BACKGROUND
the honey bee, a social insect, has received considerable attention as a model for studying neurobiology  <cit> , development  <cit> , social behavior  <cit>  and, most recently, epigenomics  <cit> .
to facilitate studies of this important biological model, the genomic sequence of the western honey bee, apis mellifera, was published in  <dig>  providing a wealth of information for understanding the molecular basis of social behavior and eusocial evolution  <cit> .
honey bees are classified in the order hymenoptera, which also includes ants, bees, sawflies, and wasps  <cit> .
the genus apis consists of eight asian species and one western species  <cit> .
ancient bees first emerged 120– <dig> million years ago  coincident with the emergence of early angiosperms  <cit> .
the ancestors of modern bees were geographically isolated in the middle east during the late pleistocene approximately 1– <dig> mya.
it was from this population that the ancestral lineage of a. mellifera spread to africa, and the ancestral lineages of a. cerana expanded throughout europe and asia  <cit> .
as a result of allopatric speciation, these two honey bee species may have evolved in different ecological environments, which gave rise to different behavioral and physiological characteristics observed in the present day  <cit> .
compared to a. mellifera, the asian honey bee, a. cerana, has several distinguishing behavioral traits .
it is able to adapt to extreme weather conditions  <cit>  and has long flight duration  <cit> , effective grooming and hygienic behaviors  <cit> , and cooperative group-level defenses  <cit> .
a well-known behavior of a. cerana is aggregation when a colony is exposed to dangers, such as predators or intruders.
in these situations, guard bees produce alarm pheromones that dictate group behavior .
in addition, a. cerana provides considerable economic benefits to the apicultural industry through its high quality bi-products, perhaps even more so than a. mellifera <cit> .table  <dig>
comparison of biological differences between
a. cerana
and
a. mellifera
a. cerana
a. mellifera
in recent years, population decreases similar to those documented in the western honey bee have also been seen in a. cerana colonies  <cit> .
in korea, more than ninety percent of a. cerana colonies were destroyed by sacbrood virus  infection  <cit> .
however, few studies have been conducted on the underlying molecular mechanisms and immune responses to this virus  <cit> .
this study reports the a. cerana genome produced with deep sequence coverage using next-generation technologies.
we generated gene sets of a. cerana using transcriptome data from seven tissues.
then, we focused on the characterization of important genes related to chemosensory reception and immunity.
this genome sequence will provide invaluable information on the novel characteristics of the honey bee species indigenous to eastern and southern asia.
the data will also provide a resource for comparative sociogenomic studies with the seven ants and western honey bee species for which genomes are already available .
RESULTS
genomic features of a. cerana
sequencing and assembly
we performed whole genome sequencing of the asian honey bee using seven drones derived from a single colony.
because the honey bee has a haplodiploid mating system, males  are haploid and females  are diploid.
to minimize possible contamination from foreign genomes such as bacteria and viruses, we eliminated mid-gut tissues from the individual drone bees prior to sequencing.
genomic sequence libraries were constructed with a combination of short reads  and two longer insert libraries , using illumina sequencing technology  .
the assembly consisted of  <dig>  scaffolds with a total length of  <dig> mb, which covered 96% of the estimated genome size   <cit> .
general information on the genome assembly is presented in table  <dig>  the n <dig> scaffold size was  <dig>  kb , much longer than the n <dig> scaffold size found in the initial and recently improved assemblies of a. mellifera   <cit> .
to assess the accuracy of the scaffolds, we compared the genome of a. mellifera and a. cerana to identify genomic synteny .
results revealed several scaffolds of a. cerana and chromosome  <dig> of a. mellifera that showed syntenic relationships with no large-scale rearrangement.
additionally, we found that the mitochondrial genome of a. mellifera  and one contig of a. cerana had high sequence similarity, ~99% .
this contig, covering the entire a. cerana mitochondrial genome, is  <dig>  bp and includes  <dig> protein-coding genes .
all sequence information was submitted in the ncbi .table  <dig>
sequencing raw data summary
the raw data were filtered by high stringency and more detailed information described in method.
apaired end sequencing, bmate-paired sequencing.
genome assembly summary
size of estimated genome and statistics of assembled scaffolds.
the n <dig> scaffod size indicated that 50% of nucleotides in the assembly occur in scaffolds of length more than or equal to the n <dig> size.
guanine plus cytosine  content
the a. cerana assembly contains 30% gc , similar to the mean gc content of a. mellifera .
in addition, six ant species  have similar gc contents ranging from 33% to 38% .
in contrast, drosophila melanogaster , nasonia vitripennis , and harpegnathos saltator  have higher gc contents compared to a. cerana <cit> .
according to comparative studies of two ant species, c. floridanus and h. saltator, organisms with more complex social traits may have at-biased genomes  <cit> .
relative at bias correlates with dna methylation, as dna methyltransferases  are almost entirely targeted to cytosine residues followed by guanines in the 5′ to 3′ orientation .
methylcytosine tends to mutate to thymine , thus the gradational accumulation of mutation that convert cpg dinucleotides to tpg dinucleotides lead to at-rich genomes .
in particular, normalized cpg observed/expected  values have a negative relationship with levels of dna methylation  <cit> .
dna methylation is one of the major part of epigenetic regulation and has functional roles in gene expression regulation in vertebrates and insects  <cit> .
in contrast to vertebrate genomes, which are depleted of cpg dinucleotides  <cit> , most hymenopteran insects, including a. cerana , a. mellifera , c. floridanus , h. saltator , and n. vitripennis , exhibit high levels of cpg o/e in their genomes  <cit> .
another intriguing discovery is that normalized cpg o/e value within protein coding sequences of a. cerana showed bimodal distribution, similar to a. mellifera  and the pea aphid acyrthosiphon pisum <cit> .
interestingly, two distinct classes of genes are documented to perform different functions  <cit> , which low-cpg genes are mainly involved in housekeeping function and high-cpg genes are involved in development.
indeed, we found that genes that are represented low-cpg classes are categorized with metabolic process, and transcriptional and translational regulation.
in contrast, high-cpg genes represented go categories that specific to biological functions.figure  <dig>
cpg analysis of protein sequence of
a. mellifera
and
a. cerana.
distributions of normalized cpg o/e content of the
a. cerana and
a. mellifera.
bimodal distributions of honey bee protein-coding sequences indicate that the genome of honey bee encoded two distinct classes of genes which are targeted by dna methylation.
the genome of a. cerana, a. mellifera, and a. pisum encode full complements of dna methylation proteins   <cit> , but, according to a recent discovery, several insects possess a full set of dnmts without any striking depletion pattern of coding exons  <cit> .
thus, this genomic feature may not be species specific, but mechanisms of epigenetic regulation may be conserved in both honey bee species.
repetitive elements
the a. cerana assembly comprised  <dig> %  repetitive elements, consisting of  <dig> %  simple repeats and  <dig> %  interspersed repeats .
seventy-five a. cerana-specific repeat elements were found using the de novo repeat finding program, repeatmodeler .
since the a. cerana genome assembly contained  <dig> % n’s, we assumed that repetitive sequences in the current assembly may be underestimated.
in comparison to a. mellifera, only long terminal repeat elements were over-represented in a. cerana, which accounted for  <dig> %  of the genome, compared to  <dig> %  in a. mellifera.
in contrast, long interspersed elements and short interspersed elements were not detected in the genome of a. cerana.
both were found in the a. mellifera genome at frequencies of  <dig> %  and  <dig> % , respectively.
dna transposons constitute  <dig> %  of the a. cerana genome and  <dig> %  of the a. mellifera genome.
mariner transposable elements, first discovered in the fruit fly, have been found across honey bee species  <cit> .
the genome of the western honey bee, a. mellifera, contained multiple copies of mariner transposons, ranging from ammar <dig> to ammar <dig> <cit> .
in contrast, the a. cerana genome contained orthologs of ammar <dig> and ammar3- <dig>  but ammar <dig> ortholog was not found.
this is consistent with the speculation that ammar <dig> and ammar <dig> were transferred to the a. mellifera genome relatively recently  <cit> .
although genome-wide repeat analyses need to be investigated further, the results of this study showed a striking reduction of transposable elements  and retrotransposons in the a. cerana genome compared to a. mellifera.
lack of tes is one of the major features of the honey bee genome, compared to other sequenced hymenoptera  <cit> .
some evidence suggests that grooming and hygienic behaviors in eusocial organisms reduced insertion of tes from foreign genomes  <cit> .
however, both social and non-social hymenopteran insect genomes, including seven ants and the parasitoid nasonia, have been sequenced, and they include significantly different quantities of repetitive elements comprising 11% to 28% of genomes  <cit> .
therefore, hygienic behavior is not the only factor influencing the accumulation of repetitive elements in genomes.
analysis of the a. ceranagene set
due to limited data on expressed sequence tags  and complementary dnas  available for a. cerana, we established a gene annotation pipeline using multiple evidence data .
first, we generated  <dig>  transcripts covering  <dig> , <dig> bp using a de novo assembly from  <dig> gb of a. cerana rna-seq reads.
second, rna-seq data was aligned to scaffold sequences, which resulted in  <dig>  gene models representing  <dig> , <dig> bp.
third, we performed computational gene prediction based on the scaffold sequence information, which generated  <dig>  genes covering  <dig> , <dig> bp.
we also employed a. mellifera gene sequences collected from the national center for biotechnology information reference sequence database  as a model to obtain homology-based gene annotation.
subsequently, we merged all predicted gene models using the maker  <cit>  program to generate a primary gene set.
all genes were queried with the ncbi non-redundant database using blastx.
lastly, we manually checked for missing genes, partial genes, or separated genes.
chemoreceptor genes, including gustatory receptors , odorant receptors , and ionotropic receptors , were investigated more carefully using analyses of functional sequence domains.
finally,  <dig>  genes were annotated as the official gene set  of a. cerana, ogs version  <dig>  , of which approximately 84% of genes were annotated with ncbi non-redundant database and 70% were annotated in the uniprot database  <cit> .
overall, the total number of genes in the a. cerana ogs v <dig>  was comparable to the number in the a. mellifera ogs v <dig>  .
however, the number is less than the current release of the a. mellifera genome, ogs v <dig>    <cit> .table  <dig>
general statistics for gene modeling
initial evaluation
rna-seq, de novo
genome sequence, de novo
a. mellifera refseqa
primary gene set
final gene set
ancbi refseq from http://www.ncbi.nlm.nih.gov/genome/48?project_id= <dig>
comparison of the official gene set of
a. cerana
and
a. mellifera
a. cerana
a. mellifera
a. mellifera
we classified genes by function using the gene ontology  and kyoto encyclopedia of genes and genomes  databases  <cit> ;  <dig>  genes  had more than one go term and  <dig>  enzymes were categorized into  <dig> pathways .
here, several interesting molecular pathways that could represent honey bee-specific molecular mechanisms were revealed.
for example, the fatty acid biosynthesis, glutathione metabolism, and cytochrome p <dig> pathways may be involved in nest-mate recognition and detoxification of pesticides   <cit> .
the surface of the honey bee is composed of fatty acids and hydrocarbons, which reflect identity, and guard bees recognize these compounds to discriminate colony members from intruders  <cit> .
kegg analyses revealed that classes of enzymes involved in fatty acid biosynthesis are shared between a. cerana and a. mellifera, and a. cerana has fewer detoxification enzymes compared to fly and mosquito but similar numbers to a. mellifera <cit> .
the contribution of pesticides to global colony losses of a. mellifera is still a controversial issue, but data indicate that a. mellifera is unusually sensitive to various insecticides  <cit> .
interestingly, colonies of a. cerana have not shown similar levels of collapse to a. mellifera, but this could be explained by other differences that may reduce exposure to pesticides, such as frequent absconding behavior, small nest architecture, and foraging in high altitude regions  <cit> .
genes unique to a. ceranaand orthologous to honey bee
to investigate whether non-orthologous genes are associated with features of a. cerana biology, we compared three hymenopteran insects, apis mellifera , apis cerana , nasonia vitripennis , and one dipteran insect, drosophila melanogaster  by orthology based clustering.
amongst  <dig>  unique genes in a. cerana , most of the significantly enriched go-terms were involved in neuromuscular junction, neuromuscular process, regulation of muscle organ development, muscle cell differentiation, and muscle tissue development .
a. cerana has a higher wing beat frequency  compared to a. mellifera  and quick, impetuous, and unpredictable flight patterns, therefore some of the enriched proteins involved in muscle movement might account for a. cerana-specific flight patterns  <cit> .
future studies should be performed to dissect this relationship.figure  <dig>
comparative analysis of orthologous protein groups among the four insect genomes.
orthology analysis of the proteins of a. cerana  with three well known insect models, d. melanogaster , n. vitripennis , and a. mellifera .
both d. melanogaster and n. vitripennis are non-social and a. mellifera and a. cerana are social insect species.
*indicates a. cerana-specific proteins.
notably, neural signaling-related go-terms, including neuron recognition, signaling receptor activity, transmembrane receptor signaling pathway, ionotropic glutamate receptor signaling pathway, and active transmembrane transporter activity, which are closely related with chemosensory reception and chemical signaling, were also enriched  in the a. cerana unique gene set .
genes involved in chemical signaling have evolved rapidly, especially in eusocial organisms  <cit> .
neural signaling processes play major roles mediating social communication in honey bee society.
a. cerana shows a number of group-level behaviors distinct from a. mellifera <cit> , including a unique defense behaviors against a hornets.
a. cerana guard bees raise their abdomens and shake or flutter, producing alarm pheromones, when hornets approach the hive  <cit> .
additional research is required to determine whether molecular regulation mechanisms found uniquely in a. cerana may be responsible for these unique social defense behaviors.
since a. mellifera and a. cerana diverged recently, we hypothesized there would be protein orthologs conserved in both honey bee species that explain shared honey bee characteristics.
a total of  <dig>  a. cerana proteins were identified with orthologs in a. mellifera but no other non-social species.
these orthologs were categorized with go-terms “sensory perception of smell”  and “sensory perception of chemical stimulus” , which are crucial features for social communication and physical interaction  <cit> .
in addition, the go-term “carbohydrate transporter activity” , which describes cuticular hydrocarbon detection  <cit> , and “regulation of short-term neuronal synaptic plasticity”  and “transmembrane signaling receptor activity” , which are involved in neuronal signaling during social interaction, were also enriched in orthologs shared by the two honey bee species .
chemoreceptor gene family
chemoreceptors play important roles in communication and social behaviors, in part by mediating detection of chemical signals from nest-mates  <cit> .
major groups of chemoreceptor genes include gustatory receptors , odorant receptors , and ionotropic receptors  .
in social insects, such as ants and honey bees, chemical communication is crucial for colony maintenance and cooperation .
here, we have characterized  <dig> new grs,  <dig> new ors, and  <dig> new irs in the a. cerana genome.
gene expression patterns, examined using rna-seq data, revealed that annotated chemoreceptor genes were well organized and comparable to those of a. mellifera <cit>  and n. vitripennis <cit> , although they were slightly underrepresented compared to the a. mellifera genome  <cit> .
the gustatory receptor family
the gustatory receptor family plays an important role in taste and is used to collect nectar and pollen for energy and brood care  <cit> .
in honey bee society, colony members have division labor and perform different tasks.
nurse bees take care of the brood and the queen, and they clean inside the nest.
forager bees collect food or resin from outside and bring it to the hive  <cit> .
peripheral and internal regulation of gr gene expression is involved in this behavioral transition  <cit> .
according to robertson and wanner  <cit> , the western honey bee, a. mellifera has  <dig> grs , a small number compared to the fruit fly d. melanogaster , the mosquito aedes aegypti , the parasitoid wasp n. vitripennis , and the ant linepithema humile .
similar to a. mellifera,  <dig> gr genes were identified in the a. cerana genome.
they were named based on their orthology to a. mellifera grs .
all identified grs in a. cerana showed simple orthologous relationships with grs in a. mellifera, and acgr <dig>   <dig>   <dig>   <dig>   <dig>   <dig>  and  <dig> also had orthologs in n. vitripennis .
these data indicated that gr genes are highly conserved among hymenopteran species.
similar to the a. mellifera gr repertoire, acgr <dig> and acgr <dig> were positioned in expanded lineages to sugar receptors of d. melanogaster, including dmgr5a, dmgr61a and dmgr64a/f  .
in addition, acgr <dig> shared a clade with dmgr43a, which functions as a fructose receptor in the periphery and a nutrient sensor in the brain of drosophila   <cit> .
in contrast, acgr <dig>   <dig>   <dig>   <dig>  and x lineages showed no apparent relationships with dmgrs, implying that they may be unique to the honey bee.
bitter taste receptors also seem to be lost in the a. cerana genome, which may be related to the evolution of flower preference in the honey bee  <cit>  compared to other social insects such as the ant in which bitter receptors are preserved  <cit> .
additionally, orthologs to drosophila carbon dioxide  receptors, gr21a and gr63a <cit> , were not present in the a. cerana genome, similar to a. mellifera <cit> .
however, honey bees are known to detect co <dig> <cit> , indicating that they may have evolved novel molecular mechanisms similar to the acid sensing mechanism found in drosophila for detecting high co <dig> concentrations  <cit> .
partial sequences of a. cerana gr <dig> and gr <dig> orthologs were located using tblastn searches.
a gr <dig> ortholog could not be found in the a. cerana genome.figure  <dig>
phylogenetic tree of the gustatory receptor  family.
phylogenetic tree constructed using a. cerana , a. mellifera , and d. melanogaster gustatory receptor proteins  relative gr gene expression profiling using rpkm values in a. cerana  and a. mellfera .
red color indicates high expression compared to blue.
expression patterns of gr orthologs in a. cerana and a. mellifera were determined by relative gene expression analyses .
surprisingly, expression patterns of gr orthologs between the two honey bee species were distinct.
candidate sugar receptors, gr <dig> and gr <dig>  were expressed higher in a. cerana compared to a. mellifera , suggesting that a. cerana may have a greater ability to sense sugars.
similarly, gr <dig> and gr <dig> were highly expressed in a. cerana compared to a. mellifera.
in contrast, gr <dig>   <dig>   <dig>  and  <dig> were more highly expressed in a. mellifera compared to a. cerana.
gr <dig> and grx were not detected in antennal transcriptome of a. cerana , implying that gr <dig> and grx might be expressed at undetectable levels or in other tissues, such as the tongue or legs.
future functional studies on grs may reveal taste sensing and internal regulation differences between the species.
the odorant receptor family
insect odorant receptors play important roles in environmental signal recognition and inter- and intra-species communication  <cit> .
honey bees use odorant receptors in contexts, including kin recognition, food navigation, and pheromone detection  <cit> .
however, despite the importance of odorant receptors, the functional identification of ors in honey bees is lacking compared to other model insects, including fly and mosquito species  <cit> .
in the a. cerana genome,  <dig> acors, including a few 5′- or 3′- partial sequences containing the odorant receptor domain, were identified.
we named a. cerana ors by sequence positions in scaffolds.
most acors were not spread evenly across scaffolds, but were clustered at a few locations in the genome.
for example, clusters of  <dig> ors,  <dig> ors, and  <dig> ors were arrayed on scaffold  <dig>   <dig>  and  <dig>  respectively .
in a. mellifera, the largest tandem array of  <dig> ors was found on chromosome  <dig>  <cit> .
this expansion of ors implies unequal crossing-over by neighboring genes occurred.
the large number of or paralogs indicate diverse roles for odorant recognition in honey bee society, such as pheromone blends, cuticular hydrocarbons, and floral odor cocktails  <cit> .
since a. mellifera and a. cerana diverged recently  <cit> , it was hypothesized that there may be synteny between or clusters.
regions of a. mellifera chromosome  <dig> with microsynteny conservation were identified by comparing the or gene arrangement in the a. cerana genome to the a. mellifera genome.
consistent with the hypothesis, conserved microsynteny and clear orthologs of a. cerana ors to a. mellifera ors were found , suggesting that honey bee or paralogs are clustered in conserved genomic regions  <cit> .figure  <dig>
phylogenetic tree of the odorant receptor  family.
phylogenetic tree constructed using a. cerana , a. mellifera , and d. melanogaster odorant receptor proteins.
relative or gene expression profiling using rpkm values in a. cerana  and a. mellfera .
red color indicates high expression compared to blue.
microsynteny between a. cerana and a. mellfera or genes.
orthologous and paralogous of a. cerana  and a. mellifera  ors were analyzed with blastz.
a. cerana scaffold number and a. mellifera chromosome number are on the left and right side, respectively.
insects have a number of variable ors, which form a chaperone with olfactory receptor co-receptor  in vivo.
in the present study, a. cerana or <dig> shared orthology with insect orcos including d. melanogaster or83b, n. vitripennis or <dig>  and a. mellifera or <dig> .
overall, identified acors showed simple orthologous relationships with amors, such as 1: <dig>  1: <dig>  and 1: <dig> .
among  <dig> a. mellifera ors, amor <dig> was functionally characterized as a queen pheromone receptor responding to 9-oxo-2-decenoic acid   <cit> .
in our study, acor <dig> showed 1: <dig> orthology to amor <dig> with  <dig> % identity , implying that queen pheromone components may be conserved between a. mellifera and a. cerana.
transcriptome data revealed that or homologs are differentially expressed between a. cerana and a. mellifera .
forty-four or homologs were more highly expressed in a. mellifera, and  <dig> or homologs were more highly expressed in a. cerana.
different expression patterns support the idea that coding sequences are well conserved among or homologs, but their promoter sequences have diverse regulatory motifs.
these data imply that the two honey bee species express different odorant spectra.
specifically, seven acors  were expressed only in a. cerana, indicating functions specific to a. cerana.
functional studies using heterologous expression systems are needed to better understand the various functions of ors in honey bees.
the ionotropic receptor family
recently, a new family of chemosensory receptors, the ionotropic receptor  family, was identified in d. melanogaster <cit> .
irs in d. melanogaster constitute distinct and divergent subfamilies of ionotropic glutamate receptors   <cit> .
sixty-six ir homologs have been identified in d. melanogaster, and  <dig> were expressed specifically in antennae  <cit> .
this suggested that irs belong to two subgroups: conserved antennal irs and species-specific divergent irs.
these subgroups represent classes of ors and grs, respectively  <cit> .
in contrast to ors, which respond broadly to alcohols, ketones, and esters, irs primarily respond to acids, amines, and carbon dioxide, which can be physiologically important in many insect species .
although the functions of these receptors are not yet known, irs may have more general function in the detection of environmental chemicals including odorants and tastes  <cit> .
the number of identified irs in insects is increasing  <cit> , and a large complement of irs has been described in the complete genomes of four hymenopteran species: a. mellifera , n. vitripennis , l. humile , and p. barbatus   <cit> .
in this study,  <dig> ir homologs were found in the a. cerana genome .
sequence comparison and phylogenetic analyses of irs with d. melanogaster and a. mellifera identified putative orthologs of conserved irs in the a. cerana genome: ir8a, ir25a, ir68a, ir75a, ir76a, and ir93a <cit> .
as expected, highly conserved orthologs of antennal irs were identified in the a. cerana genome.
these results support the hypothesis that antennal expression of ir orthologs has been conserved for over  <dig> mya since dipteran and hymenopteran insects diverged  <cit> .
other irs in a. cerana with low similarity to orthologs of other insect receptors appear to be honey bee-specific.
these irs may be used for species-specific recognition, including candidates for cuticular hydrocarbon receptors and brood pheromone receptors.
however, expression patterns for the vast majority of irs are unknown and no ligands for honey bee irs have been identified.
in this study, acir expression profiles were different in a. mellifera and a. cerana .
their functions and evolutionary basis for diversity remain to be investigated.figure  <dig>
phylogenetic tree of the ionotropic receptor  family.
phylogenetic tree constructed using a. cerana , a. mellifera , and d. melanogaster ionotropic receptor proteins.
relative ir gene expression profiling using rpkm values in a. cerana  and a. mellfera .
red color indicates high expression compared to blue.
immune-related genes
honey bees are invaluable models for studying social defense dynamics and individual molecular and behavioral defense mechanisms  <cit> .
in contrast to a. mellifera, a. cerana is not susceptible to the ectoparasitic mite, varroa destructor, one of the major vectors of bee pathogens.
in contrast, a. cerana has suffered greatly from viral and bacterial diseases in recent years  <cit> .
a recent report indicated that more than 90% of asian honey bee colonies collapsed due to sacbrood virus  infection in korea  <cit> .
many asian countries also suffered declines in a. cerana colonies for several reasons.
however, the molecular defense mechanisms of a. cerana are still unknown.
therefore, we investigated immune genes present in the a. cerana genome by comparing genomic information to other sequenced insect genomes  <cit> .
using multiple tblastn searches,  <dig> immune gene orthologs were identified in a. cerana and  <dig> additional genes were detected by manual annotation.
all major pathways were identified in a. cerana, including components of the toll, imd, jak/stat, and jnk pathways  <cit> .
notably, the fadd, dredd, and kenny, components of the imd pathway and pelle of the toll pathway were not detected in the a. cerana genome .
the total number of innate immune genes in a. cerana is similar to other social hymenoptera  <cit>  , and most immune genes in a. cerana shared higher sequence similarity with a. mellifera compared to other sequenced insect species.
this may be explained by conservation of the innate immune system between a. cerana and a. mellifera.
eusocial insects have additional social immune systems, such as cleaning behaviors , thermal defenses , and antibiotic nest architecture , which may contribute to reducing exposure to pathogens  <cit> .figure  <dig>
candidate genes of immune-related pathways in
a. cerana.
colored boxes indicate counterparts of immune pathway components in the a. cerana genome.
schematic drawing adapted from immune pathways in a. mellifera <cit> .
previous studies indicate more antimicrobial proteins are encoded in the a. cerana genome compared to a. mellifera <cit> .
indeed, defensive peptides, including venomous peptides, in a. cerana are more strongly expressed than those in a. mellifera <cit> .
in addition, some reports show the uniqueness of strong behavioral defenses of a. cerana, such as hygienic and grooming behaviors  <cit> .
together, these data indicate that a. cerana, through a combination of elaborate molecular and behavioral mechanisms, may have a more effective social defense system compared to a. mellifera.
functional studies of immune genes will inform knowledge of a. cerana-specific disease control methods and provide a valuable model for comparative studies of social insect immune systems.
CONCLUSIONS
the asian honey bee, a. cerana, a close relative of the western honey bee, a. mellifera, provides considerable economic benefits to the apicultural industry and serves as a new model for biodiversity in eastern and southern asia.
despite similarities in asian and western honey bees, differences in biological traits led us to explore the genome and transcriptome of a. cerana.
this is the first report to elucidate the whole genome sequence of the asian honey bee, a. cerana, by employing de novo assembly of the a. cerana genome and computational gene prediction followed by manual annotation.
a. cerana has unique features for muscle movement and neural signaling, reflecting the wild nature of a. cerana.
in addition, chemosensory receptors and immune-related genes, which might be responsible for sophisticated and well-organized life styles in honey bees, were identified.
comparative studies of chemoreceptor gene families showed similarities in receptor family expansions relative to a. mellifera.
however, significant differences in gene expression were also identified, potentially reflecting different capabilities for odor perception.
in addition, immune-related genes in a. cerana exhibited expression patterns that may reflect an advanced social immune system, advancing understanding of the molecular basis of social immunity.
this genome analysis will provide invaluable information on the novel characteristics of a. cerana, and contribute to the understanding of comparative sociogenomics with other sequenced social insect genomes.

 the honey bee, a social insect, has received considerable attention as a model for studying neurobiology, development, social behavior and, most recently, epigenomics. to facilitate studies of this important biological model, the genomic sequence of the western honey bee, apis mellifera, was published in providing a wealth of information for understanding the molecular basis of social behavior and eusocial evolution. honey bees are classified in the order hymenoptera, which also includes ants, bees, sawflies, and wasps. the genus apis consists of eight asian species and one western species. ancient bees first emerged 120– million years ago coincident with the emergence of early angiosperms. the ancestors of modern bees were geographically isolated in the middle east during the late pleistocene approximately 1– mya. it was from this population that the ancestral lineage of a. mellifera spread to africa, and the ancestral lineages of a. cerana expanded throughout europe and asia. as a result of allopatric speciation, these two honey bee species may have evolved in different ecological environments, which gave rise to different behavioral and physiological characteristics observed in the present day. compared to a. mellifera, the asian honey bee, a. cerana, has several distinguishing behavioral traits. it is able to adapt to extreme weather conditions and has long flight duration, effective grooming and hygienic behaviors, and cooperative group-level defenses. a well-known behavior of a. cerana is aggregation when a colony is exposed to dangers, such as predators or intruders. in these situations, guard bees produce alarm pheromones that dictate group behavior. in addition, a. cerana provides considerable economic benefits to the apicultural industry through its high quality bi-products, perhaps even more so than a. mellifera.table comparison of biological differences between a. cerana and a. mellifera a. cerana a. mellifera in recent years, population decreases similar to those documented in the western honey bee have also been seen in a. cerana colonies. in korea, more than ninety percent of a. cerana colonies were destroyed by sacbrood virus infection. however, few studies have been conducted on the underlying molecular mechanisms and immune responses to this virus. this study reports the a. cerana genome produced with deep sequence coverage using next-generation technologies. we generated gene sets of a. cerana using transcriptome data from seven tissues. then, we focused on the characterization of important genes related to chemosensory reception and immunity. this genome sequence will provide invaluable information on the novel characteristics of the honey bee species indigenous to eastern and southern asia. the data will also provide a resource for comparative sociogenomic studies with the seven ants and western honey bee species for which genomes are already available.  genomic features of a. cerana sequencing and assembly we performed whole genome sequencing of the asian honey bee using seven drones derived from a single colony. because the honey bee has a haplodiploid mating system, males are haploid and females are diploid. to minimize possible contamination from foreign genomes such as bacteria and viruses, we eliminated mid-gut tissues from the individual drone bees prior to sequencing. genomic sequence libraries were constructed with a combination of short reads and two longer insert libraries, using illumina sequencing technology. the assembly consisted of scaffolds with a total length of mb, which covered 96% of the estimated genome size. general information on the genome assembly is presented in table  the n scaffold size was kb, much longer than the n scaffold size found in the initial and recently improved assemblies of a. mellifera. to assess the accuracy of the scaffolds, we compared the genome of a. mellifera and a. cerana to identify genomic synteny. results revealed several scaffolds of a. cerana and chromosome of a. mellifera that showed syntenic relationships with no large-scale rearrangement. additionally, we found that the mitochondrial genome of a. mellifera and one contig of a. cerana had high sequence similarity, ~99%. this contig, covering the entire a. cerana mitochondrial genome, is bp and includes protein-coding genes. all sequence information was submitted in the ncbi.table sequencing raw data summary the raw data were filtered by high stringency and more detailed information described in method. apaired end sequencing, bmate-paired sequencing. genome assembly summary size of estimated genome and statistics of assembled scaffolds. the n scaffod size indicated that 50% of nucleotides in the assembly occur in scaffolds of length more than or equal to the n size. guanine plus cytosine content the a. cerana assembly contains 30% gc, similar to the mean gc content of a. mellifera. in addition, six ant species have similar gc contents ranging from 33% to 38%. in contrast, drosophila melanogaster, nasonia vitripennis, and harpegnathos saltator have higher gc contents compared to a. cerana. according to comparative studies of two ant species, c. floridanus and h. saltator, organisms with more complex social traits may have at-biased genomes. relative at bias correlates with dna methylation, as dna methyltransferases are almost entirely targeted to cytosine residues followed by guanines in the 5′ to 3′ orientation. methylcytosine tends to mutate to thymine, thus the gradational accumulation of mutation that convert cpg dinucleotides to tpg dinucleotides lead to at-rich genomes. in particular, normalized cpg observed/expected values have a negative relationship with levels of dna methylation. dna methylation is one of the major part of epigenetic regulation and has functional roles in gene expression regulation in vertebrates and insects. in contrast to vertebrate genomes, which are depleted of cpg dinucleotides, most hymenopteran insects, including a. cerana, a. mellifera, c. floridanus, h. saltator, and n. vitripennis, exhibit high levels of cpg o/e in their genomes. another intriguing discovery is that normalized cpg o/e value within protein coding sequences of a. cerana showed bimodal distribution, similar to a. mellifera and the pea aphid acyrthosiphon pisum. interestingly, two distinct classes of genes are documented to perform different functions, which low-cpg genes are mainly involved in housekeeping function and high-cpg genes are involved in development. indeed, we found that genes that are represented low-cpg classes are categorized with metabolic process, and transcriptional and translational regulation. in contrast, high-cpg genes represented go categories that specific to biological functions.figure cpg analysis of protein sequence of a. mellifera and a. cerana. distributions of normalized cpg o/e content of the a. cerana and a. mellifera. bimodal distributions of honey bee protein-coding sequences indicate that the genome of honey bee encoded two distinct classes of genes which are targeted by dna methylation. the genome of a. cerana, a. mellifera, and a. pisum encode full complements of dna methylation proteins, but, according to a recent discovery, several insects possess a full set of dnmts without any striking depletion pattern of coding exons. thus, this genomic feature may not be species specific, but mechanisms of epigenetic regulation may be conserved in both honey bee species. repetitive elements the a. cerana assembly comprised % repetitive elements, consisting of % simple repeats and % interspersed repeats. seventy-five a. cerana-specific repeat elements were found using the de novo repeat finding program, repeatmodeler. since the a. cerana genome assembly contained % n’s, we assumed that repetitive sequences in the current assembly may be underestimated. in comparison to a. mellifera, only long terminal repeat elements were over-represented in a. cerana, which accounted for % of the genome, compared to % in a. mellifera. in contrast, long interspersed elements and short interspersed elements were not detected in the genome of a. cerana. both were found in the a. mellifera genome at frequencies of % and %, respectively. dna transposons constitute % of the a. cerana genome and % of the a. mellifera genome. mariner transposable elements, first discovered in the fruit fly, have been found across honey bee species. the genome of the western honey bee, a. mellifera, contained multiple copies of mariner transposons, ranging from ammar to ammar. in contrast, the a. cerana genome contained orthologs of ammar and ammar3- but ammar ortholog was not found. this is consistent with the speculation that ammar and ammar were transferred to the a. mellifera genome relatively recently. although genome-wide repeat analyses need to be investigated further, the results of this study showed a striking reduction of transposable elements and retrotransposons in the a. cerana genome compared to a. mellifera. lack of tes is one of the major features of the honey bee genome, compared to other sequenced hymenoptera. some evidence suggests that grooming and hygienic behaviors in eusocial organisms reduced insertion of tes from foreign genomes. however, both social and non-social hymenopteran insect genomes, including seven ants and the parasitoid nasonia, have been sequenced, and they include significantly different quantities of repetitive elements comprising 11% to 28% of genomes. therefore, hygienic behavior is not the only factor influencing the accumulation of repetitive elements in genomes. analysis of the a. ceranagene set due to limited data on expressed sequence tags and complementary dnas available for a. cerana, we established a gene annotation pipeline using multiple evidence data. first, we generated transcripts covering, bp using a de novo assembly from gb of a. cerana rna-seq reads. second, rna-seq data was aligned to scaffold sequences, which resulted in gene models representing, bp. third, we performed computational gene prediction based on the scaffold sequence information, which generated genes covering, bp. we also employed a. mellifera gene sequences collected from the national center for biotechnology information reference sequence database as a model to obtain homology-based gene annotation. subsequently, we merged all predicted gene models using the maker program to generate a primary gene set. all genes were queried with the ncbi non-redundant database using blastx. lastly, we manually checked for missing genes, partial genes, or separated genes. chemoreceptor genes, including gustatory receptors, odorant receptors, and ionotropic receptors, were investigated more carefully using analyses of functional sequence domains. finally, genes were annotated as the official gene set of a. cerana, ogs version, of which approximately 84% of genes were annotated with ncbi non-redundant database and 70% were annotated in the uniprot database. overall, the total number of genes in the a. cerana ogs v was comparable to the number in the a. mellifera ogs v. however, the number is less than the current release of the a. mellifera genome, ogs v.table general statistics for gene modeling initial evaluation rna-seq, de novo genome sequence, de novo a. mellifera refseqa primary gene set final gene set ancbi refseq from http://www.ncbi.nlm.nih.gov/genome/48?project_id= comparison of the official gene set of a. cerana and a. mellifera a. cerana a. mellifera a. mellifera we classified genes by function using the gene ontology and kyoto encyclopedia of genes and genomes databases; genes had more than one go term and enzymes were categorized into pathways. here, several interesting molecular pathways that could represent honey bee-specific molecular mechanisms were revealed. for example, the fatty acid biosynthesis, glutathione metabolism, and cytochrome p pathways may be involved in nest-mate recognition and detoxification of pesticides. the surface of the honey bee is composed of fatty acids and hydrocarbons, which reflect identity, and guard bees recognize these compounds to discriminate colony members from intruders. kegg analyses revealed that classes of enzymes involved in fatty acid biosynthesis are shared between a. cerana and a. mellifera, and a. cerana has fewer detoxification enzymes compared to fly and mosquito but similar numbers to a. mellifera. the contribution of pesticides to global colony losses of a. mellifera is still a controversial issue, but data indicate that a. mellifera is unusually sensitive to various insecticides. interestingly, colonies of a. cerana have not shown similar levels of collapse to a. mellifera, but this could be explained by other differences that may reduce exposure to pesticides, such as frequent absconding behavior, small nest architecture, and foraging in high altitude regions. genes unique to a. ceranaand orthologous to honey bee to investigate whether non-orthologous genes are associated with features of a. cerana biology, we compared three hymenopteran insects, apis mellifera, apis cerana, nasonia vitripennis, and one dipteran insect, drosophila melanogaster by orthology based clustering. amongst unique genes in a. cerana, most of the significantly enriched go-terms were involved in neuromuscular junction, neuromuscular process, regulation of muscle organ development, muscle cell differentiation, and muscle tissue development. a. cerana has a higher wing beat frequency compared to a. mellifera and quick, impetuous, and unpredictable flight patterns, therefore some of the enriched proteins involved in muscle movement might account for a. cerana-specific flight patterns. future studies should be performed to dissect this relationship.figure comparative analysis of orthologous protein groups among the four insect genomes. orthology analysis of the proteins of a. cerana with three well known insect models, d. melanogaster, n. vitripennis, and a. mellifera. both d. melanogaster and n. vitripennis are non-social and a. mellifera and a. cerana are social insect species. *indicates a. cerana-specific proteins. notably, neural signaling-related go-terms, including neuron recognition, signaling receptor activity, transmembrane receptor signaling pathway, ionotropic glutamate receptor signaling pathway, and active transmembrane transporter activity, which are closely related with chemosensory reception and chemical signaling, were also enriched in the a. cerana unique gene set. genes involved in chemical signaling have evolved rapidly, especially in eusocial organisms. neural signaling processes play major roles mediating social communication in honey bee society. a. cerana shows a number of group-level behaviors distinct from a. mellifera, including a unique defense behaviors against a hornets. a. cerana guard bees raise their abdomens and shake or flutter, producing alarm pheromones, when hornets approach the hive. additional research is required to determine whether molecular regulation mechanisms found uniquely in a. cerana may be responsible for these unique social defense behaviors. since a. mellifera and a. cerana diverged recently, we hypothesized there would be protein orthologs conserved in both honey bee species that explain shared honey bee characteristics. a total of a. cerana proteins were identified with orthologs in a. mellifera but no other non-social species. these orthologs were categorized with go-terms “sensory perception of smell” and “sensory perception of chemical stimulus”, which are crucial features for social communication and physical interaction. in addition, the go-term “carbohydrate transporter activity”, which describes cuticular hydrocarbon detection, and “regulation of short-term neuronal synaptic plasticity” and “transmembrane signaling receptor activity”, which are involved in neuronal signaling during social interaction, were also enriched in orthologs shared by the two honey bee species. chemoreceptor gene family chemoreceptors play important roles in communication and social behaviors, in part by mediating detection of chemical signals from nest-mates. major groups of chemoreceptor genes include gustatory receptors, odorant receptors, and ionotropic receptors. in social insects, such as ants and honey bees, chemical communication is crucial for colony maintenance and cooperation. here, we have characterized new grs, new ors, and new irs in the a. cerana genome. gene expression patterns, examined using rna-seq data, revealed that annotated chemoreceptor genes were well organized and comparable to those of a. mellifera and n. vitripennis, although they were slightly underrepresented compared to the a. mellifera genome. the gustatory receptor family the gustatory receptor family plays an important role in taste and is used to collect nectar and pollen for energy and brood care. in honey bee society, colony members have division labor and perform different tasks. nurse bees take care of the brood and the queen, and they clean inside the nest. forager bees collect food or resin from outside and bring it to the hive. peripheral and internal regulation of gr gene expression is involved in this behavioral transition. according to robertson and wanner, the western honey bee, a. mellifera has grs, a small number compared to the fruit fly d. melanogaster, the mosquito aedes aegypti, the parasitoid wasp n. vitripennis, and the ant linepithema humile. similar to a. mellifera, gr genes were identified in the a. cerana genome. they were named based on their orthology to a. mellifera grs. all identified grs in a. cerana showed simple orthologous relationships with grs in a. mellifera, and acgr and also had orthologs in n. vitripennis. these data indicated that gr genes are highly conserved among hymenopteran species. similar to the a. mellifera gr repertoire, acgr and acgr were positioned in expanded lineages to sugar receptors of d. melanogaster, including dmgr5a, dmgr61a and dmgr64a/f. in addition, acgr shared a clade with dmgr43a, which functions as a fructose receptor in the periphery and a nutrient sensor in the brain of drosophila. in contrast, acgr and x lineages showed no apparent relationships with dmgrs, implying that they may be unique to the honey bee. bitter taste receptors also seem to be lost in the a. cerana genome, which may be related to the evolution of flower preference in the honey bee compared to other social insects such as the ant in which bitter receptors are preserved. additionally, orthologs to drosophila carbon dioxide receptors, gr21a and gr63a, were not present in the a. cerana genome, similar to a. mellifera. however, honey bees are known to detect co, indicating that they may have evolved novel molecular mechanisms similar to the acid sensing mechanism found in drosophila for detecting high co concentrations. partial sequences of a. cerana gr and gr orthologs were located using tblastn searches. a gr ortholog could not be found in the a. cerana genome.figure phylogenetic tree of the gustatory receptor family. phylogenetic tree constructed using a. cerana, a. mellifera, and d. melanogaster gustatory receptor proteins relative gr gene expression profiling using rpkm values in a. cerana and a. mellfera. red color indicates high expression compared to blue. expression patterns of gr orthologs in a. cerana and a. mellifera were determined by relative gene expression analyses. surprisingly, expression patterns of gr orthologs between the two honey bee species were distinct. candidate sugar receptors, gr and gr were expressed higher in a. cerana compared to a. mellifera, suggesting that a. cerana may have a greater ability to sense sugars. similarly, gr and gr were highly expressed in a. cerana compared to a. mellifera. in contrast, gr and were more highly expressed in a. mellifera compared to a. cerana. gr and grx were not detected in antennal transcriptome of a. cerana, implying that gr and grx might be expressed at undetectable levels or in other tissues, such as the tongue or legs. future functional studies on grs may reveal taste sensing and internal regulation differences between the species. the odorant receptor family insect odorant receptors play important roles in environmental signal recognition and inter- and intra-species communication. honey bees use odorant receptors in contexts, including kin recognition, food navigation, and pheromone detection. however, despite the importance of odorant receptors, the functional identification of ors in honey bees is lacking compared to other model insects, including fly and mosquito species. in the a. cerana genome, acors, including a few 5′- or 3′- partial sequences containing the odorant receptor domain, were identified. we named a. cerana ors by sequence positions in scaffolds. most acors were not spread evenly across scaffolds, but were clustered at a few locations in the genome. for example, clusters of ors, ors, and ors were arrayed on scaffold and respectively. in a. mellifera, the largest tandem array of ors was found on chromosome. this expansion of ors implies unequal crossing-over by neighboring genes occurred. the large number of or paralogs indicate diverse roles for odorant recognition in honey bee society, such as pheromone blends, cuticular hydrocarbons, and floral odor cocktails. since a. mellifera and a. cerana diverged recently, it was hypothesized that there may be synteny between or clusters. regions of a. mellifera chromosome with microsynteny conservation were identified by comparing the or gene arrangement in the a. cerana genome to the a. mellifera genome. consistent with the hypothesis, conserved microsynteny and clear orthologs of a. cerana ors to a. mellifera ors were found, suggesting that honey bee or paralogs are clustered in conserved genomic regions.figure phylogenetic tree of the odorant receptor family. phylogenetic tree constructed using a. cerana, a. mellifera, and d. melanogaster odorant receptor proteins. relative or gene expression profiling using rpkm values in a. cerana and a. mellfera. red color indicates high expression compared to blue. microsynteny between a. cerana and a. mellfera or genes. orthologous and paralogous of a. cerana and a. mellifera ors were analyzed with blastz. a. cerana scaffold number and a. mellifera chromosome number are on the left and right side, respectively. insects have a number of variable ors, which form a chaperone with olfactory receptor co-receptor in vivo. in the present study, a. cerana or shared orthology with insect orcos including d. melanogaster or83b, n. vitripennis or and a. mellifera or. overall, identified acors showed simple orthologous relationships with amors, such as 1: 1: and 1:. among a. mellifera ors, amor was functionally characterized as a queen pheromone receptor responding to 9-oxo-2-decenoic acid. in our study, acor showed 1: orthology to amor with % identity, implying that queen pheromone components may be conserved between a. mellifera and a. cerana. transcriptome data revealed that or homologs are differentially expressed between a. cerana and a. mellifera. forty-four or homologs were more highly expressed in a. mellifera, and or homologs were more highly expressed in a. cerana. different expression patterns support the idea that coding sequences are well conserved among or homologs, but their promoter sequences have diverse regulatory motifs. these data imply that the two honey bee species express different odorant spectra. specifically, seven acors were expressed only in a. cerana, indicating functions specific to a. cerana. functional studies using heterologous expression systems are needed to better understand the various functions of ors in honey bees. the ionotropic receptor family recently, a new family of chemosensory receptors, the ionotropic receptor family, was identified in d. melanogaster. irs in d. melanogaster constitute distinct and divergent subfamilies of ionotropic glutamate receptors. sixty-six ir homologs have been identified in d. melanogaster, and were expressed specifically in antennae. this suggested that irs belong to two subgroups: conserved antennal irs and species-specific divergent irs. these subgroups represent classes of ors and grs, respectively. in contrast to ors, which respond broadly to alcohols, ketones, and esters, irs primarily respond to acids, amines, and carbon dioxide, which can be physiologically important in many insect species. although the functions of these receptors are not yet known, irs may have more general function in the detection of environmental chemicals including odorants and tastes. the number of identified irs in insects is increasing, and a large complement of irs has been described in the complete genomes of four hymenopteran species: a. mellifera, n. vitripennis, l. humile, and p. barbatus. in this study, ir homologs were found in the a. cerana genome. sequence comparison and phylogenetic analyses of irs with d. melanogaster and a. mellifera identified putative orthologs of conserved irs in the a. cerana genome: ir8a, ir25a, ir68a, ir75a, ir76a, and ir93a. as expected, highly conserved orthologs of antennal irs were identified in the a. cerana genome. these results support the hypothesis that antennal expression of ir orthologs has been conserved for over mya since dipteran and hymenopteran insects diverged. other irs in a. cerana with low similarity to orthologs of other insect receptors appear to be honey bee-specific. these irs may be used for species-specific recognition, including candidates for cuticular hydrocarbon receptors and brood pheromone receptors. however, expression patterns for the vast majority of irs are unknown and no ligands for honey bee irs have been identified. in this study, acir expression profiles were different in a. mellifera and a. cerana. their functions and evolutionary basis for diversity remain to be investigated.figure phylogenetic tree of the ionotropic receptor family. phylogenetic tree constructed using a. cerana, a. mellifera, and d. melanogaster ionotropic receptor proteins. relative ir gene expression profiling using rpkm values in a. cerana and a. mellfera. red color indicates high expression compared to blue. immune-related genes honey bees are invaluable models for studying social defense dynamics and individual molecular and behavioral defense mechanisms. in contrast to a. mellifera, a. cerana is not susceptible to the ectoparasitic mite, varroa destructor, one of the major vectors of bee pathogens. in contrast, a. cerana has suffered greatly from viral and bacterial diseases in recent years. a recent report indicated that more than 90% of asian honey bee colonies collapsed due to sacbrood virus infection in korea. many asian countries also suffered declines in a. cerana colonies for several reasons. however, the molecular defense mechanisms of a. cerana are still unknown. therefore, we investigated immune genes present in the a. cerana genome by comparing genomic information to other sequenced insect genomes. using multiple tblastn searches, immune gene orthologs were identified in a. cerana and additional genes were detected by manual annotation. all major pathways were identified in a. cerana, including components of the toll, imd, jak/stat, and jnk pathways. notably, the fadd, dredd, and kenny, components of the imd pathway and pelle of the toll pathway were not detected in the a. cerana genome. the total number of innate immune genes in a. cerana is similar to other social hymenoptera, and most immune genes in a. cerana shared higher sequence similarity with a. mellifera compared to other sequenced insect species. this may be explained by conservation of the innate immune system between a. cerana and a. mellifera. eusocial insects have additional social immune systems, such as cleaning behaviors, thermal defenses, and antibiotic nest architecture, which may contribute to reducing exposure to pathogens.figure candidate genes of immune-related pathways in a. cerana. colored boxes indicate counterparts of immune pathway components in the a. cerana genome. schematic drawing adapted from immune pathways in a. mellifera. previous studies indicate more antimicrobial proteins are encoded in the a. cerana genome compared to a. mellifera. indeed, defensive peptides, including venomous peptides, in a. cerana are more strongly expressed than those in a. mellifera. in addition, some reports show the uniqueness of strong behavioral defenses of a. cerana, such as hygienic and grooming behaviors. together, these data indicate that a. cerana, through a combination of elaborate molecular and behavioral mechanisms, may have a more effective social defense system compared to a. mellifera. functional studies of immune genes will inform knowledge of a. cerana-specific disease control methods and provide a valuable model for comparative studies of social insect immune systems.  the asian honey bee, a. cerana, a close relative of the western honey bee, a. mellifera, provides considerable economic benefits to the apicultural industry and serves as a new model for biodiversity in eastern and southern asia. despite similarities in asian and western honey bees, differences in biological traits led us to explore the genome and transcriptome of a. cerana. this is the first report to elucidate the whole genome sequence of the asian honey bee, a. cerana, by employing de novo assembly of the a. cerana genome and computational gene prediction followed by manual annotation. a. cerana has unique features for muscle movement and neural signaling, reflecting the wild nature of a. cerana. in addition, chemosensory receptors and immune-related genes, which might be responsible for sophisticated and well-organized life styles in honey bees, were identified. comparative studies of chemoreceptor gene families showed similarities in receptor family expansions relative to a. mellifera. however, significant differences in gene expression were also identified, potentially reflecting different capabilities for odor perception. in addition, immune-related genes in a. cerana exhibited expression patterns that may reflect an advanced social immune system, advancing understanding of the molecular basis of social immunity. this genome analysis will provide invaluable information on the novel characteristics of a. cerana, and contribute to the understanding of comparative sociogenomics with other sequenced social insect genomes. 
a.cerana-specific genes were analyzed to better understand the novel characteristics of this honey bee species. in contrast, the genome of the asian honey bee, apis cerana, has not yet been sequenced. apis ceranaasian honey beegenomesocial insectchemosensory receptorshoney bee immunityissue-copyright-statement© the author 2015 here we report the first whole genome sequence of a. cerana. this first report of the whole genome sequence of a. cerana provides resources for comparative sociogenomics, especially in the field of social insect communication. a. cerana has been raised in asian countries for thousands of years and has brought considerable economic benefits to the apicultural industry. using de novo assembly methods, we produced a mbp draft of the a. cerana genome and generated genes. seventy-two percent of the a. cerana-specific genes had more than one go term, and enzymes were categorized into pathways. the honey bee is an important model system for increasing understanding of molecular and neural mechanisms underlying social behaviors relevant to the agricultural industry and basic science. the western honey bee, apis mellifera, has served as a model species, and its genome sequence has been published. these important tools will contribute to a better understanding of the complex behaviors and natural biology of the asian honey bee and to anticipate its future evolutionary trajectory. genes involved in chemoreception and immunity were carefully identified and compared to those from other sequenced insect models. a cerana has divergent biological traits compared to a. mellifera and it has played a key role in maintaining biodiversity in eastern and southern asia.
 the honey bee is an important model system for increasing understanding of molecular and neural mechanisms underlying social behaviors relevant to the agricultural industry and basic science. the western honey bee, apis mellifera, has served as a model species, and its genome sequence has been published. in contrast, the genome of the asian honey bee, apis cerana, has not yet been sequenced. a. cerana has been raised in asian countries for thousands of years and has brought considerable economic benefits to the apicultural industry. a cerana has divergent biological traits compared to a. mellifera and it has played a key role in maintaining biodiversity in eastern and southern asia. here we report the first whole genome sequence of a. cerana.  using de novo assembly methods, we produced a mbp draft of the a. cerana genome and generated genes. a.cerana-specific genes were analyzed to better understand the novel characteristics of this honey bee species. seventy-two percent of the a. cerana-specific genes had more than one go term, and enzymes were categorized into pathways. genes involved in chemoreception and immunity were carefully identified and compared to those from other sequenced insect models. these included gustatory receptors, odorant receptors, ionotropic receptors, and immune-related genes.  this first report of the whole genome sequence of a. cerana provides resources for comparative sociogenomics, especially in the field of social insect communication. these important tools will contribute to a better understanding of the complex behaviors and natural biology of the asian honey bee and to anticipate its future evolutionary trajectory. electronic supplementary material the online version of this article contains supplementary material, which is available to authorized users. keywords apis ceranaasian honey beegenomesocial insectchemosensory receptorshoney bee immunityissue-copyright-statement© the author 2015 