cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100998
title: Supporting data for "Annotation of Hox cluster and Hox cofactor genes in the Asian citrus psyllid, <i>Diaphorina citri</i> , reveals novel features"

description: Hox genes and their cofactors are essential developmental genes that specify regional identity in animals, including insects. A particularly interesting feature of Hox genes is their conserved arrangement in clusters in the same order in which they specify identity along the anterior-posterior axis. Among insects, breaks in the cluster have been reported in a few species, but these seem to be the exception rather than the rule. We have annotated the ten Hox genes of the Asian citrus psyllid, <i>Diaphorina citri</i>, and determined that there is a split in its Hox cluster between the <i>Deformed</i> and <i>Sex combs reduced</i> genes. This is the first time a break at this position has been observed in an insect Hox cluster. We have also annotated the <i>D. citri</i> orthologs of the Hox cofactor genes <i>homothorax</i>, <i>PKNOX</i> and <i>extradenticle</i>. Interestingly, we found an additional copy of <i>extradenticle</i> in <i>D. citri</i> that appears to be a retrogene. Expression data and sequence conservation suggest that the <i>extradenticle</i> retrogene may have retained the original <i>extradenticle</i> function and allowed the parental <i>extradenticle</i> gene to diverge.
DOI: 10.5524/100999
title: Supporting data for "Genome assembly of the numbat (<i>Myrmecobius fasciatus</i>), the only termitivorous marsupial"

description: The numbat (<i>Myrmecobius fasciatus</i>) is a critically endangered Australian marsupial, and the last surviving member of the Myrmecobiidae family. The numbat is unique amongst marsupials as it is the only diurnal and termitivorous species, and regularly undergoes torpor. Here we sequenced the first draft genome of the numbat using 10x Genomics chromium linked-read technology, resulting in a 3.42 Gbp genome with a scaffold N50 of 223 Kbp. A global transcriptome from liver, lung and tongue was also generated to aid genome annotation with Fgenesh++, identifying 21,465 protein-coding genes and 82.8% complete mammalian BUSCOs. To investigate adaptation to the numbats termitivorous diet and arid/semi-arid range, we interrogated the most highly expressed transcripts within the tongue and manually annotated taste, vomeronasal and aquaporin gene families. Antimicrobial proteins and proteins involved in digestion were highly expressed in the tongue, as expected. Contraction of the bitter taste receptor gene repertoire in the numbat genome, and expression of umami taste receptors in the tongue transcriptome, indicate a potential evolutionary adaptation to their specialized termitivorous diet. Vomeronasal and aquaporin gene repertoires were similar to other marsupials and have not undergone expansion or contraction. The draft numbat genome is a valuable tool for conservation and can be applied to population genetics/genomics studies and to investigate the unique biology of this interesting species.
DOI: 10.5524/101001
title: Genome sequence of the duck (<em>Anas platyrhynchos</em>).

description: Available here is the first draft genomic sequence of the duck (<em>Anas platyrhynchos</em>). Duck is a member of Anatidae, a family of birds that include geese and swans. However, duck is an economically important waterfowl serving as a source of meat, eggs and feathers; though, of special interest to agriculture and medicine is that fact that the duck is a principal natural host of influenza A viruses and harbours all subtypes of 16 haemagglutinin and 9 neuraminidase subtypes currently known, except for H13 and H16 subtypes. <br>
Using llumina Genome Analyser sequencing technology the genome of a 10-week old female Beijing duck was sequenced and a total 77 Gb of paired-end reads (approximately 64-fold coverage of the whole genome) was generated with an average length of 50 bp. Using SOAPdenovo to combine short reads, a draft genome assembly was constructed consisting of 78,487 scaffolds and covered 1.1 Gb. The contig N50 and scaffold N50 values were 26 kb and 1.2 Mb respectively. Super scaffolds were constructed and chromosomal sequences created according to the duck genetic map this resulted in 47 superscaffolds which contained 225 scaffolds and spanned 289 Mb. Transcriptomes were also generated from several different tissues, comprising 1.87 million ESTs, and approximately 121 million 75-bp and 917 million 90-bp paired-end reads, which were generated using either the 454/Roche Life Sciences Analyzer or Illumina Genome sequencing technology.
DOI: 10.5524/101002
title: Genomic data of the Little Egret (<em>Egretta garzetta</em>).

description: The Little Egret (<em>Egretta garzetta</em> (Linnaeus, 1766)) is a small white heron. An adult's average size is 5565 cm long with an 88106 cm wingspan, and weighs 350550 grams. Little egret's are mostly silent birds, but make various croaking and bubbling calls at their breeding colonies and produce a harsh alarm call when disturbed. <br>
These data have been produced as part of a project on deciphering the genomics of near extinction events, with the egret as a control species for the Ibis. DNA from a male in the Southern Qinling Mountains, Yangxian County Reserve, China. We sequenced the genome to a depth of approximately 74X with short reads from a series of libraries with various insert sizes (170bp, 500bp, 800bp, 2kb, 5kb, 10kb and 20kb). <br>
The assembled scaffolds of high quality sequences total 1.2 Gb, with the contig and scaffold N50 values of 24 kb and 3.1Mb respectively. We identified 16,585 protein-coding genes with a mean length of 18.6 kb.
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DOI: 10.5524/101006
title: Genomic data from the peregrine falcon (<em>Falco peregrinus</em>).

description: The peregrine falcon (<em>Falco peregrinus</em>) is a top predator that has unique morphological, physiological and behavioural adaptations, allowing them to be successful hunters it is also known as the worlds fastest animal. <br>The peregrine falcon genome was sequenced to further understand the evolutionary adaptation of this successful hunter. An Illumina HiSeq 2000 platform was used to generate a 128.07 Gb sequence and the initial genome size was estimated at 1.2 Gb, suggesting a genome coverage of 106.72X.<br> SOAPdenovo was used for assembly and resulted in scaffold and contig N50 values of 3.89 Mb and 28.6 kb respectively. Fosmid-based Sanger sequencing confirmed &gt;99% coverage of euchromatic DNA. These data provide insights into evolution of the peregrines predatory lifestyle.<br>
DOI: 10.5524/101007
title: Genomic data of the Killdeer (<em>Charadrius vociferus</em>).

description: The Killdeer (<em>Charadrius vociferus vociferus </em>(Linnaeus, 1758)) is a medium-sized plover (a wading bird belonging to the subfamily Charadriinae), and often uses a "broken wing act" to distract predators from their nests. <br>
These data have been produced as part of the G10K and Avian Phylogenomics Project. DNA was collected from a vouchered tissue sample (B-66055) from the Louisiana State University Museum, of a female, subspecies peruvianus, caught in Loreto, Peru. We sequenced the genome to a depth of approximately 100X with short reads from a series of libraries with various insert sizes (170bp, 500bp, 800bp, 2kb, 5kb, 10kb and 20kb). <br>
The assembled scaffolds of high quality sequences total 1.2 Gb, with the contig and scaffold N50 values of 32 kb and 3.6Mb respectively. We identified 16,856 protein-coding genes with a mean length of 19.1kb.
DOI: 10.5524/101011
title: Genomic data of the Hoatzin (<em>Opisthocomus hoazin</em>).

description: The Hoatzin (<em>Opisthocomus hoazin</em> (Müller, 1776)) is a pheasant-sized tropical bird found in swamps, forest and mangroves of the Amazon and Orinoco Delta in South America. It is known by other names, such as the Hoactzin, Stinkbird or Canje Pheasant and is notable for having chicks that possess claws on two of their wings. <br>
These data have been produced as part of the G10K and Avian Phylogenomics Project. DNA was collected from a female obtained in Lagunas, Venezuela, with the sample obtained by Maria Gloria Dominguez-Bello of the University of Puerto Rico. We sequenced the genome to a depth of approximately 100X with short reads from a series of libraries with various insert sizes (170bp, 500bp, 800bp, 2kb, 5kb, 10kb and 20kb). <br>
The assembled scaffolds of high quality sequences total 1.14Gb, with the contig and scaffold N50 values of 24kb and 2.9Mb respectively. We identified 15,702 protein-coding genes with a mean length of 20kb.
DOI: 10.5524/101012
title: Genomic data of the Downy Woodpecker (<em>Picoides pubescens</em>).

description: The Downy Woodpecker (<em>Picoides pubescens </em>(Linnaeus, 1766)) is the smallest of its kind in North America. It uses a number of vocalizations, including a short 'pik' call and produces a slow drumming sound while it pecks into trees compared with other North American woodpeckers. <br>
These data have been produced as part of the G10K and Avian Phylogenomics Project. DNA was collected from a vouchered tissue sample (B-21955) from the Louisiana State University Museum, of a female caught in Marcum Mountain, Cowell County, Montana, USA. We sequenced the genome to a depth of approximately 105X with short reads from a series of libraries with various insert sizes (170bp, 500bp, 800bp, 2kb, 5kb, 10kb and 20kb). <br>
The assembled scaffolds of high quality sequences total 1.17Gb, with the contig and scaffold N50 values of 20kb and 2Mb respectively. We identified 15,576 protein-coding genes with a mean length of 20kb.
DOI: 10.5524/101013
title: Genomic data of the Ostrich (<em>Struthio camelus australis</em>).

description: The Southern Ostrich (<em>Struthio camelus australis</em> (Gurney, 1868)) is a sub-species of The Common Ostrich (Struthio camelus) and found in southern Africa, south of the Zambezi and Cunene rivers. It is a flightless bird native to Africa and the only living member of the genus, Struthio. The Ostrich is farmed throughout the world for its meat, feathers and leather. <br>
These data have been produced as part of the G10K and Avian Phylogenomics Project. DNA was collected from a female at the San Diego Zoo in California by Oliver Ryder, of an animal originally from Botswana, Africa (ISIS ID: 202443). We sequenced the 2.16Gb genome to a depth of approximately 85X with short reads from a series of libraries with various insert sizes (170bp, 500bp, 800bp, 2kb, 5kb, 10kb and 20kb). <br>
The assembled scaffolds of high quality sequences total 1.23Gb, with the contig and scaffold N50 values of 29kb and 3.5Mb respectively. We identified 16,178 protein-coding genes with a mean length of 19.5kb.
<br><b>Update - 13-AUG-2014 -</b> A new assembly making use of the optical mapping data has been release, this improves the assembled scaffolds N50 to 17.7 Mb, the protein count is unchanged.
DOI: 10.5524/101015
title: Genomic data of the Rifleman (<em>Acanthisitta chloris</em>).

description: The Rifleman (<em>Acanthisitta chloris</em> (Sparrman, 1787)) is an endemic bird to New Zealand and is also known as New Zealand wrens, or Ttipounamu in Maori. It belongs to the Acanthisittidae family, and is one of two surviving species. The Rifleman is named after a colonial New Zealand regiment because its plumage is similar to the military uniform of a rifleman. <br>
These data have been produced as part of the Avian Phylogenomics Project. DNA was collected from an animal found dead after in earthquake in Kaikoura, South Island, New Zealand, with tissue provided by Mike Bunce and Paul Scofield. We sequenced the genome to a depth of approximately 29X.
<br> The assembled scaffolds of high quality sequences total 1.05 Gb, with the contig and scaffold N50 values of 18kb and 64kb respectively. We identified 14,596 protein-coding genes with a mean length of 13.5kb.
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DOI: 10.5524/101016
title: Genomic data of the Bar-tailed trogon (<em>Apaloderma vittatum</em>).

description: The Bar-tailed trogon (<em>Apaloderma vittatum </em>(Shelley, 1882)) belongs to the Trogonidae family of birds and lives in forests at a preferred altitude of around 1600 metres, and who's vocalisations are described "a yelping crescendo". It is found in several African countries - Angola, Burundi, Cameroon, Democratic Republic of the Congo, Equatorial Guinea, and Kenya, to name a few. <br> 
These data have been produced as part of the Avian Phylogenomics Project. DNA was collected from a vouchered tissue sample (Cat# 140150) from the Natural History Museum of Denmark, of a male collected in the Udzungwa mountains of Tanzania. We sequenced the genome to a depth of approximately 28X. <br>
The assembled scaffolds of high quality sequences total 1.08Gb, with the contig and scaffold N50 values of 19kb and 56kb respectively. We identified 13,615 protein-coding genes with a mean length of 13.5kb.
DOI: 10.5524/101019
title: Genomic data of the Chuk-will's-widow (<em>Antrostomus carolinensis</em>).

description: The Chuck-will's-widow (<em>Antrostomus carolinensis </em>(Gmelin, 1789)) is a nocturnal bird and part of the Caprimulgidae family. It's name is derived from a continuous repetitive song often heard at night, and is often confused with Whippoorwills due to their similar calls and unusual names. <br>
These data have been produced as part of the Avian Phylogenomics Project. DNA was collected from a vouchered tissue sample (B-3403) from the Louisiana State University Museum, of a male caught in East Jetty Woods, Cameron Parish, Louisiana, USA. We sequenced the genome to a depth of approximately 30X. <br>
The assembled scaffolds of high quality sequences total 1.15Gb, with the contig and scaffold N50 values of 17kb and 45kb respectively. We identified 14,676 protein-coding genes with a mean length of 12kb. <br>
DOI: 10.5524/101020
title: Genomic data of the Red-legged seriema (<em>Cariama cristata</em>).

description: The Red-legged Seriema (<em>Cariama cristata</em> (Linnaeus, 1766)) is a predatory terrestial bird in the Cariamidae family. It is also known as the Crested Cariama. It is found in the grasslands of Brazil, south of the Amazon to Uruguay and northern Argentina. The Red-legged Seriema has a song described to sound like a cross between a bark of a young dog and a clucking of turkeys. <br>
These data have been produced as part of the Avian Phylogenomics Project. DNA was collected from a male (left leg band # 295951) who had lived at the Copenhagen Zoo in Denmark (originally born in Noorder Dierenpark [Emmen Zoo] Holland), of an animal tended to by Mads Bertelsen. We sequenced the 1.5Gb genome to a depth of approximately 24X. <br>
The assembled scaffolds of high quality sequences total 1.15Gb, with the contig and scaffold N50 values of 17kb and 54kb respectively. We identified 14,216 protein-coding genes with a mean length of 13.7kb. <br>
DOI: 10.5524/100976
title: Supporting data for "Genome size evolution in the diverse insect order Trichoptera"

description: Genome size is implicated in form, function, and ecological success of a species. Two principally different mechanisms are proposed as major drivers of eukaryotic genome evolution and diversity: Polyploidy (i.e. whole genome duplication: WGD) or smaller duplication events and bursts in the activity of repetitive elements (RE). Here, we generated <i>de novo</i> genome assemblies of 17 caddisflies covering all major lineages of Trichoptera. Using these and previously sequenced genomes, we use caddisflies as a model for understanding genome size evolution in diverse insect lineages. <br>We detect approximately 14-fold variation in genome size across the order Trichoptera. While gene age distribution analyses found no evidence that ancient WGD played a major role in genome size variation in this group, we find strong evidence that transposable element (TE) expansions are the primary drivers of large caddisfly genome sizes. Using an innovative method to examine TEs associated with BUSCO genes, we find that TE expansions have a major impact on protein-coding gene regions with TE-gene associations showing a linear relationship with increasing genome size. Intriguingly, we find that expanded genomes and TE-gene associations preferentially evolved in caddisfly clades with a higher ecological diversity (i.e. various feeding modes, diversification in variable, less stable environments). <br>Our findings provide a platform to test hypotheses about the potential evolutionary roles of TE activity and TE-gene associations, particularly in groups with high species, ecological, and functional diversities.
DOI: 10.5524/100978
title: Supporting data for "A genome assembly of the Atlantic chub mackerel (<i>Scomber colias</i>): a valuable teleost fishing resource"

description: The Atlantic chub mackerel, <i>Scomber colias</i><em> </em>Gmelin, 1789, is a medium-size pelagic fish with substantial importance in the fisheries of the Atlantic Ocean and the Mediterranean Sea. Over the past decade, this species has gained special relevance being one of the main targets of pelagic fisheries in the NE Atlantic. Here, we sequenced and annotated the first high-quality draft genome assembly of <i>S. colias</i>, produced with PacBio HiFi long reads and Illumina Paired-End short reads. The estimated genome size is 814 Mb distributed into 2,028 scaffolds and 2,093 contigs with an N50 length of 4,19 and 3,34 Mb, respectively. We annotated 27,675 protein-coding genes and the BUSCO analyses indicated high completeness, with 97.3% of the single-copy orthologs in the Actinopterygii library profile. The present genome assembly represents a valuable resource to address the biology and management of this relevant fishery. Finally, this is the fourth high-quality genome assembly within the Order Scombriformes and the first in the genus <i>Scomber. </i>
DOI: 10.5524/100979
title: Supporting data for "LT1, an ONT long-read-based assembly scaffolded with Hi-C data and polished with short reads"

description: We present LT1, the first high-quality human reference genome from the Baltic States. LT1 is a female <i>de novo</i> human reference genome assembly constructed using 57x nanopore long reads and polished using 47x short paired-end reads. We utilized 72 Gb of Hi-C chromosomal mapping data for scaffolding, to maximize the assemblys contiguity and accuracy. LT1s contig assembly was 2.73 Gbp in length consisting of 4,490 contigs with an NG50 value of 12.0 Mbp. After scaffolding with Hi-C data and extensive manual curation, we produced an assembly with an NG50 value of 137 Mbp and 4,699 scaffolds. Our gene prediction quality assessment using BUSCO identified 89.3% of the single-copy orthologous genes included in the benchmark. Detailed characterization of LT1 has suggested that it has 73,744 predicted transcripts, 4.2 million autosomal SNPs, 974,616 short indels, and 12,079 large structural variants. These data are shared as a public resource without any restrictions and can be used as a benchmark for further in-depth genomic analyses of the Baltic populations.
DOI: 10.5524/100982
title: Supporting data for "A high-quality assembly reveals genomic characteristics, phylogenetic status and causal genes for leucism plumage of Indian peafowl"

description: The dazzling phenotypic characteristics of male Indian peafowl (<i>Pavo cristatus</i>) are attractive to both the female of the species and to humans. However, little is known about the evolution of the phenotypic and phylogeny of these birds at the whole-genome level. So far, there are no reports regarding the genetic mechanism of the formation of leucism plumage in this variant of Indian peafowl. <br>A draft genome of Indian peafowl was assembled, with a genome size of 1.05 Gb (the sequencing depth is 362x), and contig and scaffold N50 were up to 6.2 Mb and 11.4 Mb, respectively. Compared with other birds, Indian peafowl showed changes in terms of metabolism, immunity, skeletal development and feather development, which provided a novel insight into the phenotypic evolution of peafowl, such as the large body size and feather morphologies. Moreover, we determined that the phylogeny of Indian peafowl was more closely linked to turkey than chicken. Specifically, we first identified that <i>PMEL</i> was a potential causal gene leading to the formation of the leucism plumage variant in Indian peafowl.<br>This study provides an Indian peafowl genome of high-quality as well as a novel understanding of phenotypic evolution and phylogeny of Indian peafowl. These results provide a valuable reference for the study of avian genome evolution.
DOI: 10.5524/100987
title: Supporting data for "X-ray microtomography imaging of craniofacial hard tissues in selected reptile species with different types of dentition"

description: Reptiles exhibit a large heterogeneity in the teeth morphology. The main variability is comprised by the different tooth shape, the type of tooth attachment to the underlaying bone, or by the ability to replace the teeth. <br>Here, we provide full datasets of microtomography scans and 3D models of reptilian skulls. We selected representative species for each of nine reptilian families, based on their characteristic dental features. As there are at least four different types of tooth-bone attachments, ranging from mammalian-like thecodont attachment found in crocodilian to the simple acrodont implantation observed in some lizards, we aimed to evaluate species with different types of tooth-bone attachments. Moreover, another interesting feature varying in reptilian species is the complexity of tooth shape or the number of tooth generations, which can be associated with the type of tooth attachment to the jawbone. Therefore, selected model species also include animals with distinct tooth morphology along the jaw or different number of tooth generations. Development of tooth attachment and relationship of tooth to the jaw can be further analysed in details on large collection of pre-hatching stages of chameleon. Next, we introduce different possibilities how these datasets can be analysed with focus on the tooth-bone relationship and tooth morphology in 3D space. Moreover, these datasets can be valuable for further morphological and morphometric analyses of reptilian skulls or their individually segmented skeletal elements. <br>In conclusion, our collection of micro-computed tomography scans can bring new insight into dental or skeletal research. Broad selection of reptilian species together with their unique dental features and high quality of these scans including complete series of developmental stages of our model species, provide large opportunities of their biological reusage. Scans can be further used for virtual reality, 3D printing, or follow up usage of these models in education.
DOI: 10.5524/100990
title: Supporting data for "The Nencki-Symfonia EEG/ERP dataset: Multiple cognitive tasks and resting-state data collected in a sample of healthy adults"

description: One of the primary goals of neuropsychology is to understand the brain mechanisms underlying various aspects of attention and cognitive control. Several tasks have been developed as a part of this body of research, however their results are not always consistent. A reliable comparison of the data and a synthesis of study conclusions has been precluded by multiple methodological differences. Here, we describe a publicly available, high-density electroencephalography (EEG) dataset obtained at the Nencki Institute of Experimental Biology from a sample of 42 healthy young adults while they performed three cognitive tasks: (1) an extended Multi-Source Interference Task (MSIT+) with control, Simon, Flanker, and multi-source interference trials; (2) a 3-stimuli oddball task with frequent standard, rare target, and rare distractor stimuli; (3) a control, simple reaction task (SRT); and additionally (4) a resting-state protocol (REST). Basic demographic and psychometric information are included within the dataset (including The Amsterdam Resting-state Questionnaire (ARSQ) and UWIST Mood Adjective Check List questionnaires).