cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102625
title: Supporting data for "Genomic evidence for hybridization and introgression between blue peafowl and endangered green peafowl and molecular foundation of peafowl white plumage"

description: The blue peafowl (<i>Pavo cristatus</i>) and the green peafowl (<i>Pavo muticus</i>) have garnered significant public affection due to their stunning appearance, although the green peafowl is currently endangered. The causative mutation for the white plumage color of blue peafowl (also called white peafowl) remains unknown. <br>In this study, we generated a chromosome-level reference genome of the blue peafowl with a contig N50 of 30.6 Mb, including the autosomes, Z and W sex chromosomes, as well as a complete mitochondrial DNA sequence. Data from 77 peafowl whole genomes, 76 peafowl mitochondrial genomes and 33 peafowl W chromosome genomes provided the first substantial genetic evidence for recent hybridization between green peafowls and blue peafowls. We found three hybrid green peafowls in zoo samples rather than in wild samples, with blue peafowl genomic content of 16-34%. Maternal genetic analysis showed that two of the hybrid female green peafowls contained complete blue peafowl mitochondrial genomes and W chromosomes. Some animal protection agencies release captive green peafowls to maintain the wild population of green peafowls. Therefore, to better protect the endangered green peafowl, we suggest that purebred identification must be carried out before releasing green peafowls from zoos into the wild in order to prevent the hybrid green peafowl from contaminating the wild green peafowl. In addition, we also found that there were historical introgression events of green peafowl to blue peafowl in four zoo blue peafowl individuals. The introgressed genomic regions contain<em> </em><i>IGFBP1</i><em> </em>and <i>IGFBP3</i> genes that could affect blue peafowl body size. Finally, we identified that the nonsense mutation (g.4:12583552G&gt;A) in the <i>EDNRB2</i><em> </em>gene is the genetic causative mutation for white plumages color of blue peafowl, preventing melanocytes from being transported into plumages, thereby inhibiting melanin deposition. <br>Our research provides both theoretical and empirical support for the conservation of the endangered green peafowl. The high-quality genome and genomic data also provide valuable resource for blue peafowl genomics-assisted breeding.
DOI: 10.5524/102627
title: Supporting data for "A Telomere-To-Telomere Phased Genome of an Octoploid Strawberry Reveals a Receptor Kinase Conferring Anthracnose Resistance"

description: Cultivated strawberry (<i>Fragaria</i>×<i>ananassa</i> Duch.), an allo-octoploid species arising from at least three diploid progenitors, poses a challenge for genomic analysis due to its high levels of heterozygosity and the complex nature of its polyploid genome. <br>This study developed the complete haplotype-phased genome sequence from a short day strawberry, Florida Brilliance without parental data, assembling 56 chromosomes from telomere-to-telomere. This assembly was achieved with high-fidelity long reads and high throughput chromatic capture sequencing (Hi-C). The centromere core regions and 96,104 genes were annotated using long-read isoform RNA sequencing. Using the high-quality of haplotype phased reference genome, FaFB1, we identified the causal mutation within the gene encoding <i>Leaf Rust 10 Disease-Resistance Locus Receptor-like Protein Kinase</i> (<i>LRK10</i>) that confers resistance to anthracnose fruit rot (AFR). This disease is caused by the <i>Colletotrichum acutatum</i> species complex and results in significant economic losses in strawberry production. Comparison of resistant and susceptible haplotype assemblies and full-length transcript data revealed a 29-bp insertion at the first exon of the susceptible allele leading to a premature stop codon and loss of gene function. The functional role of <i>LRK10</i> in resistance to AFR was validated using a simplified <i>Agrobacterium</i>-based transformation method for transient gene expression analysis in strawberry fruits. Transient knock-down and overexpression of <i>LRK10</i> in fruit indicate a key role for <i>LRK10</i> in AFR resistance in strawberry. <br>The FaFB1 assembly along with other resources will be valuable for the discovery of additional candidate genes associated with disease resistance and fruit quality, which will not only advance our understanding of genes and their functions but also facilitate advancements in genome editing in strawberry.
DOI: 10.5524/102632
title: Supporting data for "Enhancing inbreeding estimation and global conservation insights through HiFi assemblies of Chinese and Malayan pangolin"

description: A high-quality reference genome coupled with resequencing data is becoming a promising strategy to address issues in conservation genomics, which has greatly enhanced the development of conservation plans for endangered species. Pangolins are fascinating animals with a range of distinctive features, but unfortunately, they are the world's most trafficked wild animals. Here, we report a haplotype-resolved and chromosome-scale genome for each of the Chinese pangolin and Malayan pangolin, the most representative reference genome for pangolin species. We found a greater improvement in evaluation of genetic diversity and inbreeding based on high-quality genomes and obtained different results in detecting genome-wide extinction risks being compared with short read assembled genomes. Moderate inbreeding and genetic diversity were verified again in these two pangolin species except for one Malayan pangolin population with the high inbreeding and low genetic diversity, which we recommend to pay special attention to the conservation and protection of this population. Additionally, our study is the first to detect relative mild genetic purging in pangolin populations that were analyzed. These two high quality reference genomes will provide valuable genomic resource for future studies on the protection and conservation for pangolins.
DOI: 10.5524/102646
title: Supporting data for "A practical DNA data storage using expanded alphabet introducing 5-methylcytosine"

description: DNA molecules are a promising next-generation data storage medium. Recently, it has been theoretically proposed that non-natural or modified bases can serve as extra molecular letters to increase the information density. However, the feasibility of the strategy is challenging due to the difficulty in synthesis, and the complex structure of non-natural DNA sequences. <br>Here, we describe a practical DNA data storage transcoding scheme named R+ based on the expanded molecular alphabet by introducing 5-methylcytosine (5mC). We also demonstrate the experimental validation by encoding one representative file into several 1.3~1.6 kbps <i>in vitro</i> DNA fragments for nanopore sequencing. The results show an average data recovery rate of 98.97% and 86.91% with and without reference respectively. This work validates the practicability of 5mC in DNA storage systems, with a potentially wide range of applications.
DOI: 10.5524/102649
title: Supporting data for "Cerebellocerebral Connectivity Predicts Body Mass Index: a New Open-Source Python-based Framework for Connectome-based Predictive Modeling"

description: The cerebellum is one of the major central-nervous structures consistently altered in obesity. Its role in higher-cognitive function, parts of which are affected by obesity, is mediated through projections to and from the cerebral cortex. We therefore investigated the relationship between body mass index (BMI) and cerebellocerebral connectivity. <br>We utilized the Human Connectome Projects Young Adults dataset including functional MRI (fMRI) and behavioral data, to perform connectome-based predictive modeling (CPM) restricted to cerebellocerebral connectivity of resting-state fMRI and task-based fMRI. We developed a Python-based open-source framework to perform CPM, a data-driven technique with built-in cross validation to establish brain-behavior relationships. Significance was assessed with permutation analysis. <br>We found that task-general cerebellocerebral connectivity predicted BMI more reliably than resting-state fMRI and individual task-based fMRI separetely. Predictive networks derived this way overlapped with established functional brain networks (namely frontoparietal networks, the somatomotor network, the salience network, and the default mode network). We found there was an inverse overlap between networks predictive of BMI and networks predictive of cognitive measures aversely affected by overweight/obesity. <br>Our results suggest obesity-specific alterations in cerebellocerebral connectivity, specifically with regard to task execution. With brain areas and brain networks relevant to task performance implicated, these alterations seem to reflect a neurobiological substrate for task performance aversely affected by obesity.
DOI: 10.5524/102651
title: Supporting data for "Genomic and transcriptomic analyses of <i>Heteropoda venatoria</i> reveal the expansion of the P450 family for starvation resistance in spider"

description: Spiders generally exhibit robust starvation resistance, with hunting spiders, represented by <i>Heteropoda venatoria</i>, being particularly outstanding in this regard. Given the challenges posed by climate change and habitat fragmentation, understanding how spiders adjust their physiology and behavior to adapt to the uncertainty of food resources is crucial for predicting ecosystem responses and adaptability. <br>We sequenced the genome of <i>H. venatoria</i> and, through comparative genomic analysis, discovered significant expansions in gene families related to lipid metabolism, such as cytochrome P450 and steroid hormone biosynthesis genes. We also systematically analyzed the gene expression characteristics of <i>H. venatoria</i> at different starvation resistance stages and found that the fat body plays a crucial role during starvation in spiders. This study indicates that during the early stages of starvation, <i>H. venatoria</i> relies on glucose metabolism to meet its energy demands. In the middle stage, gene expression stabilizes, whereas in the late stage of starvation, pathways for fatty acid metabolism and protein degradation are significantly activated, and autophagy is increased, serving as a survival strategy under extreme starvation. Additionally, analysis of expanded P450 gene families revealed that <i>H. venatoria</i> has many duplicated CYP3 clan genes that are highly expressed in the fat body, which may help maintain a low-energy metabolic state, allowing <i>H. venatoria</i> to endure longer periods of starvation. We also observed that the motifs of P450 families in <i>H. venatoria</i> are less conserved than those in insects, which may be related to the greater polymorphism of spider genomes. <br>This research not only provides important genetic and transcriptomic evidence for understanding the starvation mechanisms of spiders but also offers new insights into the adaptive evolution of arthropods.
DOI: 10.5524/102653
title: Genome assembly of the myxozoan <i>Ellipsomyxa</i> sp. fish parasite

description: The genus Ellipsomyxa was established to include the marine species <i>Ellipsomyxa</i> gobii, with subsequent descriptions of several other species that infect the gallbladders of marine or brackish fish, bringing the total number of known species to only 20. Recent studies in the Amazon Basin have revealed an increasing diversity of Ellipsomyxa parasitising fish hosts in freshwater environments, with five species already described. <br>We present two publicly available genome assemblies of the myxozoan <i>Ellipsomyxa</i> sp., with around 450 Mb (~15 fold coverage) of sequence data per assembly. The complete assemblies span around 30 Mb, with contig N50 of 758 kb. The BUSCO analysis indicates a completeness of 32.2%.
DOI: 10.5524/102656
title: Supporting data for "Healthy microbiome - moving towards functional interpretation"

description: Microbiome-based disease prediction shows promise as an early, noninvasive indicator of various health conditions linked to gut dysbiosis, aided by declining sequencing costs. Current microbiome health indices largely rely on species richness and taxonomic classification. A renewed focus on a metabolism-centric, ecological approach has revealed limitations of these traditional methods. <br>This study presents a new metagenomic health index aimed at distinguishing healthy from unhealthy microbiomes, specifically in inflammatory bowel disease (IBD). Our approach shifts from Linnean phylogenetic classification to a functional analysis of metabolic potential and ecological interactions among species. We compare our index's performance against established indices, including the Gut Microbiome Health Index (GMHI) and high-dimensional principal component analysis (hiPCA), using data from IBD cohorts and 27 additional clinical datasets. Our index outperforms GMHI and hiPCA in identifying health states, particularly in a longitudinal COVID-19 cohort, and demonstrates robustness to sequencing depth. We advocate for a functional approach to better assess microbiome health and suggest future index improvements.
DOI: 10.5524/102603
title: Supporting data for "Genomes reveal pervasive distant hybridization in nature among cyprinid fishes"

description: Genomic data has unveiled a fascinating aspect of the evolutionary past, showing that the mingling of different species through hybridization has left its mark on the histories of numerous life forms. However, the relationship between hybridization events and the origins of cyprinid fishes remains unclear. <br>In this study, we generated <i>de novo</i> assembled genomes of eight cyprinid fishes and conducted phylogenetic analyses on 24 species. Widespread allele sharing across species boundaries was observed within seven subfamilies of cyprinid fishes. Interestingly, we noted conservative divergence in the testis and incomplete reproductive isolation between the herbivorous <i>Megalobrama amblycephala</i> and the carnivorous <i>Culter alburnus</i>. Significant differences in the expression of four genes (<i>dpp2, ctrl, psb7, </i> and <i>ppce</i>) in the liver and intestine, accompanied by variations in enzyme activities, indicated swift divergence in digestive enzyme secretion. Moreover, we identified introgressed genes linked to organ development in sympatric fishes with analogous feeding habits within the <i>Cultrinae</i> and <i>Leuciscinae</i> subfamilies. <br>Our findings highlight the significant role played by incomplete reproductive isolation and frequent gene flow events, particularly those associated with the development of digestive organs, in driving speciation among cyprinid fishes in diverse freshwater ecosystems.
DOI: 10.5524/102605
title: Genome assembly of the Baikal seal <i>Pusa sibirica</i>

description: <i>Pusa sibirica</i>, the smallest true seal, is a freshwater seal that is endemic to Lake Baikal where it became landlocked some million years ago. It is a rather abundant species of least concern, with an estimated population between 80,000 to 100,000 animals, despite the limited habitat. The precise origin of the species remains ambiguous; however, the prevailing theory posits that it descends from the ringed seal, <i>Phoca hispida</i>, and indicates that the species may have experienced geographical isolation for approximately 500,000 years. <br>Until recently, research on its genetic diversity has only been done on mitochondrial genes, restriction fragment analyses, and microsatellites, before its reference genome has been published. Here we present a publicly available genome assembly of the Baikal seal <i>Pusa sibirica</i>, with 75 Gb (~32-fold coverage) of sequence data. The complete assembly spans 2.3 Gb, with contig N50 of 15 kb and scaffold N50 of 173 Mb. The BUSCO analysis indicates a completeness of 89.5%.
DOI: 10.5524/102607
title: Genome assembly of the Ringed seal <i>Pusa hispida</i>

description: The ringed seal (<i>Pusa hispida</i>) ranks among the smallest species within the phocid family. Its designation is derived from the distinctive light-colored rings that adorn its otherwise dark back. Ringed seals are found in the Arctic region, the Sea of Okhotsk, the Baltic Sea, and specific freshwater lakes in Russia or Finland. The total population of ringed seals remains largely uncertain but studies suggest that approximately 3.5 million individuals exist. <br>We present a publicly available genome assembly of the Ringed seal <i>Pusa hispida</i>, with 37 Gb (~17.3-fold coverage) of sequence data. The complete assembly spans 2.3 Gb, with contig N50 of 13 kb and scaffold N50 of 173 Mb. The BUSCO analysis indicates a completeness of 89.5%.
DOI: 10.5524/102608
title: Genome assembly of the Harbor seal <i>Phoca vitulina</i>

description: The harbour seal (<i>Phoca vitulina</i>) is classified as a small phocid seal. It is notable for having the most extensive geographical distribution of any seal species, occupying coastal waters that extend from temperate to polar regions in the Northern Hemisphere, often hauling out in groups that can consist of several hundred individuals. The population of harbour seals in the North Atlantic is estimated to be around 200,000. <br>We present a publicly available genome assembly of the Harbor seal <i>Phoca vitulina</i>, with 47 Gb (~20.5-fold coverage) of sequence data. The complete assembly spans 2.3 Gb, with contig N50 of 12 kb and scaffold N50 of 173 Mb. The BUSCO analysis indicates a completeness of 89.3%.
DOI: 10.5524/102611
title: Genome data of the cyprinid fish, <i>Megalobrama amblycephala</i> (blunt snout bream)

description: The blunt snout bream (<i>Megalobrama amblycephala</i>) is the economically most important cyprinid fish species. As an herbivore, it can be grown by eco-friendly and resource-conserving aquaculture. However, the large number of intermuscular bones in the trunk musculature is adverse to fish meat processing and consumption.[https://doi.org/10.1093/gigascience/gix039]<br>Here we present a publicly available chromosome-scale genome assembly of the blunt snout bream <i>M. amblycephala</i>. The assembled genome spans 110 Mb and exhibits a scaffold N50 value of 42.91 Mb and a contig N50 of 15.42 Mb (increased from 2.4 Mb). The BUSCO results indicated high genome assembly completeness, with 94.5% of single-copy core genes present. A total of 26,550 protein-coding genes were predicted, repetitive elements comprised 51.81% (568.18 Mb) of the assembly, and non-coding RNA was predicted in 8.76 of the genome.
DOI: 10.5524/102613
title: Genome data of the cyprinid fish, Cirrhinus molitorella (mud carp)

description: The mud carp (<i>Cirrhinus molitorella</i>) is a species of large omnivore subtropical freshwater fish in the family Cyprinidae, native to Southern China and Viet Nam and found in the Mekong River and Pearl River delta. Its cultivation has been introduced in China during the Tang dynasty and now represents up to 30% of the freshwater fish population. The mud carp exhibits a laterally compressed and elongated body structure, characterized by a rounded abdomen. Typically, adults measure approximately 15 cm in length, although some individuals can attain lengths of up to 55 cm. The dorsal region of the adult's head and back displays a greenish-grey hue, while the ventral area is silvery. Notably, the 14th and 15th scales situated above the pectoral fin are marked by crescent-shaped turquoise-blue spots. Additionally, green stripes are present at the base of the lateral scales, and all fins exhibit a purplish coloration.[Wikipedia]<br> Here we present a publicly available high quality draft genome assembly of the mud carp <i>C. molitorella</i>, with approximately 36.3 Gb of HiFi sequence data from 1 individual. This draft assembly consists of 266 contigs &gt;2kb in length, with the assembled genome spanning approximately 1066.79 Mb (contig N50 of 38.12 Mb). The BUSCO results indicated high genome assembly completeness, with 98.6% of single-copy core genes present.
DOI: 10.5524/102614
title: Genome data of the cyprinid fish, Pseudorasbora parva (Stone Moroko)

description: The stone moroko (<i>Pseudorasbora parva</i>), also known as the topmouth gudgeon, is a fish belonging to the Cyprinidae family, native to Asia, but introduced and now considered an invasive species in Europe and North America. The fish's size is rarely above 8 cm and usually 2 to 7.5 cm (0.79 to 2.95 in) long. The fish was introduced in the 1960s into ponds in Nucet, Dâmbovia County, Romania and it made its way into Danube, then spreading throughout Europe. These fish feed on eggs of locally valuable native fish species.[Wikipedia]<br> Here we present a publicly available high quality draft genome assembly of the stone moroko <i>P. parva</i>, with approximately 35.03 Gb of HiFi sequence data from 1 individual. This draft assembly consists of 234 contigs &gt;2kb in length, with the assembled genome spanning 1.29 Gb (contig N50 of 7.57 Mb). The BUSCO results indicated high genome assembly completeness, with 98.5% of single-copy core genes present.
DOI: 10.5524/102616
title: Genome data of the cyprinid fish, Elopichthys bambusa (Yellow cheek carp)

description: The yellow cheek carp (<i>Elopichthys bambusa</i>) is a large cyprinid fish native to eastern Asia. Its range spans from Russia's Amur River to Vietnam's Red and Lam Rivers, where it inhabits freshwater habitats with warm water temperatures. This fast-swimming predator reaches up to 2 meters in length and 52 kg in weight, feeding on smaller fish. Historically, its population declined significantly between the 1970s and 1990s but showed an uptick in the 2010s, the IUCN list the species as of least concern (LC).[Wikipedia]<br>Here we present a publicly available high quality draft genome assembly of the yellow cheek carp <i>E.bambusa</i>, with approximately 35.6Gb of HiFi sequence data from 1 individual. This draft assembly consists of 130 contigs &gt;2kb in length, with the assembled genome spaning approximately 863.54Mb (contig N50 of 30.38Mb), and a total of 23,553 coding genes predicted. The BUSCO results indicated high genome assembly completeness, with 98.4% of single-copy core genes present.
DOI: 10.5524/102617
title: Genome data of the cyprinid fish, <i>Ctenopharyngodon idella</i> (Grass carp)

description: The grass carp (<i>Ctenopharyngodon idella</i>) is a species of large herbivorous freshwater fish in the family Cyprinidae, native to the Pacific Far East, with a native range stretching from northern Vietnam to the Amur River on the Sino-Russian border. Whilst the grass carp are farmed for food in China (estimated five million tonnes per year), they have been widely introduced to Europe and the Americas mainly as weed control. Grass carp have elongated, chubby, torpedo-shaped bodies, and they grow rapidly with a typical adult measuring around 60-100cm, up to a maximum of 2.0m.[Wikipedia]<br>Here we present a publicly available high quality draft genome assembly of the grass carp <i>C. idella</i>, with approximately 58.8Gb of HiFi sequence data from 1 individual. This draft assembly consists of 176 contigs &gt;2kb in length, with the assembled genome spanning approximately 901.49Mb (contig N50 of 35.62Mb), and a total of 25,694 coding genes predicted. The BUSCO results indicated high genome assembly completeness, with 99.5% of single-copy core genes present.