cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100003
title: Genomic data from the crab-eating macaque/cynomolgus monkey (<em>Macaca fascicularis</em>).

description: The crab-eating macaque (<em>Macaca fascicularis</em>), also known as the Java macaque or long-tailed macaque, is a species of primate located throughout Southeast Asia. Due to the frequent usage of the genus <em>Macaca</em> in scientific research, the sequence the crab-eating macaque furthers our understanding on how it differs from other macaque species, like the Chinese rhesus macaque and the Indian rhesus macaque. This is especially relevant considering the recent trend of using crab-eating macaque (CE) and Chinese rhesus macaques rather than the Indian rhesus macaque as laboratory models.

The DNA sample for genome sequencing and analyses was from a female CE that was a captive-bred descendent of a CE from Vietnam. The genome was sequenced on the IlluminaGAIIx platform, and we obtained 162-Gb of high-quality sequence, representing 54-fold coverage. The sequencing data were processed with Illumina custom computational pipelines. The genome was <em>de novo</em> assembled using SOAPdenovo program based on the de Bruijn graph algorithm methods. The total size of the assembled genome was about 2.85 Gb, providing 54-fold coverage on average. The scaffolds were assigned to the chromosomes according to the synteny displayed with the Indian rhesus macaque and human genome sequences. About 92% of the CE scaffolds could be placed onto chromosomes.
DOI: 10.5524/100007
title: Genomic data from the domestic pigeon (<em>Columba livia</em>).

description: The domestic pigeon (<em>Columba livia domestica</em>) is one of the most common birds on planet Earth, located on every continent besides Antarctica. The sub-species sequenced was a breed known as the Danish Tumbler, a show pigeon with a distinct color markings.<br><br>The domestic pigeon genome sequence provides a better understanding of such a widespread creature, including certain mechanisms that scientists still fail to understand fully, such as the magnetosensitivity. The sequencing data also presents insight into the species similarities to and differences from other birds, and to how breeding might have shaped its genome as this sub-species was taken from Asian colonies to Denmark 400 years ago and selectively bred.<br><br>In 2010, BGI used the whole genome shotgun sequencing and IlluminaHiseq 2000 system to generate 98X short reads for a Danish Tumbler. The raw data was then used by the assembler SOAPdenovo to produce a draft assembly of 1.1 Gb with N50 scaffold length of 3.1Mb and N50 contig length of 22.4 Kb. Based on the k-mer distribution of sequencing data, the genome size of <em>Columba livia</em> is estimated to be 1.3 Gb, suggesting the current assembly is about 84% complete. The percentage of GC content (41.5%) and the percentage of repetitive content (8.7%) in the pigeon are also similar in nature to three other avian genomes (chicken, zebra finch, turkey); the uncovered regions of the genome appear to be enriched in repeats. A total of 17,300 protein-coding genes are predicted in the assembly.
DOI: 10.5524/100009
title: The genomic sequence of the Chinese hamster ovary (CHO) K1 cell line (<em>Cricetulus griseus</em>).

description: Chinese hamster ovary (CHO) K1 cells are a cell line cultured from the ovary of the Chinese hamster (<em>Cricetulus griseus</em>). CHO cells are often used in biological and medical studies and commercially in the production of therapeutic proteins, which contribute significantly to the $100 billion biopharmaceutical market.

BGI sequenced the CHO K1 genome genome using next-generation sequencing technology, assembling a 2.45G genome with 24,383 predicted genes.
DOI: 10.5524/100012
title: Genome data from sweet and grain sorghum (<em>Sorghum bicolor</em>).

description: Sorghum is produced globally as a source of food, feed, fiber, and fuel. Grain and sweet sorghums differ in a number of important traits including stem sugar and juice accumulation, plant height, and the production of grain and biomass. The first sorghum whole-genome sequences are now available for analysis, but additional genomic sequences will be required to study genome-wide and intraspecific variation for dissecting the genetic basis of these important traits and for tailor-designed breeding of this important C4 crop.

In a joint effort with scientists from the Institute of Botany of Chinese Academy of Sciences (Beijing) and Temasek Life Sciences Laboratory (Singapore), BGI resequenced two sweet and one grain sorghum inbred lines: E-Tian, Ji2731, and Keller. E-Tian (literally meaning Russian Sweet in Chinese) is a sweet sorghum line introduced into China in the early 1970s. Ji2731 is a Chinese kaoliang grain sorghum that is well adapted to Northeast China. Keller is an American-bred elite sweet sorghum line shown to perform well across a wide range of environmental conditions.

Using the re-sequencing data, a set of nearly 1,500 genes differentiating sweet and grain sorghum were identified. These genes fall into 10 major metabolic pathways involved in sugar and starch metabolisms, lignin and coumarin biosynthesis, nucleic acid metabolism, stress responses and DNA damage repair. In addition, 1,057,018 SNPs, 99,948 indels of 1-10bp in length and 16,487 presence/absence variations were uncovered, and 17,111 CNVs were detected. The majority of the SNPs, large-effect SNPs, indels and presence/absence variations resided in genes containing leucine rich repeats, PPR repeats and disease resistance R genes possessing diverse biological functions or under diversifying selection, but were absent in genes which are essential for life.

This is the first publically available data that allows the identification of genome-wide patterns of genetic variation in sorghum. The high-density SNP and indel markers presented here will be a valuable resource for future genotype and phenotype studies and the molecular breeding of this important crop and for related species.
DOI: 10.5524/100014
title: DNA methylome of human peripheral blood mononuclear cells from the YH Han Chinese individual.

description: The methylome reported and analyzed here was generated from the same sample of peripheral blood mononuclear cells (PBMCs) from a consented donor (Homo sapiens) whose genome was deciphered in the YH project. YH is an anonymous male Han Chinese individual who has no known genetic diseases, and whose genome also serves as an Asian reference genome.

Nuclear DNA was extracted and subjected to unbiased, whole-genome bisulfite sequencing (BS-seq) using the Illumina Genome Analyzer. In total, 103.5 Gbp of paired-end sequence data were generated. Of these, 70.4 Gbp (68%) were successfully aligned to either strand of the YH genome with an average mismatch rate of 1.3%, resulting in an average sequencing depth of 12.3-fold per DNA strand or a 24.7-fold overall depth. Of the 18,962,679 CpGs present in the unique haploid part (2.21 Gb) of the YH reference genome sequence, approximately 99.86% were covered by at least one unambiguously mapped read of quality score &gt;14 on either strand, and 92.62% were unambiguously covered on both strands.
DOI: 10.5524/100018
title: Genome data from the Florida carpenter ant (<em>Camponotus floridanus</em>).

description: Here we present the sequenced genome of the Florida carpenter ant (<em>Camponotus floridanus</em>), a species with an organized caste society. As an eusocial species, its genome offers interesting insights into aging, epigenetics and animal behavior.

The Illumina Genome Analyzer platform was used to sequence a genomic library of the Florida carpenter ant, obtaining more than 100-fold coverage. The draft genomic assembly reached a scaffold N50 size of ~600 Kb and covers more than 90% of the approximately 240 Mb genome.
DOI: 10.5524/100024
title: Resequencing data from 40 varieties of wild and domesticated silkworms.

description: Here we present whole-genome resequencing data of 40 domesticated and wild silkworms (<em>Bombyx</em>). The domesticated silkworm (<em>Bombyx mori</em>) is of great economic interest and has been domesticated for more the 5,000 years. An organism with a mid-range genome size (~432 Mb), it often serves as a model insect for the order Lepidoptera. A number of wild varieties of silkworms exist as well, including the Chinese wild silkworm (<em>Bombyx mandarina</em>) from which the domesticated silkworm originated.

Each of the silkworm varieties was sequenced to ~3X coverage, representing 99.88% of the genome. These sequences were then used to create a single-base pair resolution genetic variation map of the silkworm. SNP sets were obtained separately for the pool of 29 domesticated strains and the pool of 11 wild varieties. The number of SNPs in the domestic versus wild varieties was approximately 14 million and 13 million, respectively. In addition to SNPs, approximately 0.33 million small insertion-deletions (indels) and 35 thousand structural variants (SVs) were identified among the 40 varieties. Over three-fourths of the SVs overlapped with transposable elements.

A total of 1,041 candidate regions Genomic Regions of Selective Signals (GROSS) were identified. These regions cover 12.5 Mb (2.9%) of the genome and may reflect genomic footprints left by artificial selection during domestication, as they include 354 protein-coding genes that were identified as good candidates for domestication genes.

We observed that 159 genes from GROSS were expressed in on different B. mori tissues on day 3 of the fifth larval instar as a reference strain, and were enriched in tissues of silk gland, midgut, and testis. The genes expressed in silk gland are involved in the synthesis of silk proteins, including fibroin and sericin. Midgut-enriched genes are related to the metabolism of carbohydrates, amino acids and lipids. And genes enriched in the testis are annotated as having binding, catalytic, and motor activity related to reproduction.

The reference genome for this project was the Japanese wild silkworm (NCBI Accession Number NC_003395).
DOI: 10.5524/100030
title: Genomic data from the Pacific oyster (<em>Crassostrea gigas</em>).

description: The Pacific oyster (<em>Crassostrea gigas</em>) belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. In this study, DNA was extracted from an oyster derived from four generations of full-sib mating. Short-reads and a fosmid-pooling strategy were used for sequencing and assembly of the oyster genome. DNA extracted from the inbred oyster and another wild oyster was used for resequencing analysis. Finally, RNA-seq and small RNA from different organs at different developmental stages were extracted for developmental studies.
DOI: 10.5524/100034
title: Hepatocellular carcinoma genomic data from the Asia Cancer Research Group.

description: Hepatocellular carcinoma (HCC) is one of the most common solid tumors worldwide and represents the third leading cause of cancer deaths. Hepatitis B virus (HBV) is a major etiologic agent, leading to an increased risk of developing HCC, in particular those with acute liver disease and cirrhosis. The Asian Cancer Research Group (ACRG) is an independent, not-for-profit company established to accelerate research and improve treatment for patients affected with the most commonly-diagnosed cancers in Asia.

With HBV being endemic in China and Southeast Asia, and high levels of HCC being a result, the ACRG have studied the events and effects of HBV integration in the HCC genome. To do this massively parallel sequencing in a cohort of 88 Chinese patients diagnosed with HCC who underwent curative primary hepatectomy or liver transplantation at Queen Mary Hospital (Pokfulam, Hong Kong) was carried out. All patients gave written informed consent to use both tumor (T) and non-tumor (N) liver tissues for the study.

Genomic DNA was purified for at least 30-fold coverage paired-end (PE) sequencing, and PE reads were mapped on human reference genome (UCSC build hg19) and HBV (NC_003977). Two sequencing libraries with different insert size were constructed for each genomic DNA sample (200 bp and 800 bp). Paired end, 90bp read length sequencing was performed in the HiSeq 2000 sequencer according to Manufacturers instructions. Raw gene expression profiling data of these human HCC samples has also deposited to GEO with the accession number GSE25097.
DOI: 10.5524/100038
title: Updated genome assembly of YH: the first diploid genome sequence of a Han Chinese individual (version 2, 07/2012)

description: Updated genomic data from the YH <em>(Homo sapiens)</em> diploid genome the first sequenced Han Chinese individual, a representative of the Asian population. The genomic DNA used in this study came from an anonymous male Han Chinese individual who has no known genetic diseases.

The original version of the YH genome was assembled based on 3.3 billion reads using the Illumina Genome Analyzer (see dataset doi:10.5524/100015). This latest (as of 07/2012) and improved version of the YH genome was assembled based on 2.1 billion reads using the Illumina HiSeq2000. A total of 202G nucleotides data was achieved using 100 bp-long paired end reads with an insert size ranging from 180 bp to 40 kbp, and the genome was sequenced to 67.5-fold average coverage. The latest version of SOAPdenovo2 was used to reassemble, improve and update the previously assembled genome (tools and pipelines available here: doi:10.5524/100044). By aligning the short reads with SOAP, 177G nucleotides were mapped onto the NCBI reference genome and 99.99% of the genome was covered. The raw sequences, assemblies and relevant tools are released for public use under a CC0 license.

More information about the YH genome can be viewed at: http://yh.genomics.org.cn/
DOI: 10.5524/100039
title: Genomic data of the Puerto Rican Parrot (<em>Amazona vittata</em>) from a locally funded project.

description: These data represent the first assembly of a genome sequence for a critically endangered parrot (<em>Amazona vittata</em>) endemic to the United States, and also the first genome of a species from the diverse and ecologically important genus <em>Amazona</em> native to South America and the Caribbean. One sample has been selected from the non-reproductive female at Rio Abajo Breeding Facility in Puerto Rico (IACUC#201109.1), and sequenced on Illumina HiSeq platform with both fragment and paired-end sequencing approaches, resulting in a total of 42,479,499,706 bases. We predicted a total coverage depth of 26.89X of the parrots genome: 17.08X coverage for the short fragment reads, and 9.8X coverage for the mate pairs. The sequencing was initiated with the construction of two genome libraries: a short fragment library (~300 bp inserts) for sequencing the majority of the genome, and a long fragment library (~2.5 Kb inserts) to generate scaffolds to be used to order and assemble contigs derived from the short fragment library. The Illumina paired-end and mate-pairs reads were assembled together with Ray (http://denovoassembler.sourceforge.net), with the k-mer defined iteratively. In total, given that the genome size is predicted to be 1.58Gb, with the total scaffold length of 1,184, 594,388 bp, the overall coverage of the genome is around 76%, a value that might be slightly overestimated given that some of the scaffolds may be overlapping but could not be assembled. Filtering followed by assembly resulted in 259,423 contigs (N50=6,983 bp, longest = 75,003 bp), which was further combined into 148,255 scaffolds (N50 = 19,470, longest = 206,462 bp). The database contains all of the contigs, scaffolds, corresponding assembly parameters, and the annotations for the known repeats and coding sequences. The assembled scaffolds allow basic genomic annotation and comparative analyses with other available avian whole-genome sequences.
DOI: 10.5524/100004
title: Genomic data from the giant panda (<em>Ailuropoda melanoleuca</em>).

description: The giant panda (<em>Ailuropoda melanoleuca</em>) is considered a symbol of China and is a much loved animal all around the world. It is also one of the worlds most endangered species, making it a flagship species for conservation efforts. As the first fully sequenced Ursidae and the second fully sequenced carnivore after the dog, the whole genome sequence and annotation data provide an unparalleled amount of information to aid in understanding the genetic and biological underpinnings of this unique species, and will help contribute to disease control and conservation efforts.

In 2008, BGI completed a first draft of the genome sequence of a three-year old female giant panda named Jingjing, who was used as a model for the 2008 Olympics in Beijing, China (doi: 10.1038/nature08696). Using second-generation Illumina GA sequencing data, the first de novo genome assembly was created using short-read sequencing technology. Here you will find the giant panda genome sequence assembly as well as annotation information, such as gene structure and function, non-coding RNAs, and repeat elements. Also presented are polymorphism information detected in the diploid genome, including SNPs, indels, and structural variations (SVs). The assembly was done using SOAPdenovo software and the panda genome data is visualized via MapView, which is powered by the Google Web Toolkit.
DOI: 10.5524/100015
title: Genome sequence of YH: the first diploid genome sequence of a Han Chinese individual.

description: Genomic data from the YH (<em>Homo sapiens</em>) genome first diploid genome sequence of a Han Chinese, a representative of the Asian population. The genomic DNA used in this study came from an anonymous male Han Chinese individual who has no known genetic diseases.

The YH genome was assembled based on 3.3 billion reads using the Illumina Genome Analyzer. We achieved 117.7G nucleotides data and the genome was sequenced to 36-fold average coverage. By aligning the short reads with SOAP, 102.9G nucleotides were mapped onto the NCBI reference genome and 99.97% of the genome was covered. The raw sequences, alignments, consensus genome, variants and relevant tools are released for public use under a CC0 license.
DOI: 10.5524/100021
title: Genomic data from Chinese cabbage (<em>Brassica rapa</em>).

description: Available here is genomic data for the polyploid plant <em>Brassica rapa</em> ssp. pekinensis line Chiifu-401-42, a Chinese cabbage. As there are several oil and vegetable crop species in the Brassica family, this genome is of great agricultural relevance. It also provides an important resource for studying the evolution of polyploid genomes.

The <em>Brassica rapa</em> Genome Sequencing Project Consortium assembled a 283.8 Mb genome estimated to cover &gt;98% of the gene space. Using 72X coverage of paired short read sequences generated by Illumina GA II technology and 199,452 BAC-end sequences, 159 super scaffolds were produced, representing 90% of the assembled sequences with an N50 scaffold size of 1.97 Mb. Using genetic mapping of 1,427 markers in <em>B. rapa</em>, ten pseudo chromosomes that included 90% of the assembly were produced. A total of 41,174 protein-coding genes in the <em>B. rapa</em> genome were modeled, and the genome was found to have undergone genome triplication.
DOI: 10.5524/100022
title: Genome sequence of the naked mole rat (<em>Heterocephalus glaber</em>).

description: Here is the genome of the naked mole rat (<em>Heterocephalus glaber</em>), one of the only two known eusocial mammals. It is a fascinating species, due not only to its unique behavior but also to its unique physiology. Among its unusual characteristics, it has the longest lifespan of all rodent species, is a poikilotherm, is highly resistant to cancer, and does not sense certain types of pain.

The genome of an individual male naked mole rat was sequenced on the Illumina HiSeq 2000 platform and assembled using SOAPdenovo. In assembly 2.5Gb (gigabase pairs) contig sequences with N50 19.3kb (kilobase pairs) and N90 4.7kb, and 2.7Gb scaffold sequences with N50 1.6Mb (megabase pairs) and N90 0.3Mb was obtained.
DOI: 10.5524/100023
title: Genome data from the sheep.

description: This is the first version of the draft sheep (<em>Ovis aries</em>) reference genome (OAR v2.0).

A single Texel ewe and a single Texel ram were independently sequenced by next-generation sequencing platforms. The genome was assembled using a similar method to that used for the first de novo assembled genome using only next-generation sequencing platforms, the giant panda. However, here more paired-end libraries and longer insert libraries were used. Firstly, using SOAPdenovo, the 75X Texel ewe Illumina reads were assembled de novo into contigs and scaffolds. Then, 120X Illumina sequence from both the Texel ewe (BGI) and ram (Roslin) was used for gap filling so as to improve the assembly. At this point, the N50 length of contig was 18 kb, and the N50 length of the assembled scaffolds was 1.1Mb, achieving a total length of 2.71 Gb and covering ~93% of the expected ~3Gb length of the sheep genome.

The CHORI-243 BAC library end sequences were used to generate a set of super-scaffolds with an N50 of 37 Mb. Then a high density RH map and a linkage map with 39,042 SNP makers (derived from the Ovine SNP50 BeadChip) were used to anchor the super-scaffolds to chromosomes. Several rounds of manual checking and final error correction were carried out using the end sequences of the BACs in the bovine CHORI-243 library and 454 mate pair sequence data derived from 8kb and 20kb insert libraries of the male Texel (BCM). Ambiguous positions were resolved using the predicted location of the SNPs based on OARv1.0 and conserved synteny with the UMD3 bovine genome assembly. For the final release version, OAR v2.0, 95% (2.57 Gb) of the total scaffold sequence was placed onto the 26 autosomes and the X chromosome.
DOI: 10.5524/100026
title: Genomic data from an extinct Palaeo-Eskimo.

description: Available here is the genome of a male individual from an extinct Palaeo-Eskimo culture, the first known group of <em>Homo sapiens</em> to settle in Greenland.

The DNA sample was obtained from ~4,000-year-old permafrost-preserved hair, and was shown to have very low modern DNA contamination. The diploid genome was sequenced to an average depth of 20x using Illumina GAII sequencing platforms, with 79% recovery. Correct indexed reads were mapped to the human genome (hg18) with a suffix array-based method that allows for residual primer trimming. Sequencing yielded a total of 3.5 billion reads.
DOI: 10.5524/100016
title: Genomic data from the potato.

description: Available here is the genome of the potato (<em>Solanum tuberosum</em> L.), the first genome sequenced from the asterid clade. Potato is a member of the Solanaceae, a plant family that includes many other economically important species, such as tomato, petunia, eggplant, tobacco, and pepper. As the potato is both clonally propagated and the world;s most important non-grain food crop, its genome is a valuable agricultural resource.

The Potato Genome Sequencing Consortium sequenced two species: the heterozygous diploid <em>S. tuberosum</em> Group Tuberosum cultivar, RH89-039-16 (RH), and the doubled monoploid <em>S. tuberosum</em> Group Phureja clone DM1-3 516R44 (DM). The potato genome consists of 12 chromosomes, of which over 80% of the homozygous clones 844-megabase genome were assembled. Genome analysis revealed evidence of at least two genome duplication events and identified a number of asterid-specific genes. Comparison between the two clones identified frequent gene variations and mutations, which may cause inbreeding depression.