28 Works

Genomic data for the domestic cucumber (Cucumis sativus var sativus L)

S Huang, R Li, Z Zhang, L Li, X Gu, W Fan, WJ Lucas, X Wang, B Xie, P Ni, Y Ren, H Zhu, J Li, K Lin, W Jin, Z Fei, G Li, J Staub, A Kilian, EA Van Der Vossen, Y Wu, J Guo, J He, Z Jia, Y Ren … & S Li
Here we present genomic data for the domestic cucumber (Cucumis sativus var. sativus L.). The cucumber is a member of the Cucurbitaceae or cucurbit family, a family of great agricultural and horticultural importance that also includes species such as melons, gourds and squashes. A biologically interesting as well as an economically relevant species, it is used as a model system for plant sex determination and vascular biology studies. The domestic cucumber has seven pairs of...

Genomic data from the potato

Potato Genome Sequencing Consortium, X Xu, S Pan, S Cheng, B Zhang, D Mu, P Ni, G Zhang, S Yang, R Li, J Wang, G Orjeda, F Guzman, M Torres, R Lozano, O Ponce, D Martinez, G De La Cruz, SK Chakrabarti, VU Patil, KG Skryabin, BB Kuznetsov, NV Ravin, TV Kolganova, AV Beletsky … & RG Visser
Available here is the genome of the potato (Solanum tuberosum 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...

Genome data from the Tibetan antelope (Pantholops hodgsonii)

R Ge, Q Cai, Y Shen, Asan , L Ma, Y Zhang, X Yi, Y Chen, L Yang, Y Huang, B Wang, X Ou, J Xu, Y Zhang, K Wu, C Geng, G Zhang, J Wang, Y Zhang & J Wang
The Tibetan antelope (Pantholops hodgsonii) is a native of the high mountain steppes and semi-desert areas of the Tibetan plateau. It is a medium sized antelope that displays both migratory and herd behavior. Of interest, it is the only member of the genus Pantholops. The Tibetan antelope are listed as an endangered species, which is due to commercial poaching for their fine underwool, competition with local domesticated herds, and commercial development of their range land....

Genomic data from the pigeonpea (Cajanus cajan)

RK Varshney, W Chen, Y Li, AK Bharti, RK Saxena, JA Schlueter, MT Donoghue, S Azam, G Fan, AM Whaley, AD Farmer, J Sheridan, A Iwata, R Tuteja, RV Penmetsa, W Wu, HD Upadhyaya, SP Yang, T Shah, KB Saxena, T Michael, WR McCombie, B Yang, G Zhang, H Yang … & SA Jackson
Here we present the genome of the pigeonpea (Cajanus cajan), a widely farmed diploid legume species. It is an important reference genome for food crop development as many crop species, such as soybean (Glycine max), chickpea (Cicer arietinum), lentil (Lens culinaris), and alfalfa (Medicago sativa), are legumes. The genetic improvement of pigeonpea has ramifications for food protection as well, as it is cultivated primarily in small-scale holdings in semi-arid tropical regions of the developing world....

Genomic data from Escherichia coli O104:H4 isolate TY-2482

D Li, F Xi, M Zhao, W Chen, S Cao, R Xu, G Wang, J Wang, Z Zhang, Y Li, C Cui, C Chang, C Cui, Y Luo, J Qin, S Li, J Li, Y Peng, F Pu, Y Sun, Y Chen, Y Zong, X Ma, X Yang, Z Cen … & The Escherichia Coli O104:H4 TY-2482 Isolate Genome Sequencing Consortium
The May 2011 outbreak of an E. coli infection in Europe resulted in serious concerns about the potential appearance of a new deadly strain of bacteria, Escherichia coli O104:H4 TY-2482. In response to this situation, and immediately after the reports of deaths, the University Medical Centre Hamburg-Eppendorf and BGI-Shenzhen worked together to sequence the bacterium and assess its human health risk. The bacterium’s genome was first sequenced using Life Technologies; Ion Torrent sequencing platform. According...

Genomic data from the Chinese Rhesus macaque (Macaca mulatta lasiota)

G Yan, G Zhang, X Fang, Y Zhang, C Li, F Ling, DN Cooper, O Li, Y Li, AJ Van Gool, H Du, J Chen, R Chen, P Zhang, Z Huang, Thompson, Y Meng, Y Bai, J Wang, M Zhuo, T Wang, Y Huang, L Wei, J Li, Z Wang … & J Wang
The Chinese rhesus macaque (Macaca mulatta lasiota) is a subspecies of rhesus macaques that mainly resides in western and central China. Due to their anatomical and physiological similarity with human beings, macaques are a common laboratory model. Also, as several macaques species have been sequenced, such as the Indian rhesus macaque and the crab-eating macaque, examination of the Chinese rhesus macaque (CR) genome offers interesting insights into the entire Macaca genus. The DNA sample for...

DNA methylome of human peripheral blood mononuclear cells from the YH Han Chinese individual

Y Li, J Zhu, G Tian, N Li, Q Li, M Ye, H Zheng, J Yu, H Wu, J Sun, H Zhang, Q Chen, R Luo, M Chen, Y He, X Jin, Q Zhang, C Yu, G Zhou, J Sun, Y Huang, H Zheng, H Cao, X Zhou, S Guo … & X Zhang
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,...

Genomic data from the roundworm Ascaris suum

AR Jex, S Liu, B Li, ND Young, RS Hall, Y Li, L Yang, N Zeng, X Xu, Z Xiong, F Chen, X Wu, G Zhang, X Fang, Y Kang, GA Anderson, TW Harris, BE Campbell, J Vlaminck, T Wang, C Cantacessi, EM Schwarz, S Ranganathan, P Geldhof, P Nejsum … & RB Gasser
Available here is the draft genome for Ascaris suum, a roundworm species that infects pigs. It is a valuable resource for therapy and diagnostic test development for both Ascaris suum infection of pigs, and also human infection by the closely related species A. lumbricoides. The A. suum genome was sequenced at ~80-fold coverage to generate an approximately 273 million base genome sequence encoding 18,542 protein-coding genes. Compared to other metazoan genomes, it has low repeat...

Resequencing data from 40 varieties of wild and domesticated silkworms

Q Xia, Y Guo, Z Zhang, D Li, Z Xuan, Z Li, F Dai, Y Li, D Cheng, R Li, T Cheng, T Jiang, C Becquet, X Xu, C Liu, X Zha, W Fan, Y Lin, Y Shen, L Jiang, J Jensen, I Hellmann, S Tang, P Zhao, H Xu … & J Wang
Here we present whole-genome resequencing data of 40 domesticated and wild silkworms (Bombyx). The domesticated silkworm (Bombyx mori) 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 (Bombyx mandarina) from which the domesticated silkworm originated....

Genomic data from chronic hepatitis B infected humans and healthy controls

W Huang, L Peng, Q Zhao, Q Li, Y Pei, Q Liao, J Wang, Z Gao & Y Wang
Chronic hepatitis B (CHB) infection remains endemic in large parts of the world and, as such, is a major global health issue. However, a thorough understanding of the genetic variants involved in CHB infection susceptibility remains lacking. This dataset comprises the raw exome sequencing data, SNP sets and InDel sets for 50 CHB patients and 40 healthy controls. The exome sequences were captured by NimbleGen2.1M array targeting 34 Mb of the human genome, containing 180,000...

Genome data from the sheep

X Xu, W Chen, R Talbot, K Worley, Y Jiang, W Barris, B Dalrymple, J Maddox, T Farault, R Brauning, M Xie, W Zhang, A Archibald, J Kijas, N Cockett, J McEwan, H Oddy, F Nicholas, K Kristensen, J Wang & W Wang
This is the first version of the draft sheep (Ovis aries) 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...

Genome data from foxtail millet (Setaria italica)

X Liu, Z Quan, S Cheng, X Xu, S Pan, P Zeng, M Xie, Z Yue, D Zhan, Y Li, J Wang, Z Zhao & G Zhang
Foxtail millet (Setaria italica) (2n=18), is an annual grass grown both as cereal crop (grain production) and as forage food. It is primarily grown in temperate, subtropical and tropical areas. With approximately 6,000 varieties, millet is one member of the Panicoideae (grasses subfamily), which includes maize (Zea mays), sorghum (Sorghum bicolor), and sugar cane (Saccharum officinarum). It is a nutritious dietary staple, containing starch, proteins, and a number of vitamins and minerals, such as calcium,...

Transcriptome from a lymphoblastoid cell line taken from the YH Han Chinese individual

Z Tian, L Chen, Y Ou & X Hu
The transcriptome available 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. These data were used to detect RNA-editing events using a pipeline that filtered and compared RNA-seq transcriptome and whole genome sequencing...

Genomic data from the domestic pigeon (Columba livia)

C Li, G Zhang, T Gilbert & T Wang
The domestic pigeon (Columba livia domestica) 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. 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...

Genomic sequence from an Aboriginal Australian

M Rasmussen, X Guo, Y Wang, KE Lohmueller, S Rasmussen, A Albrechtsen, L Skotte, S Lindgreen, M Metspalu, T Jombart, T Kivisild, W Zhai, A Eriksson, A Manica, L Orlando, FM De La Vega, S Tridico, E Metspalu, K Nielsen, MC Avila-Arcos, JV Moreno-Mayar, C Muller, J Dortch, MT Gilbert, O Lund … & E Willerslev
Here we present Aboriginal Australian (Homo sapiens) genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. The nuclear genome was sequenced to an overall depth of 6.4-fold. It had a high degree of fragmentation, but no genotype level evidence of sample contamination by DNA from sample handlers of European descent was detected. Over 2 million SNPs were identified after genome mapping...

Genome data from sweet and grain sorghum (Sorghum bicolor)

L-Y Zheng, X-S Guo, B He, L-J Sun, Y Peng, S-S Dong, T-F Liu, S Jiang, S Ramachandran, C-M Liu & H-C Jing
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...

Genome data from the leaf-cutting ant (Acromyrmex echinatior)

S Nygaard, G Zhang, M Schitt, C Li, Y Wurm, H Hu, J Zhou, L Ji, F Qiu, M Rasmussen, H Pan, F Hauser, A Krogh, CJ Grimmelikhuijzen, J Wang & JJ Boomsma
Here is presented high-quality (>100x depth) Illumina genome sequence of the leaf-cutting ant Acromyrmex echinatior, a model species for symbiosis and reproductive conflict studies. They make a particularly good model as after humans, leaf-cutting ants form the largest and most complex animal societies on Earth. Part of the subfamily Myrmicinae, this particular species is found in the wild from Mexico to Panama and subsists mostly on a particular fungus of the genus Leucocoprinus, which it...

Genomic data from the giant panda (Ailuropoda melanoleuca)

R Li, W Fan, G Tian, H Zhu, L He, J Cai, Q Huang, Q Cai, B Li, Y Bai, Z Zhang, Y Zhang, W Wang, J Li, F Wei, H Li, M Jian, J Li, Z Zhang, R Nielsen, D Li, W Gu, Z Yang, Z Xuan, OA Ryder … & J Wang
The giant panda (Ailuropoda melanoleuca) is considered a symbol of China and is a much loved animal all around the world. It is also one of the world’s 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...

Genomic data from the polar bear (Ursus maritimus)

B Li, G Zhang, E Willersleve, J Wang & J Wang
The polar bear (Ursus maritimus) is one of the largest land carnivores, second only to the Alaskan brown bear. In an effort to adapt to the extremely cold Arctic environment, it has evolved many unique characteristics. However, ecological pressures pose a grave threat to the survival of polar bears. The polar bear genome provides significant contributions to research concerning evolution, biodiversity and climate change. In 2010, the BGI completed the first draft of the genome...

Genomic data from the Emperor penguin (Aptenodytes forsteri)

J Li, G Zhang, D Lambert & J Wang
The Emperor penguin (Aptenodytes forsteri) is a large penguin, standing over 1 meter tall, with distinctive black, yellow and white markings. Like most penguins, the emperor penguins are indigenous to Antarctica and exist between the 66th and 78th parallels. Famous for its unique social and reproductive behavior, the emperor penguin also possesses a number of other notable evolutionary qualities: its stature, its feathers, its incubation process, and its swimming capabilities. The Aptenodytes forsteri genome offers...

Genomic data from the crab-eating macaque/cynomolgus monkey (Macaca fascicularis)

G Yan, G Zhang, X Fang, Y Zhang, C Li, F Ling, DN Cooper, O Li, Y Li, AJ Van Gool, H Du, J Chen, R Chen, P Zhang, Z Huang, Thompson, Y Meng, Y Bai, J Wang, M Zhuo, T Wang, Y Huang, L Wei, J Li, Z Wang … & J Wang
The crab-eating macaque (Macaca fascicularis), 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 Macaca 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...

Genomic data from Adelie penguin (Pygoscelis adeliae)

J Li, G Zhang, D Lambert & J Wang
The Adelie penguin (Pygoscelis adeliae) is an iconic penguin of moderate stature and a tuxedo of black and white feathers. The penguins are only found in the Antarctic region and surrounding islands. Being very sensitive to climate change, and due to changes in their behavior based on minor shifts in climate, they are often used as a barometer of the Antarctic. With its status as one of the adorable and cuddly flightless birds of Antarctica,...

Genome sequence of YH: the first diploid genome sequence of a Han Chinese individual

J Wang, W Wang, R Li, Y Li, G Tian, L Goodman, W Fan, J Zhang, J Li, J Zhang, Y Guo, B Feng, H Li, Y Lu, X Fang, H Liang, Z Du, D Li, Y Zhao, Y Hu, Z Yang, H Zheng, I Hellmann, M Inouye, J Pool … & J Wang
Genomic data from the YH (Homo sapiens) 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 genomic sequence of the Chinese hamster ovary (CHO) K1 cell line (Cricetulus griseus)

X Xu, H Nagarajan, NE Lewis, S Pan, Z Cai, X Liu, W Chen, M Xie, W Wang, S Hammond, MR Andersen, N Neff, B Passarelli, W Koh, HC Fan, J Wang, Y Gui, KH Lee, MJ Betenbaugh, Quake, I Famili, BO Palsson & J Wang
Chinese hamster ovary (CHO) K1 cells are a cell line cultured from the ovary of the Chinese hamster (Cricetulus griseus). 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.

Genomic data from Chinese cabbage (Brassica rapa)

X Wang, H Wang, J Wang, R Sun, J Wu, S Liu, Y Bai, JH Mun, I Bancroft, F Cheng, S Huang, X Li, W Hua, J Wang, X Wang, M Freeling, JC Pires, AH Paterson, B Chalhoub, B Wang, A Hayward, AG Sharpe, BS Park, B Weisshaar, B Liu … & Brassica Rapa Genome Sequencing Project Consortium
Available here is genomic data for the polyploid plant Brassica rapa 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 Brassica rapa Genome Sequencing Project Consortium assembled a 283.8 Mb genome estimated to cover >98% of the gene space. Using 72X coverage of...

Registration Year

  • 2011

Resource Types

  • Dataset