Article: The sequence and de novo assembly of the giant panda genome

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TitleThe sequence and de novo assembly of the giant panda genome
AuthorsLi, R4 5
Fan, W5
Tian, G2 5
Zhu, H5
He, L8 16
Cai, J2 14
Huang, Q5
Cai, Q3 5
Li, B5
Bai, Y5
Zhang, Z17
Wang, Y
Lam, TW
Yiu, SM
Liu, S
Zhang, H
Li, D
Huang, Y
Wang, X
Yang, G
Jiang, Z
Zhang, Y
Wang, J
Qin, N
Li, L
Li, J
Bolund, L
Kristiansen, K
Wong, GKS
Olson, M
Zhang, X
Li, S
Wang, W
Yang, H
Wang, J
Wang, J
Li, J
Wei, F
Li, H
Jian, M
Li, J
Zhang, Z
Nielsen, R
Li, D
Gu, W
Yang, Z
Xuan, Z
Ryder, OA
Leung, FCC
Zhou, Y
Cao, J
Sun, X
Fu, Y
Fang, X
Guo, X
Wang, B
Hou, R
Shen, F
Mu, B
Ni, P
Lin, R
Qian, W
Wang, G
Yu, C
Nie, W
Wang, J
Wu, Z
Liang, H
Min, J
Wu, Q
Cheng, S
Ruan, J
Wang, M
Shi, Z
Wen, M
Liu, B
Ren, X
Zheng, H
Dong, D
Cook, K
Shan, G
Zhang, H
Kosiol, C
Xie, X
Lu, Z
Zheng, H
Li, Y
Steiner, CC
Lam, TTY
Lin, S
Zhang, Q
Li, G
Tian, J
Gong, T
Liu, H
Zhang, D
Fang, L
Ye, C
Zhang, J
Hu, W
Xu, A
Ren, Y
Zhang, G
Bruford, MW
Li, Q
Ma, L
Guo, Y
An, N
Hu, Y
Zheng, Y
Shi, Y
Li, Z
Liu, Q
Chen, Y
Zhao, J
Qu, N
Zhao, S
Tian, F
Wang, X
Wang, H
Xu, L
Liu, X
Vinar, T
Issue Date2010
PublisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/nature
CitationNature, 2010, v. 463 n. 7279, p. 311-317 [How to Cite?]
DOI: http://dx.doi.org/10.1038/nature08696
AbstractUsing next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes. © 2010 Macmillan Publishers Limited. All rights reserved.
ISSN0028-0836
2011 Impact Factor: 36.28
2011 SCImago Journal Rankings: 7.767
DOIhttp://dx.doi.org/10.1038/nature08696
ISI Accession Number IDWOS:000273748100035
Funding AgencyGrant Number
Shenzhen Municipal Government
Yantian District local government of Shenzhen
National Natural Science Foundation of China30725008
Danish Natural Science Research Council
Solexa project272-07-0196
Danish Strategic Research Council2106-07-0021
Funding Information:

We are indebted to the faculty and staff of Beijing Genomics Institute at Shenzhen, whose names were not included in the author list, but who contributed to this team work. This project is funded by the Shenzhen Municipal Government and the Yantian District local government of Shenzhen. This project is supported by the National Natural Science Foundation of China (30725008), Ole Romer grant from the Danish Natural Science Research Council, the Solexa project (272-07-0196), and Danish Strategic Research Council (2106-07-0021). We thank C. Wang, X. Huang and L. Luo for their assistance in collecting the blood sample. We thank D. D. Pollock for repeat content estimation. We thank M. Shi, Y. Wang and M. Ting Wong for analysis of the reproduction related genes. We also thank L. Goodman for editing the manuscript.

ReferencesReferences in Scopus
DC Field
Value
dc.contributor.authorLi, R
dc.contributor.authorFan, W
dc.contributor.authorTian, G
dc.contributor.authorZhu, H
dc.contributor.authorHe, L
dc.contributor.authorCai, J
dc.contributor.authorHuang, Q
dc.contributor.authorCai, Q
dc.contributor.authorLi, B
dc.contributor.authorBai, Y
dc.contributor.authorZhang, Z
dc.contributor.authorWang, Y
dc.contributor.authorLam, TW
dc.contributor.authorYiu, SM
dc.contributor.authorLiu, S
dc.contributor.authorZhang, H
dc.contributor.authorLi, D
dc.contributor.authorHuang, Y
dc.contributor.authorWang, X
dc.contributor.authorYang, G
dc.contributor.authorJiang, Z
dc.contributor.authorZhang, Y
dc.contributor.authorWang, J
dc.contributor.authorQin, N
dc.contributor.authorLi, L
dc.contributor.authorLi, J
dc.contributor.authorBolund, L
dc.contributor.authorKristiansen, K
dc.contributor.authorWong, GKS
dc.contributor.authorOlson, M
dc.contributor.authorZhang, X
dc.contributor.authorLi, S
dc.contributor.authorWang, W
dc.contributor.authorYang, H
dc.contributor.authorWang, J
dc.contributor.authorWang, J
dc.contributor.authorLi, J
dc.contributor.authorWei, F
dc.contributor.authorLi, H
dc.contributor.authorJian, M
dc.contributor.authorLi, J
dc.contributor.authorZhang, Z
dc.contributor.authorNielsen, R
dc.contributor.authorLi, D
dc.contributor.authorGu, W
dc.contributor.authorYang, Z
dc.contributor.authorXuan, Z
dc.contributor.authorRyder, OA
dc.contributor.authorLeung, FCC
dc.contributor.authorZhou, Y
dc.contributor.authorCao, J
dc.contributor.authorSun, X
dc.contributor.authorFu, Y
dc.contributor.authorFang, X
dc.contributor.authorGuo, X
dc.contributor.authorWang, B
dc.contributor.authorHou, R
dc.contributor.authorShen, F
dc.contributor.authorMu, B
dc.contributor.authorNi, P
dc.contributor.authorLin, R
dc.contributor.authorQian, W
dc.contributor.authorWang, G
dc.contributor.authorYu, C
dc.contributor.authorNie, W
dc.contributor.authorWang, J
dc.contributor.authorWu, Z
dc.contributor.authorLiang, H
dc.contributor.authorMin, J
dc.contributor.authorWu, Q
dc.contributor.authorCheng, S
dc.contributor.authorRuan, J
dc.contributor.authorWang, M
dc.contributor.authorShi, Z
dc.contributor.authorWen, M
dc.contributor.authorLiu, B
dc.contributor.authorRen, X
dc.contributor.authorZheng, H
dc.contributor.authorDong, D
dc.contributor.authorCook, K
dc.contributor.authorShan, G
dc.contributor.authorZhang, H
dc.contributor.authorKosiol, C
dc.contributor.authorXie, X
dc.contributor.authorLu, Z
dc.contributor.authorZheng, H
dc.contributor.authorLi, Y
dc.contributor.authorSteiner, CC
dc.contributor.authorLam, TTY
dc.contributor.authorLin, S
dc.contributor.authorZhang, Q
dc.contributor.authorLi, G
dc.contributor.authorTian, J
dc.contributor.authorGong, T
dc.contributor.authorLiu, H
dc.contributor.authorZhang, D
dc.contributor.authorFang, L
dc.contributor.authorYe, C
dc.contributor.authorZhang, J
dc.contributor.authorHu, W
dc.contributor.authorXu, A
dc.contributor.authorRen, Y
dc.contributor.authorZhang, G
dc.contributor.authorBruford, MW
dc.contributor.authorLi, Q
dc.contributor.authorMa, L
dc.contributor.authorGuo, Y
dc.contributor.authorAn, N
dc.contributor.authorHu, Y
dc.contributor.authorZheng, Y
dc.contributor.authorShi, Y
dc.contributor.authorLi, Z
dc.contributor.authorLiu, Q
dc.contributor.authorChen, Y
dc.contributor.authorZhao, J
dc.contributor.authorQu, N
dc.contributor.authorZhao, S
dc.contributor.authorTian, F
dc.contributor.authorWang, X
dc.contributor.authorWang, H
dc.contributor.authorXu, L
dc.contributor.authorLiu, X
dc.contributor.authorVinar, T
dc.date.accessioned2010-09-06T09:54:51Z
dc.date.available2010-09-06T09:54:51Z
dc.date.issued2010
dc.description.abstractUsing next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes. © 2010 Macmillan Publishers Limited. All rights reserved.
dc.description.natureLink_to_subscribed_fulltext
dc.identifier.citationNature, 2010, v. 463 n. 7279, p. 311-317 [How to Cite?]
DOI: http://dx.doi.org/10.1038/nature08696
dc.identifier.citeulike6372380
dc.identifier.doihttp://dx.doi.org/10.1038/nature08696
dc.identifier.epage317
dc.identifier.hkuros168618
dc.identifier.isiWOS:000273748100035
Funding AgencyGrant Number
Shenzhen Municipal Government
Yantian District local government of Shenzhen
National Natural Science Foundation of China30725008
Danish Natural Science Research Council
Solexa project272-07-0196
Danish Strategic Research Council2106-07-0021
Funding Information:

We are indebted to the faculty and staff of Beijing Genomics Institute at Shenzhen, whose names were not included in the author list, but who contributed to this team work. This project is funded by the Shenzhen Municipal Government and the Yantian District local government of Shenzhen. This project is supported by the National Natural Science Foundation of China (30725008), Ole Romer grant from the Danish Natural Science Research Council, the Solexa project (272-07-0196), and Danish Strategic Research Council (2106-07-0021). We thank C. Wang, X. Huang and L. Luo for their assistance in collecting the blood sample. We thank D. D. Pollock for repeat content estimation. We thank M. Shi, Y. Wang and M. Ting Wong for analysis of the reproduction related genes. We also thank L. Goodman for editing the manuscript.

dc.identifier.issn0028-0836
2011 Impact Factor: 36.28
2011 SCImago Journal Rankings: 7.767
dc.identifier.issue7279
dc.identifier.openurl
dc.identifier.pmid20010809
dc.identifier.scopuseid_2-s2.0-75149155568
dc.identifier.spage311
dc.identifier.urihttp://hdl.handle.net/10722/89279
dc.identifier.volume463
dc.languageeng
dc.publisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/nature
dc.publisher.placeUnited Kingdom
dc.relation.ispartofNature
dc.relation.referencesReferences in Scopus
dc.subject.meshAlgorithms
dc.subject.meshAnimals
dc.subject.meshChina
dc.subject.meshConserved Sequence - genetics
dc.subject.meshContig Mapping
dc.subject.meshDiet - veterinary
dc.subject.meshDogs
dc.subject.meshEvolution, Molecular
dc.subject.meshFemale
dc.subject.meshFertility - genetics - physiology
dc.subject.meshGenome - genetics
dc.subject.meshGenomics
dc.subject.meshHeterozygote
dc.subject.meshHumans
dc.subject.meshMultigene Family - genetics
dc.subject.meshPolymorphism, Single Nucleotide - genetics
dc.subject.meshReceptors, G-Protein-Coupled - genetics
dc.subject.meshSequence Alignment
dc.subject.meshSequence Analysis, DNA
dc.subject.meshSynteny - genetics
dc.subject.meshUrsidae - classification - genetics - physiology
dc.titleThe sequence and de novo assembly of the giant panda genome
dc.typeArticle
Author Affiliations
  1. Sichuan University
  2. Graduate University of Chinese Academy of Sciences
  3. Shenzhen University
  4. Københavns Universitet
  5. BGI-Shenzhen
  6. China Conservation and Research Centre for the Giant Panda
  7. The University of Hong Kong
  8. Shanghai Jiaotong University
  9. Southeast University
  10. San Diego Zoo Institute for Conservation Research
  11. University of Alberta
  12. UC Berkeley
  13. Sun Yat-Sen University
  14. Chinese Academy of Sciences
  15. Cardiff University
  16. Fudan University
  17. Chengdu Research Base of Giant Panda Breeding
  18. University of Toronto
  19. Veterinarmedizinische Universitat Wien
  20. University of Washington Seattle
  21. Comenius University
  22. South China University of Technology