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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, R5 3
Fan, W5
Tian, G5 2
Zhu, H5
He, L15 7
Cai, J2 13
Huang, Q5
Cai, Q5 1
Li, B5
Bai, Y5
Zhang, Z17
Zhang, Y13
Wang, W13
Li, J5
Wei, F4
Li, H
Jian, M5
Li, J18
Zhang, Z16
Nielsen, R5
Li, D9
Gu, W5
Yang, Z5
Xuan, Z10
Ryder, OA6
Leung, FCC5
Zhou, Y5
Cao, J9
Sun, X12
Fu, Y5
Fang, X5
Guo, X17
Wang, B17
Hou, R5
Shen, F5
Mu, B5
Ni, P5
Lin, R2 13
Qian, W5
Wang, G13
Yu, C13
Nie, W5
Wang, J5
Wu, Z5 1
Liang, H4
Min, J5 1
Wu, Q5 2
Cheng, S5
Ruan, J5
Wang, M5
Shi, Z5
Wen, M5
Liu, B5
Ren, X18
Zheng, H18
Dong, D5
Cook, K5
Shan, G19
Zhang, H9
Kosiol, C9
Xie, X5
Lu, Z5 2
Zheng, H10
Li, Y6
Steiner, CC5
Lam, TTY5
Lin, S5
Zhang, Q5
Li, G5
Tian, J9
Gong, T9
Liu, H5
Zhang, D5
Fang, L5
Ye, C12
Zhang, J12
Hu, W5
Xu, A5 13 2
Ren, Y14
Zhang, G5 2
Bruford, MW5 2
Li, Q5 2
Ma, L5
Guo, Y5 2
An, N5 2
Hu, Y7
Zheng, Y7
Shi, Y5
Li, Z5
Liu, Q5
Chen, Y5 1
Zhao, J5
Qu, N5
Zhao, S5
Tian, F5
Wang, X5
Wang, H5
Xu, L20
Liu, X23
Vinar, T6
Wang, Y22
Lam, TW8
Yiu, SM8
Liu, S8
Zhang, H5
Li, D5
Huang, Y5
Wang, X5
Yang, G5
Jiang, Z5
Wang, J5
Qin, N5
Li, L5 3
Li, J5 11
Bolund, L5
Kristiansen, K5
Wong, GKS5
Olson, M21
Zhang, X5
Li, S5
Yang, H5
Wang, J5
Wang, J5 3
 
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.
 
DescriptionErratum of this article, see link: http://hub.hku.hk/handle/10722/152427
 
ISSN0028-0836
2013 Impact Factor: 42.351
 
DOIhttp://dx.doi.org/10.1038/nature08696
 
PubMed Central IDPMC3951497
 
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 FieldValue
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.authorZhang, Y
 
dc.contributor.authorWang, W
 
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.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.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.authorYang, H
 
dc.contributor.authorWang, J
 
dc.contributor.authorWang, J
 
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_OA_fulltext
 
dc.descriptionErratum of this article, see link: http://hub.hku.hk/handle/10722/152427
 
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
 
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dc.identifier.f10002367956
 
dc.identifier.f10002367956
 
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
2013 Impact Factor: 42.351
 
dc.identifier.issue7279
 
dc.identifier.openurl
 
dc.identifier.pmcidPMC3951497
 
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
 
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Author Affiliations
  1. Shenzhen University
  2. Graduate University of Chinese Academy of Sciences
  3. Københavns Universitet
  4. Institute of Zoology Chinese Academy of Sciences
  5. BGI-Shenzhen
  6. The University of Hong Kong
  7. Shanghai Jiaotong University
  8. China Conservation and Research Centre for the Giant Panda
  9. Southeast University
  10. San Diego Zoo Institute for Conservation Research
  11. University of Alberta
  12. Sun Yat-Sen University
  13. Kunming Institute of Zoology Chinese Academy of Sciences
  14. Cardiff University
  15. Fudan University Shanghai Medical College
  16. UC Berkeley
  17. Chengdu Research Base of Giant Panda Breeding
  18. University of Toronto
  19. Veterinarmedizinische Universitat Wien
  20. Comenius University
  21. University of Washington Seattle
  22. South China University of Technology
  23. Sichuan University