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

TitleThe sequence and de novo assembly of the giant panda genome
Authors
Issue Date2010
PublisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/nature
Citation
Nature, 2010, v. 463 n. 7279, p. 311-317 How to Cite?
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.
Persistent Identifierhttp://hdl.handle.net/10722/89279
ISSN
2014 Impact Factor: 41.456
PubMed Central ID
ISI Accession Number ID
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.

References
Errata

 

DC FieldValueLanguage
dc.contributor.authorLi, Ren_HK
dc.contributor.authorFan, Wen_HK
dc.contributor.authorTian, Gen_HK
dc.contributor.authorZhu, Hen_HK
dc.contributor.authorHe, Len_HK
dc.contributor.authorCai, Jen_HK
dc.contributor.authorHuang, Qen_HK
dc.contributor.authorCai, Qen_HK
dc.contributor.authorLi, Ben_HK
dc.contributor.authorBai, Yen_HK
dc.contributor.authorZhang, Zen_HK
dc.contributor.authorXu, Aen_HK
dc.contributor.authorRen, Yen_HK
dc.contributor.authorZhang, Gen_HK
dc.contributor.authorBruford, MWen_HK
dc.contributor.authorLi, Qen_HK
dc.contributor.authorMa, Len_HK
dc.contributor.authorGuo, Yen_HK
dc.contributor.authorAn, Nen_HK
dc.contributor.authorHu, Yen_HK
dc.contributor.authorZheng, Yen_HK
dc.contributor.authorWang, Yen_HK
dc.contributor.authorShi, Yen_HK
dc.contributor.authorLi, Zen_HK
dc.contributor.authorLiu, Qen_HK
dc.contributor.authorChen, Yen_HK
dc.contributor.authorZhao, Jen_HK
dc.contributor.authorQu, Nen_HK
dc.contributor.authorZhao, Sen_HK
dc.contributor.authorTian, Fen_HK
dc.contributor.authorWang, Xen_HK
dc.contributor.authorWang, Hen_HK
dc.contributor.authorLam, TWen_HK
dc.contributor.authorXu, Len_HK
dc.contributor.authorLiu, Xen_HK
dc.contributor.authorVinar, Ten_HK
dc.contributor.authorYiu, SMen_HK
dc.contributor.authorLiu, Sen_HK
dc.contributor.authorZhang, Hen_HK
dc.contributor.authorLi, Den_HK
dc.contributor.authorHuang, Yen_HK
dc.contributor.authorWang, Xen_HK
dc.contributor.authorYang, Gen_HK
dc.contributor.authorJiang, Zen_HK
dc.contributor.authorZhang, Yen_HK
dc.contributor.authorWang, Jen_HK
dc.contributor.authorQin, Nen_HK
dc.contributor.authorLi, Len_HK
dc.contributor.authorLi, Jen_HK
dc.contributor.authorBolund, Len_HK
dc.contributor.authorKristiansen, Ken_HK
dc.contributor.authorWong, GKSen_HK
dc.contributor.authorOlson, Men_HK
dc.contributor.authorZhang, Xen_HK
dc.contributor.authorLi, Sen_HK
dc.contributor.authorWang, Wen_HK
dc.contributor.authorYang, Hen_HK
dc.contributor.authorWang, Jen_HK
dc.contributor.authorWang, Jen_HK
dc.contributor.authorLi, Jen_HK
dc.contributor.authorWei, Fen_HK
dc.contributor.authorLi, Hen_HK
dc.contributor.authorJian, Men_HK
dc.contributor.authorLi, Jen_HK
dc.contributor.authorZhang, Zen_HK
dc.contributor.authorNielsen, Ren_HK
dc.contributor.authorLi, Den_HK
dc.contributor.authorGu, Wen_HK
dc.contributor.authorYang, Zen_HK
dc.contributor.authorXuan, Zen_HK
dc.contributor.authorRyder, OAen_HK
dc.contributor.authorLeung, FCCen_HK
dc.contributor.authorZhou, Yen_HK
dc.contributor.authorCao, Jen_HK
dc.contributor.authorSun, Xen_HK
dc.contributor.authorFu, Yen_HK
dc.contributor.authorFang, Xen_HK
dc.contributor.authorGuo, Xen_HK
dc.contributor.authorWang, Ben_HK
dc.contributor.authorHou, Ren_HK
dc.contributor.authorShen, Fen_HK
dc.contributor.authorMu, Ben_HK
dc.contributor.authorNi, Pen_HK
dc.contributor.authorLin, Ren_HK
dc.contributor.authorQian, Wen_HK
dc.contributor.authorWang, Gen_HK
dc.contributor.authorYu, Cen_HK
dc.contributor.authorNie, Wen_HK
dc.contributor.authorWang, Jen_HK
dc.contributor.authorWu, Zen_HK
dc.contributor.authorLiang, Hen_HK
dc.contributor.authorMin, Jen_HK
dc.contributor.authorWu, Qen_HK
dc.contributor.authorCheng, Sen_HK
dc.contributor.authorRuan, Jen_HK
dc.contributor.authorWang, Men_HK
dc.contributor.authorShi, Zen_HK
dc.contributor.authorWen, Men_HK
dc.contributor.authorLiu, Ben_HK
dc.contributor.authorRen, Xen_HK
dc.contributor.authorZheng, Hen_HK
dc.contributor.authorDong, Den_HK
dc.contributor.authorCook, Ken_HK
dc.contributor.authorShan, Gen_HK
dc.contributor.authorZhang, Hen_HK
dc.contributor.authorKosiol, Cen_HK
dc.contributor.authorXie, Xen_HK
dc.contributor.authorLu, Zen_HK
dc.contributor.authorZheng, Hen_HK
dc.contributor.authorLi, Yen_HK
dc.contributor.authorSteiner, CCen_HK
dc.contributor.authorLam, TTYen_HK
dc.contributor.authorLin, Sen_HK
dc.contributor.authorZhang, Qen_HK
dc.contributor.authorLi, Gen_HK
dc.contributor.authorTian, Jen_HK
dc.contributor.authorGong, Ten_HK
dc.contributor.authorLiu, Hen_HK
dc.contributor.authorZhang, Den_HK
dc.contributor.authorFang, Len_HK
dc.contributor.authorYe, Cen_HK
dc.contributor.authorZhang, Jen_HK
dc.contributor.authorHu, Wen_HK
dc.date.accessioned2010-09-06T09:54:51Z-
dc.date.available2010-09-06T09:54:51Z-
dc.date.issued2010en_HK
dc.identifier.citationNature, 2010, v. 463 n. 7279, p. 311-317en_HK
dc.identifier.issn0028-0836en_HK
dc.identifier.urihttp://hdl.handle.net/10722/89279-
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.en_HK
dc.languageengen_HK
dc.publisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/natureen_HK
dc.relation.ispartofNatureen_HK
dc.subject.meshAlgorithmsen_HK
dc.subject.meshAnimalsen_HK
dc.subject.meshChinaen_HK
dc.subject.meshConserved Sequence - geneticsen_HK
dc.subject.meshContig Mappingen_HK
dc.subject.meshDiet - veterinaryen_HK
dc.subject.meshDogsen_HK
dc.subject.meshEvolution, Molecularen_HK
dc.subject.meshFemaleen_HK
dc.subject.meshFertility - genetics - physiologyen_HK
dc.subject.meshGenome - geneticsen_HK
dc.subject.meshGenomicsen_HK
dc.subject.meshHeterozygoteen_HK
dc.subject.meshHumansen_HK
dc.subject.meshMultigene Family - geneticsen_HK
dc.subject.meshPolymorphism, Single Nucleotide - geneticsen_HK
dc.subject.meshReceptors, G-Protein-Coupled - geneticsen_HK
dc.subject.meshSequence Alignmenten_HK
dc.subject.meshSequence Analysis, DNAen_HK
dc.subject.meshSynteny - geneticsen_HK
dc.subject.meshUrsidae - classification - genetics - physiologyen_HK
dc.titleThe sequence and de novo assembly of the giant panda genomeen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0028-0836&volume=463 &issue=7279&spage=311&epage=317&date=2009&atitle=The+sequence+and+de+novo+assembly+of+the+giant+panda+genomeen_HK
dc.identifier.emailLeung, FCC: fcleung@hkucc.hku.hken_HK
dc.identifier.emailLam, TW: hresltk@hkucc.hku.hken_HK
dc.identifier.emailYiu, SM: smyiu@cs.hku.hken_HK
dc.identifier.authorityLeung, FCC=rp00731en_HK
dc.identifier.authorityLam, TW=rp00135en_HK
dc.identifier.authorityYiu, SM=rp00207en_HK
dc.description.naturelink_to_OA_fulltext-
dc.identifier.doi10.1038/nature08696en_HK
dc.identifier.pmid20010809en_HK
dc.identifier.pmcidPMC3951497-
dc.identifier.scopuseid_2-s2.0-75149155568en_HK
dc.identifier.hkuros168618en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-75149155568&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume463en_HK
dc.identifier.issue7279en_HK
dc.identifier.spage311en_HK
dc.identifier.epage317en_HK
dc.identifier.isiWOS:000273748100035-
dc.publisher.placeUnited Kingdomen_HK
dc.relation.erratumdoi:10.1038/nature08846-
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