Literature DB >> 25689317

The Genome 10K Project: a way forward.

Klaus-Peter Koepfli1, Benedict Paten, Stephen J O'Brien.   

Abstract

The Genome 10K Project was established in 2009 by a consortium of biologists and genome scientists determined to facilitate the sequencing and analysis of the complete genomes of 10,000 vertebrate species. Since then the number of selected and initiated species has risen from ∼26 to 277 sequenced or ongoing with funding, an approximately tenfold increase in five years. Here we summarize the advances and commitments that have occurred by mid-2014 and outline the achievements and present challenges of reaching the 10,000-species goal. We summarize the status of known vertebrate genome projects, recommend standards for pronouncing a genome as sequenced or completed, and provide our present and future vision of the landscape of Genome 10K. The endeavor is ambitious, bold, expensive, and uncertain, but together the Genome 10K Consortium of Scientists and the worldwide genomics community are moving toward their goal of delivering to the coming generation the gift of genome empowerment for many vertebrate species.

Keywords:  amphibian; bird; fish; genome; mammal; reptile

Mesh:

Year:  2015        PMID: 25689317      PMCID: PMC5837290          DOI: 10.1146/annurev-animal-090414-014900

Source DB:  PubMed          Journal:  Annu Rev Anim Biosci        ISSN: 2165-8102            Impact factor:   8.923


  258 in total

1.  Temperature sex reversal implies sex gene dosage in a reptile.

Authors:  Alexander E Quinn; Arthur Georges; Stephen D Sarre; Fiorenzo Guarino; Tariq Ezaz; Jennifer A Marshall Graves
Journal:  Science       Date:  2007-04-20       Impact factor: 47.728

2.  Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3.

Authors:  Mira V Han; Gregg W C Thomas; Jose Lugo-Martinez; Matthew W Hahn
Journal:  Mol Biol Evol       Date:  2013-05-24       Impact factor: 16.240

Review 3.  Origin and evolution of parthenogenetic genomes in lizards: current state and future directions.

Authors:  M K Fujita; C Moritz
Journal:  Cytogenet Genome Res       Date:  2010-03-09       Impact factor: 1.636

4.  Targeted discovery of novel human exons by comparative genomics.

Authors:  Adam Siepel; Mark Diekhans; Brona Brejová; Laura Langton; Michael Stevens; Charles L G Comstock; Colleen Davis; Brent Ewing; Shelly Oommen; Christopher Lau; Hung-Chun Yu; Jianfeng Li; Bruce A Roe; Phil Green; Daniela S Gerhard; Gary Temple; David Haussler; Michael R Brent
Journal:  Genome Res       Date:  2007-11-07       Impact factor: 9.043

5.  Comparative sex chromosome genomics in snakes: differentiation, evolutionary strata, and lack of global dosage compensation.

Authors:  Beatriz Vicoso; J J Emerson; Yulia Zektser; Shivani Mahajan; Doris Bachtrog
Journal:  PLoS Biol       Date:  2013-08-27       Impact factor: 8.029

6.  Genome-wide polymorphism and comparative analyses in the white-tailed deer (Odocoileus virginianus): a model for conservation genomics.

Authors:  Christopher M Seabury; Eric K Bhattarai; Jeremy F Taylor; Ganesh G Viswanathan; Susan M Cooper; Donald S Davis; Scot E Dowd; Mitch L Lockwood; Paul M Seabury
Journal:  PLoS One       Date:  2011-01-19       Impact factor: 3.240

7.  SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.

Authors:  Ruibang Luo; Binghang Liu; Yinlong Xie; Zhenyu Li; Weihua Huang; Jianying Yuan; Guangzhu He; Yanxiang Chen; Qi Pan; Yunjie Liu; Jingbo Tang; Gengxiong Wu; Hao Zhang; Yujian Shi; Yong Liu; Chang Yu; Bo Wang; Yao Lu; Changlei Han; David W Cheung; Siu-Ming Yiu; Shaoliang Peng; Zhu Xiaoqian; Guangming Liu; Xiangke Liao; Yingrui Li; Huanming Yang; Jian Wang; Tak-Wah Lam; Jun Wang
Journal:  Gigascience       Date:  2012-12-27       Impact factor: 6.524

8.  Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations.

Authors:  Xuming Zhou; Fengming Sun; Shixia Xu; Guangyi Fan; Kangli Zhu; Xin Liu; Yuan Chen; Chengcheng Shi; Yunxia Yang; Zhiyong Huang; Jing Chen; Haolong Hou; Xuejiang Guo; Wenbin Chen; Yuefeng Chen; Xiaohong Wang; Tian Lv; Dan Yang; Jiajian Zhou; Bangqing Huang; Zhengfei Wang; Wei Zhao; Ran Tian; Zhiqiang Xiong; Junxiao Xu; Xinming Liang; Bingyao Chen; Weiqing Liu; Junyi Wang; Shengkai Pan; Xiaodong Fang; Ming Li; Fuwen Wei; Xun Xu; Kaiya Zhou; Jun Wang; Guang Yang
Journal:  Nat Commun       Date:  2013       Impact factor: 14.919

9.  Whole-genome sequencing of tibetan macaque (Macaca Thibetana) provides new insight into the macaque evolutionary history.

Authors:  Zhenxin Fan; Guang Zhao; Peng Li; Naoki Osada; Jinchuan Xing; Yong Yi; Lianming Du; Pedro Silva; Hongxing Wang; Ryuichi Sakate; Xiuyue Zhang; Huailiang Xu; Bisong Yue; Jing Li
Journal:  Mol Biol Evol       Date:  2014-03-18       Impact factor: 16.240

10.  The common marmoset genome provides insight into primate biology and evolution.

Authors: 
Journal:  Nat Genet       Date:  2014-07-20       Impact factor: 38.330

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  120 in total

Review 1.  Evolution of vertebrate sex chromosomes and dosage compensation.

Authors:  Jennifer A Marshall Graves
Journal:  Nat Rev Genet       Date:  2015-11-30       Impact factor: 53.242

2.  Reconstruction and evolutionary history of eutherian chromosomes.

Authors:  Jaebum Kim; Marta Farré; Loretta Auvil; Boris Capitanu; Denis M Larkin; Jian Ma; Harris A Lewin
Journal:  Proc Natl Acad Sci U S A       Date:  2017-06-19       Impact factor: 11.205

3.  LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly.

Authors:  Gui-Cai Xu; Tian-Jun Xu; Rui Zhu; Yan Zhang; Shang-Qi Li; Hong-Wei Wang; Jiong-Tang Li
Journal:  Gigascience       Date:  2019-01-01       Impact factor: 6.524

Review 4.  Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution.

Authors:  Sangeet Lamichhaney; Daren C Card; Phil Grayson; João F R Tonini; Gustavo A Bravo; Kathrin Näpflin; Flavia Termignoni-Garcia; Christopher Torres; Frank Burbrink; Julia A Clarke; Timothy B Sackton; Scott V Edwards
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2019-06-03       Impact factor: 6.237

Review 5.  Dissecting evolution and disease using comparative vertebrate genomics.

Authors:  Jennifer R S Meadows; Kerstin Lindblad-Toh
Journal:  Nat Rev Genet       Date:  2017-07-24       Impact factor: 53.242

6.  A golden goat genome.

Authors:  Kim C Worley
Journal:  Nat Genet       Date:  2017-03-30       Impact factor: 38.330

7.  Large numbers of vertebrates began rapid population decline in the late 19th century.

Authors:  Haipeng Li; Jinggong Xiang-Yu; Guangyi Dai; Zhili Gu; Chen Ming; Zongfeng Yang; Oliver A Ryder; Wen-Hsiung Li; Yun-Xin Fu; Ya-Ping Zhang
Journal:  Proc Natl Acad Sci U S A       Date:  2016-11-21       Impact factor: 11.205

8.  Uniclust databases of clustered and deeply annotated protein sequences and alignments.

Authors:  Milot Mirdita; Lars von den Driesch; Clovis Galiez; Maria J Martin; Johannes Söding; Martin Steinegger
Journal:  Nucleic Acids Res       Date:  2016-11-28       Impact factor: 16.971

Review 9.  LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order.

Authors:  Luca Fontanesi; Federica Di Palma; Paul Flicek; Andrew T Smith; Carl-Gustaf Thulin; Paulo C Alves
Journal:  J Hered       Date:  2016-02-26       Impact factor: 2.645

10.  Capturing Darwin's dream.

Authors:  Travis C Glenn; Brant C Faircloth
Journal:  Mol Ecol Resour       Date:  2016-09       Impact factor: 7.090

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