Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis
Rami A. Dalloul,Julie A. Long,Aleksey V. Zimin,Luqman Aslam,Kathryn Beal,Le Ann Blomberg,Pascal Bouffard,David W. Burt,Oswald Crasta,Richard P. M. A. Crooijmans,Kristal L. Cooper,Roger A. Coulombe,Supriyo De,Mary E. Delany,Jerry B. Dodgson,Jennifer J Dong,Clive Evans,Karin M. Frederickson,Paul Flicek,Liliana Florea,Otto Folkerts,Martien A. M. Groenen,Tim Harkins,Javier Herrero,Steve Hoffmann,Hendrik-Jan Megens,Andrew Jiang,Pieter J. de Jong,Peter K. Kaiser,Heebal Kim,Kyu-Won Kim,Sungwon Kim,David Langenberger,Mi-Kyung Lee,Taeheon Lee,Shrinivasrao P. Mane,Guillaume Marçais,Manja Marz,Manja Marz,A. P. McElroy,Thero Modise,Mikhail Nefedov,Cedric Notredame,Ian R. Paton,William S. Payne,Geo Pertea,Dennis Prickett,Daniela Puiu,Dan Qioa,Emanuele Raineri,Magali Ruffier,Steven L. Salzberg,Michael C. Schatz,Chantel F. Scheuring,Carl J. Schmidt,Steven Schroeder,Stephen M. J. Searle,Edward J. Smith,Jacqueline Smith,Tad S. Sonstegard,Peter F. Stadler,Hakim Tafer,Hakim Tafer,Zhijian Jake Tu,Curtis P. Van Tassell,Albert J. Vilella,Kelly P. Williams,James A. Yorke,Liqing Zhang,Hong-Bin Zhang,Xiaojun Zhang,Yang Zhang,Kent M. Reed +72 more
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TLDR
The combined application of next-generation sequencing platforms has provided an economical approach to unlocking the potential of the turkey genome.Abstract:
A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (∼1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.read more
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A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
Guillaume Marçais,Carl Kingsford +1 more
TL;DR: This work proposes a new k-mer counting algorithm and associated implementation, called Jellyfish, which is fast and memory efficient, based on a multithreaded, lock-free hash table optimized for counting k-mers up to 31 bases in length.
Journal ArticleDOI
The oyster genome reveals stress adaptation and complexity of shell formation
Guofan Zhang,Xiaodong Fang,Ximing Guo,Li Li,Ruibang Luo,Fei Xu,Pengcheng Yang,Linlin Zhang,Xiaotong Wang,Haigang Qi,Zhiqiang Xiong,Huayong Que,Yinlong Xie,Peter W. H. Holland,Jordi Paps,Yabing Zhu,Fucun Wu,Yuanxin Chen,Jiafeng Wang,Chunfang Peng,Jie Meng,Lan Yang,Jun Liu,Bo Wen,Na Zhang,Zhiyong Huang,Qihui Zhu,Yue Feng,Andrew S. Mount,Dennis Hedgecock,Zhe Xu,Yunjie Liu,Tomislav Domazet-Lošo,Yishuai Du,Xiaoqing Sun,Shoudu Zhang,Binghang Liu,Peizhou Cheng,Xuanting Jiang,Juan Li,Dingding Fan,Wei Wang,Wenjing Fu,Tong Wang,Bo Wang,Jibiao Zhang,Zhiyu Peng,Yingxiang Li,Na Li,Jinpeng Wang,Maoshan Chen,Yan He,Fengji Tan,Xiaorui Song,Qiumei Zheng,Ronglian Huang,Hailong Yang,Du Xuedi,Li Chen,Mei Yang,Patrick M. Gaffney,Shan Wang,Longhai Luo,Zhicai She,Yao Ming,Huang Wen,Shu Zhang,Baoyu Huang,Yong Zhang,Tao Qu,Peixiang Ni,Guoying Miao,Junyi Wang,Qiang Wang,Christian E. W. Steinberg,Haiyan Wang,Ning Li,Lumin Qian,Guojie Zhang,Yingrui Li,Huanming Yang,Xiao Liu,Jian Wang,Ye Yin,Jun Wang +84 more
TL;DR: The sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy and transcriptomes of development and stress response and the proteome of the shell are reported, showing that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes.
Journal ArticleDOI
Whole-genome analyses resolve early branches in the tree of life of modern birds
Erich D. Jarvis,Siavash Mirarab,Andre J. Aberer,Bo Li,Bo Li,Bo Li,Peter Houde,Cai Li,Cai Li,Simon Y. W. Ho,Brant C. Faircloth,Benoit Nabholz,Jason T. Howard,Alexander Suh,Claudia C. Weber,Rute R. da Fonseca,Jianwen Li,Fang Zhang Zhang,Hui Li,Long Zhou,Nitish Narula,Nitish Narula,Liang Liu,Ganesh Ganapathy,Bastien Boussau,Shamsuzzoha Bayzid,Volodymyr Zavidovych,Sankar Subramanian,Toni Gabaldón,Salvador Capella-Gutierrez,Jaime Huerta-Cepas,Bhanu Rekepalli,Bhanu Rekepalli,Kasper Munch,Mikkel H. Schierup,Bent E. K. Lindow,Wesley C. Warren,David A. Ray,Richard E. Green,Michael William Bruford,Xiangjiang Zhan,Xiangjiang Zhan,Andrew Dixon,Shengbin Li,Ning Li,Yinhua Huang,Elizabeth P. Derryberry,Elizabeth P. Derryberry,Mads F. Bertelsen,Frederick H. Sheldon,Robb T. Brumfield,Claudio V. Mello,Claudio V. Mello,Peter V. Lovell,Morgan Wirthlin,Maria Paula Cruz Schneider,Francisco Prosdocimi,José Alfredo Samaniego,Amhed Missael Vargas Velazquez,Alonzo Alfaro-Núñez,Paula F. Campos,Bent O. Petersen,Thomas Sicheritz-Pontén,An Pas,Thomas L. Bailey,R. Paul Scofield,Michael Bunce,David M. Lambert,Qi Zhou,Polina L. Perelman,Amy C. Driskell,Beth Shapiro,Zijun Xiong,Yongli Zeng,Shiping Liu,Zhenyu Li,Binghang Liu,Kui Wu,Jin Xiao,Xiong Yinqi,Quiemei Zheng,Yong Zhang,Huanming Yang,Jian Wang,Linnéa Smeds,Frank E. Rheindt,Michael J. Braun,Jon Fjeldså,Ludovic Orlando,F. Keith Barker,Knud A. Jønsson,Warren E. Johnson,Klaus-Peter Koepfli,Stephen J. O'Brien,David Haussler,Oliver A. Ryder,Carsten Rahbek,Eske Willerslev,Gary R. Graves,Gary R. Graves,Travis C. Glenn,John E. McCormack,Dave Burt,Hans Ellegren,Per Alström,Scott V. Edwards,Alexandros Stamatakis,David P. Mindell,Joel Cracraft,Edward L. Braun,Tandy Warnow,Tandy Warnow,Wang Jun,M. Thomas P. Gilbert,M. Thomas P. Gilbert,Guojie Zhang,Guojie Zhang +116 more
TL;DR: A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
Journal ArticleDOI
Next-generation transcriptome assembly
Jeffrey Martin,Zhong Wang +1 more
TL;DR: This Review summarizes the recent developments in transcriptome assembly approaches — reference-based, de novo and combined strategies — along with some perspectives on transcriptomeAssembly in the near future.
Journal ArticleDOI
Field guide to next-generation DNA sequencers
TL;DR: T careful thought about the desired characteristics of these systems is warranted before purchasing or using any of them, and the major characteristics of each commercially available platform are summarized.
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