Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

被引：503

作者：

Bickhart, Derek M. ^{[1
]}

Rosen, Benjamin D. ^{[2
]}

Koren, Sergey ^{[3
]}

Sayre, Brian L. ^{[4
]}

Hastie, Alex R. ^{[5
]}

Chan, Saki ^{[5
]}

Lee, Joyce ^{[5
]}

Lam, Ernest T. ^{[5
]}

Liachko, Ivan ^{[6
]}

Sullivan, Shawn T. ^{[7
]}

Burton, Joshua N. ^{[6
]}

Huson, Heather J. ^{[8
]}

Nystrom, John C. ^{[8
]}

Kelley, Christy M. ^{[9
]}

Hutchison, Jana L. ^{[2
]}

Zhou, Yang ^{[2
,10
]}

Sun, Jiajie ^{[11
]}

Crisa, Alessandra ^{[12
]}

de Leon, F. Abel Ponce ^{[13
]}

Schwartz, John C. ^{[14
]}

Hammond, John A. ^{[14
]}

Waldbieser, Geoffrey C. ^{[15
]}

Schroeder, Steven G. ^{[2
]}

Liu, George E. ^{[2
]}

Dunham, Maitreya J. ^{[6
]}

Shendure, Jay ^{[6
,16
]}

Sonstegard, Tad S. ^{[17
]}

Phillippy, Adam M. ^{[3
]}

Van Tassell, Curtis P. ^{[2
]}

Smith, Timothy P. L. ^{[9
]}

机构：

[1] USDA ARS, Cell Wall Biol & Utilizat Lab, Madison, WI USA

[2] USDA ARS, Anim Genom & Improvement Lab, Beltsville, MD USA

[3] Natl Human Genome Res Inst, Computat & Stat Genom Branch, Genome Informat Sect, Bethesda, MD USA

[4] Virginia State Univ, Dept Biol, Petersburg, VA USA

[5] BioNano Genom, San Diego, CA USA

[6] Univ Washington, Sch Med, Dept Genome Sci, Seattle, WA USA

[7] Phase Genom, Seattle, WA USA

[8] Cornell Univ, Dept Anim Sci, Ithaca, NY USA

[9] USDA ARS, Meat Anim Res Ctr, Clay Ctr, NE USA

[10] Northwest A&F Univ, Coll Anim Sci & Technol, Shaanxi Key Lab Agr Mol Biol, Yangling, Peoples R China

[11] China Agr Univ, Guangzhou, Peoples R China

[12] CREA, Anim Prod Res Ctr, Rome, Italy

[13] Univ Minnesota, Dept Anim Sci, St Paul, MN USA

[14] Pirbright Inst, Livestock Viral Dis Programme, Woking, Surrey, England

[15] USDA ARS, Warmwater Aquaculture Res Unit, Stoneville, MS USA

[16] Howard Hughes Med Inst, Seattle, WA USA

[17] Recombinet Inc, St Paul, MN USA

来源：

NATURE GENETICS | 2017年 / 49卷 / 04期

基金：

英国生物技术与生命科学研究理事会; 美国食品与农业研究所;

关键词：

CHROMOSOMES; ANNOTATION; CATTLE; RECONSTRUCTION; TRANSCRIPTOME; COMPLEXITY; ALIGNMENT; TIME;

D O I：

10.1038/ng.3802

中图分类号：

Q3 [遗传学];

学科分类号：

071007 [遗传学];

摘要：

The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus) based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a similar to 400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.

引用

页码：643 / +

页数：11

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