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

被引：0

作者：

Derek M Bickhart

Benjamin D Rosen

Sergey Koren

Brian L Sayre

Alex R Hastie

Saki Chan

Joyce Lee

Ernest T Lam

Ivan Liachko

Shawn T Sullivan

Joshua N Burton

Heather J Huson

John C Nystrom

Christy M Kelley

Jana L Hutchison

Yang Zhou

Jiajie Sun

Alessandra Crisà

F Abel Ponce de León

John C Schwartz

John A Hammond

Geoffrey C Waldbieser

Steven G Schroeder

George E Liu

Maitreya J Dunham

Jay Shendure

Tad S Sonstegard

Adam M Phillippy

Curtis P Van Tassell

Timothy P L Smith

机构：

[1] Cell Wall Biology and Utilization Laboratory,Department of Biology

[2] ARS USDA,Department of Genome Sciences

[3] Animal Genomics and Improvement Laboratory,Department of Animal Science

[4] ARS USDA,Department of Animal Science

[5] Genome Informatics Section,undefined

[6] Computational and Statistical Genomics Branch,undefined

[7] National Human Genome Research Institute,undefined

[8] Virginia State University,undefined

[9] BioNano Genomics,undefined

[10] University of Washington School of Medicine,undefined

[11] Phase Genomics,undefined

[12] Cornell University,undefined

[13] US Meat Animal Research Center,undefined

[14] ARS USDA,undefined

[15] Clay Center,undefined

[16] Shaanxi Key Laboratory of Agricultural Molecular Biology,undefined

[17] College of Animal Science and Technology,undefined

[18] Northwest A&F University,undefined

[19] South China Agricultural University,undefined

[20] Tianhe,undefined

[21] Guangzhou,undefined

[22] China.,undefined

[23] Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA)–Animal Production Research Centre,undefined

[24] University of Minnesota,undefined

[25] Livestock Viral Diseases Programme,undefined

[26] The Pirbright Institute,undefined

[27] Warmwater Aquaculture Research Unit,undefined

[28] ARS USDA,undefined

[29] Howard Hughes Medical Institute,undefined

[30] Recombinetics,undefined

[31] Inc.,undefined

来源：

Nature Genetics | 2017年 / 49卷

关键词：

D O I：

暂无

中图分类号：

学科分类号：

摘要：

Adam Phillippy, Curtis Van Tassell, Timothy Smith and colleagues present a new reference genome assembly for the domestic goat using a pipeline that improves contiguity of the assembly by more than 250-fold. The pipeline uses a combination of short- and long-read sequencing, optical mapping, and chromatin interaction mapping.

引用

页码：643 / 650

页数：7

共 42 条

[1] Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
Bickhart, Derek M.
Rosen, Benjamin D.
Koren, Sergey
Sayre, Brian L.
Hastie, Alex R.
Chan, Saki
Lee, Joyce
Lam, Ernest T.
Liachko, Ivan
Sullivan, Shawn T.
Burton, Joshua N.
Huson, Heather J.
Nystrom, John C.
Kelley, Christy M.
Hutchison, Jana L.
Zhou, Yang
Sun, Jiajie
Crisa, Alessandra
de Leon, F. Abel Ponce
Schwartz, John C.
Hammond, John A.
Waldbieser, Geoffrey C.
Schroeder, Steven G.
Liu, George E.
Dunham, Maitreya J.
Shendure, Jay
Sonstegard, Tad S.
Phillippy, Adam M.
Van Tassell, Curtis P.
Smith, Timothy P. L.
NATURE GENETICS, 2017, 49 (04) : 643 - +
[2] De novo assembly of the cattle reference genome with single-molecule sequencing
Rosen, Benjamin D.
Bickhart, Derek M.
Schnabel, Robert D.
Koren, Sergey
Elsik, Christine G.
Tseng, Elizabeth
Rowan, Troy N.
Low, Wai Y.
Zimin, Aleksey
Couldrey, Christine
Hall, Richard
Li, Wenli
Rhie, Arang
Ghurye, Jay
McKay, Stephanie D.
Thibaud-Nissen, Francoise
Hoffman, Jinna
Murdoch, Brenda M.
Snelling, Warren M.
McDaneld, Tara G.
Hammond, John A.
Schwartz, John C.
Nandolo, Wilson
Hagen, Darren E.
Dreischer, Christian
Schultheiss, Sebastian J.
Schroeder, Steven G.
Phillippy, Adam M.
Cole, John B.
Van Tassell, Curtis P.
Liu, George
Smith, Timothy P. L.
Medrano, Juan F.
GIGASCIENCE, 2020, 9 (03):
[3] De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture
Mahajan, Shivani
Wei, Kevin H. -C.
Nalley, Matthew J.
Gibilisco, Lauren
Bachtrog, Doris
PLOS BIOLOGY, 2018, 16 (07)
[4] Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies
Zhang, Lei
Cai, Xu
Wu, Jian
Liu, Min
Grob, Stefan
Cheng, Feng
Liang, Jianli
Cai, Chengcheng
Liu, Zhiyuan
Liu, Bo
Wang, Fan
Li, Song
Liu, Fuyan
Li, Xuming
Cheng, Lin
Yang, Wencai
Li, Mai-he
Grossniklaus, Ueli
Zheng, Hongkun
Wang, Xiaowu
HORTICULTURE RESEARCH, 2018, 5
[5] Hybrid error correction and de novo assembly of single-molecule sequencing reads
Sergey Koren
Michael C Schatz
Brian P Walenz
Jeffrey Martin
Jason T Howard
Ganeshkumar Ganapathy
Zhong Wang
David A Rasko
W Richard McCombie
Erich D Jarvis
Adam M Phillippy
Nature Biotechnology, 2012, 30 : 693 - 700
[6] Hybrid error correction and de novo assembly of single-molecule sequencing reads
Koren, Sergey
Schatz, Michael C.
Walenz, Brian P.
Martin, Jeffrey
Howard, Jason T.
Ganapathy, Ganeshkumar
Wang, Zhong
Rasko, David A.
McCombie, W. Richard
Jarvis, Erich D.
Phillippy, Adam M.
NATURE BIOTECHNOLOGY, 2012, 30 (07) : 692 - +
[7] Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies (vol 5, 50, 2018)
Zhang, Lei
Cai, Xu
Wu, Jian
Liu, Min
Grob, Stefan
Cheng, Feng
Liang, Jianli
Cai, Chengcheng
Liu, Zhiyuan
Liu, Bo
Wang, Fan
Li, Song
Liu, Fuyan
Li, Xuming
Cheng, Lin
Yang, Wencai
Li, Mai-he
Grossniklaus, Ueli
Zheng, Hongkun
Wang, Xiaowu
HORTICULTURE RESEARCH, 2019, 6
[8] MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
Chuan-Le Xiao
Ying Chen
Shang-Qian Xie
Kai-Ning Chen
Yan Wang
Yue Han
Feng Luo
Zhi Xie
Nature Methods, 2017, 14 : 1072 - 1074
[9] MECAT : fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
Xiao, Chuan-Le
Chen, Ying
Xie, Shang-Qian
Chen, Kai-Ning
Wang, Yan
Han, Yue
Luo, Feng
Xie, Zhi
NATURE METHODS, 2017, 14 (11) : 1072 - +
[10] De Novo Assembly of the Streptomyces sp. Strain Mg1 Genome Using PacBio Single-Molecule Sequencing
Hoefler, B. Christopher
Konganti, Kranti
Straight, Paul D.
GENOME ANNOUNCEMENTS, 2013, 1 (04)

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