Improved reference genome for the domestic horse increases assembly contiguity and composition

被引：160

作者：

Kalbfleisch, Theodore S. ^{[1
]}

Rice, Edward S. ^{[2
]}

DePriest, Michael S., Jr. ^{[1
]}

Walenz, Brian P. ^{[3
]}

Hestand, Matthew S. ^{[4
]}

Vermeesch, Joris R. ^{[4
]}

O'Connell, Brendan L. ^{[2
,16
]}

Fiddes, Ian T. ^{[2
,5
]}

Vershinina, Alisa O. ^{[6
]}

Saremi, Nedda F. ^{[2
]}

Petersen, Jessica L. ^{[7
]}

Finno, Carrie J. ^{[8
]}

Bellone, Rebecca R. ^{[8
,9
]}

McCue, Molly E. ^{[10
]}

Brooks, Samantha A. ^{[11
]}

Bailey, Ernest ^{[12
]}

Orlando, Ludovic ^{[13
,14
]}

Greene, Richard E. ^{[2
]}

Miller, Donald C. ^{[15
]}

Antczak, Douglas F. ^{[15
]}

MacLeod, James N. ^{[12
]}

机构：

[1] Univ Louisville, Sch Med, Dept Biochem & Mol Genet, Louisville, KY 40292 USA

[2] UC Santa Cruz, Dept Biomol Engn, Santa Cruz, CA 95064 USA

[3] NHGRI, Genome Informat Sect, Computat & Stat Genom Branch, NIH, Bethesda, MD 20892 USA

[4] Katholieke Univ Leuven, Ctr Human Genet, B-3000 Leuven, Belgium

[5] 10x Genomics Inc, Pleasanton, CA 94566 USA

[6] UC Santa Cruz, Dept Ecol & Evolutionary Biol, Santa Cruz, CA 95064 USA

[7] Univ Nebraska, Dept Anim Sci, Lincoln, NE 68583 USA

[8] Univ Calif Davis, Dept Populat Hlth & Reprod, Davis, CA 95616 USA

[9] Univ Calif Davis, Vet Genet Lab, Davis, CA 95616 USA

[10] Univ Minnesota, Dept Vet Populat Med, St Paul, MN 55108 USA

[11] Univ Florida, UF Genet Inst, Dept Anim Sci, Gainesville, FL 32611 USA

[12] Univ Kentucky, Gluck Equine Res Ctr, Dept Vet Sci, Lexington, KY 40546 USA

[13] Nat Hist Museum Denmark, Ctr GeoGenet, DK-1350 Copenhagen, Denmark

[14] Univ Toulouse, Univ Paul Sabatier, Lab Anthropobiol Mol & Imagerie Synth, CNRS,UMR 5288, Toulouse, France

[15] Cornell Univ, Coll Vet Med, Baker Inst Anim Hlth, Ithaca, NY 14853 USA

[16] Oregon Hlth & Sci Univ, Med & Mol Genet, Portland, OR 97239 USA

来源：

COMMUNICATIONS BIOLOGY | 2018年 / 1卷

基金：

美国国家卫生研究院;

关键词：

READ ALIGNMENT; MESSENGER-RNA; SEQUENCE; ANNOTATION; GENES;

D O I：

10.1038/s42003-018-0199-z

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. Here, we present EquCab3. The count of non-N bases in the incorporated chromosomes is improved from 2.33 Gb in EquCab2 to 2.41 Gb in EquCab3. Contiguity has also been improved nearly 40-fold with a contig N50 of 4.5 Mb and scaffold contiguity enhanced to where all but one of the 32 chromosomes is comprised of a single scaffold.

引用

页数：8

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