干旱区生态环境知识资源中心(Arid): Improving Illumina assemblies with Hi-C and long reads: An example with the North African dromedary

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DOI	10.1111/1755-0998.13020
	Improving Illumina assemblies with Hi-C and long reads: An example with the North African dromedary
	Elbers, Jean P.1; Rogers, Mark F.2; Perelman, Polina L.3,4; Proskuryakova, Anastasia A.3,4; Serdyukova, Natalia A.3,4; Johnson, Warren E.5; Horin, Petr 6; Corander, Jukka 7,8; Murphy, David 9; Burger, Pamela A.1
通讯作者	Elbers, Jean P. ; Burger, Pamela A.
来源期刊	MOLECULAR ECOLOGY RESOURCES
ISSN	1755-098X
EISSN	1755-0998
出版年	2019
卷号	19 期号:4 页码:1015-1026
英文摘要	Researchers have assembled thousands of eukaryotic genomes using Illumina reads, but traditional mate-pair libraries cannot span all repetitive elements, resulting in highly fragmented assemblies. However, both chromosome conformation capture techniques, such as Hi-C and Dovetail Genomics Chicago libraries and long-read sequencing, such as Pacific Biosciences and Oxford Nanopore, help span and resolve repetitive regions and therefore improve genome assemblies. One important livestock species of arid regions that does not have a high-quality contiguous reference genome is the dromedary (Camelus dromedarius). Draft genomes exist but are highly fragmented, and a high-quality reference genome is needed to understand adaptation to desert environments and artificial selection during domestication. Dromedaries are among the last livestock species to have been domesticated, and together with wild and domestic Bactrian camels, they are the only representatives of the Camelini tribe, which highlights their evolutionary significance. Here we describe our efforts to improve the North African dromedary genome. We used Chicago and Hi-C sequencing libraries from Dovetail Genomics to resolve the order of previously assembled contigs, producing almost chromosome-level scaffolds. Remaining gaps were filled with Pacific Biosciences long reads, and then scaffolds were comparatively mapped to chromosomes. Long reads added 99.32 Mbp to the total length of the new assembly. Dovetail Chicago and Hi-C libraries increased the longest scaffold over 12-fold, from 9.71 Mbp to 124.99 Mbp and the scaffold N50 over 50-fold, from 1.48 Mbp to 75.02 Mbp. We demonstrate that Illumina de novo assemblies can be substantially upgraded by combining chromosome conformation capture and long-read sequencing.
英文关键词	chromosome conformation capture chromosome mapping dromedary genome annotation genome assembly scaffolding
类型	Article
语种	英语
国家	Austria ; England ; Russia ; USA ; Czech Republic ; Norway ; Finland
开放获取类型	Green Published, hybrid
收录类别	SCI-E
WOS记录号	WOS:000471830200016
WOS关键词	GENOME-WIDE ASSOCIATION ; PRODUCTION TRAITS ; ANNOTATION ; SEQUENCE ; PLANT ; ARCHITECTURE ; RESOURCE ; CATTLE ; MAKER ; ABYSS
WOS类目	Biochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
WOS研究方向	Biochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/217653
作者单位	1.Vetmeduni Vienna, Res Inst Wildlife Ecol, Dept Integrat Biol & Evolut, Vienna, Austria; 2.Univ Bristol, Intelligent Syst Lab, Bristol, Avon, England; 3.RAS, SB, Inst Mol & Cellular Biol, Novosibirsk, Russia; 4.Novosibirsk State Univ, Novosibirsk, Russia; 5.Museum Support Ctr MRC 534, Walter Reed Biosystemat Unit, Smithsonian Inst, Suitland, MD USA; 6.Univ Vet & Pharmaceut Sci, Dept Anim Genet, Fac Vet Med, Ceitec VFU,RG Anim Immunogen, Brno, Czech Republic; 7.Univ Oslo, Dept Biostat, Oslo, Norway; 8.Univ Helsinki, Dept Math & Stat, Helsinki, Finland; 9.Univ Bristol, Bristol Med Sch Translat Hlth Sci, Mol Neuroendocrinol Res Grp, Bristol, Avon, England
推荐引用方式 GB/T 7714	Elbers, Jean P.,Rogers, Mark F.,Perelman, Polina L.,et al. Improving Illumina assemblies with Hi-C and long reads: An example with the North African dromedary[J],2019,19(4):1015-1026.
APA	Elbers, Jean P..,Rogers, Mark F..,Perelman, Polina L..,Proskuryakova, Anastasia A..,Serdyukova, Natalia A..,...&Burger, Pamela A..(2019).Improving Illumina assemblies with Hi-C and long reads: An example with the North African dromedary.MOLECULAR ECOLOGY RESOURCES,19(4),1015-1026.
MLA	Elbers, Jean P.,et al."Improving Illumina assemblies with Hi-C and long reads: An example with the North African dromedary".MOLECULAR ECOLOGY RESOURCES 19.4(2019):1015-1026.