Arid
DOI10.1111/1755-0998.12443
The de novo genome assembly and annotation of a female domestic dromedary of North African origin
Fitak, Robert R.1; Mohandesan, Elmira1; Corander, Jukka2; Burger, Pamela A.1
通讯作者Fitak, Robert R.
来源期刊MOLECULAR ECOLOGY RESOURCES
ISSN1755-098X
EISSN1755-0998
出版年2016
卷号16期号:1页码:314-324
英文摘要

The single-humped dromedary (Camelus dromedarius) is the most numerous and widespread of domestic camel species and is a significant source of meat, milk, wool, transportation and sport for millions of people. Dromedaries are particularly well adapted to hot, desert conditions and harbour a variety of biological and physiological characteristics with evolutionary, economic and medical importance. To understand the genetic basis of these traits, an extensive resource of genomic variation is required. In this study, we assembled at 653 coverage, a 2.06 Gb draft genome of a female dromedary whose ancestry can be traced to an isolated population from the Canary Islands. We annotated 21 167 protein-coding genes and estimated similar to 33.7% of the genome to be repetitive. A comparison with the recently published draft genome of an Arabian dromedary resulted in 1.91 Gb of aligned sequence with a divergence of 0.095%. An evaluation of our genome with the reference revealed that our assembly contains more error-free bases (91.2%) and fewer scaffolding errors. We identified similar to 1.4 million single-nucleotide polymorphisms with a mean density of 0.71 x 10(-3) per base. An analysis of demographic history indicated that changes in effective population size corresponded with recent glacial epochs. Our de novo assembly provides a useful resource of genomic variation for future studies of the camel’s adaptations to arid environments and economically important traits. Furthermore, these results suggest that draft genome assemblies constructed with only two differently sized sequencing libraries can be comparable to those sequenced using additional library sizes, highlighting that additional resources might be better placed in technologies alternative to short-read sequencing to physically anchor scaffolds to genome maps.


英文关键词adaptation Camelus dromedarius demography domestication next-generation sequencing
类型Article
语种英语
国家Austria ; Finland
收录类别SCI-E
WOS记录号WOS:000369141000030
WOS关键词REPRODUCIBLE RESEARCH ; SEQUENCING DATA ; IDENTIFICATION ; INFERENCE ; EVOLUTION ; ALIGNMENT ; PIPELINE ; CAMEL ; TOOL ; DATABASE
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/2XILL650/195100
作者单位1.Vetmeduni Vienna, Inst Populat Genet, Vet Pl 1, A-1210 Vienna, Austria;
2.Univ Helsinki, Dept Math & Stat, FIN-0014 Helsinki, Finland
推荐引用方式
GB/T 7714
Fitak, Robert R.,Mohandesan, Elmira,Corander, Jukka,et al. The de novo genome assembly and annotation of a female domestic dromedary of North African origin[J],2016,16(1):314-324.
APA Fitak, Robert R.,Mohandesan, Elmira,Corander, Jukka,&Burger, Pamela A..(2016).The de novo genome assembly and annotation of a female domestic dromedary of North African origin.MOLECULAR ECOLOGY RESOURCES,16(1),314-324.
MLA Fitak, Robert R.,et al."The de novo genome assembly and annotation of a female domestic dromedary of North African origin".MOLECULAR ECOLOGY RESOURCES 16.1(2016):314-324.
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