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Genome Assembly of ...
Genome Assembly of the Common Pheasant Phasianus colchicus : A Model for Speciation and Ecological Genomics
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- Liu, Yang (author)
- Sun Yat Sen Univ, Sch Life Sci, Coll Ecol, State Key Lab Biocontrol, Guangzhou, Peoples R China
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- Liu, Simin (author)
- Sun Yat Sen Univ, Sch Life Sci, Coll Ecol, State Key Lab Biocontrol, Guangzhou, Peoples R China
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- Zhang, Nan (author)
- Sun Yat Sen Univ, Sch Life Sci, Coll Ecol, State Key Lab Biocontrol, Guangzhou, Peoples R China
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- Chen, De (author)
- Beijing Normal Univ, Coll Life Sci, MOE Key Lab Biodivers Sci & Ecol Engn, Beijing, Peoples R China
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- Que, Pinjia (author)
- Beijing Normal Univ, Coll Life Sci, MOE Key Lab Biodivers Sci & Ecol Engn, Beijing, Peoples R China
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- Liu, Naijia (author)
- Shenzhen Univ, Coll Life Sci & Oceanog, Shenzhen, Peoples R China
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- Höglund, Jacob (author)
- Uppsala universitet,Zooekologi
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- Zhang, Zhengwang (author)
- Beijing Normal Univ, Coll Life Sci, MOE Key Lab Biodivers Sci & Ecol Engn, Beijing, Peoples R China
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- Wang, Biao (author)
- Univ Melbourne, Sch Biosci, Parkville, Vic, Australia
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(creator_code:org_t)
- 2019-11-12
- 2019
- English.
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In: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 11:12, s. 3326-3331
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https://uu.diva-port... (primary) (Raw object)
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Abstract
Subject headings
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- The commonpheasant (Phasianus colchicus) in the order Galliformes and the family Phasianidae, has 30 subspecies distributed across its native range in the Palearctic realm and has been introduced to Europe, NorthAmerica, and Australia. It is an important game bird often subjected to wildlife management as well as a model species to study speciation, biogeography, and local adaptation. However, the genomic resources for the commonpheasant are generally lacking. We sequenced a male individual of the subspecies torquatus of the common pheasant with the Illumina HiSeq platform. We obtained 94.88Gb of usable sequences by filtering out low-quality reads of the raw data generated. This resulted in a 1.02Gb final assembly, which equals the estimated genome size. BUSCO analysis using chicken as a model showed that 93.3% of genes were complete. The contig N50 and scaffold N50 sizes were 178 kb and 10.2 Mb, respectively. All these indicate that we obtained a high-quality genome assembly. We annotated 16,485 protein-coding genes and 123.3 Mb (12.05% of the genome) of repetitive sequences by ab initio and homology-based prediction. Furthermore, we applied a RAD-sequencing approach for another 45 individuals of seven representative subspecies in China and identified 4,376,351 novel single nucleotide polymorphism (SNPs) markers. Using this unprecedented data set, we uncovered the geographic population structure and genetic introgression among common pheasants in China. Our results provide the first high-quality reference genome for the common pheasant and a valuable genome-wide SNP database for studying population genomics and demographic history.
Subject headings
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Evolutionsbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Evolutionary Biology (hsv//eng)
Keyword
- common pheasant
- Phasianus colchicus
- genome sequencing
- RAD-sequencing
- SNP
- population genomics
Publication and Content Type
- ref (subject category)
- art (subject category)
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