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A chromosome-level ...
A chromosome-level assembly of the Atlantic herring : detection of a supergene and other signals of selection
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- Pettersson, Mats (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
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- Rochus, Christina Marie (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi
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- Han, Fan (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
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- Chen, Junfeng (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
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- Hill, Jason (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
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- Wallerman, Ola (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab
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- Fan, Guangyi (author)
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
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- Hong, Xiaoning (author)
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
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- Xu, Qiwu (author)
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
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- Zhang, He (author)
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
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- Liu, Shanshan (author)
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
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- Liu, Xin (author)
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
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- Haggerty, Leanne (author)
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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- Hunt, Toby (author)
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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- Martin, Fergal (author)
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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- Flicek, Paul (author)
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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- Bunikis, Ignas (author)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för immunologi, genetik och patologi
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- Folkvord, Arild (author)
- Department of Biological Sciences, University of Bergen, 5020 Bergen, Norway; Institute of Marine Research, 5018 Bergen, Norway
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- Andersson, Leif (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden;Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA
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(creator_code:org_t)
- 2019-10-24
- 2019
- English.
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In: Genome Research. - : Cold Spring Harbor Laboratory Press (CSHL). - 1088-9051 .- 1549-5469. ; 29:11, s. 1919-1928
- Related links:
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https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
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http://genome.cshlp....
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https://doi.org/10.1...
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Abstract
Subject headings
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- The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo Pacific Biosciences (PacBio) assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb, which has been corroborated by a high-resolution linkage map. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few inter-chromosomal but frequent intra-chromosomal rearrangements. The improved assembly facilitates analysis of previously intractable large-scale structural variation, allowing, for example, the detection of a 7.8-Mb inversion on Chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation.
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
- Atlantic herring
- assembly
- ecological adaptation
- supergene
Publication and Content Type
- ref (subject category)
- art (subject category)
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To the university's database
- By the author/editor
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Pettersson, Mats
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Rochus, Christin ...
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Han, Fan
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Chen, Junfeng
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Hill, Jason
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Wallerman, Ola
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show more...
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Fan, Guangyi
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Hong, Xiaoning
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Xu, Qiwu
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Zhang, He
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Liu, Shanshan
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Liu, Xin
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Haggerty, Leanne
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Hunt, Toby
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Martin, Fergal
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Flicek, Paul
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Bunikis, Ignas
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Folkvord, Arild
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Andersson, Leif
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Genetics
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Evolutionary Bio ...
- Articles in the publication
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Genome Research
- By the university
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Uppsala University