Chromosome‐level genome assembly of burbot ( Lota lota) provides insights into the evolutionary adaptations in freshwater
Abstract The burbot ( Lota lota ) is the only member of the order Gadiformes adapted solely to freshwater. This species has the widest longitudinal range among freshwater fish worldwide. Burbot serves as a good model for studies on adaptive genome evolution from marine to freshwater environments. Ho...
Published in: | Molecular Ecology Resources |
---|---|
Main Authors: | , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Wiley
2021
|
Subjects: | |
Online Access: | http://dx.doi.org/10.1111/1755-0998.13382 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13382 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13382 |
id |
crwiley:10.1111/1755-0998.13382 |
---|---|
record_format |
openpolar |
spelling |
crwiley:10.1111/1755-0998.13382 2024-06-23T07:51:06+00:00 Chromosome‐level genome assembly of burbot ( Lota lota) provides insights into the evolutionary adaptations in freshwater Han, Zhiqiang Liu, Manhong Liu, Qi Zhai, Hao Xiao, Shijun Gao, Tianxiang 2021 http://dx.doi.org/10.1111/1755-0998.13382 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13382 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13382 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Molecular Ecology Resources volume 21, issue 6, page 2022-2033 ISSN 1755-098X 1755-0998 journal-article 2021 crwiley https://doi.org/10.1111/1755-0998.13382 2024-06-11T04:39:57Z Abstract The burbot ( Lota lota ) is the only member of the order Gadiformes adapted solely to freshwater. This species has the widest longitudinal range among freshwater fish worldwide. Burbot serves as a good model for studies on adaptive genome evolution from marine to freshwater environments. However, a high‐quality reference genome of burbot has not yet been released. Here, the first chromosome‐level genome of burbot was constructed using PacBio long sequencing and Hi‐C technology. A total of 95.24 Gb polished PacBio sequences were generated, and the preliminary genome assembly was 575.83 Mb in size with a contig N50 size of 2.15 Mb. The assembled sequences were anchored to 22 pseudochromosomes by using Hi‐C data. The final assembled genome after Hi‐C correction was 575.92 Mb, with a contig N50 of 2.01 Mb and a scaffold N50 of 22.10 Mb. A total of 22,067 protein‐coding genes were predicted, 94.82% of which were functionally annotated. Phylogenetic analyses indicated that burbot diverged with the Atlantic cod approximately 43.8 million years ago. In addition, 377 putative genes that appear to be under positive selection in burbot were identified. These positively selected genes might be involved in the adaptation to the freshwater environment. These genome data provide an invaluable resource for the ecological and evolutionary study of the order Gadiformes. Article in Journal/Newspaper atlantic cod Burbot Lota lota lota Wiley Online Library Molecular Ecology Resources |
institution |
Open Polar |
collection |
Wiley Online Library |
op_collection_id |
crwiley |
language |
English |
description |
Abstract The burbot ( Lota lota ) is the only member of the order Gadiformes adapted solely to freshwater. This species has the widest longitudinal range among freshwater fish worldwide. Burbot serves as a good model for studies on adaptive genome evolution from marine to freshwater environments. However, a high‐quality reference genome of burbot has not yet been released. Here, the first chromosome‐level genome of burbot was constructed using PacBio long sequencing and Hi‐C technology. A total of 95.24 Gb polished PacBio sequences were generated, and the preliminary genome assembly was 575.83 Mb in size with a contig N50 size of 2.15 Mb. The assembled sequences were anchored to 22 pseudochromosomes by using Hi‐C data. The final assembled genome after Hi‐C correction was 575.92 Mb, with a contig N50 of 2.01 Mb and a scaffold N50 of 22.10 Mb. A total of 22,067 protein‐coding genes were predicted, 94.82% of which were functionally annotated. Phylogenetic analyses indicated that burbot diverged with the Atlantic cod approximately 43.8 million years ago. In addition, 377 putative genes that appear to be under positive selection in burbot were identified. These positively selected genes might be involved in the adaptation to the freshwater environment. These genome data provide an invaluable resource for the ecological and evolutionary study of the order Gadiformes. |
format |
Article in Journal/Newspaper |
author |
Han, Zhiqiang Liu, Manhong Liu, Qi Zhai, Hao Xiao, Shijun Gao, Tianxiang |
spellingShingle |
Han, Zhiqiang Liu, Manhong Liu, Qi Zhai, Hao Xiao, Shijun Gao, Tianxiang Chromosome‐level genome assembly of burbot ( Lota lota) provides insights into the evolutionary adaptations in freshwater |
author_facet |
Han, Zhiqiang Liu, Manhong Liu, Qi Zhai, Hao Xiao, Shijun Gao, Tianxiang |
author_sort |
Han, Zhiqiang |
title |
Chromosome‐level genome assembly of burbot ( Lota lota) provides insights into the evolutionary adaptations in freshwater |
title_short |
Chromosome‐level genome assembly of burbot ( Lota lota) provides insights into the evolutionary adaptations in freshwater |
title_full |
Chromosome‐level genome assembly of burbot ( Lota lota) provides insights into the evolutionary adaptations in freshwater |
title_fullStr |
Chromosome‐level genome assembly of burbot ( Lota lota) provides insights into the evolutionary adaptations in freshwater |
title_full_unstemmed |
Chromosome‐level genome assembly of burbot ( Lota lota) provides insights into the evolutionary adaptations in freshwater |
title_sort |
chromosome‐level genome assembly of burbot ( lota lota) provides insights into the evolutionary adaptations in freshwater |
publisher |
Wiley |
publishDate |
2021 |
url |
http://dx.doi.org/10.1111/1755-0998.13382 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13382 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13382 |
genre |
atlantic cod Burbot Lota lota lota |
genre_facet |
atlantic cod Burbot Lota lota lota |
op_source |
Molecular Ecology Resources volume 21, issue 6, page 2022-2033 ISSN 1755-098X 1755-0998 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1111/1755-0998.13382 |
container_title |
Molecular Ecology Resources |
_version_ |
1802642096372318208 |