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Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications

BACKGROUND: The relict gull (Larus relictus), was classified as vulnerable on the IUCN Red List and is a first-class national protected bird in China. Genomic resources for L. relictus are lacking, which limits the study of its evolution and its conservation. RESULTS: In this study, based on the Ill...

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Autores principales: Yang, Chao, Li, Xuejuan, Wang, Qingxiong, Yuan, Hao, Huang, Yuan, Xiao, Hong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082828/
https://www.ncbi.nlm.nih.gov/pubmed/33926388
http://dx.doi.org/10.1186/s12864-021-07616-z
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author Yang, Chao
Li, Xuejuan
Wang, Qingxiong
Yuan, Hao
Huang, Yuan
Xiao, Hong
author_facet Yang, Chao
Li, Xuejuan
Wang, Qingxiong
Yuan, Hao
Huang, Yuan
Xiao, Hong
author_sort Yang, Chao
collection PubMed
description BACKGROUND: The relict gull (Larus relictus), was classified as vulnerable on the IUCN Red List and is a first-class national protected bird in China. Genomic resources for L. relictus are lacking, which limits the study of its evolution and its conservation. RESULTS: In this study, based on the Illumina and PacBio sequencing platforms, we successfully assembled the genome of L. relictus, one of the few known reference genomes in genus Larus. The size of the final assembled genome was 1.21 Gb, with a contig N50 of 8.11 Mb. A total of 18,454 genes were predicted from the assembly results, with 16,967 (91.94%) of these genes annotated. The genome contained 92.52 Mb of repeat sequence, accounting for 7.63% of the assembly. A phylogenetic tree was constructed using 4902 single-copy orthologous genes, which showed L. relictus had closest relative of L. smithsonianus, with divergence time of 14.7 Mya estimated between of them. PSMC analyses indicated that L. relictus had been undergoing a long-term population decline during 0.01-0.1 Mya with a small effective population size fom 8800 to 2200 individuals. CONCLUSIONS: This genome will be a valuable genomic resource for a range of genomic and conservation studies of L. relictus and will help to establish a foundation for further studies investigating whether the breeding population is a complex population. As the species is threatened by habitat loss and fragmentation, actions to protect L. relictus are suggested to alleviate the fragmentation of breeding populations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07616-z.
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spelling pubmed-80828282021-04-29 Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications Yang, Chao Li, Xuejuan Wang, Qingxiong Yuan, Hao Huang, Yuan Xiao, Hong BMC Genomics Research Article BACKGROUND: The relict gull (Larus relictus), was classified as vulnerable on the IUCN Red List and is a first-class national protected bird in China. Genomic resources for L. relictus are lacking, which limits the study of its evolution and its conservation. RESULTS: In this study, based on the Illumina and PacBio sequencing platforms, we successfully assembled the genome of L. relictus, one of the few known reference genomes in genus Larus. The size of the final assembled genome was 1.21 Gb, with a contig N50 of 8.11 Mb. A total of 18,454 genes were predicted from the assembly results, with 16,967 (91.94%) of these genes annotated. The genome contained 92.52 Mb of repeat sequence, accounting for 7.63% of the assembly. A phylogenetic tree was constructed using 4902 single-copy orthologous genes, which showed L. relictus had closest relative of L. smithsonianus, with divergence time of 14.7 Mya estimated between of them. PSMC analyses indicated that L. relictus had been undergoing a long-term population decline during 0.01-0.1 Mya with a small effective population size fom 8800 to 2200 individuals. CONCLUSIONS: This genome will be a valuable genomic resource for a range of genomic and conservation studies of L. relictus and will help to establish a foundation for further studies investigating whether the breeding population is a complex population. As the species is threatened by habitat loss and fragmentation, actions to protect L. relictus are suggested to alleviate the fragmentation of breeding populations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07616-z. BioMed Central 2021-04-29 /pmc/articles/PMC8082828/ /pubmed/33926388 http://dx.doi.org/10.1186/s12864-021-07616-z Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Yang, Chao
Li, Xuejuan
Wang, Qingxiong
Yuan, Hao
Huang, Yuan
Xiao, Hong
Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications
title Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications
title_full Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications
title_fullStr Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications
title_full_unstemmed Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications
title_short Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications
title_sort genome-wide analyses of the relict gull (larus relictus): insights and evolutionary implications
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082828/
https://www.ncbi.nlm.nih.gov/pubmed/33926388
http://dx.doi.org/10.1186/s12864-021-07616-z
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