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Genome and gene evolution of seahorse species revealed by the chromosome‐level genome of Hippocampus abdominalis

Seahorses belong to the teleost family Syngnathidae that evolved a distinct body plan and unique male pregnancy compared to other teleosts. As a classic model for studying evolution of viviparity and sexual selection of teleosts, seahorse species still lack a publicly available high‐quality referenc...

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Autores principales: He, Libin, Long, Xin, Qi, Jianfei, Wang, Zongji, Huang, Zhen, Wu, Shuiqing, Zhang, Xingtan, Luo, Huiyu, Chen, Xinxin, Lin, Jinbo, Yang, Qiuhua, Huang, Shiyu, Zhou, Qi, Zheng, Leyun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9298228/
https://www.ncbi.nlm.nih.gov/pubmed/34698429
http://dx.doi.org/10.1111/1755-0998.13541
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author He, Libin
Long, Xin
Qi, Jianfei
Wang, Zongji
Huang, Zhen
Wu, Shuiqing
Zhang, Xingtan
Luo, Huiyu
Chen, Xinxin
Lin, Jinbo
Yang, Qiuhua
Huang, Shiyu
Zhou, Qi
Zheng, Leyun
author_facet He, Libin
Long, Xin
Qi, Jianfei
Wang, Zongji
Huang, Zhen
Wu, Shuiqing
Zhang, Xingtan
Luo, Huiyu
Chen, Xinxin
Lin, Jinbo
Yang, Qiuhua
Huang, Shiyu
Zhou, Qi
Zheng, Leyun
author_sort He, Libin
collection PubMed
description Seahorses belong to the teleost family Syngnathidae that evolved a distinct body plan and unique male pregnancy compared to other teleosts. As a classic model for studying evolution of viviparity and sexual selection of teleosts, seahorse species still lack a publicly available high‐quality reference genome. Here, we generated the genome assembly of the big‐belly seahorse, Hippocampus abdominalis with long‐read and Hi‐C technologies. We managed to place over 99% of the total length of 444.7 Mb of assembled genome into 21 linkage groups with almost no gaps. We reconstructed a phylogenomic tree with the big‐belly seahorse genome and other representative Syngnathidae and teleost species. We also reconstructed the historical population dynamics of four representative Syngnathidae species. We found the gene families that underwent expansion or contraction in the Syngnathidae ancestor were enriched for immune‐related or ion transporter gene ontology terms. Many of these genes were also reported to show a dynamic expression pattern during the pregnancy stages of H. abdominalis. We also identified putative positively selected genes in the Syngnathidae ancestor or in H. abdominalis, whose mouse mutants are enriched for abnormal craniofacial and limb morphological phenotypes. Overall, our study provides an important genome resource for evolutionary and developmental studies of seahorse species, and candidate genes for future experimental works.
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spelling pubmed-92982282022-07-21 Genome and gene evolution of seahorse species revealed by the chromosome‐level genome of Hippocampus abdominalis He, Libin Long, Xin Qi, Jianfei Wang, Zongji Huang, Zhen Wu, Shuiqing Zhang, Xingtan Luo, Huiyu Chen, Xinxin Lin, Jinbo Yang, Qiuhua Huang, Shiyu Zhou, Qi Zheng, Leyun Mol Ecol Resour RESOURCE ARTICLES Seahorses belong to the teleost family Syngnathidae that evolved a distinct body plan and unique male pregnancy compared to other teleosts. As a classic model for studying evolution of viviparity and sexual selection of teleosts, seahorse species still lack a publicly available high‐quality reference genome. Here, we generated the genome assembly of the big‐belly seahorse, Hippocampus abdominalis with long‐read and Hi‐C technologies. We managed to place over 99% of the total length of 444.7 Mb of assembled genome into 21 linkage groups with almost no gaps. We reconstructed a phylogenomic tree with the big‐belly seahorse genome and other representative Syngnathidae and teleost species. We also reconstructed the historical population dynamics of four representative Syngnathidae species. We found the gene families that underwent expansion or contraction in the Syngnathidae ancestor were enriched for immune‐related or ion transporter gene ontology terms. Many of these genes were also reported to show a dynamic expression pattern during the pregnancy stages of H. abdominalis. We also identified putative positively selected genes in the Syngnathidae ancestor or in H. abdominalis, whose mouse mutants are enriched for abnormal craniofacial and limb morphological phenotypes. Overall, our study provides an important genome resource for evolutionary and developmental studies of seahorse species, and candidate genes for future experimental works. John Wiley and Sons Inc. 2021-11-07 2022-05 /pmc/articles/PMC9298228/ /pubmed/34698429 http://dx.doi.org/10.1111/1755-0998.13541 Text en © 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ (https://creativecommons.org/licenses/by-nc-nd/4.0/) License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
spellingShingle RESOURCE ARTICLES
He, Libin
Long, Xin
Qi, Jianfei
Wang, Zongji
Huang, Zhen
Wu, Shuiqing
Zhang, Xingtan
Luo, Huiyu
Chen, Xinxin
Lin, Jinbo
Yang, Qiuhua
Huang, Shiyu
Zhou, Qi
Zheng, Leyun
Genome and gene evolution of seahorse species revealed by the chromosome‐level genome of Hippocampus abdominalis
title Genome and gene evolution of seahorse species revealed by the chromosome‐level genome of Hippocampus abdominalis
title_full Genome and gene evolution of seahorse species revealed by the chromosome‐level genome of Hippocampus abdominalis
title_fullStr Genome and gene evolution of seahorse species revealed by the chromosome‐level genome of Hippocampus abdominalis
title_full_unstemmed Genome and gene evolution of seahorse species revealed by the chromosome‐level genome of Hippocampus abdominalis
title_short Genome and gene evolution of seahorse species revealed by the chromosome‐level genome of Hippocampus abdominalis
title_sort genome and gene evolution of seahorse species revealed by the chromosome‐level genome of hippocampus abdominalis
topic RESOURCE ARTICLES
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9298228/
https://www.ncbi.nlm.nih.gov/pubmed/34698429
http://dx.doi.org/10.1111/1755-0998.13541
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