Pattern of New Gene Origination in a Special Fish Lineage, the Flatfishes

Origination of new genes are of inherent interest of evolutionary geneticists for decades, but few studies have addressed the general pattern in a fish lineage. Using our recent released whole genome data of flatfishes, which evolved one of the most specialized body plans in vertebrates, we identifi...

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Autores principales:	Haorong Li, Chunyan Chen, Zhongkai Wang, Kun Wang, Yongxin Li, Wen Wang
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	flatfishes phylogenomic context origin new genes Genetics QH426-470
Acceso en línea:	https://doaj.org/article/53991da3f2324c0ea0ffdebf6f64528c
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spelling	oai:doaj.org-article:53991da3f2324c0ea0ffdebf6f64528c2021-11-25T17:42:22ZPattern of New Gene Origination in a Special Fish Lineage, the Flatfishes10.3390/genes121118192073-4425https://doaj.org/article/53991da3f2324c0ea0ffdebf6f64528c2021-11-01T00:00:00Zhttps://www.mdpi.com/2073-4425/12/11/1819https://doaj.org/toc/2073-4425Origination of new genes are of inherent interest of evolutionary geneticists for decades, but few studies have addressed the general pattern in a fish lineage. Using our recent released whole genome data of flatfishes, which evolved one of the most specialized body plans in vertebrates, we identified 1541 (6.9% of the starry flounder genes) flatfish-lineage-specific genes. The origination pattern of these flatfish new genes is largely similar to those observed in other vertebrates, as shown by the proportion of DNA-mediated duplication (1317; 85.5%), RNA-mediated duplication (retrogenes; 96; 6.2%), and de novo–origination (128; 8.3%). The emergence rate of species-specific genes is 32.1 per Mya and the whole average level rate for the flatfish-lineage-specific genes is 20.9 per Mya. A large proportion (31.4%) of these new genes have been subjected to selection, in contrast to the 4.0% in primates, while the old genes remain quite similar (66.4% vs. 65.0%). In addition, most of these new genes (70.8%) are found to be expressed, indicating their functionality. This study not only presents one example of systematic new gene identification in a teleost taxon based on comprehensive phylogenomic data, but also shows that new genes may play roles in body planning.Haorong LiChunyan ChenZhongkai WangKun WangYongxin LiWen WangMDPI AGarticleflatfishesphylogenomic contextoriginnew genesGeneticsQH426-470ENGenes, Vol 12, Iss 1819, p 1819 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	flatfishes phylogenomic context origin new genes Genetics QH426-470
spellingShingle	flatfishes phylogenomic context origin new genes Genetics QH426-470 Haorong Li Chunyan Chen Zhongkai Wang Kun Wang Yongxin Li Wen Wang Pattern of New Gene Origination in a Special Fish Lineage, the Flatfishes
description	Origination of new genes are of inherent interest of evolutionary geneticists for decades, but few studies have addressed the general pattern in a fish lineage. Using our recent released whole genome data of flatfishes, which evolved one of the most specialized body plans in vertebrates, we identified 1541 (6.9% of the starry flounder genes) flatfish-lineage-specific genes. The origination pattern of these flatfish new genes is largely similar to those observed in other vertebrates, as shown by the proportion of DNA-mediated duplication (1317; 85.5%), RNA-mediated duplication (retrogenes; 96; 6.2%), and de novo–origination (128; 8.3%). The emergence rate of species-specific genes is 32.1 per Mya and the whole average level rate for the flatfish-lineage-specific genes is 20.9 per Mya. A large proportion (31.4%) of these new genes have been subjected to selection, in contrast to the 4.0% in primates, while the old genes remain quite similar (66.4% vs. 65.0%). In addition, most of these new genes (70.8%) are found to be expressed, indicating their functionality. This study not only presents one example of systematic new gene identification in a teleost taxon based on comprehensive phylogenomic data, but also shows that new genes may play roles in body planning.
format	article
author	Haorong Li Chunyan Chen Zhongkai Wang Kun Wang Yongxin Li Wen Wang
author_facet	Haorong Li Chunyan Chen Zhongkai Wang Kun Wang Yongxin Li Wen Wang
author_sort	Haorong Li
title	Pattern of New Gene Origination in a Special Fish Lineage, the Flatfishes
title_short	Pattern of New Gene Origination in a Special Fish Lineage, the Flatfishes
title_full	Pattern of New Gene Origination in a Special Fish Lineage, the Flatfishes
title_fullStr	Pattern of New Gene Origination in a Special Fish Lineage, the Flatfishes
title_full_unstemmed	Pattern of New Gene Origination in a Special Fish Lineage, the Flatfishes
title_sort	pattern of new gene origination in a special fish lineage, the flatfishes
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/53991da3f2324c0ea0ffdebf6f64528c
work_keys_str_mv	AT haorongli patternofnewgeneoriginationinaspecialfishlineagetheflatfishes AT chunyanchen patternofnewgeneoriginationinaspecialfishlineagetheflatfishes AT zhongkaiwang patternofnewgeneoriginationinaspecialfishlineagetheflatfishes AT kunwang patternofnewgeneoriginationinaspecialfishlineagetheflatfishes AT yongxinli patternofnewgeneoriginationinaspecialfishlineagetheflatfishes AT wenwang patternofnewgeneoriginationinaspecialfishlineagetheflatfishes
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Pattern of New Gene Origination in a Special Fish Lineage, the Flatfishes

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