Comparative mitochondrial genome analysis reveals intron dynamics and gene rearrangements in two Trametes species

Abstract Trametes species are efficient wood decomposers that are widespread throughout the world. Mitogenomes have been widely used to understand the phylogeny and evolution of fungi. Up to now, two mitogenomes from the Trametes genus have been revealed. In the present study, the complete mitogenom...

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Autores principales:	Cheng Chen, Qiang Li, Rongtao Fu, Jian Wang, Guangmin Deng, Xiaojuan Chen, Daihua Lu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/449982bb484a499eba8738a9c4929c83
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spelling	oai:doaj.org-article:449982bb484a499eba8738a9c4929c832021-12-02T13:57:38ZComparative mitochondrial genome analysis reveals intron dynamics and gene rearrangements in two Trametes species10.1038/s41598-021-82040-72045-2322https://doaj.org/article/449982bb484a499eba8738a9c4929c832021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-82040-7https://doaj.org/toc/2045-2322Abstract Trametes species are efficient wood decomposers that are widespread throughout the world. Mitogenomes have been widely used to understand the phylogeny and evolution of fungi. Up to now, two mitogenomes from the Trametes genus have been revealed. In the present study, the complete mitogenomes of two novel Trametes species, Trametes versicolor and T. coccinea, were assembled and compared with other Polyporales mitogenomes. Both species contained circular DNA molecules, with sizes of 67,318 bp and 99,976 bp, respectively. Comparative mitogenomic analysis indicated that the gene number, length and base composition varied between the four Trametes mitogenomes we tested. In addition, all of the core protein coding genes in Trametes species were identified and subjected to purifying selection. The mitogenome of T. coccinea contained the largest number of introns among the four Trametes species tested, and introns were considered the main factors contributing to size variations of Polyporales. Several novel introns were detected in the Trametes species we assembled, and introns identified in Polyporales were found to undergo frequent loss/gain events. Large-scale gene rearrangements were detected between closely related Trametes species, including gene inversions, insertions, and migrations. A well-supported phylogenetic tree for 77 Basidiomycetes was obtained based on the combined mitochondrial gene set using 2 phylogenetic inference methods. The results showed that mitochondrial genes are effective molecular markers for understanding the phylogeny of Basidiomycetes. This study is the first to report the mitogenome rearrangement and intron dynamics of Trametes species, which shed light on the evolution of Trametes and other related species.Cheng ChenQiang LiRongtao FuJian WangGuangmin DengXiaojuan ChenDaihua LuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Cheng Chen Qiang Li Rongtao Fu Jian Wang Guangmin Deng Xiaojuan Chen Daihua Lu Comparative mitochondrial genome analysis reveals intron dynamics and gene rearrangements in two Trametes species
description	Abstract Trametes species are efficient wood decomposers that are widespread throughout the world. Mitogenomes have been widely used to understand the phylogeny and evolution of fungi. Up to now, two mitogenomes from the Trametes genus have been revealed. In the present study, the complete mitogenomes of two novel Trametes species, Trametes versicolor and T. coccinea, were assembled and compared with other Polyporales mitogenomes. Both species contained circular DNA molecules, with sizes of 67,318 bp and 99,976 bp, respectively. Comparative mitogenomic analysis indicated that the gene number, length and base composition varied between the four Trametes mitogenomes we tested. In addition, all of the core protein coding genes in Trametes species were identified and subjected to purifying selection. The mitogenome of T. coccinea contained the largest number of introns among the four Trametes species tested, and introns were considered the main factors contributing to size variations of Polyporales. Several novel introns were detected in the Trametes species we assembled, and introns identified in Polyporales were found to undergo frequent loss/gain events. Large-scale gene rearrangements were detected between closely related Trametes species, including gene inversions, insertions, and migrations. A well-supported phylogenetic tree for 77 Basidiomycetes was obtained based on the combined mitochondrial gene set using 2 phylogenetic inference methods. The results showed that mitochondrial genes are effective molecular markers for understanding the phylogeny of Basidiomycetes. This study is the first to report the mitogenome rearrangement and intron dynamics of Trametes species, which shed light on the evolution of Trametes and other related species.
format	article
author	Cheng Chen Qiang Li Rongtao Fu Jian Wang Guangmin Deng Xiaojuan Chen Daihua Lu
author_facet	Cheng Chen Qiang Li Rongtao Fu Jian Wang Guangmin Deng Xiaojuan Chen Daihua Lu
author_sort	Cheng Chen
title	Comparative mitochondrial genome analysis reveals intron dynamics and gene rearrangements in two Trametes species
title_short	Comparative mitochondrial genome analysis reveals intron dynamics and gene rearrangements in two Trametes species
title_full	Comparative mitochondrial genome analysis reveals intron dynamics and gene rearrangements in two Trametes species
title_fullStr	Comparative mitochondrial genome analysis reveals intron dynamics and gene rearrangements in two Trametes species
title_full_unstemmed	Comparative mitochondrial genome analysis reveals intron dynamics and gene rearrangements in two Trametes species
title_sort	comparative mitochondrial genome analysis reveals intron dynamics and gene rearrangements in two trametes species
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/449982bb484a499eba8738a9c4929c83
work_keys_str_mv	AT chengchen comparativemitochondrialgenomeanalysisrevealsintrondynamicsandgenerearrangementsintwotrametesspecies AT qiangli comparativemitochondrialgenomeanalysisrevealsintrondynamicsandgenerearrangementsintwotrametesspecies AT rongtaofu comparativemitochondrialgenomeanalysisrevealsintrondynamicsandgenerearrangementsintwotrametesspecies AT jianwang comparativemitochondrialgenomeanalysisrevealsintrondynamicsandgenerearrangementsintwotrametesspecies AT guangmindeng comparativemitochondrialgenomeanalysisrevealsintrondynamicsandgenerearrangementsintwotrametesspecies AT xiaojuanchen comparativemitochondrialgenomeanalysisrevealsintrondynamicsandgenerearrangementsintwotrametesspecies AT daihualu comparativemitochondrialgenomeanalysisrevealsintrondynamicsandgenerearrangementsintwotrametesspecies
_version_	1718392256226918400

Comparative mitochondrial genome analysis reveals intron dynamics and gene rearrangements in two Trametes species

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