Intra-specific comparison of mitochondrial genomes reveals host gene fragment exchange via intron mobility in Tremella fuciformis

Youjin Deng,Baogui Xie,Wenjing Miao,Yiying Lin,Xiangzhi Lin,Longji Lin,Xunxiao Zhang,Tom Hsiang,Ray Ming,Xingtan Zhang,Yanhong Ma

doi:10.1186/s12864-020-06846-x

Youjin Deng, Baogui Xie + Show 9 more

Open Access

https://doi.org/10.1186/s12864-020-06846-x

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Abstract

BackgroundMitochondrial genomic sequences are known to be variable. Comparative analyses of mitochondrial genomes can reveal the nature and extent of their variation.ResultsDraft mitochondrial genomes of 16 Tremella fuciformis isolates (TF01-TF16) were assembled from Illumina and PacBio sequencing data. Mitochondrial DNA contigs were extracted and assembled into complete circular molecules, ranging from 35,104 bp to 49,044 bp in size. All mtDNAs contained the same set of 41 conserved genes with identical gene order. Comparative analyses revealed that introns and intergenic regions were variable, whereas genic regions (including coding sequences, tRNA, and rRNA genes) were conserved. Among 24 introns detected, 11 were in protein-coding genes, 3 in tRNA genes, and the other 10 in rRNA genes. In addition, two mobile fragments were found in intergenic regions. Interestingly, six introns containing N-terminal duplication of the host genes were found in five conserved protein-coding gene sequences. Comparison of genes with and without these introns gave rise to the following proposed model: gene fragment exchange with other species can occur via gain or loss of introns with N-terminal duplication of the host genes.ConclusionsOur findings suggest a novel mechanism of fungal mitochondrial gene evolution: partial foreign gene replacement though intron mobility.

Highlights

Mitochondrial genomic sequences are known to be variable
Mitochondrial DNA of the 16 sequenced T. fuciformis isolates was circular with a length ranging from 35,104
Intraspecific mitochondrial genomic comparison revealed that coding sequences, Transfer RNA (tRNA), and Ribosomal RNA (rRNA) genes were conserved, whereas introns and intergenic regions were variable

Summary

Introduction

Mitochondrial genomic sequences are known to be variable. The relationship between mobile elements and their host genomes is referred to as a type of parasitism at the genomic level [1,2,3]. A mobile element is a DNA sequence that can change its position within a genome or insert into another genome. It utilizes host cellular machinery for element duplication and mobility, but is traditionally regarded to have little or no benefit for the host [3, 4]. Different from nuclear introns, mitochondrial introns are typical selfish mobile elements [5]

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