Intra-specific comparison of mitochondrial genomes reveals host gene fragment exchange via intron mobility in Tremella fuciformis Brief Intron variation in mitochondrial genomes of Tremella fuciformis
Mitochondrial genomic sequences are known to be variable. Comparative analyses of mitochondrial genomes can reveal the nature and extent of their variation. Results Draft 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.
... entical 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. Conclusions Our findings suggest a novel mechanism of fungal mitochondrial gene evolution: partial foreign gene replacement though intron mobility. Background Parasitism is one of the most intricate phenomena in biology. Generally, parasitism is a nonmutualistic relationship between species, where the parasite reduces the biological fitness of the host, while it increases its own fitness by obtaining resources necessary for survival from the host. The relationship between mobile elements and their host genomes is also referred to as a type of parasitism at the genomic level [ 1-3]. 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, 4 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]. Mitochondrial genome comparisons among isolates within a species or closely related species have revealed some extra-large fragments [ 5-13]. In most cases, these fragments range from several hundred bp to several kb in size, contain one intron-encoded protein gene (IEP), and are located between exons of a conserved gene, and hence referred to as introns. These fragments did not evolve from their own genome, but resulted from parasitism by mobile elements from other genomes. When their host genes start transcription, the introns act as ribozymes to remove their own sequences from the primary transcripts, thus limiting the impact on functionality of their host [ 1]. Sometimes, one intron is invaded by another intron to form a complex intronic structure, referred to as a twintron [ 14-17]. At least two levels of parasitism exist in this situation: relationships between parasite intron and host intron, and between twintron and host gene. Based on the RNA secondary structure, introns in fungal mitochondrial genomes are classified into two major groups [ 18]. Group I introns generally encode a type of self-splicing ribozyme mostly containing 10 conserved helices and a conserved catalytic core [ 19], and spread widely through hosts by mobility and horizontal transfer. Two hypotheses are common to explain the mobility of group I introns. One hypothesis is intron homing based on the harbored homing endonuclease gene [ 19-21]. The recognition site of the homing endonuclease is located in a sequence with 14-45 nucleotides around a break point. The other hypothesis is intron invasion using an RNA intermediate for reverse splicing. According to this hypothesis, a 4-6 nt internal guide sequence is 5 employed to recognize the target region through complementarity [ 22]. Group II introns are much less common in fungal mitochondrial genomes [ 5], where splicing occurs by two transesterification steps virtually identical to nuclear pre-mRNA splicing [ 23]. Recent studies provide evidence that mobility of introns may affect their host genes, including gene structure and DNA composition. The Gigapora rosea cox1 gene is broken up into two fragments via group I intron-mediated trans-splicing. The two fragments are on the same strand in the mitochondrial genome, and are separated by a sequence of ~30 kbp, which includes 15 genes. Similar cases of group I intron-mediated trans-splicing have also been reported in the cox1 gene in Gigaspora margarita[ 24 ], Isoetes engelmannii [ 25], Selaginella moellendorffii [ 26], Helicosporidium sp. [ 27], andplacozoan animals [ 28], and in the rns gene in G. margarita [ 24]. A higher density of single nucleotide polymorphisms in exons near self-splicing introns was detected when analyzing the mitochondrial genomes of Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Lachancea kluyveri, leading to the deduction that intron mobility is a direct driver of host gene diversity (Repar and Warnecke 2017). However, no evidence has been reported that gain and loss of introns can give rise to large fragment changes in host genes. Tremella fuciformis Berk., a popular edible fungus in Asia, belongs to Tremellaceae (Tremellomycetes, Basidiomycota). This mushroom is in demand for medicinal use, such as the improvement of the immune system and anti-diabetic effects [ 29, 6 30]. In this study, we sequenced entire genomes of 16 T. fuciformis isolates using Illumina and PacBio sequencing technologies, and assembled them. We then pulled out mtDNA-related contigs and finished their assembly into complete mitochondrial molecules by more carefully examining the raw reads. Then we compared the mitochondrial genomes to investigate the types, locations and presence/absence of introns. We concentrated on the gain and loss of introns containing N-terminal duplication of the host genes. The overarching goal of this work is to investigate possible evolutionary pathways for mitochondrial protein coding genes.