Comparative Mitogenomic Analysis Reveals Dynamics of Intron Within and Between Tricholoma Species and Phylogeny of Basidiomycota

Huang, Wenli; Feng, Huiyu; Tu, Wenying; Jin, Xin; Li, Ping; Wang, Xu; Li, Qiang

doi:10.3389/fgene.2021.534871

Cited by 18 publications

(15 citation statements)

References 79 publications

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“…Positive selection signals in fungal mitochondrial rps3 genes have been reported previously ( Lin et al, 2015 , 2017 ; Kang et al, 2017 ; Wang et al, 2020 ; Zhang et al, 2020 ; Huang et al, 2021 ; Wu et al, 2021 ). Together with rps3 , genes encoding ribosomal subunits with positive AT and GC skewness are identified in the mitogenomes of brown rot fungal pathogens ( Yildiz and Ozkilinc, 2021 ).…”

Section: Discussionsupporting

confidence: 70%

Comparative Mitogenomic Analysis and the Evolution of Rhizoctonia solani Anastomosis Groups

et al. 2021

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Mitochondria are the major energy source for cell functions. However, for the plant fungal pathogens, mitogenome variations and their roles during the host infection processes remain largely unknown. Rhizoctonia solani, an important soil-borne pathogen, forms different anastomosis groups (AGs) and adapts to a broad range of hosts in nature. Here, we reported three complete mitogenomes of AG1-IA RSIA1, AG1-IB RSIB1, and AG1-IC, and performed a comparative analysis with nine published Rhizoctonia mitogenomes (AG1-IA XN, AG1-IB 7/3/14, AG3, AG4, and five Rhizoctonia sp. mitogenomes). These mitogenomes encoded 15 typical proteins (cox1-3, cob, atp6, atp8-9, nad1-6, nad4L, and rps3) and several LAGLIDADG/GIY-YIG endonucleases with sizes ranging from 109,017 bp (Rhizoctonia sp. SM) to 235,849 bp (AG3). We found that their large sizes were mainly contributed by repeat sequences and genes encoding endonucleases. We identified the complete sequence of the rps3 gene in 10 Rhizoctonia mitogenomes, which contained 14 positively selected sites. Moreover, we inferred a robust maximum-likelihood phylogeny of 32 Basidiomycota mitogenomes, representing that seven R. solani and other five Rhizoctonia sp. lineages formed two parallel branches in Agaricomycotina. The comparative analysis showed that mitogenomes of Basidiomycota pathogens had high GC content and mitogenomes of R. solani had high repeat content. Compared to other strains, the AG1-IC strain had low substitution rates, which may affect its mitochondrial phylogenetic placement in the R. solani clade. Additionally, with the published RNA-seq data, we investigated gene expression patterns from different AGs during host infection stages. The expressed genes from AG1-IA (host: rice) and AG3 (host: potato) mainly formed four groups by k-mean partitioning analysis. However, conserved genes represented varied expression patterns, and only the patterns of rps3-nad2 and nad1-m3g18/mag28 (an LAGLIDADG endonuclease) were conserved in AG1-IA and AG3 as shown by the correlation coefficient analysis, suggesting regulation of gene repertoires adapting to infect varied hosts. The results of variations in mitogenome characteristics and the gene substitution rates and expression patterns may provide insights into the evolution of R. solani mitogenomes.

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Section: Discussionsupporting

confidence: 70%

Comparative Mitogenomic Analysis and the Evolution of Rhizoctonia solani Anastomosis Groups

et al. 2021

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“…The intronic ORFs also share significant homologies with mitogenome intronic ORFs of unrelated fungal species (Supplementary Excel File 2), often outside the basidiomycetes, something commonly cited as evidence of introgression between diverse species. Similar intron dynamics were observed within the Agaricales (Huang et al, 2021).…”

Section: Introns and Accessory Mitochondrial Genessupporting

confidence: 76%

“…For M. tenuissimus, the five isolates carrying a single cox1 intronic ORF show close similarity (>99% identity) while the 3 cox1 intronic ORFs of isolates 63 and 79 show close similarity (>99% identity) in a positionally dependent manner (Figure 6B). As seen in other comparisons, the genetic relationships among these intronic ORFs across species, in some cases, also show specificity as to position within specific core genes (Huang et al, 2021). For example, the terminal GIY-YIG containing intronic ORF in cox1 shows sequence similarity (>95%) across all species except M. tenuissimus (Figure 6A).…”

Section: Introns and Accessory Mitochondrial Genessupporting

confidence: 58%

Mitochondrial Genomics of Six Cacao Pathogens From the Basidiomycete Family Marasmiaceae

et al. 2021

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Thread blight disease has recently been described as an emerging disease on cacao (Theobroma cacao) in Ghana. In Ghana, thread blight disease is caused by multiple species of the Marasmiaceae family: Marasmius tenuissimus, M. crinis-equi, M. palmivorus, and Marasmiellus scandens. Interestingly, two additional members of the Marasmiaceae; Moniliophthora roreri (frosty pod rot) and Moniliophthora perniciosa (witches’ broom disease), are major pathogens of cacao in the Western hemisphere. It is important to accurately characterize the genetic relationships among these economically important species in support of their disease management. We used data from Illumina NGS-based genome sequencing efforts to study the mitochondrial genomes (mitogenomes) of the four cacao thread blight associated pathogens from Ghana and compared them with published mitogenomes of Mon. roreri and Mon. perniciosa. There is a remarkable interspecies variation in mitogenome size within the six cacao-associated Marasmiaceae species, ranging from 43,121 to 109,103 bp. The differences in genome lengths are primarily due to the number and lengths of introns, differences in intergenic space, and differences in the size and numbers of unidentified ORFs (uORF). Among seven M. tenuissimus mitogenomes sequenced, there is variation in size and sequence pointing to divergent evolution patterns within the species. The intronic regions show a high degree of sequence variation compared to the conserved sequences of the 14 core genes. The intronic ORFs identified, regardless of species, encode GIY-YIG or LAGLIDADG domain-containing homing endonuclease genes. Phylogenetic relationships using the 14 core proteins largely mimic the phylogenetic relationships observed in gene order patterns, grouping M. tenuissimus with M. crinis-equi, and M. palmivorus with Mon. roreri and Mon. perniciosa, leaving Mar. scandens as an outlier. The results from this study provide evidence of independent expansion/contraction events and sequence diversification in each species and establish a foundation for further exploration of the evolutionary trajectory of the fungi in Marasmiaceae family.

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“… 2018 , 2019 ), but not for others (Huang et al. 2021 ). This study will help to better understand the phylogenetic status of Coprinellus and the mitogenome evolution in macrofungi, and will be of interest for further applied researches by selecting the most suitable species for biotechnological and nutritional interest.…”

mentioning

confidence: 85%

“…The size of the complete mitogenome (64,450 bp) of C. micaceus was larger than that of Coprinopsis_cinerea, 42,448 bp (NW003307477.1, Stajich et al 2010). Recent researches indicated that the genome sizes of mitochondria in Agaricales varied significantly from about 40 kb (Paxillus involutus, MK993563, Li et al 2020) to more than 120 kb (Clavaria fumosa, MT114157, Wang et al 2020), sometimes that were near in a same genera or very closed genus (Yang et al 2016； Li et al 2018, 2019, but not for others (Huang et al 2021). This study will help to better understand the phylogenetic status of Coprinellus and the mitogenome evolution in macrofungi, and will be of interest for further applied researches by selecting the most suitable species for biotechnological and nutritional interest.…”

mentioning

confidence: 99%

Characterization of the complete mitochondrial genome of Coprinellus micaceus, a wild saprobic mushroom in China

Wang

Zhang²,

et al. 2021

Mitochondrial DNA Part B

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The Glistening Inkcap (Coprinellus micaceus) is a wild saprobic mushroom in China. In this study, we assembled and annotated its complete mitochondrial genome using raw data sequenced through Illumina NovaSeq 6000 platform (Illumina, San Diego, CA). The length of the C. micaceus mitochondrial genome is 65,450 bp with 33.05% GC content. Totally, 41 genes, including 14 protein-coding genes, 25 tRNAs and 2 rRNAs were identified in the mitochondrial genome. Phylogenetic analysis showed that the mitochondrial genome relationship between C. micaceus and Coprinopsis cinerea was the closest.

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Comparative Mitogenomic Analysis Reveals Dynamics of Intron Within and Between Tricholoma Species and Phylogeny of Basidiomycota

Cited by 18 publications

References 79 publications

Comparative Mitogenomic Analysis and the Evolution of Rhizoctonia solani Anastomosis Groups

Comparative Mitogenomic Analysis and the Evolution of Rhizoctonia solani Anastomosis Groups

Mitochondrial Genomics of Six Cacao Pathogens From the Basidiomycete Family Marasmiaceae

Characterization of the complete mitochondrial genome of Coprinellus micaceus, a wild saprobic mushroom in China

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