The mitogenomes of two saprophytic Boletales species (Coniophora) reveals intron dynamics and accumulation of plasmid-derived and non-conserved genes

Wu, Peng; Bao, Zhijie; Tu, Wenying; Li, Lijiao; Jin, Xin; Li, Ping; Gui, Mingying; Huang, Wenli; Li, Qiang

doi:10.1016/j.csbj.2020.12.041

Cited by 23 publications

(15 citation statements)

References 78 publications

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“…trifurcatum, we constructed a phylogenetic tree for 15 species. The protein-coding region of 13 genes conserved in the 15 species was used to construct combined a chloroplast gene set according to previous methods (Li, Xiang, et al 2019;Wu et al 2021). Bayesian (BI) analysis method ) was used to construct the phylogenetic tree based on combined protein-coding genes of chloroplast genome as described by previous methods (Li, Yang, et al 2020;Cheng et al 2021;).…”

Section: Tibetan Hulless Barley;mentioning

confidence: 99%

Characterization of the complete chloroplast genome of Hordeum vulgare L. var. trifurcatum with phylogenetic analysis

Ren

et al. 2021

Mitochondrial DNA Part B

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In the present study, the complete chloroplast genome of Hordeum vulgare L. var. trifurcatum was sequenced, assembled and compared with closely related species. The chloroplast genome of Hordeum vulgare L. var. trifurcatum was composed of 84 protein-coding genes (PCG), 8 ribosomal RNA (rRNA) genes, and 38 transfer RNA (tRNA) genes. The Hordeum vulgare L. var. trifurcatum chloroplast genome is 136,485 bp in size, with the GC content of 38.32%. Phylogenetic analysis based on the combined chloroplast gene dataset indicated that the Hordeum vulgare L. var. trifurcatum exhibited a close relationship with Hordeum vulgare subsp. spontaneum and Hordeum vulgare subsp. vulgare.

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Section: Tibetan Hulless Barley;mentioning

confidence: 99%

Characterization of the complete chloroplast genome of Hordeum vulgare L. var. trifurcatum with phylogenetic analysis

Ren

et al. 2021

Mitochondrial DNA Part B

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“…Mitochondrial genomes are effective tools for analyzing the phylogenetic and genetic evolution of eukaryotes because they contain many available molecular markers (Burger et al, 2003;Bullerwell and Lang, 2005;Cheng et al, 2021). Besides, the arrangement of mitochondrial genes, their transfer RNA (tRNA) structure, their codon usage, and the dynamic changes of introns can also be used to infer the evolutionary status of eukaryotes (Li et al, 2018a;Wang et al, 2018Wang et al, , 2020bWu et al, 2021). With the rapid development of next-generation sequencing technologies in recent years, more and more mitochondrial genomes have been obtained (du Toit et al, 2017;Yang et al, 2018;Zhang et al, 2018;Wang et al, 2020c).…”

Section: Introductionmentioning

confidence: 99%

Characterization of the Complete Mitochondrial Genome of Basidiomycete Yeast Hannaella oryzae: Intron Evolution, Gene Rearrangement, and Its Phylogeny

Feng

et al. 2021

Front. Microbiol.

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In this study, the mitogenome of Hannaella oryzae was sequenced by next-generation sequencing (NGS) and successfully assembled. The H. oryzae mitogenome comprised circular DNA molecules with a total size of 26,444 bp. We found that the mitogenome of H. oryzae partially deleted the tRNA gene transferring cysteine. Comparative mitogenomic analyses showed that intronic regions were the main factors contributing to the size variations of mitogenomes in Tremellales. Introns of the cox1 gene in Tremellales species were found to have undergone intron loss/gain events, and introns of the H. oryzae cox1 gene may have different origins. Gene arrangement analysis revealed that H. oryzae contained a unique gene order different from other Tremellales species. Phylogenetic analysis based on a combined mitochondrial gene set resulted in identical and well-supported topologies, wherein H. oryzae was closely related to Tremella fuciformis. This study represents the first report of mitogenome for the Hannaella genus, which will allow further study of the population genetics, taxonomy, and evolutionary biology of this important phylloplane yeast and other related species.

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“…The family Peniophoraceae is primarily saprotrophic fungi. Mitochondrial genome has been widely used to understand the phylogeny, life pattern evolution and genetics of fungal species (Li et al 2020a(Li et al , 2020cWang et al 2020a;Wu et al 2021). However, up to now, no complete mitochondrial genome from the genus Peniophora has been reported.…”

mentioning

confidence: 99%

Characterization of the complete mitochondrial genome of Peniophora lycii (Russulales: Peniophoraceae) with its phylogenetic analysis

Gou

Ren

Peng

2021

Mitochondrial DNA Part B

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Peniophora lycii is a resupinate lichen-like species distributed all over the world. In the present study, we sequenced and assembled the complete mitochondrial genome of Peniophora lycii. The size of the mitochondrial genome of P. lycii was 38,296 bp, with a GC content of 25.89%. Twenty protein-coding genes, 2 ribosomal RNA genes, and 24 transfer RNA genes were identified in the mitochondrial genome of P. lycii. Phylogenetic analysis based on combined mitochondrial gene dataset indicated that the mitochondrial genome of P. lycii exhibited a close relationship with that of Heterobasidion irregulare.

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The mitogenomes of two saprophytic Boletales species (Coniophora) reveals intron dynamics and accumulation of plasmid-derived and non-conserved genes

Cited by 23 publications

References 78 publications

Characterization of the complete chloroplast genome of Hordeum vulgare L. var. trifurcatum with phylogenetic analysis

Characterization of the complete chloroplast genome of Hordeum vulgare L. var. trifurcatum with phylogenetic analysis

Characterization of the Complete Mitochondrial Genome of Basidiomycete Yeast Hannaella oryzae: Intron Evolution, Gene Rearrangement, and Its Phylogeny

Characterization of the complete mitochondrial genome of Peniophora lycii (Russulales: Peniophoraceae) with its phylogenetic analysis

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