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

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Cheng Chen ◽  
Qiang Li ◽  
Rongtao Fu ◽  
Jian Wang ◽  
Guangmin Deng ◽  
...  
Keyword(s):  
Large Scale ◽  
Core Protein ◽  
Mitochondrial Gene ◽  
Purifying Selection ◽  
Gene Rearrangements ◽  
Protein Coding ◽  
Circular Dna ◽  
Phylogeny And Evolution ◽  
Inference Methods ◽  
Shed Light

AbstractTrametes 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.

scholarly journals The complete mitochondrial genome of medicinal fungus Taiwanofungus camphoratus reveals gene rearrangements and intron dynamics of Polyporales

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xu Wang ◽  
Lihua Jia ◽  
Mingdao Wang ◽  
Hao Yang ◽  
Mingyue Chen ◽  
...  
Keyword(s):  
Large Scale ◽  
Core Protein ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Purifying Selection ◽  
Intron Loss ◽  
Gene Rearrangements ◽  
Total Size ◽  
Medicinal Fungus ◽  
Taiwanofungus Camphoratus

Abstract Taiwanofungus camphoratus is a highly valued medicinal mushroom that is endemic to Taiwan, China. In the present study, the mitogenome of T. camphoratus was assembled and compared with other published Polyporales mitogenomes. The T. camphoratus mitogenome was composed of circular DNA molecules, with a total size of 114,922 bp. Genome collinearity analysis revealed large-scale gene rearrangements between the mitogenomes of Polyporales, and T. camphoratus contained a unique gene order. The number and classes of introns were highly variable in 12 Polyporales species we examined, which proved that numerous intron loss or gain events occurred in the evolution of Polyporales. The Ka/Ks values for most core protein coding genes in Polyporales species were less than 1, indicating that these genes were subject to purifying selection. However, the rps3 gene was found under positive or relaxed selection between some Polyporales species. Phylogenetic analysis based on the combined mitochondrial gene set obtained a well-supported topology, and T. camphoratus was identified as a sister species to Laetiporus sulphureus. This study served as the first report on the mitogenome in the Taiwanofungus genus, which will provide a basis for understanding the phylogeny and evolution of this important fungus.

Large-scale mitochondrial gene rearrangements in the hermit crab Pagurus nigrofascia and phylogenetic analysis of the Anomura

Gene ◽  
2019 ◽  
Vol 695 ◽  
pp. 75-83 ◽  
Author(s):  
Li Gong ◽  
Hui Jiang ◽  
Kehua Zhu ◽  
Xinting Lu ◽  
Liqin Liu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Hermit Crab ◽  
Large Scale ◽  
Mitochondrial Gene ◽  
Gene Rearrangements

scholarly journals Characterization of the complete mitochondrial genome of Myrmus lateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses

ZooKeys ◽  
2021 ◽  
Vol 1070 ◽  
pp. 13-30
Author(s):  
Wanqing Zhao ◽  
Dajun Liu ◽  
Qian Jia ◽  
Xin Wu ◽  
Hufang Zhang
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Purifying Selection ◽  
Sister Group ◽  
Start Codon ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Inference Methods

Mitochondrial genomes (mitogenomes) are widely used in research studies on phylogenetic relationships and evolutionary history. Here, we sequenced and analyzed the mitogenome of the scentless plant bug Myrmus lateralis Hsiao, 1964 (Heteroptera, Rhopalidae). The complete 17,309 bp genome encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The mitogenome revealed a high A+T content (75.8%), a positive AT-skew (0.092), and a negative GC-skew (–0.165). All 13 PCGs were found to start with ATN codons, except for cox1, in which TTG was the start codon. The Ka/Ks ratios of 13 PCGs were all lower than 1, indicating that purifying selection evolved in these genes. All tRNAs could be folded into the typical cloverleaf secondary structure, except for trnS1 and trnV, which lack dihydrouridine arms. Phylogenetic trees were constructed and analyzed based on the PCG+rRNA from 38 mitogenomes, using maximum likelihood and Bayesian inference methods, showed that M. lateralis and Chorosoma macilentum Stål, 1858 grouped together in the tribe Chorosomatini. In addition, Coreoidea and Pyrrhocoroidea were sister groups among the superfamilies of Trichophora, and Rhopalidae was a sister group to Alydidae + Coreidae.

scholarly journals The Gene Rearrangement, Loss, Transfer, and Deep Intronic Variation in Mitochondrial Genomes of Conidiobolus

2021 ◽  
Vol 12 ◽  
Author(s):  
Yong Nie ◽  
Heng Zhao ◽  
Zimin Wang ◽  
Zhengyu Zhou ◽  
Xiaoyong Liu ◽  
...  
Keyword(s):  
Gene Rearrangement ◽  
Core Protein ◽  
Gc Content ◽  
Mitochondrial Genomes ◽  
Phylogenomic Analysis ◽  
Protein Coding ◽  
Circular Dna ◽  
Protein Coding Genes ◽  
Main Factors ◽  
Insight Into

The genus Conidiobolus s.s. was newly delimited from Conidiobolus s.l. In order to gain insight into its mitochondrial genetic background, this study sequenced six mitochondrial genomes of the genus Conidiobolus s.s. These mitogenomes were all composed of circular DNA molecules, ranging from 29,253 to 48,417 bp in size and from 26.61 to 27.90% in GC content. The order and direction for 14 core protein-coding genes (PCGs) were identical, except for the atp8 gene lost in Conidiobolus chlamydosporus, Conidiobolus polyspermus, and Conidiobolus polytocus, and rearranged in the other Conidiobolus s.s. species. Besides, the atp8 gene split the cox1 gene in Conidiobolus taihushanensis. Phylogenomic analysis based on the 14 core PCGs confirmed that all Conidiobolus s.s. species formed a monophyly in the Entomophthoromycotina lineage. The number and length of introns were the main factors contributing to mitogenomic size, and deep variations and potential transfer were detected in introns. In addition, gene transfer occurred between the mitochondrial and nuclear genomes. This study promoted the understanding of the evolution and phylogeny of the Conidiobolus s.s. genus.

scholarly journals The 287,403 bp Mitochondrial Genome of Ectomycorrhizal Fungus Tuber calosporum Reveals Intron Expansion, tRNA Loss, and Gene Rearrangement

2020 ◽  
Vol 11 ◽  
Author(s):  
Xiaolin Li ◽  
Lijiao Li ◽  
Zhijie Bao ◽  
Wenying Tu ◽  
Xiaohui He ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Fungal Species ◽  
Ectomycorrhizal Fungus ◽  
Open Reading Frames ◽  
Rrna Genes ◽  
Trna Genes ◽  
Total Size ◽  
Protein Coding

In the present study, the mitogenome of Tuber calosporum was assembled and analyzed. The mitogenome of T. calosporum comprises 15 conserved protein-coding genes, two rRNA genes, and 14 tRNAs, with a total size of 287,403 bp. Fifty-eight introns with 170 intronic open reading frames were detected in the T. calosporum mitogenome. The intronic region occupied 69.41% of the T. calosporum mitogenome, which contributed to the T. calosporum mitogenome significantly expand relative to most fungal species. Comparative mitogenomic analysis revealed large-scale gene rearrangements occurred in the mitogenome of T. calosporum, involving gene relocations and position exchanges. The mitogenome of T. calosporum was found to have lost several tRNA genes encoding for cysteine, aspartate, histidine, etc. In addition, a pair of fragments with a total length of 32.91 kb in both the nuclear and mitochondrial genomes of T. calosporum was detected, indicating possible gene transfer events. A total of 12.83% intragenomic duplications were detected in the T. calosporum mitogenome. Phylogenetic analysis based on mitochondrial gene datasets obtained well-supported tree topologies, indicating that mitochondrial genes could be reliable molecular markers for phylogenetic analyses of Ascomycota. This study served as the first report on mitogenome in the family Tuberaceae, thereby laying the groundwork for our understanding of the evolution, phylogeny, and population genetics of these important ectomycorrhizal fungi.

scholarly journals Mitochondrial Genome Structures and Phylogenetic Analyses of Two Tropical Characidae Fishes

2021 ◽  
Vol 12 ◽  
Author(s):  
Cheng-He Sun ◽  
Hong-Yi Liu ◽  
Nan Xu ◽  
Xiao-Li Zhang ◽  
Qun Zhang ◽  
...  
Keyword(s):  
Fish Species ◽  
Stop Codon ◽  
Phylogenetic Analyses ◽  
Tropical Fish ◽  
Start Codon ◽  
Protein Coding ◽  
The Family ◽  
Phylogeny And Evolution ◽  
Inference Methods ◽  
Hemigrammus Erythrozonus

The Characidae family contains the largest number of tropical fish species. Morphological similarities make species identification difficult within this family. Here, the complete mitogenomes of two Characidae fish were determined and comparatively analyzed with those of nine other Characidae fish species. The two newly sequenced complete mitogenomes are circular DNA molecules with sizes of 16,701 bp (Hyphessobrycon amandae; MT484069) and 16,710 bp (Hemigrammus erythrozonus; MT484070); both have a highly conserved structure typical of Characidae, with the start codon ATN (ATG/ATT) and stop codon TAR (TAA/TAG) or an incomplete T−−/TA−. Most protein-coding genes of the 11 Characidae mitogenomes showed significant codon usage bias, and the protein-coding gene cox1 was found to be a comparatively slow-evolving gene. Phylogenetic analyses via the maximum likelihood and Bayesian inference methods confirmed that H. amandae and H. erythrozonus belong to the family Characidae. In all Characidae species studied, one genus was well supported; whereas other two genera showed marked differentiation. These findings provide a phylogenetic basis for improved classification of the family Characidae. Determining the mitogenomes of H. erythrozonus and H. amandae improves our understanding of the phylogeny and evolution of fish species.

scholarly journals Comparative Analysis of Mitochondrial Genome Features among Four Clonostachys Species and Insight into Their Systematic Positions in the Order Hypocreales

2021 ◽  
Vol 22 (11) ◽  
pp. 5530
Author(s):  
Zhiyuan Zhao ◽  
Kongfu Zhu ◽  
Dexiang Tang ◽  
Yuanbing Wang ◽  
Yao Wang ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Purifying Selection ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Circular Dna ◽  
Genome Features ◽  
High Degree ◽  
Insight Into ◽  
Pressure Analysis ◽  
Gc Contents

The mycoparasite fungi of Clonostachys have contributed to the biological control of plant fungal disease and nematodes. The Clonostachys fungi strains were isolated from Ophiocordyceps highlandensis, Ophiocordycepsnigrolla and soil, which identified as Clonostachyscompactiuscula, Clonostachysrogersoniana, Clonostachyssolani and Clonostachys sp. To explore the evolutionary relationship between the mentioned species, the mitochondrial genomes of four Clonostachys species were sequenced and assembled. The four mitogenomes consisted of complete circular DNA molecules, with the total sizes ranging from 27,410 bp to 42,075 bp. The GC contents, GC skews and AT skews of the mitogenomes varied considerably. Mitogenomic synteny analysis indicated that these mitogenomes underwent gene rearrangements. Among the 15 protein-coding genes within the mitogenomes, the nad4L gene exhibited the least genetic distance, demonstrating a high degree of conservation. The selection pressure analysis of these 15 PCGs were all below 1, indicating that PCGs were subject to purifying selection. Based on protein-coding gene calculation of the significantly supported topologies, the four Clonostachys species were divided into a group in the phylogenetic tree. The results supplemented the database of mitogenomes in Hypocreales order, which might be a useful research tool to conduct a phylogenetic analysis of Clonostachys. Additionally, the suitable molecular marker was significant to study phylogenetic relationships in the Bionectriaceae family.

scholarly journals Comparative Mitogenomic Analysis of Five Awl Skippers (Lepidoptera: Hesperiidae: Coeliadinae) and Their Phylogenetic Implications

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 757
Author(s):  
Qi Sun ◽  
Yumeng Yang ◽  
Xiangyu Hao ◽  
Jintian Xiao ◽  
Jiaqi Liu ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Strong Support ◽  
Mitochondrial Genomes ◽  
Structural Elements ◽  
Protein Coding ◽  
Circular Dna ◽  
Phylogenetic Implications ◽  
Rna Genes ◽  
Shed Light ◽  
Complete Mitochondrial Genomes

To determine the significance of mitochondrial genome characteristics in revealing phylogenetic relationships and to shed light on the molecular evolution of the Coeliadinae species, the complete mitochondrial genomes (mitogenomes) of five Coeliadinae species were newly sequenced and analyzed, including Hasora schoenherr, Burara miracula, B. oedipodea, B. harisa, and Badamia exclamationis. The results show that all five mitogenomes are double-strand circular DNA molecules, with lengths of 15,340 bp, 15,295 bp, 15,304 bp, 15,295 bp, and 15,289 bp, respectively, and contain the typical 37 genes and a control region. Most protein-coding genes (PCGs) begin with ATN, with 3 types of stop codons including TAA, TAG, and an incomplete codon T-; most of the genes terminate with TAA. All of the transfer RNA genes (tRNAs) present the typical cloverleaf secondary structure except for the trnS1. Several conserved structural elements are found in the AT-rich region. Phylogenetic analyses based on three datasets (PCGs, PRT, and 12PRT) and using maximum likelihood (ML) and Bayesian inference (BI) methods show strong support for the monophyly of Coeliadinae, and the relationships of the five species are (B. exclamationis + ((B. harisa + (B. oedipodea + B. miracula)) + H. schoenherr)).

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