Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: May 10, 2024

Abstract In this study, we investigated the codon bias of twelve mitochondrial core protein coding genes (PCGs) in eight Pleurotus strains, two which are from same species. The results revealed that codons all strains had a preference for ending A/T. Furthermore, correlation between base compositions and adaptation index (CAI), (CBI) frequency optimal (FOP) indices was also detected, implying influence composition on bias. P. ostreatus species were found to have differences various indicators. average effective number (ENC) PCGs be less than 35, indicating strong . neutrality plot analysis PR2-Bias further suggested natural selection plays an important role Additionally, six ten (ΔRSCU > 0.08 RSCU 1) identified with UGU ACU being most widely used Finally, based combined sequence value, genetic relationship different deduced, showing large variations them. This research has improved our understanding synonymous usage characteristics evolution fungal group.

Language: Английский

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The evolutionary landscape of mitogenomes: Insights from Elsholtzia blanda and comparative analysis of ten related species

Ecological Genetics and Genomics, Journal Year: 2025, Volume and Issue: 34, P. 100328 - 100328

Published: Jan. 8, 2025

Language: Английский

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The complete mitochondrial genome of medicinally important wood-decaying fungus Tyromyces fissilis within the family Incrustoporiaceae, Polyporales

Mitochondrial DNA Part B, Journal Year: 2025, Volume and Issue: 10(4), P. 292 - 297

Published: March 13, 2025

Tyromyces fissilis (Berk. & M.A.Curtis) Donk 1933, a globally renowned white-rot basidiomycete belonging to the Polyporales order, holds significant potential for lignin degradation, yet its mitochondrial genome has received comparatively little attention. Our study concentrates on specimen designated T. NEFU_01, sourced from Forest Botanical Garden in Heilongjiang Province, China. Utilizing next-generation sequencing (NGS) technology, we have successfully delineated complete of this isolate. The is composed 15 protein-coding genes (PCGs), an array 24 transfer RNAs (tRNAs), and pair ribosomal (rRNAs), encompassing total 163,380 base pairs (bp). Additionally, encodes 28 LAGLIDADG- 10 GIY-YIG-homing endonucleases. nucleotide composition characterized by adenine (A) at 37.02%, cytosine (C) 12.91%, guanine (G) 13.04%, thymine (T) 37.03%, culminating GC content 25.95%. Subsequently, undertook phylogenetic analysis, employing dataset 25 genomes construct tree. This research represents first comprehensive foray into understanding relationships with Basidiomycete kin, particularly sister-group relationship Phlebia radiata Fr. (1821), thereby laying substantive groundwork subsequent evolutionary taxonomic studies within mycological cohort.

Language: Английский

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Multichromosomal mitochondrial genome of Punica granatum: comparative evolutionary analysis and gene transformation from chloroplast genomes

BMC Plant Biology, Journal Year: 2023, Volume and Issue: 23(1)

Published: Oct. 25, 2023

Abstract Background Punica granatum is a fundamentally important fruit tree that has economic, medicinal and ornamental properties. At present, there are few reports on the mitochondrial genome of pomegranate. Hence, in this study P. mitogenome was sequenced assembled to further understanding organization, variation, evolution mitogenomes species. Results The structure multi-chromosomes with seven circular contigs, measuring 382,774 bp length 45.91% GC content. It contained 74 genes, including 46 protein-coding 25 tRNA three rRNA genes. There were 188 pairs dispersed repeats lengths 30 or greater, primarily consisting reverse complementary repeats. analysis identified 114SSRs 466 RNA editing sites. Analyses codon usage, nucleotide diversity gene migration from chloroplast also conducted. collinear comparative structures between its proximal species indicated ‘Taishanhong’ closely related ‘Qingpitian’ Lagerstroemia indica. Phylogenetic examination based confirmed evolutionary relationship. Conclusion results offered crucial information biology pomegranate highlighted ways promote utilization species’ germplasm.

Language: Английский

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Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species

Plants, Journal Year: 2024, Volume and Issue: 13(4), P. 468 - 468

Published: Feb. 6, 2024

Heat shock protein 20 (HSP20) serves as a chaperone and plays roles in numerous biological processes, but the codon usage bias (CUB) of its genes has remained unexplored. This study identified 140 HSP20 from four cruciferous species, Arabidopsis thaliana, Brassica napus, rapa, Camelina sativa, that were Ensembl plants database, we subsequently investigated their CUB. As result, base composition analysis revealed overall GC content was below 50%. The significantly correlated with constituents at three positions, implying both mutation pressure natural selection might contribute to relatively high ENc values suggested CUB species weak. Subsequently, exhibited negative correlation gene expression levels. Analyses, including ENc-plot analysis, neutral PR2 bias, mainly shaped patterns these species. In addition, total 12 optimal codons (ΔRSCU > 0.08 RSCU 1) across A neighbor-joining phylogenetic based on coding sequences (CDS) showed strictly distinctly clustered into subfamilies. Principal component cluster relative synonymous (RSCU) supported fact pattern consistent genetic relationship level (or) These results will not only enrich resource also advance our understanding genes, which may underlie theoretical basis for exploration evolutionary pattern.

Language: Английский

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Comparative analysis of the whole mitochondrial genomes of four species in sect. Chrysantha (Camellia L.), endemic taxa in China

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: Oct. 12, 2024

The sect. Chrysantha Chang of plants with yellow flowers Camellia species as the "Queen Tea Family", most these are narrowly distributed endemics China and currently listed Grde-II in National Key Protected Wild Plant China. They commercially important horticultural medicinal scientific research value. However, study genetics still its infancy, to date, mitochondrial genome has been unexplored.

Language: Английский

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Correlations of gene expression, codon usage bias, and evolutionary rates of the mitochondrial genome show tissue differentiation in Ophioglossum vulgatum

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: Feb. 1, 2025

Mitochondria are crucial for energy production in plant tissues, but their quantity and activity vary different tissues developmental processes. Determining the factors underlying differential molecular evolutionary rates has long been a central question biology, with expression level emerging as prime predictor. Although we have previously observed an anti-correlation between (E) rate (R) chloroplast genes, it remains unclear whether such exists mitochondrial genes. Ophioglossum vulgatum is typical belonging to Ophioglossaceae, characterized by its unique morphology only single leaf above ground. It holds significant scientific medicinal value. Using genome transcriptome data of O. vulgatum, first analyzed correlation gene expression, codon usage bias, tissues. Our findings indicated that was strongest stem leaf, while weakest sporangium root. Kruskal-Wallis tests revealed differences across various tissue types. Codon bias influenced both mutation selection, selection exerting greater impact. The Spearman's rank coefficients adaptation index levels sporangium, stem, root were 0.1178, 0.3926, 0.4463, 0.2945, respectively, significance (P < 0.05). nonsynonymous substitution (dN) -0.0840, -0.1786, -0.1714, -0.0857, yet none statistically significant. coefficient synonymous (dS) negative, whereas those dS positive, although they not dN/dS ratio exhibited negative For time, our study well rates, vulgatum. Moreover, also provide novel insights into understanding effects on patterns.

Language: Английский

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Comparative Mitochondrial Genomic Analysis of Longhorn Beetles (Coleoptera: Chrysomeloidea) with Phylogenetic Implications

Arthropod Systematics & Phylogeny, Journal Year: 2024, Volume and Issue: 82, P. 133 - 150

Published: March 22, 2024

Longhorn beetles (Cerambycidae) play a vital role in global ecosystems. Some of them contribute to nutrient cycling and pollination, while others, pose threat forestry production. Despite their ecological importance, there has been lack comprehensive analyses on the mitochondrial genomes Cerambycidae beetles. In this study, we have conducted genome sequencing annotation for four beetles: Monochamus sutor , guerryi galloprovincialis latefasciatus . Our analysis revealed high degree conservation these genomes, with rare gene rearrangements observed across family. Additionally, notable bias towards AT content was identified, most genes using ATN as start codon TAA stop codon. Except trnS1, all tRNA showed typical cloverleaf secondary structures. Phylogenetic IQ-TREE Phylobayes consistently produced congruent topologies. At level analyses, our results highlighted remarkable COX1 gene. Furthermore, at species level, strong adaptability Spondylidinae Lepturinae subfamilies. We also offer insights into contentious aspects phylogeny. Overall, research contributes deeper understanding phylogeny evolution Cerambycidae, laying groundwork future population genetic investigations.

Language: Английский

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Comparative Chloroplast Genome Analyses of Six Hemlock Trees in East Asia: Insights into Their Genomic Characterization and Phylogenetic Relationship

Forests, Journal Year: 2023, Volume and Issue: 14(11), P. 2136 - 2136

Published: Oct. 26, 2023

Hemlocks (Pinaceae: Tsuga) are widely distributed in North America and East Asia, forming a reticulate evolutionary structure Asia with significant ecological importance. To clarify the chloroplast genome characteristics phylogenetic relationships among Tsuga species, we analyzed genomes of T. chinensis var. tchekiangensis, chinensis, diversifolia, dumosa, forrestii, sieboldii, performing associated analyses. The results reveal that lengths six species vary from 120,520 to 121,010 bp, encompassing about 108 112 genes, including 35/32 tRNA genes 4 rRNA genes. A codon usage analysis highlighted preference for A/U-ending codons, all nucleotide types have A/T bases prevalence mononucleotides. Notably, exhibit inverted repeat (IR) contractions possess unique hexanucleotides absent other Pinaceae, potentially making them more susceptible gene recombination or rearrangement during evolution. While most variations observed non-coding regions, particularly intergenic fragments, substantial variation sites also present within tree, constructed using genomes, substantiates sister taxa relationship between Nothotsuga. Furthermore, it confirms tchekiangensis exhibits closer forrestii than chinensis. These findings not only provide partial evidence may constitute monophyletic but underscore necessity reevaluating taxonomic status tchekiangensis. In addition, while RSCU cluster is basically consistent analysis, highlights distinct differentiation Nothotsuga Tsuga. This study provides molecular-level classification Pinaceous genera via analyses offers compelling further exploring delimitation hemlocks Asia.

Language: Английский

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Comparative analysis of mitochondrial genomes in Ceratocystis fimbriata complex across diverse hosts

Gene, Journal Year: 2024, Volume and Issue: 921, P. 148539 - 148539

Published: May 6, 2024

Language: Английский

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