Analysis of synonymous codon usage patterns in mitochondrial genomes of nine Amanita species

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: March 8, 2023

Codon basis is a common and complex natural phenomenon observed in many kinds of organisms.In the present study, we analyzed base bias 12 mitochondrial core protein-coding genes (PCGs) shared by nine Amanita species.The results showed that codons all species tended to end A/T, demonstrating preference for this codon. In addition, detected correlation between codon composition adaptation index (CAI), (CBI), frequency optimal (FOP) indices, indicating influence on bias. The average effective number (ENC) PCGs 30.81, which <35, strong Amanita. neutrality plot analysis PR2-Bias further demonstrated selection plays an important role obtained 5-10 (ΔRSCU > 0.08 RSCU 1) species, GCA AUU were most widely used codons. Based combined sequence value, deduced genetic relationship different found large variations them.This study promoted understanding synonymous usage characteristics evolution fungal group.

Language: Английский

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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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Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: May 4, 2023

Codon usage bias is a prevalent phenomenon observed across various species and genes. However, the specific attributes of codon in mitochondrial genome Ganoderma remain unknown.In this study, we investigated 12 core protein-coding genes (PCGs) 9 species, including 13 strains.The codons all strains showed preference for ending A/T. Additionally, correlations between base composition adaptation index (CAI), (CBI) frequency optimal (FOP) were identified, demonstrating impact on bias. Various indicators found to vary or within strains, GC3s, CAI, CBI, FOP. The results also revealed that PCGs have an average effective number (ENC) lower than 35, indicating strong toward certain codons. Evidence from neutrality plot PR2-bias analysis indicates natural selection major factor affecting Ganoderma. 11 22 (ΔRSCU>0.08 RSCU>1) identified with GCA, AUC, UUC being most widely used By analyzing combined sequences relative synonymous (RSCU) values, genetic relationships determined, variations them. Nevertheless, RSCU-based illustrated intra- interspecies species.This study deepens our insight into characteristics, genetics, evolution important fungal group.

Language: Английский

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Mitogenome evolution in Trichoderma afroharzianum strains: for a better understanding of distinguishing genus

Genome, Journal Year: 2023, Volume and Issue: 67(5), P. 139 - 150

Published: Dec. 20, 2023

Trichoderma afroharzianum ( Hypocreales) is known as an important mycoparasite and biocontrol fungus feeds on fungal material by parasitizing other fungi. Recent studies indicate that this species also ear rot pathogen in Europe. Here, the complete mitochondrial genome of three T. strains was sequenced using next-generation sequencing comparatively characterized reported mitogenomes. mitogenomes were varying between 29 511 bp 517 length, with average A + T content 72.32%. These contain 14 core protein coding genes (PCGs), 22 tRNAs, two rRNAs, one gene encoding ribosomal S3, or four including conserved domains for homing endonucleases (HEGs; GIY-YIG type LAGLIDADG type). All PCGs are initiated ATG codons, except atp8, all terminated TAA. significant correlation observed nucleotide composition codon preference. Four introns belonging to group I intron class predicted, accounting about 14.54% size Phylogenetic analyses confirmed positions within genus supported a sister relationship simmonsii. The recovered trees monophyly included families Acremonium. characterization contributes understanding phylogeny evolution Hypocreales.

Language: Английский

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Codon Usage Bias in the Photolyase Gene of Amsacta moorei Entomopoxvirus

Biology Bulletin, Journal Year: 2024, Volume and Issue: 51(S1), P. S52 - S65

Published: Dec. 1, 2024

Language: Английский

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