Analysis of codon usage bias in mitochondrial CO gene among platyhelminthes

Mazumder, Gulshana A.; Uddin, Arif; Chakraborty, Supriyo

doi:10.1016/j.molbiopara.2021.111410

Cited by 4 publications

(2 citation statements)

References 88 publications

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“…The difference in synonymous codons is mainly reflected in the difference in the third codon. In this study, we found that all core PCGs of Amanita species tend to end with A/T, which is consistent with the rule of mitochondrial codon usage in many eukaryotes ( Mazumder et al, 2021 ; Montana-Lozano et al, 2023 ). Most high-frequency codons parsed by RSCU also end with A/T, which further proves the tendency of using the third codon of Amanita .…”

Section: Discussionsupporting

confidence: 85%

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

Luo

Sha

et al. 2023

Front. Microbiol.

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

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Section: Discussionsupporting

confidence: 85%

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

Luo

Sha

et al. 2023

Front. Microbiol.

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“…The majority of the differences in codon usage were observed at the third codon. It was also noted that the core PCGs of Ganoderma species typically terminate with A/T, which is consistent with the mitochondrial codon usage pattern observed in some other eukaryotes ( Mazumder et al, 2021 ; Montana-Lozano et al, 2022 ). Additionally, there was a disparity in base usage between different species and genes.…”

Section: Discussionsupporting

confidence: 82%

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

Xiao

Luo

et al. 2023

Front. Microbiol.

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

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

Özkale,

Doğan,

Budak

et al. 2024

Genome

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

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Analysis of codon usage bias in mitochondrial CO gene among platyhelminthes

Cited by 4 publications

References 88 publications

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

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

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

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

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