Analysis of mitochondrial protein‐coding genes of <i>Antheraea assamensis</i>: Muga silkworm of Assam

Uddin, Arif; Chakraborty, Supriyo

doi:10.1002/arch.21750

Cited by 3 publications

(3 citation statements)

References 41 publications

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“…5 ), indicating that mutation pressure effect accounted only 1.69%–23.46%. Therefore, the above results suggested that natural selection might have played a dominant role, whereas mutation pressure and other factors might have played a lesser role in shaping CUB ( Uddin & Chakraborty, 2020 ).…”

Section: Resultsmentioning

confidence: 91%

Comparative analysis of codon usage patterns and phylogenetic implications of five mitochondrial genomes of the genus Japanagallia Ishihara, 1955 (Hemiptera, Cicadellidae, Megophthalminae)

Li,

Wang,

Dai

et al. 2023

PeerJ

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Japanagallia is a genus of Cicadomorpha in the family of leafhoppers that are plant piercing-sucking insects, and it is difficult to distinguish by morphological characteristics. So far, only one complete mitochondrial genome data has been reported for the genus Japanagallia. Therefore, in order to better understand this group, we assembled and annotated the complete mitochondrial genomes of five Japanagallia species, and analyzed their codon usage patterns. Nucleotide composition analysis showed that AT content was higher than GC content, and the protein-coding sequences preferred to end with A/T at the third codon position. Relative synonymous codon usage analysis revealed most over-represented codon ends with A or T. Parity plot analysis revealed the codon usage bias of mitochondrial genes was influenced by both natural selection and mutation pressure. In the neutrality plot, the slopes of regression lines were < 0.5, suggesting that natural selection was playing a major role while mutation pressure was of minor importance. The effective number of codons showed that the codon usage bias between genes and genomes was low. Correspondence analysis revealed that the codon usage pattern differed among 13 protein-coding genes. Phylogenetic analyses based on three datasets using two methods (maximum likelihood and Bayesian inference), restored the Megophthalminae monophyly with high support values (bootstrap support values (BS) = 100, Bayesian posterior probability (PP) = 1). In the obtained topology, the seven Japanagallia species were clustered into a monophyletic group and formed a sister group with Durgade. In conclusion, our study can provide a reference for the future research on organism evolution, identification and phylogeny relationships of Japanagallia species.

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Section: Resultsmentioning

confidence: 91%

Comparative analysis of codon usage patterns and phylogenetic implications of five mitochondrial genomes of the genus Japanagallia Ishihara, 1955 (Hemiptera, Cicadellidae, Megophthalminae)

Li,

Wang,

Dai

et al. 2023

PeerJ

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“…Other many factors also could affect codon usage bias, e.g., selection for optimized translation, gene expression, codon location within genes, and the secondary structural of DNA [ 44 ]. Generally, mutation pressure and natural selection are considered to be two main factors affecting codon usage [ 45 , 46 ]. As was found in other insects [ 46 , 47 ], our results of the RSCU analyses also indicated that the third codon positions had a higher frequency in the usage of A and T relative to G and C, which may have led to the high codon bias observed.…”

Section: Discussionmentioning

confidence: 99%

Comparative mitogenomic analysis provides evolutionary insights into Formica (Hymenoptera: Formicidae)

Liu,

Hu,

et al. 2024

PLoS ONE

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Formica is a large genus in the family Formicidae with high diversity in its distribution, morphology, and physiology. To better understand evolutionary characteristics of Formica, the complete mitochondrial genomes (mitogenomes) of two Formica species were determined and a comparative mitogenomic analysis for this genus was performed. The two newly sequenced Formica mitogenomes each included 37 typical mitochondrial genes and a large non-coding region (putative control region), as observed in other Formica mitogenomes. Base composition, gene order, codon usage, and tRNA secondary structure were well conserved among Formica species, whereas diversity in sequence size and structural characteristics was observed in control regions. We also observed several conserved motifs in the intergenic spacer regions. These conserved genomic features may be related to mitochondrial function and their highly conserved physiological constraints, while the diversity of the control regions may be associated with adaptive evolution among heterogenous habitats. A negative AT-skew value on the majority chain was presented in each of Formica mitogenomes, indicating a reversal of strand asymmetry in base composition. Strong codon usage bias was observed in Formica mitogenomes, which was predominantly determined by nucleotide composition. All 13 mitochondrial protein-coding genes of Formica species exhibited molecular signatures of purifying selection, as indicated by the ratio of non-synonymous substitutions to synonymous substitutions being less than 1 for each protein-coding gene. Phylogenetic analyses based on mitogenomic data obtained fairly consistent phylogenetic relationships, except for two Formica species that had unstable phylogenetic positions, indicating mitogenomic data are useful for constructing phylogenies of ants. Beyond characterizing two additional Formica mitogenomes, this study also provided some key evolutionary insights into Formica.

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“…The overall codon usage pattern represented by ENC plot of M. hyorinis resembles that of M. bovis [46]. With respect to investigations of roles neutral selection caused by nucleotide composition variations at gene level in evolutionary approach of micro‐organisms, neutrality plot analysis provided some new genetic insights into interplay between nucleotide and CUB [56,57]. Neutrality plot analysis also reveals that nucleotide composition constraint derived from mutation pressure and translational selection involved in natural selection function together on shaping codon usages for gene population of M. hyorinis .…”

Section: Discussionmentioning

confidence: 99%

The nucleotide usages significantly impact synonymous codon usage inMycoplasma hyorhinis

Jin

et al. 2021

J Basic Microbiol

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Five annotated genomes of Mycoplasma hyorhinis were analyzed for clarifying evolutionary dynamics driving the overall codon usage pattern. Information entropy used for estimating nucleotide usage pattern at the gene level indicates that multiple evolutionary dynamics participate in forcing nucleotide usage bias at every codon position. Moreover, nucleotide usage bias directly contributes to synonymous codon usage biases with two different extremes. The overrepresented codons tended to have A/T in the third codon position, and the underrepresented codons strongly used G/C in the third position. Furthermore, correspondence analysis and neutrality plot reflect an obvious interplay between mutation pressure and natural selection mediating codon usage in M. hyorhinis genome. Due to significant bias in usages between A/T and G/C at the gene level, different selective forces have been proposed to contribute to codon usage preference in M. hyorhinis genome, including nucleotide composition constraint derived from mutation pressure, translational selection involved in natural selection, and strand-specific mutational bias represented by different nucleotide skew index. The systemic analyses of codon usage for M. hyorhinis can enable us to better understand the mechanisms of evolution in this species.

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Analysis of mitochondrial protein‐coding genes of Antheraea assamensis: Muga silkworm of Assam

Cited by 3 publications

References 41 publications

Comparative analysis of codon usage patterns and phylogenetic implications of five mitochondrial genomes of the genus Japanagallia Ishihara, 1955 (Hemiptera, Cicadellidae, Megophthalminae)

Comparative analysis of codon usage patterns and phylogenetic implications of five mitochondrial genomes of the genus Japanagallia Ishihara, 1955 (Hemiptera, Cicadellidae, Megophthalminae)

Comparative mitogenomic analysis provides evolutionary insights into Formica (Hymenoptera: Formicidae)

The nucleotide usages significantly impact synonymous codon usage inMycoplasma hyorhinis

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