Compositional features and pattern of codon usage for mitochondrial CO genes among reptiles

Chakraborty, Supriyo; Basumatary, Priyanka; Nath, Durbba; Paul, Subrata; Uddin, Arif

doi:10.1016/j.mito.2021.11.004

Cited by 6 publications

(9 citation statements)

References 56 publications

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“…Earlier investigations on codon usage bias in Harpago chiragra and Lambis lambis (Gastropoda: Stromboidea) also revealed that the mitochondria genes were subjected to different mutational pressures which signi ed compositional constraints (Jiang et al 2019). Similar ndings were observed in reptiles (Chakraborty et al 2022), cotton species (Wang et al 2018), and bivalves (Gerdol et al 2015).…”

Section: Discussionsupporting

confidence: 80%

“…Narrow GC content, which was less than 50%, further suggests that natural selection was the most signi cant factor for codon usage pattern of MT-COI gene in Potamidids. In support of these ndings, other studies in reptiles (Chakraborty et al 2022) and amphibians (P. A. Barbhuiya et al 2021) concluded that natural selection and mutation pressure were the major and minor evolutionary forces respectively, responsible for shaping CUB in mitochondrial genes.…”

Section: Discussionmentioning

confidence: 62%

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Compositional properties and codon usage pattern of mitochondrial cytochrome c oxidase I gene among Potamidids

Shabani

Mfilinge

Mpenda

2022

Preprint

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Codon usage bias refers to the phenomenon where there is unequal occurrence of specific synonymous codons in a genome, the frequency of which varies within and among species. Molecular evolutionary researches suggest that CUB studies are significant in interpreting evolutionary trends of species or genes. A number of studies on codon usage bias are emerging in different organisms. However, such information remained unclear for organisms in the family Potamididae. This study systematically examined compositional features and codon usage patterns in MT-COI gene among potamidids to identify factors shaping codon usage bias. Quantification of codon usage bias and the identification of causative factors was performed by assessing various parameters such as nucleotide composition, effective number of codons (ENC), relative synonymous codon usage (RSCU), parity rule (PR2) analysis, neutrality plot analysis as well as a multivariate statistical approach of correspondence analysis (CoA). The results from neutrality plot suggested that natural selection is the dominant evolutionary factor for CUB in MT-COI gene among the different genera of potamidids. Correspondence analysis (CoA), parity plot and ENC analyses indicated the existence of mutational pressure with minor contribution. Nucleotide composition investigations indicated that, most codons are AT rich, with T nucleotides count being highly presented. Thus, compositional restraint was shown as among the reasons behind the pattern of codon usage in MT-COI gene of species in the family Potamididae.

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Section: Discussionsupporting

confidence: 80%

Section: Discussionmentioning

confidence: 62%

Compositional properties and codon usage pattern of mitochondrial cytochrome c oxidase I gene among Potamidids

Shabani

Mfilinge

Mpenda

2022

Preprint

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“…Comparative in-sillico analysis revealed that the mononucleotide repeats A/T were dominant over the G/C. This type of mononucleotide distribution has been observed in human mitochondria (Chakraborty et al, 2022). However, the chromosome-wide distribution of mononucleotide SSR Crassostrea was exactly the opposite (Sahu et al, 2023).…”

Section: Discussionmentioning

confidence: 87%

Purifying selection and intraspecies recombination may drive the speciation in Crassostrea: evidence from complete mitochondria sequence ofCrassostrea hongkongensisand comparative genomic analysis

Sahu,

Fazil,

Panda

et al. 2024

Preprint

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Repeat dynamics and recombination play a crucial role during the evolution of the mitochondrial genome in plants and animals. However, this phenomenon has got less attention within Crassostrea, a complex marine species found worldwide having high commercial value as well as efficient carbon neutralizer. During this study, we characterized the whole mitochondrial genomes of C. hongkongensis retrieved from transcriptome data (GenBank acc. no. MZ073671). The current mitochondrial genome (18,616 bp) was composed of a non-coding control region (D-loop region), 2 ribosomal RNA (rRNA genes), 12 protein-coding genes (PCGs), and 23 transfer RNA (tRNA). Furthermore, comparative genomics analysis revealed that the present isolate is closely related to the Chinese isolate (NC_011518) with 99.82% similarity. Microsatellite analysis within the mitochondrial genome revealed its bias towards mononucleotide repeat A/T, di-nucleotide AG followed by AT and AC, trinucleotide AAT followed by AAG, ATC, and ATG. The recombination analysis deciphered the lack of interspecific recombination, but the presence of intraspecific recombination within ND1, ND2, and ND4L of Crassostrea species. Selection pressure analysis revealed the presence of purifying selection within maximum genes which drive the evolution of the species.

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“…We found that ATG appeared in 11 protein-coding genes (except for COI and ND3), and 9 genes used onlyATG as the start codon. The start codon GTG was commonly used in COI and ND5, ATA was only used in ND3, but it was frequently observed in other species, and CTA was only used in ND6 ( Chakraborty et al, 2022 ; Uddin, Choudhury & Chakraborty, 2018 ).…”

Section: Resultsmentioning

confidence: 99%

Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris

Chen

Miao

Wang

et al. 2022

PeerJ

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Background The genus Calidris (Charadriiformes, Scolopacidae) includes shorebirds known as dunlin, knots, and sanderlings. The relationships between species nested within Calidris, including Eurynorynchus, Limicola and Aphriza, are not well-resolved. Methods Samples were collected from Xiaoyangkou, Rudong County, Jiangsu Province, China. Mitogenomes were sequenced using the Illumina Novaseq 6000 platform for PE 2 × 150 bp sequencing, and then checked for PCR products. Protein-coding genes were determined using an Open Reading Frame Finder. tRNAscan-SE, MITOS, and ARWEN were used to confirm tRNA and rRNA annotations. Bioinformatic analyses were conducted using DnaSP 5.1 and MEGA X. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses. Results We sequenced and annotated the mitogenome of five species and obtained four complete mitogenomes and one nearly complete mitogenome. Circular mitogenomes displayed moderate size variation, with a mean length of 16,747 bp, ranging from 16,642 to 16,791 bp. The mitogenome encoded a control region and a typical set of 37 genes containing two rRNA genes, 13 protein-coding genes, and 22 tRNA genes. There were four start codons, four stop codons, and one incomplete stop codon (T–). The nucleotide composition was consistently AT-biased. The average uncorrected pairwise distances revealed heterogeneity in the evolutionary rate for each gene; the COIII had a slow evolutionary rate, whereas the ATP8 gene had a fast rate. dN/dS analysis indicated that the protein-coding genes were under purifying selection. The genetic distances between species showed that the greatest genetic distance was between Eurynorhynchus pygmeus and Limicola falcinellus (22.5%), and the shortest was between E. pygmeus and Calidris ruficollis (12.8%). Phylogenetic trees revealed that Calidris is not a monophyletic genus, as species from the genera Eurynorynchus and Limicola were nested within Calidris. The molecular data obtained in this study are valuable for research on the taxonomy, population genetics, and evolution of birds in the genus Calidris.

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Compositional features and pattern of codon usage for mitochondrial CO genes among reptiles

Cited by 6 publications

References 56 publications

Compositional properties and codon usage pattern of mitochondrial cytochrome c oxidase I gene among Potamidids

Compositional properties and codon usage pattern of mitochondrial cytochrome c oxidase I gene among Potamidids

Purifying selection and intraspecies recombination may drive the speciation in Crassostrea: evidence from complete mitochondria sequence ofCrassostrea hongkongensisand comparative genomic analysis

Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris

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