Similarities and dissimilarities of codon usage in mitochondrial ATP genes among fishes, aves, and mammals

Uddin, Arif; Mazumder, Tarikul Huda; Barbhuiya, Parvin A.; Chakraborty, Supriyo

doi:10.1002/iub.2231

Cited by 29 publications

(12 citation statements)

References 64 publications

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“…Based on the regression coefficient, the role of mutation pressure was highest in fishes compared to reptiles, birds, and mammals. In ATP genes, the role of natural selection was higher than mutation pressure, and based on the regression coefficient, the role of mutation pressure was highest in fishes in compared to birds and mammals, supporting our results [ 64 ].…”

Section: Discussionsupporting

confidence: 88%

Analysis of Codon Usage of Speech Gene FoxP2 among Animals

Mazumder¹,

Alqahtani

et al. 2021

Biology

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The protein-coding gene FoxP2 (fork head box protein P2) plays a major role in communication and evolutionary changes. The present study carried out a comprehensive codon usage bias analysis in the FoxP2 gene among a diverse group of animals including fishes, birds, reptiles, and mammals. We observed that in the genome of fishes for the FoxP2 gene, codons ending with C or G were most frequently used, while in birds, reptiles, and mammals, codons ending with T or A were most frequently used. A higher ENC value was observed for the FoxP2 gene indicating a lower CUB. Parity role two-bias plots suggested that apart from mutation pressure, other factors such as natural selection might have influenced the CUB. The frequency distribution of the ENC observed and ENC expected ratio revealed that mutation pressure plays a key role in the patterns of codon usage of FoxP2. Besides, correspondence analysis exposed the composition of the nucleobase under mutation bias affects the codon usage of the FoxP2 gene. However, neutrality plots revealed the major role of natural selection over mutation pressure in the CUB of FoxP2. In addition, the codon usage patterns for FoxP2 among the selected genomes suggested that nature has favored nearly all the synonymous codons for encoding the corresponding amino acid. The uniform usage of 12 synonymous codons for FoxP2 was observed among the species of birds. The amino acid usage frequency for FoxP2 revealed that the amino acids Leucine, Glutamine, and Serine were predominant over other amino acids among all the species of fishes, birds, reptiles, and mammals.

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Section: Discussionsupporting

confidence: 88%

Analysis of Codon Usage of Speech Gene FoxP2 among Animals

Mazumder¹,

Alqahtani

et al. 2021

Biology

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“…The % of GC content was lower than AT content, that is, the genes were rich in AT. This result supports our previous studies on mitochondrial ND1 gene (Uddin et al, 2017) and ATP6 and ATP8 gene (Uddin et al, 2020) among pisces, aves, and mammals. Furthermore, AT richness was also reported in genome of Bombyx mori L. (S.-J.…”

Section: Phylogenetic Treesupporting

confidence: 93%

“…Nevertheless, the neutrality plot suggested a narrow distribution of GC3 along with diagonal distribution at some points. All these findings together suggested that the CUB in the mitochondrial genes of Muga silkworm might be influenced by both two evolutionary forces namely mutation pressure and natural selection and these findings supported the results of our earlier studies Uddin et al, , 2019Uddin et al, , 2020L. Wei et al, 2014).…”

Section: Phylogenetic Treesupporting

confidence: 89%

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

Uddin¹,

Chakraborty

2020

Arch Insect Biochem Physiol

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To understand the synonymous codon usage pattern in mitochondrial genome of Antheraea assamensis, we analyzed the 13 mitochondrial protein-coding genes of this species using a bioinformatic approach as no work was reported yet. The nucleotide composition analysis suggested that the percentages of A, T, G,and C were 33.73, 46.39, 9.7 and 10.17, respectively and the overall GC content was 19.86, that is, lower than 50% and the genes were AT rich. The mean effective number of codons of mitochondrial protein-coding genes was 36.30 and it indicated low codon usage bias (CUB). Relative synonymous codon usage analysis suggested overrepresented and underrepresented codons in each gene and the pattern of codon usage was different among genes. Neutrality plot analysis revealed a narrow range of distribution for GC content at the third codon position and some points were diagonally distributed, suggesting both mutation pressure and natural selection influenced the CUB.

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“…In this work, we studied the patterns of the CUB across 224 protein coding genes involved in human autophagy upon the impact of two major evolutionary forces, namely, mutation and natural selection [ 28 ]. Recently, research was made on patterns of the CUB in human tumor suppressor genes [ 55 ]; Y-linked genes [ 56 ]; and mitochondrial ATP genes in mammals, fishes, and aves [ 57 ], but no work has been reported in autophagy-related genes so far, which makes our research significant in providing molecular insights of genes linked with autophagy in humans. Analyzing our current study, the average ENC value for genes involved in human autophagy was found to be 45.05, indicating a low CUB.…”

Section: Discussionmentioning

confidence: 99%

Analysis of the Compositional Features and Codon Usage Pattern of Genes Involved in Human Autophagy

Jamil

Uddin²,

Alam

et al. 2022

Cells

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Autophagy plays an intricate role in paradigmatic human pathologies such as cancer, and neurodegenerative, cardiovascular, and autoimmune disorders. Autophagy regulation is performed by a set of autophagy-related (ATG) genes, first recognized in yeast genome and subsequently identified in other species, including humans. Several other genes have been identified to be involved in the process of autophagy either directly or indirectly. Studying the codon usage bias (CUB) of genes is crucial for understanding their genome biology and molecular evolution. Here, we examined the usage pattern of nucleotide and synonymous codons and the influence of evolutionary forces in genes involved in human autophagy. The coding sequences (CDS) of the protein coding human autophagy genes were retrieved from the NCBI nucleotide database and analyzed using various web tools and software to understand their nucleotide composition and codon usage pattern. The effective number of codons (ENC) in all genes involved in human autophagy ranges between 33.26 and 54.6 with a mean value of 45.05, indicating an overall low CUB. The nucleotide composition analysis of the autophagy genes revealed that the genes were marginally rich in GC content that significantly influenced the codon usage pattern. The relative synonymous codon usage (RSCU) revealed 3 over-represented and 10 under-represented codons. Both natural selection and mutational pressure were the key forces influencing the codon usage pattern of the genes involved in human autophagy.

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Similarities and dissimilarities of codon usage in mitochondrial ATP genes among fishes, aves, and mammals

Cited by 29 publications

References 64 publications

Analysis of Codon Usage of Speech Gene FoxP2 among Animals

Analysis of Codon Usage of Speech Gene FoxP2 among Animals

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

Analysis of the Compositional Features and Codon Usage Pattern of Genes Involved in Human Autophagy

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