Genetic evolution and codon usage analysis of NKX-2.5 gene governing heart development in some mammals

Malakar, Arup Kr.; Halder, Binata; Pavlidis, Paul; Deka, Himangshu; Chakraborty, Supriyo

doi:10.1016/j.ygeno.2019.07.023

Cited by 11 publications

(4 citation statements)

References 68 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These intricate correlation patterns suggest the influence of mutation (major) and selection pressure (minor) is shaping the CUB of EC-responsive genes. Our findings corroborated with the results reported elsewhere [ 23 ].…”

Section: Resultssupporting

confidence: 94%

“…Interestingly, a significant positive correlation was observed between the GC3 and ENc (r=0.56, p <0.05), suggest genes with higher GC3 have a lower CUB. A similar finding was reported by Malaker et al 2020 in a study conducted on mammalian genes [ 23 ]. Furthermore, GC showed strong positive correlations with GC endings codons (Table 2 - see PDF).…”

Section: Discussionsupporting

confidence: 89%

See 1 more Smart Citation

Codon usage bias analysis of genes linked with esophagus cancer

Bordoloi¹

2021

Bioinformation

View full text Add to dashboard Cite

Esophageal cancer involves multiple genetic alternations. A systematic codon usage bias analysis was completed to investigate the bias among the esophageal cancer responsive genes. GC-rich genes were low (average effective number of codon value was 49.28). CAG and GTA are over-represented and under-represented codons, respectively. Correspondence analysis, neutrality plot, and parity rule 2 plot analysis confirmed the dominance over mutation pressure in modulating the codon usage pattern of genes linked with esophageal cancer.

show abstract

Section: Resultssupporting

confidence: 94%

Section: Discussionsupporting

confidence: 89%

Codon usage bias analysis of genes linked with esophagus cancer

Bordoloi¹

2021

Bioinformation

View full text Add to dashboard Cite

show abstract

“…In most of the species a significant negative correlation between Nc and GC3 was depicted, a trend well in line with the standard notion of Nc-GC3 relationship (Hassan et al, 2009;Pandit and Sinha, 2011;Prabha et al, 2012;Malakar et al, 2016Malakar et al, , 2019Song et al, 2017b). The results of the correlation analysis is shown in Supplementary Table 3.…”

Section: Analysis Of Cub Pattern Of Whole Genomesupporting

confidence: 81%

Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes

Saha

Sarkar

et al. 2019

Front. Microbiol.

View full text Add to dashboard Cite

“…Here, the evolution of the atg13 genes in different eukaryotic species represents the species-specific model at synonymous codon usages (Figure 7), strongly suggesting that genetic changes of synonymous codon usage in the atg13 gene benefit the corresponding protein products with functional fit to perform the proper biological functions in specific species. Given that genetic changes in genes can alter phenotypes and even result in diseases, the synonymous codon usage bias has a strong correlation with protein biological functions (Chakraborty et al, 2017;Chakraborty et al, 2019;De Mandal et al, 2020;Malakar et al, 2020). With the ongoing analyses for the genetic signatures of atg genes, some members have been regarded as markers for predicting some diseases (such as cancers) (Baradaran Ghavami et al, 2019;Chen et al, 2020;Yang et al, 2020;Lai et al, 2020;Wang et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages

Wang

et al. 2021

Front. Cell. Infect. Microbiol.

View full text Add to dashboard Cite

Synonymous codon usage bias is a universal characteristic of genomes across various organisms. Autophagy-related gene 13 (atg13) is one essential gene for autophagy initiation, yet the evolutionary trends of the atg13 gene at the usages of nucleotide and synonymous codon remains unexplored. According to phylogenetic analyses for the atg13 gene of 226 eukaryotic organisms at the nucleotide and amino acid levels, it is clear that their nucleotide usages exhibit more genetic information than their amino acid usages. Specifically, the overall nucleotide usage bias quantified by information entropy reflected that the usage biases at the first and second codon positions were stronger than those at the third position of the atg13 genes. Furthermore, the bias level of nucleotide ‘G’ usage is highest, while that of nucleotide ‘C’ usage is lowest in the atg13 genes. On top of that, genetic features represented by synonymous codon usage exhibits a species-specific pattern on the evolution of the atg13 genes to some extent. Interestingly, the codon usages of atg13 genes in the ancestor animals (Latimeria chalumnae, Petromyzon marinus, and Rhinatrema bivittatum) are strongly influenced by mutation pressure from nucleotide composition constraint. However, the distributions of nucleotide composition at different codon positions in the atg13 gene display that natural selection still dominates atg13 codon usages during organisms’ evolution.

show abstract

Genetic evolution and codon usage analysis of NKX-2.5 gene governing heart development in some mammals

Cited by 11 publications

References 68 publications

Codon usage bias analysis of genes linked with esophagus cancer

Codon usage bias analysis of genes linked with esophagus cancer

Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes

Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages

Contact Info

Product

Resources

About