Genome-wide characterization and identification of synonymous codon usage patterns in <i>Plasmodium knowlesi</i>

Yadav, Manoj Kumar; Gajbhiye, Shivani

doi:10.1101/2021.01.01.425038

Cited by 3 publications

(1 citation statement)

References 48 publications

(51 reference statements)

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“…The amount of ENC varies between 20 to 61, and the higher the ENC value, the weaker the CUB. The ENC of the Brassica LysM-RLKs ranged from 48.97 to 59.64, indicating that the codons of this family are not affected by strong codon bias and there are various synonymous codons [ 118 ]. The CAI index varies from 0 to 1, which is typically applied to measure expression levels [ 119 ].…”

Section: Discussionmentioning

confidence: 99%

Analyses of Lysin-motif Receptor-like Kinase (LysM-RLK) Gene Family in Allotetraploid Brassica napus L. and Its Progenitor Species: An In Silico Study

Abedi

Hajiahmadi

Kordrostami

et al. 2021

Cells

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The LysM receptor-like kinases (LysM-RLKs) play a crucial role in plant symbiosis and response to environmental stresses. Brassica napus, B. rapa, and B. oleracea are utilized as valuable vegetables. Different biotic and abiotic stressors affect these crops, resulting in yield losses. Therefore, genome-wide analysis of the LysM-RLK gene family was conducted. From the genome of the examined species, 33 LysM-RLK have been found. The conserved domains of Brassica LysM-RLKs were divided into three groups: LYK, LYP, and LysMn. In the Brassica LysM-RLK gene family, only segmental duplication has occurred. The Ka/Ks ratio for the duplicated pair of genes was less than one indicating that the genes’ function had not changed over time. The Brassica LysM-RLKs contain 70 cis-elements, indicating that they are involved in stress response. 39 miRNA molecules were responsible for the post-transcriptional regulation of 12 Brassica LysM-RLKs. A total of 22 SSR loci were discovered in 16 Brassica LysM-RLKs. According to RNA-seq data, the highest expression in response to biotic stresses was related to BnLYP6. According to the docking simulations, several residues in the active sites of BnLYP6 are in direct contact with the docked chitin and could be useful in future studies to develop pathogen-resistant B. napus. This research reveals comprehensive information that could lead to the identification of potential genes for Brassica species genetic manipulation.

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Section: Discussionmentioning

confidence: 99%

Analyses of Lysin-motif Receptor-like Kinase (LysM-RLK) Gene Family in Allotetraploid Brassica napus L. and Its Progenitor Species: An In Silico Study

Abedi

Hajiahmadi

Kordrostami

et al. 2021

Cells

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Genome-wide survey of catalase genes in Brassica rapa, Brassica oleracea, and Brassica napus: identification, characterization, molecular evolution, and expression profiling of BnCATs in response to salt and cadmium stress

2022

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Fitness difference between two synonymous mutations of Phytophthora infestans ATP6 gene

Nkurikiyimfura,

Waheed,

Fang

et al. 2024

BMC Ecol Evo

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Background Sequence variation produced by mutation provides the ultimate source of natural selection for species adaptation. Unlike nonsynonymous mutation, synonymous mutations are generally considered to be selectively neutral but accumulating evidence suggests they also contribute to species adaptation by regulating the flow of genetic information and the development of functional traits. In this study, we analysed sequence characteristics of ATP6, a housekeeping gene from 139 Phytophthora infestans isolates, and compared the fitness components including metabolic rate, temperature sensitivity, aggressiveness, and fungicide tolerance among synonymous mutations. Results We found that the housekeeping gene exhibited low genetic variation and was represented by two major synonymous mutants at similar frequency (0.496 and 0.468, respectively). The two synonymous mutants were generated by a single nucleotide substitution but differed significantly in fitness as well as temperature-mediated spatial distribution and expression. The synonymous mutant ending in AT was more common in cold regions and was more expressed at lower experimental temperature than the synonymous mutant ending in GC and vice versa. Conclusion Our results are consistent with the argument that synonymous mutations can modulate the adaptive evolution of species including pathogens and have important implications for sustainable disease management, especially under climate change.

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Genome-wide characterization and identification of synonymous codon usage patterns in Plasmodium knowlesi

Cited by 3 publications

References 48 publications

Analyses of Lysin-motif Receptor-like Kinase (LysM-RLK) Gene Family in Allotetraploid Brassica napus L. and Its Progenitor Species: An In Silico Study

Analyses of Lysin-motif Receptor-like Kinase (LysM-RLK) Gene Family in Allotetraploid Brassica napus L. and Its Progenitor Species: An In Silico Study

Genome-wide survey of catalase genes in Brassica rapa, Brassica oleracea, and Brassica napus: identification, characterization, molecular evolution, and expression profiling of BnCATs in response to salt and cadmium stress

Fitness difference between two synonymous mutations of Phytophthora infestans ATP6 gene

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