Genome-Wide Analysis of Codon Usage Bias in Epichloë festucae

Song, Hui; Yu, Kuang; Chen, Shuihong; Tian, Pei; Li, Chunjie; Zhang, Nan

doi:10.3390/ijms17071138

Cited by 28 publications

(24 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The ENC in grape bHLH genes ranged from 30.28 to 60.96, with an average of 53.25. Among the 94 grape bHLH genes, only one gene (VvbHLH091) exhibited high codon bias (ENC < 35), indicating that in general, grape bHLH genes reflect random codon usage without strong codon bias (Li et al, 2016 ). Codon usage bias could be affected by many stressors including mutation pressure and natural selection (Li, 1987 ).…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Characterization of bHLH Genes in Grape and Analysis of their Potential Relevance to Abiotic Stress Tolerance and Secondary Metabolite Biosynthesis

et al. 2018

View full text Add to dashboard Cite

Basic helix-loop-helix (bHLH) transcription factors are involved in many abiotic stress responses as well as flavonol and anthocyanin biosynthesis. In grapes (Vitis vinifera L.), flavonols including anthocyanins and condensed tannins are most abundant in the skins of the berries. Flavonols are important phytochemicals for viticulture and enology, but grape bHLH genes have rarely been examined. We identified 94 grape bHLH genes in a genome-wide analysis and performed Nr and GO function analyses for these genes. Phylogenetic analyses placed the genes into 15 clades, with some remaining orphans. 41 duplicate gene pairs were found in the grape bHLH gene family, and all of these duplicate gene pairs underwent purifying selection. Nine triplicate gene groups were found in the grape bHLH gene family and all of these triplicate gene groups underwent purifying selection. Twenty-two grape bHLH genes could be induced by PEG treatment and 17 grape bHLH genes could be induced by cold stress treatment including a homologous form of MYC2, VvbHLH007. Based on the GO or Nr function annotations, we found three other genes that are potentially related to anthocyanin or flavonol biosynthesis: VvbHLH003, VvbHLH007, and VvbHLH010. We also performed a cis-acting regulatory element analysis on some genes involved in flavonoid or anthocyanin biosynthesis and our results showed that most of these gene promoters contained G-box or E-box elements that could be recognized by bHLH family members.

show abstract

Section: Resultsmentioning

confidence: 99%

Genome-Wide Characterization of bHLH Genes in Grape and Analysis of their Potential Relevance to Abiotic Stress Tolerance and Secondary Metabolite Biosynthesis

et al. 2018

View full text Add to dashboard Cite

show abstract

“…A recent study on codon usage bias in E. festucae showed that both natural selection and mutation pressure played a role in forming codon usage bias in E. festucae , and that codon usage bias was influenced by CDS length (Li et al, 2016 ). There are 43 Epichloë species that have been reported to date, but it is not clear whether Epichloë species share similar codon usage bias.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Analysis of Codon Usage Bias in Seven Epichloë Species and Their Peramine-Coding Genes

et al. 2017

Self Cite

View full text Add to dashboard Cite

Codon usage bias plays an important role in shaping genomes and genes in unicellular species and multicellular species. Here, we first analyzed codon usage bias in seven Epichloë species and their peramine-coding genes. Our results showed that both natural selection and mutation pressure played a role in forming codon usage bias in seven Epichloë species. All seven Epichloë species contained a peramine-coding gene cluster. Interestingly, codon usage bias of peramine-coding genes were not affected by natural selection or mutation pressure. There were 13 codons more frequently found in Epichloë genome sequences, peramine-coding gene clusters and orthologous peramine-coding genes, all of which had a bias to end with a C nucleotide. In the seven genomes analyzed, codon usage was biased in highly expressed coding sequences (CDSs) with shorter length and higher GC content. Genes in the peramine-coding gene cluster had higher GC content at the third nucleotide position of the codon, and highly expressed genes had higher GC content at the second position. In orthologous peramine-coding CDSs, high expression level was not significantly correlated with CDS length and GC content. Analysis of selection pressure identified that the genes orthologous to peramine genes were under purifying selection. There were no differences in codon usage bias and selection pressure between peramine product genes and non-functional peramine product genes. Our results provide insights into understanding codon evolution in Epichloë species.

show abstract

“…The analysis showed that the GC3s was positively correlated with the GC12s (r ¼ 0.2239, p ¼ 0.3045). The slope of the neutrality plot was 0.03608, meaning that mutation pressure accounted for 3.608% of shaping the codon usage pattern and the influence from other factors was 96.392% [26].…”

Section: Neutrality Plot Analysismentioning

confidence: 99%

Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Senecavirus A evolution

Chen

Tan

et al. 2017

Microbial Pathogenesis

View full text Add to dashboard Cite

Senecavirus A (SVA) infection was recently confirmed in pigs in Brazil, United States of America and Canada. To better understand the molecular characteristics of isolated SVA genomes, we first reported genome-wide comprehensive analyses of codon usage and various factors that have contribute to the molecular evolution in SVA. The effective number of codons (ENC) ranged from 54.51 to 55.54 with an average of 54.87 ± 0.285, which reveals a relatively stable nucleotide composition. We found that codon usage bias of the SVA was low. Mutational pressure acted as an increasingly dominant factor for the evolution of the virus compared with the natural selection. Notably, codon usage bias was also affected by the geographic distribution and isolated time. The first systemic analysis on the codon usage bias of the SVA provides important information for the understanding of the evolution of the SVA and has fundamental and theoretical benefits.

show abstract

Genome-Wide Analysis of Codon Usage Bias in Epichloë festucae

Cited by 28 publications

References 50 publications

Genome-Wide Characterization of bHLH Genes in Grape and Analysis of their Potential Relevance to Abiotic Stress Tolerance and Secondary Metabolite Biosynthesis

Genome-Wide Characterization of bHLH Genes in Grape and Analysis of their Potential Relevance to Abiotic Stress Tolerance and Secondary Metabolite Biosynthesis

Comprehensive Analysis of Codon Usage Bias in Seven Epichloë Species and Their Peramine-Coding Genes

Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Senecavirus A evolution

Contact Info

Product

Resources

About