Scholarlink

<p>Millets are crops that grow well in dry land and have much nutrition, but little is known regarding comprehensive research on the chloroplast genomic architecture. In this study, we look at codon usage bias in chloroplast DNA of eight millet types: <i>Echinochloa esculenta</i>, <i>Eleusine coracana</i>, <i>Panicum miliaceum</i>, <i>Panicum sumatrense</i>, <i>Paspalum scrobiculatum</i>, <i>Pennisetum glaucum</i>, <i>Setaria italica</i>, and <i>Sorghum bicolor</i>. We use different codon bias measures like RSCU, ENC, GC content, and neutrality plots to understand what affects codon use, whether mutation or selection. The analysis revealed strong A/T-ending codon usage preference, and interestingly, the third codon position GC3 revealed ~ 29–30%, supporting compositional bias. Thirty high-frequency codons (RSCU &gt; 1) were identified and ended in A or T. Some codons, like TGT, CCT, and TTA are common in all species, but many optimal codons are different between species. ENC and neutrality results revealed that natural selection played a key role in shaping codon usage bias relative to mutations. The PR2 plot also shows a preference for T and G at the third codon position. Correspondence analysis revealed many genes similarly use codons, but some genes are different, maybe because of environment or gene function. This research helps to understand the evolution of chloroplasts in millets and can help future work in transgene, phylogeny and make better millet crops with codon optimization for more stress resistance and nutrition.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Comprehensive Analysis of Codon Usage Bias Pattern in Chloroplast Genomes of Eight Millet Species

  • 期刊论文

  • 发表日期：

    2026年3月24日

查看全文
  • J. Bevin Nishanth,
  • Raju Balaji,
  • Ganesan Govindhan,
  • Suji Somasundaram

摘要

Millets are crops that grow well in dry land and have much nutrition, but little is known regarding comprehensive research on the chloroplast genomic architecture. In this study, we look at codon usage bias in chloroplast DNA of eight millet types: Echinochloa esculenta, Eleusine coracana, Panicum miliaceum, Panicum sumatrense, Paspalum scrobiculatum, Pennisetum glaucum, Setaria italica, and Sorghum bicolor. We use different codon bias measures like RSCU, ENC, GC content, and neutrality plots to understand what affects codon use, whether mutation or selection. The analysis revealed strong A/T-ending codon usage preference, and interestingly, the third codon position GC3 revealed ~ 29–30%, supporting compositional bias. Thirty high-frequency codons (RSCU > 1) were identified and ended in A or T. Some codons, like TGT, CCT, and TTA are common in all species, but many optimal codons are different between species. ENC and neutrality results revealed that natural selection played a key role in shaping codon usage bias relative to mutations. The PR2 plot also shows a preference for T and G at the third codon position. Correspondence analysis revealed many genes similarly use codons, but some genes are different, maybe because of environment or gene function. This research helps to understand the evolution of chloroplasts in millets and can help future work in transgene, phylogeny and make better millet crops with codon optimization for more stress resistance and nutrition.