Scholarlink

<p>Self-incompatibility genes, a critical genetic mechanism in flowering plants, enforce cross-pollination by preventing self-fertilization through specific pollen-pistil recognition mediated by the S-locus. In <i>Brassica rapa</i>, this system is initiated through specific recognition between the pollen determinant gene <i>BrSP11</i> (S-locus protein 11)<i>/BrSCR</i> (S-locus cysteine-rich protein) and the pistil determinant gene <i>BrSRK</i> (S-locus receptor kinase). Additionally, <i>BrSLG</i> (S-locus glycoprotein) enhances the intensity of this recognition response. To elucidate the evolutionary dynamics and codon usage characteristics of these genes, we systematically analyzed 37 <i>BrSRK</i>, 16 <i>BrSLG</i>, and 17 <i>BrSP11/BrSCR</i> alleles through computational approaches (Codon W, Mega, and SPSS). The codon usage bias was further analyzed through PR2 plot, ENC-GC3 plot, neutrality plot, and multivariate statistical analysis to explore the evolutionary forces driving its formation. Phylogenetic relationships were reconstructed using hierarchical clustering and neighbor-joining algorithms, with congruence validated against coding sequence (CDS) phylogenies. The results showed that the S-domains of <i>BrSRK</i>, <i>BrSLG</i>, and <i>BrSP11/BrSCR</i> exhibited pronounced AT-richness, and the codon prefer to end with A/T, with a low preference for codon usage, which is affected by natural selection (a main factor), mutational pressure (a secondary factor), and the abundance of dinucleotides. Based on the relative synonymous codon usage (RSCU) values, two, three and eleven over-represented codons of <i>BrSRK</i>, <i>BrSLG</i>, and <i>BrSP11/SCR</i> were identified, respectively. Cluster analysis based on RSCU could accurately classify class I and class II haplotypes and accurately reflect the relationships among <i>BrSRK</i>, <i>BrSLG</i>, and <i>BrSP11</i>/<i>BrSCR</i> alleles in <i>B. rapa</i>, which was consistent and reliable with CDS clustering. According to the codon usage patterns and clustering results, the self-incompatibility genes <i>BrSRK</i>, <i>BrSLG</i>, and <i>BrSP11</i>/<i>BrSCR</i> may be coevolutionary in their codon usage patterns.</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

Codon usage bias analysis of self-incompatibility genes BrSRK, BrSLG, and BrSP11/BrSCR in Brassica rapa reveals insights into their coevolution

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年5月29日

查看全文
  • Yi-zhong Zhang,
  • Min Ji,
  • Lin-qiong Deng,
  • Li-kun Lian,
  • Li Jian,
  • Rong-xian Zhang

摘要

Self-incompatibility genes, a critical genetic mechanism in flowering plants, enforce cross-pollination by preventing self-fertilization through specific pollen-pistil recognition mediated by the S-locus. In Brassica rapa, this system is initiated through specific recognition between the pollen determinant gene BrSP11 (S-locus protein 11)/BrSCR (S-locus cysteine-rich protein) and the pistil determinant gene BrSRK (S-locus receptor kinase). Additionally, BrSLG (S-locus glycoprotein) enhances the intensity of this recognition response. To elucidate the evolutionary dynamics and codon usage characteristics of these genes, we systematically analyzed 37 BrSRK, 16 BrSLG, and 17 BrSP11/BrSCR alleles through computational approaches (Codon W, Mega, and SPSS). The codon usage bias was further analyzed through PR2 plot, ENC-GC3 plot, neutrality plot, and multivariate statistical analysis to explore the evolutionary forces driving its formation. Phylogenetic relationships were reconstructed using hierarchical clustering and neighbor-joining algorithms, with congruence validated against coding sequence (CDS) phylogenies. The results showed that the S-domains of BrSRK, BrSLG, and BrSP11/BrSCR exhibited pronounced AT-richness, and the codon prefer to end with A/T, with a low preference for codon usage, which is affected by natural selection (a main factor), mutational pressure (a secondary factor), and the abundance of dinucleotides. Based on the relative synonymous codon usage (RSCU) values, two, three and eleven over-represented codons of BrSRK, BrSLG, and BrSP11/SCR were identified, respectively. Cluster analysis based on RSCU could accurately classify class I and class II haplotypes and accurately reflect the relationships among BrSRK, BrSLG, and BrSP11/BrSCR alleles in B. rapa, which was consistent and reliable with CDS clustering. According to the codon usage patterns and clustering results, the self-incompatibility genes BrSRK, BrSLG, and BrSP11/BrSCR may be coevolutionary in their codon usage patterns.