Scholarlink

<p>Coffee is among the most widely consumed beverages worldwide, with diverse <i>Coffea</i> species displaying a broad spectrum of flavors and important agronomic traits. Despite recent advances in genomics and the availability of assembled coffee genomes, comparative genomic analyses remain underutilized for crop improvement. In this study, we conducted comprehensive orthology and orthogroup evolution analyses across 24 plant species–four Gentianales, including three <i>Coffea</i> species (<i>Coffea arabica</i>, <i>Coffea canephora</i>, and <i>Coffea eugenioides</i>), twelve Lamiales, and eight Solanales–to identify lineage-specific genomic features associated with adaptation and coffee quality traits. Using OrthoFinder in conjunction with gene family evolution models (CAFE5 and COUNT), we identified 1,552 orthogroups that are either specific to <i>Coffea</i> or have undergone significant expansion or contraction. Disease‑resistance genes were the most prominent among rapidly expanded orthogroups, reflecting an ongoing evolutionary arms race with pathogens. We also observed asymmetric patterns of orthogroup evolution, including contraction of light and ethylene signaling orthogroups in <i>C. canephora</i>, contrasted by their expansion in <i>C. arabica</i> and <i>C. eugenioides</i>, which may contribute to their adaptation to shaded, high-altitude environments. Further analysis using COUNT identified twelve <i>Coffea</i>-specific orthogroup expansions associated with secondary metabolite biosynthesis, including key enzymes for caffeine and chlorogenic acid production. Our comprehensive catalog of lineage-specific orthogroups, supported by functional enrichment and phylogenetic analyses, provides a valuable genomic resource to support breeding programs focused on enhancing stress resilience, disease resistance, and cup quality in cultivated coffee.</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

Lineage-specific genomic signatures in Coffea identified through comparative gene family evolution

  • 期刊论文

  • 发表日期：

    2026年5月9日

查看全文
  • Sunchung Park,
  • Ezekiel Ahn,
  • Sookyung Oh,
  • Dapeng Zhang,
  • Lyndel W. Meinhardt

摘要

Coffee is among the most widely consumed beverages worldwide, with diverse Coffea species displaying a broad spectrum of flavors and important agronomic traits. Despite recent advances in genomics and the availability of assembled coffee genomes, comparative genomic analyses remain underutilized for crop improvement. In this study, we conducted comprehensive orthology and orthogroup evolution analyses across 24 plant species–four Gentianales, including three Coffea species (Coffea arabica, Coffea canephora, and Coffea eugenioides), twelve Lamiales, and eight Solanales–to identify lineage-specific genomic features associated with adaptation and coffee quality traits. Using OrthoFinder in conjunction with gene family evolution models (CAFE5 and COUNT), we identified 1,552 orthogroups that are either specific to Coffea or have undergone significant expansion or contraction. Disease‑resistance genes were the most prominent among rapidly expanded orthogroups, reflecting an ongoing evolutionary arms race with pathogens. We also observed asymmetric patterns of orthogroup evolution, including contraction of light and ethylene signaling orthogroups in C. canephora, contrasted by their expansion in C. arabica and C. eugenioides, which may contribute to their adaptation to shaded, high-altitude environments. Further analysis using COUNT identified twelve Coffea-specific orthogroup expansions associated with secondary metabolite biosynthesis, including key enzymes for caffeine and chlorogenic acid production. Our comprehensive catalog of lineage-specific orthogroups, supported by functional enrichment and phylogenetic analyses, provides a valuable genomic resource to support breeding programs focused on enhancing stress resilience, disease resistance, and cup quality in cultivated coffee.