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<p><i>Epidendrum ibaguense</i> is a representative epiphytic orchid of high ornamental and horticultural value. Here, we report the complete plastome of <i>E. ibaguense</i> (147,596&#xa0;bp), which represents the smallest plastome reported in the genus. The genome exhibits a typical quadripartite structure with conserved inverted repeat/single-copy (IR/SC) junctions. Most NADH dehydrogenase (<i>ndh</i>) genes are pseudogenized or lost in <i>E. ibaguense</i>, while comparative analyses across <i>Epidendrum</i> species revealed lineage-specific variation in <i>ndh</i> gene content and integrity. Core photosynthetic genes remain intact under strong purifying selection, and codon usage analysis revealed gene-specific biases consistent with mutational and translational constraints. Phylogenomic reconstruction based on complete plastomes placed <i>E. ibaguense</i> in a strongly supported clade with <i>E. porpax</i>, <i>E. eburneum</i>, and <i>E. avicula</i>. Across <i>Epidendrum</i> plastomes, 981 non-redundant SSRs were identified at the genus level, 464 of which exhibit length polymorphisms, predominantly in intergenic regions. Both SSR polymorphisms and lineage-specific <i>ndh</i> variation represent promising sources of molecular markers for conservation, breeding, and horticultural applications. These findings enhance our understanding of plastome evolution in orchids and provide valuable genomic resources for future marker development in <i>Epidendrum</i>.</p>

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The complete plastid genome of Epidendrum ibaguense (Orchidaceae): insights into plastome evolution and molecular marker resources

  • 期刊论文

  • 发表日期：

    2026年1月14日

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  • Chang Shengxin,
  • Han Wei,
  • Yu Baiyin,
  • Luo Jiayi,
  • Luo Youhui,
  • Li Chunxia

摘要

Epidendrum ibaguense is a representative epiphytic orchid of high ornamental and horticultural value. Here, we report the complete plastome of E. ibaguense (147,596 bp), which represents the smallest plastome reported in the genus. The genome exhibits a typical quadripartite structure with conserved inverted repeat/single-copy (IR/SC) junctions. Most NADH dehydrogenase (ndh) genes are pseudogenized or lost in E. ibaguense, while comparative analyses across Epidendrum species revealed lineage-specific variation in ndh gene content and integrity. Core photosynthetic genes remain intact under strong purifying selection, and codon usage analysis revealed gene-specific biases consistent with mutational and translational constraints. Phylogenomic reconstruction based on complete plastomes placed E. ibaguense in a strongly supported clade with E. porpax, E. eburneum, and E. avicula. Across Epidendrum plastomes, 981 non-redundant SSRs were identified at the genus level, 464 of which exhibit length polymorphisms, predominantly in intergenic regions. Both SSR polymorphisms and lineage-specific ndh variation represent promising sources of molecular markers for conservation, breeding, and horticultural applications. These findings enhance our understanding of plastome evolution in orchids and provide valuable genomic resources for future marker development in Epidendrum.