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<p><i>Gomesa recurva</i> (Orchidaceae: Cymbidieae, Oncidiinae), the type species of the genus <i>Gomesa</i>, is an important species with ornamental value and distributed from northeastern Argentina to northeastern Brazil. In the present study, we assembled the complete plastid genome (plastome) of <i>G. recurva</i> based on genome skimming data, and we conducted comparative plastome analyses to study the evolutionary pattern in the tribe Cymbidieae. The plastome of <i>G. recurva</i> is a molecule with 145,807&#xa0;bp arranged in the typical quadripartite structure: the large single-copy (LSC) has 83,519&#xa0;bp, each inverted repeat (IR) has 25,113&#xa0;bp, and the small single-copy (SSC) has 12,062&#xa0;bp. It encodes 112 unique genes, including 78 protein-coding genes, 30 tRNA, and four rRNA. From the referenced annotation of plastid genes of <i>G. recurva</i>, we verified the presence of premature stop codons and sub functionalisation in <i>ndh</i> genes. Comparative analyses revealed no major structural differences between plastomes of species of tribe Cymbidieae, although differences were evident in genome size, gene content, as well as inverted repeat (IR) region expansion and contraction. Ten cpDNA markers, <i>ndhI</i>, <i>ccsA</i>-<i>ndhD</i>, <i>trnR</i>-<i>atpA</i>, <i>trnS</i>-<i>trnG</i>, <i>ycf1</i>-<i>rpl32</i>, <i>psbl</i>-<i>trnG</i>, <i>psaC</i>-<i>ndhE</i>, <i>ndhG</i>, <i>rps16</i>-<i>trnQ</i>, <i>trnK</i>-<i>rpl16</i>, were identified with relatively high levels of variation within Cymbidieae.</p>

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The complete plastid genome of Gomesa recurva (Orchidaceae: Oncidiinae) and comparative analysis of species in tribe Cymbidieae: genome structure, sequence divergence, and phylogenomic analysis

  • 期刊论文

  • 发表日期：

    2025年6月4日

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  • Fernanda Witt Cidade,
  • Leila do Nascimento Vieira,
  • Viviane da Silva-Pereira,
  • Eric Camargo de Smidt

摘要

Gomesa recurva (Orchidaceae: Cymbidieae, Oncidiinae), the type species of the genus Gomesa, is an important species with ornamental value and distributed from northeastern Argentina to northeastern Brazil. In the present study, we assembled the complete plastid genome (plastome) of G. recurva based on genome skimming data, and we conducted comparative plastome analyses to study the evolutionary pattern in the tribe Cymbidieae. The plastome of G. recurva is a molecule with 145,807 bp arranged in the typical quadripartite structure: the large single-copy (LSC) has 83,519 bp, each inverted repeat (IR) has 25,113 bp, and the small single-copy (SSC) has 12,062 bp. It encodes 112 unique genes, including 78 protein-coding genes, 30 tRNA, and four rRNA. From the referenced annotation of plastid genes of G. recurva, we verified the presence of premature stop codons and sub functionalisation in ndh genes. Comparative analyses revealed no major structural differences between plastomes of species of tribe Cymbidieae, although differences were evident in genome size, gene content, as well as inverted repeat (IR) region expansion and contraction. Ten cpDNA markers, ndhI, ccsA-ndhD, trnR-atpA, trnS-trnG, ycf1-rpl32, psbl-trnG, psaC-ndhE, ndhG, rps16-trnQ, trnK-rpl16, were identified with relatively high levels of variation within Cymbidieae.