High-throughput sequencing yields the complete plastid genome of the endemic species Phragmipedium kovachii (Orchidaceae) from northeastern Peru.

Pub Date : 2024-09-02 eCollection Date: 2024-01-01 DOI:10.1080/23802359.2024.2397979

Jois V Carrion, Jhordy Perez, Daniel Tineo, Martha S Calderon, Ligia Garcia, Manuel Oliva, Oscar Gamarra Torres, Danilo E Bustamante

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Abstract

Phragmipedium kovachii is a species of orchid endemic to the Amazonas and San Martín regions. Unfortunately, its excessive extraction has made it a critically endangered species. In this study, we performed next-generation sequencing of P. kovachii (GenBank accession number OR348669) and assembled its complete chloroplast genome. The complete chloroplast genome of P. kovachii is A + T-rich (64.3%), measuring 152,918 bp in length. This plastid genome contains a total of 124 genes (77 protein-coding genes, 39 tRNAs, and eight rRNAs) and five pseudogenes, including a pair of inverted repeats (IRs) 25,116 bp in size and separated by a large single-copy (LSC) region of 89,216 bp and a small single-copy (SSC) region of 13,470 bp. This genome has a typical quadripartite organization following the structure of other Orchidaceae plastomes. Phylogenetic analyses revealed the close relationship between P. kovachii and P. besseae. This study contributes to the understanding of the phylogenetic relationships of the monophyletic group Cypripedioideae.

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高通量测序获得了秘鲁东北部特有物种Phragmipedium kovachii（兰科）的完整质体基因组。

Phragmipedium kovachii 是亚马逊和圣马丁地区特有的一种兰花。不幸的是，由于过度采挖，该物种已濒临灭绝。在这项研究中，我们对 P. kovachii（GenBank登录号 OR348669）进行了下一代测序，并组装了其完整的叶绿体基因组。Kovachii 的完整叶绿体基因组富含 A + T（64.3%），长度为 152,918 bp。该质体基因组共包含 124 个基因（77 个蛋白质编码基因、39 个 tRNA 和 8 个 rRNA）和 5 个假基因，其中包括一对大小为 25,116 bp 的倒位重复序列（IR），并由一个 89,216 bp 的大单拷贝（LSC）区域和一个 13,470 bp 的小单拷贝（SSC）区域分隔开来。该基因组具有典型的四方组织结构，与其他兰科植物质体的结构相同。系统进化分析表明 P. kovachii 与 P. besseae 关系密切。这项研究有助于人们了解单系群Cypripedioideae的系统发育关系。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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