Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae.

Huyen-Trang Vu,Thanh-Diem Nguyen,Minh-Tri Le,Quoc-Luan Vu,Ngan Tran,My-Huyen Bui,Ly Le

doi:10.3390/plants9010061

Abstract

Paphiopedilum delenatii is a native orchid of Vietnam with highly attractive floral traits. Unfortunately, it is now listed as a critically endangered species with a few hundred individuals remaining in nature. In this study, we performed next-generation sequencing of P. delenatii and assembled its complete chloroplast genome. The whole chloroplast genome of P. delenatii was 160,955 bp in size, 35.6% of which was GC content, and exhibited typical quadripartite structure of plastid genomes with four distinct regions, including the large and small single-copy regions and a pair of inverted repeat regions. There were, in total, 130 genes annotated in the genome: 77 coding genes, 39 tRNA genes, 8 rRNA genes, and 6 pseudogenes. The loss of ndh genes and variation in inverted repeat (IR) boundaries as well as data of simple sequence repeats (SSRs) and divergent hotspots provided useful information for identification applications and phylogenetic studies of Paphiopedilum species. Whole chloroplast genomes could be used as an effective super barcode for species identification or for developing other identification markers, which subsequently serves the conservation of Paphiopedilum species.

Highlights

The sequence of chloroplast genomes can provide information for studying genetic relationships, gene transfer, cloning, and domestication of species [1]
To verify the plastid genome sequence, we independently compared it to four barcoded markers, i.e., matK, trnL-UAA, rpoB, and rpoC1 (GenBank accessions MK792631, MK787353, MK876160, and MK792704, respectively), belonging to the chloroplast genome of the same P. delenatii sample that was sequenced by the Sanger method in our previous study [25]
We aimed to expand the genetic resource of the endangered species P. delenatii by next-generation sequencing and chloroplast genome assembly

Summary

Introduction

The sequence of chloroplast (cp) genomes can provide information for studying genetic relationships, gene transfer, cloning, and domestication of species [1]. The project of chloroplast genome sequencing and barcoding Fritillaria [2]. The sequencing of the chloroplast genome of the rice variety Nagina-22 [3] enriched genetic resources to support the breeding and crossbreeding of next-generation rice varieties. Na Tian et al (2018) sequenced and analyzed the chloroplast genome of Epipremum aureum that contributed to the propagation and support of gene transfer of this medicinal plant [4]. The sequencing and analysis of cp genomes helped explain phylogenetic relationships and the evolutionary path of Orchidaceae [6,7]

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