Characterization of the complete chloroplast genome of Gastrochilus sinensis (Orchidaceae, Epidendroideae), a beautiful epiphytic orchid from China

Abstract Gastrochilus sinensis is a beautiful epiphytic orchid with high ornamental value. In this study, the first complete chloroplast genome sequence of G. sinensis was determined using next-generation sequencing (NGS). The de novo assembled chloroplast genome was 148,020 bp in length, including a pair of inverted repeat regions (IRs; 25,987 bp), a small single-copy region (SSC; 11,045 bp), and a large single-copy region (LSC; 85,001 bp). The chloroplast genome encodes 109 unique genes, including 75 protein-coding genes (PCGs), 30 tRNA genes, and four rRNA genes. The total GC content of the chloroplast genome was 36.8%. The phylogenetic analysis showed a close relationship between G. sinensis and G. formosanus species. The complete chloroplast genome provides fundamental information for genetic diversity and phylogenetic relationships in Gastrochilus.


Introduction
Gastrochilus sinensis Z.H. Tsi 1996, is a beautiful epiphytic orchid and distributed in southern China (Tsi 1996;Chen et al. 2009;Cheng et al. 2022).It has a showy labellum, which is divided into a recurved epichile and a saccate hypochile, with high ornamental value (Pridgeon et al. 2014;Liao et al. 2022).With rapid development of the second-generation sequencing technology, the chloroplast genome information was widely used for studying taxonomy, phylogeny, evolution, conservation, and ecology in plants (Jheng et al. 2012;Zhang, Liao, et al. 2022).Until now, only 10 plastid genomes of Gastrochilus have been reported (Liu et al. 2020), which has greatly hindered the aforementioned studies in this genus.Therefore, we reported the first complete chloroplast genome of G. sinensis based on the whole-genome Illumina sequencing dataset in this study.

Materials and methods
Fresh leaves of Gastrochilus sinensis (Figure 1; voucher ZJY181; contact person: Bo Xu, xubo@cib.ac.cn) were collected from Sanjiang (31 � 7 0 14.95 00 N, 103 � 13 0 25.60 00 E), Wenchuan County, Sichuan Province, China, and a voucher specimen was deposited at the Herbarium of Chengdu Institute of Biology (CDBI).Total genomic DNA was extracted from silica-gel dried leaves through Plant DNA Isolation Kit (Cat.No. DE-06111, Foregene, Chengdu, China).Next-generation sequencing (NGS) was performed via Illumina paired-end technology.De novo assembly of the chloroplast genome was carried out using GetOrganelle v1.7.2 (Jin et al. 2020).The average read mapping depths of the assembled genome were 2729� (Figure S1).The assembled chloroplast genome was annotated using PGA (Qu et al. 2019) and manually corrected for the start and stop codons.The final genome map of G. sinensis was generated using CPGview (http://www.1kmpg.cn/cpgview).The annotated chloroplast genome was submitted to the GenBank under the accession number OQ784257.

Discussion
The genome size, gene content, and order are not significantly different from other published chloroplast genomes in Gastrochilus (Liu et al. 2020).The inferred phylogenetic tree analysis also confirmed the systematic position of G. sinensis supported by data on filtered plastid and nuclear loci (Zhang, Cheng, et al. 2022), that G. sinensis is a member of the monophyletic genus Gastrochilus in the subtribe Aeridinae of the tribe Vandeae of Orchidaceae.The other species of this genus have been clearly distinguished, but the topology of the inferred phylogeny is different from those of recently published phylogenies (Liu et al. 2019), such as the systematic positions of the clade C and D are opposite to Liu et al. (2019) and Zhang et al. (2023), suggesting that further research on phylogenetic relationships in Gastrochilus is necessary.The research results will be used for authenticating the plant materials of G. sinensis and for analyzing the genetic diversity and phylogenetic relationships in Gastrochilus.

Figure 1 .
Figure 1.Flowering plant image of Gastrochilus sinensis (this unpublished photo, taken in Sanjiang, Wenchuan County, Sichuan Province, China by Mr. Yuehong Cheng, is used with permission).

Figure 2 .
Figure 2. The circle map of complete chloroplast genome of Gastrochilus sinensis.The map was generated by CPGView.located on the inner and outer of circle are transcribed clockwise and anticlockwise, respectively.The dark grey inner circle indicates GC content.Large single-copy (LSC), small single-copy (SSC), and inverted repeats (IRA and IRB) are indicated in the inner layer.The functional classification of the genes is provided in the bottom left corner.