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. 2021 Mar 26;6(3):1245–1246. doi: 10.1080/23802359.2021.1906171

The complete plastid genome of Thrixspermum centipeda (Orchidaceae, Aeridinae)

Meng-Wei Chi 1, Ding-Kun Liu 1, Cheng-Yuan Zhou 1, Ming-He Li 1, Si-Ren Lan 1,✉
PMCID: PMC8008882  PMID: 33829096

Abstract

The complete plastid genome of the type species of Thrixspermum, Th. centipeda, was determined and analyzed in this work. The plastome was 147,888 bp in length with 85,899 bp of the large single-copy (LSC) region, 11,055 bp of the small single-copy (SSC) region and 25,467 bp of the invert repeats (IR) regions. The genome contained 120 genes, including 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis divided 18 Aeridinae plastomes into four groups, and Th. centipeda was sister to Th. tsii.

Keywords: Aeridinae, chloroplast genome, phylogeny, Thrixspermum

The Thrixspermum comprises about 160 species and is one of the largest genera of Aeridinae (Chase et al. 2015). This genus is distributed in the subtropical and tropical regions from Asia to Australia (Pridgeon et al. 2014). The intergeneric and intrageneric phylogenetic relationships of Thrixspermum remain unresolved (Pridgeon et al. 2014; Zou et al. 2015). Here, the plastid genome of the type species of Thrixspermum, Th. centipeda, was sequenced and assembled for phylogeny and evolution research.

Fresh leaf sample of Th. centipeda was acquired from Menghai County, Yunnan Province of China (21°55′N, 100°07′E). The voucher specimen deposited at Fujian Agriculture and Forestry University (specimen code MH Li or081). DNA extraction, library constructing, sequencing and data filtering were carried out following the methods described by Liu et al. (2019). The paired-end reads were filtered with GetOrganelle pipe-line (Jin et al. 2020) to get plastid-like reads using the reference of Th. japonicum (KX871234). The plastid-like reads were assembled by SPAdes version 3.10 (Bankevich et al. 2012) to get the ‘fastg.’ The final ‘fastg’ files were filtered by the script of GetOrganelle to obtain pure plastid contigs, and the De Brujin graphs were viewed and edited by Bandage (Wick et al. 2015). Assembled plastid genome was annotated using the reference of Th. japonicum by GENEIOUS v11.1.5 (Biomatters Ltd., Auckland, New Zealand) (Kearse et al. 2012). According to Zou et al. (2015) and Liu et al. (2020), a matrix of 18 representative species of Aeridinae and three outgroup species (Calanthe triplicata, C. davidii and Cattleya crispata) were aligned using MAFFT v7.307 (Katoh and Standley 2013). The phylogenetic tree was constructed by the maximum likelihood software IQ-TREE (Nguyen et al. 2015) based on the complete plastid genomes, and branch supports with the ultrafast bootstrap (Hoang et al. 2018).

The complete plastid genome sequence of Th. centipeda (GenBank accession MW057769) was 147,888 bp in length, with a large single-copy (LSC) region of 85,899 bp, a small single-copy (SSC) region of 11,055 bp, and a pair of inverted repeats (IR) regions of 25,467 bp. The complete genome GC content was 36.4% (LSC, 33.5%; SSC, 27.2%; IR, 43.2%) and the plastome contained 120 genes, including 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes.

The phylogenetic analysis divided Th. centipeda and 17 Aeridinae plastomes into four groups, and Th. centipeda was sister to Th. tsii with full support (Figure 1). Clade I contained four species of Phalaenopsis. Clade II comprised three species of Thrixspermum and it was sister to clade III plus clade IV. Clade III contained two species of Gastrochilus and Pelatantheria scolopendrifolia. Clade IV contained two species of Vanda and six species of Holcoglossum.

Figure 1.

Figure 1.

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The Maximum-Likelihood (ML) tree based on the plastid genomes of Th. centipeda and the other 17 species of Aeridinae. Numbers near the nodes mean bootstrap support value.

Funding Statement

The present research was financially supported by National Key R&D Program of China [2019YFD1000400].

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The complete plastid genome of Th. centipeda is available in NCBI GenBank database (https://www.ncbi.nlm.nih.gov) with the accession number is MW057769. It is also available at Mendeley Data (http://dx.doi.org/10.17632/wj96wzmsm6.1).

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The complete plastid genome of Th. centipeda is available in NCBI GenBank database (https://www.ncbi.nlm.nih.gov) with the accession number is MW057769. It is also available at Mendeley Data (http://dx.doi.org/10.17632/wj96wzmsm6.1).

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