The complete chloroplast genome sequence of Acer cinnamomifolium (Aceraceae), a plant species endemic to China

Abstract

Acer cinnamomifolium (Aceraceae) is a plant species endemic to China. In our present study, the complete chloroplast (cp) genome sequence of Acer cinnamomifolium was assembled from Illumina pair-end sequencing data. The complete cp genome sequence of A. cinnamomifolium was 156,227 bp in size. Totally, 139 genes were identified, including 88 protein-coding genes, 40 transfer RNAs, 8 ribosomal RNA genes, and 3 pseudogenes (infA, ycf1, and rps2). Phylogenetic analysis results showed that A. cinnamomifolium is sister to Acer sino-oblongum, with a support rate of 100%.

Acer cinnamomifolium is an evergreen tree species endemic to China. It is mainly distributed in Zhejiang, Fujiang, Jiangxi, Hubei, Hunan, Guangdong, and Guangxi province. It features grey to blackish-grey bark, leathery leaves, yellowish-green petals, and brownish-yellow fruit. Acer cinnamomifolium mainly grows in broadleaf forests at altitudes of 300–1200 m and this tree species can be used as a promising ornamental garden plant. The chloroplast (cp) genome of A. cinnamomifolium has not been reported. In this study, we assembled the complete cp genome of A. cinnamomifolium and generated a phylogenetic tree to understand its relationship with other Acer species.

Leaves were collected at an altitude of 811 m in Yandangshan mountain (28°21′47′′N, 121°03′11′′E), Yueqing City, Wenzhou, Zhejiang province, China. The sample was sealed in a plastic bag and taken to the laboratory. The voucher (CHS2017085) is stored at the Molecular Biology Laboratory at Taizhou University. Leaf DNA was extracted following Doyle and Doyle (1987). A 150 bp paired-end DNA library was constructed, and it was sequenced on an Illumina Hiseq X Ten platform (Illumina, San Diego, CA). A total of 7.2 Gb raw reads were obtained, and the clean reads were de novo assembled by NOVOPlasty (Dierckxsens et al. 2017).

The plastome sequence was annotated using Dual Organellar GenoMe Annotator (DOGMA), tRNAscan-SE, and ARAGORN (Lowe and Eddy 1997; Laslett and Canback, 2004; Wyman et al. 2004). The whole length of A. cinnamomifolium cp genome (GenBank accession: MN414240) is 156,227 bp, and its overall GC content is 37.9%. The genome is comprised of two inverted repeats (IRs), a large single copy (LSC), and a small single copy (SSC), and their sizes are 26,079, 85,928, and 18,121 bp, respectively. There are 89 protein-coding genes, 40 tRNAs, 8 rRNAs, and 3 pseudogenes in the plastome genome. Most genes occur as single-copy, while 22 genes contain two copies, these include ndhB, orf42, rpl2, rpl32, rps7, rps12, rrn4.5, rrn5, rrn16, rrn23, trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnM-CAU, trnN-GUU, trnR-ACG, trnT-GGU, trnV-GAC, ycf1, ycf2, and ycf15. Three genes, infA, ycf1, and rps2, are proved to be pseudogenes.

A maximum-likelihood (ML) phylogenetic tree including A. cinnamomifolium and other 12 Acer species was generated using PhyML 3.1 (Guindon et al. 2010), with Dipteronia sinensis (Aceraceae) as the outgroup. The Acer plant species for ML tree construction were Acer laevigatum, Acer palmatum, Acer wilsonii, Acer buergerianum, Acer truncatum, Acer miaotaiense, Acer catalpifolium, Acer davidii, Acer morrisonense, Acer griseum, and Acer sino-oblongum. Our results indicated that A. cinnamomifolium grouped with A. sino-oblongum, and the bootstrap support value was 100%, revealing their close phylogenetic relationship (Figure 1).

Figure 1.

The maximum-likelihood tree generated using the complete chloroplast genome sequences of Acer cinnamomifolium and other 12 Acer plants, with Dipteronia sinensis (Aceraceae) as the outgroup. The numbers next to nodes are bootstrap support values.

Disclosure statement

No potential conflict of interest was reported by the authors.