The complete chloroplast genome of Wurfbainia neoaurantiaca (Zingiberaceae: Zingiberea) from Yunnan Province, China

Abstract Wurfbainia neoaurantiaca is a medicinal plant endemic to Yunnan Province, China. In this study, its complete chloroplast genome was assembled and characterized. The total genome size of W. neoaurantiaca was 158,484 bp in length, consisting of a large single-copy region (LSC), a small single-copy region (SSC) and two inverted repeat regions (IRs) with 88,605 bp, 15,285 bp and 29,822 bp, respectively. Its GC content was 36.08%. The chloroplast genome encoded 113 unique genes, including 79 protein-coding, 30 tRNA, and four rRNA genes. The result of the phylogenetic analysis indicated that W. neoaurantiaca was related to W. villosa var. xanthioides and supported de Boer’s classification that W. compacta, W. longiligularis, W. neoaurantiaca, W. villosa, W. villosa var. xanthioides and Amomum krervanh belonged to the Wurfbainia Clade.

Wurfbainia neoaurantiaca (former Latin names: Amomum aurantiacum H. T. Tsai & S. W. Zhao, 1979, Amomum neoaurantiacum T. L. Wu, K. Larsen & N. J. Turland, 2000) is a perennial medicinal herb classified in the family Zingiberaceae, which is endemic to the Yunnan Province of China (de Boer et al. 2018;Wu and Turland 2001). Its fruits are used as herbal medicine and have been used to treat gastrointestinal diseases (Ma et al. 2018). It is difficult to distinguish W. neoaurantiaca from its related species such as Wurfbainia. villosa, W. villosa var. xanthioides and W. longiligularis due to their similar morphological characters. In recent years, the chloroplast genome as a superbarcode has been shown to be an efficient method to distinguish species (Abdullah et al. 2019;Liang et al. 2019), and phylogenetic analysis of chloroplast genomes has been successfully used to identify Wurfbainia species . In this study, the chloroplast genome of W. neoaurantiaca was assembled, annotated, characterized, and a phylogenetic analysis was performed to investigate its evolutionary relationship with other Wurfbainia species and confirm its phylogenetic position in the family location.
The plants of W. neoaurantiaca were collected from Jinghong (100 52 0 44ʺE; 21 48 0 56ʺN), Yunnan Province, China. Voucher specimen (Y20180726015) and its DNA (DNA-Y20180726015) were deposited in the Herbaria and Medicinal Plant Cultivation Research Center of Yunnan Branch Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, respectively (www.yn-implad.ac.cn, contacts: Dr. Haitao Li, email contact: lhtxyl@126.com). The genomic DNA was extracted from the leaves using the DNeasy Plant Mini Kit (Qiagen, Dusseldorf, Germany). The quality of the DNA was assessed using a Nanodrop One C spectrophotometer (Thermo Scientific, Madison, USA) and determined by 1.5% agarose gel electrophoresis.
A paired-end library of 350 bp was constructed and sequenced on the NovaSeq system (Illumina, San Diego, USA). A total of 8.5 Gb reads were generated and used to assemble the chloroplast genome using the default settings in NOVOplasty 4.0 (Dierckxsens et al. 2017). Annotation of the chloroplast genome was executed using GeSeq (Tillich et al. 2017) and corrected manually.
The chloroplast genome sequences of 23 species (including W. neoaurantiaca) from Zingiberaceae and three outgroup taxa from the Musaceae were aligned with MAFFT 7.307 (Katoh and Standley 2013). A phylogenetic tree was constructed using RAxML 8.2.12 (Stamatakis 2014) with 1000 Bootstrap replicates and using the GTR þ FþR2 model according to ModelFinder (Kalyaanamoorthy et al. 2017

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

Data availability
The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under the accession no. MW145134. The associated BioProject, Bio-Sample and SRA numbers are PRJNA699991, SAMN17817191 and SRP304958, respectively.