Abstract
Antirhea chinensis is a plant of the family Rubiaceae. So far, there is no study on the genome of A. chinensis. Here we report and characterize the complete plastid genome sequence of A. chinensis in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 155,616 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat regions of 25,690 bp, a large single copy region of 86,252 bp and a small single copy region of 17,984 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of A. chinensis is 62.40%. The complete plastome sequence of A. chinensis will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Rubiaceae.
Antirhea chinensis (Champ. ex Benth.) Forbes et Hemst. is a plant of the family Rubiaceae. It is a wild shrub and distributed in Guangdong, Hainan and Hongkong, province of China (Chen and Charlotte Citation2011) and tropical Asia, Australia, Madagascar, Mascarene Islands, Pacific islands. A. chinensis is with high medicinal value. The bark of A.chinensis is with the function of bringing down a fever. So far, there have been no studies on the genome of A. chinensis. Consequently, the genetic and genomic information is urgently needed to promote its systematics research and the development of conservation value of A. chinensis. Here, we report and characterize the complete plastid genome sequence of A. chinensis (GenBank accession number: this study) in an effort to provide genomic resources useful for promoting its conservation.
In this study, A. chinensis was sampled from Diaoluo Mountain (18.67°N, 109.88°E), which is a National Nature Reserve of Hainan, China. A voucher specimen (Wang et al. B47) was deposited in the Herbarium of the Institute of Tropical Agriculture and Forestry (HUTB), Hainan University, Haikou, China.
The experiment procedure is as reported in Zhu et al. (Citation2018). Around 6 Gb clean data were assembled against the plastome of Mitragyna speciosa (NC_034698.1) (Zhang and Handy Citation2016) using MITO bim v1.8 (Hahn et al. Citation2013). The plastome was annotated using Geneious R8.0.2 (Biomatters Ltd., Auckland, New Zealand) against the plastome of M. speciosa (NC_034698.1). The annotation was corrected with DOGMA (Wyman et al. Citation2004).
The plastome of A. chinensis was found to possess a total length 155,616 bp with the typical quadripartite structure of angiosperms, containing two inverted repeats (IRs) of 25,690 bp, a large single copy (LSC) region of 86,252 bp, and a small single copy (SSC) region of 17,984 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. The overall A/T content in the plastome of A. chinensis is 62.40%, which the corresponding value of the LSC, SSC, and IR region were 64.50%, 68.60%, and 56.80%, respectively.
We used RAxML (Stamatakis Citation2006) with 1000 bootstraps under the GTRGAMMAI substitution model to reconstruct a maximum likelihood (ML) phylogeny of 8 published complete plastomes of Rubiaceae, using Gentiana officinalis (Rubiales, Gentianable) as an outgroup. The phylogenetic analysis indicated that A. chinensis is closer to M. speciosa (). Most nodes in the plastome ML trees were strongly supported. The complete plastome sequence of A. chinensis will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Rubiaceae.
Figure 1. The best ML phylogeny recovered from 10 complete plastome sequences by RAxML. Accession numbers: Antirhea chinensis (this study), Emmenopterys henryi NC_036300.1, Galium mollugo NC_036970.1, Mitragyna speciosa NC_034698.1, Gynochthodes nanlingensis NC_028614.1, Morinda officinalis NC_028009.1, Coffea arabica NC_008535.1, Galium aparine NC_036969.1, Coffea canephora NC_030053.1, outgroup: Gentiana officinalis MH261261.1.
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References
- Chen T, Charlotte MT. 2011. Flora of China. Vol. 19. Beijing: Science Press; p. 74–75.
- Hahn C, Bachmann L, Chevreux B. 2013. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads-a baiting and iterative mapping approach. Nucleic Acids Res. 41:e129
- Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22:2688–2690.
- Wyman SK, Jansen RK, Boore JL. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 20:3252–3255.
- Zhang N, Handy SM. 2016 (Submitted). College Park (MD): Center of Food Safety and Nutrition, Food and Drug Adminstration.
- Zhu ZX, Mu WX, Wang JH, Zhang JR, Zhao KK, Friedman CR, Wang HF. 2018. Complete plastome sequence of Dracaena cambodiana (Asparagaceae): a species considered “Vulnerable” in Southeast Asia. Mitochondrial DNA B Resour. 3:620–621.