Abstract
The complete chloroplast genome sequences of Artocarpus hypargyreus was reported in this study. The length of the sequence was 160,952 bp in length with a large single copy (LSC) region of 89,476 bp, the small single copy (SSC) region of 20,070 bp and two inverted repeat (IR) regions of 25,703 bp. The complete genome contains 129 genes including 84 protein-coding genes, 8 rRNA genes and 37 tRNA genes. Phylogenetic analysis of the Moraceae based on 8 plastome sequence shows that A. hypargyreus is most related to Morus cathayana.
Keywords: Artocarpus hypargyreus, Moraceae, chloroplast genome, phylogenomic tree
Artocarpus hypargyreus Hance is an endangered species, which belongs to the genus Artocarpus in the family Moraceae (Fu 1992). It is endemic to China, and only scattered in evergreen broad-leaved forests in Guangdong, Fujian, Jiangxi, Hunan, and Yunnan (Li et al. 2011). A. hypargyreus has high economic value and is widely used in our life. Its wood can be used as furniture; its fruits and seeds can be eaten raw, or be used as raw materials for candied fruit or beverages (Shen 2011). The roots of A. hypargyreus are widely used in northern Guangdong and western Yunnan for the treatment of rheumatoid arthritis and chronic back pain (Ouyang et al. 2010). In recent years, research on A. hypargyreus has focused on the chemical composition (He et al. 2016), screening and mechanism of effective medicinal parts (Shen et al. 2011), community structure (Tan et al. 2017), breeding technology (Li et al. 2010) and genetic diversity (Fan 2010). In this study, we reported and characterized the complete chloroplast genome sequence of A. hypargyreus to contribute to further phylogenetical and protective studies of this plant.
The fresh leaves of Artocarpus hypargyreus was collected from Xiafu village (:25°0′33″N, 113°42′06″E, Altitude: 106 m) in Shaoguan, Guangdong, China. And the Voucher specimens were deposited in the Herbarium of Shaoguan university, the accession number is Li-201904. Total DNA was extracted from the fresh young leaves using the Plants Genomic DNA Kit (DP305, Tiangen Biotech Co., Ltd., Beijing, China). The plastome sequences was generated using Illumina HiSeq 2500 platform (Illumina Lnc., San Diego, CA, USA). In total, 5.5 Gb raw reads were obtained. The filtered reads were assembled with the program NOVOPlasty 3.1 (Dierckxsens et al. 2017) with a part of rbcL gene of Antiaris toxicaria (NC 042884), and then the sequence of A. hypargyreus was annotated using DOGMA (Wyman et al. 2004). The annotated sequence was submitted to NCBI, the accession number is MN720648.
The complete chloroplast genome of A. hypargyreus is 160,952 bp in length, including a large single-copy (LSC) region of 89,476 bp, the small single copy region of 20,070 bp, and two inverted repeat (IR) regions of 25703 bp. The complete genome of A. hypargyreus contains 129 genes, including 84 protein-coding genes, 8 rRNA genes and 37 tRNA genes, the GC content of this genome was 35.80%.To further investigate the phylogenetic position of A. hypargyreus in Moraceae family, 8 of complete chloroplast genomes in family was download from NCBI, and then the maximum-likelihood (ML) phylogenetic tree was generated by MEGA 7.0 (Kumar et al. 2016), with Antiaris toxicaria as outgroup. The results in Figure 1 shows that A. hypargyreus is closed to Morus cathayana. Our study here could be further applied for the evolutionary and phylogenetic studies of this endangered plant.
Figure 1.
Maximum likelihood tree based on the sequences of eight complete chloroplast genomes. Numbers in the nodes were bootstrap values from 1000 replicates. Scale in substitutions per site.
Funding Statement
This study was supported by the National Science Foundation of Hainan Province [319QN214] and PhD research startup foundation of Shaoguan University [99000612].
Disclosure statement
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
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