Abstract
The complete chloroplast (cp) genome sequence of Actinidia callosa var. henryi was assembled and characterize by Illumina paired-end data in this study. The assembled plastome was 156,826 bp in length, containing a large single copy region (LSC) of 88,604 bp and a small single copy region (SSC) of 22,510 bp, which was separated by a pair of 23,866 bp inverted repeat regions (IR). The genome possessed 127 genes, including 82 protein-coding genes, 37 tRNA genes, 8 ribosomal RNA genes. The phylogenetic position based on the chloroplast genome showed that Actinidia callosa var. henryi was sister to the group A. eriantha, A. deliciosa, and A. chinensis.
The species Actinidia callosa var. henryi (ACH) is an attractive special folk medicinal plant in southern China, which has been widely used as antipyretic and analgesic to treat abdominal pain, anti-inflammatory and remove dampness (Liao et al. Citation2012). Berries of ACH are also tasted and rich in vitamins P and C, trace elements and a variety of amino acids and enzymes. Furthermore, ACH berries have a smooth pericarp with obvious light brown dots, therefore, it can be eaten as a whole, just like hardy kiwi. ACH is thought to be a promising crop plant and essential genetic resources in Actinidia species. In this study, we reported the complete chloroplast genome of ACH based on the next generation sequencing data and uncovered its phylogenetic relationship with 8 Actinidiaceae species, of which complete chloroplast genomes are available.
The voucher specimen of ACH was stored at Shanghai Chen Shan botanical Herbarium (CSH). Fresh leaves of ACH were collected from Shifang, Sichuan, China (31°13′45″ N, 104°0′55″ E). We isolated the total genomic DNA from fresh leaves using a modified CTAB method (Doyle and Doyle Citation1987) and sequenced it based on the Illumina pair-end technology. Then, we used the program NOVO-Plasty to assemble the filtered reads (Dierckxsens et al. Citation2017) and used the sequenced cp genome of its close relative A. eriantha as the reference. The assembled cp genome was annotated using program Plann (Huang and Cronk Citation2015). The annotation was corrected by using Geneious (Kearse et al. Citation2012). The new annotated complete chloroplast genome was submitted to GenBank under the accession number of MK088177.
The complete cp genome of ACH is 156,826 base pairs (bp) in length. The genome exhibits a typical quadripartite structure, with a large single-copy region (LSC) of 88,604 bp, a small single-copy region (SSC) of 22,510 bp, and two inverted repeat regions (IR) (IRa and IRb, 23,866 bp). In addition, the plastome possesses 127 genes in total, including 82 protein-coding genes, 8 rRNA genes, and 37 distinct tRNA genes. Most of these genes are in a single copy, however, 4 rRNA genes (i.e. 4.5S, 5S, 16S and 23S rRNA), 5 protein-coding genes, and 8 tRNA genes occur in double copies. The overall GC-content of the whole plastome is 37.9%.
The phylogenetic position of ACH was determined using a neighbour-joining (NJ) tree (Saitou and Nei Citation1987) which was constructed based on complete cp genome sequences of 9 Actinidiaceae plants using MEGA7 software with 1000 bootstrap replicates (Kumar et al. Citation2016). Here, all cp genome sequences were first aligned using MAFFT (Katoh and Standley Citation2013). Our results showed that ACH was closely related to the species of A. eriantha and is sister to the group A. eriantha, A. deliciosa, and A. chinensis ().
Figure 1. The phylogenetic tree based on the 9 complete chloroplast genome sequences. Accession numbers: Actinidia chinensis (NC026690), A. deliciosa (NC026691), A. eriantha (NC034914), A. tetramera (NC031187), A. arguta (NC034913), A. polygama (NC031186), A. kolomikta (NC034915), Clematoclethra scandens subsp. Hemsleyi (KX345299).
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The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article.
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References
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