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Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Sinojackia Sarcocarpa, an Endemic Plant in Southwest China

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Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Sinojackia Sarcocarpa, an Endemic Plant in Southwest China Mitochondrial DNA Part B Resources ISSN: (Print) 2380-2359 (Online) Journal homepage: https://www.tandfonline.com/loi/tmdn20 Complete chloroplast genome sequence and phylogenetic analysis of Sinojackia sarcocarpa, an endemic plant in Southwest China Jing Fan, Qin-Chao Fu & Zi Liang To cite this article: Jing Fan, Qin-Chao Fu & Zi Liang (2019) Complete chloroplast genome sequence and phylogenetic analysis of Sinojackiasarcocarpa, an endemic plant in Southwest China, Mitochondrial DNA Part B, 4:1, 1350-1351, DOI: 10.1080/23802359.2019.1597652 To link to this article: https://doi.org/10.1080/23802359.2019.1597652 © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. Published online: 02 Apr 2019. Submit your article to this journal View Crossmark data Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=tmdn20 MITOCHONDRIAL DNA PART B 2019, VOL. 4, NO. 1, 1350–1351 https://doi.org/10.1080/23802359.2019.1597652 MITOGENOME ANNOUNCEMENT Complete chloroplast genome sequence and phylogenetic analysis of Sinojackia sarcocarpa, an endemic plant in Southwest China Jing Fan, Qin-Chao Fu and Zi Liang College of Life Sciences, Leshan Normal University, Leshan, PR China ABSTRACT ARTICLE HISTORY Sinojackia sarcocarpa is an endangered plant endemic to China. Here, the complete chloroplast gen- Received 13 February 2019 ome of S. sarcocarpa was sequenced and characterized. The total genome size is 158,737 bp, with a Accepted 13 March 2019 typical quadripartite structure including a pair of inverted repeat regions (IRs, 26,090 bp) separated by KEYWORDS a large single copy (LSC, 88,002 bp) region and a small single copy (SSC, 18,555 bp) region. The gen- Sinojackia sarcocarpa; ome contains 137 genes, including 90 protein-coding genes, 38 transfer RNA genes, and 8 ribosomal S. sarcocarpa Sinojackia xylocarpa chloroplast genome; RNA genes. Phylogenetic analysis revealed that is closely related to styracaceae; illu- and Sinojackia rehderiana, but forms an independent evolutionary branch. mina sequencing Sinojackia sarcocarpa is a Styracaceae plant endemic to fresh leaves using SDS method. The complete chloroplast Sichuan province, China (Luo 1992). Sinojackia sarcocarpa has genome of S. sarcocarpa was sequenced by Illumina HiSeq good ornamental value and can be used as a garden tree Xten platform, the Illumina raw sequence reads were edited species. In addition, it contains effective anticancer com- by the NGS QC tool Kit v2.3.3, the percentage of cut-off val- pounds and can be used as an important plant source for ues for read length and phred quality score were 80 and 30, the extraction of drug active substances (Wang et al. 2011). respectively (Patel and Jain 2012). 20 (Bankevich et al. 2012). However, the number of existing wild individuals is very Annotations were performed with the plann software (Huang small, S. sarcocarpa is, therefore, under state protection (cat- and Cronk 2015). The complete chloroplast genome of S. sar- egory II) in China. A good knowledge of its phylogeny and cocarpa (GenBank accession number MK351986) is taxonomy is necessary for the protection and utilization of S. 158,737 bp in length, which has a GC content of 37.24%, sarcocarpa. Molecular systematics has become an important including a large single-copy area (LSC, 88,002 bp) and a method of taxonomic research. In the past, system evolution small single-copy area (SSC, 18,555 bp), as well as two reverse was usually inferred by selecting individual or several genes, repetition zones (IRs) of 26,090 bp. The complete chloroplast however, single-gene data lacks sufficient genetic information genome encodes 137 genes, including 90 protein-coding when compared to the multi-gene data (Thorne and Kishino genes, 8 ribosomal RNA genes, and 38 transfer RNA genes, 2002). The chloroplast genome structure is conservative, 15 genes contain an intron, 2 genes contain two introns, and rarely recombinant, and mutated, and is uniparental inherit- 1 rps12 gene has trans splicing. ance in most cases, so it is of great practical value to study To ascertain the phylogenetic evolution of S. sarcocarpa, the evolution of plant system (He et al. 2019). However, at the fasta format file containing all the chloroplast genome present, no complete chloroplast genome sequence of S. sar- sequences of 24 plants was treated by MAFFT 7.037 software cocarpa is available in the NCBI GenBank. This work is the and then aligned in automatic mode (Katoh and Standley first to report on the chloroplast genome sequence of S. sar- 2013). The neighbour-joining (NJ) phylogenetic tree was con- cocarpa, which can better understand the genetic back- structed by MEGA 6.0 software (Tamura et al. 2013), the par- ground of S. sarcocarpa and contribute to the conservation ameter settings were as follows: the stability of branches was of the species. evaluated with 1,000 bootstrap replications, nucleotide sub- The samples of S. sarcocarpa were collected from botan- stitution model was computed using the p-distance method, ical garden in Leshan, Sichuan Province, China and the speci- the substitution included a variety of transitions and transver- mens were stored in the herbarium of Leshan normal sions, and the gaps/missing data treatments were set to university. Total genomic DNA was extracted from 50 mg complete deletion. The results of phylogenetic analysis show CONTACT Jing Fan [email protected] College of Life Sciences, Leshan normal University, No778 Binhe Road, Shizhong District, Leshan, 614004, Sichuan province, PR China ß 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MITOCHONDRIAL DNA PART B 1351 Figure 1. The NJ phylogeny constructed from 24 complete plastome sequences using MEGA6.0 software. Note: Numbers near each node represent the percentage of support when the nodes occurred among 1000 bootstraps. that S. sarcocarpa forms a separate branch when compared new genome assembly algorithm and its applications to single-cell with other plants in this study, which is more closely related sequencing. J Comput Biol. 19:455–477. Sinojackia He P, Ma Q, Dong M, Yang Z, Liu L. 2019. The complete chloroplast gen- to two other species (Figure 1). The complete plas- Berberidaceae S. sarcocarpa ome of Leontice incerta and phylogeny of . tome sequence of provides an important data Mitochondrial DNA B. 4:101–102. set for the conservation genetics of this species. Huang DI, Cronk QC. 2015. Plann: a command-line application for anno- tating plastome sequences. Appl Plant Sci. 3:1500026. Katoh K, Standley DM. 2013. MAFFT Multiple sequence alignment soft- Disclosure statement ware version 7: improvements in performance and usability. Mol Biol Evol. 30:772–780. The authors confirm this article content has no conflict of interest and Luo LQ. 1992. A new species of Sinojackia from Sichuan. Acta Sci Nat all the authors are responsible for the content of this article. Univ Sunyatseni. 31:78–79. Patel RK, Jain M. 2012. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 7:e30619. Funding Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: This work was supported by Leshan Normal University under Grant molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 30: – JG2018-1-ZF-21. 2725 2729. Thorne JL, Kishino H. 2002. Divergence time and evolutionary rate esti- mation with multilocus data. Syst Biol. 51:689–702. References Wang O, Liu S, Zou J, Lu L, Chen L, Qiu S, Li H, Lu X. 2011. Anticancer activity of 2a,3a,19b,23b-tetrahydroxyurs-12-en-28-oic acid (THA), a Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, novel triterpenoid isolated from Sinojackia sarcocarpa. PLoS One. 6: Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. 2012. SPAdes: a e21130..
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