Comparative chloroplast genomics of the important resource plant Kadsura coccinea

ZHAI Xuechang, PENG Li, YAN Haifei, ZHU Kefan, ZHANG Shuyan, ZHANG Caiyun, LU Xiankai

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2024, Vol. 48 ›› Issue (6) : 71-78.

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南京林业大学学报（自然科学版）
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JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2024, Vol. 48 ›› Issue (6) : 71-78. DOI: 10.12302/j.issn.1000-2006.202404014

Comparative chloroplast genomics of the important resource plant Kadsura coccinea

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Abstract

【Objective】This study aims to investigate the chloroplast genomes and SSR loci of Kadsura coccinea, an important plant resource in China, to establish a basis for assessing its genetic diversity and germplasm resources.【Method】The study obtained and analyzed the chloroplast genomes of five individuals of K. coccinea through genetical annotation, nucleotide polymorphism analysis, and SSR analysis using bioinformatics methods. Additionally, the phylogenetic analysis of Kadsura were reconstructed using two Schisandra spp. as outgroups.【Result】The chloroplast genome of K. coccinea showed a typical quadripartite structure, with genome lengths ranging from 145 413 to 145 903 base pairs (bp). The large single-copy region (LSC) spaned from 94 457 to 94 757 bp, while the small single-copy region (SSC) encompassed 18 032 to 18 047 bp. It encodes a total of 125 genes, including 82 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. The genome had a total GC content of 39.7% and demonstrated substantial nucleotide polymorphisms (Pi > 0.03) in the intergenic regions of petN-psbM and trnS-GCU-trnG-UCC. A total of 212 single sequence repeat (SSR) loci were identified across the chloroplast genomes of this species. Mononucleotide repeats were the most prevalent, followed by trinucleotide repeats, and pentanucleotide repeats were the least frequent. Among these loci, 24 polymorphic SSR loci were found among five individuals of K. coccinea, indicating their potential utility in future. Phylogenetic analysis robustly clusters K. coccinea individuals into a distinct group, revealing no close relationship with other congeneric species.【Conclusion】This study presents the first systematic comparison of chloroplast genomes among multiple K. coccinea individuals. Our findings identified highly variable regions and SSR loci that can be valuable for evaluating the genetic diversity and germplasm resource of this species.

Key words

Kadsura coccinea / plastid genome / genetic diversity / SSR loci / phylogeny

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ZHAI Xuechang , PENG Li , YAN Haifei , et al . Comparative chloroplast genomics of the important resource plant Kadsura coccinea[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2024, 48(6): 71-78 https://doi.org/10.12302/j.issn.1000-2006.202404014

References

List( Publishing order | Descend order by publishing year | Descend order by cited within ) Chart analysis
[1]
XIA N H, LIU Y H, SOUNDERS R M K. Schisandraceae[C]// WU Z Y, RAVEN P H, HONG D Y. Floral of China. Beijing: Science Press, 2008: 39-47.
Cited in this article [4]
[2]
林祁, 段林东, 姚炳矾. 南五味子属(五味子科)三种植物之补记[J]. 植物分类学报, 2005, 43(6):567-570.
LIN Q, DUAN L D, YAO B F. Notes on three species of the genus Kadsura Juss.(Schisandraceae)[J]. Acta Phytotaxon Sin, 2005, 43(6):567-570.
Cited in this article [1]
[3]
黄珊珊, 黄晓玲, 宋卉, 等. 中药黑老虎的研究进展[J]. 海峡药学, 2021, 33(11):38-40.
HUANG S S, HUANG X L, SONG H, et al. Advances in traditional Chinese medicine Kadsura coccinea[J]. Strait Pharm J, 2021, 33(11):38-40.DOI: 10.3969/j.issn.1006-3765.2021.11.012.
Cited in this article [1]
[4]
苏维, 王欣悦, 付港, 等. 南五味子属植物的化学成分、药理作用及临床应用研究进展[J]. 中国中药杂志, 2024, 49(1):26-38.
SU W, WANG X Y, FU G, et al. Research progress on chemical constituents from Kadsura genus and its pharmacological activities and clinical application[J]. China J Chin Mater Med, 2024, 49(1):26-38.DOI: 10.19540/j.cnki.cjcmm.20230718.201.
Cited in this article [1]
[5]
杨赛男, 戴斌, 潘清平, 等. 黑老虎植物资源利用研究进展[J]. 湖南生态科学学报, 2022, 9(3):112-120.
YANG S N, DAI B, PAN Q P, et al. Research progress on the application value and comprehensive utilization of Kadsura coccinea resources[J]. J Hunan Ecol Sci, 2022, 9(3):112-120.DOI: 10.3969/j.issn.2095-7300.2022.03.015.
Cited in this article [1]
[6]
杨芝干. 地标奇果:通道“黑老虎”[J]. 生命世界, 2019(9):66-69.
YANG Z G. Landmark fruit-tongdao “Black Tiger”[J]. Life World, 2019(9):66-69.
Cited in this article [1]
[7]
林旭俊, 陆文, 李善志, 等. 药用植物黑老虎的资源调查[J]. 热带林业, 2019, 47(2):34-36.
LIN X J, LU W, LI S Z, et al. Investigation on the resources of medicinal plant Kadsura coccinea[J]. Trop For, 2019, 47(2):34-36.DOI: 10.3969/j.issn.1672-0938.2019.02.009.
Cited in this article [1]
[8]
韦霄, 梁惠凌, 唐辉, 等. 广西南五味子属植物的分布与利用[J]. 广西农业科学, 2006, 37(2):117-119.
WEI X, LIANG H L, TANG H, et al. Distribution and utilization of Kadsura in Guangxi[J]. Guangxi Agric Sci, 2006, 37(2):117-119.DOI: 10.3969/j.issn.2095-1191.2006.02.006.
Cited in this article [1]
[9]
邹建文, 罗先权, 饶红欣, 等. 常绿木质藤本植物黑老虎基因组SSR特征分析及引物开发[J]. 中南林业科技大学学报, 2021, 41(4):130-138.
ZOU J W, LUO X Q, RAO H X, et al. Characters of genomic SSRs and development of 28 SSR markers for Kadsura coccinea,an evergreen woody vine[J]. J Cent South Univ For Technol, 2021, 41(4):130-138.DOI: 10.14067/j.cnki.1673-923x.2021.04.015.
Cited in this article [1]
[10]
ZOU J W, HE R H, RAO H X, et al. Genetic diversity and population genetic structure in Kadsura coccinea (Schisandraceae),an evergreen woody vine from Hunan,China[J]. J For Res, 2023, 28(5):364-373.DOI: 10.1080/13416979.2023.2220192.
Cited in this article [1]
[11]
DONG Y Q, WEI X P, QIANG T Y, et al. RAD-Seq and ecological niche reveal genetic diversity,phylogeny,and geographic distribution of Kadsura interior and its closely related species[J]. Front Plant Sci, 2022,13:857016.DOI: 10.3389/fpls.2022.857016.
Cited in this article [1]
[12]
赵儒楠, 褚晓洁, 刘维, 等. 鹅耳枥属树种叶绿体基因组结构及变异分析[J]. 南京林业大学学报(自然科学版), 2021, 45(2):25-34.
ZHAO R N, CHU X J, LIU W, et al. Structure and variation analyses of chloroplast genomes in Carpinus[J]. J Nanjing For Univ (Nat Sci Ed), 2021, 45(2):25-34.DOI: 10.12302/j.issn.1000-2006.202009007.
Cited in this article [1]
[13]
袁钰晨, 谢旭强, 徐立清, 等. 不同年龄阶段胡桃楸天然更新幼树的光合生理特性[J]. 森林工程, 2023, 39(4):29-37.
YUAN Y C, XIE X Q, XU L Q, et al. Photosynthetic physiological characteristics of naturally regenerated Juglans mandshurica saplings at different ages[J]. For Eng, 2023, 39(4):29-37.
Cited in this article [1]
[14]
WANG J, KAN S L, LIAO X Z, et al. Plant organellar genomes:much done,much more to do[J]. Trends Plant Sci, 2024, 29(7):754-769.DOI: 10.1016/j.tplants.2023.12.014.
Cited in this article [1]
[15]
邓叶, 李翔, 李平, 等. 黑老虎种质资源与分子生物学研究进展[J]. 湖南生态科学学报, 2024, 11(1):96-104.
DENG Y, LI X, LI P, et al. Research progress on germplasm resources and molecular biology of Kadsura coccinea[J]. J Hunan Ecol Sci, 2024, 11(1):96-104.DOI: 10.3969/j.issn.2095-7300.2024.01.012.
Cited in this article [3]
[16]
LIU L Y, FU Y P, LI Y Q, et al. The complete chloroplast genome sequence of Kadsura ananosma[J]. Mitochondrial DNA B Resour, 2020, 5(1):768-769.DOI: 10.1080/23802359.2020.1715866.
Cited in this article [3]
[17]
QIN H Z, DENG L L, SHI Y C. Complete chloroplast genome of Kadsura coccinea (Lem.) A.C.Sm.(Schisandraceae):genome structure and evolution[J]. Mitochondrial DNA B Resour, 2021, 6(3):1222-1223.DOI: 10.1080/23802359.2021.1904798.
Cited in this article [3]
[18]
YANG J, WANG X A, GAO M Y, et al. The complete chloroplast genome of ‘black tiger 2’ (Kadsura coccinea (Lem.) A.C.Smith) in southeast of China and phylogenetic relationships[J]. Mitochondrial DNA B Resour, 2019, 5(1):296-297.DOI: 10.1080/23802359.2019.1698328.
Cited in this article [3]
[19]
DOYLE J J, DOYLE J L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue[J]. Phytochem Bull, 1987, 19:11-15
Cited in this article [1]
[20]
WANG Q H, WANG H, FU Y P, et al. The complete chloroplast genome sequence of Kadsura heteroclita[J]. Mitochondrial DNA B Resour, 2020, 5(3):2197-2198.DOI: 10.1080/23802359.2020.1768963.
Cited in this article [2]
[21]
FU Y P, LI Y Q, CHEN W, et al. The complete chloroplast genome sequence of Kadsura interior[J]. Mitochondrial DNA B Resour, 2020, 5(1):515-516.DOI: 10.1080/23802359.2019.1710297.
Cited in this article [2]
[22]
JIN L, LIU J J, XIAO T W, et al. Plastome-based phylogeny improves community phylogenetics of subtropical forests in China[J]. Mol Ecol Resour, 2022, 22(1):319-333.DOI: 10.1111/1755-0998.13462.
Cited in this article [2]
[23]
WEI X P, LI H J, CHE P, et al. Comparing chloroplast genomes of traditional Chinese herbs Schisandra sphenanthera and S.chinensis[J]. Chin Herb Med, 2020, 12(3):247-256.DOI: 10.1016/j.chmed.2019.09.009.
Cited in this article [2]
[24]
GUO H J, LIU J S, LUO L, et al. Complete chloroplast genome sequences of Schisandra chinensis:genome structure,comparative analysis,and phylogenetic relationship of basal angiosperms[J]. Sci China Life Sci, 2017, 60(11):1286-1290.DOI: 10.1007/s11427-017-9098-5.
Cited in this article [2]
[25]
JIN J J, YU W B, YANG J B, et al. GetOrganelle:a fast and versatile toolkit for accurate de novo assembly of organelle genomes[J]. Genome Biol, 2020, 21(1):241.DOI: 10.1186/s13059-020-02154-5.
Cited in this article [1]
[26]
TILLICH M, LEHWARK P, PELLIZZER T, et al. GeSeq-versatile and accurate annotation of organelle genomes[J]. Nucleic Acids Res, 2017, 45(W1):W6-W11.DOI: 10.1093/nar/gkx391.
Cited in this article [1]
[27]
KEARSE M, MOIR R, WILSON A, et al. Geneious basic:an integrated and extendable desktop software platform for the organization and analysis of sequence data[J]. Bioinformatics, 2012, 28(12):1647-1649.DOI: 10.1093/bioinformatics/bts199.
Cited in this article [1]
[28]
LOHSE M, DRECHSEL O, BOCK R. OrganellarGenomeDRAW (OGDRAW):a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes[J]. Curr Genet, 2007, 52(5/6):267-274.DOI: 10.1007/s00294-007-0161-y.
Cited in this article [1]
[29]
KATOH K, STANDLEY D M. MAFFT multiple sequence alignment software version 7:improvements in performance and usability[J]. Mol Biol Evol, 2013, 30(4):772-780.DOI: 10.1093/molbev/mst010.
Cited in this article [2]
[30]
ROZAS J, FERRER-MATA A, SÁNCHEZ-DELBARRIO J C, et al. DnaSP 6:DNA sequence polymorphism analysis of large data sets[J]. Mol Biol Evol, 2017, 34(12):3299-3302.DOI: 10.1093/molbev/msx248.
Cited in this article [2]
[31]
BEIER S, THIEL T, MÜNCH T, et al. MISA-web:a web server for microsatellite prediction[J]. Bioinformatics, 2017, 33(16):2583-2585.DOI: 10.1093/bioinformatics/btx198.
Cited in this article [1]
[32]
STAMATAKIS A. RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies[J]. Bioinformatics, 2014, 30(9):1312-1313.DOI: 10.1093/bioinformatics/btu033.
Cited in this article [1]
[33]
GOULD S B, WALLER R R, MCFADDEN G I. Plastid evolution[J]. Annu Rev Plant Biol, 2008, 59: 491-517. DOI:10.1146/annurev.arplant.59.032607.092915
Cited in this article [1]
[34]
杨圆圆, 于世河, 卜鹏图, 等. 不同培育模式下日本落叶松林灌草和土壤养分特征研究[J]. 森林工程, 2023, 39(6):12-25.
YANG Y Y, YU S H, BU P T, et al. Study on shrub-grass and soil nutrient characteristics of Larix kaempferi forest under different cultivation modes[J]. For Eng, 2023, 39(6):12-25.
Cited in this article [1]
[35]
JANSEN R K, RUHLMAN T A. Plastid genomes of seed plants[M]//BOCK R, KNOOP V. Advances in Photosynthesis and Respiration. Dordrecht: Springer Netherlands,2012:103-126.DOI: 10.1007/978-94-007-2920-9_5.
Cited in this article [1]
[36]
SAUNDERS R M. Monograph of Kadsura (Schisandraceae)[C]// ANDERSON C. Systematic Botany Monographs. St. Louis: Missouri Botanical Garden Press, 1998.
Cited in this article [4]
[37]
刘玉壶. 木兰科[C]//中国科学院中国植物志编辑委员会. 中国植物志. 北京: 科学出版社, 1996.
LIU Y H. Magnoliaceae[C]//The Agenda of the Chinese Academy. Flora Reipublicae Popularis Sinicae. Beijing: Science Press,1996
Cited in this article [1]
[38]
SMITH A C. The families Illiciaceae and Schisandraceae[J]. Sargentia, 1947, 7:1-224.DOI: 10.5962/p.265318.
Cited in this article [1]
[39]
毕海燕, 林祁, 刘长江, 等. 南五味子属(五味子科)的种子形态及其分类学意义[J]. 植物分类学报, 2002, 40(6):501-510.
BI H Y, LIN Q, LIU C J, et al. Seed morphology of Kadsura Juss.(Schisandraceae) in relation to its taxonomic significance[J]. Acta Phytotaxon Sin, 2002, 40(6):501-510.
Cited in this article [1]
[40]
LIU Z, HAO G, LUO Y B, et al. Phylogeny and androecial evolution in Schisandraceae,inferred from sequences of nuclear ribosomal DNA ITS and chloroplast DNA trnL-F regions[J]. Int J Plant Sci, 2006, 167(3):539-550.DOI: 10.1086/501476.
Cited in this article [1]
[41]
GUO H J, LI X W, QI Y D, et al. Identification of Dian Ji Xue Teng (Kadsura interior) with DNA barcodes[J]. World J Tradit Chin Med, 2017, 3(1):11-15.DOI: 10.15806/j.issn.2311-8571.2016.0017.
Cited in this article [1]
[42]
HAO G, CHYE M L, SAUNDERS R M K. A phylogenetic analysis of the Schisandraceae based on morphology and nuclear ribosomal ITS sequences[J]. Bot J Linn Soc, 2001, 135(4):401-411.DOI: 10.1006/bojl.2000.0420.
Cited in this article [1]
[43]
CHASE M W, SOLTIS D E, OLMSTEAD R G, et al. Phylogenetics of seed plants:an analysis of nucleotide sequences from the plastid gene rbcL[J]. Ann Mo Bot Gard, 1993, 80(3):528-580.DOI: 10.2307/2399846.
Cited in this article [1]
[44]
QIU Y L, LEE J, BERNASCONI-QUADRONI F, et al. The earliest angiosperms:evidence from mitochondrial,plastid and nuclear genomes[J]. Nature, 1999, 402(6760):404-407.DOI: 10.1038/46536.
Cited in this article [1]
[45]
SOLTIS D E, SOLTIS P S, CHASE M W, et al. Angiosperm phylogeny inferred from 18S rDNA,rbcL,and atpB sequences[J]. Bot J Linn Soc, 2000, 133(4):381-461.DOI: 10.1111/j.1095-8339.2000.tb01588.x.
Cited in this article [1]
[46]
SHAW J, LICKEY E B, BECK J T, et al. The tortoise and the hare Ⅱ:relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis[J]. Am J Bot, 2005, 92(1):142-166.DOI: 10.3732/ajb.92.1.142.
Cited in this article [1]
[47]
SHAW J, LICKEY E B, SCHILLING E E, et al. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms:the tortoise and the hare Ⅲ[J]. Am J Bot, 2007, 94(3):275-288.DOI: 10.3732/ajb.94.3.275.
Cited in this article [1]
[48]
SHAW J, SHAFER H L, LEONARD O R, et al. Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms:the tortoise and the hare Ⅳ[J]. Am J Bot, 2014, 101(11):1987-2004.DOI: 10.3732/ajb.1400398.
Cited in this article [1]
[49]
WEISING K. DNA fingerprinting in plants:principles,methods,and applications[M].2nd ed.Boca Raton, FL: Taylor & Francis Group, 2005.
Cited in this article [2]
[50]
YAN H F. Phylogeographic structure of Primula obconica (Primulaceae) inferred from chloroplast microsatellites (cpSSRs) markers[J]. Acta Phytotaxon Sin, 2007, 45(4):488-496.DOI: 10.1360/aps06214.
Cited in this article [1]
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