[1]林锦杭,耿晓姗,郭艺鹏,等.基于全基因组的假蒟叶绿体进化:特征及系统发育分析[J].江苏农业学报,2025,(10):1907-1919.[doi:doi:10.3969/j.issn.1000-4440.2025.10.004]
　LIN Jinhang,GENG Xiaoshan,GUO Yipeng,et al.Evolutionary characteristics and phylogenetic analysis of chloroplasts in Piper sarmentosum based on whole genome sequencing[J].,2025,(10):1907-1919.[doi:doi:10.3969/j.issn.1000-4440.2025.10.004]
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基于全基因组的假蒟叶绿体进化:特征及系统发育分析()

江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2025年10期
页码:
1907-1919
栏目:
遗传育种·生理生化
出版日期:
2025-10-31

文章信息/Info

Title:
Evolutionary characteristics and phylogenetic analysis of chloroplasts in Piper sarmentosum based on whole genome sequencing
作者:
林锦杭1; 耿晓姗2; 郭艺鹏1; 刘秦2
(1.玉林师范学院/广西壮族自治区设施农业工程中心,广西玉林537000；2.广西农业职业技术大学农业工程学院,广西南宁530000)
Author(s):
LIN Jinhang1; GENG Xiaoshan2; GUO Yipeng1; LIU Qin2
(1.Yulin Normal University/Guangxi Zhuang Autonomous Region Engineering Research Center of Facility Agriculture, Yulin 537000, China;2.College of Agricultural Engineering, Guangxi Vocational University of Agriculture, Nanning 530000, China)
关键词:
假蒟; 胡椒属; 叶绿体基因组; 密码子偏好性; 系统发育分析
Keywords:
Piper sarmentosum; Piper L.; chloroplast genome; codon usage bias; phylogenetic analysis
分类号:
Q949.732.3
DOI:
doi:10.3969/j.issn.1000-4440.2025.10.004
文献标志码:
A
摘要:
为了明确假蒟的基因组学信息,本研究对假蒟叶绿体基因组进行de novo测序、组装和注释,并对其基因组结构、基因组成、重复序列特征、简单重复序列（SSR)位点以及系统发育关系进行全面分析。结果显示,假蒟叶绿体基因组碱基序列总长度为161 389 bp,具有典型的四分体结构,即大单拷贝区(LSC)、小单拷贝区(SSC)和2个反向重复区(IRa和IRb),总G+C含量为38.30%,包含82个蛋白质编码基因。在对其散在重复序列鉴定中共检测到16个正向重复序列、24个回文重复序列、2个反向重复序列和2个互补重复序列,而在SSR检测中,共发现51个SSR位点,其核苷酸重复类型主要为A/T。密码子偏好性分析结果表明,编码亮氨酸(Leu)的密码子使用频率最高,而编码半胱氨酸(Cys)的密码子使用频率最低,在高频密码子中多使用A或U结尾。通过属内叶绿体基因组IR边界比较分析,结果发现胡椒属IR边界区域相对保守,仅存在微小的变异。核苷酸多态性分析共检测出胡椒属存在6个高变异区：rps16(exon1)-trnQ、psbZ-trnG、rps4-trnT、petA-psbJ、psbJ-psbL以及ndhF-rpl32,这些高变异区可用于开发胡椒属物种系统发育和DNA条形码研究的分子标记。基于胡椒目植物叶绿体基因组的系统发育分析确定假蒟与蒌叶、海南蒟、变叶胡椒的亲缘关系较近。本研究结果为这种重要药食同源植物的系统发育和叶绿体基因工程研究提供了宝贵信息。
Abstract:
To elucidate the genomic information of Piper sarmentosum, this study conducted de novo sequencing, assembly, and annotation of its chloroplast genome, followed by a comprehensive analysis of its genomic structure, gene composition, repetitive sequence characteristics, simple sequence repeat (SSR) loci, and phylogenetic relationships. The results showed that the total length of the chloroplast genome sequence of Piper sarmentosum was 161 389 bp, exhibiting a typical quadripartite structure consisting of a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeat (IRa and IRb) regions. The overall G+C content was 38.30%, and the genome contained 82 protein-coding genes. A total of 16 forward repeats, 24 palindromic repeats, two reverse repeats, and two complementary repeats were identified during the analysis of its dispersed repetitive sequences. Meanwhile, 51 SSR loci were detected, with A/T nucleotides being the predominant repeat type. The results of codon usage bias analysis revealed that codons encoding leucine (Leu) were the most frequently used, while those encoding cysteine (Cys) were the least frequent. Among the high-frequency codons, most ended with A or U. Through comparative analysis of chloroplast genome IR boundaries within the genus, it was found that the IR boundary regions of Piper were relatively conserved, with only minor variations. Six highly variable regions were detected in the Piper genus through nucleotide polymorphism analysis: rps16(exon1)-trnQ, psbZ-trnG, rps4-trnT, petA-psbJ, psbJ-psbL, and ndhF-rpl32. These regions can be utilized to develop molecular markers for phylogenetic and DNA barcoding research in Piper. Phylogenetic analysis based on chloroplast genomes of Piperales plants confirmed that Piper sarmentosum was closely related to Piper betle, Piper hainanense, and Piper mutabile. The results of this study provide valuable information for the phylogeny and chloroplast genetic engineering of this important plant with both medicinal and edible values.

参考文献/References:

[1]ZHANG Y, TIAN L, LU C M. Chloroplast gene expression:recent advances and perspectives[J]. Plant Communications,2023,4(5):100611.
[2]ARMBRUSTER U, PESARESI P, PRIBIL M, et al. Update on chloroplast research:new tools,new topics,and new trends[J]. Molecular Plant,2011,4(1):1-16.
[3]ARCHIBALD J M. Genomic perspectives on the birth and spread of plastids[J]. Proceedings of the National Academy of Sciences of the United States of America,2015,112(33):10147-10153.
[4]TIMMIS J N, AYLIFFE M A, HUANG C Y, et al. Endosymbiotic gene transfer:organelle genomes forge eukaryotic chromosomes[J]. Nature Reviews Genetics,2004,5(2):123-135.
[5]DANIELL H, LIN C S, YU M, et al. Chloroplast genomes:diversity,evolution,and applications in genetic engineering[J]. Genome Biology,2016,17(1):134.
[6]WHITNEY S M, HOUTZ R L, ALONSO H. Advancing our understanding and capacity to engineer nature’s CO2-sequestering enzyme,Rubisco[J]. Plant Physiology,2011,155(1):27-35.
[7]PARRY M A J, JOHN ANDRALOJC P, SCALES J C, et al. Rubisco activity and regulation as targets for crop improvement[J]. Journal of Experimental Botany,2013,64(3):717-730.
[8]NOURI M Z, MOUMENI A, KOMATSU S. Abiotic stresses:insight into gene regulation and protein expression in photosynthetic pathways of plants[J]. International Journal of Molecular Sciences,2015,16(9):20392-20416.
[9]龚秋怡,董姝洁,许琴,等. 牛茄子叶绿体全基因组特征及系统发育分析[J]. 中草药,2024,55(12):4150-4158.
[10]梁莹莹,吴文如,彭晓祺,等. 苹婆叶绿体全基因组序列特征及苹婆属系统发育分析[J]. 中草药,2024,55(19):6721-6729.
[11]任玉玲,李幸儿,梁佳林,等. 鲜黄小檗叶绿体基因组特征及系统发育分析[J]. 西北植物学报,2024,44(10):1616-1625.
[12]黄祥,何梦瑶,王子煊,等. 紫叶风箱果叶绿体基因组特征及绣线菊亚科系统发育分析[J]. 草业学报,2024,33(3):161-173.
[13]VERMA D, DANIELL H. Chloroplast vector systems for biotechnology applications[J]. Plant Physiology,2007,145(4):1129-1143.
[14]CLARKE J L, DANIELL H. Plastid biotechnology for crop production:present status and future perspectives[J]. Plant Molecular Biology,2011,76(3/4/5):211-220.
[15]AN Y Q, WANG Y, WANG X W, et al. Development of chloroplast transformation and gene expression regulation technology in land plants[J]. Frontiers in Plant Science,2022,13:1037038.
[16]SUN X L, CHEN W H, DAI W, et al. Piper sarmentosum Roxb.:a review on its botany,traditional uses,phytochemistry,and pharmacological activities[J]. Journal of Ethnopharmacology,2020,263:112897.
[17]HUSSAIN K, HASHMI F K, LATIF A, et al. A review of the literature and latest advances in research of Piper sarmentosum[J]. Pharmaceutical Biology,2012,50(8):1045-1052.
[18]NURUL, SANUSI N A, UMAR R, et al. Chemical compositions and antimicrobial properties of Piper sarmentosum-a review[J]. IOSR Journal of Dental and Medical Sciences,2017,16:62-65.
[19]ZAINAL ARIFFIN S H, WAN OMAR W H, ZAINAL ARIFFIN Z, et al. Intrinsic anticarcinogenic effects of Piper sarmentosum ethanolic extract on a human hepatoma cell line[J]. Cancer Cell International,2009,9:6.
[20]UGUSMAN A, ZAKARIA Z, HUI C K, et al. Flavonoids of Piper sarmentosum and its cytoprotective effects against oxidative stress[J]. EXCLI Journal,2012,11:705-714.
[21]HAMIL M S R, MEMON A H, MAJID A M S A, et al. Simultaneous determination of two isomers of asarone in Piper sarmentosum Roxburgh (Piperaceae) extracts using different chromatographic columns[J]. Tropical Journal of Pharmaceutical Research,2016,15(1):157.
[22]POREBSKI S, BAILEY L G, BAUM B R. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components[J]. Plant Molecular Biology Reporter,1997,15(1):8-15.
[23]BOLGER A M, LOHSE M, USADEL B. Trimmomatic:a flexible trimmer for Illumina sequence data[J]. Bioinformatics,2014,30(15):2114-2120.
[24]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 Biology,2020,21(1):241.
[25]LIU C, SHI L C, ZHU Y J, et al. CpGAVAS,an integrated web server for the annotation,visualization,analysis,and GenBank submission of completely sequenced chloroplast genome sequences[J]. BMC Genomics,2012,13:715.
[26]BEIER S, THIEL T, MNCH T, et al. MISA-web:a web server for microsatellite prediction[J]. Bioinformatics,2017,33(16):2583-2585.
[27]KURTZ S, CHOUDHURI J V, OHLEBUSCH E, et al. REPuter:the manifold applications of repeat analysis on a genomic scale[J]. Nucleic Acids Research,2001,29(22):4633-4642.
[28]YAO J C, ZHENG Z H, XU T, et al. Chloroplast genome sequencing and comparative analysis of six medicinal plants of Polygonatum[J]. Ecology and Evolution,2025,15(1):70831.
[29]SHARP P M, LI W H. The Codon adaptation index:a measure of directional synonymous Codon usage bias,and its potential applications[J]. Nucleic Acids Research,1987,15(3):1281-1295.
[30]WU J, ZHANG J, GUO X H, et al. Comprehensive analysis of complete chloroplast genome sequence of Plantago asiatica L.(Plantaginaceae)[J]. Plant Signaling & Behavior,2023,18(1):2163345.
[31]LI H E, GUO Q Q, XU L, et al. CPJSdraw:analysis and visualization of junction sites of chloroplast genomes[J]. Peer J,2023,11:15326.
[32]FUSARI C M, LIA V V, ESTEBAN HOPP H, et al. Identification of single nucleotide polymorphisms and analysis of linkage disequilibrium in sunflower elite inbred lines using the candidate gene approach[J]. BMC Plant Biology,2008,8:7.
[33]ZHANG D, GAO F L, JAKOVLIC I, et al. PhyloSuite:an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies[J]. Molecular Ecology Resources,2020,20(1):348-355.
[34]GAIKWAD A B, KAILA T, MAURYA A, et al. The chloroplast genome of black pepper (Piper nigrum L.) and its comparative analysis with related Piper species[J]. Frontiers in Plant Science,2023,13:1095781.
[35]WEI F, TANG D F, WEI K H, et al. The complete chloroplast genome sequence of the medicinal plant Sophora tonkinensis[J]. Scientific Reports,2020,10(1):12473.
[36]NGUYEN H Q, NGUYEN T N L, DOAN T N, et al. Complete chloroplast genome of novel Adrinandra megaphylla Hu species:molecular structure,comparative and phylogenetic analysis[J]. Scientific Reports,2021,11(1):11731.
[37]张健,张宏祥. 新疆野苹果叶绿体基因组特征及其进化历史[J]. 干旱区研究,2024,41(12):2110-2119.
[38]HUANG R, XIE X N, CHEN A M, et al. The chloroplast genomes of four Bupleurum (Apiaceae) species endemic to Southwestern China,a diversity center of the genus,as well as their evolutionary implications and phylogenetic inferences[J]. BMC Genomics,2021,22(1):714.
[39]SERRES-GIARDI L, BELKHIR K, DAVID J, et al. Patterns and evolution of nucleotide landscapes in seed plants[J]. The Plant Cell,2012,24(4):1379-1397.
[40]TANG J M, ZOU R, HUANG K, et al. Comparative and phylogenetic analyses of the complete chloroplast genomes of four Ottelia species[J]. Horticulturae,2024,10(6):603.
[41]WENG M L, BLAZIER J C, GOVINDU M, et al. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements,repeats,and nucleotide substitution rates[J]. Molecular Biology and Evolution,2014,31(3):645-659.
[42]ELLEGREN H. Microsatellites:simple sequences with complex evolution[J]. Nature Reviews Genetics,2004,5(6):435-445.
[43]POMBERT J F, OTIS C, LEMIEUX C, et al. The chloroplast genome sequence of the green Alga pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages[J]. Molecular Biology and Evolution,2005,22(9):1903-1918.
[44]YUE F, CUI L Y, DEPAMPHILIS C W, et al. Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat[J]. BMC Genomics,2008,9(1):25.
[45]HABERLE R C, MATTHEW FOURCADE H, BOORE J L, et al. Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes[J]. Journal of Molecular Evolution,2008,66(4):350-361.
[46]SHABALINA S A, SPIRIDONOV N A, KASHINA A. Sounds of silence:synonymous nucleotides as a key to biological regulation and complexity[J]. Nucleic Acids Research,2013,41(4):2073-2094.
[47]LABELLA A L, OPULENTE D A, STEENWYK J L, et al. Variation and selection on Codon usage bias across an entire subphylum[J]. PLoS Genetics,2019,15(7):1008304.
[48]WANG L J, ROOSSINCK M J. Comparative analysis of expressed sequences reveals a conserved pattern of optimal Codon usage in plants[J]. Plant Molecular Biology,2006,61(4/5):699-710.
[49]朱艳,韩长志. 普通核桃与深纹核桃中叶绿体基因组密码子使用特征对比[J]. 江苏农业学报,2024,40(8):1507-1520.
[50]PARVATHY S T, UDAYASURIYAN V, BHADANA V. Codon usage bias[J]. Molecular Biology Reports,2022,49(1):539-565.
[51]KRMER C, BOEHM C R, LIU J H, et al. Removal of the large inverted repeat from the plastid genome reveals gene dosage effects and leads to increased genome copy number[J]. Nature Plants,2024,10(6):923-935.
[52]XUE S, SHI T, LUO W J, et al. Comparative analysis of the complete chloroplast genome among Prunus mume,P.armeniaca,and P.salicina[J]. Horticulture Research,2019,6:89.
[53]DOWNIE S R, JANSEN R K. A comparative analysis of whole plastid genomes from the Apiales:expansion and contraction of the inverted repeat,mitochondrial to plastid transfer of DNA,and identification of highly divergent noncoding regions[J]. Systematic Botany,2015,40(1):336-351.
[54]LIU L K, DU J X, LIU Z H, et al. Comparative and phylogenetic analyses of nine complete chloroplast genomes of Orchidaceae[J]. Scientific Reports,2023,13:21403.
[55]ZHANG L, MENG Y, WANG D, et al. Plastid genome data provide new insights into the dynamic evolution of the tribe Ampelopsideae (Vitaceae)[J]. BMC Genomics,2024,25(1):247.
[56]ZHAO X Q, YAN M, DING Y, et al. Characterization and comparative analysis of the complete chloroplast genome sequence from Prunus avium ‘Summit’[J]. Peer J,2019,7:8210.
[57]VOETS A M, VAN DEN BOSCH B J C, Stassen A P, et al. Large scale mtDNA sequencing reveals sequence and functional conservation as major determinants of homoplasmic mtDNA variant distribution[J]. Mitochondrion,2011,11(6):964-972.
[58]YANG Z, NIELSEN R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models[J]. Molecular Biology and Evolution,2000,17(1):32-43.
[59]WITHARANA E P, IWASAKI T, SAN M H, et al. Subfamily evolution analysis using nuclear and chloroplast data from the same reads[J]. Scientific Reports,2025,15(1):687.
[60]QIN H T, MLLER M, MILNE R, et al. Multiple paternally inherited chloroplast capture events associated with Taxus speciation in the Hengduan Mountains[J]. Molecular Phylogenetics and Evolution,2023,189:107915.
[61]KUROIWA T. Mechanisms of maternal inheritance of chloroplast DNA:an active digestion hypothesis[J]. Microbiological Sciences,1985,2(9):267-270.
[62]TUCKER S C, DOUGLAS A W, LIANG H X. Utility of ontogenetic and conventional characters in determining phylogenetic relationships of Saururaceae and Piperaceae (Piperales)[J]. Systematic Botany,1993,18(4):614.
[63]HILLIS D M. Phylogenetic analysis[J]. Current Biology,1997,7(3):129-131.
[64]SMITH J F, STEVENS A C, TEPE E J, et al. Placing the origin of two species-rich genera in the Late Cretaceous with later species divergence in the tertiary:a phylogenetic,biogeographic and molecular dating analysis of Piper and Peperomia (Piperaceae)[J]. Plant Systematics and Evolution,2008,275(1):9-30.
[65]SIMMONDS S E, SMITH J F, DAVIDSON C, et al. Phylogenetics and comparative plastome genomics of two of the largest genera of angiosperms,Piper and Peperomia (Piperaceae)[J]. Molecular Phylogenetics and Evolution,2021,163:107229.

备注/Memo

备注/Memo:
收稿日期：2025-04-24基金项目：国家自然科学基金项目(32101691)；广西自然科学基金项目(2025GXNSFAA069625)；2023年度广西高校中青年教师基础能力提升项目(2023KY05604)作者简介：林锦杭(2002-),男,广东潮州人,本科,主要从事植物基因组学研究。(E-mail)15919529485@163.com通讯作者：刘秦,(E-mail)liuqin@ylu.edu.cn；郭艺鹏,(E-mail)514508412@qq.com
更新日期/Last Update: 2025-11-17