WANG Jiyue,BAI Yu,SHI Denghong,et al.Reseach Progress on Chloroplast Genome of Moraceae Plant[J].Northern Horticulture,2021,(08):124-130.[doi:10.11937/bfyy.20200520]
桑科植物叶绿体基因组研究进展
- Title:
- Reseach Progress on Chloroplast Genome of Moraceae Plant
- Keywords:
- Moraceae plants; chloroplast genome; systematic evolution
- 文献标志码:
- A
- 摘要:
- 叶绿体基因组具有半自主性和母性遗传特征，揭示其功能对于研究植物起源、系统进化及物种鉴定、分类具有十分重要的作用。桑科植物具有食用、药用、生态修复及作为工业原料等多种用途。其叶绿体基因组为双链环状结构，由4个部分组成，即1个大的单拷贝区域（large single-copy，LSC）、1个小的单拷贝区域（small single-copy，SSC）、2个反向重复区域（inverted repeat，IRs）。基因组大小约160 kb，编码110~130个基因，包括蛋白质编码基因、tRNA＼rRNA＼ncRNA等。桑科植物叶绿体基因组上存在SSR和SNP位点，同时还发现有密码子使用偏好性。该研究对近年来桑科植物叶绿体基因组的研究现状、应用以及发展趋势进行了综述，为进一步理解桑科植物叶绿体的功能机制提供参考依据。
- Abstract:
- Chloroplast genomes are characterized by semi-autonomy and maternal heredity.Revealing plant chloroplast genome played an important role in the study of origin,phylogeny,identification and classification of species in plant.The chloroplast genome of Moraceae plants had a double chain structure,composed of four parts,incluing a large single-copy (LSC),a small single-copy(SSC),and twoinverted repeat (IRs).SSRs and SNPs,and codon useD preferenceare found in chloroplast genome.The present status,applications,and developing trends of chloroplast genome reasrch of Moraceae plants were briefly summarized in this review.It provided a reference for further understanding the functional mechanism of chloroplast in Moraceae plants.
参考文献/References:
[1]张秀实.中国植物志(第32卷第1分册)[M].北京:科学出版社,1998.[2]吴征镒,路安民,汤彦承,等.中国被子植物科属综论[M].北京:科学出版社,2003．[3]路丹桂,邱丽氚,常虹,等.中国桑科植物属的空间分布及多样性[J].西北植物学报,2019,39(6):1127-1134.[4]中国科学院中国植物志编辑委员会.中国植物志(第23卷第1分册)[M].北京:科学出版社,1998.[5]BOCK R.Genetic engineering of the chloroplast:Novel tools and new applications[J].Current Opinion in Biotechnology,2014,26:7-13.[6]PETER C,PERER G F,MARTIN T E,et al.Analyses of charophyte chloroplast genomes helpcharacterize the ancestral chloroplast genome of land plants[J].Genome Biol.Evol,2014,(4):897-911.[7]RAVI V,KHURNANA J P,TYAGI A K,et al.The chloroplast genome of mulberry:Complete nucleotide sequence,gene organization and comparative analysis[J].Tree Genet Genomes,2006(3):49-59.[8]RAVI V,TYAG AK,KHURNANA JP,et al.Rosales sister to Fabales:Towards resolving the rosid puzzle[J].Molecular Phylogenetics and Evolution,2007,44:488-493.[9]KIM T H,JUNG J,KIM J H.Comparative analysis of the complete genomes of three Ficus L.(Moraceae) species and its implication[J].The Plant Resources Society of Korea,2019,29:41-61.[10]AVSAR B,ALIABADI D E.A comparison study of chloroplast genomes:Ficus species versus its close relatives[J].Journal of Molecular Biology and Biotechnology,2018,2(2):28-31.[11]LIU J,NIU F Y,NI S B,et al.The complete chloroplast genome of Artocarpus heterophyllus (Moraceae)[J].Mitochondrial DNA Part B,2018,3(1):13-14.[12]LI Y R,SONG Y.The chloroplast genome of an endangeredtree Artocarpus nanchuanensis (Moraceae)[J].Mitochondrial DNA Part B,2019,4(1):893-894.[13]LUO J,WANG Y Y,ZHAO Z J A.The completechloroplast genome of Morusalba (Moraceae:Morus),the herbal medicine species in China[J].Mitochondrial DNA Part B,2019,4(2):2467-2468.[14]LIU Y R,CHEN W N,LI F,et al.The complete chloroplast genome sequence of Ficus hirta (Moraceae)[J].Mitochondrial DNA Part B,2019,4(2):4041-4042.[15]WANG J Y,SHI D H,BAI Y,et al.High-throughput sequencing uncover Ficus tikoua Bur.chloroplast genome[J].Journal of Plant Biochemistry and Biotechnology,2020,12(3):66-75.[16]DONG W,LIU H,XU C,et al.A chloroplast genomic strategy fordesigning taxon specific DNA mini-barcodes:A case study onginsengs[J].BMC Genetics,2014(15):138.[17]JO Y D,PARK J,KIM J,et al.Complete sequencingand comparative analyses of the pepper (Capsicum annuum L.) plastome revealedhigh frequency of tandem repeats and large insertion/deletions on pepper plastome[J].Plant Cell Reports,2011,30:217-229.[18]KONG W Q,YANG J H.The complete chloroplast genome sequence of Morus cathayana and Morus multicaulis,and comparative analysis within genus Morus L.[J].Peer Journal,2017(5):30-37.[19]YANG Y,YUAN D,QING L,et al.Complete chloroplastgenome sequence of poisonous and medicinal plant datura stramonium:Orga-nizations and implications for genetic engineering[J].PLoS One,2014,9(11):e110656.[20]SHAW J,LICKEY E B,SCHILLIMG 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].American Journal of Botany,2007,94:275-288.[21]WORBERG A,QUANDT D,BAMISKE A M,et al.Phylogeny of basal eudicots:Insights from non-coding and rapidly evolving DNA[J].Organisms Diversity & Evolution,2007(7):55-77.[22]SABLOK G,NAYAK K C,VAZQUEZ F,et al.Synonymous codon usage,GC3,and evolutionary patterns across plastomes of three pooid model species:Emerging grass genome models for monocots[J].Molecular Biotechnology,2011,49:116-128.[23]OLEJNICZAK S A,OJEWSKA E,KOWZLCZYK T,et al.Chloroplasts:State of research and practical applications of plastome sequencing[J].Planta,2016,244(3):517-27.[24]BRUUN-LUND S,CLEMENT W L,KJELLBERG F,et al.First plastid phylogenomic study reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L.(Moraceae)[J].Mol Phylogenet Evol,2017,109:93-104.[25]WON H.Test of the hybrid origin of Broussonetia×kazinoki (Moraceae) in Korea using molecular markers[J].Korean Journal of Plant Taxonomists,2019,49(4):282-293.[26]RAVI V,TYAGI A K,KHURNANA J P,et al.An update on chloroplast genomes[J].Plant Systematics and Evolution,2008,271:101-122.[27]张剑锋,李阳,金静静,等.烟草叶绿体基因工程研究进展[J].烟草科技,2017,50(6):88-98.[28]SHARMA S,MEHRA R,BAS F.Molecular phylogeography of Ficus benghalensis Linnaeus using nrDNA ITS 1,cpDNA trnL and cpDNA rps16 from the Indian subcontinent[J].Current Science,2019,117(2):293-298.[29]李双双,张迎新,范成明,等.单倍型分析技术研究进展[J].生物工程学报,2018,34(6):852-861.[30]KAUPPI L,BARCHI M,LANGE J,et al Numerical constraints and feedback control of double-strand breaks in mouse meiosis[J].Genes & Development,2013,27(8):873-886.[31]ZHANG L F,ZANG Z,WANG X M,et al.Molecular phylogeny of the Ficus auriculata complex (Moraceae)[J].Phytotaxa,2019,362(1):39-54.[32]KHURANA P,CHECKER V G.The advent of genomics in mulberry and perspectives for productivity enhancement[J].Plant Cell Rep,2011,30:825-838.[33]TOEWS D P L,BRELSFORD A.The biogeography of mitochon-drial and nuclear discordance in animals[J].Molecular Ecology,2012(21):3907-3930.[34]BOWHM C,BOCL R.Recent advances and current challenges in synthetic biology of the plastid genetic system and metabolism[J].Plant Physiology,2019,179:794-802.[35]DAUVILLEE D,HILBIG L,PREISS S,et al.Minimal extent of sequence homology required for homologous recombination at the psbA locus in Chlamydomonas reinhardtii chloroplasts using PCR-generated DNA fragments[J].Photosynthesis Research,2004,79:219-224.[36]ROGALKI M,RUF S,BOCL R.Tobacco plastid ribosomal protein S18 is essential for cell survival[J].Nucleic Acids Res,2006,34:4537-4545.[37]BROPHY J A N,VOIGT C A.Principles of genetic circuit design[J].Nature Methods,2014(11):508-520.[38]SHI C,WANG S,XIA E H,et al.Full transcription of the chloroplast genome in photosynthetic eukaryotes[J].Scientific Reports,2016(6):30-35.[39]VENAYK N,ANESIADIS N,CLUNTT W R,et al.Engineering metabolism through dynamic control[J].Current Opinion in Biotechnology,2015,34:142-152.[40]VERHOUNIG A,KARCHER D,BOCK R.Inducible gene expression from the plastid genome by a synthetic riboswitch[J].Proceedings of the National Academy of Sciences of the United States of America,2010,107:6204-6209.[41]GLOAGUEN P,BOUMAIS S,ALBANL C,et al.ChloroKB:A web application for the integration of knowledge related to chloroplast metabolic network[J].Plant Physiology,2017,174:922-934.[42]GREINER S,BOCK R.Tuning a ménage à trois:Co-evolution and co-adaptation of nuclear and organellar genomes in plants[J].Bio Essays,2013,35:354-365[43]BALLARD J W O,MELVIN R G.Linking the mitochondrial genotype to the organismal phenotype[J].Molecular Ecology,2010(19):1523-1539.[44]LLOPART A,HERRIG D,BRUND E,et al.Sequentialadaptive introgression of the mitochondrial genome in Drosophilayakuba and Drosophila santomea[J].Molecular Ecology,2014(23):1124-1236.[45]TOEWS D P L,MANDIC M,RICHARDS J G,et al.Migra-tion,mitochondria and the yellow-rumped warbler[J].Evolution,2013,68:241-255.[46]IRWIN D E.Local adaptation along smooth ecological gradients causes phylogeographic breaks and phenotypic clus-tering[J].The American Naturalist,2012,180:35-49.[47]FUENTES I,STEGEMAN S,GOLCZYK H,et al.Horizontal genome transfer as an asexual path to the formation of new species[J].Nature,2014,511:232-235.[48]BOCL D G,ANDREW R L,RIESEBERG L H.On the adaptive value of cytoplasmic genomes in plants[J].Molecular Ecology,2014,23(20):4899-4911.[49]USAI G,MASCAGNI F,GIORDANI T,et al.Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome[J].Plant Journal,2020,102(3):234-250.
相似文献/References:
[1]吴东洋,业宁,徐逸卿,等.狗枣猕猴桃叶绿体基因组微卫星特征分析[J].北方园艺,2018,42(09):30.[doi:10.11937/bfyy.20174592]
WU Dongyang,YE Ning,XU Yiqing,et al.Microsatellite Characteristic Analysis of Chloroplast Genome of Actinidia kolomikta[J].Northern Horticulture,2018,42(08):30.[doi:10.11937/bfyy.20174592]
[2]李昂,金亮,朱惠琴,等.田葛缕子叶绿体基因组微卫星特征分析[J].北方园艺,2023,(16):96.[doi:10.11937/bfyy.20224010]
LI Ang,JIN Liang,ZHU Huiqin,et al.Characterization Analysis of Microsatellite in Chloroplast Genome of Carum buriaticum Turcz.[J].Northern Horticulture,2023,(08):96.[doi:10.11937/bfyy.20224010]
[3]王宏霞,郑文霞.韭（Allium tuberosum）叶绿体基因组及其特征分析[J].北方园艺,2023,(24):16.[doi:10.11937/bfyy.20231522]
WANG Hongxia,ZHENG Wenxia.Chloroplast Genome and Characteristics Analysis of Allium tuberosum[J].Northern Horticulture,2023,(08):16.[doi:10.11937/bfyy.20231522]
备注/Memo
第一作者简介：王继玥（1984-），男，博士，副教授，现主要从事植物分子育种等研究工作。E-mail:acute2803764@126.com.基金项目：国家级大学生创新创业训练资助项目（2018109760007，2018109760008）；贵州省区域内一流培育建设学科生态学资助项目（黔教科研发[2017]85号）；贵州省科技计划资助项目（黔科合基础[2017]1004）；生态学省级重点学科资助项目（黔学位合字ZDXK[2013]08）；贵州省大学生创新训练资助项目（2018520777，2018520778，2018520831，2018520861）；贵阳市财政支持贵阳学院学科建设与研究生教育资助项目(SH-2020）。收稿日期：2020-02-15