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野生六棱大麦(Hordeum agriocrithon)广泛分布在青藏高原上，被认为是六棱栽培大麦的野生祖先。为揭示野生六棱大麦叶绿体基因组(chloroplast DNA,cpDNA)结构特征和系统发育关系，利用Illumina Hiseq 6000测序平台对其进行高通量测序，并以钝稃野大麦(H.spontaneum)叶绿体基因组为参考进行序列组装及质控；利用生物信息学手段，对野生六棱大麦的叶绿体基因组进行注释及特征分析；同时，以玉米(Zea mays)和禾本科(Gramineae)针茅属(Stipa)物种Stipa lipskyi为外类群，通过MEGA X软件构建最大似然法(maximum likelihood method,ML)系统发育树，分析野生六棱大麦系统发育关系。研究表明，野生六棱大麦叶绿体基因组总G+C含量为38.32%,全长136 462 bp,包含1对长度为21 582 bp的反向重复区(inverted repeats region, IRs),1个长度为80 597 bp的大单拷贝区(large single copy region, LSC)和1个长度为12 701 bp的小单拷贝区(small single copy region, SSC),为典型的四分体结构。在野生六棱大麦叶绿体基因组中共检测到129个基因，分别是83个编码基因、 38个tRNA基因和8个rRNA基因；另外，共检测到46个散在重复序列(dispersedrepeated sequences)和178个简单重复序列(simple sequence repeats, SSR)位点，大部分SSR是由A/T组成的单碱基重复序列。密码子偏好性分析结果表明，野生六棱大麦有偏好性，且偏好使用以A/U结尾的密码子。结合IR边界分析和序列比较分析，结果表明，除碱大麦(Hordeum marinum)外，野生六棱大麦、栽培二棱大麦(Hordeum distichon)、钝稃野大麦和大麦(Hordeum vulgare)的叶绿体基因组结构具有较高保守性，且序列变异主要发生在LSC的非编码序列上。系统发育分析结果表明野生六棱大麦与大麦属(Hordeum)物种聚类在一起，且与大麦亲缘关系最近。本研究获得了野生六棱大麦的叶绿体基因组序列，明确了与小麦族(Triticeae)物种间的亲缘关系，为研究大麦属物种的系统进化及物种鉴定提供科学依据。
Abstract：Hordeum agriocrithon is considered as the wild progenitor of six-rowed cultivated barley and is widely distributed in the Qinghai-Tibet Plateau. In order to reveal the structural characteristics and phylogenetic relationship of chloroplast DNA(cpDNA) of H. agriocrithon, the H. agriocrithon cpDNA was sequenced by using the Illumina Hiseq 6000 sequencing platform, and the cpDNA of H. spontaneum was used as a reference to sequence assembly and quality control. The cpDNA of H. agriocrithon was annotated and characterized by bioinformatics. Meanwhile, the maximum likelihood method(ML) phylogenetic tree was constructed by MEGA X software, with Zea mays and Gramineae Stipa species Stipa lipskyi as outgroups, to analyze the phylogenetic relationships of Hordeum agriocrithon. The results showed that the cpDNA of H. agriocrithon was 136 462 bp in length, with a G+C content of 38.32%, which was a typical tetrad structure, including a pair of inverted repeats region(IRs) of 21 582 bp, a large single copy region(LSC) of 80 597 bp, and a small single copy region(SSC) of 12 701 bp. A total of 129 genes were identified in the cpDNA of H. agriocrithon, including 83 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. A total of 46 dispersed repeated sequences and 178 simple sequence repeats(SSR) loci were detected, most of SSR were single base repeats composed of A/T. Codon usage bias analysis showed that H. agriocrithon had a preference and preferred to use the codons ending with A/U. IR boundary analysis combined with comparative sequence analysis showed that the chloroplast genome structures of H. agriocrithon, H. distichon, H. spontaneum, and H. vulgare were highly conserved, in which the sequence variation mainly occurred in the non-coding sequence of the LSC, except for H. marinum. The phylogenetic analysis showed that the H. agriocrithon clustered with Hordeum species and had the closest genetic relationship with H. vulgare. In this study, the complete chloroplast genome sequence of H. agriocrithon was obtained, which clarified the affinities between the Triticeae and provided the scientific basis for the study of the phylogeny and species identification of H. agriocrithon.
林汇源，何楚扬，张启赢，等，2023.植物基因组重复DNA序列与基因组大小.分子植物育种，(2023-04-26)[2023-11-13],https://kns.cnki.net/kcms/detail/46.1068.S.20230425.1450.019.html.[LIN H Y,HE C Y,ZHANG Q Y,et al.,2023.Plant genome repetitive DNA sequences and genome size.Molecular Plant Breeding,(2023-04-26)[2023-11-13],https://kns.cnki.net/kcms/detail/46.1068.S.20230425.1450.019.html.]
芦永昌，张鑫，张璐燕，等，2023.辽东丁香完整叶绿体基因组的结构与特征.植物研究，43(1):120-130.[LU Y C,ZHANG X,ZHANG L Y,et al.,2023.Complete chloroplast genome structure and characterization of Syringa villosa subsp.Wolfi.Bulletin of Botanical Research,43(1):122-130.]
马得泉，1997.中国野生六棱大麦(H.agriocrithon ?berg)分类和分布的研究.大麦科学，(2):7-10.[MA D Q,1997.The research on classification and distribution of six-rowed wild barley (H.agriocrithon ?berg) in China.Barley and Cereal Sciences,(2):7-10.]
牛迎凤，李国华，刘紫艳，等，2020.光亮橡胶树叶绿体基因组测序组装与注释.经济林研究，38(4):62-71.[NIU Y F,LI G H,LIU Z Y,et al.,2020.Sequencing,assembly and annotation of chloroplast genome of Hevea nitida.Non-wood Forest Research,38(4):62-71.]
苏丹丹，刘玉萍，刘涛，等，2022.苦马豆叶绿体基因组结构及其特征分析.植物研究，42(3):446-454.[SU D D,LIU Y P,LIU T,et al.,2022.Structure of chloroplast genome and its characteristics of Sphaerophysa salsula.Bulletin of Botanical Research,42(3):446-454.]
苏宁，何兆峰，欧平和，等，2020.小麦属植物叶绿体基因组结构的比较分析.麦类作物学报，40(1):55-64.[SU N,HE Z F,OU P H,et al.,2020.Comparative analysis of the chloroplast genome in Triticum species.Journal of Triticeae Crops,40(1):55-64.]
王震，张占平，孔令阳，等，2023.白鲜叶绿体高通量测序组装及系统进化分析.植物科学学报，41(2):139-148.[WANG Z,ZHANG Z P,KONG L Y,et al.,2023.Characterization and phylogenetic analysis of the complete chloroplast genome of Dictamnus dasycarpus Turcz.Plant Science Journal,41(2):139-148.]
杨芮，2019.三个树莓类资源叶绿体基因组比较分析，硕士学位论文.雅安：四川农业大学.[YANG R,2019.Complete chloroplast genome and comparative analyses of three bramble resources (Rubus),Thesis for M.S.Yaan:Sichuan Agricultural University.]
张昊，2023.五加属植物叶绿体基因组测序分析及系统发育研究，硕士学位论文.牡丹江：牡丹江师范学院.[ZHANG H,2023.The chloroplast genome sequencing and phylogenetic studies of Eleutherococcus plants,Thesis for M.S.Mudanjiang:Mudanjiang Normal University.]
张瑞，张天留，宋美华，等，2021.重复序列在牛亚科中的研究进展.中国畜牧杂志，57(4):33-38.[ZHANG R,ZHANG T L,SONG M H,et al.,2021.Research progress in the repetitive sequences of bovinae.Chinese Journal of Animal Science,57(4):33-38.]
周红，2020.野生大麦重要农艺性状的遗传解析及ceRNA调控网络挖掘，博士学位论文.雅安：四川农业大学.[ZHOU H,2020.The genetic analysis for important agronomic traits from wild barley and construction of ceRNA regulatory networks,Dissertation for Ph.D.Yaan:Sichuan Agricultural University.]
AMIRYOUSEFI A,HYV?NEN J,POCZAI P,2018.IRscope:an online program to visualize the junction sites of chloroplast genomes.Bioinformatics,34(17):3030-3031.
BARAK P,RAI A,RAI P,et al.,2013.Quantitative optical trapping on single organelles in cell extract.Nat.Methods,10(1):68-70.
BEIER S,THIEL T,MüNCH T,et al.,2017.MISA-web:a web server for microsatellite prediction.Bioinformatics,33(16):2583-2585.
CHEN Z J,JIN Y Y,LI X Z,et al.,2021.Characterization of the complete chloroplast genome of Hordeum jubatum (Poaceae:Pooideae:Triticeae) and phylogenetic analysis.Mitochondrial DNA B Resour.,6(10):2933-2935.
EBERT D,PEAKALL R,2009.Chloroplast simple sequence repeats (cpSSRs):technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant species.Mol.Ecol.Resour.,9(3):673-690.
GAWEL N J,JARRET R L,1991.A modified CTAB DNA extraction procedure for Musa and Ipomoea.Plant Mol.Biol.Report.,9(3):262-266.
GOUY M,GAUTIER C,1982.Codon usage in bacteria:correlation with gene expressivity.Nucleic Acids Res.,10(22):7055-7074.
GREINER S,LEHWARK P,BOCK R,2019.OrganellarGenomeDRAW (OGDRAW) version 1.3.1:expanded toolkit for the graphical visualization of organellar genomes.Nucleic Acids Res.,47(W1):W59-W64.
HUANG J,YANG X T,ZHANG C M,et al.,2015.Development of chloroplast microsatellite markers and analysis of chloroplast diversity in Chinese jujube (Ziziphus jujuba Mill.) and wild jujube (Ziziphus acidojujuba Mill.).PLoS ONE,10(9):e0134519.
JANSEN R K,RAUBESON L A,BOORE J L,et al.,2005.Methods for obtaining and analyzing whole chloroplast genome sequences.Methods Enzymol.,395:348-384.
KATOH K,STANDLEY D M,2013.MAFFT multiple sequence alignment software version 7:improvements in performance and usability.Mol.Biol.Evol.,30(4):772-780.
KLEIN S J,O′NEILL R J,2018.Transposable elements:genome innovation,chromosome diversity,and centromere conflict.Chromosome Res.,26(1-2):5-23.
KUMAR S,STECHER G,LI M,et al.,2018.MEGA X:molecular evolutionary genetics analysis across computing platforms.Mol.Biol.Evol.,35(6):1547-1549.
LI L,HU Y F,HE M,et al.,2021.Comparative chloroplast genomes:insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia.BMC Genom.,22(1):138.
LIU S X,XUE D Y,CHENG R,et al.,2014.The complete mitogenome of Apocheima cinerarius (Lepidoptera:Geometridae:Ennominae) and comparison with that of other lepidopteran insects.Gene,547(1):136-144.
PEDEN J F,1999.Analysis of codon usage,Dissertation for Ph.D.Nottingham:University of Nottingham.
REN Y H,XIA H,LU L D,et al.,2021.Characterization of the complete chloroplast genome of Hordeum vulgare L.var.trifurcatum with phylogenetic analysis.Mitochondrial DNA B Resour.,6(7):1852-1854.
SU X X,ZHAO J,WANG Z Y,2020.The complete chloroplast genome of Hordeum brevisubulatum.Mitochondrial DNA B Resour.,5(3):2988-2989.
XIE J B,QIAN K C,SI J N,et al.,2018.Conserved noncoding sequences conserve biological networks and influence genome evolution.Heredity,120(5):437-451.
YU X L,LI X,YAO X H,et al.,2021.The complete chloroplast genome sequence of Hordeum distichon (Poales:Poaceae).Mitochondrial DNA B Resour.,6(12):3482-3484.
ZENG Q X,YUAN J H,WANG L Y,et al.,2017.The complete chloroplast genome of Tibetan hulless barley.Mitochondrial DNA A DNA Mapp.Seq.Anal.,28(3):324-325.
基本信息:
DOI：10.13417/j.gab.043.000788
中图分类号:S512.3
引用信息:
[1]余鑫莲,李新.野生六棱大麦叶绿体基因组特征及系统发育分析[J].基因组学与应用生物学,2024,43(05):788-802.DOI:10.13417/j.gab.043.000788.
基金信息:
青海大学省部共建三江源生态与高原农牧业国家重点实验室自主课题项目(2022-ZZ-07); 青海省自然科学基金计划——创新团队项目(2022-ZJ-902); 青海省科技创新平台建设专项(2023-1-5)共同资助
2024-01-02
2024-01-02
2024-01-02