生物多样性 ›› 2019, Vol. 27 ›› Issue (4): 366-372.doi: 10.17520/biods.2018332

• 研究报告 • 上一篇    下一篇

直刺变豆菜叶绿体全基因组及其特征

陈志祥1, 姚雪莹1, Stephen R.Downie2, 王奇志1, *()   

  1. 1 华侨大学化工学院园艺系, 福建厦门 361021
    2 Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana 61801
  • 收稿日期:2018-12-18 接受日期:2019-01-09 出版日期:2019-04-20
  • 通讯作者: 王奇志 E-mail:wqz@hqu.edu.cn
  • 基金项目:
    国家自然科学基金(31500162);国家标本平台教学标本子平台项目(2005DKA21403-JK);华侨大学研究生科研创新能力培育计划资助项目(1611315007);中国大学校园植物网的构建与示范Ⅱ(20180947)

Assembling and analysis of Sanicula orthacantha chloroplast genome

Chen Zhixiang1, Yao Xueying1, Stephen R. Downie2, Wang Qizhi1, *()   

  1. 1 Department of Horticulture, Huaqiao University, Xiamen, Fujian 361021, China
    2 Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana 61801
  • Received:2018-12-18 Accepted:2019-01-09 Online:2019-04-20
  • Contact: Wang Qizhi E-mail:wqz@hqu.edu.cn

直刺变豆菜(Sanicula orthacantha)是中国广泛分布的多年生草本植物, 也是一味著名的民族药。本文通过二代高通量测序平台Illumina HiSeq PE150对直刺变豆菜叶绿体全基因组进行测序, 并通过生物信息学方法对其结构特征进行分析。结果表明: 直刺变豆菜叶绿体全基因组大小为157,163 bp, 包括大单拷贝区(large single copy, LSC)、小单拷贝区(small single copy, SSC)和2个反向重复序列(inverted repeat sequence, IRa和IRb), 长度分别为87,547 bp、17,122 bp和26,247 bp, 具有典型被子植物叶绿体基因组环状四分体结构; 共注释得到129个基因, 包括8个核糖体RNA (rRNA)基因、37个转运RNA (tRNA)基因和84个蛋白质编码基因。直刺变豆菜在叶绿体基因组结构、基因种类、排列顺序上与其他伞形科植物基本一致。直刺变豆菜叶绿体全基因组测序的成功为变豆菜属植物完整叶绿体基因组组装及其特征分析提供了新的方法。

关键词: 高通量测序, 变豆菜属, 基因组装, 系统发育分析

Sanicula orthacantha is a perennial herb widely distributed in China and is a widely used for medicinal purposes. In this study, the whole chloroplast genome was sequenced and analyzed using bioinformatics methods. The results showed that it was a circular molecule 157,163 bp in length with a typical quadripartite structure including a pair of inverted repeats (IRa and IRb) of 26,247 bp that were separated by large and small single copy regions (LSC and SSC) of 87,547 bp and 17,122 bp, respectively. A total of 129 predicted genes, including 84 protein-coding genes, 37 tRNA genes and eight rRNA genes were identified. Compared with other Apiaeceae species, the S. orthacantha chloroplast genome had few differences in size, order and structure. The success of sequencing the S. orthacantha chloroplast genome provides a new method for the complete chloroplast genome assembly and characterization of Sanicula species, providing a methodological guide for the study of Sanicula plant evolution and phylogeny.

Key words: high-throughput sequencing, Sanicula L., gene assembly, phylogenetic analysis

图1

直刺变豆菜叶绿体全基因组。外圈基因逆时针方向转录, 内圈基因顺时针方向转录, 不同的颜色表明基因不同的功能, 小圈中深灰色表示GC含量, 浅灰色表示AT含量。"

表1

直刺变豆菜叶绿体基因组所编码的基因"

基因分类
Category for genes
基因分组
Group of genes
基因名称
Name of genes
表达相关基因
Self replication
核糖体RNA基因 Ribosomal RNAs rrn4.5(×2), rrn5(×2), rrn16(×2), rrn 23(×2)
转运RNA基因 Transfer RNAs trnA-UGC(×2), trnC-GCA, trnD-GUG, trnE-UCC, trnF-GAA, trnfM-CAU, trnG-GCC, trnG-UCC, trnH-GUG, trnI-CAU(×2), trnI-GAU(×2), trnK- UUU, trnL-CAA(×2), trnL-UAA, trnL-UAG, trnM-CAU, trnN-GUU (×2) trnP-UGG, trnQ-UUC, trnR-ACG(×2) trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC(×2), trnV-UAC, trnW-CCA, trnY-GUA
核糖体小亚基基因
Ribosomal small subunit (SSU)
rps16, rps2, rps14, rps4, rps18, rps11, rps8, rps3, rps19, rps7(×2), rps12, rps15
核糖体大亚基基因
Ribosomal large subuni (LSU)
rpl33, rpl20, rpl36, rpl14, rpl16, rpl22, rpl2(×2), rpl23(×2), rpl32
RNA聚合酶亚基基因 RNA polymerase rpoA, rpoB, rpoC1, rpoC2
光合作用相关基因
Genes for
photosynthesis
光合系统I基因 Photosystem I psaA, psaB, psaC, psaI, psaJ
光合系统II基因 Photosystem II psbA, psbB, psbK, psbI, psbM, psbD, psbC, psbE, psbJ, psbL, psbT, psbH, psbN, psbF, psbZ, psbJ
细胞色素复合物基因 Cytochrome b/f complex petA, petD, petG, petL, petN
ATP合酶基因 ATP synthase atpA, atpF, atpH, atpI, atpE, atpB
依赖ATP的蛋白酶单元p基因
ATP-dependent protease subunit p gene
clpP
二磷酸核酮糖羧化酶大亚基基因
RubiscoCO large subunit
rbcL
NADH脱氢酶基因 NADH dehydrogenase ndhJ, ndhK, ndhC, ndhB(×2), ndhF, ndhD, ndhE, ndhG, ndhI, ndhA, ndhH
其他基因
Other genes
成熟酶基因 Maturase matK
包裹膜蛋白基因 Envelop membrane protein cemA
乙酰辅酶A羧化酶亚基基因
Subunit of acetyl-CoA-carboxylase
accD
c型细胞色素合成基因
c-type cytochrome synthesis ccsA gene
ccsA
转录起始因子基因
Transcription initiation factor IF-1
InfA
未知功能基因
Genes of unknown
function
保守开放阅读框
Conserved open reading frames
ycf1, ycf2(×2), ycf3, ycf4

图2

基于叶绿体全基因组序列用最大似然法构建的15个物种的系统进化树"

[1] Andrews S ( 2013) Babraham Bioinformatics FastQC: A Quality Control Tool for High Throughput Sequence Data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc.
[2] Bayly MJ, Rigault P, Spokevicius A, Ladiges PY, Ades PK, Anderson C, Bossinger G, Merchant A, Udovicic F, Woodrow IE ( 2013) Chloroplast genome analysis of Australian eucalypts—Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae). Molecular Phylogenetics & Evolution, 69, 704-716.
[3] Clegg MT, Gaut BS, Learn G, Morton BR ( 1994) Rates and patterns of chloroplast DNA evolution. Proceedings of the National Academy of Sciences, USA, 91, 6795-6801.
doi: 10.1073/pnas.91.15.6795
[4] Daniell H, Lin CS, Ming Y, Chang WJ ( 2016) Chloroplast genomes: Diversity, evolution, and applications in genetic engineering. Genome Biology, 17, 134-163.
doi: 10.1186/s13059-016-1004-2
[5] Dierckxsens N, Mardulyn P, Smits G ( 2017) NOVO-Plasty: De novo assembly of organelle genomes from whole genome data. Nucleic Acids Research, 45, e18.
doi: 10.1093/nar/gkw1060
[6] Downie SR, Jansen RK ( 2015) 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. Systematic Botany, 40, 336-351.
doi: 10.1600/036364415X686620
[7] Ge L, Shen LQ, Chen QY, Li XM, Zhang L ( 2017) The complete chloroplast genome sequence of Hydrocotyle sibthorpioides (Apiales: Araliaceae). Mitochondrial DNA Part B, 2, 29-30.
doi: 10.1080/23802359.2016.1241676
[8] Jansen RK, Raubeson LA, Boore JL, Depamphilis CW, Chumley TW, Haberle RC, Wyman SK, Alverson AJ, Peery R, Herman SJ ( 2005) Methods for obtaining and analyzing whole chloroplast genome sequences. Methods in Enzymology, 395, 348-384.
doi: 10.1016/S0076-6879(05)95020-9
[9] Kazutaka K, Kazuharu M, Kei-Ichi K, Takashi M ( 2002) MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30, 3059-3066.
doi: 10.1093/nar/gkf436
[10] Kearse M, Moir R, Wilson A, Stoneshavas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C ( 2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28, 1647-1649.
doi: 10.1093/bioinformatics/bts199
[11] Kim KJ, Lee HL ( 2005) Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Research, 11, 247-261.
[12] Kumar S, Stecher G, Tamura K ( 2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology & Evolution, 33, 1870-1874.
[13] Lohse M, Drechsel O, Kahlau S, Bock R ( 2013) OrganellarGenomeDRAW—A suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Research, 41, W575.
doi: 10.1093/nar/gkt289
[14] Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Qi P, Liu Y ( 2012) SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler. GigaScience, 1, 18.
doi: 10.1186/2047-217X-1-18
[15] McCauley DE, Stevens JE, Peroni PA, Raveill JA ( 1996) The spatial distribution of chloroplast DNA and allozyme polymorphisms within a population of Silene alba (Caryophyllaceae). American Journal of Botany, 83, 727-731.
doi: 10.1002/j.1537-2197.1996.tb12761.x
[16] Peden JF ( 1999) CodonW. PhD Dissertation, University of Nottingham, Nottinghamshire, UK.
[17] Ruhlman T, Lee SB, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H ( 2006) Complete plastid genome sequence of Daucus carota: Implications for biotechnology and phylogeny of angiosperms. BMC Genomics, 7, 222-235.
doi: 10.1186/1471-2164-7-222
[18] Shan RH, She ML ( 1979) Flora Reipublicae Popularis Sinicae, Tomus 14, pp. 12-67. Science Press, Beijing. (in Chinese)
[ 单人骅, 佘孟兰 ( 1979) 中国植物志, 第十四卷, 12-67页. 科学出版社, 北京.]
[19] Sichuan Provincial Health Department (1979) Sichuan Chinese Herbal Medicine Standard (Trial Draft). Sichuan Provincial Health Department, Chengdu. (in Chinese)
[ 四川省卫生局 ( 1979) 四川省中草药标准(试行稿). 四川省卫生局, 成都.]
[20] Small RL, Cronn RC, Wendel JF ( 2004) Use of nuclear genes for phylogeny reconstruction in plants. Australian Systematic Botany, 17, 145-170.
doi: 10.1071/SB03015
[21] Soltis PS, Soltis DE ( 2000) The role of genetic and genomic attributes in the success of polyploids. Proceedings of the National Academy of Sciences, USA, 97, 7051-7057.
doi: 10.1073/pnas.97.13.7051
[22] Thiel T, Michalek W, Varshney R, Graner A ( 2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical & Applied Genetics, 106, 411-422.
[23] Wang L, Dong WP, Zhou SL ( 2012) Structural mutations and reorganizations in chloroplast genomes of flowering plants. Acta Botanica Boreali-Occidentalia Sinica. 32, 1282-1288. (in Chinese with English abstract)
[ 王玲, 董文攀, 周世良 ( 2012) 被子植物叶绿体基因组的结构变异研究进展. 西北植物学报, 32, 1282-1288.]
[24] Xie ZW ( 1996) The Compilation of Chinese Herbal Medicine. People’s Medical Publishing House, Beijing. (in Chinese)
[ 谢宗万 ( 1996) 全国中草药汇编. 人民卫生出版社, 北京.]
[25] Xing SC, Clarke JL ( 2008) Process in chloroplast genome analysis. Progress in Biochemistry and Biophysics, 35, 21-28. (in Chinese with English abstract)
[ 邢少辰 , Clarke JL ( 2008) 叶绿体基因组研究进展. 生物化学与生物物理进展, 35, 21-28.]
[26] Zhang HY ( 1994) Annals of Chinese Traditional Medicine Resources. Science Press, Beijing. (in Chinese)
[ 张惠源 ( 1994) 中国中药资源志要. 科学出版社, 北京.]
[27] Zhang T, Fang Y, Wang X, Deng X, Zhang X, Hu S, Yu J ( 2012) The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica: Insights into the evolution of plant organellar genomes. PLoS ONE, 7, e30531.
doi: 10.1371/journal.pone.0030531
[28] Zhao YB, Yin JL, Guo HY, Zhang YY, Xiao W, Sun C, Wu JY, Qu XB, Yu J, Wang XM, Xiao JF ( 2015) The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng. Frontiers in Plant Science, 5, 696-709.
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