Comparative Analyses of Indels Based on the Whole Chloroplast Genome of Cuscuta reflexa between European and Asian Populations

doi:10.7677/ynzwyj201312070

Abstract

Abstract:

We determined the complete nucleotide sequence of the chloroplast genome of Asian Cuscuta reflexa which is a world distributed dodder using shotgun method at Illumina’s Genome Analyzer, and then compared it with the corresponding published sequence of the same species that distributed in Europe. The chloroplast genome length was 120972bp, which was 549bp shorter than the European one, with a large single copy (LSC) region of 79499bp, a small single copy (SSC) region of 8369bp and two inverted repeats (IR) of 16552bp each. The overall GC content was 38.3%, which is slightly higher than European C.reflexa. The chloroplast genome of C.reflexa from both area encoded identical functional genes in the same order. On the other hand, detailed analyses revealed 251 insertions and 210 deletions. The length of indels substitution sum to 7649bp and the largest insertion and deletion reached 426bp and 435bp respectively. Meanwhile, 3720bp base substitution events were found in the entire chloroplast genome of Asian C.reflaxa. Majority of the indels observed were singlebase but four large length mutations longer than 200bp were also detected, including two deletions in ycf2 region, one insertion in trnFpsbE and another insertion in matKtrnQ. Most indels located in the intergenic regions of the LSC region while rare in the IR region. This research initially compared the whole chloroplast genome of same heterotrophic plants distributed in different continents.

Key words: Cuscuta reflexa, Chloroplast genome, Indels, Comparative analysis

摘要：

运用鸟枪法在Illumina测序仪上对亚洲分布的大花菟丝子(Cuscuta reflexa)叶绿体基因组核苷酸全序列进行测定，并与已经发表的分布于欧洲的大花菟丝子进行了比较分析。研究结果表明亚洲分布的大花菟丝子叶绿体基因组总长度为120972bp，由79499bp的长单拷贝区，8369bp的短单拷贝区，以及两个16552bp的反向重复区组成，其长度比欧洲分布的大花菟丝子小了549bp；基因组总GC含量为38.3%，稍高于欧洲分布的大花菟丝子。两地区的大花菟丝子叶绿体全基因组编码的功能基因完全相同，且基因排列顺序也完全一致。另外，经过进一步序列比对后发现亚洲分布的大花菟丝子与欧洲分布的存在251个插入和210个缺失现象，总插入缺失及碱基替换长度分别为7649bp和3720bp，最大的插入和缺失长度分别为426bp和435bp。很多插入缺失都是单碱基，但仍然存在四个长度超过200bp的大突变，两个大的缺失发生在ycf2基因中，两个大的插入分别发生在trnFpsbE和matKtrnQ间隔区，详细的对比后发现大量的插入缺失都发生在大单拷贝区的基因间隔区，且插入缺失在反向重复区的发生频率较低。本研究首次报道不同大洲分布的同种异养植物的叶绿体全基因组比较分析，为研究这两个区域的居群多样性提供了基础资料。

关键词: 大花菟丝子, 叶绿体基因组, 插入缺失, 对比分析

CLC Number:

Q 75

WANG Chao-Bo-, GONG Xun. Comparative Analyses of Indels Based on the Whole Chloroplast Genome of Cuscuta reflexa between European and Asian Populations[J]. Plant Diversity, 2013, 35(2): 158-164.

王朝波1、2, 龚洵1. 欧亚大陆分布的大花菟丝子叶绿体基因组插入缺失分析[J]. Plant Diversity, 2013, 35(2): 158-164.

References

Asano T, Tsudzuki T, Takahashi S et al., 2004. Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: a comparative analysis of four monocot chloroplast genomes［J］. DNA Research, 11 (2): 93—99
Calsa Júnior T, Carraro DM, Benatti MR et al., 2004. Structural features and transcriptediting analysis of sugarcane (Saccharum officinarum L.) chloroplast genome［J］. Current Genetics, 46 (6): 366—373
Chung HJ, Jung JD, Park HW et al., 2006. The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241bp deletion in cultivated potato chloroplast DNA sequence［J］. Plant Cell Reports, 25 (12): 1369—1379
Delannoy E, Fujii S, Colas des FrancsSmall C et al., 2011. Rampant gene loss in the underground orchid Rhizanthella gardneri highlights evolutionary constraints on plastid genomes［J］. Molecular Biology and Evolution, 28 (7): 2077—2086
Funk HT, Berg S, Krupinska K et al., 2007. Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii［J］. BMC Plant Biology, 7 (45): 1—12
Guisinger MM, Kuehl JV, Boore JL et al., 2011. Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage［J］. Molecular Biology and Evolution, 28 (1): 583—600
Haberle RC, Fourcade HM, Boore JL et al., 2008. Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes［J］. Journal of Molecular Evolution, 66 (4): 350—361
Hirao T, Watanabe A, Kurita M et al., 2008. Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species［J］. BMC Plant Biology, 8 (70): 1—20
Hiratsuka J, Shimada H, Whittier R et al., 1989. The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals［J］. Molecular and General Genetics, 217 (2-3): 185—194
Jo YD, Park J, Kim J et al., 2011. Complete sequencing and comparative analyses of the pepper (Capsicum annuum L.) plastome revealed high frequency of tandem repeats and large insertion/deletions on pepper plastome［J］. Plant Cell Reports, 30 (2): 217—229
Katoh K, Toh H, 2008. Recent developments in the MAFFT multiple sequence alignment program［J］. Briefings in Bioinformatics, 9 (4): 286—298
Kelchner SA, 2000. The evolution of noncoding chloroplast DNA and its application in plant systematics［J］. Annals of The Missouri Botanical Garden, 87 (4): 482—498
Krause K, 2011. Piecing together the puzzle of parasitic plant plastome evolution［J］. Planta, 234 (4): 647—656
Kumar S, Hahn FM, McMahan CM et al., 2009. Comparative analysis of the complete sequence of the plastid genome of Parthenium argentatum and identification of DNA barcodes to differentiate Parthenium species and lines［J］. BMC Plant Biology, 9 (131): 1—12
Lee HL, Jansen RK, Chumley TW et al., 2007. Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions［J］. Molecular Biology and Evolution, 24 (5-6): 1161—1180
Li RQ, Yu C, Li YR et al., 2009. SOAP2: an improved ultrafast tool for short read alignment［J］. Bioinformatics, 25 (15): 1966—1967
Librado P, Rozas J, 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data［J］. Bioinformatics, 25 (11): 1451—1452
Logacheva MD, Schelkunov MI, Penin AA, 2011. Sequencing and analysis of plastid genome in mycoheterotrophic orchid Neottia nidusavis［J］. Genome Biology and Evolution, 3 (1): 1296—1303
Lohse M, Drechsel O, Bock R, 2007. OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of highquality custom graphical maps of plastid and mitochondrial genomes［J］. Current Genetics, 52 (5-6): 267—274
Madoka Y, Tomizawa K, Mizoi J et al., 2002. Chloroplast transformation with modified accD operon increases acetylCoA carboxylase and causes extension of leaf longevity and increase in seed yield in tobacco［J］. Plant and Cell Physiology, 43 (12): 1518—1525
Maier RM, Neckermann K, Igloi GL et al., 1995. Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing［J］. Journal of Molecular Biology, 251 (5): 614—628
Matsuoka Y, Yamazaki Y, Ogihara Y et al., 2002. Whole chloroplast genome comparison of rice, maize, and wheat: implications for chloroplast gene diversification and phylogeny of cereals［J］. Molecular Biology and Evolution, 19 (12): 2084—2091
McNeal JR, Kuehl JV, Boore JL et al., 2007. Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta［J］. BMC Plant Biology, 7 (57): 1—22
Moore MJ, Soltis PS, Bell CD et al., 2010. Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots［J］. Proceedings of the National Academy of Sciences, 107 (10): 4623—4628
Ogihara Y, Isono K, Kojima T et al., 2002. Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA［J］. Molecular Genetics and Genomics, 266 (5): 740—746
Plader W, Yukawa Y, Sugiura M et al., 2007. The complete structure of the cucumber (Cucumis sativus L.) chloroplast genome: its composition and comparative analysis［J］. Cellular & Molecular Biology Letters, 12 (4): 584—594
Saski C, Lee SB, Daniell H et al., 2005. Complete chloroplast genome sequence of Gycine max and comparative analyses with other legume genomes［J］. Plant Molecular Biology, 59 (2): 309—322
Shahid MM, Nishikawa T, Fukuoka S et al., 2004. The complete nucleotide sequence of wild rice (Oryza nivara) chloroplast genome: first genome wide comparative sequence analysis of wild and cultivated rice［J］. Gene, 340 (1): 133—139
Triboush SO, Danilenko NG, Davydenko OG, 1998. A method for isolation of chloroplast DNA and mitochondrial DNA from sunflower［J］. Plant Molecular Biology, 16 (2): 183—183
Wicke S, Schneeweiss GM, dePamphilis CW et al., 2011. The evolution of the plastid chromosome in land plants: gene content, gene order, gene function［J］. Plant Molecular Biology, 76 (3-5): 273—297
Wolfe KH, Morden CW, Palmer JD, 1992. Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant［J］. Proceedings of the National Academy of Sciences, 89 (22): 10648—10652
Wyman S, Jansen R, Boore J, 2004. Automatic annotation of organellar genomes with DOGMA［J］. Bioinformatics, 20 (1): 3252—3255

[1]	Jiangshan Lai (赖江山), Yan He (何雁), Mi Hou (侯蜜, Aiying Zhang (张爱英), Gang Wang (王刚), Lingfeng Mao (毛岭峰). Evaluating the relative importance of phylogeny and predictors in phylogenetic generalized linear models using the phylolm.hp R package [J]. Plant Diversity, 2025, 47(05): 709-717.
[2]	Ibrokhimjon Ergashov, Ziyoviddin Yusupov, Alireza Dolatyari, Mina Khorasani, İsmail Eker, Nazgul Turdumatova, Georgy Lazkov, Farruhbek Rasulov, Hang Sun, Tao Deng, Komiljon Tojibaev. New insights into the molecular phylogeny and biogeographical history of Allium subgenus Melanocrommyum (Amaryllidaceae) based on plastome and nuclear sequences [J]. Plant Diversity, 2025, 47(04): 561-575.
[3]	Hai-Su Hu, Jiu-Yang Mao, Xue Wang, Yu-Ze Liang, Bei Jiang, De-Quan Zhang. Plastid phylogenomics and species discrimination in the “Chinese” clade of Roscoea (Zingiberaceae) [J]. Plant Diversity, 2023, 45(05): 523-534.
[4]	Na Su, Richard G.J. Hodel, Xi Wang, Jun-Ru Wang, Si-Yu Xie, Chao-Xia Gui, Ling Zhang, Zhao-Yang Chang, Liang Zhao, Daniel Potter, Jun Wen. Molecular phylogeny and inflorescence evolution of Prunus (Rosaceae) based on RAD-seq and genome skimming analyses [J]. Plant Diversity, 2023, 45(04): 397-408.
[5]	Ying-Min Zhang, Li-Jun Han, Cong-Wei Yang, Zi-Li Yin, Xing Tian, Zi-Gang Qian, Guo-Dong Li. Comparative chloroplast genome analysis of medicinally important Veratrum (Melanthiaceae) in China: Insights into genomic characterization and phylogenetic relationships [J]. Plant Diversity, 2022, 44(01): 70-82.
[6]	Hanqing Tang, Lu Tang, Shicheng Shao, Yulan Peng, Lu Li, Yan Luo. Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae, Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution [J]. Plant Diversity, 2021, 43(05): 350-361.
[7]	Ziyoviddin Yusupov, Tao Deng, Sergei Volis, Furkat Khassanov, Dilmurod Makhmudjanov, Komiljon Tojibaev, Hang Sun. Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion [J]. Plant Diversity, 2021, 43(02): 102-110.
[8]	Virginia M. Mwanzia, Ding-Xuan He, Andrew W. Gichira, Yan Li, Boniface K. Ngarega, Mwihaki J. Karichu, Peris W. Kamau, Zhi-Zhong Li. The complete plastome sequences of five Aponogeton species (Aponogetonaceae): Insights into the structural organization and mutational hotspots [J]. Plant Diversity, 2020, 42(05): 334-342.
[9]	JIN Gui-Hua, CHEN Shi-Yun, YI Ting-Shuang, ZHANG Shu-Dong. Characterization of the Complete Chloroplast Genome of Apple (Malus × domestica, Rosaceae)* [J]. Plant Diversity, 2014, 36(04): 468-484.
[10]	ZHANG Yu-Xiao-, HU Yu-Xing-, MA Peng-Fei-, ZHANG Li-Na-, LI De-Zhu. Selection of Potential Plastid DNA Barcodes for Bambusoideae (Poaceae) [J]. Plant Diversity, 2013, 35(6): 743-750.
[11]	ZHANG Yun-Jie, LI De-Zhu. Advances in Phylogenomics Based on Complete Chloroplast Genomes [J]. Plant Diversity, 2011, 33(4): 365-375.

Comparative Analyses of Indels Based on the Whole Chloroplast Genome of Cuscuta reflexa between European and Asian Populations

欧亚大陆分布的大花菟丝子叶绿体基因组插入缺失分析

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 11

Recommended Articles

Metrics

Comments