马铃薯‘合作88’自交分离群体叶绿体基因组遗传组成分析

doi:10.16420/j.issn.0513-353x.2022-0721

摘要/Abstract

摘要：

为了从基因组水平解析马铃薯品种‘合作88’（Solanum tuberosum‘Cooperation 88’）叶绿体基因组多态性和遗传多样性，了解其自交分离群体叶绿体基因组遗传组成和变异，通过对‘合作88’及其30个自交分离群体材料的叶绿体基因组测序组装，并与其他11个茄科物种、拟南芥和水稻的叶绿体基因组序列进行比较分析。结果表明，‘合作88’叶绿体基因组为典型环状结构，长度为160 323 bp，GC含量为38.6%，共注释29个tRNA基因和77个蛋白质编码基因。30个自交后代叶绿体基因组大小在160 331 ~ 162 120 bp之间，注释预测基因数95 ~ 106个，GC含量36.7% ~ 38.6%。进一步分析表明，‘合作88’和其30个自交后代叶绿体类型均为W型，未呈现出多态性。‘合作88’和其自交后代均偏好使用以A/U结尾的密码子，子代叶绿体基因组密码子4种碱基使用频率不同，推断其相对同义密码子使用度、有效密码子数和高频密码子数的差异为叶绿体基因组随机突变和翻译自然选择所导致。此外，16个正向重复序列中有12个存在于‘合作88’及所有自交后代中，另有4个为子代中新出现的。UPGMA聚类分析和共线性分析发现重复序列的出现和基因丢失使得自交后代叶绿体基因组遗传多样性增加。

关键词: 马铃薯, 自交分离群体, 叶绿体基因组, 重复序列, 密码子偏好性

Abstract:

In order to analyze the chloroplast genome polymorphism and genetic diversity of potato ‘Cooperation 88’at the genome level and to understand the genetic composition and variation of the chloroplast genome of the selfing population of‘Cooperation 88’，this study assembled the chloroplast genomes of‘Cooperation 88’and 30 selfing progenies and comparatively analyzed them with the chloroplasts genomes of 11 other Solanaceae species，Arabidopsis thaliana and Oryza sativa. The results showed that the assembled chloroplast genome of the‘Cooperation 88’was a typical circular structure with a length of 160 323 bp and the GC content of 38.6%，including a total of 29 annotated tRNA genes and 77 protein-coding genes. The size of the chloroplast genome of the 30 selfing progenies ranged from 160 331 bp to 162 120 bp，the number of genes predicted was 95-106，and the GC content was 36.7%-38.6%. Further analysis showed that the chloroplast types of the parent and 30 selfing progeny were all W-type，showing no polymorphism. Both parent and selfing progenies prefer to use codons ending with A/U，and the progenies chloroplasts genomes codon pairs used different frequencies of the four bases，indicating that the relative synonymous codon usage and effective codons in the chloroplast genome of selfing progenies variations in the number of codons and high-frequency codons were caused by random mutation and translational natural selection in the chloroplast genome. In addition，12 repeats existing in the parent were also present in all progenies but four repeats were new appeared in progeny. UPGMA analysis and collinearity analysis also found that the evolutionary level of the Solanum chloroplast genome was highly conserved, but the appearance of repeats and the loss of genes changed the size of the progeny chloroplast genome and increased their genetic diversity.

Key words: potato, selfing population, chloroplast genome, repeat sequence, codon bias

王荣艳, 李清, 徐灵, 王秋洁, 宋昱, 母昌冉, 唐唯, 郝大海. 马铃薯‘合作88’自交分离群体叶绿体基因组遗传组成分析[J]. 园艺学报, 2023, 50(8): 1649-1663.

WANG Rongyan, LI Qing, XU Ling, WANG Qiujie, SONG Yu, MU Changran, TANG Wei, HAO Dahai. Genetic Analysis of Chloroplast Genome Characteristics of Potato‘Cooperation 88’Selfing Population[J]. Acta Horticulturae Sinica, 2023, 50(8): 1649-1663.

图/表 11

参考文献 58

[1]	Ames M, Salas A, Spooner D M. 2007. The discovery and phylogenetic implications of a novel 41 bp plastid DNA deletion in wild potatoes. Plant Systematics and Evolution, 268:159-175. doi: 10.1007/s00606-007-0567-5 URL
[2]	Amiryousefi A, Hyvönen J, Poczai P. 2018. The chloroplast genome sequence of bittersweet(Solanum dulcamara):plastid genome structure evolution in Solanaceae. Public Library of Science, 13 (4):e0196069.
[3]	Birky C W J. 1995. Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution. Proceedings of the National Academy of Sciences of the United States of America, 92 (25):11331-11338.
[4]	Chimote V P, Chakrabarti S K, Pattanayak D, Pandey S K, Naik P S. 2008. Molecular analysis of cytoplasm type in Indian potato varieties. Euphytica, 162:69-80. doi: 10.1007/s10681-007-9563-7 URL
[5]	Choudhary A, Wright L, Ponce O, Chen J, Prashar A, Sanchez-Moran E, Luo Z, Compton L. 2020. Varietal variation and chromosome behaviour during meiosis in Solanum tuberosum. Heredity(Edinb), 125 (4):212-226.
[6]	Chung H J, Jung J D, Park H W, Kim J H, Cha H W, Min S R, Jeong W J, Liu J R. 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. Plant Cell Reports, 25 (12):1369-1379. doi: 10.1007/s00299-006-0196-4 URL
[7]	Darling A C, Mau B, Blattner F R, Perna N T. 2004. Mauve:multiple alignment of conserved genomic sequence with rearrangements. Genome Research, 14 (7):1394-1403. doi: 10.1101/gr.2289704 pmid: 15231754
[8]	de Oliveira J L, Morales A C, Hurst L D, Urrutia A O, Thompson C R L, Wolf J B. 2021. Inferring adaptive codon preference to understand sources of selection shaping codon usage bias. Molecular Biology and Evolution, 38 (8):3247-3266. doi: 10.1093/molbev/msab099 pmid: 33871580
[9]	Ding Zhijie, Bao Jinbo, Rouxian Guli, Zhu Tiantian, Li Xueli, Miao Haoyu, Tian Xinmin. 2022. Comparative chloroplast genome study of Mallus servisii‘Red Delicious’and‘Golden Delicious’. Acta Horticulturae Sinica, 49 (9):1977-1990. (in Chinese) doi: 10.16420/j.issn.0513-353x.2021-0378
	丁志杰, 包金波, 柔鲜古丽, 朱甜甜, 李雪丽, 苗浩宇, 田新民. 2022. 新疆野苹果与‘元帅’‘金冠’的叶绿体基因组比对研究. 园艺学报, 49 (9):1977-1990. doi: 10.16420/j.issn.0513-353x.2021-0378
[10]	Doyle J J, Doyle J L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull, 19:11-15.
[11]	Endelman J B, Jansky S H. 2016. Genetic mapping with an inbred line-derived F₂ population in potato. Theoretical and Applied Genetics, 129 (5):935-943. doi: 10.1007/s00122-016-2673-7 pmid: 26849236
[12]	Feng S, Zheng K, Jiao K, Cai Y, Chen C, Mao Y, Wang L, Zhan X, Ying Q, Wang H. 2020. Complete chloroplast genomes of four Physalis species(Solanaceae):lights into genome structure,comparative analysis,and phylogenetic relationships. BMC Plant Biology, 20 (1):242. doi: 10.1186/s12870-020-02429-w
[13]	Greiner S, Lehwark P, Bock R. 2019. OrganellarGenomeDRAW(OGDRAW)version 1.3.1:expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research, 47 (W1):W59-W64.
[14]	Guan Xi-jin, Zhu Zhi-guo, Zheng Hao-ji, Yan Li-jun, Zhu Guang-tao. 2021. Comparative analysis of plastid genomes between potato and its wild relatives. Journal of Yunnan Normal University(Natural Sciences Edition), 41 (4):33-40. (in Chinese)
	关惜今, 朱智国, 郑昊吉, 严丽君, 祝光涛. 2021. 马铃薯与其野生近缘种叶绿体基因组差异分析. 云南师范大学学报(自然科学版), 41 (4):33-40.
[15]	Harris R S. 2007. Improved pairwise alignment of genomic DNA[Ph. D. Dissertation]. Statechurch:The Pennsylvania State University.
[16]	Hosaka K, Hanneman R E. 1987. A rapid and simple method for determination of potato chloroplast DNA type. American Potato Journal, 64:345-353. doi: 10.1007/BF02853596 URL
[17]	Hosaka K, Sanetomo R. 2012. Development of a rapid identification method for potato cytoplasm and its use for evaluating Japanese collections. Theoretical and Applied Genetics, 125 (6):1237-1251. doi: 10.1007/s00122-012-1909-4 pmid: 22696007
[18]	Hosaka K, Sanetomo R. 2020. Creation of a highly homozygous diploid potato using the S locus inhibitor(Sli)gene. Euphytica, 216:169. doi: 10.1007/s10681-020-02699-3
[19]	Hosaka K. 2002. Distribution of the 241 bp deletion of chloroplast DNA in wild potato species. American Journal of Potato Research, 79:119-123. doi: 10.1007/BF02881520 URL
[20]	Jiang Sisi, Yuan Jun, Zhou Wenjun, Niu Genhua, Zhou Junqin. 2022. Complete chloroplast genome sequence and characteristics analysis of Carya illinoinensis. Acta Horticulturae Sinica, 49 (8):1772-1784. (in Chinese)
	蒋思思, 袁军, 周文君, 钮根花, 周俊琴. 2022. 薄壳山核桃(Carya illinoinensis)叶绿体基因组及其特征分析. 园艺学报, 49 (8):1772-1784. doi: 10.16420/j.issn.0513-353x.2021-0389
[21]	Jiao Kai-li, Zheng Kai-xin, Zhu Yu-jia, Wang Hui-zhong, Feng Shang-guo. 2019. Advances in chloroplast genome research of Solanaceae plants. Journal of Hangzhou Normal University(Natural Science Edition), 18 (2):160-167. (in Chinese)
	焦凯丽, 郑凯欣, 朱宇佳, 王慧中, 冯尚国. 2019. 茄科植物叶绿体基因组研究进展. 杭州师范大学学报(自然科学版), 18 (2):160-167.
[22]	Jo Y D, Parkk J, Kim J, Song W, Hur C G, Lee Y H, Kang B C. 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. Plant Cell Reports, 30 (2):217-229. doi: 10.1007/s00299-010-0929-2 URL
[23]	Kahlau S, Aspinall S, Gray J C, Bock R. 2006. Sequence of the tomato chloroplast DNA and evolutionary comparison of Solanaceous plastid genomes. Journal of Molecular Evolution, 63 (2):194-207. doi: 10.1007/s00239-005-0254-5 pmid: 16830097
[24]	Khan A R, Park C E, Park G S, Seo Y J, So J H, Shin J H. 2017. The whole chloroplast genome sequence of black nightshade plant(Solanum nigrum). Mitochondrial DNA Part A:DNA Mapping,Sequencing,and Analysis, 28 (2):169-170.
[25]	Koichiro T, Glen S, Sudhir K. 2021. MEGA11:molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38 (7):3022-3027. doi: 10.1093/molbev/msab120 pmid: 33892491
[26]	Li C H, Wang J, Chien D H, Song B, Vanderzaag P. 2011. Cooperation 88:a high yielding,multi-purpose,late blight resistant cultivar growing in southwest China. American Journal of Potato Research, 88:190-194. doi: 10.1007/s12230-010-9174-z URL
[27]	Li Guo-bin, Wang Wei-wei, Shi Cong-xian, Bai Jin-lian, Li Can-hui, Tang Wei. 2019. Identification of potato variety resources and construction of molecular fingerprint in Yunnan Province. Molecular Plant Breeding, 17 (14):4679-4691. (in Chinese)
	李国彬, 王伟伟, 史聪仙, 白瑾琏, 李灿辉, 唐唯. 2019. 云南省马铃薯品种资源鉴定及分子指纹图谱的建立. 分子植物育种, 17 (14):4679-4691.
[28]	Linneweber C S, Regel R, Du T G, Hupfer H, Herrmann R G, Maier R M. 2002. The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum:the role of RNA editing in generating divergence in the process of plant speciation. Molecular Biology and Evolution, 19 (9):1602-1612. doi: 10.1093/oxfordjournals.molbev.a004222 URL
[29]	Liu Chao, Han Li-hong, Dai Xiao-bo, Liu Chen-yu. 2022. Chloroplast genome characteristics and evolution of Capsicum. Chinese Journal of Tropical Crops, 43 (3):447-454. (in Chinese)
	刘潮, 韩利红, 代小波, 刘宸语. 2022. 辣椒属叶绿体基因组特征及进化. 热带作物学报, 43 (3):447-454.
[30]	Liu Y. 2020. A code within the genetic code:codon usage regulates co-translational protein folding. Cell Communication and Signaling, 18 (1):145. doi: 10.1186/s12964-020-00642-6 pmid: 32907610
[31]	Lössl A, Adler N, Hom R, Frei U, Wenzel. 1999. Chondriome-type characterization of potato:mt α,β,γ,δ,ɛ and novel plastid-mitochondrial configurations in somatic hybrids. Theoretical and Applied Genetics, 99:1-10.
[32]	Lössl A, Götz M, Braun A, Wenzel G. 2000. Molecular markers for cytoplasm in potato:male sterility and contribution of different plastid-mitochondrial configurations to starch production. Euphytica, 116:221-230. doi: 10.1023/A:1004039320227 URL
[33]	Luo Jie, Tang Wei, Wang Pei, Tang Fei,Li Can-hui. 2018. Genotype analysis of PVY and PLRV resistance genes in tetraploid potato‘Cooperation 88’. Journal of Anhui Agricultural Sciences, 46 (17):98-101,128. (in Chinese)
	罗杰, 唐唯, 王培, 唐飞, 李灿辉. 2018. 四倍体马铃薯‘合作88’PVY、PLRV抗性基因的基因型分析. 安徽农业科学, 46 (17):98-101,128.
[34]	Lynch M, Marinov G K. 2015. The bioenergetic costs of a gene. Proceedings of the National Academy of Sciences of the United States of America, 112 (51):15690-15695.
[35]	Marais G, Mouchiroud D, Duret L. 2003. Neutral effect of recombination on base composition in Drosophila. Genetical Research, 81 (2):79-87. doi: 10.1017/S0016672302006079 URL
[36]	Mehmood F, Abdullah, Shahzadi I, Ahmed I, Waheed M T, Mirza B. 2020. Characterization of Withania somnifera chloroplast genome and its comparison with other selected species of Solanaceae. Genomics, 112 (2):1522-1530. doi: 10.1016/j.ygeno.2019.08.024 URL
[37]	Myrick S N B. 2016. An economic impact assessment of Cooperation 88 potato variety in the Yunnan Province of China[Ph. D. Dissertation]. Blacksburg:Virginia Polytechnic Institute and State University.
[38]	Parvathy S T, Udayasuriyan V, Bhadana V. 2022. Codon usage bias. Molecular Biology Reports, 49 (1):539-565. doi: 10.1007/s11033-021-06749-4
[39]	Qu X J, Moore M J, Li D Z, Yi T S. 2019. PGA:a software package for rapid,accurate,and flexible batch annotation of plastomes. Plant Methods, 15:50. doi: 10.1186/s13007-019-0435-7
[40]	Quax T E, Claassens N J, Söll D, Vander O J. 2015. Codon bias as a means to fine-tune gene expression. Molecular Cell, 59 (2):149-161. doi: 10.1016/j.molcel.2015.05.035 pmid: 26186290
[41]	Randall T A, Dwyer R A, Huitema E, Beyer K, Cvitanich C, Kelkar H, Fong A M, Gates K, Roberts S, Yatzkan E, Gaffney T, Law M, Testa A, Torto-Alalibo T, Zhang M, Zheng L, Mueller E, Windass J, Binder A, Birch P R, Gisi U, Govers F, Gow N A, Mauch F, van West P, Waugh M E, Yu J, Boller T, Kamoun S, Lam S T, Judelson H S. 2005. Large-scale gene discovery in the oomycete Phytophthora infestans reveals likely components of phytopathogenicity shared with true fungi. Molecular Plant-Microbe Interactions, 18 (3):229-243. pmid: 15782637
[42]	Ren T, Yang Y, Zhou T, Liu Z L. 2018. Comparative plastid genomes of Primula species:sequence divergence and phylogenetic relationships. International Journal of Molecular Sciences, 19 (4):1050. doi: 10.3390/ijms19041050 URL
[43]	Shahid M M, Nishikawa T, Fukuoka S, Njenga P K, Tsudzuki T, Kadowaki K. 2004. The complete nucleotide sequence of wild rice(Oryza nivara)chloroplast genome:first genome wide comparative sequence analysis of wild and cultivated rice. Gene, 340 (1):133-139. pmid: 15556301
[44]	Spooner D M, Mclean, Ramsay G, Waugh R, Bryan G J. 2005. A single domestication for potato based on multilocus amplified fragment length polymorphism genotyping. Proceedings of the National Academy of Sciences of the United States of America, 102 (41):14694-14699.
[45]	Tang Chenqian, Qiu Zhixin, Tan Chao, Qian Yuming, Chen Xin. 2022. Sorbus koehneana(Rosaceae):its complete chloroplast genome and phylogenetic relationship with S. unguiculata. Acta Horticulturae Sinica, 49 (3):641-654. (in Chinese) doi: 10.16420/j.issn.0513-353x.2020-1021
	汤晨茜, 仇志欣, 檀超, 钱羽铭, 陈昕. 2022. 陕甘花楸叶绿体基因组及其与爪瓣花楸的系统关系. 园艺学报, 49 (3):641-654. doi: 10.16420/j.issn.0513-353x.2020-1021
[46]	Tang D, Wei F, Cai Z, Wei Y, Khan A, Miao J, Wei K. 2021. Analysis of codon usage bias and evolution in the chloroplast genome of Mesona chinensis Benth. Development Genes and Evolution, 231:1-9. doi: 10.1007/s00427-020-00670-9
[47]	Tang Ping, Wang Qiang, Chen Jian-qun. 2008. The patterns and influences of insertions,deletions and nucleotide substitutions in Solanaceae chloroplast genome. Hereditas(Beijing),(11):1506-1512. (in Chinese) pmid: 19073561
	唐萍, 王强, 陈建群. 2008. 茄科植物叶绿体基因组插入、缺失和核苷酸替代的发生方式及影响. 遗传,(11):1506-1512. pmid: 19073561
[48]	Uijtewaal B A, Huigen D J, Hermsen J G. 1987. Production of potato monohaploids(2n = x =12)through prickle pollination. Theoretical and Applied Genetics, 73 (5):751-758. doi: 10.1007/BF00260786 pmid: 24241201
[49]	Wang Ling, Dong Wen-pan, Zhou Shi-liang. 2012. Structural mutations and reorganizations in chloroplast genomes of floweing plants. Acta Botanica Boreali-Occidentalia Sinica, 32 (6):1282-1288. (in Chinese)
	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 (6):1282-1288.
[50]	Wang L, Xing H, Yuan Y, Wang X, Saeed M, Tao J, Feng W, Zhang G, Song X, Sun X. 2018. Genome-wide analysis of codon usage bias in four sequenced cotton species. PLoS ONE, 13 (3):e0194372. doi: 10.1371/journal.pone.0194372 URL
[51]	Wang Z, Xu B, Li B, Zhou Q, Wang G, Jiang X, Wang C, Xu Z. 2020. Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species. PeerJ, 8:e8251. doi: 10.7717/peerj.8251 URL
[52]	Wicke S, Schneeweiss G M, DePamphilis C W, Müller K L, Quandt D. 2011. The evolution of the plastid chromosome in land plants:gene content,gene order,gene function. Plant Molecular Biology, 76:273-297. doi: 10.1007/s11103-011-9762-4 URL
[53]	Wu Z Q, Ge S. 2012. The phylogeny of the BEP clade in grasses revisited:evidence from the whole-genome sequences of chloroplasts. Molecular Phylogenetics and Evolution, 62 (1):573-578. doi: 10.1016/j.ympev.2011.10.019 URL
[54]	Xiao M Z, Jun R W, Li F, Sha L, Hong B P, Lan Q, Jing L, Yan S, Wei H Q, Li F Z, Yun L C, Qing W Y. 2017. Inferring the evolutionary mechanism of the chloroplast genome size by comparing whole-chloroplast genome sequences in seed plants. Scientific Reports, 7 (1):1555. doi: 10.1038/s41598-017-01518-5 pmid: 28484234
[55]	Ye M, Peng Z, Tang D, Yang Z, Li D, Xu Y, Zhang C, Huang S. 2018. Generation of self-compatible diploid potato by knockout of S-RNase. Nature Plants, 4 (9):651-654. doi: 10.1038/s41477-018-0218-6
[56]	Yi Jing. 2016. Molecular marker-based identification of potato germplasms and association analysis with important biological traits[M. D. Dissertation]. Kunming: Yunnan Normal University. (in Chinese)
	易靖. 2016. 马铃薯品种资源分子标记检测及其与重要生物学性状的关联分析[硕士论文]. 昆明: 云南师范大学.
[57]	Zalucki Y M, Power P M, Jennings M P. 2007. Selection for efficient translation initiation biases codon usage at second amino acid position in secretory proteins. Nucleic Acids Research, 35 (17):5748. pmid: 17717002
[58]	Zeng J, Huang C, Liu Y, Yuan C, Yu H, Song B. 2021. The complete chloroplast genome sequence of Nicotiana debneyi(Solanaceae). Mitochondrial DNA Part B:Resources, 6 (3):1042-1043.

物种 Species	基因组大小/bp Genome size	反向重复长度/bp IR size	GC含量/% GC content	基因数 Number of genes	登录号 Accession No.
马铃薯Potato
合作88 Cooperation 88	160 323	25 575	38.6	106	ON921079
大西洋 Atlantic	155 296	25 593	37.9	134	GWHAORW01000000
底西瑞 Desiree	155 312	25 595	37.0	130	DQ231562
夏波蒂Shepody	155 296	25 593	37.9	132	MW307949
费乌瑞它 Favorita	155 296	25 593	37.9	132	MW307948
番茄 Solanum lycopersicum	155 461	25 611	37.9	134	DQ347959
龙葵 Solanum nigrum	155 432	25 589	38.0	125	KM489055
茄子 Solanum melongena	154 289	25 566	37.9	125	KU682719
烟草 Nicotiana debneyi	156 073	25 410	38.4	129	MT985319
枸杞 Lycium ruthenicum	154 996	25 395	37.9	111	MG976805
辣椒 Capsicum annuum	156 781	25 783	37.7	135	JX270811
黄灯笼辣椒 Capsicum chinense	156 807	25 803	37.7	134	KU041709
拟南芥 Arabidopsis thaliana	154 478	26 264	37.9	131	AP000423
水稻 Oryza sativa	134 503	20 804	39.0	148	MG252500

物种 Species	基因组大小/bp Genome size	反向重复长度/bp IR size	GC含量/% GC content	基因数 Number of genes	登录号 Accession No.
马铃薯Potato
合作88 Cooperation 88	160 323	25 575	38.6	106	ON921079
大西洋 Atlantic	155 296	25 593	37.9	134	GWHAORW01000000
底西瑞 Desiree	155 312	25 595	37.0	130	DQ231562
夏波蒂Shepody	155 296	25 593	37.9	132	MW307949
费乌瑞它 Favorita	155 296	25 593	37.9	132	MW307948
番茄 Solanum lycopersicum	155 461	25 611	37.9	134	DQ347959
龙葵 Solanum nigrum	155 432	25 589	38.0	125	KM489055
茄子 Solanum melongena	154 289	25 566	37.9	125	KU682719
烟草 Nicotiana debneyi	156 073	25 410	38.4	129	MT985319
枸杞 Lycium ruthenicum	154 996	25 395	37.9	111	MG976805
辣椒 Capsicum annuum	156 781	25 783	37.7	135	JX270811
黄灯笼辣椒 Capsicum chinense	156 807	25 803	37.7	134	KU041709
拟南芥 Arabidopsis thaliana	154 478	26 264	37.9	131	AP000423
水稻 Oryza sativa	134 503	20 804	39.0	148	MG252500

基因分类 Category of genes	基因分组 Group of genes	基因名称 Gene name
光合作用相关 Photosynthesis related	光系统ⅠPhotosystemⅠ	psaJ，psaI，psaA，psaB，psaC
	光系统Ⅱ PhotosystemⅡ	psbA，psbB，psbC，psbD，psbE，psbF，psbH，psbI，psbJ，psbK，psbL，psbM，psbN，psbT，psbZ
	ATP合酶 ATP synthase	atpF，atpH，atpA，atpB，atpE，atpI
	细胞色素Cytochrome	petA，petL，petG，petB，petD，petN
	NADH脱氢酶NADH dehydrogenase	ndhJ，ndhK，ndhF，ndhE，ndhG，ndhI，ndhH，ndhC，ndhA
	二磷酸核酮糖羧化酶大亚基 Rubis CO large subunit	rbcL
转录和翻译相关 Transcription and translation related	RNA 聚合酶RNA polymerase	rpoA，rpoB，rpoC1，rpoC2
	ATP依赖性clp蛋白酶 ATP-dependent clp protease	clpP
	成熟酶K Maturase K	matK
	核糖体大亚基Large subunit of ribosome	rpl33，rpl20，rpl36，rpl14，rpl16，rpl22，rpl23⁽²⁾ ，rpl2，rpl32
	核糖体小亚基Small subunit of ribosome	rps16，rps4，rps18，rps11，rps8，rps3，rps19，rps7，rps15，rps2，rps14，rps12
	tRNA	trnL-CAA，trnI-CAU，trnR-ACG，trnV-GAC，trnL-UAG，trnN-GUU，trnV-GAC，trnR-ACG，trnN-GUU，trnI-CAU，trnL-CAA，trnP-UGG，trnW-CCA，trnF-GAA，trnM-CAU，trnT-UGU、trnS-GGA，trnfM-CAU，trnG-GCC，trnS-UGA，trnT-GGU，trnC-GCA，trnE-UUC，trnD-GUC，trnY-GUA，trnR-UCU，trnS-GCU，trnQ-UUG，trnH-GUG
其他基因 Other genes	假设叶绿体阅读框架 Hypothetical chloroplast reading frames (ycf)	ycf1，ycf2，ycf3，ycf4
	C型细胞色素合成基因 C-type cytochrome synthesis gene	ccsA
	包膜膜蛋白 Envelope membrane protein	cemA
	乙酰辅酶A羧化酶亚基 Subunit of Acetyl-CoA carboxylase	accD

基因分类 Category of genes	基因分组 Group of genes	基因名称 Gene name
光合作用相关 Photosynthesis related	光系统ⅠPhotosystemⅠ	psaJ，psaI，psaA，psaB，psaC
	光系统Ⅱ PhotosystemⅡ	psbA，psbB，psbC，psbD，psbE，psbF，psbH，psbI，psbJ，psbK，psbL，psbM，psbN，psbT，psbZ
	ATP合酶 ATP synthase	atpF，atpH，atpA，atpB，atpE，atpI
	细胞色素Cytochrome	petA，petL，petG，petB，petD，petN
	NADH脱氢酶NADH dehydrogenase	ndhJ，ndhK，ndhF，ndhE，ndhG，ndhI，ndhH，ndhC，ndhA
	二磷酸核酮糖羧化酶大亚基 Rubis CO large subunit	rbcL
转录和翻译相关 Transcription and translation related	RNA 聚合酶RNA polymerase	rpoA，rpoB，rpoC1，rpoC2
	ATP依赖性clp蛋白酶 ATP-dependent clp protease	clpP
	成熟酶K Maturase K	matK
	核糖体大亚基Large subunit of ribosome	rpl33，rpl20，rpl36，rpl14，rpl16，rpl22，rpl23⁽²⁾ ，rpl2，rpl32
	核糖体小亚基Small subunit of ribosome	rps16，rps4，rps18，rps11，rps8，rps3，rps19，rps7，rps15，rps2，rps14，rps12
	tRNA	trnL-CAA，trnI-CAU，trnR-ACG，trnV-GAC，trnL-UAG，trnN-GUU，trnV-GAC，trnR-ACG，trnN-GUU，trnI-CAU，trnL-CAA，trnP-UGG，trnW-CCA，trnF-GAA，trnM-CAU，trnT-UGU、trnS-GGA，trnfM-CAU，trnG-GCC，trnS-UGA，trnT-GGU，trnC-GCA，trnE-UUC，trnD-GUC，trnY-GUA，trnR-UCU，trnS-GCU，trnQ-UUG，trnH-GUG
其他基因 Other genes	假设叶绿体阅读框架 Hypothetical chloroplast reading frames (ycf)	ycf1，ycf2，ycf3，ycf4
	C型细胞色素合成基因 C-type cytochrome synthesis gene	ccsA
	包膜膜蛋白 Envelope membrane protein	cemA
	乙酰辅酶A羧化酶亚基 Subunit of Acetyl-CoA carboxylase	accD

样本名称 Sample name	基因组大小/bp Genome size	基因数 Number of genes	蛋白质编码基因 Protein-coding gene	转移RNA tRNA gene	GC含量/% GC content	反向重复序列/bp Inverted repeat
样本名称 Sample name	基因组大小/bp Genome size	基因数 Number of genes	蛋白质编码基因 Protein-coding gene	转移RNA tRNA gene	GC含量/% GC content	IRA	IRB
合作88 Cooperation 88	160 323	106	77	29	38.6	25 583	25 567
C88-18	160 331	106	77	29	38.6	25 599	25 579
C88-20	161 341	100	76	24	36.7	25 735	26 053
C88-24	161 157	100	76	24	37.2	25 548	26 053
C88-35	161 150	99	76	23	36.9	25 532	26 049
C88-61	161 157	101	76	25	36.9	25 633	25 960
C88-68	161 387	100	74	26	36.9	25 659	26 177
C88-69	161 220	99	75	24	36.8	25 733	25 930
C88-71	161 418	99	75	24	37.0	25 804	26 041
C88-84	161 599	100	76	24	36.8	25 839	26 190
C88-88	161 663	101	76	25	36.9	25 856	26 196
C88-96	161 431	98	74	24	36.9	25 765	26 109
C88-106	161 349	99	76	23	36.9	25 687	26 107
C88-107	161 375	101	76	25	37.1	25 656	26 163
C88-109	161 343	101	76	25	36.9	25 587	26 207
C88-111	161 630	100	75	25	37.0	26 002	26 076
C88-115	161 226	100	75	25	37.1	25 426	26 197
C88-118	161 175	100	75	25	37.0	25 623	25 997
C88-119	161 706	99	75	24	36.9	25 901	26 162
C88-132	161 326	100	75	25	36.9	25 697	26 041
C88-138	161 880	101	74	27	36.8	25 943	26 361
C88-141	161 577	101	76	25	36.8	25 689	26 330
C88-143	161 832	102	76	26	36.8	26 095	26 163
C88-144	161 228	95	73	22	36.7	25 579	26 081
C88-151	161 527	101	75	26	36.8	25 693	26 286
C88-157	161 568	101	75	26	37.0	25 718	26 286
C88-160	161 418	103	77	26	37.0	25 719	26 102
C88-161	162 120	100	75	25	36.9	26 218	26 345
C88-182	161 806	96	72	24	37.2	25 768	26 492
C88-187	160 484	100	74	26	37.5	25 292	25 636
C88-209	161 259	99	74	25	37.2	25 551	26 158