黑籽南瓜的叶绿体基因组特征及系统发育分析

doi:10.7668/hbnxb.20195785

摘要/Abstract

摘要：

为揭示黑籽南瓜与其他葫芦科植物的系统进化关系,对黑籽南瓜叶绿体基因组进行组装、注释和分析。使用Illumina NovaSeq 6000平台对黑籽南瓜进行测序,并对其序列特征、基因类型、基因重复序列、密码子偏好性及物种进化等进行了分析。黑籽南瓜的叶绿体基因组全长是157 631 bp,GC含量为37.15%;注释到60.99%蛋白质编码基因、33.33% tRNA基因以及5.67% rRNA基因,共141个基因,分为光合作用基因、自我复制基因、其他基因和未知功能基因4类。对黑籽南瓜叶绿体进行简单重复序列分析,共检测到SSR位点192个。密码子偏好性分析发现,RSCU值大于1.00的密码子共有31个,以A或U结尾的密码子有29个。黑籽南瓜与其他8个葫芦科物种的边界基因存在差异,扩张和收缩现象在IR区和LSC区明显存在。进化分析结果表明,黑籽南瓜与中国南瓜、印度南瓜、西葫芦、墨西哥南瓜、臭瓜、阿克丘宾南瓜、伦德尔南瓜属于同一分支,与葫芦科的其他物种亲缘关系较远。组装完成了黑籽南瓜的叶绿体基因组,注释到141个基因,检测到192个SSR位点,进化上与所选葫芦科物种亲缘关系较远,为黑籽南瓜系统进化和分子育种提供理论依据。

关键词: 黑籽南瓜, 叶绿体基因组, 结构特征, 系统进化

Abstract:

The chloroplast genome of Cucurbita ficifolia was assembled,annotated and analyzed to reveal the phylogenetic relationship between C.ficifolia and other Cucurbitaceae plants.The Illumina NovaSeq 6000 platform was used to sequence C.ficifolia,and its sequence characteristics,gene type,gene repeat sequence,codon preference and species evolution were analyzed.The chloroplast genome of C.ficifolia was 157 631 bp in length with a GC content of 37.15%.A total of 141 genes were annotated,comprising 60.99% protein-coding genes,33.33% tRNA genes,and 5.67% rRNA genes.These genes were categorized into four groups:photosynthesis-related genes,self-replication genes,other genes,and genes of unknown function.Simple sequence repeat analysis was performed on the chloroplasts of C.ficifolia,and a total of 192 SSR loci were detected.Codon preference analysis showed that there were 31 codons with RSCU values greater than 1.00,and 29 codons ended with A or U.The boundary genes of C.ficifolia were different from those of 8 other Cucurbitaceae species,and the expansion and contraction phenomena were obvious in the IR region and LSC region.The results of evolutionary analysis showed that C.ficifolia was in the same branch with C.moschata,C.maxima,C.pepo,C.argyrosperma var. palmeri,C.foetidissima,C.okeechobeensis subsp. martinezii and C.lundelliana.C.ficifolia was distant in relationship with other species of Cucurbitaceae.The chloroplast genome of C.ficifolia was assembled,and annotated with 141 genes and 192 SSR loci.Its evolutionary relationship is relatively distant with the selected Cucurbitaceae species.This study provides a theoretical basis for phyletic evolution and molecular breeding strategies in C.ficifolia.

Key words: Cucurbita ficifolia, Chloroplast genome, Structural characteristics, Phyletic evolution

中图分类号:

康家香, 彭聪归, 昂海燕, 荆赞革, 杨正安, 谢秀锋, 汪雨欣, 裴徐梨. 黑籽南瓜的叶绿体基因组特征及系统发育分析[J]. 华北农学报, 2026, 41(3): 48-56. doi: 10.7668/hbnxb.20195785.

KANG Jiaxiang, PENG Conggui, ANG Haiyan, JING Zange, YANG Zhengan, XIE Xiufeng, WANG Yuxin, PEI Xuli. Chloroplast Genome Characteristics and Phylogenetic Analysis of Cucurbita ficifolia[J]. Acta Agriculturae Boreali-Sinica, 2026, 41(3): 48-56. doi: 10.7668/hbnxb.20195785.

http://www.hbnxb.net/CN/Y2026/V41/I3/48

图/表 6

参考文献 41

[1]	陈丽, 李耕耘, 张竞, 符强, 蒲鹏, 吴航, 贺水莲. 云南黑籽南瓜种子形态特征及其与环境因子的相关性分析[J]. 种子, 2024, 43(10):13-19.doi:10.16590/j.cnki.1001-4705.2024.10.013.
	Chen L, Li G Y, Zhang J, Fu Q, Pu P, Wu H, He S L. The seed morphological characteristics of Cucurbita ficifolia in Yunnan and the analysis on its correlation with environmental factors[J]. Seed, 2024, 43(10):13-19.
[2]	吴航, 李耕耘, 陈丽, 王瑞梅, 田雪鸿, 闫杨垚, 贺水莲. 不同类型黄瓜嫁接砧木对枯萎病菌胁迫的响应[J]. 贵州农业科学, 2025, 53(3):85-92.doi:10.3969/j.issn.1001-3601.2025.03.011.
	Wu H, Li G Y, Chen L, Wang R M, Tian X H, Yan Y Y, He S L. Response of different types of cucumber grafted rootstocks to Fusarium wilt stress[J]. Guizhou Agricultural Sciences, 2025, 53(3):85-92.
[3]	梁祖珍, 潘玲华, 赵兵, 陈安琪, 邓飞鹏, 李刚. 3种砧木春季嫁接对黄瓜生长、品质与抗枯萎病的影响[J]. 南方园艺, 2014, 25(1):7-8.doi:10.3969/j.issn.1674-5868.2014.01.002.
	Liang Z Z, Pan L H, Zhao B, Chen A Q, Deng F P, Li G. Effects of three rootstocks grafting in spring on growth,quality and Fusarium wilt resistance of cucumber[J]. Southern Horticulture, 2014, 25(1):7-8.
[4]	谭占明, 轩正英, 张娟, 朱洒洒, 刘义飞, 熊仁次. 不同砧木嫁接对黄瓜产量和品质的影响[J]. 分子植物育种, 2021, 19(2):679-686.doi:10.13271/j.mpb.019.000679.
	Tan Z M, Xuan Z Y, Zhang J, Zhu S S, Liu Y F, Xiong R C. Effects of different rootstocks on the yield and quality of cucumber[J]. Molecular Plant Breeding, 2021, 19(2):679-686.
[5]	陶美奇, 周刚, 姚超宇, 俞晟, 束胜, 郭世荣. 砧木种类对嫁接黄瓜生长、品质和产量的影响[J]. 长江蔬菜, 2018(2):54-59.doi:10.3865/j.issn.1001-3547.2018.02.020.
	Tao M Q, Zhou G, Yao C Y, Yu S, Shu S, Guo S R. Effects of different kinds of rootstock grafting on growth,quality and yield of cucumber[J]. Journal of Changjiang Vegetables, 2018(2):54-59.
[6]	丁玉梅, 高婷, 暴会会, 谢俊俊, 姚春馨, 周晓罡, 侯思名, 杨正安. 黑籽南瓜NBS类抗病基因的鉴别及关键基因分析[J]. 植物生理学报, 2020, 56(9):1833-1844.doi:10.13592/j.cnki.ppj.2020.0183.
	Ding Y M, Gao T, Bao H H, Xie J J, Yao C X, Zhou X G, Hou S M, Yang Z A. The identification and key genes analysis of NBS type disease-resistance gene from Cucurbita ficifotia[J]. Plant Physiology Journal, 2020, 56(9):1833-1844.
[7]	杨正安, 孟平红, 代贤, 杨立芳, 张兴国. 云南黑籽南瓜种质遗传多样性的RAPD和ISSR分析[J]. 植物遗传资源学报, 2011, 12(6):860-864.doi:10.13430/j.cnki.jpgr.2011.06.027.
	Yang Z A, Meng P H, Dai X, Yang L F, Zhang X G. Genetic diversity of Cucurbita ficifolia bauche based on RAPD and ISSR[J]. Journal of Plant Genetic Resources, 2011, 12(6):860-864.
[8]	高婷, 张杰, 马瑞红, 杨正安, 谢俊俊. NaCl胁迫对黑籽南瓜生长和生理特性的影响[J]. 江苏农业科学, 2020, 48(6):122-124,137.doi:10.15889/j.issn.1002
	Gao T, Zhang J, Ma R H, Yang Z A, Xie J J. Effects of salt stress on growth and physiological characteristics of Cucurbita ficifolia[J]. Jiangsu Agricultural Sciences, 2020, 48(6):122-124,137.
[9]	郭铭炎, 马海霞, 乔天乐, 殷钰, 王欣维, 李金洺, 封烁. 葱属植物叶绿体基因组比较分析[J]. 草地学报, 2025, 33(12):3920-3932.doi:10.11733/j.issn.1007-0435.2025.12.006.
	Guo M Y, Ma H X, Qiao T L, Yin Y, Wang X W, Li J M, Feng S. Comparative analysis of chloroplast genomes of Allium species[J]. Acta Agrestia Sinica, 2025, 33(12):3920-3932.
[10]	汪慧玲, 张呈彦, 王远丽, 张琴, 李艳宾. 荒漠产油微藻Chlorella sp. DT025叶绿体基因组特征及系统发育分析[J]. 分子植物育种, 2025, 23(11):3746-3753.doi:10.13271/j.mpb.023.003746.
	Wang H L, Zhang C Y, Wang Y L, Zhang Q, Li Y B. Chloroplast genome structure characteristic and phylogenetic analysis of Chlorella sp.DT025 in desert oil-producing microalgae[J]. Molecular Plant Breeding, 2025, 23(11):3746-3753.
[11]	郭晓雨, 张晓慧, 马宗新, 李文峰, 李慧慧. 玉铃铛枣叶绿体基因组特征及密码子偏性[J]. 分子植物育种, 2023, 21(8):2488-2498.doi:10.13271/j.mpb.021.002488.
	Guo X Y, Zhang X H, Ma Z X, Li W F, Li H H. Chloroplast genome characteristics and codon usage bias of yulingdang jujuba[J]. Molecular Plant Breeding, 2023, 21(8):2488-2498.
[12]	陈春梅, 马春雷, 马建强, 刘声传, 陈亮. 茶树cpDNA测序及基于cpDNA序列的山茶属植物亲缘关系研究[J]. 茶叶科学, 2014, 34(4):371-380.doi:10.13305/j.cnki.jts.2014.04.008.
	Chen C M, Ma C L, Ma J Q, Liu S C, Chen L. Sequencing of chloroplast genome of Camellia sinensis and genetic relationship for Camellia plants based on chloroplast DNA sequences[J]. Journal of Tea Science, 2014, 34(4):371-380.
[13]	Zhu Q L, Gao P, Liu S, Amanullah S, Luan F S. Comparative analysis of single nucleotide polymorphisms in the nuclear,chloroplast,and mitochondrial genomes in identification of phylogenetic association among seven melon(Cucumis melo L.) cultivars[J]. Breeding Science, 2016, 66(5):711-719.doi:10.1270/jsbbs.16066. URL
[14]	江转转, 胡淑宝, 杨浩东, 郭晶. 基于叶绿体基因组比较栝楼属植物的演化[J]. 安庆师范大学学报(自然科学版), 2023, 29(2):87-95.doi:10.13757/j.cnki.cn34-1328/n.2023.02.015.
	Jiang Z Z, Hu S B, Yang H D, Guo J. Comparative evolution of Trichosanthes based on chloroplast genomes[J]. Journal of Anqing Normal University(Natural Science Edition), 2023, 29(2):87-95.
[15]	马宗新. 马泡瓜叶绿体基因组测序[J]. 分子植物育种, 2023, 21(1):138-147.doi:10.13271/j.mpb.021.000138.
	Ma Z X. Sequencing of chloroplast genome of Cucumis melo L.var.agrestis Naud[J]. Molecular Plant Breeding, 2023, 21(1):138-147.
[16]	Xu H X, Yu G M, Dong X, Yang J X, Peninah C R, Tan Y, Cai X Z, Hu G W. Correction:the complete chloroplast genome of Lagenaria abyssinica(Hook.f.)C.Jeffrey: comparative and phylogenetic analysis[J]. Genetic Resources and Crop Evolution, 2025, 72(S1):25-49.doi:10.1007/S10722-025-02611-9.
[17]	Plᶏder W, Yukawa Y, Sugiura M, Malepszy S. The complete structure of the cucumber(Cucumis sativus L.) chloroplast genome:its composition and comparative analysis[J]. Cellular and Molecular Biology Letters, 2007, 12(4):584-594.doi:10.2478/s11658-007-0029-7.
[18]	Jansen R K, Raubeson L A, Boore J L, de Pamphilis C W, Chumley T W, Haberle R C, Wyman S K, Alverson A J, Peery R, Herman S J, Fourcade H M, Kuehl J V, McNeal J R, Leebens-Mack J, Cui L Y. Methods for obtaining and analyzing whole chloroplast genome sequences[M]//Molecular Evolution: Producing the Biochemical Data. Amsterdam:Elsevier,2005:348-384.doi:10.1016/s0076-6879(05)95020-9.
[19]	Chen J, Guo Y J, Hu X W, Zhou K B. Comparison of the chloroplast genome sequences of 13 oil-tea Camellia samples and identification of an undetermined oil-tea Camellia species from Hainan Province[J]. Frontiers in Plant Science, 2022, 12:798581.doi:10.3389/fpls.2021.798581. URL
[20]	朱恒星, 戴前莉, 魏卓, 卢敏, 黄飞逸, 陈本文. 17种楠属植物叶绿体基因组密码子偏好性分析[J]. 南方农业学报, 2024, 55(12):3646-3655.doi:10.3969/j.issn.2095-1191.2024.12.014.
	Zhu H X, Dai Q L, Wei Z, Lu M, Huang F Y, Chen B W. Codon usage bias in chloroplast genomes of 17 Phoebe species[J]. Journal of Southern Agriculture, 2024, 55(12):3646-3655.
[21]	黄超婷, 孙豪良, 盛文涛. 荞麦属五种植物叶绿体基因组的结构变异与分子进化研究[J]. 种子, 2023, 42(10):83-88,98.doi:10.16590/j.cnki.1001
	Huang C T, Sun H L, Sheng W T. Structural variation and molecular evolution of chloroplast genomes in five species of Fagopyrum[J]. Seed, 2023, 42(10):83-88,98.
[22]	Huang X J, Xia C L, Zhao Y, Xu L. The first complete chloroplast genome of Haymondia wallichii(Fabaceae)and its phylogenetic analysis[J]. Mitochondrial DNA Part B, 2021, 6(7):1865-1866.doi:10.1080/23802359.2021.1923415. URL
[23]	Sun H H, Wu S, Zhang G Y, Jiao C, Guo S G, Ren Y, Zhang J, Zhang H Y, Gong G Y, Jia Z C, Zhang F, Tian J X, Lucas W J, Doyle J J, Li H Z, Fei Z J, Xu Y. Karyotype stability and unbiased fractionation in the paleo-allotetraploid Cucurbita genomes[J]. Molecular Plant, 2017, 10(10):1293-1306.doi:10.1016/j.molp.2017.09.003. URL
[24]	邓港, 吴田泽, 高冉冉, 王梦月, 刘霞, 向丽. 红花龙胆叶绿体基因组特征及适应性进化分析[J]. 药学学报, 2022, 57(10):3240-3253.doi:10.16438/j.0513-4870.2022-0537.
	Deng G, Wu T Z, Gao R R, Wang M Y, Liu X, Xiang L. Characteristics and adaptive evolution analysis of the chloroplast genome of Gentiana rhodantha[J]. Acta Pharmaceutica Sinica, 2022, 57(10):3240-3253.
[25]	邢钰, 冯慧喆. 叶绿体基因组的比较分析及系统发育研究[J]. 乡村科技, 2021, 12(24):82-83.doi:10.3969/j.issn.1674-7909.2021.24.040.
	Xing Y, Feng H Z. Comparative analysis and phylogenetic study of chloroplast genome[J]. Rural Science and Technology, 2021, 12(24):82-83.
[26]	朱强龙. 西瓜与甜瓜细胞器比较基因组学研究[D]. 哈尔滨: 东北农业大学, 2018.doi:10.7666/d.Y3431369.
	Zhu Q L. Comparative genomics Research on the organellar genome of watermelon and melon[D]. Harbin: Northeast Agricultural University, 2018.
[27]	Mishra A K, Agarwal S, Jain C K, Rani V. High GC content:critical parameter for predicting stress regulated miRNAs in Arabidopsis thaliana[J]. Bioinformation, 2009, 4(4):151-154.doi:10.6026/97320630004151. URL
[28]	童一涵, 郑倩, 杜新明, 冯士令, 周莉君, 丁春邦, 陈涛. 多齿红山茶叶绿体基因组序列特征分析[J]. 植物资源与环境学报, 2022, 31(5):27-36.doi:10.3969/j.issn.1674-7895.2022.05.04.
	Tong Y H, Zheng Q, Du X M, Feng S L, Zhou L J, Ding C B, Chen T. Analysis on sequence characteristics of chloroplast genome of Camellia polyodonta[J]. Journal of Plant Resources and Environment, 2022, 31(5):27-36.
[29]	王飞, 赵文植, 董章宏, 马路遥, 李卫英, 李宗艳, 辛培尧. 丝兰属6种植物叶绿体基因组特征分析[J]. 植物研究, 2023, 43(1):109-119.doi:10.7525/j.issn.1673-5102.2023.01.012.
	Wang F, Zhao W Z, Dong Z H, Ma L Y, Li W Y, Li Z Y, Xin P Y. Analysis of the chloroplast genome characteristics of 6 species of Yucca[J]. Bulletin of Botanical Research, 2023, 43(1):109-119.
[30]	龚意辉, 周桂花, 李丽梅, 曾永贤, 陈致印. 黄桃叶绿体基因组的组装与序列分析[J]. 热带作物学报, 2022, 43(8):1545-1553.doi:10.3969/j.issn.1000-2561.2022.08.003.
	Gong Y H, Zhou G H, Li L M, Zeng Y X, Chen Z Y. Assembly and sequence analysis of chloroplast genome of Amygdalus persica[J]. Chinese Journal of Tropical Crops, 2022, 43(8):1545-1553.
[31]	Tong W, Kim T S, Park Y J. Rice chloroplast genome variation architecture and phylogenetic dissection in diverse Oryza species assessed by whole-genome resequencing[J]. Rice, 2016, 9(1):57.doi:10.1186/s12284-016-0129-y. pmid: 27757948
[32]	George B, Bhatt B S, Awasthi M, George B, Singh A K. Comparative analysis of microsatellites in chloroplast genomes of lower and higher plants[J]. Current Genetics, 2015, 61(4):665-677.doi:10.1007/s00294-015-0495-9. pmid: 25999216
[33]	冉然, 张晓明, 宛涛, 伊卫东. 密码子偏好性的相关研究及方法分析[J]. 草原与草业, 2022, 34(3):5-10,43.doi:10.3969/j.issn.2095
	Ran R, Zhang X M, Wan T, Yi W D. Method analysis of codon usage bias and its related research[J]. Grassland and Prataculture, 2022, 34(3):5-10,43.
[34]	杨玉霞, 魏泽昶, 李小阳, 李静婷, 吕梁. 野鸦椿叶绿体基因组特征及系统发育研究[J]. 西南农业学报, 2025, 38(11):2306-2314.
	Yang Y X, Wei Z C, Li X Y, Li J T, Lyu L. Characterization and phylogenetic study of the chloroplast genome in Chinese Toon(Toon chinensis)[J]. Southwest Agricultural Journal, 2025, 38(11):2306-2314.doi:10.16213/j.cnki.scjas.2025.11.004.
[35]	胡晓聪, 刘秀云, 胥明, 王可, 金亮. 白灵山红山茶叶绿体基因组特征分析[J]. 西北林学院学报, 2024, 39(6):34-44.doi:10.3969/j.issn.1001-7461.2024.06.05.
	Hu X C, Liu X Y, Xu M, Wang K, Jin L. Chloroplast genomic characterization of Camellia bailinshanica[J]. Journal of Northwest Forestry University, 2024, 39(6):34-44.
[36]	张乐, 金国龙, 罗玲, 王跃平, 董志敏, 孙守红, 邱丽娟. 大豆基因组和转录组的核基因密码子使用偏好性分析[J]. 作物学报, 2011, 37(6):965-974.doi:10.3724/SP.J.1006.2011.00965.
	Zhang L, Guo Y, Luo L, Wang Y P, Dong Z M, Sun S H, Qiu L J. Analysis of nuclear gene codon bias on soybean genome and transcriptome[J]. Acta Agronomica Sinica, 2011, 37(6):965-974.
[37]	Feng S G, Zheng K X, Jiao K L, Cai Y C, Chen C L, Mao Y Y, Wang L Y, Zhan X R, Ying Q C, Wang H Z. Complete chloroplast genomes of four Physalis species(Solanaceae):lights into genome structure,comparative analysis,and phylogenetic relationships[J]. BMC Plant Biology, 2020, 20(1):242.doi:10.1186/s12870-020-02429-w.
[38]	郭豪杰, 刘久石, 罗丽, 魏雪苹, 张进, 齐耀东, 张本刚, 刘海涛, 肖培根. 五味子叶绿体基因组结构解析与比较分析[J]. 中国科学:生命科学, 2017, 47(7):728-739.
	Guo H J, Liu J S, Luo L, Wei X P, Zhang J, Qi Y D, Zhang B G, Liu H T, Xiao P G. Complete chloroplast genome sequences of Schisandra chinensis:genome structure,comparative analysis,and phylogeneticrelationship of basal angiosperms[J]. Scientia Sinica(Vitae), 2017, 47(7):728-739.
[39]	Gong Y H, Wei Y Y, Zhou G H, Ou Y L, Zhang C M, Li P. The complete chloroplast genome of white towel gourd(Luffa cylindrica)and phylogenetic analysis[J]. Genetic Resources and Crop Evolution, 2024, 71(7):3315-3329.doi:10.1007/s10722-023-01842-y.
[40]	Gong L, Stift G, Kofler R, Pachner M, Lelley T. Microsatellites for the genus Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L.[J]. Theoretical and Applied Genetics, 2008, 117(1):37-48.doi:10.1007/s00122-008-0750-2. pmid: 18379753
[41]	Wyatt L E, Strickler S R, Mueller L A, Mazourek M. An acorn squash(Cucurbita pepo ssp.ovifera)fruit and seed transcriptome as a resource for the study of fruit traits in Cucurbita[J]. Horticulture Research, 2015, 2:14070.doi:10.1038/hortres.2014.70.

基因功能分类 Gene functional category	基因组 Genome	基因名 Gene name		基因数量 Gene number
自我复制相关基因	核糖体大亚基	rpl14、rpl16^、rpl2^、rpl20、rpl22、rpl23(2)、rpl32、rpl33、rpl36		10
Self-replication related genes	核糖体小亚基	rps11、rps12^*(2)、rps14、rps15、rps16^、rps18、rps19、rps2、rps3、rps4、rps7(2)、rps8		14
	DNA 依赖核酸聚合酶	rpoA、rpoB、rpoC1^、rpoC2*		4
	核糖体RNA	rrn16(2)、rrn23(2)、rrn4.5(2)、rrn5(2)		8
	转运RNA	trnA-UGC^(2)、trnC-GCA、trnD-GUC、trnE-UUC、trnF-GAA、trnG-GCC、trnG-UCC^、trnH-GUG、trnI-CAU(4)、trnI-GAU^(2)、trnK-UUU^、trnL-CAA(4)、trnL-UAA^、trnL-UAG、trnM-CAU、trnN-GUU(4)、trnP-UGG、trnQ-UUG、trnR-ACG(4)、trnR-UCU、trnS-GCU、trnS-GGA、trnS-UGA、trnT-GGU、trnT-UGU、trnV-GAC(4)、trnV-UAC^、trnW-CCA、trnY-GUA、trnfM-CAU		47
光合作用有关基因	亚光系统Ⅰ		psaA、psaB、psaC、psaI、psaJ	5
Photosynthesis related genes	亚光系统Ⅱ		psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、psbJ、psbK、psbL、psbM、psbN、psbT、psbZ	15
	NADH 脱氢酶亚基		ndhA^、ndhB^(2)、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK	12
	细胞色素复合物b/f亚基		petA、petB^、petD^、petG、petL、petN	6
	ATP 合酶亚基		atpA、atpB、atpE、atpF^、atpH、atpI*	6
	Rubisco 酶大亚基		rbcL	1
其他基因	成熟酶		matK	1
Other genes	蛋白酶		clpP^**	1
	包裹膜蛋白		cemA	1
	乙酰辅酶A羧化酶亚基		accD	1
	c型细胞色素合成		ccsA	1
	转录起始因子		infA	1
未知功能基因	假定叶绿体阅读框		ycf1、ycf15(2)、ycf2(2)、ycf3^*、ycf4*	7
Genes of unknown function
总计Total				141

基因功能分类 Gene functional category	基因组 Genome	基因名 Gene name		基因数量 Gene number
自我复制相关基因	核糖体大亚基	rpl14、rpl16^、rpl2^、rpl20、rpl22、rpl23(2)、rpl32、rpl33、rpl36		10
Self-replication related genes	核糖体小亚基	rps11、rps12^*(2)、rps14、rps15、rps16^、rps18、rps19、rps2、rps3、rps4、rps7(2)、rps8		14
	DNA 依赖核酸聚合酶	rpoA、rpoB、rpoC1^、rpoC2*		4
	核糖体RNA	rrn16(2)、rrn23(2)、rrn4.5(2)、rrn5(2)		8
	转运RNA	trnA-UGC^(2)、trnC-GCA、trnD-GUC、trnE-UUC、trnF-GAA、trnG-GCC、trnG-UCC^、trnH-GUG、trnI-CAU(4)、trnI-GAU^(2)、trnK-UUU^、trnL-CAA(4)、trnL-UAA^、trnL-UAG、trnM-CAU、trnN-GUU(4)、trnP-UGG、trnQ-UUG、trnR-ACG(4)、trnR-UCU、trnS-GCU、trnS-GGA、trnS-UGA、trnT-GGU、trnT-UGU、trnV-GAC(4)、trnV-UAC^、trnW-CCA、trnY-GUA、trnfM-CAU		47
光合作用有关基因	亚光系统Ⅰ		psaA、psaB、psaC、psaI、psaJ	5
Photosynthesis related genes	亚光系统Ⅱ		psbA、psbB、psbC、psbD、psbE、psbF、psbH、psbI、psbJ、psbK、psbL、psbM、psbN、psbT、psbZ	15
	NADH 脱氢酶亚基		ndhA^、ndhB^(2)、ndhC、ndhD、ndhE、ndhF、ndhG、ndhH、ndhI、ndhJ、ndhK	12
	细胞色素复合物b/f亚基		petA、petB^、petD^、petG、petL、petN	6
	ATP 合酶亚基		atpA、atpB、atpE、atpF^、atpH、atpI*	6
	Rubisco 酶大亚基		rbcL	1
其他基因	成熟酶		matK	1
Other genes	蛋白酶		clpP^**	1
	包裹膜蛋白		cemA	1
	乙酰辅酶A羧化酶亚基		accD	1
	c型细胞色素合成		ccsA	1
	转录起始因子		infA	1
未知功能基因	假定叶绿体阅读框		ycf1、ycf15(2)、ycf2(2)、ycf3^*、ycf4*	7
Genes of unknown function
总计Total				141

氨基酸 Amino acid	密码子 Codon	数量 Quantity	RSCU	氨基酸 Amino acid	密码子 Codon	数量 Quantity	RSCU	氨基酸 Amino acid	密码子 Codon	数量 Quantity	RSCU
Ter	UAA	55	1.918 5	Ile	AUA	685	0.917 7	Arg	AGA	466	1.801 8
	UAG	16	0.558 0		AUC	472	0.632 4		AGG	170	0.657 0
	UGA	15	0.523 2		AUU	1 082	1.449 9		CGA	361	1.395 6
Ala	GCA	378	1.093 2	Lys	AAA	1 014	1.498 8		CGU	345	1.333 8
	GCC	225	0.650 8		AAG	339	0.501 2	Ser	AGC	124	0.363 0
	GCG	151	0.436 8	Leu	CUA	383	0.835 2		AGU	414	1.211 4
	GCU	629	1.819 2		CUC	187	0.408 0		UCA	419	1.225 8
Cys	UGC	81	0.540 0		CUG	179	0.390 6		UCC	320	0.936 0
	UGU	219	1.460 0		CUU	580	1.264 8		UCG	195	0.570 6
Asp	GAC	226	0.408 0		UUA	855	1.864 8		UCU	579	1.693 8
	GAU	882	1.592 0		UUG	567	1.236 6	Thr	ACA	388	1.176 8
Glu	GAA	1 045	1.498 2	Met	AUG	622	1.996 8		ACC	242	0.734 0
	GAG	350	0.501 8	Asn	AAC	298	0.465 2		ACG	155	0.470 0
Phe	UUC	528	0.720 4		AAU	983	1.534 8		ACU	534	1.619 6
	UUU	938	1.279 6	Pro	CCA	311	1.147 6	Val	GUA	515	1.456 8
Gly	GGA	718	1.630 8		CCC	199	0.734 4		GUC	188	0.532 0
	GGC	171	0.388 4		CCG	160	0.590 4		GUG	192	0.543 2
	GGG	281	0.638 4		CCU	414	1.527 6		GUU	519	1.468 0
	GGU	591	1.342 4	Gln	CAA	724	1.538 8	Trp	UGG	453	1.000 0
His	CAC	153	0.491 2		CAG	217	0.461 2	Tyr	UAC	192	0.396 6
	CAU	470	1.508 8						UAU	776	1.603 4

氨基酸 Amino acid	密码子 Codon	数量 Quantity	RSCU	氨基酸 Amino acid	密码子 Codon	数量 Quantity	RSCU	氨基酸 Amino acid	密码子 Codon	数量 Quantity	RSCU
Ter	UAA	55	1.918 5	Ile	AUA	685	0.917 7	Arg	AGA	466	1.801 8
	UAG	16	0.558 0		AUC	472	0.632 4		AGG	170	0.657 0
	UGA	15	0.523 2		AUU	1 082	1.449 9		CGA	361	1.395 6
Ala	GCA	378	1.093 2	Lys	AAA	1 014	1.498 8		CGU	345	1.333 8
	GCC	225	0.650 8		AAG	339	0.501 2	Ser	AGC	124	0.363 0
	GCG	151	0.436 8	Leu	CUA	383	0.835 2		AGU	414	1.211 4
	GCU	629	1.819 2		CUC	187	0.408 0		UCA	419	1.225 8
Cys	UGC	81	0.540 0		CUG	179	0.390 6		UCC	320	0.936 0
	UGU	219	1.460 0		CUU	580	1.264 8		UCG	195	0.570 6
Asp	GAC	226	0.408 0		UUA	855	1.864 8		UCU	579	1.693 8
	GAU	882	1.592 0		UUG	567	1.236 6	Thr	ACA	388	1.176 8
Glu	GAA	1 045	1.498 2	Met	AUG	622	1.996 8		ACC	242	0.734 0
	GAG	350	0.501 8	Asn	AAC	298	0.465 2		ACG	155	0.470 0
Phe	UUC	528	0.720 4		AAU	983	1.534 8		ACU	534	1.619 6
	UUU	938	1.279 6	Pro	CCA	311	1.147 6	Val	GUA	515	1.456 8
Gly	GGA	718	1.630 8		CCC	199	0.734 4		GUC	188	0.532 0
	GGC	171	0.388 4		CCG	160	0.590 4		GUG	192	0.543 2
	GGG	281	0.638 4		CCU	414	1.527 6		GUU	519	1.468 0
	GGU	591	1.342 4	Gln	CAA	724	1.538 8	Trp	UGG	453	1.000 0
His	CAC	153	0.491 2		CAG	217	0.461 2	Tyr	UAC	192	0.396 6
	CAU	470	1.508 8						UAU	776	1.603 4

选择文件类型/文献管理软件名称

选择包含的内容