野生稻叶绿体基因组组装与密码子偏好性分析及系统发育研究

doi:10.16819/j.1001-7216.2025.240612

中国水稻科学 ›› 2025, Vol. 39 ›› Issue (6): 801-812.DOI: 10.16819/j.1001-7216.2025.240612

野生稻叶绿体基因组组装与密码子偏好性分析及系统发育研究

李荣欣¹^,², 王波², 肖素勤², 殷富有², 张建红³, 钟巧芳², 陈玲², 李金璐², 杨和生³, 程在全²^,^*(), 刘丽²^,^*()

¹云南大学资源植物研究院，昆明 650504
²云南省农业科学院生物技术与种质资源研究所，昆明 650205
³云南省陆良县种子管理站，云南陆良 655699

收稿日期:2024-06-19 修回日期:2024-07-12 出版日期:2025-11-10 发布日期:2025-11-19
通讯作者: * email:czquan-99@163.com;liuliyaas@163.com
基金资助:
国家重点研发计划资助项目(2021YFD1200102-02);云南省农业联合专项－重点项目(202301BD070001-149);云南省种子种业联合实验室项目(202205AR070001-01);云南省杨庆文专家工作站项目(202305AF150161)

Assembly, Codon Usage Bias, and Phylogenetic Analysis of Chloroplast Genome of Oryza meyeriana

LI Rongxin¹^,², WANG Bo², XIAO Suqin², YIN Fuyou², ZHANG Jianhong³, ZHONG Qiaofang², CHEN Ling², LI Jinlu², YANG Hesheng³, CHENG Zaiquan²^,^*(), LIU Li²^,^*()

¹Institute of Plant Resources, Yunnan University, Kunming 650504, China
²Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
³Seed Management Station of Luliang County, Yunnan Province, Luliang 655699, China

Received:2024-06-19 Revised:2024-07-12 Online:2025-11-10 Published:2025-11-19
Contact: * email:czquan-99@163.com;liuliyaas@163.com

摘要/Abstract

摘要：

【目的】疣粒野生稻是稻属中唯一的旱生且保存较多原始性状的耐荫野生稻。本研究旨在丰富疣粒野生稻的遗传基础，为疣粒野生稻优异基因的载体构建提供信息参考。【方法】采用二代测序技术对云南疣粒野生稻叶绿体基因组进行测序、组装和注释，进而运用RStudio和MEGA分析其密码子偏好性及系统发育。【结果】疣粒野生稻叶绿体基因组全长135,937 bp，总GC含量39.0%，有效密码子（ENC）平均值为48.09，密码子偏好性较弱；ENC-plot、PR2-plot及中性绘图分析显示选择压力对疣粒野生稻叶绿体基因组密码子偏好性有重要决定作用，且密码子偏好性主要调控自我复制与光合系统相关基因；共鉴定出16个优势密码子，其中14个以A/U结尾，2个以G/C结尾；通过系统发育分析明确了疣粒野生稻叶绿体基因组与短药野生稻的亲缘关系较近。【结论】本研究丰富了疣粒野生稻基因组的基本组成和遗传信息，为水稻优异光合基因挖掘及物种进化研究奠定了基础。

关键词: 云南疣粒野生稻, 叶绿体基因组, 密码子偏好性, 系统发育

Abstract:

【Objective】 Oryza meyeriana, which is shade-tolerant and retains many primitive traits, is the only xerophytic type of wild rice in the genus Oryza. This study aims to enrich the genetic foundation of O. meyeriana and provide reference for vector construction of its superior genes. 【Methods】 The chloroplast genome of Yunnan O. meyeriana was sequenced using second-generation sequencing technology, followed by assembly and annotation. Codon usage bias and phylogenetic relationships were analyzed with RStudio and MEGA. 【Results】 The results showed that the total length of the chloroplast genome was 135,937 bp, with a GC content of 39.0%. The average effective number of codons(ENC) value was 48.09, indicating weak codon usage bias. ENC-plot, PR2-plot, and neutral plot analyses revealed that selection pressure plays a major role in shaping the chloroplast codon usage bias in Oryza meyeriana, and that this bias mainly regulates genes involved in self-replication and the photosynthetic system. A total of 16 optimal codons were identified, among which 14 ended with A/U and 2 ended with G/C. Phylogenetic analysis based on the chloroplast genome showed that Oryza meyeriana is closely related to O. brachyantha.【Conclusion】 This study enriches our understanding of the genomic composition and genetic information of Oryza meyeriana. The findings provide a basis for mining favorable genes related to photosynthesis and for investigating the evolution of wild rice species.

Key words: Yunnan Oryza meyeriana, chloroplast genome, codon usage bias, phylogeny

李荣欣, 王波, 肖素勤, 殷富有, 张建红, 钟巧芳, 陈玲, 李金璐, 杨和生, 程在全, 刘丽. 野生稻叶绿体基因组组装与密码子偏好性分析及系统发育研究[J]. 中国水稻科学, 2025, 39(6): 801-812.

LI Rongxin, WANG Bo, XIAO Suqin, YIN Fuyou, ZHANG Jianhong, ZHONG Qiaofang, CHEN Ling, LI Jinlu, YANG Hesheng, CHENG Zaiquan, LIU Li. Assembly, Codon Usage Bias, and Phylogenetic Analysis of Chloroplast Genome of Oryza meyeriana[J]. Chinese Journal OF Rice Science, 2025, 39(6): 801-812.

图/表 12

参考文献 31

[1]	Kirchhoff H. Chloroplast ultrastructure in plants[J]. New Phytologist, 2019, 223(2): 565-574.
[2]	Bandaranayake P C G, Naranpanawa N, Chandrasekara CHWMRB, Samarakoon H, Lokuge S, Jayasundara S, Bandaranayake A U, Pushpakumara DKNG, Wijesundara D S A. Chloroplast genome, nuclear ITS regions, mitogenome regions, and skmer analysis resolved the genetic relationship among Cinnamomum species in Sri Lanka[J]. PLoS One, 2023, 18(9): e0291763.
[3]	Zhang E, Liu Y, Wang Y, Zhang X, Wei Y, Zhang L. Characterization of the complete chloroplast genome of Cynanchum acutum subsp. sibiricum (Apocynaceae)[J]. Mitochondrial DNA Part B: Resources, 2023, 8(9): 993-997.
[4]	Testone G, Lamprillo M, Gonnella M, Arnesi G, Sobolev A P, Aiese C R, Giannino D. The chloroplast genome of endive (Cichorium endivia L.): Cultivar structural variants and transcriptome responses to stress due to rain extreme events[J]. Genes (Basel), 2023, 14(9): 1829-1844.
[5]	Kousar M, Park J. Comparative analysis of the chloroplast genome of Sicyos angulatus with other seven species of Cucurbitaceae family[J]. Genes (Basel), 2023, 14(9): 1776-1788.
[6]	Xu C, Cai X N, Chen Q Z, Zhou H X, Cai Y, Ben A L. Factors affecting synonymous codon usage bias in chloroplast genome of Oncidium Gower Ramsey[J]. Evolutionary Bioinformatics, 2011, 7(7): 271-278.
[7]	Doherty A, Mcinerney J O. Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates[J]. Molecular Biology and Evolution, 2013, 30(10): 2263-2267.
[8]	Fages-Lartaud M, Hundvin K, Hohmann-Marriott M F. Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii[J]. The Plant Journal, 2022, 112(4): 919-945.
[9]	高立志, 张寿洲, 周毅, 葛颂, 洪德元. 中国野生稻的现状调查[J]. 生物多样性, 1996, 4(3): 160-166.
	Gao L Z, Zhang S Z, Zhou Y, Ge S, Hong D Y. A survey of the current status of wild rice in China[J]. Chinese Biodiversity, 1996, 4(3): 160-166. (in Chinese with English abstract)
[10]	刘学思, 殷富有, 张敦宇, 熊子璇, 刘鑫, 李玉琢, 李俊, 杨顺发, 杨和生, 白成星, 彭钰婷, 刘丽, 钟巧芳, 程在全, 肖素勤. 云南省4个州(市)疣粒野生稻的调查、收集与保护[J]. 杂交水稻, 2023, 38(5): 20-25.
	Liu X S, Yin F Y, Zhang D Y, Xiong Z X, Liu X, Li X Z, Li J, Yang S F, Yang H S, Bai C X, Peng Y T, Liu L, Zhong Q F, Cheng Z Q, Xiao S Q. Investigation, collection and protection of Oryza meyeriana in four prefectures (cities) of Yunnan Province[J]. Hybrid Rice, 2023, 38(5): 20-25. (in Chinese with English abstract)
[11]	肖素勤, 殷富有, 张绍松, 余腾琼, 陈玲, 柯学, 付坚, 张敦宇, 钟巧芳, 李定琴, 陈越, 孙治旭, 岳英, 郭顺云, 王玲仙, 黄兴奇, 杨雅云, 王波, 曾民, 李娥贤, 程在全. 云南野生稻资源及其保护[J]. 植物遗传资源学报, 2017, 18(3): 494-502.
	Xiao S Q, Yin F Y, Zhang S Y, Yu T Q, Chen L, Ke X, Fu J, Zhang D Y, Zhong Q F, Li D Q, Chen Y, Sun Z X, Yue Y, Guo S Y, Wang L X, Huang X Q, Yang Y Y, Wang B, Zeng M, Li E X, Cheng Z Q. Genetic resources and conservation of Yunnan wild rice species[J]. Journal of Plant Genetic Resources, 2017, 18(3): 494-502. (in Chinese with English abstract)
[12]	Masoomi-Aladizgeh F, Masoomi-Aladizgeh F, Jabbari L, Khayam Nekouei R, Aalami A, Atwell B J, Haynes P A. A universal protocol for high-quality DNA and RNA isolation from diverse plant species[J]. PLoS One, 2023, 18(12): e0295852.
[13]	Zhang P, Xu W, Lu X, Wang L. Analysis of codon usage bias of chloroplast genomes in Gynostemma species[J]. Physiology and Molecular Biology of Plants, 2021, 27(12): 2727-2737.
[14]	Wu K Q, Qian J, Song J Y, Gao H H, Zhu Y J, Xu J, Pang X H, Yao H, Sun C, Li X E, Li C Y, Liu J Y, Xu H B, Chen S L. The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza[J]. PLoS One, 2013, 8(2): e57607.
[15]	Yuan S, Nie C, Jia S, Liu T, Zhao J, Peng J, Kong W, Liu W, Gou W, Lei X, Xiong Y, Xiong Y, Yu Q, Ling Y, Ma X. Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: Genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis[J]. Frontiers in Plant Science, 2023, 14: 1170004-1170020.
[16]	Li H, Wu M, Lai Q, Zhou W, Song C. Complete chloroplast of four Sanicula taxa (Apiaceae) endemic to China: lights into genome structure, comparative analysis, and phylogenetic relationships[J]. BMC Plant Biology, 2023, 23(1): 444-460.
[17]	Ogihara Y, Isono K, Kojima T, Endo A, Hanaoka M, Shiina T, Terachi T, Utsugi S, Murata M, Mori N, Takumi S, Ikeo K, Gojobori T, Murai R, Murai K, Matsuoka Y, Ohnishi Y, Tajiri H, Tsunewaki K. Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA[J]. Molecular Genetics and Genomics, 2002, 266(5): 740-746.
[18]	Maier R M, Neckermann K, Igloi G L, Ssel H K. 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, 1995, 251(5): 614-628.
[19]	Saski C, Lee S B, Fjellheim S, Guda C, Jansen R K, Luo H, Tomkins J, Rognli O A, Daniell H, Clarke J L. Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes[J]. Theoretical and Applied Genetics, 2007, 115(4): 571-590.
[20]	Middleton C P, Senerchia N, Stein N, Akhunov E D, Keller B, Wicker T, Kilian B. Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe[J]. PLoS One, 2014, 9(3): e85761.
[21]	Song Y, Chen Y, Lv J, Xu J, Zhu S, Li M, Chen N. Development of chloroplast genomic resources for Oryza species discrimination[J]. Frontiers in Plant Science, 2017, 8: 1854-1863.
[22]	Wambugu P W, Brozynska M, Furtado A, Waters D L, Henry R J. Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences[J]. Scientific Reports, 2015, 5: 13957-13965.
[23]	Hao J, Liang Y, Ping J, Li J, Shi W, Su Y, Wang T. Chloroplast gene expression level is negatively correlated with evolutionary rates and selective pressure while positively with codon usage bias in Ophioglossum vulgatum L[J]. BMC Plant Biology, 2022, 22(1): 580-592.
[24]	Chi X, Zhang F, Dong Q, Chen S. Insights into comparative genomics, codon usage bias, and phylogenetic relationship of species from Biebersteiniaceae and Nitrariaceae based on complete chloroplast genomes[J]. Plants (Basel), 2020, 9(11): 1065-1079.
[25]	Li C, Zhou L, Nie J, Wu S, Li W, Liu Y, Liu Y. Codon usage bias and genetic diversity in chloroplast genomes of Elaeagnus species (Myrtiflorae: Elaeagnaceae)[J]. Physiology and Molecular Biology of Plants, 2023, 29(2): 239-251.
[26]	Shen L, Chen S, Liang M, Qu S, Feng S, Wang D, Wang G. Comparative analysis of codon usage bias in chloroplast genomes of ten medicinal species of Rutaceae[J]. BMC Plant Biology, 2024, 24(1): 424-437.
[27]	Kaiser E, Correa Galvis V, Armbruster U. Efficient photosynthesis in dynamic light environments: A chloroplast's perspective[J]. The Biochemical Journal, 2019, 476(19): 2725-2741.
[28]	Cejudo F J, Gonzalez M C, Perez-Ruiz J M. Redox regulation of chloroplast metabolism[J]. Plant Physiology, 2021, 186(1): 9-21.
[29]	Vaughan D A. The Wild Relative of Rice: A Genetic Resources Handbook[M]. 1994.
[30]	Asaf S, Waqas M, Khan A L, Khan M A, Kang S M, Imran Q M, Shahzad R, Bilal S, Yun B W, Lee I J. The complete chloroplast genome of wild rice (Oryza minuta) and its comparison to related species[J]. Frontiers in Plant Science, 2017, 8: 304-318.
[31]	Gao L L, Hong Z H, Wang Y, Wu G Z. Chloroplast proteostasis: A story of birth, life, and death[J]. Plant Communications, 2023, 4(1): 100424-100448.

种类 Category	基因分组 Gene group	基因名 Gene name
光合系统 Photosynthesis	光系统Ⅰ Subunits of photosystem Ⅰ	psaA, psaB, psaC, psaI, psaJ
	光系统Ⅱ Subunits of photosystem Ⅱ	psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ
	NADH脱氢酶亚基 Subunits of NADH dehydrogenase	ndhA, ndhB(2), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH(2), ndhI, ndhJ, ndhK
	细胞色素b/f复合体亚基 Subunits of cytochrome b/f complex	petA, petB, petD, petG, petL, petN
	ATP合成酶 Subunits of ATP synthase	atpA, atpB, atpE, atpF, atpH, atpI*
	Rubisco大亚基 Large subunit of rubisco	rbcL
自我复制 Self-replication	核糖体蛋白大亚基 Large ribosomal subunit	rpl14, rpl16, rpl2(2), rpl20, rpl22, rpl23(2), rpl32, rpl33, rpl36
	核糖体蛋白小亚基 Small ribosomal subunit	rps11, rps12(3), rps14, rps15(2), rps16, rps18, rps19(2), rps2, rps3, rps4, rps7(2), rps8
	RNA聚合酶亚基 Subunits of RNA polymerase	rpoA, rpoB, rpoC1, rpoC2
	核糖体RNA Ribosomal RNAs	rrn16S(2), rrn23S(2), rrn4.5S(2), rrn5S(2)
	转运RNA Transfer RNAs	trnA-UGC(2), trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-UCC, trnH-GUG(2), trnI-CAU(2), trnI-GAU(2), trnK-UUU, trnL-CAA(2), trnL-UAA, trnL-UAG, trnM-CAU, trnN-GUU(2), trnP-UGG, trnQ-UUG, trnR-ACG(2), trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC(2), trnV-UAC, trnW-CCA, trnY-GUA, trnfM-CAU*
其他基因 Other gene	成熟酶 Maturase	matK
	蛋白酶 Protease	clpP
	外膜蛋白 Envelope membrane protein	cemA
	乙酰辅酶A羧化酶亚基 Acetyl-CoA carboxylase	accD
	c型细胞色素合成基因 Synthesis factor of c-cytochrome	ccsA
	翻译起始因子 Initiation factor of translation	infA
未知功能基因 Unknown function gene	保守开放阅读框 Conserve open reading frame	ycf3, ycf4, ycf68(2)
：有一个内含子的基因；：有两个内含子的基因；括号中数字表示多拷贝基因的拷贝数。 , Gene with one intron; **, Gene with two introns; Values in the brackets refer to number of copies of multi-copy genes.

种类 Category	基因分组 Gene group	基因名 Gene name
光合系统 Photosynthesis	光系统Ⅰ Subunits of photosystem Ⅰ	psaA, psaB, psaC, psaI, psaJ
	光系统Ⅱ Subunits of photosystem Ⅱ	psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ
	NADH脱氢酶亚基 Subunits of NADH dehydrogenase	ndhA, ndhB(2), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH(2), ndhI, ndhJ, ndhK
	细胞色素b/f复合体亚基 Subunits of cytochrome b/f complex	petA, petB, petD, petG, petL, petN
	ATP合成酶 Subunits of ATP synthase	atpA, atpB, atpE, atpF, atpH, atpI*
	Rubisco大亚基 Large subunit of rubisco	rbcL
自我复制 Self-replication	核糖体蛋白大亚基 Large ribosomal subunit	rpl14, rpl16, rpl2(2), rpl20, rpl22, rpl23(2), rpl32, rpl33, rpl36
	核糖体蛋白小亚基 Small ribosomal subunit	rps11, rps12(3), rps14, rps15(2), rps16, rps18, rps19(2), rps2, rps3, rps4, rps7(2), rps8
	RNA聚合酶亚基 Subunits of RNA polymerase	rpoA, rpoB, rpoC1, rpoC2
	核糖体RNA Ribosomal RNAs	rrn16S(2), rrn23S(2), rrn4.5S(2), rrn5S(2)
	转运RNA Transfer RNAs	trnA-UGC(2), trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-UCC, trnH-GUG(2), trnI-CAU(2), trnI-GAU(2), trnK-UUU, trnL-CAA(2), trnL-UAA, trnL-UAG, trnM-CAU, trnN-GUU(2), trnP-UGG, trnQ-UUG, trnR-ACG(2), trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC(2), trnV-UAC, trnW-CCA, trnY-GUA, trnfM-CAU*
其他基因 Other gene	成熟酶 Maturase	matK
	蛋白酶 Protease	clpP
	外膜蛋白 Envelope membrane protein	cemA
	乙酰辅酶A羧化酶亚基 Acetyl-CoA carboxylase	accD
	c型细胞色素合成基因 Synthesis factor of c-cytochrome	ccsA
	翻译起始因子 Initiation factor of translation	infA
未知功能基因 Unknown function gene	保守开放阅读框 Conserve open reading frame	ycf3, ycf4, ycf68(2)
：有一个内含子的基因；：有两个内含子的基因；括号中数字表示多拷贝基因的拷贝数。 , Gene with one intron; **, Gene with two introns; Values in the brackets refer to number of copies of multi-copy genes.

基因 Gene	GC1(%)	GC2(%)	GC3(%)	GC_all(%)	有效密码子数 ENC	基因 Gene	GC1(%)	GC2(%)	GC3(%)	GC_all(%)	有效密码子数ENC
rps12	53.78	48.74	27.73	43.42	46.66	petA	53.89	35.20	33.64	40.91	48.83
psbA	49.44	43.22	35.03	42.56	39.47	rps18	34.76	39.02	26.83	33.54	42.30
matK	41.07	31.68	30.76	34.50	47.22	rpl20	41.67	39.17	30.00	36.94	55.84
psbD	53.11	43.50	36.72	44.44	46.90	clpP	53.00	38.25	39.17	43.47	52.57
psbC	53.59	44.94	33.12	43.88	44.81	psbB	54.22	46.17	32.02	44.14	47.85
rpoB	49.91	38.20	31.60	39.90	49.02	petB	48.61	41.20	29.17	39.66	42.27
rpoC1	49.34	38.21	30.01	39.19	50.15	petD	51.55	39.13	30.43	40.37	48.26
rpoC2	48.37	36.36	31.12	38.62	50.40	rpoA	46.15	36.69	29.59	37.48	50.54
rps2	40.93	40.93	33.33	38.40	50.78	rps11	50.00	57.64	22.22	43.29	41.59
atpI	47.58	36.29	32.26	38.71	50.79	infA	45.37	37.04	42.59	41.67	61.00
atpF	47.83	33.70	32.07	37.86	48.81	rps8	41.61	41.61	27.74	36.98	41.83
atpA	55.91	39.96	31.10	42.32	46.79	rpl14	54.84	37.10	26.61	39.52	53.66
rps14	41.35	45.19	32.69	39.74	40.55	rpl16	51.09	54.01	26.28	43.80	37.23
psaB	48.57	43.13	33.74	41.81	49.64	rps3	43.75	30.00	25.42	33.06	46.49
psaA	52.06	43.54	36.09	43.90	49.60	rpl22	40.00	36.67	34.67	37.11	46.54
ycf3	47.95	37.43	33.33	39.57	58.34	ndhB	42.27	38.94	33.07	38.10	46.72
rps4	48.51	37.13	25.74	37.13	49.23	rps7	50.32	45.22	23.57	39.70	47.03
ndhJ	48.75	36.88	31.87	39.17	48.30	ndhH	50.76	34.52	27.92	37.73	47.00
ndhK	42.11	43.72	30.36	38.73	47.60	ndhF	37.69	38.78	25.31	33.92	44.56
ndhC	52.07	34.71	32.23	39.67	59.96	ccsA	33.85	40.99	26.40	33.75	43.62
atpE	52.90	39.13	36.23	42.75	57.29	ndhD	40.52	36.73	31.74	36.33	45.12
atpB	54.71	41.48	30.46	42.22	47.32	ndhE	40.20	32.35	25.49	32.68	50.51
rbcL	57.53	43.93	31.59	44.35	47.59	ndhG	46.89	34.46	25.42	35.59	41.40
ycf4	49.46	40.32	34.95	41.58	46.13	ndhI	38.12	38.67	28.73	35.17	50.78
cemA	42.42	27.71	32.03	34.05	51.88	ndhA	42.70	36.64	25.07	34.80	44.99
GC1, GC2, GC3和GC_all分别代表第1位、第2位、第3位碱基和所有碱基GC含量。下同。 GC1, GC2, GC3, and GC_all represent the GC content of the first, second, and third codon positions as well as the overall GC content of all bases, respectively. The same below.

基因 Gene	GC1(%)	GC2(%)	GC3(%)	GC_all(%)	有效密码子数 ENC	基因 Gene	GC1(%)	GC2(%)	GC3(%)	GC_all(%)	有效密码子数ENC
rps12	53.78	48.74	27.73	43.42	46.66	petA	53.89	35.20	33.64	40.91	48.83
psbA	49.44	43.22	35.03	42.56	39.47	rps18	34.76	39.02	26.83	33.54	42.30
matK	41.07	31.68	30.76	34.50	47.22	rpl20	41.67	39.17	30.00	36.94	55.84
psbD	53.11	43.50	36.72	44.44	46.90	clpP	53.00	38.25	39.17	43.47	52.57
psbC	53.59	44.94	33.12	43.88	44.81	psbB	54.22	46.17	32.02	44.14	47.85
rpoB	49.91	38.20	31.60	39.90	49.02	petB	48.61	41.20	29.17	39.66	42.27
rpoC1	49.34	38.21	30.01	39.19	50.15	petD	51.55	39.13	30.43	40.37	48.26
rpoC2	48.37	36.36	31.12	38.62	50.40	rpoA	46.15	36.69	29.59	37.48	50.54
rps2	40.93	40.93	33.33	38.40	50.78	rps11	50.00	57.64	22.22	43.29	41.59
atpI	47.58	36.29	32.26	38.71	50.79	infA	45.37	37.04	42.59	41.67	61.00
atpF	47.83	33.70	32.07	37.86	48.81	rps8	41.61	41.61	27.74	36.98	41.83
atpA	55.91	39.96	31.10	42.32	46.79	rpl14	54.84	37.10	26.61	39.52	53.66
rps14	41.35	45.19	32.69	39.74	40.55	rpl16	51.09	54.01	26.28	43.80	37.23
psaB	48.57	43.13	33.74	41.81	49.64	rps3	43.75	30.00	25.42	33.06	46.49
psaA	52.06	43.54	36.09	43.90	49.60	rpl22	40.00	36.67	34.67	37.11	46.54
ycf3	47.95	37.43	33.33	39.57	58.34	ndhB	42.27	38.94	33.07	38.10	46.72
rps4	48.51	37.13	25.74	37.13	49.23	rps7	50.32	45.22	23.57	39.70	47.03
ndhJ	48.75	36.88	31.87	39.17	48.30	ndhH	50.76	34.52	27.92	37.73	47.00
ndhK	42.11	43.72	30.36	38.73	47.60	ndhF	37.69	38.78	25.31	33.92	44.56
ndhC	52.07	34.71	32.23	39.67	59.96	ccsA	33.85	40.99	26.40	33.75	43.62
atpE	52.90	39.13	36.23	42.75	57.29	ndhD	40.52	36.73	31.74	36.33	45.12
atpB	54.71	41.48	30.46	42.22	47.32	ndhE	40.20	32.35	25.49	32.68	50.51
rbcL	57.53	43.93	31.59	44.35	47.59	ndhG	46.89	34.46	25.42	35.59	41.40
ycf4	49.46	40.32	34.95	41.58	46.13	ndhI	38.12	38.67	28.73	35.17	50.78
cemA	42.42	27.71	32.03	34.05	51.88	ndhA	42.70	36.64	25.07	34.80	44.99
GC1, GC2, GC3和GC_all分别代表第1位、第2位、第3位碱基和所有碱基GC含量。下同。 GC1, GC2, GC3, and GC_all represent the GC content of the first, second, and third codon positions as well as the overall GC content of all bases, respectively. The same below.

组段区间 Class range	频数 Frequency number	频率 Frequency(%)
[−0.20，−0.05）	4	8
[−0.05，0.05）	9	18
[0.05，0.15）	25	50
[0.15，0.25）	10	20
[0.25，0.35）	2	4

野生稻叶绿体基因组组装与密码子偏好性分析及系统发育研究

Assembly, Codon Usage Bias, and Phylogenetic Analysis of Chloroplast Genome of Oryza meyeriana

RichHTML

PDF

可视化

摘要/Abstract

引用本文

使用本文

图/表 12

参考文献 31

相关文章 2

编辑推荐

Metrics

氨基酸 AA	密码子 Codon	RSCU高表达 RSCU high expression	RSCU低表达 RSCU low expression	RSCU差值 △RSCU	RSCU值 RSCU value
Phe	UUU	1.06	1.27	−0.21	1.30
	UUC*	0.94	0.73	0.21	0.70
Leu	UUA***	2.08	1.35	0.73	2.00
	UUG*	1.44	1.16	0.28	1.13
	CUU	1.36	1.45	−0.09	1.29
	CUC	0.00	0.48	−0.48	0.42
	CUA	0.80	0.87	−0.07	0.82
	CUG	0.32	0.68	−0.36	0.35
Ile	AUU**	1.66	1.31	0.35	1.51
	AUC	0.53	0.58	−0.05	0.59
	AUA	0.81	1.11	−0.30	0.91
Met	AUG	1.00	1.00	0.00	1.00
Val	GUU	2.05	2.00	0.05	1.54
	GUC	0.10	0.44	−0.34	0.46
	GUA***	1.74	1.11	0.63	1.47
	GUG	0.10	0.44	−0.34	0.53
Ser	UCU***	1.85	1.08	0.77	1.60
	UCC***	1.32	0.77	0.55	1.20
	UCA	0.44	1.38	−0.94	1.03
	UCG	0.18	0.62	−0.44	0.53
Pro	CCU***	2.00	0.70	1.30	1.51
	CCC	0.90	1.39	−0.49	0.95
	CCA	0.70	0.87	−0.17	1.08
	CCG	0.40	1.04	−0.64	0.46
Thr	ACU***	1.92	0.89	1.03	1.68
	ACC	0.92	1.04	−0.12	0.76
	ACA	0.92	0.89	0.03	1.09
	ACG	0.25	1.19	−0.94	0.47
Ala	GCU***	2.17	1.66	0.51	1.77
	GCC	0.54	0.68	−0.14	0.56
	GCA	1.02	1.13	−0.11	1.19
	GCG	0.27	0.53	−0.26	0.48
Tyr	UAU	1.40	1.63	−0.23	1.56
	UAC*	0.60	0.37	0.23	0.44
Ter	UAA***	2.40	1.80	0.60	1.44
	UAG	0.00	0.60	−0.60	0.84
His	CAU	1.16	1.20	−0.04	1.45
	CAC	0.84	0.80	0.04	0.55
Gln	CAA*	1.45	1.29	0.16	1.52
	CAG	0.55	0.71	−0.16	0.48
Asn	AAU	0.89	1.46	−0.57	1.47
	AAC***	1.11	0.54	0.57	0.53
Lys	AAA**	1.35	1.03	0.32	1.46
	AAG	0.65	0.97	−0.32	0.54
Asp	GAU	1.38	1.71	−0.33	1.54
	GAC**	0.63	0.29	0.34	0.46
Glu	GAA	1.37	1.64	−0.27	1.48
	GAG*	0.63	0.36	0.27	0.52
Cys	UGU	1.71	2.00	−0.29	1.47
	UGC*	0.29	0.00	0.29	0.53
Ter	UGA	0.60	0.60	0.00	0.72
Trp	UGG	1.00	1.00	0.00	1.00
Arg	CGU***	1.58	0.87	0.71	1.39
	CGC	0.33	0.55	−0.22	0.54
	CGA	1.52	1.64	−0.12	1.32
	CGG	0.40	0.87	−0.47	0.49
Ser	AGU*	1.76	1.54	0.22	1.27
	AGC	0.44	0.62	−0.18	0.38
Arg	AGA**	1.98	1.53	0.45	1.68
	AGG	0.20	0.55	−0.35	0.59
Gly	GGU***	1.82	1.09	0.73	1.27
	GGC	0.55	0.48	0.07	0.43
	GGA	1.39	1.58	−0.19	1.53
	GGG	0.24	0.85	−0.61	0.77

登录号 GenBank code	物种 Species	登录号 GenBank code	物种 Species
MZ323108.1	Arabidopsis thaliana	NC027676.1	Oryza punctata
NC034764.1	Oryza ridleyi	NC030298.1	Oryza minuta
NC034763.1	Oryza longiglumis	KM088024.1	Oryza longistaminata
KF359917.1	Oryza brachyantha	KM103377.1	Oryza glaberrima
NC053277.1	Oryza schlechteri	NC027460.1	Oryza barthii
NC024608.1	Oryza australiensis	NC008155.1	Oryza sativa indica Group
NC027463.1	Oryza officinalis	NC005973.1	Oryza nivara
NC034759.1	Oryza eichingeri	KF562709.1	Oryza rufipogon (Dongxiang)
NC034761.1	Oryza grandiglumis	MW001303.1	Oryza sativa temperate japonica
NC034760.1	Oryza alta	KT289404.1	Oryza sativa tropical japonica
NC036934.1	Oryza coarctata	LC739565.1	Oryza sativa japonica Group

[1]	陈涛,张震,柴荣耀,王教瑜,毛雪琴,邱海萍,杜新法,姜华,王立安. 浙江省水稻纹枯病菌的遗传分化与致病力研究[J]. 中国水稻科学, 2010, 24(1): 67-72 .
[2]	王玲,黄世文 ,王全永,鄂志国,王磊,张建萍,朱德峰,傅强. 稗草病原真菌AAE的分子鉴定及其粗蛋白诱导水稻的稻瘟病抗性[J]. 中国水稻科学, 2008, 22(3): 327-330 .