茶树大面白叶绿体基因组特征、密码子偏好性及其系统发育分析

尹明华; 张嘉欣; 乐芸; 何凡凡; 黄添慧; 张牧彤

doi:10.13305/j.cnki.jts.2024.03.009

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茶叶科学 ›› 2024, Vol. 44 ›› Issue (3) : 411-430. DOI: 10.13305/j.cnki.jts.2024.03.009

研究报告

茶树大面白叶绿体基因组特征、密码子偏好性及其系统发育分析

尹明华^1,2,3,4, 张嘉欣¹, 乐芸¹, 何凡凡¹, 黄添慧¹, 张牧彤¹

作者信息 +

Genomic Characteristics, Codon Preference, and Phylogenetic Analysis of Chloroplasts of Camellia sinensis cv. ‘Damianbai’

YIN Minghua^1,2,3,4, ZHANG Jiaxin¹, LE Yun¹, HE Fanfan¹, HUANG Tianhui¹, ZHANG Mutong¹

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文章历史 +

摘要

茶树大面白（Camellia sinensis cv. ‘Damianbai’）在1985年被全国农作物品种审定委员会认定为国家品种,其起源以及与其他茶树品种之间的进化关系尚不清晰。以茶树大面白为试验材料,采用高通量测序技术对茶树大面白叶绿体全基因组进行测序、组装、注释,采用生物信息学软件对其叶绿体的基因组特征、系统发育和密码子偏好性进行分析。结果表明,茶树大面白叶绿体基因组全长157 129 bp,为典型的四分体结构,包括1个LSC区（86 687 bp）、1个SSC区（18 282 bp）和2个IR区（包括IRa和IRb,均为26 080 bp）。大面白叶绿体基因组共注释到135个功能基因,包括90个CDS基因;8个rRNA基因和37个tRNA基因。共检测到52个SSR和50个Longrepeat,SSR只有A/T单核苷酸重复序列,Longrepeat只存在正向重复和回文重复2种类型。茶树大面白叶绿体基因组密码子使用偏性主要受自然选择的影响,受内部突变压力的影响小。茶树大面白叶绿体基因有14个最优密码子（AAU、GAU、UGU、AAA、UAA、GCA、GCU、GGU、CCU、GUA、CGU、CUU、AGU、UCU）。茶树大面白与凤凰单丛茶白银（Camellia sinensis isolated Baiyin cultivar Phoenix Dancong Tea,OL690374）亲缘关系较近。本研究分析了大面白茶树叶绿体基因组序列特征及系统发育进化关系,为加强茶树大面白种质鉴定及其资源多样性的开发利用提供了参考依据。

Abstract

‘Damianbai’ was approved as a national tea cultivar by the National Crop Variety Approval Committee in 1985, but its origin and evolutionary relationship with other tea resources are still unclear. Using ‘Damianbai’ as the experimental material, high-throughput sequencing technology was used to sequence, assemble and annotate the entire chloroplast genome of ‘Damianbai’. In order to provide a basis for studying its phylogenetic evolutionary relationship, bioinformatics software was used to analyze the characteristics, phylogeny, and codon preference of its chloroplast genome. The results show that the chloroplast genome of the tea cultivar ‘Damianbai’ had a total length of 157 129 bp and was a typical tetrad structure, including 1 LSC region (86 687 bp), 1 SSC region (18 282 bp), and 2 IR regions (including IRa and IRb, both of which were 26 080 bp). A total of 135 functional genes were annotated in the chloroplast genome of ‘Damianbai’, including 90 CDS genes, 8 rRNA genes, and 37 tRNA genes. A total of 52 SSRs and 50 Longrepeat sequences were detected in the chloroplast genome of ‘Damianbai’. The SSRs had only A/T single nucleotide repeat sequences, while Longrepeat sequences had only two types: forward repeat and palindrome repeat. The codon usage bias in the chloroplast genome of tea cultivar ‘Damianbai’ was mainly influenced by natural selection, and was less affected by internal mutation pressure. The chloroplast gene of tea cultivar ‘Damianbai’ had 14 optimal codons (AAU, GAU, UGU, AAA, UAA, GCA, GCU, GGU, CCU, GUA, CGU, CUU, AGU, UCU). The Camellia sinensis cv. ‘Damianbai’ had a close genetic relationship with Camellia sinensis isolate Baiyin cultivar Phoenix Dancong Tea (OL690374). This study analyzed the chloroplast genome sequence characteristics and phylogenetic relationships of ‘Damianbai’, which provided a reference basis for strengthening the identification of tea cultivar ‘Damianbai’ and the development and utilization of its resource diversity.

导出引用

尹明华, 张嘉欣, 乐芸, 何凡凡, 黄添慧, 张牧彤. 茶树大面白叶绿体基因组特征、密码子偏好性及其系统发育分析[J]. 茶叶科学. 2024, 44(3): 411-430 https://doi.org/10.13305/j.cnki.jts.2024.03.009

YIN Minghua, ZHANG Jiaxin, LE Yun, HE Fanfan, HUANG Tianhui, ZHANG Mutong. Genomic Characteristics, Codon Preference, and Phylogenetic Analysis of Chloroplasts of Camellia sinensis cv. ‘Damianbai’[J]. Journal of Tea Science. 2024, 44(3): 411-430 https://doi.org/10.13305/j.cnki.jts.2024.03.009

中图分类号： S571.1 S326

参考文献

[1] Li W X, Shi X G, Guo W X, et al.Characterization of the complete chloroplast genome of Camellia granthamiana (Theaceae), a Vulnerable species endemic to China[J]. Mitochondrial DNA B Resource, 2018, 3(2): 1139-1140.
[2] 杨雨青, 谭娟, 汪芳, 等. 茶树叶绿体基因组的研究与应用进展[J]. 生物技术通报, 2024, 40(2): 1-11.
Yang Y Q, Tan J, Wang F, et al.Research and application progress in chloroplast genome of tea plant (Camellia sinensis)[J]. Biotechnology Bulletin, 2024, 40(2): 1-11.
[3] Xia E H, Tong W, Wu Q, et al.Tea plant genomics: achievements, challenges and perspectives[J]. Horticulture Research, 2020, 7(1): 7. doi: 10.1038/s41438-019-0225-4.
[4] 闫明慧, 刘柯, 王满, 等. 信阳10号叶绿体基因组及其系统进化[J]. 茶叶科学, 2021, 41(6): 777-788.
Yan M H, Liu K, Wang M, et al.Complete chloroplast genome of Camellia sinensis cv. Xinyang 10 and its phylogenetic evolution[J]. Journal of Tea Science, 2021, 41(6): 777-788.
[5] 王士圻. 名茶新魁——上饶白眉[J]. 蚕桑茶叶通讯, 1986(1): 31-32.
Wang S Q.Famous tea new leader: Shangrao white eyebrow[J]. Newsletter of Sericulture and Tea, 1986(1): 31-32.
[6] 王士圻. 上饶“白眉”炒制技术要点[J]. 茶业通报, 1983(6): 44.
Wang S Q.Key points of frying techniques for Shangrao white eyebrows[J]. Journal of Tea Business, 1983(6): 44.
[7] 黄奋文, 黄积安. 福丁大毫、上饶大面白不同行距种植对茶叶产量的影响[J]. 蚕桑茶叶通讯, 1988(4): 4-7.
Huang F W, Huang J A.The effect of different row spacing planting on tea yield in Fuding Damao and Shangrao Damanbai[J]. Newsletter of Sericulture and Tea, 1988(4): 4-7.
[8] 王士圻. 茶树良种——大面白的选育及其鉴定报告[J]. 茶业通报, 1981(5): 40-45.
Wang S Q.Breeding and identification report of a good tea tree variety: Damianbai[J]. Journal of Tea Business, 1981(5): 40-45.
[9] 王士圻. 茶树良种——上饶大面白[J].蚕桑茶叶通讯, 1978(2): 4-5.
Wang S Q.Excellent tea tree variety: Shangrao Damianbai[J]. Newsletter of Sericulture and Tea, 1978(2): 4-5.
[10] Cao P H, Wang D, Gao S, et al.OsDXR interacts with OsMORF1 to regulate chloroplast development and the RNA editing of chloroplast genes in rice[J]. Journal of Integrative Agriculture, 2023, 22(3): 669-678.
[11] Zhang G L, Feng C, Kou J, et al.Phylogeny and divergence time estimation of the genus Didymodon (Pottiaceae) based on nuclear and chloroplast markers[J]. Journal of Systematics and Evolution, 2023, 61(1): 115-126.
[12] Park T.Complete chloroplast genome sequence of Solanum iopetalum, one of the tuber-bearing wild potato relatives[J]. Mitochondrial DNA Part B, 2023, 8: 347-351.
[13] Li B Z, Li Y, Li Z F, et al.The complete chloroplast genome of Impatiens mengtszeana (Balsaminaceae), an endemic species in China[J]. Mitochondrial DNA Part B, 2022, 7(2): 367-369.
[14] Bourret J, Borvető F, Bravo I G.Subfunctionalisation of paralogous genes and evolution of differential codon usage preferences: the showcase of polypyrimidine tract binding proteins[J]. Journal of Evolutionary Biology, 2023, 36(10): 1375-1392.
[15] Tan F, Banerjee A K, Deng J, et al.Characterization of the complete chloroplast genome of Firmiana hainanensis (Malvaceae), an endemic and vulnerable tree species of China[J]. Mitochondrial DNA Part B, 2023, 8(1): 57-60.
[16] Singhal S, Kumar U, Alqahtani T, et al.An insight into codon pattern analysis of autophagy genes associated with virus infection[J]. Current Pharmaceutical Design, 2023, 29(14): 1105-1120.
[17] Chu D, Wei L.Characterizing the heat response of Arabidopsis thaliana from the perspective of codon usage bias and translational regulation[J]. Journal of Plant Physiology, 2019, 240: 153012. doi: 10.1016/j.jplph.2019.153012.
[18] Zhu Y A, Wang S, Xie J, et al.The complete chloroplast genome of Rubus ellipticus var. obcordatus, an edible and medicinal dual-purpose plant[J]. Mitochondrial DNA Part B, 2022, 7(2): 406-408.
[19] 赵许朋, 崔奎, 耿苗苗, 等. 贵定鸟王茶的叶绿体基因组特征[J]. 西南农业学报, 2023, 36(11): 2348-2357.
Zhao X P, Cui K, Geng M M, et al.Chloroplast genome characteristics of Guiding Niaowang tea[J]. Southwest China Journal of Agricultural Sciences, 2023, 36(11): 2348-2357.
[20] 佟岩, 黄荟, 王雨华. 森林茶园古茶树大理茶叶绿体基因组密码子偏好性及系统发育研究[J]. 茶叶科学, 2023, 43(3): 297-309.
Tong Y, Huang H, Wang Y H.Analysis of codon usage bias and phylogenesis in the chloroplast genome of ancient tea tree Camellia taliensis in forest-tea garden[J]. Journal of Tea Science, 2023, 43(3): 297-309.
[21] 黎巷汝, 赵雅琦, 张艳, 等. 武夷名丛叶绿体基因组序列特征及系统发育分析[J]. 南方农业学报, 2023, 54(5): 1352-1362.
Li X R, Zhao Y Q, Zhang Y, et al.Chloroplast genome sequence features and phylogenetic analysis of Wuyi Mingcong[J]. Journal of Southern Agriculture, 2023, 54(5): 1352-1362.
[22] 刘振, 赵洋, 杨培迪, 等. 三倍体茶树‘西莲1号’叶绿体基因组特征及系统发育分析[J]. 茶叶通讯, 2023, 50(2): 166-175.
Liu Z, Zhao Y, Yang P D, et al.Characterization and phylogenetic analysis of the complete chloroplast genome of triploid tea plant Xilian 1[J]. Journal of Tea Communicatio, 2023, 50(2): 166-175.
[23] 叶晓倩, 赵忠辉, 朱全武, 等. 茶树‘龙井43’叶绿体基因组测序及其系统进化[J]. 浙江大学学报(农业与生命科学版), 2014, 40(4): 404-412.
Ye X Q, Zhao Z H, Zhu Q W, et al.Entire chloroplast genome sequence of tea (Camellia sinensis cv.Longjing 43): a molecular phylogenetic analysis[J]. Journal of Zhejiang University (Agriculture & Life Sciences), 2014, 40(4): 404-412.
[24] Li L, Hu Y F, Wu L, et al.The complete chloroplast genome sequence of Camellia sinensis cv. Dahongpao: a most famous variety of Wuyi tea (Synonym: Thea bohea L.)[J]. Mitochondrial DNA Part B, 2021, 6(1): 3-5.
[25] Peng J, Zhao Y L, Dong M, et al.Exploring the evolutionary characteristics between cultivated tea and its wild relatives using complete chloroplast genomes[J]. BMC Ecology and Evolution, 2021, 21(1): 71. doi: 10.1186/s12862-021-01800-1.
[26] Doyle J J.A rapid DNA isolation procedure for small quantities of fresh leaf tissue[J]. Phytochem Bull, 1987, 19(1): 11-15.
[27] Dierckxsens N, Mardulyn P, Smits G.NOVOPlasty: de novo assembly of organelle genomes from whole genome data[J]. Nucleic Acids Research, 2016, 45(4): e18. doi: 10.1093/nar/gkw955.
[28] Chen S F, Zhou Y Q, Chen Y R, et al.Fastp: an ultra-fast all-in-one FASTQ preprocessor[J]. Bioinformatics, 2018, 34(17): i884-i890.
[29] Tillich M, Lehwark P, Pellizzer T, et al.GeSeq: versatile and accurate annotation of organelle genomes[J]. Nucleic Acids Research, 2017, 45(W1): W6-W11.
[30] Lowe T M, Eddy S R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence[J]. Nucleic Acids Research, 1997, 25(5): 955-964.
[31] Lohse M, Drechsel O, Bock R.OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes[J]. Current Genetics, 2007, 52(5/6): 267-274.
[32] Grant J R, Stothard P.The CGView Server: a comparative genomics tool for circular genomes[J]. Nucleic Acids Research, 2008, 36: 181-184.
[33] Thiel T, Michalek W, Varshney R, et al.Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)[J]. Theoretical & Applied Genetics, 2003, 106(3): 411-422.
[34] Kurtz S, Choudhuri J V, Ohlebusch E, et al.REPuter: the manifold applications of repeat analysis on a genomic scale[J]. Nucleic Acids Research, 2001, 29(22): 4633-4642.
[35] Sharp P M, Li W H.Codon usage in regulatory genes in Escherichia coli does not reflect selection for ‘rare’ codons[J]. Nucleic Acids Research, 1986, 14(19): 7737-7749.
[36] Domselaar G V.Interactive microbial genome visualization with GView[J]. Bioinformatics, 2010, 26(24): 3125-3126.
[37] Amiryousefi A, Hyvönen J, Poczai P.IRscope: an online program to visualize the junction sites of chloroplast genomes[J]. Bioinformatics, 2018, 34(17): 3030-3031.
[38] Rozas J, Rozas R.DnaSP, DNA sequence polymorphism: an interactive program for estimating population genetics parameters from DNA sequence data[J]. Bioinformatics, 1995, 11(6): 621-625.
[39] Katoh K, Standley D M.MAFFT multiple sequence alignment software version 7: improvements in performance and usability[J]. Molecular Biology and Evolution. 2013, 30(4): 772-780.
[40] Price M N, Dehal P S, Arkin A P.FastTree 2-approximately maximum-likelihood trees for large alignments[J]. Plos One, 2010, 5(3): e9490. doi: 10.1371/journal.pone.0009490.
[41] Zhang C, Li S Q, Xie H H, et al.Comparative plastid genome analyses of Rosa: Insights into the phylogeny and gene divergence[J]. Tree Genetics & Genomes, 2022, 18(3): 20. doi: 10.1007/s11295-022-01549-8.
[42] 纵丹, 黄嘉城, 段晓盟, 等. 无籽刺梨及其近缘种叶绿体基因组序列比较分析[J]. 福建农林大学学报(自然科学版), 2024, 53(1): 39-47.
Zong D, Huang J C, Duan X M, et al.Comparative analyses on chloroplast genome sequence of Rosa sterilis and its related species[J]. Journal of Fujian Agriculture and Forestry University (Natural Science Edition), 2024, 53(1): 39-47.
[43] Kaila T, Chaduvla P K, Saxena S, et al.Chloroplast genome sequence of pigeonpea (Cajanus cajan (L.) Millspaugh) and Cajanus scarabaeoides (L.) Thouars: genome organization and comparison with other legumes[J]. Frontiers in Plant Science, 2016, 7: 1847. doi: 10.3389/fpls.2016.01847.
[44] Park I, Yang S, Kim W J, et al.The Complete chloroplast genomes of six Ipomoea species and indel marker development for the discrimination of authentic pharbitidis semen (seeds of I. nil or I. purpurea)[J]. Frontiers in Plant Science, 2018, 9: 965. doi: 10.3389/fpls.2018.00965.
[45] Yang Y, Dang Y Y, Li Q, et al.Complete chloroplast genome sequence of poisonous and medicinal plant Datura stramonium: organizations and implications for genetic engineering[J]. Plos One, 2014, 9(11): e110656. doi: 10.1371/journal.pone.0110656. eCollection 2014.
[46] Fan L, Li L, Hu Y F, et al.Complete chloroplast genomes of five classical Wuyi tea varieties (Camellia sinensis, Synonym: Thea bohea L.), the most famous oolong tea in China[J]. Mitochondrial DNA Part B, 2022, 7(4): 655-657.
[47] Li X W, Gao H H, Wang Y T, et al.Complete chloroplast genome sequence of Magnolia grandiflora and comparative analysis with related species[J]. Science China Life Sciences, 2013, 56(2): 189-198.
[48] Huang H, Shi C, Liu Y, et al.Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships[J]. BMC Evolutionary Biology, 2014, 14(1): 151. doi: 10.1186/1471-2148-14-151.
[49] Geng X S, Huang N, Zhu Y L, et al.Codon usage bias analysis of the chloroplast genome of cassava[J]. South African Journal of Botany, 2022, 151: 970-975.
[50] Ramesh G A, Mathew D, John K J, et al.Chloroplast gene matK holds the barcodes for identification of Momordica (Cucurbitaceae) species from Indian subcontinent[J]. Horticultural Plant Journal, 2022, 8(1): 89-98.
[51] Yang C J, Wang K, Zhang H, et al.Analysis of the chloroplast genome and phylogenetic evolution of three species of Syringa[J]. Molecular Biology Reports, 2023, 50(1): 665-677.
[52] Rawal H C, Kumar P M, Bera B, et al.Decoding and analysis of organelle genomes of Indian tea (Camellia assamica) for phylogenetic confirmation[J]. Genomics, 2020, 112(1): 659-668.