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猫尾草叶绿体基因组结构及其解析

吴民富 李莎 高柔敏 吴民华 黄琼林

吴民富,李莎,高柔敏,等. 猫尾草叶绿体基因组结构及其解析 [J]. 福建农业学报,2023,38(9):1094−1102 doi: 10.19303/j.issn.1008-0384.2023.09.011
引用本文: 吴民富,李莎,高柔敏,等. 猫尾草叶绿体基因组结构及其解析 [J]. 福建农业学报,2023,38(9):1094−1102 doi: 10.19303/j.issn.1008-0384.2023.09.011
WU M F, LI S, GAO R M, et al. Structure of Uraria crinita Chloroplast Genome [J]. Fujian Journal of Agricultural Sciences,2023,38(9):1094−1102 doi: 10.19303/j.issn.1008-0384.2023.09.011
Citation: WU M F, LI S, GAO R M, et al. Structure of Uraria crinita Chloroplast Genome [J]. Fujian Journal of Agricultural Sciences,2023,38(9):1094−1102 doi: 10.19303/j.issn.1008-0384.2023.09.011

猫尾草叶绿体基因组结构及其解析

doi: 10.19303/j.issn.1008-0384.2023.09.011
基金项目: 广东省基础与应用基础研究基金项目(2020A1515110332);湛江市科技计划项目(2019A01008)
详细信息
    作者简介:

    吴民富(1986 —),男,博士,副教授,主要从事食品质量与安全研究,E-mail:wmf@fspt.edu.cn

    通讯作者:

    黄琼林(1986 —),男,博士,副教授,主要从事医学生物化学研究,E-mail:perfecthql@163.com

  • 中图分类号: S541

Structure of Uraria crinita Chloroplast Genome

  • 摘要:   目的  阐明岭南药食两用植物猫尾草的叶绿体基因组结构特征,为猫尾草资源的保护、利用和开发提供理论依据。  方法  采用高通量测序技术开展猫尾草叶绿体基因组测序,并通过生物信息方法进行拼接、注释、解析以及系统进化分析。  结果  猫尾草叶绿体基因组是149 774 bp的环状双链四段式分子,包含128个基因,GC含量为38.2%。猫尾草叶绿体基因组含有26 015个密码子,偏好以A或T结尾;存在110个简单重复序列,以A或T单核苷酸重复居多。序列比对和进化分析显示猫尾草与同属狸尾豆的亲缘关系最近。  结论  首次报道猫尾草叶绿体基因组的全序列,并明确其结构特点,为猫尾草的栽培育种、遗传多样性和资源利用等奠定基础。
  • 图  1  猫尾草叶绿体基因组

    Figure  1.  Chloroplast genome of U. crinita

    图  2  猫尾草叶绿体基因组的相对同义密码子使用情况

    Ala-丙氨酸; Arg-精氨酸; Asn-天冬酰胺; Asp-天冬氨酸; Cys-半胱氨酸; Glu-谷氨酸; Gln-谷氨酰胺; Gly-甘氨酸;His-组氨酸; Ile-异亮氨酸; Leu-亮氨酸; Lys-赖氨酸; Met-甲硫氨酸; Phe-苯丙氨酸; Pro-脯氨酸; Ser-丝氨酸; Thr-苏氨酸; Trp-色氨酸; Tyr-络氨酸; Val-缬氨酸; end-终止密码子。

    Figure  2.  Relative synonymous codon usage of U. crinita chloroplast genome

    Ala: alanine; Arg: arginine; Asn: asparagine; Asp: aspartate; Cys: cysteine; Glu: glutamate; Gln: glutamine; Gly: glycine; His: histidine; Ile: isoleucine; Leu: leucine; Lys: lysine; Met: methionine; Phe: phenylalanine; Pro: proline; Ser: serine; Thr: threonine; Trp: tryptophan; Tyr: tyrosine; Val: valine; end: ending codon.

    图  3  5种植物的叶绿体基因组SC/IR边界的比较

    Figure  3.  Comparison on boundaries of SC/IR in chloroplast genomes of 5 plants

    图  4  豆科蝶形亚科山蚂蝗族5种植物叶绿体基因组序列差异分析

    Figure  4.  Sequence differentiations among 5 chloroplast genomes from trib. Lespedezinae

    图  5  基于叶绿体基因组构建的猫尾草系统进化树

    Figure  5.  Phylogenetic tree of U. crinita based on chloroplast genome

    表  1  猫尾草叶绿体基因及其注释和功能归类

    Table  1.   Composition and classification of genes in U. crinita chloroplast genome

    分类
    Category
    功能
    Function
    基因
    Gene
    蛋白质编码基因
    Protein-coding gene
    ATP 合成酶
    ATP synthase
    atpA, atpB, atpE, atpF1, atpH, atpI
    细胞色素b/f复合物
    Cytochrome b/f complex
    petA, petB1, petD1, petG, petL, petN
    NADH脱氢酶
    NADH dehydrogenase
    ndhA1, ndhB1*, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK
    光系统I
    Photosystem I
    psaA, psaB, psaC, psaI, psaJ
    光系统II
    Photosystem II
    psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ
    核糖体蛋白质大亚基
    Ribosomal proteins large submit
    rps2, rps3, rps4, rps7*, rps8, rps11,rps12#*, rps14, rps15,rps161, rps18, rps19*
    核糖体蛋白质小亚基
    Ribosomal proteins small submit
    rpl21*, rpl14, rpl161, rpl20,rpl22*, rpl23*, rpl32,rpl33, rpl36
    RNA集合酶
    RNA polymerase
    rpoA, rpoB, rpoC11, rpoC2
    其他基因
    Other genes
    accD, ccsA, cemA, clpP2, matK, rbcL, infA
    假定叶绿体阅读框
    Hypothetical chloroplast reading frame
    ycf1, ycf2*, ycf32, ycf4
    核糖体RNA
    Ribosomal RNAs
    rrn4.5*, rrn5*, rrn16*, rrn23*
    转运RNA
    Transfer RNAs
    trnH-GUG, trnK-UUU1, trnM-CAU, trnM-CAU, trnV-UAC1, trnF-GAA, trnL-UAA1, trnT-UGU, trnS-GGA, trnfM-CAU, trnG-GCC, trnS-UGA, trnT-GGU, trnD-GUC, trnY-GUA, trnE-UUC, trnC-GCA, trnR-UCU, trnG-UCC1, trnS-GCU, trnQ-UUG, trnW-CCA, trnP-UGG, trnI-CAU, trnL-CAA*, trnV-GAC*, trnI-GAU1*, trnA-UGC1*, trnR-ACG*, trnN-GUU*, trnL-UAG
    基因右上角的数字表示该基因所含的内含子数;#表示该基因存在反式剪接情况;*表示该基因为双拷贝基因。
    Data on upper right corner stand for intron number in genes; # denotes trans-splicing in genes; * represents genes with two copies.
    下载: 导出CSV

    表  2  猫尾草叶绿体基因组SSR统计

    Table  2.   SSR information on U. crinita chloroplast genome

    类型
    Type
    重复基序
    Motif
    数量
    Number
    比例
    Ratio/%
    单核苷酸 Mononucleotide A/T 54 98.2
    C/G 1 1.8
    二核苷酸 Dinucleotide AG/CT 1 2.4
    AT/AT 41 97.6
    三核苷酸 Trinucleotide AAT/ATT 6 100.0
    四核苷酸 Tetranucleotide AAAT/ATTT 4 57.1
    AAGG/CCTT 1 14.3
    AAGT/ACTT 1 14.3
    AGAT/ATCT 1 14.3
    总计 Total 110
    下载: 导出CSV
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出版历程
  • 收稿日期:  2023-05-26
  • 修回日期:  2023-07-04
  • 网络出版日期:  2023-10-25
  • 刊出日期:  2023-09-28

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