Volume 41 Issue 2
Apr.  2024
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Article Navigation >  Journal of Zhejiang A&F University  > 2024  >  41(2): 297-305

XU Ya’ nan, SONG Chengwei, ZHANG Lixia, et al. Dynamic analysis of mineral elements across the growth cycle of Paeonia ostii ‘Feng Dan’[J]. Journal of Zhejiang A&F University, 2021, 38(1): 128-137. DOI: 10.11833/j.issn.2095-0756.20200303
Citation: WU Minhua, YE Xiaoxia, TAN Jingyi, et al. Analysis on chloroplast genome of Wikstroemia indica[J]. Journal of Zhejiang A&F University, 2024, 41(2): 297-305. DOI: 10.11833/j.issn.2095-0756.20230412
shu

Analysis on chloroplast genome of Wikstroemia indica

DOI: 10.11833/j.issn.2095-0756.20230412
  • 1.

    School of Basic Medicine, Guangdong Medical University, Zhanjiang 524023, Guangdong, China

  • 2.

    School of Pharmacy, Guangdong Medical University, Zhanjiang 524023, Guangdong, China

  • 3.

    The First Clinic Medical College, Guangdong Medical University, Zhanjiang 524023, Guangdong, China

  • Received Date: 2023-07-24
  • Accepted Date: 2023-12-22
  • Rev Recd Date: 2023-12-13
    • Available Online: 2024-03-21
  • Publish Date: 2024-04-01
  •   Objective  This study is aimed to clarify the structure traits of chloroplast genome and phylogenetic status of medicinal plant Wikstroemia indica, providing a scientific basis for the resource protection and sustainable utilization of W. indica.   Method  An Illumina high-throughput sequencing platform was employed to acquire the chloroplast genome sequence which was then assembled, annotated, compared and analyzed using bioinformatics technologies and software.   Result  The chloroplast genome of W. indica was an annular quadripartite molecule with a length of 149 864 bp and composed of a large single copy (LSC, 86 347 bp), a small single copy (SSC, 10 601 bp) and a couple of inverted repeat (IR, 26 458 bp) and 124 genes were annotated in the chloroplast genome. In the chloroplast genome there were a total of 24 180 codon, which were divided into 64 types of which 30 types of codon were used frequently and 29 of them ended with A/T. Altogether 93 chloroplast simple sequence repeat (SSR) were identified from the chloroplast genome with Mononucleotide being the predominate type taking up a number of 72 and the motifs formed by A/T contributing the most and obvious variations were observed in IR boundary between W. indica and closely related plants whereas sequence alignment and phylogenetic tree revealed that W. indica shared high sequence identity with W. nutans.   Conclusion  The chloroplast genome of W. indica exhibited typical structure of plant chloroplast genome, and possessed codon preference and several SSRs with rich polymorphism. Additionally, the chloroplast genome of W. indica showed the closest similarity to W. nutans. [Ch, 5 fig. 2 tab. 24 ref.]
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Analysis on chloroplast genome of Wikstroemia indica

doi: 10.11833/j.issn.2095-0756.20230412
  • 1. School of Basic Medicine, Guangdong Medical University, Zhanjiang 524023, Guangdong, China
  • 2. School of Pharmacy, Guangdong Medical University, Zhanjiang 524023, Guangdong, China
  • 3. The First Clinic Medical College, Guangdong Medical University, Zhanjiang 524023, Guangdong, China
  • Received Date: 2023-07-24
  • Accepted Date: 2023-12-22
  • Rev Recd Date: 2023-12-13
  • Available Online: 2024-03-21
  • Publish Date: 2024-04-01

Abstract:   Objective  This study is aimed to clarify the structure traits of chloroplast genome and phylogenetic status of medicinal plant Wikstroemia indica, providing a scientific basis for the resource protection and sustainable utilization of W. indica.   Method  An Illumina high-throughput sequencing platform was employed to acquire the chloroplast genome sequence which was then assembled, annotated, compared and analyzed using bioinformatics technologies and software.   Result  The chloroplast genome of W. indica was an annular quadripartite molecule with a length of 149 864 bp and composed of a large single copy (LSC, 86 347 bp), a small single copy (SSC, 10 601 bp) and a couple of inverted repeat (IR, 26 458 bp) and 124 genes were annotated in the chloroplast genome. In the chloroplast genome there were a total of 24 180 codon, which were divided into 64 types of which 30 types of codon were used frequently and 29 of them ended with A/T. Altogether 93 chloroplast simple sequence repeat (SSR) were identified from the chloroplast genome with Mononucleotide being the predominate type taking up a number of 72 and the motifs formed by A/T contributing the most and obvious variations were observed in IR boundary between W. indica and closely related plants whereas sequence alignment and phylogenetic tree revealed that W. indica shared high sequence identity with W. nutans.   Conclusion  The chloroplast genome of W. indica exhibited typical structure of plant chloroplast genome, and possessed codon preference and several SSRs with rich polymorphism. Additionally, the chloroplast genome of W. indica showed the closest similarity to W. nutans. [Ch, 5 fig. 2 tab. 24 ref.]

XU Ya’ nan, SONG Chengwei, ZHANG Lixia, et al. Dynamic analysis of mineral elements across the growth cycle of Paeonia ostii ‘Feng Dan’[J]. Journal of Zhejiang A&F University, 2021, 38(1): 128-137. DOI: 10.11833/j.issn.2095-0756.20200303
Citation: WU Minhua, YE Xiaoxia, TAN Jingyi, et al. Analysis on chloroplast genome of Wikstroemia indica[J]. Journal of Zhejiang A&F University, 2024, 41(2): 297-305. DOI: 10.11833/j.issn.2095-0756.20230412
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  • 叶绿体基因组为植物质体遗传体系之一，是由大单拷贝区(LSC)、小单拷贝区(SSC)以及穿插在它们之间的一对碱基组成相同、排列方向相反的反向重复区(IR)构成的环状双链四分体，通常编码约130个主要与光合作用以及叶绿体自身复制相关的基因[1−2]。叶绿体基因组是研究植物物种鉴别、进化生物学和遗传多样性的新思路，并且已有较多的应用实例。SONG等[3]比较了27种安息香属Styrax植物的叶绿体基因组序列，筛选出6个高突变序列，其中ycf1b和trnT-trnL是安息香属物种鉴别的特异性DNA条形码。LIU等[4]利用叶绿体基因组序列探讨了11种燕麦属Avena植物的系统进化关系，支持燕麦属的单系性，并且认为该属包括2个遗传支系。JO等[5]基于饲料作物大花野豌豆Vicia bungei的叶绿体简单重复序列(SSR)开发出232个分子标记，并将其中39个分子标记应用于野豌豆属Vicia中7个物种的遗传多样性分析。

    了哥王Wikstroemia indica是瑞香科Thymelaeaceae荛花属Wikstroemia常绿灌木植物，全株有毒，分布于中国广东、广西、海南、福建、湖南、浙江、云南、贵州、四川以及台湾等大部分省区，多见于海拔1 500 m以下开旷的林下或石山上，野生时一般分布在山坡灌木丛中或路边、村边等[6]。了哥王的干燥根及根皮可入药，能清热解毒、消肿散结、止痛，多用来治疗支气管炎、肺炎、乳腺炎等多种炎症以及跌打损伤[7]，已被开发成了哥王片、了哥王胶囊、了哥王颗粒、祛伤消肿酊等制剂。了哥王含有黄酮、木质素、香豆素、甾体、挥发油等化学成分，具有抗炎、抗菌、抗病毒、抗肿瘤等药理活性[8−9]。了哥王根叶煮汁可作杀虫剂，茎皮纤维可以制作高级纸张和人造棉[6]。了哥王还是一种观赏性园林植物[10]。因此，了哥王具有较高的药用、经济和社会价值。

    了哥王原以野生采收为主要来源，随着市场需求的快速增加，了哥王遭到过度开采，不少产地的野生蕴藏量急剧下降，出现资源匮乏甚至枯竭的情况[11]。本研究分析了哥王叶绿体基因组序列的结构和基因组成、密码子偏好性、SSR等特征，比较了哥王与近缘植物的叶绿体基因组序列差异，并基于叶绿体基因组探究了哥王的进化位置，旨在为了哥王的品种鉴定、育种栽培、遗传背景和系统进化等资源保护和可持续利用提供科学依据。

    • 1.   材料与方法

      1.1.   了哥王的采集和处理

    • 了哥王植株于2022年6月采自广西壮族自治区钦州市钦北区，经广东医科大学天然药物研究与开发重点实验室吴科锋研究员鉴定。取了哥王植株的新鲜叶片，使用北京康为世纪生物科技公司生产的磁珠法植物DNA提取试剂盒提取了哥王的总DNA，随后采用美国Illumina公司生产的NexteraXT DNA测序文库制备试剂盒构建了哥王的叶绿体基因组测序文库。

      • 1.2.   叶绿体基因组测序、拼接、基因注释和图谱绘制

    • 通过美国Illumina公司的Novaseq 6000高通量测序平台完成了哥王叶绿体基因组测序。测得的原始序列经滤除试剂盒附带的接头序列和含有无法确定碱基的劣质序列后，获得合格的可分析读序。采用SPAdes软件对可分析读序进行序列拼接，并运用plastid genome annotator软件对序列中含有的基因进行功能注释。拼接和注释后的了哥王叶绿体基因组序列和基因信息提交至GenBank保存(序列登记号为OQ831641)，并提交到OGDRAW在线工具(https://chlorobox.mpimp-golm.mpg.de/OGDraw.html)绘制物理图谱。

      • 1.3.   密码子偏好性和SSR分析

    • 参照黄琼林[12]的研究，采用CodonW v1.3软件计算了哥王叶绿体基因组全部密码子的相对同义密码子使用情况(RSCU)值，评价其使用频率，RSCU＞1为高频使用密码子。参照吴民华等[13]的研究，使用MISA软件(https://webblast.ipk-gatersleben.de/misa/)检索了哥王的SSR，分析其类型、组成基序、数量和分布等特点。

      • 1.4.   序列比对分析

    • 利用IRscope在线软件(https://irscope.shinyapps.io/irapp/)比较了哥王与同属植物细轴荛花W. nutans (MW393702)、荛花W. canescens (MW073911)、头序荛花W. capitate (MW073909)以及同科植物长柱瑞香Daphne championii (MT648376)叶绿体基因组IR边界(即IR贴近相邻LSC或SSC的碱基)的位置差异。采用设置为Shuffle-LAGAN模式的mVISTA软件(https://genome.lbl.gov/vista/index.shtml)进行前述5种瑞香科植物叶绿体基因组的多重序列比对，明确它们之间的碱基差异。

      • 1.5.   系统进化分析

    • 为探究了哥王在荛花属和瑞香科内的进化关系，在GenBank中下载已公开发布的瑞香科及其相关类群菱科Trapaceae、桃金娘科Myrtaceae植物叶绿体基因组序列，并以与了哥王亲缘关系较远的单子叶植物高良姜Alpinia officinarum的叶绿体基因序列作为外群，将所有下载序列与本研究测得的了哥王叶绿体基因组序列一起提交到MAFFT软件进行多重比对及对齐，随后导入设置为GTRGAMMA模型的RAxML软件构建系统进化树。

    2.   结果与分析

      2.1.   叶绿体基因组的结构和基因特点

    • 如图1所示：了哥王叶绿体基因组由位于1~86 347 bp的LSC、86 348~112 805 bp的IRA、112 806~123 407 bp的SSC和123 408~149 864 bp的IRB依顺时针排列而成，呈现为149 864 bp的环状双链四分体分子。了哥王叶绿体基因组的GC含量较低，仅为37.5%。

      Figure 1.  Chloroplast geome of W. indica

      从表1可见：了哥王叶绿体共有124个基因，包括79个蛋白质编码基因、8个核糖体RNA基因和37个转运RNA基因。这些基因中有14个基因(trnK-UUU、rps16、trnG-UCC、atpF、rpoC1、trnL-UAA、trnV-UAC、petB、petD、rpl16、rpl2、ndhB、trnI-GAU、trnA-UGC)含有1个内含子，1个基因(ycf3)存在2个内含子；17个基因(ndhB、rps7、rpl2、rpl23、ycf1、ycf2、rrn4.5、rrn5、rrn16、rrn23、trnI-CAU、trnL-CAA、trnV-GAC、trnI-GAU、trnA-UGC、trnR-ACG、trnN-GUU)具有2个拷贝。

      基因类别基因功能基因名称
      蛋白质编码基因
      		 ATP合成酶 atpA, atpB, atpE, atpF1, atpH, atpI
      细胞色素b/f复合物 petA, petB1, petD1, petG, petL, petN
      NADH脱氢酶 ndhB1*, ndhD, ndhE, ndhF, ndhH, ndhK
      光合系统Ⅰ psaA, psaB, psaC, psaI, psaJ
      光合系统Ⅱ psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ
      核糖体蛋白质小亚基 rps2, rps3, rps4, rps7*, rps8, rps11, rps12#, rps14, rps15, rps161, rps18, rps19
      核糖体蛋白质大亚基 rpl21*, rpl14, rpl161, rpl20, rpl22, rpl23*, rpl32, rpl33, rpl36
      RNA 聚合酶 rpoA, rpoB, rpoC11, rpoC2
      假定叶绿体阅读框 ycf1*, ycf2*, ycf32, ycf4
      其他基因 matK, rbcL, cemA, accD, ccsA, clpP
      核糖体RNAs rrn4.5*, rrn5*, rrn16*, rrn23*
      转运RNAs trnH-GUG, trnK-UUU1, trnM-CAU, trnI-CAU*, trnV-UAC1, trnF-GAA, trnL-UAA1, trnT-UGU, trnS-　GGA, trnfM-CAU, trnG-GCC, trnS-UGA, trnT-GGU, trnE-UUC, trnY-GUA, trnD-GUC, trnC-GCA, 　trnR-UCU, trnG-UCC1, trnS-GCU, trnQ-UUG, trnW-CCA, trnP-UGG, trnL-CAA*, trnV-GAC*, 　trnI-GAU1*, trnA-UGC1*, trnR-ACG*, trnN-GUU*, trnL-UAG
      　　说明：上标1表示含有1个内含子，上标2表示含有2个内含子，#表示反式剪接基因，*表示双拷贝基因。

      Table 1.  Gene composition and annotation in W. indica chloroplast genome

      • 2.2.   密码子偏好性分析

    • 通过CodonW软件，在了哥王叶绿体基因组的编码区共找到24 180个密码子，包括24 100个氨基酸编码密码子和80个终止密码子。如图2所示：61种氨基酸编码密码子编码20种氨基酸，终止密码子有3种。编码相同氨基酸的多种密码子即称为同义密码子，除了甲硫氨酸(Met)和色氨酸(Trp)外，其余18种氨基酸均有2~6种同义密码子。除了AUG (单独编码Met)和UGG (单独编码Trp)的RSCU为1外，有30种密码子的RSCU＞1，为高频使用密码子；其余32种密码子的RSCU＜1，属于低频使用密码子。在30种高频使用密码子中，有29种的第3位碱基是A/T，表明了哥王叶绿体基因组偏好使用A/T结尾的密码子。

      Figure 2.  RSCU value of all codon in W. indica chloroplast genome

      • 2.3.   SSR分析

    • 以设定的参数通过MISA软件查找，在了哥王叶绿体基因组中发现93个SSR，由72个单核苷酸、11个二核苷酸、4个三核苷酸、5个四核苷酸以及1个五核苷酸组成(表2)。在各类SSR中，A/T、AT/AT、AAT/ATT、AAAT/ATTT、AATAG/ATTCT分别是优势基序，数量依次是72、9、3、3、1个，分别占单核苷酸的100.0%、二核苷酸的81.2%、三核苷酸的75.0%、四核苷酸的60.0%和五核苷酸的100.0%。可见，由A/T及组合形成的基序数量最多，分别包括72个单核苷酸、9个二核苷酸、3个三核苷酸、4个四核苷酸，共占SSR总数的94.6%。因此，了哥王以A/T及组合形成的SSR居多，与其叶绿体基因组低GC含量的情况相符。在分布区域上来看，了哥王SSR主要分布在LSC，而SSC和IR较少；从所有位置上来看，这些SSR主要位于基因间隔区(IGS)，基因内含子次之，编码区(CDS)则最少。说明了哥王叶绿体SSR分布广泛且不均匀，多态性较为丰富。

      类型重复基序数量分布区域所在位置
      LSCSSCIRIGSIntronCDS
      单核苷酸 A/T 72 56 8 8 48 14 10
      二核苷酸 AT/AT 9 9 0 0 5 3 1
      AC/GT 1 1 0 0 1 0 0
      AG/CT 1 1 0 0 1 0 0
      三核苷酸 AAT/ATT 3 1 0 2 1 2 0
      AAG/CTT 1 1 0 0 0 1 0
      四核苷酸 AAAT/ATTT 3 2 1 0 1 1 1
      AATC /ATTG 1 0 1 0 0 0 1
      AATT/AATT 1 1 0 0 0 0 1
      五核苷酸 AATAG/ATTCT 1 1 0 0 1 0 0
      合计　　 93 73 10 10 58 21 14
      说明：LSC为大单拷贝区；SSC为小单拷贝区；IR为反向重复区；IGS基因间隔区；Intron为内含子；CDS为编码区。

      Table 2.  Summaries of SSR loci in W. indica chloroplast genome

      • 2.4.   IR边界比较

    • 叶绿体基因组的2个IR在邻近LSC、SSC的位置形成边界，分别称作JLB (IRB-LSC)、JSB (IRB-SSC)、JSA (IRA-SSC)和JLA (IRA-LSC)。如图3所示：了哥王等4种荛花属植物的JLB均处于rpl19和rpl2之间的IGS，瑞香属Daphne植物长柱瑞香的JLB则在rpl16内。了哥王的JSB在ycf1内，细轴荛花的JSB在ycf1和rpl132之间的IGS，其余植物的JSB则在ndhF内。了哥王和细轴荛花的JSA都在ycf1内，且都在距离该基因5′端的1 085 bp处，其余植物的JSA则在rpl132和trnL之间的IGS。了哥王等4种荛花属植物的JLA均落在rpl2和trnH之间的IGS，长柱瑞香的JLA则位于rps3和trnH之间的IGS。由此可见，了哥王与其他4种植物的IR边界存在较为明显的差异(尤其是JSB)，说明叶绿体基因组在了哥王等瑞香科植物进化过程中发生了不同程度的IR扩张和收缩。

      Figure 3.  IR boundaries divergence of chloroplast genomes from 5 Thymelaeaceae plants

      • 2.5.   序列比对

    • 如图4所示：了哥王与细轴荛花的序列相似度最高，仅在psbE-petL、atpF-atpH等IGS看到少量的碱基突变，并且编码区的序列完全一致。了哥王与另外2种荛花属植物荛花、头序荛花有着较明显的序列差异，几乎所有的IGS、内含子等非编码区序列均可见碱基突变，而且psbA、trnK-UUU、rpoC2、rpoC1、rpoB、accD、rpoA等多个基因也可见变异。了哥王与不同属的长柱瑞香则存在更加显著的序列差异，说明叶绿体基因序列差异与物种的亲缘关系密切相关。

      Figure 4.  Multiple alignment of chloroplast genome sequences from 5 Thymelaeaceae plants

      • 2.6.   系统进化分析

    • 从图5可见：在科水平上，瑞香科、菱科、桃金娘科均形成独立的分支，并与外群高良姜分开。在瑞香科内，沉香属Aquilaria、荛花属和瑞香属各自形成分支，其中荛花属与瑞香属聚在一起，说明这2个属的亲缘关系更近。在荛花属内，9个物种大致聚成3个类群，类群Ⅰ包括荛花和互生叶荛花Wikstroemia canescens，类群Ⅱ含有小黄构W. micrantha、革叶荛花W. scytophylla和一把香W. dolichantha，类群Ⅲ则有了哥王、细轴荛花、北江荛花W. monnula、河朔荛花W. chamaedaphne和头序荛花。了哥王与细轴荛花最先聚成一个分支，表明它们具有最近的亲缘关系。

      Figure 5.  Phylogenetic tree among various plants including W. indica

    3.   讨论

    • 研究发现：了哥王叶绿体基因组由LSC、SSC和两者之间的一对IR形成，呈现为陆生植物叶绿体基因组典型的环状双链四分体结构[14−15]。了哥王叶绿体基因组长度为149 864 bp，也介于被子植物叶绿体基因组110~160 kb范围内[16]。了哥王叶绿体基因组的GC含量为37.5%，与被子植物如瑞香科瑞香属[17]、豆科Leguminosae和蝶形亚科Papilionoideae[18]、兰科Orchidaceae[19]等物种的叶绿体基因组普遍存在的较低GC含量相符。叶绿体基因组作为执行光合作用的细胞器，容易受到光照等自然因素造成的选择压力的影响，在长期的进化过程中，叶绿体基因组可能发生了碱基替换和基因重组，导致其GC含量降低。此外，较低GC含量的DNA更容易解链，推测可以促进叶绿体基因组的重组，从而更好适应自然选择。在基因数量和组成上，了哥王叶绿体基因组共有124个基因，以与光合作用相关的基因及叶绿体自身复制所需的基因为主，也符合被子植物叶绿体基因组的基因构成[20]。因此，了哥王叶绿体基因组具有植物叶绿体基因组的共性特征。

      植物在自然选择、碱基突变的作用下会形成一套与其自身进化相适应的常用密码子，以执行编码氨基酸或终止氨基酸翻译的功能。本研究在了哥王叶绿体基因组发现30种高频使用密码子(RSCU＞1)，包括29种氨基酸编码密码子和1种终止密码子，这些高频使用密码子比其他同义密码子更常被使用。除了编码亮氨酸(Leu)的UUG，其他高频密码子的末位碱基都是A/T。而且，在编码Leu的6种同义密码子中，UUG是使用频率较高的密码子(RSCU=1.26)，排第3位，最高的是UUA (RSCU=1.84)，其次是CUU (RSCU=1.30)。由此可见，了哥王叶绿体基因组编码20种氨基酸以及终止密码子最常用都是末位碱基为A/T的密码子，具有一定的密码子使用偏好性。相同的密码子偏好性也出现在金银花大毛花Lonicera japonica ‘Damaohua’[21]、高良姜[12]、菠萝Ananas comosus[22]等植物中。

      SSR为一种具有丰富多态性的显性DNA标记，是研究植物品种鉴别、多样性分析以及构建遗传图谱、辅助分子育种的有效手段。利用MISA软件对了哥王叶绿体SSR进行定位和统计，发现了哥王含93个叶绿体SSR，且以A或T碱基及其组成的基序，尤其是polyA或polyT单核苷酸为优势类型，以分布在LSC和IGS为主，与北陵鸢尾Iris typhifolia[23]、露兜树Pandanus tectorius[13]、闭鞘姜Helenia speciosa [24]等植物的SSR特点相同。

      IR被认为是叶绿体基因组中序列最为保守的区域，但IR经常会发生扩张和收缩，从而引起IR乃至整个叶绿体基因组长度的变化。因此，IR边界是比较物种叶绿体基因组差异的重要指标。本研究发现：了哥王与细轴荛花同属近缘植物的IR边界特别是SSC和IRB之间的JSB具有明显的不同。并且全序列比对显示：了哥王与细轴荛花同属近缘植物在IGS (如psbE-petL、atpF-atpH)等非编码区具有碱基变异。这些结果提示叶绿体基因组序列可以为了哥王及其近缘物种的鉴别提供依据。此外，系统进化树也直观地展示了了哥王的进化位置及其与相关近缘植物的亲缘关系，聚类效果良好。

    4.   结论

    • 本研究结果表明：了哥王叶绿体基因组为149 864 bp的环状双链四分体分子，GC含量为37.5%，含124个基因；偏好使用以A/T结尾的密码子；SSR以polyA或polyT单核苷酸为主。了哥王与细轴荛花具有最近的亲缘关系。

Reference (24)

Catalog

  • HTML

  • 1.   材料与方法

  • 1.1.   了哥王的采集和处理

  • 1.2.   叶绿体基因组测序、拼接、基因注释和图谱绘制

  • 1.3.   密码子偏好性和SSR分析

  • 1.4.   序列比对分析

  • 1.5.   系统进化分析

  • 2.   结果与分析

  • 2.1.   叶绿体基因组的结构和基因特点

  • 2.2.   密码子偏好性分析

  • 2.3.   SSR分析

  • 2.4.   IR边界比较

  • 2.5.   序列比对

  • 2.6.   系统进化分析

  • 3.   讨论
  • 4.   结论

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