入侵植物薇甘菊的转录组分析及其群体遗传特征初探
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摘要
薇甘菊Mikania micrantha H.B.K.为菊科假泽兰属植物,是世界上最有害的100种外来入侵物种之一。它原产于热带美洲,现广布于亚洲热带。作为一种典型的已造成严重生态危害的入侵杂草,研究薇甘菊具有重要的现实意义和科学价值。近年来国内外已相继开展了大量关于薇甘菊的生理生态、群落结构以及生态效应等各方面的研究。但相对而言,关于薇甘菊入侵遗传机制的研究则少得多。随着近年来新一代高通量测序技术的发展,从基因组层面探讨薇甘菊入侵性相关的分子基础、认识入侵性表达的分子调控机制、揭示外来种成功入侵的机理和“后适应”进化机制已成为可能。
本研究作为一种在基因(转录)组水平上对非模式入侵植物进行入侵分子机制探讨的尝试,首先采用第二代高通量测序技术(Illumina GAII),以薇甘菊作为研究对象来进行转录组水平上的拼接和组装,并进一步探讨其入侵特性的分子基础。本论文研究内容包括以下两个部分,结果如下:
1.薇甘菊个体转录组的分析:以个体薇甘菊全株为材料提取总RNA,反转录后采用新一代高通量测序技术(Solexa)进行测序,利用所得到的32百万对经过质量过滤的reads并采用多种拼接方法的整合,本研究成功组装了51,782条平均长度在734 nt、最大长度达到7,324nt的参考转录本拼接序列,72.9%的特异组装序列与NCBI数据库里的序列具有显著同源性,其中25,478条序列能够进行基因分类(gene ontology assignments),这项研究中所获得的序列代表了第一次大规模的涉及入侵杂草的表达基因的序列数据。进一步的研究结果鉴定出大量高表达并与入侵特性相关的候选基因:如基因组进化基因,可塑性基因,次生代谢和防御反应基因等。这一转录组资源提供了重要信息以促进有关薇甘菊的入侵生物学的研究。
2.薇甘菊原产地与入侵地两个种群的群体遗传特性比较:选取中美洲哥斯达黎加群体(14),东莞以及广州(12)两个群体作为原产地与入侵地种群的代表,它们的幼苗在相同环境中培养一个月,将两个群体中个体的总RNA分别等量混和测序,以前一部分研究中所获得的个体薇甘菊转录组作为参考序列进行拼接和校正,寻找并验证SNP,根据群体转录组在参考转录本上的比对信息,在约7.8百万个序列位点中筛选出约27万个候选的SNP位点。在此基础上,进一步计算θ和π等群体遗传参数,其中,哥斯达黎加群体的θ和π分别为5.7‰和4.1‰,而在广东群体则分别为4.8‰和3.0‰,本研究获得了薇甘菊群体基因(转录)组水平遗传多样性的宝贵信息,同时得到了薇甘菊原产地群体的遗传多样性水平略高于入侵地群体的初步结论,并为进一步的研究提供了大量可供利用的SNP遗传信息。
本研究成功应用了第二代测序技术Illumina GAII对典型入侵杂草薇甘菊的转录组进行了测序和自组装,并进一步在群体水平上获得了薇甘菊原产地与入侵地两个不同种群的遗传多样性信息和群体SNP位点信息。该结果对利用第二代测序技术研究非模式入侵生物的群体遗传学、转录组测序和自组装提供了重要的参考价值。该方法的应用将成为系统和全面研究基因(转录)组水平的入侵遗传特性提供了一种新的思路。
Mikania micrantha H.B.K. of Asteraceae has been listed as the first batch of alien invasive species in China. This species is such a highly hazardous weed that it has been listed as the world's 100 worst invasive alien species. M. micrantha is of the new world origin and is widely naturalized in the old world tropics. As a typical invasive weed, M. micrantha resulted in great ecological loss in China. The studies on M. micrantha could be of important practical significance and scientific value. In recent years, a large number of studies about M. micrantha have been reported, in which the fields such as the physiological ecology, community structure and ecological effects has been involved.
However, the study of the genetic mechanisms of biological invasion is much less reported. With the development of next-generation high-throughput sequencing technology, it is possible to investigate the molecular mechanisms of biological invasions, through revealing the regulation of invasive expression and the molecular evolutionary process of "post-adaptation" on the basis of the genome data of invasive species, M. micrantha. However, the EST library construction and consequential sequencing on the genome level is based on the traditional Sanger methods which is laborious and cost a lot. With the advances of sequencing technology, a new generation of high-throughput sequencing technology which is more efficient and cost-effective has been used gradually in the field of invasive biology. However, de novo assembly of genome or transcriptome of non-model organisms is not only a difficult task but also a challenge considering only the short read length (75-90 nt) is available by the high-throughput sequencing technology nowadays. As an initial step towards understanding the molecular mechanisms by which plants become invasive, we present here the first transcriptome analysis for an invasive weed (i.e. Mikania micrantha) for which no prior genomic information was available. We further explored its molecular basis of invasion characteristics. This thesis consists of the following two parts:
1. The transcriptome analysis of individual M. micrantha: The entire plant, including roots, was used for RNA extraction. Paired-end short read sequencing was done on one lane of the Illumina GAII system after reverse transcription. The analysis was based on the 75-nucloetide short reads data generated. A total of 51,782 unique sequences with an average length of 734 nt and a maximum length of 7,324 nt were assembled de novo based on 32 million filtered paired-end sequence reads for the transcriptome of an individual M. micrantha growing in the field. Seventy-three percent of the unique sequences showed significant similarity to existing proteins in the NCBI database, and 25,478 could be grouped based on gene ontology assignments. The sequences obtained in this study represent the first large-scale dataset of expressed genes in an invasive weed. Of particular interest are the sequences that share homology with genes involved in genome evolution, plasticity, secondary metabolism, and defense responses. This resource provides essential information to support the investigation of numerous questions regarding the invasive biology of M. micrantha and related species.
2. Comparison of population genetic characteristics of source population and invasion population of M. micrantha: In this thesis, the population from Costa Rica in Central America (14 individuals) and population from Dongguan and Guangzhou (12 individuals) have been treated as the representatives of source population and invasion population of M. micrantha, respectively. The seedlings from different sources were cultured in the common garden for one month. Then we pooled two groups of individuals with equal amount of individual RNA respectively and sequenced the two RNA mixtures by Illumina GAII system. De novo assembling the transcriptome of population of M. micrantha and SNP identification were carried out on the basis of the reference sequence which comes from individual transcriptome obtained before. A total of 270,000 candidate SNP sites were screened from about 7.8 million loci based on the comparison results. The population genetic parameters such asθandπwere estimated for source population and invasion population of M. micrantha respectively (θ= 5.7‰,π= 4.1‰in population of Costa Rica,θ= 4.8‰,π= 3.0‰in population of Guangdong). The genetic diversity of population of Costa Rica was slightly higher than that of population of Guangdong. Our result also provided a wealth of SNP information available for the further research.
The present study demonstrated a successful application of second-generation high-through sequencing technologies on the transcriptome analysis of non-model typical invasive species Mikania micrantha. The important population parameters such as the genetic diversity of populations and SNP loci were estimated based on the transcriptome analysis of M. micrantha Our study has revealed that next-generation DNA sequencing technologies can be used effectively for de novo sequencing of transcriptomes of non-model invasive species, making it possible to carry out rapid and low-cost sequencing for other important plant species. With these genomic approaches, it is possible to dissect the invasiveness-related genes and their expression and regulation patterns, identify invasive genotypes and hence understand plant invasiveness, which can be used to disassemble plant invasion mechanisms and define the evolutionary patterns during plant invasions.
本研究作为一种在基因(转录)组水平上对非模式入侵植物进行入侵分子机制探讨的尝试,首先采用第二代高通量测序技术(Illumina GAII),以薇甘菊作为研究对象来进行转录组水平上的拼接和组装,并进一步探讨其入侵特性的分子基础。本论文研究内容包括以下两个部分,结果如下:
1.薇甘菊个体转录组的分析:以个体薇甘菊全株为材料提取总RNA,反转录后采用新一代高通量测序技术(Solexa)进行测序,利用所得到的32百万对经过质量过滤的reads并采用多种拼接方法的整合,本研究成功组装了51,782条平均长度在734 nt、最大长度达到7,324nt的参考转录本拼接序列,72.9%的特异组装序列与NCBI数据库里的序列具有显著同源性,其中25,478条序列能够进行基因分类(gene ontology assignments),这项研究中所获得的序列代表了第一次大规模的涉及入侵杂草的表达基因的序列数据。进一步的研究结果鉴定出大量高表达并与入侵特性相关的候选基因:如基因组进化基因,可塑性基因,次生代谢和防御反应基因等。这一转录组资源提供了重要信息以促进有关薇甘菊的入侵生物学的研究。
2.薇甘菊原产地与入侵地两个种群的群体遗传特性比较:选取中美洲哥斯达黎加群体(14),东莞以及广州(12)两个群体作为原产地与入侵地种群的代表,它们的幼苗在相同环境中培养一个月,将两个群体中个体的总RNA分别等量混和测序,以前一部分研究中所获得的个体薇甘菊转录组作为参考序列进行拼接和校正,寻找并验证SNP,根据群体转录组在参考转录本上的比对信息,在约7.8百万个序列位点中筛选出约27万个候选的SNP位点。在此基础上,进一步计算θ和π等群体遗传参数,其中,哥斯达黎加群体的θ和π分别为5.7‰和4.1‰,而在广东群体则分别为4.8‰和3.0‰,本研究获得了薇甘菊群体基因(转录)组水平遗传多样性的宝贵信息,同时得到了薇甘菊原产地群体的遗传多样性水平略高于入侵地群体的初步结论,并为进一步的研究提供了大量可供利用的SNP遗传信息。
本研究成功应用了第二代测序技术Illumina GAII对典型入侵杂草薇甘菊的转录组进行了测序和自组装,并进一步在群体水平上获得了薇甘菊原产地与入侵地两个不同种群的遗传多样性信息和群体SNP位点信息。该结果对利用第二代测序技术研究非模式入侵生物的群体遗传学、转录组测序和自组装提供了重要的参考价值。该方法的应用将成为系统和全面研究基因(转录)组水平的入侵遗传特性提供了一种新的思路。
Mikania micrantha H.B.K. of Asteraceae has been listed as the first batch of alien invasive species in China. This species is such a highly hazardous weed that it has been listed as the world's 100 worst invasive alien species. M. micrantha is of the new world origin and is widely naturalized in the old world tropics. As a typical invasive weed, M. micrantha resulted in great ecological loss in China. The studies on M. micrantha could be of important practical significance and scientific value. In recent years, a large number of studies about M. micrantha have been reported, in which the fields such as the physiological ecology, community structure and ecological effects has been involved.
However, the study of the genetic mechanisms of biological invasion is much less reported. With the development of next-generation high-throughput sequencing technology, it is possible to investigate the molecular mechanisms of biological invasions, through revealing the regulation of invasive expression and the molecular evolutionary process of "post-adaptation" on the basis of the genome data of invasive species, M. micrantha. However, the EST library construction and consequential sequencing on the genome level is based on the traditional Sanger methods which is laborious and cost a lot. With the advances of sequencing technology, a new generation of high-throughput sequencing technology which is more efficient and cost-effective has been used gradually in the field of invasive biology. However, de novo assembly of genome or transcriptome of non-model organisms is not only a difficult task but also a challenge considering only the short read length (75-90 nt) is available by the high-throughput sequencing technology nowadays. As an initial step towards understanding the molecular mechanisms by which plants become invasive, we present here the first transcriptome analysis for an invasive weed (i.e. Mikania micrantha) for which no prior genomic information was available. We further explored its molecular basis of invasion characteristics. This thesis consists of the following two parts:
1. The transcriptome analysis of individual M. micrantha: The entire plant, including roots, was used for RNA extraction. Paired-end short read sequencing was done on one lane of the Illumina GAII system after reverse transcription. The analysis was based on the 75-nucloetide short reads data generated. A total of 51,782 unique sequences with an average length of 734 nt and a maximum length of 7,324 nt were assembled de novo based on 32 million filtered paired-end sequence reads for the transcriptome of an individual M. micrantha growing in the field. Seventy-three percent of the unique sequences showed significant similarity to existing proteins in the NCBI database, and 25,478 could be grouped based on gene ontology assignments. The sequences obtained in this study represent the first large-scale dataset of expressed genes in an invasive weed. Of particular interest are the sequences that share homology with genes involved in genome evolution, plasticity, secondary metabolism, and defense responses. This resource provides essential information to support the investigation of numerous questions regarding the invasive biology of M. micrantha and related species.
2. Comparison of population genetic characteristics of source population and invasion population of M. micrantha: In this thesis, the population from Costa Rica in Central America (14 individuals) and population from Dongguan and Guangzhou (12 individuals) have been treated as the representatives of source population and invasion population of M. micrantha, respectively. The seedlings from different sources were cultured in the common garden for one month. Then we pooled two groups of individuals with equal amount of individual RNA respectively and sequenced the two RNA mixtures by Illumina GAII system. De novo assembling the transcriptome of population of M. micrantha and SNP identification were carried out on the basis of the reference sequence which comes from individual transcriptome obtained before. A total of 270,000 candidate SNP sites were screened from about 7.8 million loci based on the comparison results. The population genetic parameters such asθandπwere estimated for source population and invasion population of M. micrantha respectively (θ= 5.7‰,π= 4.1‰in population of Costa Rica,θ= 4.8‰,π= 3.0‰in population of Guangdong). The genetic diversity of population of Costa Rica was slightly higher than that of population of Guangdong. Our result also provided a wealth of SNP information available for the further research.
The present study demonstrated a successful application of second-generation high-through sequencing technologies on the transcriptome analysis of non-model typical invasive species Mikania micrantha. The important population parameters such as the genetic diversity of populations and SNP loci were estimated based on the transcriptome analysis of M. micrantha Our study has revealed that next-generation DNA sequencing technologies can be used effectively for de novo sequencing of transcriptomes of non-model invasive species, making it possible to carry out rapid and low-cost sequencing for other important plant species. With these genomic approaches, it is possible to dissect the invasiveness-related genes and their expression and regulation patterns, identify invasive genotypes and hence understand plant invasiveness, which can be used to disassemble plant invasion mechanisms and define the evolutionary patterns during plant invasions.
引文
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