二斑叶螨与灰飞虱的微卫星开发及种群遗传结构研究
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摘要
朱砂叶螨Tetranychus cinnabarinus (Boisduval)和二斑叶螨T. urticae Koch属于蛛形纲Arachnida、蜱螨亚纲Acari、真螨目Acariformes、叶螨科Tetranychidae,是农林生产中十分重要的害螨。这两种叶螨具有多种扩散机制,由于叶螨无翅,通常依靠爬行进行扩散;但它们也可以借助风和人类活动进行远距离的传播；叶螨复杂的扩散机制可能导致复杂的种群遗传结构。但是,由于这两种叶螨体内可用的分子标记较少,导致我国这两种叶螨的种群遗传多样和种群遗传结构的研究相对滞后。此外,在中国,朱砂叶螨与二斑叶螨两种叶螨并存,红色型被认为是本地种,而绿色型的变种被认为是入侵种。朱砂叶螨和二斑叶螨在欧美被认为是二斑叶螨的不同色型,因为两者可以自由交配,形态学和线粒体DNA水平上难以找出差别；而在中国等亚洲国家两者被认为是两种不同的螨类,理由是成螨体色差异较大,遗传杂交实验常得到不亲和的结果。二者的分类地位一直存在较大争论。
针对以上问题笔者首先通过抑制PCR的方法成功构建了微卫星富集文库来,开发叶螨微卫星分子标记；并结合以前报道的微卫星分子标记研究了我国25个地理种群的二斑叶螨和朱砂叶螨的种群遗传多样性和种群遗传结构,比较了两者种群遗传多样性和种群遗传结构的差异,并从种群生态学的角度探讨朱砂叶螨与二斑叶螨的分类进化地位,获得以下结果与结论：
1)通过叶螨的基因组DNA提取纯化、酶切、接头连接及抑制PCR扩增等步骤成功构建了二斑叶螨微卫星富集文库,挑取180个阳性克隆成功测序,并设计了53对微卫星引物,最后成功获得2个多态性较好的微卫星标记。本研究是首次通过抑制PCR的方法构建叶螨的微卫星富集文库来开发微卫星,通过此研究,我们得出结论,叶螨体内微卫星变异速率较低严重的影响了微卫星开发效率。
2)结合笔者刚开发的2个微卫星及以前报道的6个微卫星,对中国18个朱砂叶螨种群和7个二斑叶螨种群,共计1055个叶螨样本进行了种群遗传多样性和种群遗传结构分析。8个微卫星位点共检测到109个等位基因。平均每个位点13.63个等位基因。然而,平均每个种群每个位点等位基因丰富度和杂合度都较低,表明我国的叶螨种群遗传多样性较差。对朱砂叶螨和二班叶螨的等位基因丰富度和预期杂合度的T测验发现：我国的二斑叶螨的多样性显著低于朱砂叶螨,这可能是由于朱砂叶螨是本地种,而二斑叶螨是入侵种,在入侵过程中发生瓶颈效应造成的。通过等位基因丰富度和预期杂合度(AR和HE)与地理坐标(经度和纬度)之间的皮尔逊相关性分析表明,朱砂叶螨的遗传多样性与纬度成正相关性,这是由于低纬度地区的朱砂叶螨每年发生的代数较多,维持了较高的遗传多样性。Hardy-Weinberg平衡测试显示25个种群里面有23个种群因为杂合体缺失而偏离了平衡,进一步分析发现无效等位基因的存在是引起偏离平衡的重要因素。
3)25个叶螨种群的总体分化指数FST为0.506,种群之间高度遗传分化。种群间基因流较小,种群多样性较差及存在地理隔离效应是引起朱砂叶螨种群分化的重要因素。通过构建NJ系统发育树、贝叶斯聚类及分子变异模型分析(AMOVA),结果显示我国的叶螨种群分为五个分支,其中朱砂叶螨的聚类结果与地理分布有很好的相关性。此外,我们的遗传数据不支持将两种形式的叶螨分成两个物种,因为两者的分化水平处于不同地理种群的分化水平,两者在DNA组成上没有实质的不同,体色的差异可能由于表观遗传方式的不同造成的。
灰飞虱Laodelphax striatellus (Fallen)属半翅目飞虱科,世界范围内主要分布在温带地区,广泛分布于东亚、东南亚、欧洲和北非等地,可在温带地区安全越冬。国内分布遍及全国各地,以长江流域和华北稻区发生较多。灰飞虱除以成虫、若虫刺吸危害外,还是多种植物病毒病害的重要媒介昆虫,可传播多种病毒病害,其传毒危害造成的损失远远大于其刺吸危害。尽管灰飞虱的经济地位重要,但是对于灰飞虱的种群遗传学的研究报道却比较少。原因在于灰飞虱上可用的遗传标记较少,且不能提供足够的遗传学信息。而微卫星(microsatellite)分子标记由于广泛地在基因组中分布、良好的重复性和保真性、较高的变异频率、呈孟德尔式遗传、共显性等优点,已成为种群遗传学研究中应用最为广泛的分子标记。但是,目前尚未有灰飞虱微卫星的开发的报道。基于以上原因,笔者分别通过褐飞虱EST数据库和抑制PCR构建微卫星富集文库来开发灰飞虱的微卫星,并应用新开发的9个微卫星标记和一段线粒体COI基因的序列对中国17个地理种群共计720个灰飞虱个体展开种群遗传多样性和种群遗传结构的研究,并得到相关的结果与结论：
1)由于国际无灰飞虱微卫星的报道,基于EST微卫星具有较高的不同种属之间的转移性、开发成本低和效率高的特性,首先根据褐飞虱的EST数据库开发褐飞虱的微卫星,然后验证在其灰飞虱上的转移性。笔者通过搜索褐飞虱的EST数据库,设计引物并PCR验证,最终开发了12个多态性较好的褐飞虱微卫星标记。微卫星等位基因的测序结果揭示了微卫星复杂的变异机制。对这12对微卫星引物在灰飞虱上面的转移性研究结果发现：这12对卫星引物高度专属于褐飞虱,不能够用于灰飞虱。我们得出结论：灰飞虱与褐飞虱属于不同的属,分化时间较长,且进化速度较快,两者的基因组信息差异太大,导致两者之间的微卫星不能相互转移。
2)通过抑制PCR的方法构建了灰飞虱(TC)6(AC)5和(AG)6(AC)5的复合型微卫星富集文库,挑取200个阳性克隆测序,设计了100对微卫星引物,最终成功开发了9个多态性较好的微卫星,通过三个地理种群对新开发的微卫星进行检测,结果显示每个位点具有13到30个等位基因。平均表观杂合度和预期杂合度分别在在0.255～0.833和0.392～0.929之间,这9个微卫星位点具有高度的多态性,新开发的微卫星位点将为灰飞虱种群遗传结构的研究提供有效的分子标记手段,本研究首次在国际上报道了9个灰飞虱微卫星,填补了国际无灰飞虱微卫星的空白。
3)运用9个微卫星分子标记对17个地理种群的灰飞虱种群遗传结构的研究,结果显示每个种群平均每个位点的等位基因个数在12.111～16.333之间。所有种群的表观杂合度介于0.536～0.683之间,预期杂合度介于0.742～0.840之间。说明我国的灰飞虱具有较高水平的遗传多样性,并且华东种群和华北种群较东北种群和华南种群的多样性要高。由于灰飞虱的近交导致大部分种群因杂合体缺失而偏离Hardy-Weinberg平衡。除了华南的永福和南宁种群外,其他种群都具有私有等位基因,这可能是由于华南地区的分析样本较少造成的。基于FST统计显示种群间分化较小或无分化,总体FST为0.004,只有东北的黑龙江HLJ种群和辽宁的丹东DD种群与其他种群有较微弱的显著分化,贝叶斯聚类及NJ分析结果同样显示17个种群具有不稳定的种群遗传结构黑龙江HLJ种群和辽宁的丹东DD种群与其他种群有较微弱的差异。AMOVA分析结果表明灰飞虱的微弱变异主要来自个体之间的差异,而种群间及4个区域间的遗传分化极小。与地理距离的相关性分析结果表明,尽管灰飞虱的遗传分化水平较低,但是与地理距离还有较弱的负相关性,说明地理距离在灰飞虱种群分化中起一定作用。
4)基于线粒体一段COI基因序列对种群的研究发现,COI基因经比对并去掉引物及测序较差的部分后,最终得到了769bp的片段,没有终止密码子碱基的插入或缺失出现,共有33个变异位点,占总序列的4.2%,其中简约信息位点15个。总体来说灰飞虱多样性较好,在720个个体中共发现了37个单倍型,单倍型多样性指数0.159～0.764之间,平均0.642；核酸多样性较差,在0.101%～0.320%之间,平均0.217%。与微卫星的结果相似,华东种群较东北种群和华南种群的多样性要高；东北地区的灰飞虱多样性较差,平均每个种群有5.5个单倍型,并且这四个种群中无私有单倍型存在。其中最差的是黑龙江HLJ种群,只有3个单倍型。COI基因的FST统计比微卫星的结果稍大,但还是处于较低分化的水平,平均分化指数为0.055,表明灰飞虱的确分化较小或无分化。COI的分析同样表明东北的黑龙江种群与其他种群有显著分化。AMOVA分析结果同样显示灰飞虱的微弱变异主要来自个体之间的差异。
5)根据微卫星和COI基因对灰飞虱种群遗传结构的研究,我们得出结论：灰飞虱种群分化水平较低,分化程度与具有迁飞习性的东亚飞蝗相似,种群间基因流较强,灰飞虱可能具有远距离迁飞习性。基于COI基因的分析发现37个单倍型在各个种群中分布不均匀,这可能是由于环境选择压力的不同造成,单倍型与灰飞虱的适合度及迁飞是否有某种联系需要进一步的实验验证,另外,我们还发现灰飞虱感染的Wolbachia没有引起单倍型多样性的降低,但导致了核酸多样性的降低,这是由于Wolbachia对线粒体拉升效应造成的。
Both the two-spotted spider mite Tetranychus urticae Koch and the carmine spider mite T. cinnabarinus (Boisduval), which belong to Arachnida, Acari, Acariformes, Tetranychidae, Tetranychus, are very important mite pests. The two species have multiple dispersal mechanisms. They are wingless and usually rely on crawling for their dispersal. But they can also be carried for long distance by the wind and by human activities. Due to the complex dispersal mechanisms of T. urticae, the population structure and diversity would be complex. However, due to the limited number of markers used to analyse geographic populations and individuals, the information that they provided was insufficient to understand the genetic diversity and population structure clearly. In addition to questions about the population structure and genetic diversity of T. urticae in China, there is a big question about its taxonomy. Due to reproductive compatibility, difficult to find out the differences in morphology and mitochondrial DNA levels, T. cinnabarinus and T. urticae are considered to be the single species in Europe and the United States. However, in China and other Asian countries, they are considered to be two different species of mites. The reasons are the differences of body color and reproductive incompatibility between them. Therefore, whether they constitute one or two species has been debated for long time.
To address the above issues, a microsatellites-enriched DNA library was constructed using a suppression-PCR procedure. We genotyped25populations of spider mites in China using eight microsatellite loci, including2newly developed by ourselves and6previously reported. We also compared the difference of the genetic diversity and population structure of the two types of mites, and try to clarify the taxonomic status of the two types of mites from a population genetic structure perspective. The main results and conclusions are as follows:
1) We successfully constructed the microsatellites-enriched DNA library of the spider mite using a suppression-PCR procedure. Of the180clones sequenced,53sequences flanking microsatellites were selected for primer design. Finally, two microsatellites with good polymorphism was isolated from the genome of the spider mite. This is the first time to use the suppression-PCR procedure for microsatellites isolation in spider mites. Low mutation rate of the mite microsatellites bring the isolation efficiency down.
2) We genotyped a total of1055individuals from18T. cinnabarinus populations and7T.urticae populations in China using eight microsatellite loci. One hundred alleles were identified in the8loci, with13.63in each locus across the25populations. However, the low values of heterozygosity and allelic richness implies the low level of genetic diversity of the spider mites. In addition, genetic diversity of the red form mites was found to be higher than the green form. Pearson correlations between statistics of variation (AR and He) and geographic co-ordinates (latitude and longitude) showed that the genetic diversity of T. cinnabarinus was correlated with latitude. The declining genetic diversity of T. cinnabarinus with increasing latitude may be because the northern populations have fewer generations per year. Twenty-three of the25populations used in this study deviated from HWE, and of these,19populations displayed significant heterozygote deficiency. Further analysis revealed that the deficit in heterozygotes were due to null allele.
3) We found a highly significant genetic differentiation among the25populations with global FST=0.506. Spider mites possess low levels of genetic diversity, limited gene flow between populations and significant IBD (isolation by distance) effect. These factors in turn contribute to the strong subdivision of genetic structure. Based on the results of NJ tree, Bayesian analysis and AMOVA, we conclude that five clades likely exist in China. In addition, the population genetic structures of the two forms of mites do not support their separation into two species. The morphological difference between the two forms of mites may be the result of epigenetic effects.
The small brown planthopper (SBPH) Laodelphax striatellus Fallen is an important agricultural pest, which is widely distributed in temperate zones such as East Asia, Southeast Asia, Europe and Northern Africa, and can overwinter safely in these areas. This pest is one of the most serious pest insects of rice plant and many other kinds of gramineous plants. Besides the direct sucking damage, the agricultural significance of SBPH lies in its ability to spread the damaging plant disease, Rice stripe virus (RSV). Despite the economic importance of this pest, the population genetic structure and genetic diversity were little known. In recent years, due to the characteristics of high level of polymorphism, co-dominant Mendelian inheritance, high frequency of occurrence, and ease of detection by PCR, microsatellites or simple sequence repeats (SSR) have been widely used in population genetic studies. However, no microsatellites primers developed specifically for the SBPH bottlenecked the process of population genetic study for the SBPH. To resolve the aforementioned issues, we tried to develop microsatellites through searching the EST database of the brown planthopper (BPH), Nilaparvata lugens (Stal) and construction the microsatellites-enriched libraries. Employing9new microsatellites developed in this study and COI gene, we investigated the genetic structure of17L. striatellus populations in China. The main results are as follows:
1) An enormous number of ESTs are now available in the public sequence database, and can be exploited to identify markers inexpensively. Compared with conventional markers derived from genomic DNA, EST-derived markers are easy to develop, and highly transferable. In this study, we mined existing BPH ESTs for new microsatellites, and validated the transferability from BPH to SBPH. Finally we developed and characterized12polymorphic microsatellites from the expressed sequence tags database of the brown planthopper (BPH), Nilaparvata lugens (Stal). Microsatellites sequencing revealed complex mechanisms of mutations of the12microsatellites loci. The fact of failed transferability of the new microsatellites from BPH to SBPH may be due to that the two species had diverged long time ago, and evolved quickly.
2) Nine microsatellites loci were isolated from the genome of Laodelphax striatellus (Fallen)(Homoptera:Delphacidae) by constructing (TC)6(AC)5and (AG)6(AC)5compound SSR enriched libraries using suppression-PCR procedure. These loci developed in this study were high polymorphism with13to30alleles per locus in three tested populations. The observed and expected heterozygosities ranged from0.255to0.833and0.392to0.929respectively. These microsatellites markers can be used for population genetic structure and genetic diversity research of L. striatellus.
3) The results of the microsatellites implied L. striatellus populations possess high levels of genetic diversity. The allele numbers of each locus in each population were ranged from12.111to16.333. The observed heterozygosity and expected heterozygosity were0.536-0.683and0.742-0.840respectively. The L. striatellus populations in East China have much higher levels of genetic diversity than the populations in Northeast China and South China. Most microsatellites displayed a significant departure from Hardy-Weinberg equilibrium (HWE) in most populations due to serious inbreeding. Private alleles were identified in all populations except YF and NN, which are all located in South China. This may be due to the limited number of analyzed samples in the two populations. Little genetic differentiation among almost all the populations, with global FST=0.004. However, HLJ and DD show slightly but significant differentiation with some other populations. This was also evidences by the results of NJ tree and Bayesian analysis. AMOVA results indicate that genetic variation mainly comes from the individuals' level. Although the level of population differentiation was very low, there were also mild IBD effects among L. striatellus populations. Which means geographical distance plays a role in population differentiation.
4) All sequences were truncated to the same length (769bp) to eliminate missing data. The sequences had33polymorphic sites (accounting4.2%), of which15were parsimony informative. In general, L. striatellus populations have high levels of genetic diversity. An alignment the COI gene from720individuals from17populations across China revealed37haplotypes. The haplotype diversity ranged between0.159and0.764with mean0.642. However, the nucleotide diversity was relatively low, which was ranged between0.101%and0.320%(mean0.217). The L. striatellus populations in East China and North China also showed much higher levels of genetic diversity than the populations in Northeast China and South China based on the COI gene. With5.5haplotypes per populations and no private haplotypes, the Northeast China populations posses the lowest levels of genetic diversity. Among which, HLJ was the lowest one, only3haplotypes were identified in this population. The COI also revealed little genetic differentiation among populations, although the values of FST calculated by COI gene (mean0.055) were slightly larger than by microsatellites. HLJ populations also displayed significant differentiation with some other populations according to the COI gene. AMOVA results also indicate that genetic variation mainly comes from the individuals' level.
6) According to the research on the population structure of L. striatellus by SSR and COI, we concluded that:the L. striatellus population shows a relative low level of genetic differentiation, which is similar with the migratory species Locusta migratoria manilensis (Meyen), while there is a strong gene flow among these populations indicating that the L. striatellus may have Long-distance migratory ability. Based on the COI we found that37haplotypes distribute unevenly among populations. This could be explained by the environmental selection pressures. However, whether there is a linkage between the haplotypes and the fitness, migration of L. striatellus requires further experimental verification. Furthermore, we found that individuals infected with Wolbachia don't cause a reduction in the diversity of haplotypes but the nuclear polymorphisms, which can be reasoned by the hitchhiking.
针对以上问题笔者首先通过抑制PCR的方法成功构建了微卫星富集文库来,开发叶螨微卫星分子标记；并结合以前报道的微卫星分子标记研究了我国25个地理种群的二斑叶螨和朱砂叶螨的种群遗传多样性和种群遗传结构,比较了两者种群遗传多样性和种群遗传结构的差异,并从种群生态学的角度探讨朱砂叶螨与二斑叶螨的分类进化地位,获得以下结果与结论：
1)通过叶螨的基因组DNA提取纯化、酶切、接头连接及抑制PCR扩增等步骤成功构建了二斑叶螨微卫星富集文库,挑取180个阳性克隆成功测序,并设计了53对微卫星引物,最后成功获得2个多态性较好的微卫星标记。本研究是首次通过抑制PCR的方法构建叶螨的微卫星富集文库来开发微卫星,通过此研究,我们得出结论,叶螨体内微卫星变异速率较低严重的影响了微卫星开发效率。
2)结合笔者刚开发的2个微卫星及以前报道的6个微卫星,对中国18个朱砂叶螨种群和7个二斑叶螨种群,共计1055个叶螨样本进行了种群遗传多样性和种群遗传结构分析。8个微卫星位点共检测到109个等位基因。平均每个位点13.63个等位基因。然而,平均每个种群每个位点等位基因丰富度和杂合度都较低,表明我国的叶螨种群遗传多样性较差。对朱砂叶螨和二班叶螨的等位基因丰富度和预期杂合度的T测验发现：我国的二斑叶螨的多样性显著低于朱砂叶螨,这可能是由于朱砂叶螨是本地种,而二斑叶螨是入侵种,在入侵过程中发生瓶颈效应造成的。通过等位基因丰富度和预期杂合度(AR和HE)与地理坐标(经度和纬度)之间的皮尔逊相关性分析表明,朱砂叶螨的遗传多样性与纬度成正相关性,这是由于低纬度地区的朱砂叶螨每年发生的代数较多,维持了较高的遗传多样性。Hardy-Weinberg平衡测试显示25个种群里面有23个种群因为杂合体缺失而偏离了平衡,进一步分析发现无效等位基因的存在是引起偏离平衡的重要因素。
3)25个叶螨种群的总体分化指数FST为0.506,种群之间高度遗传分化。种群间基因流较小,种群多样性较差及存在地理隔离效应是引起朱砂叶螨种群分化的重要因素。通过构建NJ系统发育树、贝叶斯聚类及分子变异模型分析(AMOVA),结果显示我国的叶螨种群分为五个分支,其中朱砂叶螨的聚类结果与地理分布有很好的相关性。此外,我们的遗传数据不支持将两种形式的叶螨分成两个物种,因为两者的分化水平处于不同地理种群的分化水平,两者在DNA组成上没有实质的不同,体色的差异可能由于表观遗传方式的不同造成的。
灰飞虱Laodelphax striatellus (Fallen)属半翅目飞虱科,世界范围内主要分布在温带地区,广泛分布于东亚、东南亚、欧洲和北非等地,可在温带地区安全越冬。国内分布遍及全国各地,以长江流域和华北稻区发生较多。灰飞虱除以成虫、若虫刺吸危害外,还是多种植物病毒病害的重要媒介昆虫,可传播多种病毒病害,其传毒危害造成的损失远远大于其刺吸危害。尽管灰飞虱的经济地位重要,但是对于灰飞虱的种群遗传学的研究报道却比较少。原因在于灰飞虱上可用的遗传标记较少,且不能提供足够的遗传学信息。而微卫星(microsatellite)分子标记由于广泛地在基因组中分布、良好的重复性和保真性、较高的变异频率、呈孟德尔式遗传、共显性等优点,已成为种群遗传学研究中应用最为广泛的分子标记。但是,目前尚未有灰飞虱微卫星的开发的报道。基于以上原因,笔者分别通过褐飞虱EST数据库和抑制PCR构建微卫星富集文库来开发灰飞虱的微卫星,并应用新开发的9个微卫星标记和一段线粒体COI基因的序列对中国17个地理种群共计720个灰飞虱个体展开种群遗传多样性和种群遗传结构的研究,并得到相关的结果与结论：
1)由于国际无灰飞虱微卫星的报道,基于EST微卫星具有较高的不同种属之间的转移性、开发成本低和效率高的特性,首先根据褐飞虱的EST数据库开发褐飞虱的微卫星,然后验证在其灰飞虱上的转移性。笔者通过搜索褐飞虱的EST数据库,设计引物并PCR验证,最终开发了12个多态性较好的褐飞虱微卫星标记。微卫星等位基因的测序结果揭示了微卫星复杂的变异机制。对这12对微卫星引物在灰飞虱上面的转移性研究结果发现：这12对卫星引物高度专属于褐飞虱,不能够用于灰飞虱。我们得出结论：灰飞虱与褐飞虱属于不同的属,分化时间较长,且进化速度较快,两者的基因组信息差异太大,导致两者之间的微卫星不能相互转移。
2)通过抑制PCR的方法构建了灰飞虱(TC)6(AC)5和(AG)6(AC)5的复合型微卫星富集文库,挑取200个阳性克隆测序,设计了100对微卫星引物,最终成功开发了9个多态性较好的微卫星,通过三个地理种群对新开发的微卫星进行检测,结果显示每个位点具有13到30个等位基因。平均表观杂合度和预期杂合度分别在在0.255～0.833和0.392～0.929之间,这9个微卫星位点具有高度的多态性,新开发的微卫星位点将为灰飞虱种群遗传结构的研究提供有效的分子标记手段,本研究首次在国际上报道了9个灰飞虱微卫星,填补了国际无灰飞虱微卫星的空白。
3)运用9个微卫星分子标记对17个地理种群的灰飞虱种群遗传结构的研究,结果显示每个种群平均每个位点的等位基因个数在12.111～16.333之间。所有种群的表观杂合度介于0.536～0.683之间,预期杂合度介于0.742～0.840之间。说明我国的灰飞虱具有较高水平的遗传多样性,并且华东种群和华北种群较东北种群和华南种群的多样性要高。由于灰飞虱的近交导致大部分种群因杂合体缺失而偏离Hardy-Weinberg平衡。除了华南的永福和南宁种群外,其他种群都具有私有等位基因,这可能是由于华南地区的分析样本较少造成的。基于FST统计显示种群间分化较小或无分化,总体FST为0.004,只有东北的黑龙江HLJ种群和辽宁的丹东DD种群与其他种群有较微弱的显著分化,贝叶斯聚类及NJ分析结果同样显示17个种群具有不稳定的种群遗传结构黑龙江HLJ种群和辽宁的丹东DD种群与其他种群有较微弱的差异。AMOVA分析结果表明灰飞虱的微弱变异主要来自个体之间的差异,而种群间及4个区域间的遗传分化极小。与地理距离的相关性分析结果表明,尽管灰飞虱的遗传分化水平较低,但是与地理距离还有较弱的负相关性,说明地理距离在灰飞虱种群分化中起一定作用。
4)基于线粒体一段COI基因序列对种群的研究发现,COI基因经比对并去掉引物及测序较差的部分后,最终得到了769bp的片段,没有终止密码子碱基的插入或缺失出现,共有33个变异位点,占总序列的4.2%,其中简约信息位点15个。总体来说灰飞虱多样性较好,在720个个体中共发现了37个单倍型,单倍型多样性指数0.159～0.764之间,平均0.642；核酸多样性较差,在0.101%～0.320%之间,平均0.217%。与微卫星的结果相似,华东种群较东北种群和华南种群的多样性要高；东北地区的灰飞虱多样性较差,平均每个种群有5.5个单倍型,并且这四个种群中无私有单倍型存在。其中最差的是黑龙江HLJ种群,只有3个单倍型。COI基因的FST统计比微卫星的结果稍大,但还是处于较低分化的水平,平均分化指数为0.055,表明灰飞虱的确分化较小或无分化。COI的分析同样表明东北的黑龙江种群与其他种群有显著分化。AMOVA分析结果同样显示灰飞虱的微弱变异主要来自个体之间的差异。
5)根据微卫星和COI基因对灰飞虱种群遗传结构的研究,我们得出结论：灰飞虱种群分化水平较低,分化程度与具有迁飞习性的东亚飞蝗相似,种群间基因流较强,灰飞虱可能具有远距离迁飞习性。基于COI基因的分析发现37个单倍型在各个种群中分布不均匀,这可能是由于环境选择压力的不同造成,单倍型与灰飞虱的适合度及迁飞是否有某种联系需要进一步的实验验证,另外,我们还发现灰飞虱感染的Wolbachia没有引起单倍型多样性的降低,但导致了核酸多样性的降低,这是由于Wolbachia对线粒体拉升效应造成的。
Both the two-spotted spider mite Tetranychus urticae Koch and the carmine spider mite T. cinnabarinus (Boisduval), which belong to Arachnida, Acari, Acariformes, Tetranychidae, Tetranychus, are very important mite pests. The two species have multiple dispersal mechanisms. They are wingless and usually rely on crawling for their dispersal. But they can also be carried for long distance by the wind and by human activities. Due to the complex dispersal mechanisms of T. urticae, the population structure and diversity would be complex. However, due to the limited number of markers used to analyse geographic populations and individuals, the information that they provided was insufficient to understand the genetic diversity and population structure clearly. In addition to questions about the population structure and genetic diversity of T. urticae in China, there is a big question about its taxonomy. Due to reproductive compatibility, difficult to find out the differences in morphology and mitochondrial DNA levels, T. cinnabarinus and T. urticae are considered to be the single species in Europe and the United States. However, in China and other Asian countries, they are considered to be two different species of mites. The reasons are the differences of body color and reproductive incompatibility between them. Therefore, whether they constitute one or two species has been debated for long time.
To address the above issues, a microsatellites-enriched DNA library was constructed using a suppression-PCR procedure. We genotyped25populations of spider mites in China using eight microsatellite loci, including2newly developed by ourselves and6previously reported. We also compared the difference of the genetic diversity and population structure of the two types of mites, and try to clarify the taxonomic status of the two types of mites from a population genetic structure perspective. The main results and conclusions are as follows:
1) We successfully constructed the microsatellites-enriched DNA library of the spider mite using a suppression-PCR procedure. Of the180clones sequenced,53sequences flanking microsatellites were selected for primer design. Finally, two microsatellites with good polymorphism was isolated from the genome of the spider mite. This is the first time to use the suppression-PCR procedure for microsatellites isolation in spider mites. Low mutation rate of the mite microsatellites bring the isolation efficiency down.
2) We genotyped a total of1055individuals from18T. cinnabarinus populations and7T.urticae populations in China using eight microsatellite loci. One hundred alleles were identified in the8loci, with13.63in each locus across the25populations. However, the low values of heterozygosity and allelic richness implies the low level of genetic diversity of the spider mites. In addition, genetic diversity of the red form mites was found to be higher than the green form. Pearson correlations between statistics of variation (AR and He) and geographic co-ordinates (latitude and longitude) showed that the genetic diversity of T. cinnabarinus was correlated with latitude. The declining genetic diversity of T. cinnabarinus with increasing latitude may be because the northern populations have fewer generations per year. Twenty-three of the25populations used in this study deviated from HWE, and of these,19populations displayed significant heterozygote deficiency. Further analysis revealed that the deficit in heterozygotes were due to null allele.
3) We found a highly significant genetic differentiation among the25populations with global FST=0.506. Spider mites possess low levels of genetic diversity, limited gene flow between populations and significant IBD (isolation by distance) effect. These factors in turn contribute to the strong subdivision of genetic structure. Based on the results of NJ tree, Bayesian analysis and AMOVA, we conclude that five clades likely exist in China. In addition, the population genetic structures of the two forms of mites do not support their separation into two species. The morphological difference between the two forms of mites may be the result of epigenetic effects.
The small brown planthopper (SBPH) Laodelphax striatellus Fallen is an important agricultural pest, which is widely distributed in temperate zones such as East Asia, Southeast Asia, Europe and Northern Africa, and can overwinter safely in these areas. This pest is one of the most serious pest insects of rice plant and many other kinds of gramineous plants. Besides the direct sucking damage, the agricultural significance of SBPH lies in its ability to spread the damaging plant disease, Rice stripe virus (RSV). Despite the economic importance of this pest, the population genetic structure and genetic diversity were little known. In recent years, due to the characteristics of high level of polymorphism, co-dominant Mendelian inheritance, high frequency of occurrence, and ease of detection by PCR, microsatellites or simple sequence repeats (SSR) have been widely used in population genetic studies. However, no microsatellites primers developed specifically for the SBPH bottlenecked the process of population genetic study for the SBPH. To resolve the aforementioned issues, we tried to develop microsatellites through searching the EST database of the brown planthopper (BPH), Nilaparvata lugens (Stal) and construction the microsatellites-enriched libraries. Employing9new microsatellites developed in this study and COI gene, we investigated the genetic structure of17L. striatellus populations in China. The main results are as follows:
1) An enormous number of ESTs are now available in the public sequence database, and can be exploited to identify markers inexpensively. Compared with conventional markers derived from genomic DNA, EST-derived markers are easy to develop, and highly transferable. In this study, we mined existing BPH ESTs for new microsatellites, and validated the transferability from BPH to SBPH. Finally we developed and characterized12polymorphic microsatellites from the expressed sequence tags database of the brown planthopper (BPH), Nilaparvata lugens (Stal). Microsatellites sequencing revealed complex mechanisms of mutations of the12microsatellites loci. The fact of failed transferability of the new microsatellites from BPH to SBPH may be due to that the two species had diverged long time ago, and evolved quickly.
2) Nine microsatellites loci were isolated from the genome of Laodelphax striatellus (Fallen)(Homoptera:Delphacidae) by constructing (TC)6(AC)5and (AG)6(AC)5compound SSR enriched libraries using suppression-PCR procedure. These loci developed in this study were high polymorphism with13to30alleles per locus in three tested populations. The observed and expected heterozygosities ranged from0.255to0.833and0.392to0.929respectively. These microsatellites markers can be used for population genetic structure and genetic diversity research of L. striatellus.
3) The results of the microsatellites implied L. striatellus populations possess high levels of genetic diversity. The allele numbers of each locus in each population were ranged from12.111to16.333. The observed heterozygosity and expected heterozygosity were0.536-0.683and0.742-0.840respectively. The L. striatellus populations in East China have much higher levels of genetic diversity than the populations in Northeast China and South China. Most microsatellites displayed a significant departure from Hardy-Weinberg equilibrium (HWE) in most populations due to serious inbreeding. Private alleles were identified in all populations except YF and NN, which are all located in South China. This may be due to the limited number of analyzed samples in the two populations. Little genetic differentiation among almost all the populations, with global FST=0.004. However, HLJ and DD show slightly but significant differentiation with some other populations. This was also evidences by the results of NJ tree and Bayesian analysis. AMOVA results indicate that genetic variation mainly comes from the individuals' level. Although the level of population differentiation was very low, there were also mild IBD effects among L. striatellus populations. Which means geographical distance plays a role in population differentiation.
4) All sequences were truncated to the same length (769bp) to eliminate missing data. The sequences had33polymorphic sites (accounting4.2%), of which15were parsimony informative. In general, L. striatellus populations have high levels of genetic diversity. An alignment the COI gene from720individuals from17populations across China revealed37haplotypes. The haplotype diversity ranged between0.159and0.764with mean0.642. However, the nucleotide diversity was relatively low, which was ranged between0.101%and0.320%(mean0.217). The L. striatellus populations in East China and North China also showed much higher levels of genetic diversity than the populations in Northeast China and South China based on the COI gene. With5.5haplotypes per populations and no private haplotypes, the Northeast China populations posses the lowest levels of genetic diversity. Among which, HLJ was the lowest one, only3haplotypes were identified in this population. The COI also revealed little genetic differentiation among populations, although the values of FST calculated by COI gene (mean0.055) were slightly larger than by microsatellites. HLJ populations also displayed significant differentiation with some other populations according to the COI gene. AMOVA results also indicate that genetic variation mainly comes from the individuals' level.
6) According to the research on the population structure of L. striatellus by SSR and COI, we concluded that:the L. striatellus population shows a relative low level of genetic differentiation, which is similar with the migratory species Locusta migratoria manilensis (Meyen), while there is a strong gene flow among these populations indicating that the L. striatellus may have Long-distance migratory ability. Based on the COI we found that37haplotypes distribute unevenly among populations. This could be explained by the environmental selection pressures. However, whether there is a linkage between the haplotypes and the fitness, migration of L. striatellus requires further experimental verification. Furthermore, we found that individuals infected with Wolbachia don't cause a reduction in the diversity of haplotypes but the nuclear polymorphisms, which can be reasoned by the hitchhiking.
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