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首页> 外文期刊>Polish Journal of Environmental Studies >Genetic Diversity and RNA-seq Transcriptome Analysis of Tricholoma matsutake from Sichuan Province, China
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Genetic Diversity and RNA-seq Transcriptome Analysis of Tricholoma matsutake from Sichuan Province, China

机译：四川松茸的遗传多样性和RNA-seq转录组分析

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摘要

The sequences of the internal transcribed spacer (ITS) regions of ectomycorrhizal fungi collected from Sichuan Province were analyzed using a PCR primer pair specific to T. matsutake. The amplified fragments were sequenced and compared with each other to build a phylogenetic tree. The mRNA deep sequencing approach was adopted to identify differentially expressed T. matsutake genes among the transcriptomes developed from a Xiaojin sample. A phylogenetic analysis of the aligned sequences was performed using maximum-likelihood (ML) and neighbor-joining (NJ) analyses. The results clearly showed that the KD (KM657344) and BT (KM657342) strains were more closely related to each other than to other strains. Moreover, T. matsutake from Sichuan differed from those specimens derived from Heilongjiang, Yunnam, and Guizhou provinces of China, Finland, and Japan. Furthermore, there was extremely high homology among these T. matsutake samples, despite some genetic variation. In addition, the genome of T. matsutake was sequenced using Illumina sequencing technology (RNA-seq). In all, a total of 24,549,990 reads were obtained that yielded 18,266,492 high-quality clean reads. The quality reads were excluded later. The BLAST analysis of the sequence reads against the NR database indicated that T. matsutake shared a high number of contigs with Laccaria bicolor. The results also indicated that catalytic activity, metabolic processes, metabolic pathways, and biosynthesis of secondary metabolites were the main functions identified by gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Phylogenetic analysis showed that T. matsutake growing in Sichuan differed from samples growing in other regions. The differences in secondary metabolites between the Sichuan and Xiaojin samples may be due to differences in metabolic pathways. Thus the study provides a foundation for understanding T. matsutake biogeography and origins, and identifies DEGs in the Xiaojin sample to help elucidate the molecular mechanisms in secondary metabolite synthesis.
机译：使用特异于松茸的PCR引物对分析了四川省外生菌根真菌的内部转录间隔区（ITS）区域的序列。对扩增的片段进行测序并相互比较以构建系统发育树。采用mRNA深度测序方法在从小金样品产生的转录组中鉴定差异表达的松茸基因。使用最大似然（ML）和邻居加入（NJ）分析对比对序列进行系统发育分析。结果清楚地表明，KD（KM657344）和BT（KM657342）菌株之间的亲缘关系比其他菌株更紧密。此外，来自四川的松茸与来自中国的黑龙江，云南和贵州，芬兰和日本的标本不同。此外，尽管有一些遗传变异，这些松茸样品之间的同源性极高。此外，使用Illumina测序技术（RNA-seq）对松茸的基因组进行了测序。总共获得了24,549,990个读取，产生了18,266,492个高质量的纯净读取。稍后将排除质量读数。针对NR数据库读取的序列的BLAST分析表明，松茸T. matsutake与双色紫胶菌共享大量重叠群。研究结果还表明，次要代谢产物的催化活性，代谢过程，代谢途径和生物合成是通过基因本体论（GO）和《京都基因与基因组百科全书》（KEGG）途径分析确定的主要功能。系统发育分析表明，四川省的松茸生长与其他地区的样品不同。四川和小金样品之间次生代谢产物的差异可能是由于代谢途径的差异。因此，该研究为了解松茸的生物地理和起源提供了基础，并鉴定了小金样品中的DEG，以帮助阐明次级代谢产物合成的分子机制。

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  • 来源
    《Polish Journal of Environmental Studies》 |2016年第6期|2327-2338|共12页
  • 作者

    Ding Xiang; Wang Panpan; Hou Yiling; Wang Mei; Hou Wanru; Li Yuming;

  • 作者单位

    Mianyang Normal Univ, Ecol Secur & Protect Key Lab Sichuan Prov, Mianyang 621000, Peoples R China|China West Normal Univ, Coll Life Sci, Minist Educ, Key Lab Southwest China Wildlife Resources Conser, Nanchong 637009, Peoples R China;

    China West Normal Univ, Coll Life Sci, Minist Educ, Key Lab Southwest China Wildlife Resources Conser, Nanchong 637009, Peoples R China;

    China West Normal Univ, Coll Life Sci, Minist Educ, Key Lab Southwest China Wildlife Resources Conser, Nanchong 637009, Peoples R China;

    Nanchong Acad Agr Sci, Natl Ctr Sweet Potato Improvement Ctr Nanchong, Nanchong 637001, Peoples R China;

    China West Normal Univ, Coll Life Sci, Minist Educ, Key Lab Southwest China Wildlife Resources Conser, Nanchong 637009, Peoples R China;

    Nanchong Acad Agr Sci, Natl Ctr Sweet Potato Improvement Ctr Nanchong, Nanchong 637001, Peoples R China;

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  • 正文语种 eng
  • 中图分类
  • 关键词

    Tricholoma matsutake; ITS; phylogenetic; RNA-seq; differentially expressed gene; Sichuan; China;

    机译：松茸ITS的系统发育RNA序列差异表达基因四川;

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