向日葵锈菌转录组SNP位点挖掘及所在基因功能注释

doi:10.7668/hbnxb.2018.03.015

摘要/Abstract

摘要： 为了解向日葵锈菌基因组中SNP所在基因功能及其致病性，使用SOAPsnp软件对向日葵锈菌330小种不同萌发阶段（0，4，8 h）的转录组测序结果拼接得到的59 409条Unigene序列进行SNP检测，计算其发生频率并对其进行Nr、Nt注释、GO分类、COG分类、KEGG代谢通路注释与PHI比对。结果发现，共有29 966个SNP位点分别分布在8 321条Unigene上，SNP发生的频率为1/2 764 bp，其中转换19 599个，颠换10 367个。在所有变异类型中，A/G和C/T发生频率最高，分别达32.80%和32.60%。注释结果表明，分别有79.46%，43.00%的序列被注释到Nr、Nt数据库中，基因中涉及最多的为遗传信息过程通路，以翻译为主；最后将这些含SNP Unigene与病原菌寄主互作数据库PHI比对，共筛选到961条可能与向日葵锈菌致病性相关的含SNP的序列，因而认为，锈菌的致病性是由真菌细胞壁修饰蛋白和潜在的致病效应蛋白所致。结果可为以后进一步开发SNP遗传多态性、遗传图谱的构建提供理论依据，为研究向日葵锈菌毒力与功能奠定基础，并对向日葵的抗病育种研究具有重大意义。

关键词: 向日葵锈菌, 转录组, 单核苷酸多态性, 功能注释

Abstract: To understand the function and pathogenicity of the single nucleotide polymorphisms(SNP) gene in the Puccinia helianthi Schw., we used SOAPsnp to search for the SNP of 59 409 Unigenes sequence in the transcriptome data of different germination stages (0, 4, 8 h) of race 330 of P. helianthi. The frequency of sequences with SNP was calculated. Nr,Nt annotation,GO classification,COG classification,KEGG metabolic pathway annotation,and PHI(Pathogen Host Interaction)alignment were performed. The SNP-containing Unigenes were independently assessed for homology matches against NCBI's non-redundant nucleotide database,non-redundant protein database and for orthologs against the Cluster Orthologous Groups of proteins(COG)database using Blast search strategies. And Blast analysis of the PHI database. A total of 29 966 SNPs was identified in 8 321 Unigenes,the frequency of SNPs was 1/2 764 bp,including transition 19 599 and transversion 10 367. A/G and C/T were the main types,accounting for 32.80% and 32.60% of all the SNPs. The annotation results showed that there were 79.64% and 43.00% Unigene annotated to Nr and Nt libraries,genes involved in genetic information process pathways are mostly of translation. Finally,the SNP-containing Unigenes were predicted to have pathogenic function by Blast analysis of the PHI database,there were 961 Unigenes which might be related to pathogenicity of sunflower rust. Therefore,we believed that the pathogenicity of rust is caused by fungal cell wall modification proteins and potential caused by effector protein. This will provide a theoretical basis for the development of SNP genetic polymorphism and construction of genetic maps and lay the foundation for further studies on the virulence and function of sunflower rust,and is of great significance for the study of sunflower disease resistance breeding.

Key words: Puccinia helianthi Schw., Transcriptome group, Single nucleotide polymorphism, Functional annotation

中图分类号:

S435.655
Q78

王妍, 景岚, 李鑫淳. 向日葵锈菌转录组SNP位点挖掘及所在基因功能注释[J]. 华北农学报, 2018, 33(3): 92-98. doi: 10.7668/hbnxb.2018.03.015.

WANG Yan, JING Lan, LI Xinchun. SNP Mining and Gene Functional Annotation in Puccinia helianthi Transcriptome Group[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2018, 33(3): 92-98. doi: 10.7668/hbnxb.2018.03.015.

http://www.hbnxb.net/CN/Y2018/V33/I3/92

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