Comparative transcriptome analysis of candidate secretory effector proteins from Colletotrichum falcatum infecting sugarcane

Q1 Agricultural and Biological Sciences

Agri Gene Pub Date : 2019-09-01 DOI:10.1016/j.aggene.2019.100089

C. Naveen Prasanth, R. Viswanathan, P. Malathi, A. Ramesh Sundar

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引用次数: 10

Abstract

The ascomycete Colletotrichum falcatum is the causal agent of red rot of sugarcane, infecting stalks which are economically important for extraction of sugar. Since the pathogen is considered as the most destructive disease in many sugarcane growing countries it gained much attention to decipher its lifestyle. In this study, we have sequenced in planta transcriptome of C. falcatum under Illumina Hi-Seq platform and expanded our search towards finding the Small Secretory Proteins (SSPs) expressed during the host-pathogen interactions. Our previous reports from genome and transcriptome of C.falcatum data provided 768 and 884 SSPs were predicted respectively. The in planta secretory proteins were further mapped and localized with the help of bioinformatics pieplines such as TargetP and SignalP with the default parameters resulted in localizing 739 sequences to secretory pathway, 27 as mitochondrion and two contained chloroplast signal peptides. Further, the predicted secretory proteins were grouped into classical and non-classical proteins and these secreted proteins and 56 transmembrane helices were classified using GO, which revealed that signal peptides have a probable role in stabilizing fungal secretory proteins in the host system during pathogenesis. These small secreted proteins were further identified as crucial key pathogenic determinants from in planta transcriptome analysis. The repertoire of C. falcatum effectors prediction from in vitro and in planta transcriptome identified several putative genes which are involved in biotrophy-necrotrophy in functionally diverse patterns and this will facilitate further analysis of stage specific genes, fungal pathogenicity determinants and characterizing the expression of SSPs in in planta.

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镰形炭疽杆菌感染甘蔗候选分泌效应蛋白的比较转录组分析

甘蔗红腐病的病原是子囊菌镰孢炭疽菌，其侵染的甘蔗秸秆具有重要的经济价值。由于这种病原体被认为是许多甘蔗种植国最具破坏性的疾病，因此破译其生活方式受到了广泛关注。在这项研究中，我们在Illumina的高通量测序平台上对C. falcatum的植物转录组进行了测序，并扩大了我们对宿主-病原体相互作用过程中表达的小分泌蛋白(ssp)的研究。我们之前的报告从镰状镰刀菌的基因组和转录组数据中分别预测了768和884个ssp。在TargetP和SignalP等生物信息学管道的帮助下，利用默认参数进一步定位了植物分泌蛋白，结果发现739个序列定位于分泌通路，27个序列定位于线粒体，2个序列定位于叶绿体信号肽。此外，将预测的分泌蛋白分为经典蛋白和非经典蛋白，并使用氧化石墨烯对这些分泌蛋白和56个跨膜螺旋进行分类，这表明信号肽可能在发病过程中稳定宿主系统中的真菌分泌蛋白。这些小分泌蛋白在植物转录组分析中被进一步鉴定为关键的致病决定因素。通过体外和植物转录组对金黄色葡萄球菌 效应物的预测，确定了几个可能以不同功能模式参与生物营养-坏死的基因，这将有助于进一步分析阶段特异性基因、真菌致病性决定因素和表征植物中ssp的表达。

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来源期刊

Agri Gene Agricultural and Biological Sciences-Agricultural and Biological Sciences (miscellaneous)

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期刊介绍： Agri Gene publishes papers that focus on the regulation, expression, function and evolution of genes in crop plants, farm animals, and agriculturally important insects and microorganisms. Agri Gene strives to be a diverse journal and topics in multiple fields will be considered for publication so long as their main focus is on agriculturally important organisms (plants, animals, insects, or microorganisms). Although not limited to the following, some examples of potential topics include: Gene discovery and characterization. Genetic markers to guide traditional breeding. Genetic effects of transposable elements. Evolutionary genetics, molecular evolution, population genetics, and phylogenetics. Profiling of gene expression and genetic variation. Biotechnology and crop or livestock improvement. Genetic improvement of biological control microorganisms. Genetic control of secondary metabolic pathways and metabolic enzymes of crop pathogens. Transcription analysis of beneficial or pest insect developmental stages Agri Gene encourages submission of novel manuscripts that present a reasonable level of analysis, functional relevance and/or mechanistic insight. Agri Gene also welcomes papers that have predominantly a descriptive component but improve the essential basis of knowledge for subsequent functional studies, or which provide important confirmation of recently published discoveries provided that the information is new.