1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
A reference transcriptome for walnut anthracnose pathogen, Ophiognomonia leptostyla
Paper ID : 1227-ICB10
Authors:
Fatemeh Khelghatibana *1, Mohammad Javan nikkhah2, Naser Safaie3, Ehsan Sari4, Ahmad Sobhani5, Somayeh Shams6
1Plant Pathology department, Iranian Research Institute of Plant Protection, Tehran, Iran
22 Department of Plant Protection, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
3Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
4Wheat Genomics and Pathology ,Durum Wheat Breeding and Genetic Team, Crop Development Centre University of Saskatchewan, Saskatoon, Canada
5Agricultural Biotechnology Research Institute of Iran - Isfahan Branch, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box: 85135-487, Isfahan, Iran.
6Department of Plant Production and Genetic Engineering, Lorestan University
Abstract:
Despite the economic losses due to Ophiognomonia leptostyla on walnut trees, no genome or transcriptome reference for the pathogen has yet been available. In the present study, the transcriptome of O. leptostyla isolate SA-SE was assembled using four assemblers i.e., Trinity, Oases, SOAPdenovo-Trans and Bridger. RNA sequencing of fungal mycelia grown on axenic culture and the leaf samples of Persian walnut (cv. Chandler) inoculated with the fungal conidia and sampled at three time points 48h, 96h and 144h post inoculation. The completeness and contiguity of assemblies were assessed by tools such as Transrate and BUSCO to identify the superior assembly [1,2]. In most of the assessment criteria such as N50, Transrate score, number of ORFs with known description in gene bank, the percentage reads mapped back to the transcript (RMBT), BUSCO features, SwissProt coverage bin and RESM-EVAL score, the Bridger assembly was the superior assembler. Next, the expression of transcript was profiled over sampling time point to understand how O. leptostyla deploys transcriptome for infection and colonization within host plants. K-means clustering [3] of expressed transcripts resulted in transcripts grouped in four different clusters over three sampling time points. Candidate effectors [4] and Cazyme [5] were identified in silico and their co-expression pattern was examined to identify candidate key genes in infection and host colonization.
Keywords:
Keywords: Juglans. Regia (cv Chandler), Ophiognomonia leptostylaRNA-seq, de novo assembly, K-mean analysis, effector
Status : Paper Accepted (Poster Presentation)