Whole genome sequencing and pathogenesis analysis of xanthomonas oryzae pv. oryzae strains

Name: Thitima Chintaganon

LCSH: Kasetsart University -- Theses. M.S. (Agricultural Biotechnology) 2022

Classification :.LCCS: SB608.R5

LCSH: Kasetsart University. -- Interdisciplinary Graduate Program -- Theses

LCSH: Rice -- Diseases and pests

LCSH: Rice -- Genetics

LCSH: Xanthomonas diseases

LCSH: Pathogenic bacteria

LCSH: Genome

Abstract: Bacterial leaf blight disease (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious diseases in rice production worldwide. In this study, 50 strains of Xoo collected from 14 provinces in Thailand from 2008 to 2018 were subjected to whole-genome sequencing using the Illumina HiSeq platform. The genome sequence of 50 Thai Xoo strains and reference strains: KACC10331 from Korea, ITCCBB0002 from India, and PXO99A from the Philippines, were compared to SK2-3 (NZ_CP019515). The draft genomes of 50 Xoo strains found in Thailand contained 4.2-4.4 Mb, consisting of 3,787-3,945 protein-coding genes. The sequence comparisons showed that 30,140 SNPs and 3,156 indels were observed in these 50 Thai strains. Among these variants, only 21,181 SNPs were observed across these samples. Principal component and neighbor-joining clustering analysis showed that Thai Xoo strains could be divided into eight subgroups, of which five clusters corresponded well with their geographic distribution. The multigene phylogeny built based on 38 Xoo pathogenesis-related genes also showed the correspondence between genetic variation and geographic distribution, in which ten out of 13 showed this agreement. Furthermore, some clades in the single-gene phylogenies of rpfC, rpfF, gumG, raxX, and xopZ genes showed correlations between genetic variation and the type of resistance gene in rice. However, the relationship between genetic variation and geographic distribution in these clades wasn't clear as some contained foreign Xoo strains. The correlation between genetic variation, geographic distribution, and resistance genes in rice suggested that information regarding Xoo strain genetic variation would be useful for selecting suitable resistant rice varieties for growing in each region of Thailand.

Kasetsart University. Office of the University Library

Address: Bangkok

Email: tdckulib@ku.ac.th

Name: Sujin Patarapuwadol

Role: Thesis Advisor

Name: Passorn Wonnapinij

Role: Thesis CO-Advisor

Role: Thesis CO-Advisor

Created: 2022

Modified: 2025-07-21

Issued: 2025-07-21

วิทยานิพนธ์/Thesis

application/pdf

URL: https://www.lib.ku.ac.th/KUthesis/2564/thitima-chi-all.pdf

CallNumber: SB608.R5 .T46

eng

DegreeName: Master of Science

Level: Master's Degree

Descipline: Agricultural Biotechnology

Grantor: Kasetsart University

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