|
Draft Genome Sequence and Population Structure of Xanthomonas oryzae pv. oryzae Causing Bacterial Blight Disease on Rice in Thailand |
|---|---|
| รหัสดีโอไอ | |
| Creator | Thitima Chintaganon |
| Title | Draft Genome Sequence and Population Structure of Xanthomonas oryzae pv. oryzae Causing Bacterial Blight Disease on Rice in Thailand |
| Contributor | Jutatape Watcharachaiyakup, Passorn Wonnapinij, Pumipat Tongyoo |
| Publisher | Department of Agriculture |
| Publication Year | 2565 |
| Journal Title | Thai Agricultural Research Journal |
| Journal Vol. | 40 |
| Journal No. | 1 |
| Page no. | 45-58 |
| Keyword | bacterial blight disease, Xanthomonas oryzae pv. oryzae, genome analysis |
| URL Website | https://at.doa.go.th/journal |
| Website title | Thai Agricultural Research Journal |
| ISSN | 0125-8389 |
| Abstract | Bacterial blight disease (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious diseases of rice production worldwide. The virulence of disease can cause severe yield losses as high as 50 percent. Xoo is genetically diverse and some strains can destroy more than 10 rice resistance genes. Xoo genome analysis can provide comparative information on genetic relationships and population structure. In this study, fifty strains of Xoo collected from 14 provinces in Thailand during 2008 to 2018 were subjected to whole-genome sequencing byusing Illumina HiSeq platform. The obtained sequence reads were assembled, mapped, and compared to the genomes of Xoo reference strains including KACC10331, ITCCBB0002, PXO99A and SK2-3 strains from Korea, India, Philippines and Thailand, respectively. The draft genomes of the 50 strains of Xoo in Thailand contained 4,219,315-4,366,829 basepairs which consisted of 3,787-3,945 coding regions of gene (CDS). We identified 30,140 single nucleotide polymorphisms (SNPs) and 3,156 insertion-deletion (indels). The analysis of Xoo population structure and genetic correlations using the 21,181 SNP positions based on principal component analysis and neighbor-joining clustering revealed that most of Thai Xoo populations were genetically distinct from reference strains. However, xa5-breaking strains from Sukhothai province and 12 strains from Chiang Rai were genetically related to the Indian strain (ITCCBB0002). Furthermore, the highly genetic diversity within the Thai Xoo population was found. Thai Xoo strains in this study were divided into 8 subgroups, in relation to the geography for 5 subgroups, and 39 percent of all Thai strains were in subgroup 1. Based on population genomics, we found that there was a general correspondence between the areas of Xoo isolated and genomic structure. This suggests that the geographical factors as affected by climate, soil types, may influence on the diversity of Xoo. |
