Single molecule real-time sequencing of Xanthomonas oryzae genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships

Abstract

Pathogen-injected, direct transcriptional activators of host genes, TAL (transcription activator-like) effectors play determinative roles in plant diseases caused by Xanthomonas spp. A large domain of nearly identical, 33–35 aa repeats in each protein mediates DNA recognition. This modularity makes TAL effectors customizable and thus important also in biotechnology. However, the repeats render TAL effector (tal) genes nearly impossible to assemble using next-generation, short reads. Here, we demonstrate that long-read, single molecule real-time (SMRT) sequencing solves this problem. Taking an ensemble approach to first generate local, tal gene contigs, we correctly assembled de novo the genomes of two strains of the rice pathogen X. oryzae completed previously using the Sanger method and even identified errors in those references. Sequencing two more strains revealed a dynamic genome structure and a striking plasticity in tal gene content. Our results pave the way for population-level studies to inform resistance breeding, improve biotechnology and probe TAL effector evolution.

An operon for production of bioactive gibberellin A4 phytohormone with wide distribution in the bacterial rice leaf streak pathogen Xanthomonas oryzae pv. oryzicola

“…Bioinformatic searches of the sequence information currently available for X. oryzae indicated that the GA biosynthetic operon is present in Xoc, but not those for the closely related and other major pathovar X. oryzae pv. oryzae (Xoo) whose genomes have been fully sequenced (Lee et al, 2005;Ochiai et al, 2005;Salzberg et al, 2008;Booher et al, 2015;Quibod et al, 2016). In Xoc, examination of the available genome sequences (Bogdanove et al, 2011;Wilkins et al, 2015) revealed that the GA biosynthetic operon is flanked by multiple insertion sequence (IS) elements.…”

Population genomic insights into variation and evolution of Xanthomonas oryzae pv. oryzae

“…Phylogenomic tree of Indian Xoo strains along with other Asian strains [XOOK59, XOOM60, XOOP61, PXO8662, PXO8363, XO35933 (NCBI accession number: AXVI00000000), XOC_BLS25664], African strains (XOO_NAI865, XOC_MAI1065, XOC_CFBP734262) and the USA strains (X8-1A56, X11-5A56) was obtained using 31 phylogenomic marker genes14, extracted from each genome and concatenated. Mega 7.0 was used for obtaining multiple sequence alignment of the concatenated sequences as well as to obtain phylogenetic tree66.…”

Using Ecology, Physiology, and Genomics to Understand Host Specificity inXanthomonas

“…The recent sequencing and resequencing of several X. oryzae strains indeed revealed a dynamic genome structure and an important plasticity in TAL effector genes through HGT, duplication, and recombination (19). More generally, broad sequence analyses of genes coding for pathogenicity determinants together with their genomic environment will help to determine not only their functions but also the mechanisms by which they appear and evolve in a given population (88,124).…”