Complete Genome Sequencing Provides Novel Insight Into the Virulence Repertories and Phylogenetic Position of Dry Beans Pathogen<i>Curtobacterium flaccumfaciens</i>pv.<i>flaccumfaciens</i>

Abstract

Bacterial wilt of dry beans (family Fabaceae) caused by the actinobacterial agent <i>Curtobacterium flaccumfaciens</i> pv. <i>flaccumfaciens</i> is one of the most important diseases threatening edible legume production around the globe. Despite the economic losses due to the bacterial wilt disease, the pathogen has not so far been investigated for its genomic features, pathogenicity determinants, and virulence strategies. Here we present the first complete genome sequence of a highly virulent bacteriocin-producing <i>C. flaccumfaciens</i> pv. <i>flaccumfaciens</i> strain P990. The bacterium has a circular chromosome consisting of 3,736 kbp with the G+C% content of 71.0%. Furthermore, a 147-kbp circular plasmid (pCff1) with 66.1% G+C% content as well as two circular plasmid-like DNAs with sizes of 25 and 22 kbp were detected within the genomic contents of <i>C. flaccumfaciens</i> pv. <i>flaccumfaciens</i>. Phylogenetic analyses revealed that only a few number of <i>Curtobacterium</i> sp. strains deposited in the public databases could be classified within the species <i>C. flaccumfaciens</i>. Comparative genomics of <i>C. flaccumfaciens</i> pv. <i>flaccumfaciens</i> using the genome sequences of actinobacterial plant pathogens revealed the presence of a set of unique low G+C% content genomic islands in the <i>C. flaccumfaciens</i> pv. <i>flaccumfaciens</i> genome. Homologs of pathogenicity-determinant loci capable of producing 1,4-beta-xylanase (<i>xysA</i>), pectate lyase (<i>pelA1</i> and <i>pelA2</i>), serine protease (<i>chpC</i>, <i>chpG</i>, and <i>pat-1</i>), and sortase (<i>srtA</i>) were detected in <i>C. flaccumfaciens</i> pv. <i>flaccumfaciens</i> genome. The genomic data presented here extend our understanding of the <i>C. flaccumfaciens</i> pv. <i>flaccumfaciens</i> genomic features and pave the ways of research on functional and interaction genetics to combat the risk of bacterial wilt disease in the 21st century's dry bean industry.