Two ‘Candidatus Liberibacter asiaticus’ Strains Recently Found in California Harbor Different Prophages

Abstract

'Candidatus Liberibacter asiaticus' (CLas), an α-proteobacterium, is associated with citrus Huanglongbing (HLB; yellow shoot disease). In California, two cases of CLas have been detected in Los Angeles County, one in Hacienda Heights in 2012 and the other in San Gabriel in 2015. Although all infected trees were destroyed in compliance with a state mandate, citrus industry stakeholder concerns about HLB in California are high. Little is known about the biology of CLas, particularly the California strains, hindering effective HLB management efforts. In this study, next-generation sequencing technology (Illumina MiSeq) was employed to characterize the California CLas strains. Data sets containing >4 billion (Giga) bp of sequence were generated from each CLas sample. Two prophages (P-HHCA1-2 and P-SGCA5-1) were identified by the MiSeq read mapping technique referenced to two known Florida CLas prophage sequences, SC1 and SC2. P-HHCA1-2 was an SC2-like or Type 2 prophage of 38,989 bp in size. P-SGCA5-1 was an SC1-like or Type 1 prophage of 37,487 bp in size. Phylogenetic analysis revealed that P-HHCA1-2 was part of an Asiatic lineage within the Type 2 prophage group. Similarly, P-SGCA5-1 was part of an Asiatic lineage within Type 1 prophage group. The Asiatic relatedness of both P-HHCA1-2 and P-SGCA5-1 was further presented by single nucleotide polymorphism analysis at terL (encoding prophage terminase) that has been established for CLas strain differentiation. The presence of different prophages suggests that the two California CLas strains could have been introduced from different sources. An alternative explanation is that there was a mixed CLas population containing the two types of prophages, and limited sampling in a geographic region may not accurately depict the true CLas diversity. More accurate pathway analysis may be achieved by including more strains collected from the regions.

Functional and comparative genomic analysis of integrated prophage-like sequences inCandidatus Liberibacter asiaticus

“…[15,11,10], whether of Type 1, 2, or 3. These phage types can be used to compare evolutionary dynamics [12,9], and to predict the origin of strains [17,14,9]. Nonetheless, prior work has leveraged read-mapping based approaches to identify new prophage-like sequences, albeit those that resemble Type 1 or 2 phage.…”

“…Strains A4 and gxpsy have a Type 2 classified sequence. Strain YNJS7C harbours a sequence that resembles a Type 3 prophage [12,23]. Novel prophage-like sequences of Type 1 were found in strains TX1712 and TX2351, while Type 2 sequences were also found in strain TX2351.…”

“…The CLas genome includes genes involved in cell motility and active transport [5,6], despite the presence of these genes, only passive movement has been observed in the phloem sap [6]. Furthermore, prophage sequences have also been identified in multiple CLas strains [7,8,9,10,11,12,13,14,15]. The interest in Clas prophage stems from observations that a prophage-encoded peroxidase is an effector that suppresses plant defenses [3].…”

“…Type 1, 2 or 3. Current methods to identify prophage in CLas genomes rely on read mapping against known prophages [12,9]. As a consequence, failure of read-mapping has been interpreted to mean that a genome is prophage free (e.g., as in the Ishi-1 strain [16]).…”

Understanding the Physiology of <b><i>Liberibacter asiaticus</i></b>: An Overview of the Demonstrated Molecular Mechanisms

“…The citrus industry is on the precipice of obliteration. A successful, sustainable treatment method for HLB remains elusive; yet, new Liberibacter species and subspecies continues to emerge [Morris et al, 2017;Roberts et al, 2015;Roberts and Pietersen, 2017;Wu et al, 2015;Zheng et al, 2017]. A variety of important crops are infected by this bacteria genus, the Solanaceae family is probably the most representative and economically significant [Hawkes, 1999].…”