A novel Microviridae phage (CLasMV1) from "Candidatus Liberibacter asiaticus"

Authors: ZHANG, L, - South China Agricultural University; LI, Z. - South China Agricultural Univerisity; BAO, M - South China Agricultural Univerisity; LI, T. - South China Agricultural Univerisity; FANG, F. - South China Agricultural Univerisity; ZHENG, Y. - South China Agricultural Univerisity; LIU, Y. - South China Agricultural Univerisity; XU, M. - South China Agricultural Univerisity; Chen, Jianchi; DENG, X. - South China Agricultural Univerisity; ZHENG, Z. - South China Agricultural Univerisity

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/7/2021
Publication Date: 10/13/2021
Citation: Zhang, L., Li, Z., Bao, M., Li, T., Fang, F., Zheng, Y., Liu, Y., Xu, M., Chen, J., Deng, X., Zheng, Z. 2021. A novel Microviridae phage (CLasMV1) from "Candidatus Liberibacter asiaticus". Frontiers in Microbiology. 12. Article 754245. https://doi.org/10.3389/fmicb.2021.754245.
DOI: https://doi.org/10.3389/fmicb.2021.754245

Interpretive Summary: Candidatus Liberibacter asiaticus (CLa) is the scientific name of the bacterium associated with the disorder in citrus called Huanglongbing (HLB), which is also known as citrus greening disease. HLB threatens citrus production worldwide. Learning about the microbiology of CLa is critical to manage HLB. This research publication describes the discovery by genomic methods of a new virus we named CLasMV1 that infected CLa. CLasMV1 has only eight genes and belongs to a single-stranded DNA virus group. This is the first report of a virus infecting CLa. Information about CLasMV1 enriches our knowledge of CLa and opens new avenues to manage HLB.

Technical Abstract: “Candidatus Liberibacter asiaticus” (CLas) is an unculturable phloem-limited a-proteobacterium associated with citrus Huanglongbing (HLB, yellow shoot disease). HLB is currently threatening citrus production worldwide. Understanding the CLas biology is critical for HLB management. In this study, a novel single-stranded DNA phage, CLasMV1, was identified and characterized in CLas strain GDHZ11 from Guangdong Province of China through a metagenomic analysis. The CLasMV1 phage had a circular genome of 8,869 bp with eight open reading frames (ORFs), among which, six ORFs remained as encoding uncharacterized putative proteins, ORF6 encoded a replication initiation protein (RIP) and ORF8 encoded a major capsid protein (MCP). Based on BLASTp search against GenBank database, the amino acid sequences of both MCP and RIP shared similarities (Length Coverage > 50% and Nucleotide Identity > 25%) to those of phages in Microviridae, a single-stranded DNA phage Family. Phylogenetic analysis revealed that both MCP and RIP sequences clustered with those from CLas and “Ca. L. solanacearum” published in GenBank database, forming a distinct lineage, designated as Subfamily Libervirinae. No complete integration form but partial sequences of CLasMV1 was found in the chromosome of CLas strain GDHZ11. Read-mapping analyses were performed on additional HiSeq data sets of 15 CLas strains. Eight strains were detected to harbor complete CLasMV1 sequences with low level variations in single nucleotide polymorphisms (SNPs) and small sequence insertions/deletions (InDels). PCR tests using CLasMV1 specific primer set detected the phage in 557 out of the 1,006 (57%) CLas strains collected from southern China. This is the first report of Microviridae phage in CLas, which will have significant impact on current CLas phage research.