A Novel Microviridae Phage (CLasMV1) From “Candidatus Liberibacter asiaticus”
“Candidatus Liberibacter asiaticus” (CLas) is an unculturable phloem-limited α-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 n...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-10-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2021.754245/full |
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| author | Ling Zhang Ziyi Li Minli Bao Tao Li Fang Fang Yongqin Zheng Yaoxin Liu Meirong Xu Jianchi Chen Xiaoling Deng Zheng Zheng |
| author_facet | Ling Zhang Ziyi Li Minli Bao Tao Li Fang Fang Yongqin Zheng Yaoxin Liu Meirong Xu Jianchi Chen Xiaoling Deng Zheng Zheng |
| author_sort | Ling Zhang |
| collection | DOAJ |
| description | “Candidatus Liberibacter asiaticus” (CLas) is an unculturable phloem-limited α-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 (ssDNA) phage, CLasMV1, was identified in a 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). While six ORFs remain uncharacterized, ORF6 encoded a replication initiation protein (RIP), and ORF8 encoded a major capsid protein (MCP). Based on BLASTp search against GenBank database, amino acid sequences of both MCP and RIP shared similarities (coverage > 50% and identity > 25%) to those of phages in Microviridae, an ssDNA phage family. Phylogenetic analysis revealed that CLasMV1 MCP and RIP sequences were clustered with genes from CLas and “Ca. L. solanacearum” (CLso) genomes and formed a unique phylogenetic lineage, designated as a new subfamily Libervirinae, distinct to other members in Microviridae family. No complete integration form but partial sequence (∼1.9 kb) of CLasMV1 was found in the chromosome of strain GDHZ11. Read-mapping analyses on additional 15 HiSeq data sets of CLas strains showed that eight strains harbored complete CLasMV1 sequence with variations in single-nucleotide polymorphisms (SNPs) and small sequence insertions/deletions (In/Dels). PCR tests using CLasMV1-specific primer sets detected CLasMV1 in 577 out of 1,006 CLas strains (57%) from southern China. This is the first report of Microviridae phage associated with CLas, which expands our understanding of phage diversity in CLas and facilitates current research in HLB. |
| first_indexed | 2024-12-22T04:41:56Z |
| format | Article |
| id | doaj.art-ee3e903a8b64414ba3d7d4369ecbc832 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-22T04:41:56Z |
| publishDate | 2021-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-ee3e903a8b64414ba3d7d4369ecbc8322022-12-21T18:38:44ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2021-10-011210.3389/fmicb.2021.754245754245A Novel Microviridae Phage (CLasMV1) From “Candidatus Liberibacter asiaticus”Ling Zhang0Ziyi Li1Minli Bao2Tao Li3Fang Fang4Yongqin Zheng5Yaoxin Liu6Meirong Xu7Jianchi Chen8Xiaoling Deng9Zheng Zheng10Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, ChinaGuangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, ChinaChina-United States Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, ChinaGuangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, ChinaGuangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, ChinaGuangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, ChinaHorticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, ChinaGuangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, ChinaUnited States Department of Agriculture, San Joaquin Valley Agricultural Sciences Center, Agricultural Research Service, Parlier, CA, United StatesGuangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, ChinaGuangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China“Candidatus Liberibacter asiaticus” (CLas) is an unculturable phloem-limited α-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 (ssDNA) phage, CLasMV1, was identified in a 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). While six ORFs remain uncharacterized, ORF6 encoded a replication initiation protein (RIP), and ORF8 encoded a major capsid protein (MCP). Based on BLASTp search against GenBank database, amino acid sequences of both MCP and RIP shared similarities (coverage > 50% and identity > 25%) to those of phages in Microviridae, an ssDNA phage family. Phylogenetic analysis revealed that CLasMV1 MCP and RIP sequences were clustered with genes from CLas and “Ca. L. solanacearum” (CLso) genomes and formed a unique phylogenetic lineage, designated as a new subfamily Libervirinae, distinct to other members in Microviridae family. No complete integration form but partial sequence (∼1.9 kb) of CLasMV1 was found in the chromosome of strain GDHZ11. Read-mapping analyses on additional 15 HiSeq data sets of CLas strains showed that eight strains harbored complete CLasMV1 sequence with variations in single-nucleotide polymorphisms (SNPs) and small sequence insertions/deletions (In/Dels). PCR tests using CLasMV1-specific primer sets detected CLasMV1 in 577 out of 1,006 CLas strains (57%) from southern China. This is the first report of Microviridae phage associated with CLas, which expands our understanding of phage diversity in CLas and facilitates current research in HLB.https://www.frontiersin.org/articles/10.3389/fmicb.2021.754245/full“Candidatus Liberibacter asiaticus,”Microviridaephagegenomic characterizationprevalenceevolution |
| spellingShingle | Ling Zhang Ziyi Li Minli Bao Tao Li Fang Fang Yongqin Zheng Yaoxin Liu Meirong Xu Jianchi Chen Xiaoling Deng Zheng Zheng A Novel Microviridae Phage (CLasMV1) From “Candidatus Liberibacter asiaticus” Frontiers in Microbiology “Candidatus Liberibacter asiaticus,” Microviridae phage genomic characterization prevalence evolution |
| title | A Novel Microviridae Phage (CLasMV1) From “Candidatus Liberibacter asiaticus” |
| title_full | A Novel Microviridae Phage (CLasMV1) From “Candidatus Liberibacter asiaticus” |
| title_fullStr | A Novel Microviridae Phage (CLasMV1) From “Candidatus Liberibacter asiaticus” |
| title_full_unstemmed | A Novel Microviridae Phage (CLasMV1) From “Candidatus Liberibacter asiaticus” |
| title_short | A Novel Microviridae Phage (CLasMV1) From “Candidatus Liberibacter asiaticus” |
| title_sort | novel microviridae phage clasmv1 from candidatus liberibacter asiaticus |
| topic | “Candidatus Liberibacter asiaticus,” Microviridae phage genomic characterization prevalence evolution |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2021.754245/full |
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