Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “<italic toggle="yes">Candidatus</italic> Liberibacter asiaticus”

ABSTRACT Huanglongbing disease (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen “Candidatus Liberibacter asiaticus” is an alphaproteobacterium of the Rhizobiaceae family that has been identified as the causative agent of HLB. The virulence o...

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Autores principales:	Marian Dominguez-Mirazo, Rong Jin, Joshua S. Weitz
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	One Health bioinformatics environmental microbiology microbial ecology phage ecology phytopathology Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/6b3a4723142f407780f885b604962902
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spelling	oai:doaj.org-article:6b3a4723142f407780f885b6049629022021-11-15T15:22:24ZFunctional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “<italic toggle="yes">Candidatus</italic> Liberibacter asiaticus”10.1128/mSphere.00409-192379-5042https://doaj.org/article/6b3a4723142f407780f885b6049629022019-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00409-19https://doaj.org/toc/2379-5042ABSTRACT Huanglongbing disease (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen “Candidatus Liberibacter asiaticus” is an alphaproteobacterium of the Rhizobiaceae family that has been identified as the causative agent of HLB. The virulence of “Ca. Liberibacter asiaticus” has been attributed, in part, to prophage-carried genes. Prophage and prophage-like elements have been identified in 12 of the 15 available “Ca. Liberibacter asiaticus” genomes and are classified into three prophage types. Here, we reexamined all 15 “Ca. Liberibacter asiaticus” genomes using a de novo prediction approach and expanded the number of prophage-like elements from 16 to 33. Further, we found that all of the “Ca. Liberibacter asiaticus” genomes contained at least one prophage-like sequence. Comparative analysis revealed a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 “Ca. Liberibacter asiaticus” strain that had previously been reported as lacking prophages. Our findings provide both a resource for data and new insights into the evolutionary relationship between phage and “Ca. Liberibacter asiaticus” pathogenicity. IMPORTANCE Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is “Candidatus Liberibacter asiaticus.” Prior work using mapping-based approaches identified prophage-like sequences in some “Ca. Liberibacter asiaticus” genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in “Ca. Liberibacter asiaticus” from 16 to 33 and identified at least one prophage-like sequence in all “Ca. Liberibacter asiaticus” strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage—expanding the number of prophage types in “Ca. Liberibacter asiaticus” from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of “Ca. Liberibacter asiaticus.”Marian Dominguez-MirazoRong JinJoshua S. WeitzAmerican Society for MicrobiologyarticleOne Healthbioinformaticsenvironmental microbiologymicrobial ecologyphage ecologyphytopathologyMicrobiologyQR1-502ENmSphere, Vol 4, Iss 6 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	One Health bioinformatics environmental microbiology microbial ecology phage ecology phytopathology Microbiology QR1-502
spellingShingle	One Health bioinformatics environmental microbiology microbial ecology phage ecology phytopathology Microbiology QR1-502 Marian Dominguez-Mirazo Rong Jin Joshua S. Weitz Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “<italic toggle="yes">Candidatus</italic> Liberibacter asiaticus”
description	ABSTRACT Huanglongbing disease (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen “Candidatus Liberibacter asiaticus” is an alphaproteobacterium of the Rhizobiaceae family that has been identified as the causative agent of HLB. The virulence of “Ca. Liberibacter asiaticus” has been attributed, in part, to prophage-carried genes. Prophage and prophage-like elements have been identified in 12 of the 15 available “Ca. Liberibacter asiaticus” genomes and are classified into three prophage types. Here, we reexamined all 15 “Ca. Liberibacter asiaticus” genomes using a de novo prediction approach and expanded the number of prophage-like elements from 16 to 33. Further, we found that all of the “Ca. Liberibacter asiaticus” genomes contained at least one prophage-like sequence. Comparative analysis revealed a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 “Ca. Liberibacter asiaticus” strain that had previously been reported as lacking prophages. Our findings provide both a resource for data and new insights into the evolutionary relationship between phage and “Ca. Liberibacter asiaticus” pathogenicity. IMPORTANCE Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is “Candidatus Liberibacter asiaticus.” Prior work using mapping-based approaches identified prophage-like sequences in some “Ca. Liberibacter asiaticus” genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in “Ca. Liberibacter asiaticus” from 16 to 33 and identified at least one prophage-like sequence in all “Ca. Liberibacter asiaticus” strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage—expanding the number of prophage types in “Ca. Liberibacter asiaticus” from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of “Ca. Liberibacter asiaticus.”
format	article
author	Marian Dominguez-Mirazo Rong Jin Joshua S. Weitz
author_facet	Marian Dominguez-Mirazo Rong Jin Joshua S. Weitz
author_sort	Marian Dominguez-Mirazo
title	Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “<italic toggle="yes">Candidatus</italic> Liberibacter asiaticus”
title_short	Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “<italic toggle="yes">Candidatus</italic> Liberibacter asiaticus”
title_full	Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “<italic toggle="yes">Candidatus</italic> Liberibacter asiaticus”
title_fullStr	Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “<italic toggle="yes">Candidatus</italic> Liberibacter asiaticus”
title_full_unstemmed	Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “<italic toggle="yes">Candidatus</italic> Liberibacter asiaticus”
title_sort	functional and comparative genomic analysis of integrated prophage-like sequences in “<italic toggle="yes">candidatus</italic> liberibacter asiaticus”
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/6b3a4723142f407780f885b604962902
work_keys_str_mv	AT mariandominguezmirazo functionalandcomparativegenomicanalysisofintegratedprophagelikesequencesinitalictoggleyescandidatusitalicliberibacterasiaticus AT rongjin functionalandcomparativegenomicanalysisofintegratedprophagelikesequencesinitalictoggleyescandidatusitalicliberibacterasiaticus AT joshuasweitz functionalandcomparativegenomicanalysisofintegratedprophagelikesequencesinitalictoggleyescandidatusitalicliberibacterasiaticus
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Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “<italic toggle="yes">Candidatus</italic> Liberibacter asiaticus”

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