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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #411895
Research Project: Identifying Vulnerabilities in Vector-host-pathogen Interactions of Grapevine and Citrus Pathosystems to Advance Sustainable Management Strategies

Location: Crop Diseases, Pests and Genetics Research

Title: The complete genome sequence of ‘Candidatus Liberibacter asiaticus’ strain 9PA and its application in characterization of the prevalent strains in the Brazilian citriculture

Author
item DUTRA, MICHELE - Universidade Estadual Paulista (UNESP)
item SILVA, PRISCILA - Universidade De Campinas (UNICAMP)
item Chen, Jianchi
item WULFF, NELSON - Fundecitrus - Brazil

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/8/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary: Citrus huanglongbing (HLB) is a severe disease affecting citrus production around the world. The disease is caused by a non-culturable bacterium. Genome sequences of HLB pathogen are key resources for academic research and disease control. This study reports the complete whole genome sequence of HLB pathogen strain 9PA from Brazil, along sequences of three viruses infecting the HLB pathogen. Highly variable regions in the 9PA genomes were found. The variation information from these regions was used to evaluate 68 samples from high HLB incidence areas in Sao Paulo state, Brazil. The new genome resource and knowledge derived from sequence analyses will have important impact on HLB management in Brazil and citrus production countries around the world.

Technical Abstract: The unculturable alfa-proteobacterium 'Candidatus Liberibacter asiaticus' is associated citrus huanglongbing (HLB), a severe disease with global implications, particularly affecting citrus production in Brazil. This study reports the complete genome of the first Brazilian strain of CLas, known as 9PA. Within this strain, two prophages, P-9PA-1 and P-9PA-3, were identified. P-9PA-1 was found to be both integrated and circularized, while P-9PA-3 occurs exclusively in a circularized form. Notably, these prophages show high identity with their cognate prophages, SC1 (83%) from Florida and P-JXGC-3 (98%). Comparative analysis of the 9PA strain with 13 other complete genomes in GenBank revealed 9,091 mismatches and 992 gaps/insertions, highlighting eight locally collinear blocks, among which, six are in the prophage region. The whole genome phylogenetic analysis categorized the 13 CLas genomes into two clusters with 9PA belonging to a cluster primarily represented by strains from China and the USA. Moreover, whole-genomic comparison found six Hyper Variable Regions (HVRs), three in the prophage region and three in chromosome. These HVRs were used to assess 68 samples from high HLB incidence areas in Sao Paulo state. Strain 9PA is in the second most prevalent group (A), accounting for 20.6% of samples, while the most prevalent group (B) made up 41.2%. Three HVRs, namely HVR_4, HVR_6, and HVR_7, can be employed to determine prophage occurrence in CLas strains based on fragment analysis. On the other hand, HVR_M is a region encompassing a novel Microviridae recently reported in CLas genomes. Characterizing these HVRs in CLas may yield insights into their interactions with prophage elements, evolutionary processes, and adaptation to host plants and insects.