Draft Whole-Genome Sequence of “Candidatus Liberibacter asiaticus” Strain TX1712 from Citrus in Texas

Cai, Weili; Yan, Z.; Rascoe, J.; Stulberg, Michael J.

doi:10.1128/genomea.00554-18

Cited by 7 publications

(1 citation statement)

References 10 publications

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“…Raw read data sets of C Las genomes derived from citrus tissues were accessed from the National Center for Biotechnology and Information (NCBI) Sequence Read Archive (SRA) 42 using accession numbers SRR016816, SRR7050882, SRR8177702, SRR9641236, and SRR9673120. These Illumina reads represent C Las genomic data from an unknown C Las strain identified in Citrus sinensis in Florida, USA, strain TX1712 collected from C. sinensis in Texas, USA 43 , strain YNJS7C identified in C. sinensis from Yunnan province, China 44 , strain AHCA17 identified in C. maxima (pummelo) in California, USA 45 , and strain TaiYZ2 collected from C. maxima (pummelo) in Songkhla province, Thailand 46 , respectively.…”

Section: Methodsmentioning

confidence: 99%

Direct DNA sequencing of ‘Candidatus Liberibacter asiaticus’ from Diaphorina citri, the Asian citrus psyllid, and its implications for citrus greening disease management

Higgins

Mann

Heck

2022

Preprint

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The Asian citrus psyllid, Diaphorina citri is an invasive insect 1 and a vector of ’Candidatus Liberibacter asiaticus’ (CLas), a bacterium whose growth in Citrus species results in citrus greening disease 2,3. Methods to enrich and sequence CLas from D. citri often rely on biased genome amplification 4 and nevertheless contain significant quantities of host DNA 5,6. To overcome these hurdles, we developed a simple pre-treatment DNase and filtration (hereafter PDF) protocol to directly sequence CLas and the complete, primarily uncultivable, microbiome from D. citri adults. The PDF protocol yielded CLas abundances upwards of 60% and enabled detection of 156 genetic variants in these strains compared to progenitor strains in Florida, which included prophage encoding regions with key functions in CLas pathogenesis, putative antibiotic resistance loci, and a single secreted effector. These variants suggest laboratory propagation of CLas may result in different phenotypic trajectories among laboratories, and may confound CLas physiology or therapeutic design and evaluation if these differences remain undocumented. Finally, we obtained genetic signatures affiliated with Citrus nuclear and organellar genomes, entomopathogenic fungal mitochondria, and commensal bacteria from laboratory-reared and field-collected D. citri adults. Hence, the PDF protocol can inform agricultural management strategies related to pathogen evolution 7, insect microbiome surveillance 8, antibiotic resistance screening 9, and gut content analysis 10.

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Section: Methodsmentioning

confidence: 99%

Direct DNA sequencing of ‘Candidatus Liberibacter asiaticus’ from Diaphorina citri, the Asian citrus psyllid, and its implications for citrus greening disease management

Higgins

Mann

Heck

2022

Preprint

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Decreasing detection frequency of MITE (MCLas-A) in the population of ‘Candidatus Liberibacter asiaticus’ recently collected in southern China

Cui

Zeng

Liu

et al. 2020

Journal of Integrative Agriculture

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SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus

Cai

Nunziata

Rascoe

et al. 2019

Sci Rep

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Huanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘Candidatus Liberibacter asiaticus’ (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.

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Draft Whole-Genome Sequence of “Candidatus Liberibacter asiaticus” Strain TX1712 from Citrus in Texas

Cited by 7 publications

References 10 publications

Direct DNA sequencing of ‘Candidatus Liberibacter asiaticus’ from Diaphorina citri, the Asian citrus psyllid, and its implications for citrus greening disease management

Direct DNA sequencing of ‘Candidatus Liberibacter asiaticus’ from Diaphorina citri, the Asian citrus psyllid, and its implications for citrus greening disease management

Decreasing detection frequency of MITE (MCLas-A) in the population of ‘Candidatus Liberibacter asiaticus’ recently collected in southern China

SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus

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