scholarly journals Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “Candidatus Liberibacter asiaticus”

mSphere ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Marian Dominguez-Mirazo ◽  
Rong Jin ◽  
Joshua S. Weitz
Keyword(s):  
Causative Agent ◽  
De Novo ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Sequence Type ◽  
Comparative Genomic ◽  
Citrus Production ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
Prediction Approach

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.”

scholarly journals Functional and comparative genomic analysis of integrated prophage-like sequences in Candidatus Liberibacter asiaticus

2019 ◽  
Author(s):  
Marian Dominguez-Mirazo ◽  
Rong Jin ◽  
Joshua S. Weitz
Keyword(s):  
De Novo ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Sequence Type ◽  
Comparative Genomic ◽  
Candidatus Liberibacter Asiaticus ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
Prediction Approach

AbstractHuanglongbing (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen Candidatus Liberibacter asiaticus (CLas) is an alphapro-teobacterium of the Rhizobiaceae family that has been identified as the cause. The virulence of CLas has been attributed, in part, to prophage encoded genes. Prophage and prophage like elements have been identified in 12 of the 15 CLas available genomes, and are classified into three prophage types. Here, we re-examined all 15 CLas genomes using a de novo prediction approach and expanded the number of prophage like elements from 16 to 33. Further, we find that all CLas contain at least one prophage-like sequence. Comparative analysis reveals 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 CLas strain that had previously been reported as lacking prophages. Our findings provide both a resource and new insights into the evolutionary relationship between phage and CLas pathogenicity.

scholarly journals Discovery of Novel GMPS Inhibitors of Candidatus Liberibacter Asiaticus by Structure Based Design and Enzyme Kinetic

Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 594
Author(s):  
Jing Nan ◽  
Shaoran Zhang ◽  
Ping Zhan ◽  
Ling Jiang
Keyword(s):  
Folic Acid ◽  
Enzyme Assay ◽  
De Novo ◽  
Enzyme Kinetic ◽  
Candidatus Liberibacter Asiaticus ◽  
De Novo Synthesis ◽  
Citrus Production ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
High Inhibition

Citrus production is facing an unprecedented problem because of huanglongbing (HLB) disease. Presently, no effective HLB-easing method is available when citrus becomes infected. Guanosine 5′-monophosphate synthetase (GMPS) is a key protein in the de novo synthesis of guanine nucleotides. GMPS is used as an attractive target for developing agents that are effective against the patogen infection. In this research, homology modeling, structure-based virtual screening, and molecular docking were used to discover the new inhibitors against CLas GMPS. Enzyme assay showed that folic acid and AZD1152 showed high inhibition at micromole concentrations, with AZD1152 being the most potent molecule. The inhibition constant (Ki) value of folic acid and AZD1152 was 51.98 µM and 4.05 µM, respectively. These results suggested that folic acid and AZD1152 could be considered as promising candidates for the development of CLas agents.

scholarly journals Evidence that inconsistent gene prediction can mislead analysis of algal genomes

2019 ◽  
Author(s):  
Yibi Chen ◽  
Raúl A. González-Pech ◽  
Timothy G. Stephens ◽  
Debashish Bhattacharya ◽  
Cheong Xin Chan
Keyword(s):  
De Novo ◽  
Gene Prediction ◽  
Genomic Analysis ◽  
Gene Families ◽  
Comparative Genomic ◽  
Homologous Gene ◽  
Genome Data ◽  
Biological Interpretation ◽  
Gene Models ◽  
Prediction Approach

AbstractComparative algal genomics often relies on predicted gene models from de novo assembled genomes. However, the artifacts introduced by different gene-prediction approaches, and their impact on comparative genomic analysis, remain poorly understood. Here, using available genome data from six dinoflagellate species in Symbiodiniaceae, we identified potential methodological biases in the published gene models that were predicted using different approaches. We developed and applied a comprehensive customized workflow to predict genes from these genomes. The observed variation among predicted gene models resulting from our workflow agreed with current understanding of phylogenetic relationships among these taxa, whereas those published earlier were largely biased by the distinct approaches used in each instance. Importantly, these biases mislead the inference of homologous gene families and synteny among genomes, thus impacting biological interpretation of these data. Our results demonstrate that a consistent gene-prediction approach is critical for comparative genomics, particularly for non-model algal genomes.

scholarly journals Susceptibility of Sixteen Citrus Genotypes to ‘Candidatus Liberibacter asiaticus’

Plant Disease ◽  
2016 ◽  
Vol 100 (6) ◽  
pp. 1080-1086 ◽  
Author(s):  
Greg McCollum ◽  
Mark Hilf ◽  
Mike Irey ◽  
Weiqi Luo ◽  
Tim Gottwald
Keyword(s):  
The United States ◽  
Insect Vector ◽  
Candidatus Liberibacter Asiaticus ◽  
Citrus Germplasm ◽  
Citrus Production ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
Florida Citrus ◽  
Citrus Macrophylla ◽  
Free Ranging

Huanglongbing (HLB) disease is the most serious threat to citrus production worldwide and, in the last decade, has devastated the Florida citrus industry. In the United States, HLB is associated with the phloem-limited α-proteobacterium ‘Candidatus Liberibacter asiaticus’ and its insect vector, the Asian citrus psyllid (ACP; Diaphorina citri). Significant effort is being put forth to develop novel citrus germplasm that has a lower propensity to succumb to HLB than do currently available varieties. Effective methods of screening citrus germplasm for susceptibility to HLB are essential. In this study, we exposed small, grafted trees of 16 citrus types to free-ranging ACP vectors and ‘Ca. L. asiaticus’ inoculum in the greenhouse. During 45 weeks of exposure to ACP, the cumulative incidence of ‘Ca. L. asiaticus’ infection was 70%. Trees of Citrus macrophylla and C. medica were most susceptible to ‘Ca. L. asiaticus’, with 100% infection by the end of the test period in three trials, while the complex genetic hybrids ‘US 1-4-59’ and ‘Fallglo’ consistently were least susceptible, with approximately 30% infection. Results obtained in this greenhouse experiment showed good agreement with trends observed in the orchard, supporting the validity of our approach for screening citrus germplasm for susceptibility to HLB.

scholarly journals Genomic analysis of Landes goose origin goose hemorrhagic polyomavirus, China

2021 ◽  
Author(s):  
Ling Luo ◽  
Xinglong Yu ◽  
Xiang Qu ◽  
Fei Zhao ◽  
Yan Ding ◽  
...  
Keyword(s):  
Causative Agent ◽  
Mainland China ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Laboratory Diagnostics ◽  
First Time ◽  
Landes Geese ◽  
Hatching Rates

A goose hemorrhagic polyomavirus (GHPV) outbreak occurred in a Goose Farm in Hunan, China, between January and July 2021. Approximately 1,500 breeding goose died, and hatching rates dropped from the previous 85% to about 50% in this outbreak. GHPV HUN-01, isolated from the liver of infected Landes geese, shared a close evolutionary relationship with the Toulouse Goose 2000 and 14234 strain, isolated from geese in France and Hungary. The isolation of GHPV from the livers of dead embryos also demonstrates that the virus can be transmitted vertically. In conclusion, clinical and laboratory diagnostics of the diseased geese in this outbreak were consistent with GHPV being the causative agent. We learned that this is the first time that GHPV has been isolated from geese in mainland China.

scholarly journals Genome assembly of the JD17 soybean provides a new reference genome for Comparative genomics

2021 ◽  
Author(s):  
Xinxin Yi ◽  
Jing Liu ◽  
Shengcai Chen ◽  
Hao Wu ◽  
Min Liu ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
High Quality ◽  
Genome Wide ◽  
A Genome ◽  
Cultivated Soybean

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromsome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with three published soybeans (WM82, ZH13 and W05) , which identified five large inversions and two large translocations specific to JD17, 20,984 - 46,912 PAVs spanning 13.1 - 46.9 Mb in size, and 5 - 53 large PAV clusters larger than 500kb. 1,695,741 - 3,664,629 SNPs and 446,689 - 800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation (SNF) genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.

scholarly journals Historical Perspectives, Management, and Current Research of Citrus HLB in Guangdong Province of China, Where the Disease has been Endemic for Over a Hundred Years

2018 ◽  
Vol 108 (11) ◽  
pp. 1224-1236 ◽  
Author(s):  
Zheng Zheng ◽  
Jianchi Chen ◽  
Xiaoling Deng
Keyword(s):  
Southern China ◽  
Candidatus Liberibacter Asiaticus ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
Historical Perspectives ◽  
Citrus Production ◽  
Candidatus Liberibacter ◽  
Citrus Huanglongbing ◽  
Liberibacter Asiaticus ◽  
Generation Sequencing

Citrus huanglongbing (HLB) is a highly destructive disease currently threatening citrus production worldwide. In China, the disease is exclusively associated with ‘Candidatus Liberibacter asiaticus’, a nonculturable proteobacterium. HLB was observed in Guangdong of China over a hundred years ago. Researchers and citrus growers have been battling with the disease through vigorous research and have exercised various control practices. Much of the early work was not well known outside China. This review is intended to fill in gaps of historical information by reviewing selected literature records. Along the way, the HLB system within southern China was evaluated. Emphases were on comparison of symptomatology, evolution of etiology, control practices, and impacts of using next-generation sequencing technology for ‘Ca. L. asiaticus’ research and detection.

scholarly journals Screen Mesh Size for Exclusion of Diaphorina citri (Hemiptera: Liviidae) in Citrus Production

2020 ◽  
Vol 113 (4) ◽  
pp. 2026-2030
Author(s):  
Timothy A Ebert ◽  
Laura Waldo ◽  
Daniel Stanton ◽  
Arnold W Schumann
Keyword(s):  
Tree Mortality ◽  
Mesh Size ◽  
Diaphorina Citri ◽  
Short Side ◽  
Vector Management ◽  
Citrus Production ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
Pass Through ◽  
Individual Trees

Abstract Huanglongbing is a citrus disease that reduces yield, crop quality, and eventually causes tree mortality. The putative causal agent, Candidatus Liberibacter asiaticus (Rhizobiales: Rhizobiaceae), is vectored by the Asian citrus psyllid, Diaphorina citri Kuwayama. Disease management is largely through vector control, but the insect is developing pesticide resistance. A nonchemical approach to vector management is to grow citrus under screen cages either as bags over individual trees or enclosures spanning many acres. The enclosing screen reduces wind, alters temperature relative to ambient, and excludes a variety of pests that are too large to pass through the screen. Here we evaluated the potential of six screens to exclude D. citri. We conclude that screens with rectangular openings need to limit the short side to no more than 384.3 µm with a SD of 36.9 µm (40 mesh) to prevent psyllids from passing through the screen. The long side can be at least 833 µm, but the efficacy of screens exceeding this value should be tested before using in the field.

scholarly journals Genome Sequence Resource of “Candidatus Liberibacter asiaticus” strain Myan16 from Myanmar

Plant Disease ◽  
2020 ◽  
Author(s):  
Yongqin Zheng ◽  
jun guo ◽  
Xiaoling Deng ◽  
Zheng Zheng
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Sequence Database ◽  
Candidatus Liberibacter Asiaticus ◽  
Genome Sequence Database ◽  
Citrus Production ◽  
Candidatus Liberibacter ◽  
Citrus Huanglongbing ◽  
Liberibacter Asiaticus

“Candidatus Liberibacter asiaticus” (CaLas), an uncultured α-proteobacterium, is associated with citrus Huanglongbing (HLB, yellow shoot disease), a destructive disease threatening citrus production worldwide. Here, we reported the draft genome sequence of CaLas strain Myan16 from a HLB-affected lime tree in Myitkyina, Kachin State, Myanmar. The strain Myan16 genome is 1,229,102 bp with an average G+C content of 36.4%, along with a circular prophage: P-Myan16-2 (36,303 bp, Type 2). This is the first genome sequence of CaLas strain from Myanmar, which will enrich the current CaLas genome sequence database and facilitate HLB epidemiology research in Asia and world.

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