Computer Science Applications


Publications
35

Integrated Transcriptome and Metabolome Analysis Reveals Phenylpropanoid Biosynthesis and Phytohormone Signaling Contribute to “Candidatus Liberibacter asiaticus” Accumulation in Citrus Fruit Piths (Fluffy Albedo)

Citation
Cui et al. (2022). International Journal of Molecular Sciences 23 (24)
Names
Ca. Liberibacter asiaticus
Abstract
“Candidatus Liberibacter asiaticus” (CLas) is a phloem-restricted α-proteobacterium that is associated with citrus huanglongbing (HLB), which is the most destructive disease that affects all varieties of citrus. Although midrib is usually used as a material for CLas detection, we recently found that the bacterium was enriched in fruits, especially in the fruit pith. However, no study has revealed the molecular basis of these two parts in responding to CLas infection. Therefore, we performed tran

Biological Features and In Planta Transcriptomic Analyses of a Microviridae Phage (CLasMV1) in “Candidatus Liberibacter asiaticus”

Citation
Wang et al. (2022). International Journal of Molecular Sciences 23 (17)
Names
Ca. Liberibacter asiaticus
Abstract
“Candidatus Liberibacter asiaticus” (CLas) is the causal agent of citrus Huanglongbing (HLB, also called citrus greening disease), a highly destructive disease threatening citrus production worldwide. A novel Microviridae phage (named CLasMV1) has been found to infect CLas, providing a potential therapeutic strategy for CLas/HLB control. However, little is known about the CLasMV1 biology. In this study, we analyzed the population dynamics of CLasMV1 between the insect vector of CLas, the Asian c

Transgenic Sweet Orange Expressing the Sarcotoxin IA Gene Produces High-Quality Fruit and Shows Tolerance to ‘Candidatus Liberibacter asiaticus’

Citation
Longhi et al. (2022). International Journal of Molecular Sciences 23 (16)
Names
Ca. Liberibacter asiaticus
Abstract
Huanglongbing (otherwise known as HLB or greening) is currently the most devastating citrus disease worldwide. HLB is primarily associated with the phloem-inhabiting bacterium ‘Candidatus Liberibacter asiaticus’ (CLas). Currently, there are no citrus species resistant to CLas. Genetic transformation is one of the most effective approaches used to induce resistance against plant diseases. Antimicrobial peptides (AMPs) have shown potential breakthroughs to improve resistance to bacterial diseases

Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus “CandidatusAccumulibacter”

Citation
Petriglieri et al. (2022). mSystems 7 (3)
Names
“Accumulibacter” “Accumulibacter adiacens” “Accumulibacter meliphilus” “Accumulibacter propinquus” “Accumulibacter contiguus” “Accumulibacter vicinus” “Accumulibacter cognatus” “Accumulibacter affinis” “Accumulibacter proximus” “Accumulibacter necessarius” “Accumulibacter iunctus” “Accumulibacter similis” “Accumulibacter conexus” “Propionivibrio dominans” “Accumulibacter adjunctus” “Proximibacter danicus” “Proximibacter”
Abstract
“CandidatusAccumulibacter” is the most studied PAO, with a primary role in biological nutrient removal. However, the species-level taxonomy of this lineage is convoluted due to the use of different phylogenetic markers or genome sequencing approaches. Here, we redefined the phylogeny of these organisms, proposing a comprehensive approach which could be used to address the classification of other diverse and uncultivated lineages.

The Upregulated Expression of the Citrus RIN4 Gene in HLB Diseased Citrus Aids Candidatus Liberibacter Asiaticus Infection

Citation
Cheng et al. (2022). International Journal of Molecular Sciences 23 (13)
Names
Liberibacter Ca. Liberibacter asiaticus
Abstract
The citrus industry has been threatened by Huanglongbing (HLB) for over a century. Here, an HLB-induced Arabidopsis RPM1-interacting protein 4 (RIN4) homologous gene was cloned from Citrus clementina, and its characteristics and function were analyzed to determine its role during citrus–Candidatus Liberibacter asiaticus (CLas) interactions. Quantitative real-time PCR showed that RIN4 was expressed in roots, stems, leaves and flowers, with the greatest expression level in leaves. Its expression w

The Longitudinal Dividing Bacterium Candidatus Thiosymbion Oneisti Has a Natural Temperature-Sensitive FtsZ Protein with Low GTPase Activity

Citation
Wang et al. (2022). International Journal of Molecular Sciences 23 (6)
Names
Ca. Thiosymbion Ca. Thiosymbion oneisti
Abstract
FtsZ, the bacterial tubulin-homolog, plays a central role in cell division and polymerizes into a ring-like structure at midcell to coordinate other cell division proteins. The rod-shaped gamma-proteobacterium Candidatus Thiosymbion oneisti has a medial discontinuous ellipsoidal “Z-ring.” Ca. T. oneisti FtsZ shows temperature-sensitive characteristics when it is expressed in Escherichia coli, where it localizes at midcell. The overexpression of Ca. T. oneisti FtsZ interferes with cell division a

Structure of Lipopolysaccharide from Liberibacter crescens Is Low Molecular Weight and Offers Insight into Candidatus Liberibacter Biology

Citation
Black et al. (2021). International Journal of Molecular Sciences 22 (20)
Names
Liberibacter Ca. Liberibacter asiaticus
Abstract
Huanglongbing (HLB) disease, also known as citrus greening disease, was first reported in the US in 2005. Since then, the disease has decimated the citrus industry in Florida, resulting in billions of dollars in crop losses and the destruction of thousands of acres of citrus groves. The causative agent of citrus greening disease is the phloem limited pathogen Candidatus Liberibacter asiaticus. As it has not been cultured, very little is known about the structural biology of the organism. Liberib

Deciphering Symbiotic Interactions of “ Candidatus Aenigmarchaeota” with Inferred Horizontal Gene Transfers and Co-occurrence Networks

Citation
Li et al. (2021). mSystems 6 (4)
Names
Ca. Aenigmarchaeota
Abstract
Recent advances in sequencing technology promoted the blowout discovery of super tiny microbes in the Diapherotrites , Parvarchaeota , Aenigmarchaeota , Nanoarchaeota , and Nanohaloarchaeota (DPANN) superphylum. However, the unculturable properties of the majority of microbes impeded our investigation of their behavior and symbiotic lifestyle in the corresponding c

Comparative Genomics Reveals Thermal Adaptation and a High Metabolic Diversity in “ Candidatus Bathyarchaeia”

Citation
Qi et al. (2021). mSystems 6 (4)
Names
Bathyarchaeia
Abstract
Ca . Bathyarchaeia MAGs from terrestrial hot spring habitats are poorly revealed, though they have been studied extensively in marine ecosystems.

Differential Response of Grapevine to Infection with ‘Candidatus Phytoplasma solani’ in Early and Late Growing Season through Complex Regulation of mRNA and Small RNA Transcriptomes

Citation
Dermastia et al. (2021). International Journal of Molecular Sciences 22 (7)
Names
Ca. Phytoplasma solani
Abstract
Bois noir is the most widespread phytoplasma grapevine disease in Europe. It is associated with ‘Candidatus Phytoplasma solani’, but molecular interactions between the causal pathogen and its host plant are not well understood. In this work, we combined the analysis of high-throughput RNA-Seq and sRNA-Seq data with interaction network analysis for finding new cross-talks among pathways involved in infection of grapevine cv. Zweigelt with ‘Ca. P. solani’ in early and late growing seasons. While t