Computer Science Applications


Publications
33

Metagenomics Revealed a New Genus ‘Candidatus Thiocaldithrix dubininis’ gen. nov., sp. nov. and a New Species ‘Candidatus Thiothrix putei’ sp. nov. in the Family Thiotrichaceae, Some Members of Which Have Traits of Both Na+- and H+-Motive Energetics

Citation
Ravin et al. (2023). International Journal of Molecular Sciences 24 (18)
Names
Ca. Thiothrix putei Ca. Thiocaldithrix dubininis
Abstract
Two metagenome-assembled genomes (MAGs), GKL-01 and GKL-02, related to the family Thiotrichaceae have been assembled from the metagenome of bacterial mat obtained from a sulfide-rich thermal spring in the North Caucasus. Based on average amino acid identity (AAI) values and genome-based phylogeny, MAG GKL-01 represented a new genus within the Thiotrichaceae family. The GC content of the GKL-01 DNA (44%) differed significantly from that of other known members of the genus Thiothrix (50.1–55.6%).

Effects of Candidatus Liberibacter asiaticus infection on metagenome of Diaphorina citri gut endosymbiont

Citation
Pan et al. (2023). Scientific Data 10 (1)
Names
Ca. Liberibacter asiaticus
Abstract
AbstractAsian citrus psyllid (Diaphorina citri, D. citri) is the important vector of “Candidatus Liberibacter asiaticus” (CLas), associated with Huanglongbing, the most devastating citrus disease worldwide. CLas can affect endosymbiont abundance of D. citri. Here, we generated the high-quality gut endosymbiont metagenomes of Diaphorina citri on the condition of CLas infected and uninfected. The dataset comprised 6616.74 M and 6586.04 M raw reads, on overage, from CLas uninfected and infected psy

Diversity Analysis and Function Prediction of Bacterial Communities in the Different Colored Pericarp of Citrus reticulata cv. ‘Shatangju’ Due to ‘Candidatus Liberibacter asiaticus’ Infection

Citation
Wang et al. (2023). International Journal of Molecular Sciences 24 (14)
Names
Ca. Liberibacter asiaticus Liberibacter
Abstract
Huanglongbing (HLB), caused by the Candidatus Liberibacter spp., is the most devastating disease in the citrus industry. HLB significantly affects and alters the microbial community structure or potential function of the microbial community of leaves and roots. However, it is unknown how the microbial community structure of the pericarp with different pigments is affected by Candidatus Liberibacter asiaticus (CLas). This study identified the enriched taxa of the microbial community in the citrus

Distribution, abundance, and ecogenomics of the Palauibacterales , a new cosmopolitan thiamine-producing order within the Gemmatimonadota phylum

Citation
Aldeguer-Riquelme et al. (2023). mSystems
Names
Palauibacter ramosifaciens Palauibacter polyketidifaciens Kutchimonas denitrificans Ts Carthagonibacter metallireducens Ts Palauibacter denitrificans Palauibacter irciniicola Palauibacter australiensis Palauibacter poriticola Palauibacter rhopaloidicola Palauibacter scopulicola Palauibacter soopunensis Ts Benthicola azotiphorus Indicimonas acetifermentans Ts Benthicola marisminoris Ts Caribbeanibacter nitroreducens Ts Humimonas hydrogenitrophica Ts Kutchimonas Indicimonas Carthagonibacter Caribbeanibacter Humimonas Benthicola Palauibacter Palauibacterales Palauibacteraceae
Abstract
ABSTRACT The phylum Gemmatimonadota comprises mainly uncultured microorganisms that inhabit different environments such as soils, freshwater lakes, marine sediments, sponges, or corals. Based on 16S rRNA gene studies, the group PAUC43f is one of the most frequently retrieved Gemmatimonadota in marine samples. However, its physiology and ecological roles are completely unknown since, to date, not a single PAUC43f isolate or me

Spatial Distribution and Temporal Dynamics of Candidatus Liberibacter Asiaticus in Different Stages of Embryos, Nymphs and Adults of Diaphorina citri

Citation
Nian et al. (2023). International Journal of Molecular Sciences 24 (10)
Names
Ca. Liberibacter asiaticus Liberibacter
Abstract
Huanglongbing, a globally devastating citrus disease, is associated with Candidatus Liberibacter asiaticus (CLas) and is mainly transmitted by Diaphorina citri. Verification of the distribution and dynamics of CLas in D. citri is critical to understanding CLas transmitted by vectors in nature. Here, the distribution and titers of CLas in different sexes and tissues of D. citri adults were investigated by fluorescence in-situ hybridization (FISH) and quantitative real-time PCR (qRT-PCR). Results

Metagenomic Discovery of “ Candidatus Parvarchaeales”-Related Lineages Sheds Light on Adaptation and Diversification from Neutral-Thermal to Acidic-Mesothermal Environments

Citation
Rao et al. (2023). mSystems 8 (2)
Names
“Rehaiarchaeum” “Jingweiarchaeales” “Haiyanarchaeaceae” “Jingweiarchaeum” “Haiyanarchaeum” “Parvarchaeum tengchongense” “Jingweiarchaeum tengchongense” “Haiyanarchaeum thermophilum” “Parvarchaeales”
Abstract
“ Candidatus Parvarchaeales” microbes may represent a lineage uniquely distributed in extreme environments such as AMD and hot springs. However, little is known about the strategies and processes of how they adapted to these extreme environments.

Identification of the Actin-Binding Region and Binding to Host Plant Apple Actin of Immunodominant Transmembrane Protein of ‘Candidatus Phytoplasma mali’

Citation
Boonrod et al. (2023). International Journal of Molecular Sciences 24 (2)
Names
Ca. Phytoplasma mali
Abstract
‘Candidatus Phytoplasma mali’ (‘Ca. P. mali’) has only one major membrane protein, the immunodominant membrane protein (Imp), which is regarded as being close to the ancestor of all phytoplasma immunodominant membrane proteins. Imp binds to actin and possibly facilitates its movement in the plant or insect host cells. However, protein sequences of Imp are quite diverse among phytoplasma species, thus resulting in difficulties in identifying conserved domains across species. In this work, we comp

Comparative Genomic Insights into the Evolution of Halobacteria -Associated “ Candidatus Nanohaloarchaeota”

Citation
Zhao et al. (2022). mSystems 7 (6)
Names
Ca. Nanohaloarchaeota
Abstract
The DPANN superphylum is a group of archaea widely distributed in various habitats. They generally have small cells and have a symbiotic lifestyle with other archaea.

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