Publications

3805

The complete genome sequence of “ Candidatus Phytoplasma aurantifolia” TB2022, which consists of one 670,073-bp circular chromosome, is presented in this work. This bacterium is associated with sweet potato little leaf disease in Fujian Province, China.

Here, we announce the draft genome sequence of “ Candidatus Liberibacter asiaticus” strain GZQL4, which was collected from Guizhou, China. The GZQL4 strain has a genome size of 1,234,029 bp, a G+C content of 36.5%, 1,204 predicted open reading frames, and 53 RNA genes.

AbstractDuring the past two decades, a high mortality of coconut palms was observed in the coastal areas of Equatorial Guinea. Reportedly, the palm population has been reduced by 60%–70%, and coconut production has decreased accordingly. To identify the cause of the mortality, a survey was carried out in April 2021 in various localities of the coconut belt. Molecular analyses carried out on 16S rRNA and secA genes detected phytoplasma presence in the majority of the samples. Sequencing and BLAST search of the 16S rRNA gene sequences showed >99% identity of the detected phytoplasmas to ‘Candidatus Phytoplasma palmicola’. The RFLP analyses of 16S ribosomal gene using Tru1I and TaqI enzymes led to assign these phytoplasmas to subgroup 16SrXXII‐A. In all samples that tested positive, including one from a hybrid coconut palm and two from oil palm the same phytoplasma was identified. The phylogenetic analyses of 16S rRNA and secA genes confirmed respectively 99.98%–100% and 97.94%–100% identity to ‘Ca. P. palmicola’. RFLP analyses using MboII enzyme on the secA gene amplicon differentiated the phytoplasma found in Equatorial Guinea from those present in Ghana and Ivory Coast. The Equatorial Guinean phytoplasma strain resulted to be identical to the strains from Mozambique, confirming the presence of a geographic differentiation among phytoplasma strains in the coastal areas of Western and Central Africa. The identified phytoplasma is different from the ‘Ca. P. palmicola’ strains found in Ghana and Ivory Coast and represents the first identification a 16SrXXII‐A strain in Equatorial Guinea and in Central Africa. Strict monitoring and surveillance procedures for early detection of the pathogen are strongly recommended to reduce its impact and further spread in the country and permit the recovery of coconut plantations.

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 pericarp with normal or abnormal pigment and determine the effects of HLB on the pericarp microbial community using 16S rRNA-seq. The alpha and beta diversity and composition of microbial communities were significantly different between normal and abnormal pigment pericarp tissues of ripe fruits infected by CLas. Firmicutes, Actinobacteriota, Bacteroidota, Acidobacteriota, and Desulfobacterota dominated the pericarp microbiota composition in WDYFs (whole dark yellow fruits) samples. The relative abundance of most genera in WDYFs was higher than 1%, such as Burkholderia, and Pelomonas. However, with the exception of the HLB pathogen, the relative abundance of most genera in the abnormal-colored pericarp samples was less than 1%. CLas decreased the relative abundance of pericarp taxonomic. The predicted function of microbial was more plentiful and functional properties in the WDYF sample, such as translation, ribosomal structure and biogenesis, amino acid transport and metabolism, energy production and conversion, and some other clusters of orthologous groups (COG) except for cell motility. The results of this study offer novel insights into understanding the composition of microbial communities of the CLas-affected citrus pericarps and contribute to the development of biological control strategies for citrus against Huanglongbing.

Abstract Objectives: “Candidatus Liberibacter asiaticus” (CLas) is an un-culturable α-proteobacterium that caused citrus Huanglongbing (HLB), a destructive disease threatening citrus production worldwide. In China, the presence of HLB was first reported in Chaoshan region of Guangdong province, China around a century ago. Thus, whole genome information of CLas strains from Chaoshan area become the most important resource to understand the population diversity and evaluation of CLas in China. Data description: CLas strain GDCZ was originally from Chaozhou city (Chaoshan area) and sequenced using Pacbio Sequel long-read sequencing and Illumina short-read sequencing. The genome of strain GDCZ comprised of 1,230,507 bp with an average G+C content of 36.4%, along with a circular CLasMV1 phage: CLasMV1_GDCZ (8,869 bp). The CLas strain GDCZ contained a Type 2 prophage (37,452 bp) and encoded a total of 1,057 open reading frames and 53 RNA genes. The whole genome sequence of CLas strain GDCZ from the historical HLB endemic region in China will serve as a useful resource for further analyses of CLas evolution and HLB epidemiology in China and world.

AbstractCandidatusLiberibacter asiaticus (CLas) is the causal agent of the devastating citrus Huanglongbing (HLB) disease. Our understanding of the pathogenicity mechanism and biology of CLas remain limited because CLas has not been cultured in artificial media. CLas encodes 1136 proteins of which 415 have unknown functions. Since genetic studies of CLas genes with unknown functions are impossible, we utilized genome-wide protein-protein interactions (PPIs) yeast-two-hybrid (Y2H) assays to help solve the mystery. PPIs are fundamental to all cellular processes and machinery and instrumental in investigating uncharacterized proteins and inferring biological pathways. In total, 916 bait and 936 prey proteins were included in the three-phase screening, which identified 4245 interactions. The false positive rate of the Y2H assay was estimated to be 3.1%. Pull-down assays confirmed the robustness of our Y2H. The average interactions per node for CLas Y2H interactome were approximately 15.6, significantly higher than free-living bacteria, indicating genome reduction has led to a multi-function of proteins. PPIs provide clues for functions of 371 uncharacterized proteins of CLas. Forty HUB node proteins were identified which might play critical roles in CLas, including a quinone oxidoreductase and LysR that are known to protect bacteria against oxidative stress. This explains why CLas survives well in the phloem even though it triggers immune-mediated disease, systemic and chronic production of reactive oxygen species, and phloem cell death. This PPI database facilitates the investigation of CLas cellular biochemistry and physiology, functions of uncharacterized proteins, and pathogenicity mechanisms of the pathogen.

Bamboo is used for making structures, furniture, handicrafts, and ropes, as well as a source of food in the Philippines. One of the emerging diseases of bamboo in the country is the bamboo witches’ broom (BWB), which has been occasionally noted in three genera of bamboo – including Dendrocalamus, Gigantochloa, and Schizostachyum from various provinces in the Philippines (Ilocos Norte, Laguna, Batangas, Quezon, Agusan del Sur, Bukidnon, and South Cotabato) since the 1990s. However, studies and information about BWB in the country remain lacking and largely unexplored. In this study, we report a similar disease affecting Dendrocalamus and Gigantochloa bamboo species from Bohol and Davao and – for the first time – in Dendrocalamus merrillianus ("bayog") and Bambusa spinosa ("kawayan-tinik") from Isabela and Nueva Vizcaya. As a result of the surveys conducted from 1999–2019, the disease is now identified in six species across four genera of bamboo – namely, Gigantochloa spp. (G. levis and G. atter), Dendrocalamus spp. (D. asper and D. merrillianus), Schizostachyum lumampao, and Bambusa spinosa recorded in 11 provinces in the Philippines. The BWB symptoms include clustering of leaves forming a rosette-like structure, leaf proliferation, excessive limb formation from a single node, and shortening of internodes. Nested PCR using the universal primers P1/P7 and R16MF2/R1 targeting the phytoplasma 16S ribosomal RNA gene revealed positive amplification in five symptomatic BWB samples from Isabela, Philippines. Subsequent sequencing (~ 1.3kbp) and phylogenetic analysis using the representative BWB isolates from Isabela revealed > 98.65% genetic similarity and clustering to Candidatus Phytoplasma luffae, which belongs to the 16SrVIII group (Loofah Witches’ Broom Group). This paper determined the distribution of BWB in different species of bamboo in the Philippines, as well as the association of 'Ca. Phytoplasma luffae'-related strain (16SrVIII) to BWB.