Biology subjects

Kuo, C.-H.

Publications and source records attributed to Kuo, C.-H..

At least 19 recordsLinked to original sources

bioRxiv2026

Rhizobia transform legume nodules via native T-DNA transfer systems

Agrobacteria can deliver transfer DNA (T-DNA) into plant cells, causing tumorous growth. This process, agrobacteria-mediated transformation (AMT), underlies plant genetic engineering and has been regarded as an evolutionary innovation specific to these pathogens. By screening 63,759 alphaproteobacterial genomes for T-DNA border sequences, we identify mini-T-DNAs in diverse rhizobial genera. Each typically encodes a single cargo, a RolB/RolC family protein or a distant rhizobial homologue. We show that native rhizobia-mediated transformation (RMT) systems deliver these mini-T-DNAs into the root nodules of common bean, pea, and chickpea, where the cargo genes are expressed, with no signal in adjacent root tissue. RMT systems share VirG-dependent activation of the core virulence regulon but respond to distinct upstream signals. Our genome screen identifies many additional candidate T-DNA transfer systems, and phylogenetic analysis places their genes into two of the many type IV secretion system (T4SS) clades. RMT systems occur in both clades, together with other systems unrelated to T-DNA transfer, and typically have an ancestral-like T4SS configuration. In contrast, AMT systems occupy a single subclade, consistent with later acquisition of their T4SS module. AMT and RMT thus represent two specialized outcomes of an older, more widespread capability for bacteria-to-plant DNA transfer.

microbiology↗

bioRxiv2026

A broad-host-range Rhizobium rhizogenes strain enables transient expression across diverse crops and establishes functional assays in faba bean

Agrobacterium-mediated transient expression has revolutionized plant research, enabling numerous landmark discoveries across diverse areas of plant biology. Yet this powerful approach remains largely confined to solanaceous species, leaving most economically important crop families without a comparable rapid assay platform. Here, we show that an engineered Rhizobium rhizogenes strain, AS109, mediates efficient transient expression across diverse dicot species spanning multiple taxonomic families, consistently outperforming commonly used laboratory agrobacterial strains. Leveraging the broad host range of AS109, we establish a suite of functional assays in faba bean (Vicia faba), including protein localisation, RNA interference-mediated gene silencing, cell-surface elicitor recognition screens, nucleotide-binding leucine-rich repeat receptor (NLR) activation, and infection cell biology at the host-pathogen interface. We further demonstrate that both singleton NLRs and sensor-helper NLR pairs from Solanaceae retain effector recognition and cell death activity when transferred into faba bean, establishing a rapid platform for evaluating cross-family transferability of disease-resistance genes. AS109 thus provides an accessible and versatile chassis for functional genomics in non-model crops, bridging the widening gap between hypothesis generation and experimental validation across diverse plant species.

plant biology↗

bioRxiv2025

Comparative genomics of a poinsettia-associated phytoplasma and functional validation of its SAP11-homologous effectors that induce plant branching

Phytoplasmas are insect-transmitted plant pathogens that manipulate host development through secreted effector proteins. While they are notorious for causing agricultural losses, in the ornamental plant poinsettia (Euphorbia pulcherrima), phytoplasma infection is uniquely harnessed to induce the commercially desirable free-branching trait. However, the effectors responsible for this phenotype have remained unknown. To address this question, we sequenced and analyzed the genome of Candidatus Phytoplasma pruni PR2021, a strain associated with the high-branching cultivar Princettia Pink. Comparative genomics confirmed its species assignment and revealed an unusual effector repertoire. PR2021 lacks most previously described effectors but encodes two distinct SAP11 homologs, a family of effectors known to induce plant branching. Genomic context analysis showed that one homolog is located within a potential mobile unit (PMU) and is nearly identical to the SAP11 of the distantly related Ca. P. asteris, while the other is located outside PMU regions and is divergent in sequence and predicted structure. Functional assays using Agrobacterium-mediated transient expression in Nicotiana benthamiana demonstrated that each homolog independently induced significant branching, whereas co-expression did not enhance the phenotype, indicating overlapping functions. These findings establish a direct connection between poinsettia branching and SAP11-homologous effectors, providing the first experimental evidence linking phytoplasma effector activity to this horticulturally important trait. This work expands understanding of phytoplasma effector diversity and mobility, while offering a functional framework for developing pathogen-free strategies to modulate ornamental plant architecture. IMPACT STATEMENTPhytoplasmas are uncultivated bacterial pathogens that reprogram host development through secreted effectors. While they are notorious for causing agricultural losses, phytoplasma infection is uniquely harnessed to induce the desirable free-branching trait in poinsettia, although the molecular basis has remained unresolved. Through analysis of the complete genome of Candidatus Phytoplasma pruni PR2021, a strain associated with a high-branching cultivar, we identified two SAP11-homologous effectors with contrasting genomic and evolutionary contexts. One appears vertically inherited and divergent from previously characterized homologs, whereas the other is embedded in a potential mobile unit and likely acquired through horizontal transfer. Importantly, both homologs induce branching despite substantial sequence divergence. Taken together, this work advances understanding of phytoplasma genome evolution and effector diversity, while providing experimental evidence that links effector function to host developmental manipulation. Beyond its horticultural relevance, it illustrates how horizontal gene transfer and lineage-specific retention shape phytoplasma effector complements, offering a foundation for future efforts to dissect and re-engineer effector-host interactions. DATA SUMMARYAll genome assemblies analyzed in this study were obtained from the National Center for Biotechnology Information (NCBI) Genome Database. The accession numbers are provided in Table S1.

genomics↗

bioRxiv2025

Comparative Transcriptomics Reveals Context- and Strain-Specific Regulatory Programs of Agrobacterium During Plant Colonization

Agrobacterium is a genus of plant-associated bacteria capable of transferring DNA into host genomes to induce tumorigenesis. The process has been primarily studied in a few model strains, particularly C58, and developed into Agrobacterium-mediated transformation (AMT) for genetic manipulation. However, the diversity of wild-type strains and their context-specific regulatory responses remain poorly characterized. Here, we evaluated five wild-type strains and identified 1D1108 as superior in tumorigenesis on legumes and transient transformation in Nicotiana benthamiana. Under in vitro virulence induction with acetosyringone (AS), we identified 126 differentially expressed genes (DEGs) in 1D1108. Although the number of DEGs was comparable to those in C58 and the legume isolate 1D1609 under the same condition, only 22 DEGs, primarily within the vir regulon, were conserved, indicating extensive divergence among these Agrobacterium strains. Leaf infiltration of N. benthamiana revealed 1,134 DEGs specifically regulated in planta for 1D1108. These included genes involved in attachment, virulence regulation, type IV pilus, succinoglycan biosynthesis, and diverse nutrient transporters, providing new evidence on expression regulation during colonization. Comparative analyses of in planta transcriptomes with C58 and Pseudomonas syringae DC3000 revealed distinct secretion systems required for pathogenesis, namely type IV for Agrobacterium and type III for Pseudomonas, and only approximately 5-19% of DEGs were conserved. These limited transcriptomic overlaps underscore the importance of studying gene expression in strains and conditions directly relevant to the biological context, rather than relying on model systems. Together, this work reveals how environmental and host-associated cues shape transcriptional responses in plant-associated bacteria. IMPORTANCEAgrobacterium is a key tool for plant genetic engineering, yet much of our knowledge about its biology comes from a few strains studied under artificial conditions. This work combines tumor formation assays on legumes and transient transformation in Nicotiana benthamiana with transcriptomic analyses to explore how diverse Agrobacterium strains, particularly the high-performing wild-type strain 1D1108, respond to host and environmental cues. By comparing gene expression under in vitro and in planta conditions, we found that the bacterial response within plant tissue is more complex than previously appreciated. Cross-strain comparisons further revealed limited conservation in gene expression regulation, even under similar conditions. Comparative analysis with Pseudomonas syringae revealed the activation of distinct secretion systems for pathogenesis and differences in regulatory programs used during plant colonization. These findings underscore the importance of studying bacteria in biologically relevant contexts and highlight the limitations of relying solely on model strains to infer regulatory responses.

microbiology↗

bioRxiv2025

Floral Stage Optimization and Immune Evasion Enhance Agrobacterium-Mediated Genome Editing in Arabidopsis

O_LIAgrobacterium-mediated transformation via floral inoculation (AMT-FI) enables genetic engineering without tissue culture. It is widely used in the model plant Arabidopsis thaliana, yet its efficiency and broader applicability remain limited. C_LIO_LIHere, we used a dual-reporter system (RUBY and hygromycin resistance) to identify key floral stages and engineered Agrobacterium strains to evade plant immunity, leading to enhanced transient expression and genome editing. C_LIO_LIWe determined that flowers opened at 6 day-post-inoculation (DPI) are optimal for high transformation efficiency, with nearly 100% of siliques harboring transformants. However, Agrobacterium infection induced ovule abortion, particularly in wild-type (Col-0) plants, whereas efr mutants lacking the EF-Tu receptor (EFR)-mediated pattern-triggered immunity (PTI) showed reduced ovule abortion. Notably, efr mutants exhibited more RUBY-positive ovules and significantly enhanced genome editing efficiency. Two engineered stealth Agrobacterium strains (AS201 and AS202) expressing a chimeric EF- Tu for evading recognition by EFR enhanced both transient transformation and genome editing efficiency. Remarkably, genome-edited T1 plants could be recovered based on phenotype or direct sequencing without the need for antibiotic selection when targeting flowers opened at 6 DPI. C_LIO_LIBy integrating floral stage selection, immune evasion, and Agrobacterium engineering, this study provides a practical and versatile platform to advance plant genome engineering. C_LI

plant biology↗

bioRxiv2025

Comparative genomic analysis of a novel heat-tolerant and euryhaline strain of unicellular marine cyanobacterium Cyanobacterium sp. DS4 from a high-temperature lagoon

BackgroundCyanobacteria have diversified through their long evolutionary history and occupy a wide range of environments on Earth. To advance our understanding of their adaption mechanisms in extreme environments, we performed stress tolerance characterizations, whole genome sequencing, and comparative genomic analyses of a novel heat-tolerant and euryhaline strain of the unicellular cyanobacterium Cyanobacterium sp. Dongsha4 (DS4). This strain was isolated from a lagoon on Dongsha Island in the South China Sea, a habitat with fluctuations in temperature, salinity, light intensity, and nutrient supply. ResultsDS4 cells can tolerate long-term high-temperature up to 50 and salinity from 0 to 6.6 %, which is similar to the results previously obtained for Cyanobacterium aponinum. In contrast, most mesophilic cyanobacteria cannot survive under these extreme conditions. Based on the 16S rRNA gene phylogeny, DS4 is most closely related to Cyanobacterium sp. NBRC 102756 isolated from Iwojima Island, Japan, and Cyanobacterium sp. MCCB114 isolated from Vypeen Island, India. For comparison with strains that have genomic information available, DS4 is most similar to Cyanobacterium aponinum strain PCC 10605 (PCC10605), sharing 81.7% of the genomic segments and 92.9% average nucleotide identity (ANI). Gene content comparisons identified multiple distinct features of DS4. Unlike related strains, DS4 possesses the genes necessary for nitrogen fixation. Other notable genes include those involved in photosynthesis, central metabolisms, cyanobacterial starch metabolisms, stress tolerances, and biosynthesis of novel secondary metabolites. ConclusionsThese findings promote our understanding of the physiology, ecology, evolution, and stress tolerance mechanisms of cyanobacteria. The information is valuable for future functional studies and biotechnology applications of heat-tolerant and euryhaline marine cyanobacteria.

genomics↗

bioRxiv2024

Rhizobium rhizogenes A4-derived strains mediate hyper-efficient transient gene expression in Nicotiana benthamiana and other solanaceous plants

Agroinfiltration, a method utilizing agrobacteria to transfer DNA into plant cells, is widely used for transient gene expression in plants. Besides the commonly used Agrobacterium strains, Rhizobium rhizogenes can also introduce foreign DNA into host plants for gene expression. While many R. rhizogenes strains have been known for inducing hairy root symptoms, their use for transient expression has not been fully explored. Here, we showed that R. rhizogenes A4 outperformed all other tested agrobacterial strains in agroinfiltration experiments on leaves of Nicotiana benthamiana and other solanaceous plants. By conducting an agroinfiltration screening in N. benthamiana leaves using various agrobacterial strains carrying the RUBY reporter gene cassette, we discovered that A4 mediates the strongest and fastest transient expression. Utilizing the genomic information, we developed a collection of disarmed and modified strains derived from A4. By performing vacuum infiltration assays, we demonstrated that these A4-derived strains efficiently transiently transform 6-week-old N. benthamiana leaves, showing less sensitivity to the age of plants compared to the laboratory strain GV3101. Furthermore, we performed agroinfiltration using AS109, an A4-derived disarmed strain, on the leaves of tomato, pepper, and eggplant. Remarkably, AS109 mediated transient gene expression on tested solanaceous plants more effectively than all the tested commonly used agrobacterial strains. This discovery paves the way for establishing R. rhizogenes A4-derived strains as a new option for enhancing transient expression in N. benthamiana and facilitating the functional study of plant genes in other solanaceous species.

plant biology↗

bioRxiv2024

Population genomics of a thermophilic cyanobacterium revealed divergence at subspecies level and possible adaptation genes

BackgroundCyanobacteria are diverse phototrophic microbes with ecological importance and potential for biotechnology applications. One species of thermophilic cyanobacteria, Thermosynechococcus taiwanensis, has been studied for biomass pyrolysis, estrogen degradation, and the production of bioethanol, monosaccharide, and phycocyanin. To better understand the diversity and evolution of this species, we sampled across different regions in Taiwan for strain isolation and genomic analysis. ResultsA total of 27 novel strains were isolated from nine of the 12 hot springs sampled and subjected to whole genome sequencing. Including strains studied previously, our genomic analyses encompassed 32 strains from 11 hot springs. Genome sizes among these strains ranged from 2.64 to 2.70 Mb, with an average of 2.66 Mb. Annotation revealed between 2,465 and 2,576 protein-coding genes per genome, averaging 2,537 genes. Core-genome phylogeny, gene flow estimates, and overall gene content divergence consistently supported the within-species divergence into two major populations. While isolation by distance partially explained the within-population divergence, the factors driving divergence between populations remain unclear. Nevertheless, this species likely has a closed pan-genome comprising approximately 3,030 genes, with our sampling providing sufficient coverage of its genomic diversity. To investigate the divergence and potential adaptations, we identified genomic regions with significantly lower nucleotide diversity, indicating loci that may have undergone selective sweeps within each population. We identified 149 and 289 genes within these regions in populations A and B, respectively. Only 16 genes were common to both populations, suggesting that selective sweeps primarily targeted different genes in the two populations. Key genes related to functions such as carbon fixation, photosynthesis, motility, and ion transport were highlighted. ConclusionsThis work provides a population genomics perspective on a hot spring cyanobacterial species in Taiwan. Beyond advancing our understanding of microbial genomics and evolution, the strains collected and genome sequences generated in this work provide valuable materials for future development and utilization of biological resources.

genomics↗

bioRxiv2024

Endophytic pyrroloquinoline quinone enhances banana growth and immunity against Fusarium wilt for plant-microbe mutualisms

Fusarium wilt has a substantial impact on global banana production, posing a threat to food security worldwide. However, breeding new Fusarium-resistant cultivars is difficult and time-consuming. Alternatively, endophytic biostimulants that could combat such pervasive plant diseases provide possible novel solutions. Our prior research demonstrated that a pyrroloquinoline quinone (PQQ)-producing endophytic bacterium, Burkholderia seminalis 869T2, can enhance the growth of various plant species and protect bananas from Fusarium wilt in the field. PQQ is a peptide-derived redox cofactor known to stimulate mitochondrial biogenesis and metabolism in animals, but its molecular roles, especially in plants, remain to be elucidated. In this study, multi-omics approaches were employed to explore the potential mechanisms through which PQQ influences banana plants. The result of in situ imaging mass spectrometry revealed that the endophytic metabolite PQQ does not function through direct antagonism against Fusarium. The follow-up transcriptomic profiling shows it could regulate plant respiration, TCA cycle, oxidative phosphorylation, NAD/NADP-dependent dehydrogenases, MAPK signalling, and various phytohormone signalling pathways. Furthermore, PQQ appeared to trigger plant systemic immunity, thereby enhancing plant health and resistance to biotic stress. Beyond that, the complete genome of 869T2 was determined for follow-up comparative genomics analyses, revealing its genetic contexts, potential evolutionary events of PQQ operons among the Burkholderia species, and the absence of human virulence-facilitating genes within those PQQ-producing agricultural isolates. In summary, this study facilitates our understanding of PQQ in plant-microbe mutualisms and provides scientific evidence for its future application in agriculture. Significance StatementFusarium wilt is caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), a notorious soil-borne pathogen that attacks bananas vascular system, which critically threatens global banana production and food security. A potential PQQ-producing endophytic strain has been confirmed to protect bananas through in planta biocontrol, reducing the morbidity of Banana Fusarium Wilt (BFW) disease in the field and promoting the growth of banana plants simultaneously. Our results revealed that the endophytic metabolite PQQ does not function through direct antagonism but triggers plant systemic immunity and coordinates energetic metabolisms, thereby improving the overall health of host plants and enhancing their resistance against Fusarium wilt.

plant biology↗

bioRxiv2024

Delineating bacterial genera based on gene content analysis: a case study of the Mycoplasmatales-Entomoplasmatales clade within the class Mollicutes

Genome-based analysis allows for large-scale classification of diverse bacteria and has been widely adopted for delineating species. Unfortunately, for higher taxonomic ranks such as genus, establishing a generally accepted approach based on genome analysis is challenging. While core-genome phylogenies depict the evolutionary relationships among species, determining the correspondence between clades and genera may not be straightforward. For genotypic divergence, percentage of conserved proteins (POCP) and genome-wide average amino acid identity (AAI) are commonly used, but often do not provide a clear threshold for classification. In this work, we investigated the utility of global comparisons and data visualization in identifying clusters of species based on their overall gene content, and rationalized that such patterns can be integrated with phylogeny and other information such as phenotypes for improving taxonomy. As a proof of concept, we selected 177 representative genome sequences from the Mycoplasmatales-Entomoplasmatales clade within the class Mollicutes for a case study. We found that the clustering patterns corresponded to the current understanding of these organisms, namely the split into three above-genus groups: Hominis, Pneumoniae, and Spiroplasma-Entomoplasmataceae-Mycoides (SEM). However, at the genus level, several important issues were found. For example, recent taxonomic revisions that split the Hominis group into three genera and Entomoplasmataceae into five genera are problematic, as those newly described or emended genera lack clear differentiations in gene content from one another. Moreover, several cases of mis-classification were identified. These findings demonstrated the utility of this approach and the potential application for other bacteria. Impact statementTaxonomy provides a foundation for communication that involves biological entities. As such, robust classification and standardized nomenclature are critical. In recent years, genome analysis has been widely adopted for delineating species, but generally accepted approaches for delineating higher taxonomic ranks such as genus are lacking. In this work, we demonstrated that the comparison of overall gene content among species provides an intuitive method for identifying groups of similar organisms that can correspond to genera. Moreover, several critical issues were identified when we applied the method to evaluate recent taxonomic revisions that affected many pathogens with biomedical or economic importance. These findings serve as a cautionary tale against the over-reliance of core-genome centered approaches in taxonomy. Data SummaryThe 183 genome assemblies analyzed in this study were obtained from the National Center for Biotechnology Information (NCBI) Genome Database. The accession numbers are provided in Table S1.

genomics↗

bioRxiv2023

A cyclic dipeptide for salinity stress alleviation and the trophic flexibility of an endophyte reveal niches in salt marsh plant-microbe interactions

In response to climate change, the nature of endophytes and their applications in sustainable agriculture has attracted the attention of academia and agro-industries. We focused on the endophytic halophiles of the endangered Taiwanese salt marsh plant, Bolboschoenus planiculmis, and evaluated the functions of the isolates through in planta salinity stress alleviation assay using Arabidopsis. An endophytic strain Priestia megaterium BP01R2 that could promote plant growth and salinity tolerance was further characterised through multi-omics approaches. The transcriptomics results suggested that BP01R2 could function by tuning hormone signal transduction, energy-producing metabolism, multiple stress responses, etc. In addition, a cyclodipeptide, cyclo(L-Ala-Gly), identified by metabolomics analysis was later confirmed to contribute to salinity stress alleviation in stressed plants by exogenous supplementation. Here we provide a new perspective on host-microbe interactions in the wetland biome based on the multi-omics investigation and mixotrophic character of BP01R2. This study revealed a biostimulant-based plant-endophyte symbiosis with potential application in sustainable agriculture and facilitated our understanding of those enigmatic cross-kingdom relationships.

microbiology↗

bioRxiv2023

Depletion of tropomyosin 1.6 promotes matrix-degrading phenotype in TGF-β1-induced myofibroblast

Fibroblasts can be transformed into myofibroblasts under pro-fibrotic conditions, which is characterized by increased contractility and reduced matrix degradation. The relationship between contractile activity and matrix degradation is not fully understood. We found that TGF-{beta}1-induced myofibroblast activation occurs on a culture dish, favoring stress fiber formation and inhibiting podosome structures due to high matrix stiffness. To mimic physiological conditions, we cultured fibroblasts on collagen gel. Blocking actomyosin signaling significantly reduced TGF-{beta}1-induced myofibroblast activation. Tpm1.6, an actomyosin-associated contractile unit, was specifically upregulated by TGF-{beta}1 on soft collagen substrates. Depletion of Tpm1.6 attenuated TGF-{beta}1-induced increase of -SMA, N-cadherin, and {beta}1-integrin, indicating its crucial role in early myofibroblast activation during fibrosis progression. Tpm1.6 depletion reduced TGF-{beta}1-induced cell contractility and enhanced collagen degradation. Notably, in Tpm1.6-depleted fibroblasts, TGF-{beta}1 triggered formation of distinct -SMA dot structures enriched with MMP9, promoting collagen degradation. Our study highlights the pivotal role of Tpm1.6 in TGF-{beta}1-induced myofibroblast activation and collagen degradation. Depletion of Tpm1.6 triggers robust collagen degradation through distinct -SMA dots, presenting a potential therapeutic approach for chronic kidney disease.

cell biology↗

bioRxiv2022

Rapid and accurate discrimination of Mycobacterium abscessus subspecies based on matrix-assisted laser desorption ionization-time of flight spectrum and machine learning

BackgroundMycobacterium abscessus complex (MABC) has been reported to cause considerable complicated infections. Subspecies identification of MABC is crucial for adequate treatment due to different antimicrobial resistance property amid the subspecies. However, long incubation days is needed for the traditional antibiotic susceptibility testing (AST) method. Effective antibiotics administration often delayed considerably and caused unfavorable outcomes. Thus, we proposed a novel and accurate method to identify subspecies and its potential antibiotics resistance, to guide clinical treatment within hours. MethodsSubspecies of the MABC isolates were determined by secA1, rpoB, and hsp65. AST was tested by using microdilution method, as well as sequencing of erm(41) and rrl genes. MALDI-TOF mass spectrometry (MS) spectra were analyzed. The informative peaks on MS spectra were detected by random forest (RF) importance. Machine learning (ML) algorithms were used to build models for classifying MABC subspecies based on MALDI-TOF spectrum. The models were developed and validated by nested five-fold cross-validation to avoid over-fitting. ResultsIn total, 102 MABC isolates (52 subspecies abscessus and 50 subspecies massiliense) were analyzed. Top informative peaks including m/z 6715, 4739, 2805, etc. were identified. RF model attained AUROC of 0.9166 (95% CI: 0.9072-0.9196) and outperformed other algorithms in discriminating subspecies abscessus from massiliense. ConclusionWe developed a MALDI-TOF based ML model for rapid and accurate MABC subspecies identification. The novel diagnostic tool would guide a more accurate and timely MABC subspecies-specific treatment.

microbiology↗

bioRxiv2021

Comparative Genome Analysis of 'Candidatus Phytoplasma luffae' Reveals the Influential Roles of Potential Mobile Units in Phytoplasma Evolution

Phytoplasmas are insect-transmitted plant pathogens that cause substantial losses in agriculture. In addition to economic impact, phytoplasmas induce distinct disease symptoms in infected plants, thus attracting attention for research on molecular plant-microbe interactions and plant developmental processes. Due to the difficulty of establishing an axenic culture of these bacteria, culture-independent genome characterization is a crucial tool for phytoplasma research. However, phytoplasma genomes have strong nucleotide composition biases and are repetitive, which make it challenging to produce complete assemblies. In this study, we utilized Illumina and Oxford Nanopore sequencing technologies to obtain the complete genome sequence of Candidatus Phytoplasma luffae strain NCHU2019 that is associated with witches broom disease of loofah (Luffa aegyptiaca) in Taiwan. The fully assembled circular chromosome is 769 kb in size and is the first representative genome sequence of group 16SrVIII phytoplasmas. Comparative analysis with other phytoplasmas revealed that NCHU2019 has an exceptionally repetitive genome, possessing a pair of 75 kb repeats and at least 13 potential mobile units (PMUs) that account for ~25% of its chromosome. This level of genome repetitiveness is exceptional for bacteria, particularly among obligate pathogens with reduced genomes. Our genus-level analysis of PMUs demonstrated that these phytoplasma-specific mobile genetic elements can be classified into three major types that differ in gene organization and phylogenetic distribution. Notably, PMU abundance explains nearly 80% of the variance in phytoplasma genome sizes, a finding that provides a quantitative estimate for the importance of PMUs in phytoplasma genome variability. Finally, our investigation found that in addition to horizontal gene transfer, PMUs also contribute to intra-genomic duplications of effector genes, which may provide redundancy for neofunctionalization or subfunctionalization. Taken together, this work improves the taxon sampling for phytoplasma genome research and provides novel information regarding the roles of mobile genetic elements in phytoplasma evolution.

genomics↗

bioRxiv2021

Species boundaries in the Agrobacterium tumefaciens complex and multi-level modular evolution of their antibacterial type VI secretion system and tumor-inducing plasmids

BackgroundMany bacterial taxa are species complexes and uncertainties regarding the organization of their genetic diversity challenge research efforts. We utilized Agrobacterium tumefaciens, a taxon known for its phytopathogenicity and applications in transformation, as a study system and devised strategies for investigating genome diversity and evolution of species complexes. ResultsWe utilized 35 genome assemblies to achieve a comprehensive and balanced sampling of A. tumefaciens. Our confident inference of gene content and core-genome phylogeny supported a quantitative guideline for delineating 12 species and allowed for robust investigations of genes critical in fitness and ecology. For the type VI secretion system (T6SS) involved in interbacterial competition and thought to be conserved, we detected multiple losses and one horizontal gene transfer. For the tumor-inducing plasmids (pTi) and pTi-encoded type IV secretion system (T4SS) that are essential for agrobacterial phytopathogenicity, we uncovered novel diversity and hypothesized their involvement in shaping this species complex. Intriguingly, for both T6SS and T4SS, genes encoding structural components are highly conserved, whereas extensive diversity exists for genes encoding effectors and other proteins. ConclusionsWe demonstrated that the combination of a phylogeny-guided sampling scheme and an emphasis on high-quality assemblies provides a cost-effective approach for robust analysis in evolutionary genomics. Our strategies for multi-level investigations at scales that range from whole-genomes to intragenic domains and phylogenetic depths of between- and within-species are applicable to other bacteria. Finally, modularity observed in the molecular evolution of genes and domains is useful for inferring functional constraints and informing experimental works.

genomics↗

bioRxiv2021

Genetic differentiation of Xylella fastidiosa following the introduction into Taiwan

The economically important plant pathogen Xylella fastidiosa has been reported in multiple regions of the globe during the last two decades, threatening a growing list of crops and industries. Xylella fastidiosa subspecies fastidiosa causes disease in grapevines (Pierces disease of grapevines, PD), a current problem in the United States (US), Spain, and Taiwan. We studied PD-causing subsp. fastidiosa populations and compared the genome sequences of 33 isolates found in Central Taiwan with 171 isolates from the US and two from Spain. Phylogenetic relationships, haplotype network, and genetic diversity analyses confirm that subsp. fastidiosa was recently introduced into Taiwan from the Southeast US (i.e., the PD-I lineage in Georgia based on available data). Recent core genome recombination events were detected among introduced subsp. fastidiosa isolates in Taiwan and contributed to the development of genetic diversity, particularly in the Houli District of Taichung City in Central Taiwan. Unexpectedly, despite comprehensive sampling of all regions with high PD incidences in Taiwan, the genetic diversity observed include contributions through recombination from unknown donors, suggesting that higher diversity exists in the region. Nevertheless, no recombination event was detected between X. fastidiosa subsp. fastidiosa and the endemic sister species Xylella taiwanensis. In summary, this study improved our understanding of the genetic diversity of PD-causing subsp. fastidiosa after invasion to a new region.

genomics↗

bioRxiv2021

Complete genome sequence of Xylella taiwanensis and comparative analysis of virulence gene content with Xylella fastidiosa

The bacterial genus Xylella contains plant pathogens that are major threats to agriculture in America and Europe. Although extensive research was conducted to characterize different subspecies of Xylella fastidiosa (Xf), comparative analysis at above-species levels were lacking due to the unavailability of appropriate data sets. Recently, a bacterium that causes pear leaf scorch (PLS) in Taiwan was described as the second Xylella species (i.e., Xylella taiwanensis; Xt). In this work, we report the complete genome sequence of Xt type strain PLS229T. The genome-scale phylogeny provided strong support that Xf subspecies pauca (Xfp) is the basal lineage of this species and Xylella was derived from the paraphyletic genus Xanthomonas. Quantification of genomic divergence indicated that different Xf subspecies share [~]87-95% of their chromosomal segments, while the two Xylella species share only [~]66-70%. Analysis of overall gene content suggested that Xt is most similar to Xf subspecies sandyi (Xfs). Based on the existing knowledge of Xf virulence genes, the homolog distribution among 28 Xylella representatives was examined. Among the 11 functional categories, those involved in secretion and metabolism are the most conserved ones with no copy number variation. In contrast, several genes related to adhesins, hydrolytic enzymes, and toxin-antitoxin systems are highly variable in their copy numbers. Those virulence genes with high levels of conservation or variation may be promising candidates for future studies. In summary, the new genome sequence and analysis reported in this work contributed to the study of several important pathogens in the family Xanthomonadaceae. Contribution to the FieldXylella fastidiosa is a plant-pathogenic bacterium with multiple subspecies that are major threats to agriculture in America and Europe. Although extensive research has been conducted, comparative analysis of this species with other bacteria is lacking due to the unavailability of known close relatives. In this work, we report the complete genome sequence of Xylella taiwanensis, a newly described species within the same genus. This new data set and our focused analysis helped to better understand the evolutionary relationships among different Xylella lineages and their genomic diversity. Moreover, detailed examination of their virulence genes identified those that are either highly conserved or variable, providing promising candidates for future studies to further investigate the molecular mechanisms of Xylella virulence.

genomics↗

bioRxiv2021

Parasite co-opts a ubiquitin receptor to induce a plethora of developmental changes

Obligate parasites can induce complex and substantial phenotypic changes in their hosts in ways that favour their transmission to other trophic levels. However, mechanisms underlying these changes remain largely unknown. Here, we demonstrate how SAP05 protein effectors from insect-vectored plant pathogenic phytoplasmas take control of several plant developmental processes to simultaneously prolong host lifespan and induce witchs broom-like proliferations of leaf and sterile shoots, organs colonized by phytoplasmas and vectors. SAP05 acts by mediating the concurrent degradation of SPL and GATA developmental regulators via a process that uniquely relies on hijacking the plant ubiquitin receptor RPN10 independently of substrate lysine ubiquitination. RPN10 is highly conserved among eukaryotes, but SAP05 does not bind insect vector RPN10. A two-amino-acid substitution within plant RPN10 generates a functional variant that is resistant to SAP05 activities. Therefore, one effector protein enables obligate parasitic phytoplasmas to induce a plethora of developmental phenotypes in their hosts.

molecular biology↗