Biology subjects

Chen, A.-P.

Publications and source records attributed to Chen, A.-P..

4 recordsLinked to original sources

bioRxiv2023

Transcriptome and translatome comparison of tissues from Arabidopsis thaliana

Translation is one of the multiple complementary steps that orchestrates gene activity. In contrast to the straightforwardness of transcriptional surveys, genome-wide profiles of the translational landscape of plant cells remain technically challenging and are less well explored. Protein-coding genes are expressed at a variable degree of efficiency, resulting in pronounced discordance among the regulatory levels that govern gene activity. Ribo-Seq provides an extremely useful tool for estimating translation efficiency, but limited data sets are available for plants. Here, we provide comparative inventories of expressed and translated RNA populations, generated by mRNA sequencing (RNA-Seq) and ribosome footprinting (Ribo-Seq) of shoots and roots of Arabidopsis thaliana seedlings. Our data set provides information on the translational fitness of protein-coding mRNAs and lncRNAs that may aid in obtaining a comprehensive picture of the regulatory levels governing genes activity across the genome.

plant biology↗

bioRxiv2023

Botrytis cinerea small RNAs are associated with tomato AGO1 and silence tomato target genes supporting cross-kingdom RNAi between the fungal pathogen B. cinerea and its tomato host

Cross-kingdom or cross-species RNA interference (RNAi) is broadly present in many interacting systems between microbes/parasites and their plant and animal hosts. A recent study by Qin et al. (2022) performed correlation analysis using global sRNA- and mRNA-deep sequencing data of cultured B. cinerea and B. cinerea-infected tomato leaves and claimed that cross-kingdom RNAi may not occur in B. cinerea-tomato interaction (Qin et al., 2022). Here, we use experimental evidence and additional bioinformatics analysis of the datasets produced by Qin et al. (2022) to identify the key reasons why a discrepancy between the conclusion of Qin et al. 2022 and previously published findings occurred. We also provided additional experimental evidence to support the presence of cross-kingdom RNAi between tomato and B. cinerea. We believe it is important to clarify the basic concept and mechanism of cross-kingdom/cross-species sRNA trafficking and illustrate proper bioinformatics analyses in this regard for all the scientists and researchers in this field.

plant biology↗

bioRxiv2022

The antibacterial T6SS of Agrobacterium tumefacien promotes disease occurrence and influences crown gall microbiota composition

The type VI secretion system (T6SS) is deployed by many proteobacteria to secrete effector proteins into bacterial competitors for competition or eukaryotic cells for pathogenesis. Agrobacteria, a group of soil-borne phytopathogens causing crown gall disease on various plant species, deploys the T6SS to attack closely- and distantly-related bacterial species in vitro and in planta. Current evidence suggests that the T6SS is not essential for pathogenesis under direct inoculation but it remains unknown whether the T6SS influences natural disease incidence or the microbial community within crown galls (i.e., gallobiome). To address these two key questions, we established a soil inoculation method on wounded tomato seedlings that mimics natural infections and developed a bacterial 16S rRNA gene amplicon enrichment sequencing platform. By comparing the Agrobacterium wild-type strain C58 with two T6SS mutants, we demonstrate that the T6SS influences both disease occurrence and gallobiome composition. Based on multiple inoculation trials across seasons, all three strains could induce tumors but the mutants had significantly lower disease incidences. The season of inoculation played a more important role than the T6SS in shaping the gallobiome. The influence of T6SS was evident in summer, in which two Sphingomonas species and the family Burkhoderiaceae were enriched in the gallobiome induced by the mutants. Further in vitro competition and colonization assay demonstrated the T6SS-mediated antagonism to a Sphingomonas sp. R1 strain isolated from tomato rhizosphere in this study. In conclusion, this work demonstrates that the Agrobacterium T6SS promotes tumorigenesis in infection process and provides competitive advantages in gall-associated microbiota. IMPORTANCEThe T6SS is widespread among Proteobacteria and used for interbacterial competition by agrobacteria, which are soil inhabitants and opportunistic bacterial pathogens causing crown gall disease in a wide range of plants. Current evidence indicates that the T6SS is not required for gall formation when agrobacteria are inoculated directly on plant wounding sites. However, in natural settings, agrobacteria may need to compete with other bacteria in bulk soil to gain access to plant wounds and influence microbial community inside crown galls. The role of the T6SS in these critical aspects of disease ecology have remained largely unknown. In this study, we successfully developed a Soil Inoculation method coupled with Blocker-mediated enrichment of Bacterial 16S rRNA gene Amplicon Sequencing, named as SI-BBacSeq, to address these two important questions. We provided evidence that the T6SS promotes disease occurrence and influences crown gall microbiota composition by interbacterial competition.

microbiology↗

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↗