Junyang Yue

Draft genome of the kiwifruit Actinidia chinensis

The kiwifruit (Actinidia chinensis) is an economically and nutritionally important fruit crop with remarkably high vitamin C content. Here we report the draft genome sequence of a heterozygous kiwifruit, assembled from ~140-fold next-generation sequencing data. The assembled genome has a total length of 616.1 Mb and contains 39,040 genes. Comparative genomic analysis reveals that the kiwifruit has undergone an ancient hexaploidization event (γ) shared by core eudicots and two more recent whole-genome duplication events. Both recent duplication events occurred after the divergence of kiwifruit from tomato and potato and have contributed to the neofunctionalization of genes involved in regulating important kiwifruit characteristics, such as fruit vitamin C, flavonoid and carotenoid metabolism. As the first sequenced species in the Ericales, the kiwifruit genome sequence provides a valuable resource not only for biological discovery and crop improvement but also for evolutionary and comparative genomics analysis, particularly in the asterid lineage.

Comprehensive Transcriptome Profiling Reveals Long Noncoding RNA Expression and Alternative Splicing Regulation during Fruit Development and Ripening in Kiwifruit (Actinidia chinensis)

Genomic and transcriptomic data on kiwifruit (Actinidia chinensis) in public databases are very limited despite its nutritional and economic value. Previously, we have constructed and sequenced nine fruit RNA-Seq libraries of A. chinensis “Hongyang” at immature, mature, and postharvest ripening stages of fruit development, and generated over 66.2 million paired-end and 24.4 million single-end reads. From this dataset, here we have identified 7051 long noncoding RNAs (lncRNAs), 29,327 alternative splicing (AS) events and 2980 novel protein-coding genes that were not annotated in the draft genome of “Hongyang.” AS events were demonstrated in genes involved in the synthesis of nutritional metabolites in fruit, such as ascorbic acids, carotenoids, anthocyanins, and chlorophylls, and also in genes in the ethylene signaling pathway, which plays an indispensable role in fruit ripening. Additionally, transcriptome profiles and the contents of sugars, organic and main amino acids were compared between immature, mature, and postharvest ripening stages in kiwifruits. A total of 5931 differentially expressed genes were identified, including those associated with the metabolism of sugar, organic acid, and main amino acids. The data generated in this study provide a foundation for further studies of fruit development and ripening in kiwifruit, and identify candidate genes and regulatory elements that could serve as targets for improving important agronomic traits through marker assisted breeding and biotechnology.

PTIR: Predicted Tomato Interactome Resource

Protein-protein interactions (PPIs) are involved in almost all biological processes and form the basis of the entire interactomics systems of living organisms. Identification and characterization of these interactions are fundamental to elucidating the molecular mechanisms of signal transduction and metabolic pathways at both the cellular and systemic levels. Although a number of experimental and computational studies have been performed on model organisms, the studies exploring and investigating PPIs in tomatoes remain lacking. Here, we developed a Predicted Tomato Interactome Resource (PTIR), based on experimentally determined orthologous interactions in six model organisms. The reliability of individual PPIs was also evaluated by shared gene ontology (GO) terms, co-evolution, co-expression, co-localization and available domain-domain interactions (DDIs). Currently, the PTIR covers 357,946 non-redundant PPIs among 10,626 proteins, including 12,291 high-confidence, 226,553 medium-confidence, and 119,102 low-confidence interactions. These interactions are expected to cover 30.6% of the entire tomato proteome and possess a reasonable distribution. In addition, ten randomly selected PPIs were verified using yeast two-hybrid (Y2H) screening or a bimolecular fluorescence complementation (BiFC) assay. The PTIR was constructed and implemented as a dedicated database and is available at http://bdg.hfut.edu.cn/ptir/index.html without registration.

FR database 1.0: a resource focused on fruit development and ripening

Fruits form unique growing period in the life cycle of higher plants. They provide essential nutrients and have beneficial effects on human health. Characterizing the genes involved in fruit development and ripening is fundamental to understanding the biological process and improving horticultural crops. Although, numerous genes that have been characterized are participated in regulating fruit development and ripening at different stages, no dedicated bioinformatic resource for fruit development and ripening is available. In this study, we have developed such a database, FR database 1.0, using manual curation from 38 423 articles published before 1 April 2014, and integrating protein interactomes and several transcriptome datasets. It provides detailed information for 904 genes derived from 53 organisms reported to participate in fleshy fruit development and ripening. Genes from climacteric and non-climacteric fruits are also annotated, with several interesting Gene Ontology (GO) terms being enriched for these two gene sets and seven ethylene-related GO terms found only in the climacteric fruit group. Furthermore, protein–protein interaction analysis by integrating information from FR database presents the possible function network that affects fleshy fruit size formation. Collectively, FR database will be a valuable platform for comprehensive understanding and future experiments in fruit biology. Database URL: http://www.fruitech.org/

Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics

The Kiwifruit Information Resource (KIR) is dedicated to maintain and integrate comprehensive datasets on genomics, functional genomics and transcriptomics of kiwifruit (Actinidiaceae). KIR serves as a central access point for existing/new genomic and genetic data. KIR also provides researchers with a variety of visualization and analysis tools. Current developments include the updated genome structure of Actinidia chinensis cv. Hongyang and its newest genome annotation, putative transcripts, gene expression, physical markers of genetic traits as well as relevant publications based on the latest genome assembly. Nine thousand five hundred and forty-seven new transcripts are detected and 21 132 old transcripts are changed. At the present release, the next-generation transcriptome sequencing data has been incorporated into gene models and splice variants. Protein–protein interactions are also identified based on experimentally determined orthologous interactions. Furthermore, the experimental results reported in peer-reviewed literature are manually extracted and integrated within a well-developed query page. In total, 122 identifications are currently associated, including commonly used gene names and symbols. All KIR datasets are helpful to facilitate a broad range of kiwifruit research topics and freely available to the research community. Database URL: http://bdg.hfut.edu.cn/kir/index.html.

Identification of Conserved and Novel MicroRNAs in Blueberry

MicroRNAs (miRNAs) are a class of small endogenous RNAs that play important regulatory roles in cells by negatively affecting gene expression at both transcriptional and post-transcriptional levels. There have been extensive studies aiming to identify miRNAs and to elucidate their functions in various plant species. In the present study, we employed the high-throughput sequencing technology to profile miRNAs in blueberry fruits. A total of 9,992,446 small RNA tags with sizes ranged from 18 to 30 nt were obtained, indicating that blueberry fruits have a large and diverse small RNA population. Bioinformatic analysis identified 412 conserved miRNAs belonging to 29 families, and 35 predicted novel miRNAs that are likely to be unique to blueberries. Among them, expression profiles of five conserved miRNAs were validated by stem loop qRT-PCR. Furthermore, the potential target genes of conserved and novel miRNAs were predicted and subjected to Gene Ontology (GO) annotation. Enrichment analysis of the GO-represented biological processes and molecular functions revealed that these target genes were potentially involved in a wide range of metabolic pathways and developmental processes. Particularly, anthocyanin biosynthesis has been predicted to be directly or indirectly regulated by diverse miRNA families. This study is the first report on genome-wide miRNA profile analysis in blueberry and it provides a useful resource for further elucidation of the functional roles of miRNAs during fruit development and ripening.

PCPPI: a comprehensive database for the prediction of Penicillium–crop protein–protein interactions

Penicillium expansum, the causal agent of blue mold, is one of the most prevalent post-harvest pathogens, infecting a wide range of crops after harvest. In response, crops have evolved various defense systems to protect themselves against this and other pathogens. Penicillium–crop interaction is a multifaceted process and mediated by pathogen- and host-derived proteins. Identification and characterization of the inter-species protein–protein interactions (PPIs) are fundamental to elucidating the molecular mechanisms underlying infection processes between P. expansum and plant crops. Here, we have developed PCPPI, the Penicillium-Crop Protein–Protein Interactions database, which is constructed based on the experimentally determined orthologous interactions in pathogen–plant systems and available domain–domain interactions (DDIs) in each PPI. Thus far, it stores information on 9911 proteins, 439 904 interactions and seven host species, including apple, kiwifruit, maize, pear, rice, strawberry and tomato. Further analysis through the gene ontology (GO) annotation indicated that proteins with more interacting partners tend to execute the essential function. Significantly, semantic statistics of the GO terms also provided strong support for the accuracy of our predicted interactions in PCPPI. We believe that all the PCPPI datasets are helpful to facilitate the study of pathogen-crop interactions and freely available to the research community. Database URL: http://bdg.hfut.edu.cn/pcppi/index.html

PAAS: Fast Retrieval of Plant Amino Acid Substitutions and Their Effects on Comparative Phenomics

PAAS (Plant Amino Acid Substitutions) is a web database that provides a comprehensive collection of single amino acid substitutions and plant phenotype effects. It gives direct access to the query for comparative phenotype among different species. From here, users can obtain detailed annotation of each variants, substitution combination, and corresponding protein effects. Currently, PAAS covers 4,749 manually curated single amino acid substitutions scattered throughout 1,313 proteins from 111 plant species. PAAS should be an efficient resource for researchers to facilitate gene function understanding, produce rationally designed protein, as well as improve plant desirable traits. The database is implemented in PHP MySQL JavaScript and can be accessed at http://paas.fruitech.org/ without registration.

Transcriptome analysis of differentially expressed unigenes involved in flavonoid biosynthesis during flower development of Chrysanthemum morifolium ‘Chuju’

Chrysanthemum morifolium is an ornamentally and medicinally important plant species. Up to date, molecular and genetic investigations have largely focused on determination of flowering time in the ornamental species. However, little is known about gene regulatory networks for the biosynthesis of flavonoids in the medicinal species. In the current study, we employed the high-throughput sequencing technology to profile the genome-wide transcriptome of C. morifolium ‘Chuju’, a famous medicinal species in traditional Chinese medicine. A total of 63,854 unigenes with an average length of 741 bp were obtained. Bioinformatic analysis has identified a great number of structural and regulatory unigenes potentially participating in the flavonoid biosynthetic pathway. According to the comparison of digital gene expression, 8,370 (3,026 up-regulated and 5,344 down-regulated), 1,348 (717 up-regulated and 631 down-regulated) and 944 (206 up-regulated and 738 down-regulated) differentially expressed unigenes (DEUs) were detected in the early, middle and mature growth phases, respectively. Among them, many DEUs were implicated in controlling the biosynthesis and composition of flavonoids from the budding to full blooming stages during flower development. Furthermore, the expression patterns of 12 unigenes involved in flavonoid biosynthesis were generally validated by using quantitative real time PCR. These findings could shed light on the molecular basis of flavonoid biosynthesis in C. morifolium ‘Chuju’ and provide a genetic resource for breeding varieties with improved nutritional quality.

DFR1-Mediated Inhibition of Proline Degradation Pathway Regulates Drought and Freezing Tolerance in Arabidopsis

Proline accumulation is one of the most important adaptation mechanisms for plants to cope with environmental stresses, such as drought and freezing. However, the molecular mechanism of proline homeostasis under these stresses is largely unknown. Here, we identified a mitochondrial protein, DFR1, involved in the inhibition of proline degradation in Arabidopsis. DFR1 was strongly induced by drought and cold stresses. The dfr1 knockdown mutants showed hypersensitivity to drought and freezing stresses, whereas the DFR1 overexpression plants exhibited enhanced tolerance, which was positively correlated with proline levels. DFR1 interacts with proline degradation enzymes PDH1/2 and P5CDH and compromises their activities. Genetic analysis showed that DFR1 acts upstream of PDH1/2 and P5CDH to positively regulate proline accumulation. Our results demonstrate a regulatory mechanism by which, under drought and freezing stresses, DFR1 interacts with PDH1/2 and P5CDH to abrogate their activities to maintain proline homeostasis, thereby conferring drought and freezing tolerance.