RARGE II: an integrated phenotype database of Arabidopsis mutant traits using a controlled vocabulary

Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences

Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021-22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org.

Identification of growth regulators using cross-species network analysis in plants

With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.

Metabolization and sequestration of plant specialized metabolites in insect herbivores: Current and emerging approaches

Herbivorous insects encounter diverse plant specialized metabolites (PSMs) in their diet, that have deterrent, anti-nutritional, or toxic properties. Understanding how they cope with PSMs is crucial to understand their biology, population dynamics, and evolution. This review summarizes current and emerging cutting-edge methods that can be used to characterize the metabolic fate of PSMs, from ingestion to excretion or sequestration. It further emphasizes a workflow that enables not only to study PSM metabolism at different scales, but also to tackle and validate the genetic and biochemical mechanisms involved in PSM resistance by herbivores. This review thus aims at facilitating research on PSM-mediated plant-herbivore interactions.

R2R3-MYBs in Durum Wheat: Genome-Wide Identification, Poaceae-Specific Clusters, Expression, and Regulatory Dynamics Under Abiotic Stresses

MYB transcription factors (TFs) represent one of the biggest TF families in plants, being involved in various specific plant processes, such as responses to biotic and abiotic stresses. The implication of MYB TFs in the tolerance mechanisms to abiotic stress is particularly interesting for crop breeding, since environmental conditions can negatively affect growth and productivity. Wheat is a worldwide-cultivated cereal, and is a major source of plant-based proteins in human food. In particular, durum wheat plays an important role in global food security improvement, since its adaptation to hot and dry conditions constitutes the base for the success of wheat breeding programs in future. In the present study, a genome-wide identification of R2R3-MYB TFs in durum wheat was performed. MYB profile search and phylogenetic analyses based on homology with Arabidopsis and rice MYB TFs led to the identification of 233 R2R3-TdMYB (Triticum durum MYB). Three Poaceae-specific MYB clusters were detected, one of which had never been described before. The expression of eight selected genes under different abiotic stress conditions, revealed that most of them responded especially to salt and drought stress. Finally, gene regulatory network analyses led to the identification of 41 gene targets for three TdR2R3-MYBs that represent novel candidates for functional analyses. This study provides a detailed description of durum wheat R2R3-MYB genes and contributes to a deeper understanding of the molecular response of durum wheat to unfavorable climate conditions.

Non-CG DNA methylation-deficiency mutations enhance mutagenesis rates during salt adaptation in cultured Arabidopsis cells

Much has been learned about how plants acclimate to stressful environments, but the molecular basis of stress adaptation and the potential involvement of epigenetic regulation remain poorly understood. Here, we examined if salt stress induces mutagenesis in suspension cultured plant cells and if DNA methylation affects the mutagenesis using whole genome resequencing analysis. We generated suspension cell cultures from two Arabidopsis DNA methylation-deficient mutants and wild-type plants, and subjected the cultured cells to stepwise increases in salt stress intensity over 40 culture cycles. We show that ddc (drm1 drm2 cmt3) mutant cells can adapt to grow in 175 mM NaCl-containing growth medium and exhibit higher adaptability compared to wild type Col-0 and nrpe1 cells, which can adapt to grow in only 125 mM NaCl-containing growth medium. Salt treated nrpe1 and ddc cells but not wild type cells accumulate more mutations compared with their respective untreated cells. There is no enrichment of stress responsive genes in the list of mutated genes in salt treated cells compared to the list of mutated genes in untreated cells. Our results suggest that DNA methylation prevents the induction of mutagenesis by salt stress in plant cells during stress adaptation.

Genome Evolutionary Dynamics Meets Functional Genomics: A Case Story on the Identification of SLC25A44

Gene clusters are becoming promising tools for gene identification. The study reveals the purposive genomic distribution of genes toward higher inheritance rates of intact metabolic pathways/phenotypes and, thereby, higher fitness. The co-localization of co-expressed, co-interacting, and functionally related genes was found as genome-wide trends in humans, mouse, golden eagle, rice fish, Drosophila, peanut, and Arabidopsis. As anticipated, the analyses verified the co-segregation of co-localized events. A negative correlation was notable between the likelihood of co-localization events and the inter-loci distances. The evolution of genomic blocks was also found convergent and uniform along the chromosomal arms. Calling a genomic block responsible for adjacent metabolic reactions is therefore recommended for identification of candidate genes and interpretation of cellular functions. As a case story, a function in the metabolism of energy and secondary metabolites was proposed for Slc25A44, based on its genomic local information. Slc25A44 was further characterized as an essential housekeeping gene which has been under evolutionary purifying pressure and belongs to the phylogenetic ETC-clade of SLC25s. Pathway enrichment mapped the Slc25A44s to the energy metabolism. The expression of peanut and human Slc25A44s in oocytes and Saccharomyces cerevisiae strains confirmed the transport of common precursors for secondary metabolites and ubiquinone. These results suggest that SLC25A44 is a mitochondrion-ER-nucleus zone transporter with biotechnological applications. Finally, a conserved three-amino acid signature on the cytosolic face of transport cavity was found important for rational engineering of SLC25s.

Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators

Gene regulation is a dynamic process in which transcription factors (TFs) play an important role in controlling spatiotemporal gene expression. To enhance our global understanding of regulatory interactions in Arabidopsis thaliana, different regulatory input networks capturing complementary information about DNA motifs, open chromatin, TF-binding and expression-based regulatory interactions were combined using a supervised learning approach, resulting in an integrated gene regulatory network (iGRN) covering 1,491 TFs and 31,393 target genes (1.7 million interactions). This iGRN outperforms the different input networks to predict known regulatory interactions and has a similar performance to recover functional interactions compared to state-of-the-art experimental methods. The iGRN correctly inferred known functions for 681 TFs and predicted new gene functions for hundreds of unknown TFs. For regulators predicted to be involved in reactive oxygen species (ROS) stress regulation, we confirmed in total 75% of TFs with a function in ROS and/or physiological stress responses. This includes 13 ROS regulators, previously not connected to any ROS or stress function, that were experimentally validated in our ROS-specific phenotypic assays of loss- or gain-of-function lines. In conclusion, the presented iGRN offers a high-quality starting point to enhance our understanding of gene regulation in plants by integrating different experimental data types.

A multilayered cross-species analysis of GRAS transcription factors uncovered their functional networks in plant adaptation to the environment

Introduction

Environmental stress is both a major force of natural selection and a prime factor affecting crop qualities and yields. The impact of the GRAS [gibberellic acid-insensitive (GAI), repressor of GA1-3 mutant (RGA), and scarecrow (SCR)] family on plant development and the potential to resist environmental stress needs much emphasis.

Objectives

This study aims to investigate the evolution, expansion, and adaptive mechanisms of GRASs of important representative plants during polyploidization.

Methods

We explored the evolutionary characteristics of GRASs in 15 representative plant species by systematic biological analysis of the genome, transcriptome, metabolite, protein complex map and phenotype.

Results

The GRAS family was systematically identified from 15 representative plant species of scientific and agricultural importance. The detection of gene duplication types of GRASs in all species showed that the widespread expansion of GRASs in these species was mainly contributed by polyploidization events. Evolutionary analysis reveals that most species experience independent genome-wide duplication (WGD) events and that interspecies GRAS functions may be broadly conserved. Polyploidy-related Chenopodium quinoa GRASs (CqGRASs) and Arabidopsis thaliana GRASs (AtGRASs) formed robust networks with flavonoid pathways by crosstalk with auxin and photosynthetic pathways. Furthermore, Arabidopsis thaliana population transcriptomes and the 1000 Plants (OneKP) project confirmed that GRASs are components of flavonoid biosynthesis, which enables plants to adapt to the environment by promoting flavonoid accumulation. More importantly, the GRASs of important species that may potentially improve important agronomic traits were mapped through TAIR and RARGE-II publicly available phenotypic data. Determining protein interactions and target genes contributes to determining GRAS functions.

Conclusion

The results of this study suggest that polyploidy-related GRASs in multiple species may be a target for improving plant growth, development, and environmental adaptation.

A quick protocol for the identification and characterization of early growth mutants in tomato

Root system architecture (RSA) manipulation may improve water and nutrient capture by plants under normal and extreme climate conditions. With the aim of initiating the genetic dissection of RSA in tomato, we established a defined ontology that allowed the curated annotation of the observed phenotypes on 12 traits at four consecutive growth stages. In addition, we established a quick approach for the molecular identification of the mutations associated with the trait-of-interest by using a whole-genome sequencing approach that does not require the building of an additional mapping population. As a proof-of-concept, we screened 4543 seedlings from 300 tomato M₃ lines (Solanum lycopersicum L. cv. Micro-Tom) generated by chemical mutagenesis with ethyl methanesulfonate. We studied the growth and early development of both the root system (primary and lateral roots) and the aerial part of the seedlings as well as the wound-induced adventitious roots emerging from the hypocotyl. We identified 659 individuals (belonging to 203 M₃ lines) whose early seedling and RSA phenotypes differed from those of their reference background. We confirmed the genetic segregation of the mutant phenotypes affecting primary root length, seedling viability and early RSA in 31 M₄ families derived from 15 M₃ lines selected in our screen. Finally, we identified a missense mutation in the SlCESA3 gene causing a seedling-lethal phenotype with short roots. Our results validated the experimental approach used for the identification of tomato mutants during early growth, which will allow the molecular identification of the genes involved.

Identification of QTLs for Domestication-Related Traits in Zombi Pea [Vigna vexillata (L.) A. Rich], a Lost Crop of Africa

Zombi pea [Vigna vexillata (L.) A. Rich] is a legume crop found in Africa. Wild zombi pea is widely distributed throughout the tropical and subtropical regions, whereas domesticated zombi pea is rarely cultivated. Plant domestication is an evolutionary process in which the phenotypes of wild species, including seed dormancy, pod shattering, organ size, and architectural and phenological characteristics, undergo changes. The molecular mechanism underlying the domestication of zombi pea is relatively unknown. In this study, the genetic basis of the following 13 domestication-related traits was investigated in an F₂ population comprising 198 individuals derived from a cross between cultivated (var. macrosperma) and wild (var. vexillata) zombi pea accessions: seed dormancy, pod shattering, days-to-flowering, days-to-maturity, stem thickness, stem length, number of branches, leaf area, pod length, 100-seed weight, seed width, seed length, and seeds per pod. A genetic map containing 6,529 single nucleotide polymorphisms constructed for the F₂ population was used to identify quantitative trait loci (QTLs) for these traits. A total of 62 QTLs were identified for the 13 traits, with 1-11 QTLs per trait. The major QTLs for days-to-flowering, stem length, number of branches, pod length, 100-seed weight, seed length, and seeds per pod were clustered in linkage group 5. In contrast, the major QTLs for seed dormancy and pod shattering belonged to linkage groups 3 and 11, respectively. A comparative genomic analysis with the cowpea [Vigna unguiculata (L.) Walp.] genome used as the reference sequence (i.e., the genome of the legume species most closely related to zombi pea) enabled the identification of candidate genes for the major QTLs. Thus, we revealed the genomic regions associated with domestication-related traits and the candidate genes controlling these traits in zombi pea. The data presented herein may be useful for breeding new varieties of zombi pea and other Vigna species.

Proxies of CRISPR/Cas9 Activity To Aid in the Identification of Mutagenized Arabidopsis Plants

CRISPR/Cas9 has become the preferred gene-editing technology to obtain loss-of-function mutants in plants, and hence a valuable tool to study gene function. This is mainly due to the easy reprogramming of Cas9 specificity using customizable small non-coding RNAs, and to the possibility of editing several independent genes simultaneously. Despite these advances, the identification of CRISPR-edited plants remains time and resource-intensive. Here, based on the premise that one editing event in one locus is a good predictor of editing event/s in other locus/loci, we developed a CRISPR co-editing selection strategy that greatly facilitates the identification of CRISPR-mutagenized Arabidopsis thaliana plants. This strategy is based on targeting the gene/s of interest simultaneously with a proxy of CRISPR-Cas9-directed mutagenesis. The proxy is an endogenous gene whose loss-of-function produces an easy-to-detect visible phenotype that is unrelated to the expected phenotype of the gene/s under study. We tested this strategy via assessing the frequency of co-editing of three functionally unrelated proxy genes. We found that each proxy predicted the occurrence of mutations in each surrogate gene with efficiencies ranging from 68 to 100%. The selection strategy laid out here provides a framework to facilitate the identification of multiplex edited plants, thus aiding in the study of gene function when functional redundancy hinders the effort to define gene-function-phenotype links.

Comparative transcriptomics enables the identification of functional orthologous genes involved in early leaf growth

Leaf growth is a complex trait for which many similarities exist in different plant species, suggesting functional conservation of the underlying pathways. However, a global view of orthologous genes involved in leaf growth showing conserved expression in dicots and monocots is currently missing. Here, we present a genome-wide comparative transcriptome analysis between Arabidopsis and maize, identifying conserved biological processes and gene functions active during leaf growth. Despite the orthology complexity between these distantly related plants, 926 orthologous gene groups including 2829 Arabidopsis and 2974 maize genes with similar expression during leaf growth were found, indicating conservation of the underlying molecular networks. We found 65% of these genes to be involved in one-to-one orthology, whereas only 28.7% of the groups with divergent expression had one-to-one orthology. Within the pool of genes with conserved expression, 19 transcription factor families were identified, demonstrating expression conservation of regulators active during leaf growth. Additionally, 25 Arabidopsis and 25 maize putative targets of the TCP transcription factors with conserved expression were determined based on the presence of enriched transcription factor binding sites. Based on large-scale phenotypic data, we observed that genes with conserved expression have a higher probability to be involved in leaf growth and that leaf-related phenotypes are more frequently present for genes having orthologues between dicots and monocots than clade-specific genes. This study shows the power of integrating transcriptomic with orthology data to identify or select candidates for functional studies during leaf development in flowering plants.

Candidate Domestication-Related Genes Revealed by Expression Quantitative Trait Loci Mapping of Narrow-Leafed Lupin (Lupinus angustifolius L.)

The last century has witnessed rapid domestication of the narrow-leafed lupin (Lupinus angustifolius L.) as a grain legume crop, exploiting discovered alleles conferring low-alkaloid content (iucundus), vernalization independence (Ku and Julius), and reduced pod shattering (lentus and tardus). In this study, a L. angustifolius mapping population was subjected to massive analysis of cDNA ends (MACE). The MACE yielded 4185 single nucleotide polymorphism (SNP) markers for linkage map improvement and 30,595 transcriptomic profiles for expression quantitative trait loci (eQTL) mapping. The eQTL highlighted a high number of cis- and trans-regulated alkaloid biosynthesis genes with gene expression orchestrated by a regulatory agent localized at iucundus locus, supporting the concept that ETHYLENE RESPONSIVE TRANSCRIPTION FACTOR RAP2-7 may control low-alkaloid phenotype. The analysis of Ku shed light on the vernalization response via FLOWERING LOCUS T and FD regulon in L. angustifolius, providing transcriptomic evidence for the contribution of several genes acting in C-repeat binding factor (CBF) cold responsiveness and in UDP-glycosyltransferases pathways. Research on lentus selected a DUF1218 domain protein as a candidate gene controlling the orientation of the sclerified endocarp and a homolog of DETOXIFICATION14 for purplish hue of young pods. An ABCG transporter was identified as a hypothetical contributor to sclerenchyma fortification underlying tardus phenotype.

A Similarity Searching System for Biological Phenotype Images Using Deep Convolutional Encoder-decoder Architecture

Background:

The BLAST (Basic Local Alignment Search Tool) algorithm has been widely used for sequence similarity searching. Analogously, the public phenotype images must be efficiently retrieved using biological images as queries and identify the phenotype with high similarity. Due to the accumulation of genotype-phenotype-mapping data, a system of searching for similar phenotypes is not available due to the bottleneck of image processing.

Objective:

In this study, we focus on the identification of similar query phenotypic images by searching the biological phenotype database, including information about loss-of-function and gain-of-function.

Methods:

We propose a deep convolutional autoencoder architecture to segment the biological phenotypic images and develop a phenotype retrieval system to enable a better understanding of genotype–phenotype correlation.

Results:

This study shows how deep convolutional autoencoder architecture can be trained on images from biological phenotypes to achieve state-of-the-art performance in a phenotypic images retrieval system.

Conclusion:

Taken together, the phenotype analysis system can provide further information on the correlation between genotype and phenotype. Additionally, it is obvious that the neural network model of image segmentation and the phenotype retrieval system is equally suitable for any species, which has enough phenotype images to train the neural network.

Computational aspects underlying genome to phenome analysis in plants

Recent advances in genomics technologies have greatly accelerated the progress in both fundamental plant science and applied breeding research. Concurrently, high-throughput plant phenotyping is becoming widely adopted in the plant community, promising to alleviate the phenotypic bottleneck. While these technological breakthroughs are significantly accelerating quantitative trait locus (QTL) and causal gene identification, challenges to enable even more sophisticated analyses remain. In particular, care needs to be taken to standardize, describe and conduct experiments robustly while relying on plant physiology expertise. In this article, we review the state of the art regarding genome assembly and the future potential of pangenomics in plant research. We also describe the necessity of standardizing and describing phenotypic studies using the Minimum Information About a Plant Phenotyping Experiment (MIAPPE) standard to enable the reuse and integration of phenotypic data. In addition, we show how deep phenotypic data might yield novel trait-trait correlations and review how to link phenotypic data to genomic data. Finally, we provide perspectives on the golden future of machine learning and their potential in linking phenotypes to genomic features.

The role of Arabidopsis thaliana RASD1 gene in ABA-dependent abiotic stress response

Abiotic stress is one of the key parameters affecting plant productivity. Drought and soil salinity, in particular, challenge plants to activate various response mechanisms to withstand these adverse growth conditions. While the molecular events that take place are complex and to a large extent unclear, the plant hormone abscisic acid (ABA) is considered a major player in mediating the adaptation of plants to stress. Here we report the identification of an ABA-insensitive mutant from Arabidopsis thaliana. A combination of molecular, genetic and physiology approaches were implemented, to characterise the AtRASD1 locus (RESPONSIVENESS TO ABA SALT AND DROUGHT 1) and to investigate its role in plant development. RASD1 is expressed predominantly in the vascular system of A. thaliana and encodes a peptide of unknown function with no similarity to any known sequence to date. The protein is localised in the nucleus and the cytoplasm, and RASD1-impaired plants are drought-intolerant and insensitive to exogenous ABA and NaCl during germination and root growth. Our data indicate that RASD1 is involved in ABA-dependent signal transduction pathways and therefore in enabling plants to activate response mechanisms related to seed germination and abiotic stress.

Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes

Algae are smaller organisms than land plants and offer clear advantages in research over terrestrial species in terms of rapid production, short generation time and varied commercial applications. Thus, studies investigating the practical development of effective algal production are important and will improve our understanding of both aquatic and terrestrial plants. In this study we estimated multiple physicochemical and secondary structural properties of protein sequences, the predicted presence of post-translational modification (PTM) sites, and subcellular localization using a total of 510,123 protein sequences from the proteomes of 31 algal and three plant species. Algal species were broadly selected from green and red algae, glaucophytes, oomycetes, diatoms and other microalgal groups. The results were deposited in the Algal Protein Annotation Suite database (Alga-PrAS; http://alga-pras.riken.jp/), which can be freely accessed online.

In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae

Recent proteome analyses have reported that intrinsically disordered regions (IDRs) of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs) has been reported. The genomes of various eukaryotic algae as common ancestors of plants have also been sequenced. However, no analysis of the relationship to protein properties such as structure and PTMs in algae has been reported. Here, we describe correlations between IDR content and the number of PTM sites for phosphorylation, glycosylation, and ubiquitination, and between IDR content and regions rich in proline, glutamic acid, serine, and threonine (PEST) and transmembrane helices in the sequences of 20 algae proteomes. Phosphorylation, O-glycosylation, ubiquitination, and PEST preferentially occurred in disordered regions. In contrast, transmembrane helices were favored in ordered regions. N-glycosylation tended to occur in ordered regions in most of the studied algae; however, it correlated positively with disordered protein content in diatoms. Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae. Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups.

MOROKOSHI: transcriptome database in Sorghum bicolor

In transcriptome analysis, accurate annotation of each transcriptional unit and its expression profile is essential. A full-length cDNA (FL-cDNA) collection facilitates the refinement of transcriptional annotation, and accurate transcription start sites help to unravel transcriptional regulation. We constructed a normalized FL-cDNA library from eight growth stages of aerial tissues in Sorghum bicolor and isolated 37,607 clones. These clones were Sanger sequenced from the 5' and/or 3' ends and in total 38,981 high-quality expressed sequence tags (ESTs) were obtained. About one-third of the transcripts of known genes were captured as FL-cDNA clone resources. In addition to these, we also annotated 272 novel genes, 323 antisense transcripts and 1,672 candidate isoforms. These clones are available from the RIKEN Bioresource Center. After obtaining accurate annotation of transcriptional units, we performed expression profile analysis. We carried out spikelet-, seed- and stem-specific RNA sequencing (RNA-Seq) analysis and confirmed the expression of 70.6% of the newly identified genes. We also downloaded 23 sorghum RNA-Seq samples that are publicly available and these are shown on a genome browser together with our original FL-cDNA and RNA-Seq data. Using our original and publicly available data, we made an expression profile of each gene and identified the top 20 genes with the most similar expression. In addition, we visualized their relationships in gene co-expression networks. Users can access and compare various transcriptome data from S, bicolor at http://sorghum.riken.jp.

A maize database resource that captures tissue-specific and subcellular-localized gene expression, via fluorescent tags and confocal imaging (Maize Cell Genomics Database)

Maize is a global crop and a powerful system among grain crops for genetic and genomic studies. However, the development of novel biological tools and resources to aid in the functional identification of gene sequences is greatly needed. Towards this goal, we have developed a collection of maize marker lines for studying native gene expression in specific cell types and subcellular compartments using fluorescent proteins (FPs). To catalog FP expression, we have developed a public repository, the Maize Cell Genomics (MCG) Database, (http://maize.jcvi.org/cellgenomics), to organize a large data set of confocal images generated from the maize marker lines. To date, the collection represents major subcellular structures and also developmentally important progenitor cell populations. The resource is available to the research community, for example to study protein localization or interactions under various experimental conditions or mutant backgrounds. A subset of the marker lines can also be used to induce misexpression of target genes through a transactivation system. For future directions, the image repository can be expanded to accept new image submissions from the research community, and to perform customized large-scale computational image analysis. This community resource will provide a suite of new tools for gaining biological insights by following the dynamics of protein expression at the subcellular, cellular and tissue levels.

Plant-PrAS: a database of physicochemical and structural properties and novel functional regions in plant proteomes

Arabidopsis thaliana is an important model species for studies of plant gene functions. Research on Arabidopsis has resulted in the generation of high-quality genome sequences, annotations and related post-genomic studies. The amount of annotation, such as gene-coding regions and structures, is steadily growing in the field of plant research. In contrast to the genomics resource of animals and microorganisms, there are still some difficulties with characterization of some gene functions in plant genomics studies. The acquisition of information on protein structure can help elucidate the corresponding gene function because proteins encoded in the genome possess highly specific structures and functions. In this study, we calculated multiple physicochemical and secondary structural parameters of protein sequences, including length, hydrophobicity, the amount of secondary structure, the number of intrinsically disordered regions (IDRs) and the predicted presence of transmembrane helices and signal peptides, using a total of 208,333 protein sequences from the genomes of six representative plant species, Arabidopsis thaliana, Glycine max (soybean), Populus trichocarpa (poplar), Oryza sativa (rice), Physcomitrella patens (moss) and Cyanidioschyzon merolae (alga). Using the PASS tool and the Rosetta Stone method, we annotated the presence of novel functional regions in 1,732 protein sequences that included unannotated sequences from the Arabidopsis and rice proteomes. These results were organized into the Plant Protein Annotation Suite database (Plant-PrAS), which can be freely accessed online at http://plant-pras.riken.jp/.

Arabidopsis thaliana phosphoinositide-specific phospholipase C isoform 3 (AtPLC3) and AtPLC9 have an additive effect on thermotolerance

The heat stress response is an important adaptation, enabling plants to survive challenging environmental conditions. Our previous work demonstrated that Arabidopsis thaliana Phosphoinositide-Specific Phospholipase C Isoform 9 (AtPLC9) plays an important role in thermotolerance. During prolonged heat treatment, mutants of AtPLC3 showed decreased heat resistance. We observed no obvious phenotypic differences between plc3 mutants and wild type (WT) seedlings under normal growth conditions, but after heat shock, the plc3 seedlings displayed a decline in thermotolerance compared with WT, and also showed a 40-50% decrease in survival rate and chlorophyll contents. Expression of AtPLC3 in plc3 mutants rescued the heat-sensitive phenotype; the AtPLC3-overexpressing lines also exhibited much higher heat resistance than WT and vector-only controls. The double mutants of plc3 and plc9 displayed increased sensitivity to heat stress, compared with either single mutant. In transgenic lines containing a AtPLC3:GUS promoter fusion, GUS staining showed that AtPLC3 expresses in all tissues, except anthers and young root tips. Using the Ca(2+)-sensitive fluorescent probe Fluo-3/AM and aequorin reconstitution, we showed that plc3 mutants show a reduction in the heat-induced Ca(2+) increase. The expression of HSP genes (HSP18.2, HSP25.3, HSP70-1 and HSP83) was down-regulated in plc3 mutants and up-regulated in AtPLC3-overexpressing lines after heat shock. These results indicated that AtPLC3 also plays a role in thermotolerance in Arabidopsis, and that AtPLC3 and AtPLC9 function additionally to each other.