KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research

A database (DB) describing the relationships between species and their metabolites would be useful for metabolomics research, because it targets systematic analysis of enormous numbers of organic compounds with known or unknown structures in metabolomics. We constructed an extensive species-metabolite DB for plants, the KNApSAcK Core DB, which contains 101,500 species-metabolite relationships encompassing 20,741 species and 50,048 metabolites. We also developed a search engine within the KNApSAcK Core DB for use in metabolomics research, making it possible to search for metabolites based on an accurate mass, molecular formula, metabolite name or mass spectra in several ionization modes. We also have developed databases for retrieving metabolites related to plants used for a range of purposes. In our multifaceted plant usage DB, medicinal/edible plants are related to the geographic zones (GZs) where the plants are used, their biological activities, and formulae of Japanese and Indonesian traditional medicines (Kampo and Jamu, respectively). These data are connected to the species-metabolites relationship DB within the KNApSAcK Core DB, keyed via the species names. All databases can be accessed via the website http://kanaya.naist.jp/KNApSAcK_Family/. KNApSAcK WorldMap DB comprises 41,548 GZ-plant pair entries, including 222 GZs and 15,240 medicinal/edible plants. The KAMPO DB consists of 336 formulae encompassing 278 medicinal plants; the JAMU DB consists of 5,310 formulae encompassing 550 medicinal plants. The Biological Activity DB consists of 2,418 biological activities and 33,706 pairwise relationships between medicinal plants and their biological activities. Current statistics of the binary relationships between individual databases were characterized by the degree distribution analysis, leading to a prediction of at least 1,060,000 metabolites within all plants. In the future, the study of metabolomics will need to take this huge number of metabolites into consideration.     

HoSeqI: automated homologous sequence identification in gene family databases

We present a web service allowing to automatically assign sequences to homologous gene families from a set of databases. After identification of the most similar gene family to the query sequence, this sequence is added to the whole alignment and the phylogenetic tree of the family is rebuilt. Thus, the phylogenetic position of the query sequence in its gene family can be easily identified. AVAILABILITY: http://pbil.univ-lyon1.fr/software/HoSeqI/.     

Reconciling gene and genome duplication events: using multiple nuclear gene families to infer the phylogeny of the aquatic plant family Pontederiaceae

Most plant phylogenetic inference has used DNA sequence data from the plastid genome. This genome represents a single genealogical sample with no recombination among genes, potentially limiting the resolution of evolutionary relationships in some contexts. In contrast, nuclear DNA is inherently more difficult to employ for phylogeny reconstruction because major mutational events in the genome, including polyploidization, gene duplication, and gene extinction can result in homologous gene copies that are difficult to identify as orthologs or paralogs. Gene tree parsimony (GTP) can be used to infer the rooted species tree by fitting gene genealogies to species trees while simultaneously minimizing the estimated number of duplications needed to reconcile conflicts among them. Here, we use GTP for five nuclear gene families and a previously published plastid data set to reconstruct the phylogenetic backbone of the aquatic plant family Pontederiaceae. Plastid-based phylogenetic studies strongly supported extensive paraphyly of Eichhornia (one of the four major genera) but also depicted considerable ambiguity concerning the true root placement for the family. Our results indicate that species trees inferred from the nuclear genes (alone and in combination with the plastid data) are highly congruent with gene trees inferred from plastid data alone. Consideration of optimal and suboptimal gene tree reconciliations place the root of the family at (or near) a branch leading to the rare and locally restricted E. meyeri. We also explore methods to incorporate uncertainty in individual gene trees during reconciliation by considering their individual bootstrap profiles and relate inferred excesses of gene duplication events on individual branches to whole-genome duplication events inferred for the same branches. Our study improves understanding of the phylogenetic history of Pontederiaceae and also demonstrates the utility of GTP for phylogenetic analysis.     

Ancient signals: comparative genomics of plant MAPK and MAPKK gene families

MAPK signal transduction modules play crucial roles in regulating many biological processes in plants, and their components are encoded by highly conserved genes. The recent availability of genome sequences for rice and poplar now makes it possible to examine how well the previously described Arabidopsis MAPK and MAPKK gene family structures represent the broader evolutionary situation in plants, and analysis of gene expression data for MPK and MKK genes in all three species allows further refinement of those families, based on functionality. The Arabidopsis MAPK nomenclature appears sufficiently robust to allow it to be usefully extended to other well-characterized plant systems.     

CRAWview: for viewing splicing variation, gene families, and polymorphism in clusters of ESTs and full-length sequences.

MOTIVATION: DNA sequence clustering has become a valuable method in support of gene discovery and gene expression analysis. Our interest lies in leveraging the sequence diversity within clusters of expressed sequence tags (ESTs) to model gene structure for the study of gene variants that arise from, among other things, alternative mRNA splicing, polymorphism, and divergence after gene duplication, fusion, and translocation events. In previous work, CRAW was developed to discover gene variants from assembled clusters of ESTs. Most importantly, novel gene features (the differing units between gene variants, for example alternative exons, polymorphisms, transposable elements, etc.) that are specialized to tissue, disease, population, or developmental states can be identified when these tools collate DNA source information with gene variant discrimination. While the goal is complete automation of novel feature and gene variant detection, current methods are far from perfect and hence the development of effective tools for visualization and exploratory data analysis are of paramount importance in the process of sifting through candidate genes and validating targets. RESULTS: We present CRAWview, a Java based visualization extension to CRAW. Features that vary between gene forms are displayed using an automatically generated color coded index. The reporting format of CRAWview gives a brief, high level summary report to display overlap and divergence within clusters of sequences as well as the ability to 'drill down' and see detailed information concerning regions of interest. Additionally, the alignment viewing and editing capabilities of CRAWview make it possible to interactively correct frame-shifts and otherwise edit cluster assemblies. We have implemented CRAWview as a Java application across windows NT/95 and UNIX platforms. AVAILABILITY: A beta version of CRAWview will be freely available to academic users from Pangea Systems (http://www.pangeasystems.com). Contact :     

An ESTs description of the new Vanin gene family conserved from fly to human

Circulation and tissue colonization are essential properties of lymphoid cells and involve major families of adhesion molecules (e.g. , integrin, selectin, mucin-like, and molecules from the immunoglobulin superfamily). The mouse Vanin-1 molecule was recently identified and found to be involved in the colonization of the thymus by hematopoietic precursor cells. Here we show based on computational analysis of EST sequence database resources that Vanin-1 belongs to a new family of related molecules present from drosophila to human. This family includes the amidase enzyme Biotinidase, and a central protein domain is shared between Vanin and Nitrilase families, suggesting that Vanin molecules might bear an enzymatic activity. Five of these molecules were new uncharacterized cDNA sequences only described as ESTs. The three human Vanin genes map to the same region of Chromosome 6q. The detailed results are consultable at the VANIN web page (http://tagc. univ-mrs.fr/pub/vanin/).     

Food-plant families of British insects and mites: the influence of life form and plant family

The dissimilarities between 107 British plant families with respect to the insect and mite species which feed on them were analysed using a principal co-ordinates analysis. The relationships between the plant families were strongly influenced by the plant life forms. Major groups were woody plants (trees and shrubs), aquatic plants and herbs. A wet to dry gradient was distinguished, as were evergreen plants, and early successional plant families with weeds and annuals. Taxonomically, plant families of the same order were closer together if they were predominantly of the same life form. Fagales and several orders of monocotyledons formed particularly clear groups. The three 'nearest neighbours' of each plant family based on the dissimilarities measures were listed. These provide some interesting, but conjectural, data on evolutionary aspects of plant families. This was illustrated briefly by the Cornaceae and Euphorbiaceae. The underlying progressive evolution of plants from woody species and wetter areas to herbs and annual plants of dry and cold places may be reflected by insect and mite food plant family associations.     

Function and evolution of the plant MADS-box gene family

The function of MADS-box genes in flower and fruit development has been uncovered at a rapid pace over the past decade. Evolutionary biologists can now analyse the expression pattern of MADS-box genes during the development of different plant species, and study the homology of body parts and the evolution of body plans. These studies have shown that floral development is conserved among divergent species, and indicate that the basic mechanism of floral patterning might have evolved in an ancient flowering plant.     

Chromosome numbers and differentiation of centrospermous families

The patterns of variation of chromosome numbers in theCentrospermae suggest a common ancestry of centrospermous anthocyanin and betalain families. Phylogenetic divergence in the order may have originated with progenitors similar to extantMolluginaceae, Aizoaceae orPhytolaccaceae taxa with x = 9. Evolutionary radiation and advancement in several lines then seems to have been paralleled by trends for increasing chromosome base numbers through dysploidy and polyploidy, e.g. towardsCaryophyllaceae, Portulacaceae-Basellaceae, Hectorellaceae, Cactaceae, Didieraceae, Nyctaginaceae andChenopodiaceae-Amaranthaceae. Presented in the Symposium Evolution of Centrospermous Families, during the XIIth International Botanical Congress, Leningrad, July 8, 1975.     

Genome-wide enzyme annotation with precision control: catalytic families (CatFam) databases

In this article, we present a new method termed CatFam (Catalytic Families) to automatically infer the functions of catalytic proteins, which account for 20-40% of all proteins in living organisms and play a critical role in a variety of biological processes. CatFam is a sequence-based method that generates sequence profiles to represent and infer protein catalytic functions. CatFam generates profiles through a stepwise procedure that carefully controls profile quality and employs nonenzymes as negative samples to establish profile-specific thresholds associated with a predefined nominal false-positive rate (FPR) of predictions. The adjustable FPR allows for fine precision control of each profile and enables the generation of profile databases that meet different needs: function annotation with high precision and hypothesis generation with moderate precision but better recall. Multiple tests of CatFam databases (generated with distinct nominal FPRs) against enzyme and nonenzyme datasets show that the method's predictions have consistently high precision and recall. For example, a 1% FPR database predicts protein catalytic functions for a dataset of enzymes and nonenzymes with 98.6% precision and 95.0% recall. Comparisons of CatFam databases against other established profile-based methods for the functional annotation of 13 bacterial genomes indicate that CatFam consistently achieves higher precision and (in most cases) higher recall, and that (on average) CatFam provides 21.9% additional catalytic functions not inferred by the other similarly reliable methods. These results strongly suggest that the proposed method provides a valuable contribution to the automated prediction of protein catalytic functions. The CatFam databases and the database search program are freely available at http://www.bhsai.org/downloads/catfam.tar.gz.     

The evolution of a plant globin gene family

Summary We have analyzed the sequences of soybean leghemoglobin genes as an initial step toward understanding their mode of evolution. Alignment of the sequences of plant globin genes with those of animals reveals that (i) based on the proportion of nucleotide substitutions that have occurred at the first, second, and third codon positions, the time of divergence of plant and animal globin gene families appears to be extremely remote (between 900 million and 1.4 billion years ago, if one assumes constancy of evolutionary rate in both the plant and animal lineages) and (ii) in addition to the normal regulatory sequences on the 5 end, an approximately 30-base-pair sequence, specific to globin genes, that surrounds the cap site is conserved between the plant and animal globin genes. Comparison of the leghemoglobin sequences with one another shows that (i) the relative amount of sequence divergence in various coding and noncoding regions is roughly similar to that found for animal globin genes and (ii) as in animal globin genes, the positions of insertions and deletions in the intervening sequences often coincide with the locations of direct repeats. Thus, the mode of evolution of the plant globin genes appears to resemble, in many ways, that of their animal counterparts. We contrast the overall intergenic organization of the plant globin genes with that of animal genes, and discuss the possibility of the concerted evolution of the leghemoglobin genes.