The SOL Genomics Network Model: Making Community Annotation Work

The concept of community annotation is a growing discipline for achieving participation of the research community in depositing up‐to‐date knowledge in biological databases.
The Solanaceae Genomics Network ("SGN":http://sgn.cornell.edu/) is a clade‐oriented database (COD) focusing on plants of the nightshade family, including tomato, potato, pepper, eggplant, and tobacco, and is one of the bioinformatics nodes of the international tomato genome sequencing project. One of our major efforts is linking Solanaceae phenotype information with the underlying genes, and subsequently the genome. As part of this goal, SGN has introduced a database for locus names and descriptors, and a database for phenotypes of natural and induced variation. These two databases have web interfaces that allow cross references, associations with tomato gene models, and in‐house curated information of sequences, literature, ontologies, gene networks, and the Solanaceae biochemical pathways database ("SolCyc":http://solcyc.sgn.cornell.edu). All of our curator tools are open for online community annotation, through specially assigned “submitter” accounts. 

Currently the community database consists of 5,548 phenotyped accessions, and 5,739 curated loci, out of which more than 300 loci where contributed or annotated by 66 active submitters, creating a database that is truly community driven.
This framework is easily adaptable for other projects working on other taxa (for example see "http://chlamybase.org":http://chlamybase.org), greatly expanding the application of this user‐friendly online annotation system. Community participation is fostered by an active outreach program that includes contacting potential submitters via emails, at meetings and conferences, and by promoting featured user submitted annotations on the SGN homepage. The source code and database schema for all SGN functionalities are freely available. Please contact SGN at "sgn‐feedback[at]sgn.cornell.edu":mailto:[email protected] for more information

Description and molecular diagnosis of a new species of Brunfelsia (Solanaceae) from the Bolivian and Argentinean Andes

Brunfelsia plowmaniana N.Filipowicz & M.Nee sp. nov., a species from humid and cloud forests of the Bolivian and Argentinean Andes, is described and provided with a molecular diagnosis, using provisions available in the recently approved International Code of Nomenclature for algae, fungi and plants. Specimens belonging to the new species were previously placed in the polymorphic B. uniflora (Pohl) D.Don, which a molecular phylogeny revealed as polyphyletic. Revision of numerous collections revealed clear morphological differences between the new species and B. uniflora, the type locality of which is in the state of São Paulo, Brazil

INDEPENDENT ORIGINATION OF FLORAL ZYGOMORPHY, A PREDICTED ADAPTIVE RESPONSE TO POLLINATORS: DEVELOPMENTAL AND GENETIC MECHANISMS

Observations of floral development indicate that floral organ initiation in pentapetalous flowers more commonly results in a medially positioned abaxial petal (MAB) than in a medially positioned adaxial petal (MAD), where the medial plane is defined by the stem and the bract during early floral development. It was proposed that the dominant MAB petal initiation might impose a developmental constraint that leads to the evolution of limited patterns of floral zygomorphy in Asteridae, a family in which the floral zygomorphy develops along the medial plane and results in a central ventral (CV) petal in mature flowers. Here, I investigate whether the pattern of floral organ initiation may limit patterns of floral zygomorphy to evolve in pentapetalous angiosperms. I analyzed floral diagrams representing 405 species in 330 genera of pentapetalous angiosperms to reconstruct the evolution of floral organ initiation and the evolution of developmental processes that give rise to floral zygomorphy on a phylogenetic framework. Results indicate that MAB petal initiation is the most common; it occupies 86.2% of diversity and represents the ancestral state of floral organ initiation in pentapetalous angiosperms. The MAD petal initiation evolved 28 times independently from the ancestral MAB petal initiation. Among the 34 independent originations of floral zygomorphy, 76.5% of these clades represent MAB petal initiation, among which only 47% of the clades result a CV petal in mature flowers. The discrepancy is explained by the existence of developmental processes that result in floral zygomorphy along oblique planes of floral symmetry in addition to along the medial plane. Findings suggest that although the early floral organ initiation plays a constraining role to the evolution of patterns of floral zygomorphy, the constraint diverges along phylogenetically distantly related groups that allow the independent originations of floral zygomorphy through distinct development processes in pentapetalous angiosperms. In additional study, the butterfly-like flowers of Schizanthus are adapted to pollination by bees, hummingbirds, and moths. I investigated the genetic basis of the zygomorphic corolla, for which development is key to the explosive pollen release mechanism found in the species of Schizanthus adapted to bee pollinators. I examined differential gene expression profiles across the zygomorphic corolla of Schizanthus pinnatus, a bee-pollinated species, by analyzing RNA transcriptome sequencing (RNA- seq). Data indicated that CYC2 is not expressed in the zygomorphic corolla of Sc. pinnatus, suggesting CYC2 is not involved in the development of floral zygomorphy in Schizanthus (Solanaceae). The data also indicated that a number of genes are differentially expressed across the corolla

Tomato prosystemin gene in other Solanaceae

Systemin, an octadeca-peptide isolated from tomato, is a signalling molecule involved in local and systemic wound response. It regulates the activation of more than twenty defensive genes in tomato plants in response to herbivore attacks. Systemin derives from the C-terminal region of a precursor of 200 amino acids, known as prosystemin. Prosystemin homologues have been found in other Solanaceae species such as potato (Solanum tuberosum), black nightshade (Solanum nigrum) and bell pepper (Capsicum annum), all members of the Solaneae subtribe, whereas they were not identified in tobacco, which belongs to the Nicotianae subtribe. Tobacco possesses two hydroxyproline-rich peptides released from the same precursor (preproTobHypSys) that show systemin-like activity. However, those peptides and their precursors are not similar in sequence to the tomato prosystemin. Even if it was previously showed that tobacco does not respond to tomato systemin when externally applied, it has been recently found that wild type tobacco cells are sensitive to systemin. Furthermore, a recent finding indicate that the constitutive expression of the tomato prosystemin in tobacco plants increases the expression of a number of proteins involved in plant defence against pathogens and oxidative stress. The aim of this project was to increase the understanding of the possible biotechnological role of the tomato prosystemin, with a particular emphasis to the exploitation of this precursor to increase the endogenous resistance against biotic stress. To this goal, the tomato prosystemin cDNA was expressed in tobacco and potato. Moreover, a mutated prosystemin cDNA lacking the 3’ terminal systemin encoding exon was also expressed to understand the possible function of the N-terminal region prosystemin precursor in the activation of the defence response. Transgenic tobacco plants expressing either of the prosystemin genes were already available. Transgenic potato plants were obtained after an Agrobacterium-mediated plant transformation. Tobacco and potato transformants were characterized and a group of genes involved in plant response against biotic stress was analysed by Real Time PCR. The modification in gene expression registered in MZ transgenic plants (expressing the tomato prosystemin cDNA) and PRO8 plants (expressing the deleted prosystemin) showed that HSP, GST, Pin II and TobHypSys, all related to plant response to stress, are over-expressed in tobacco transformants. Among the gene tested, GST gene was over-expressed only in MZ transgenic plants. Furthermore, in tobacco, the over-expression level induced by prosystemin of HSP and Pin II is similar to the effect of wounding. A bioassay with the pathogenic fungus Botrytis cinerea showed a moderate increase in resistance in the PRO8 tobacco plants. The expression of prosystemin gene in potato does not affect pathogen-related genes as GluB2 and PR1b nor the defence-related potato endogenous systemins, PotProsys and prePotHypSys genes. A effect was observed for Lox3 that was over-expressed in potato in both MZ and PRO8 transgenic plants. These data imply that the modification in gene expression in tobacco and potato is not only due to the Sys sequence and that the N-terminus is also involved

Molecular studies on a complex of potyviruses infecting solanaceous crops, and some specific virus-host interactions

This thesis constitutes a comprehensive analysis of the molecular and biological characteristics of three potyviruses (genus Potyvirus, family Potyviridae) naturally occurring in cultivated and wild species of family Solanaceae: Peru tomato virus (PTV), Potato virus V (PVV) and Wild potato mosaic virus (WPMV). In addition, the studies presented in this thesis focus on the genetic variability of isolates of PTV and PVV and on the role of the Potato virus A (PVA) 6K2 protein as a host-specific determinant of virus movement and symptom induction. Determination of the complete genomic sequences of PVV, PTV and WPMV demonstrated that these viruses are typical members of the genus Potyvirus. Furthermore, comparison of the polyprotein amino acid sequences and the biological and serological characteristics of these three viruses supported their current taxonomic position as independent species of the genus Potyvirus. The nucleotide sequences of the P1 protein, coat protein and non-translated regions of European and South American PVV isolates were determined and compared. Results showed limited genetic variability among the European isolates, in contrast to the higher variability found among the South American isolates of PVV. Phylogenetic analysis defined two distinct clusters, grouping the European isolates together but placing two South American isolates to a different group; these two isolates of PVV did not induce a hypersensitive response in an Nv gene-carrying potato cultivar in contrast to the European PVV isolates. Thus, European and South American PVV isolates belong to different strain groups. In addition, great genetic variability was detected among PTV isolates. Analysis of phylogenetic relationships among PTV, PVV, WPMV and other members of the genus Potyvirus commonly found infecting solanaceous crop plants showed that PTV, PVV and WPMV are the most closely related viruses which together with Potato virus Y, Pepper mottle virus, Pepper severe mosaic virus and Pepper yellow mosaic virus constitute a group distinguishable from other potyviruses. Thus, members of this group seem to share a common ancestor. The 6K2 protein of PVA was modified by deleting various portions or by introducing six histidine residues (6xHis) into various positions of this protein. These modifications disturbed functions required for viral infection in Nicotiana tabacum. Furthermore, inoculation of the insertion constructs to N. benthamiana plants did not result in systemic infection with the exception of one plant. This plant lacked typical PVA symptoms but had virus titers similar to the plants infected with the wild type virus: a single point mutation (Gly2 ® Cys2) in the 6xHis-containing 6K2 had restored the viral movement functions. However, partial deletion of the 6xHis-tag to gain the original size of the 6K2 protein was required to restore the induction of symptoms in N. benthamiana and to enable systemic infection of N. tabacum. Taken together, these results indicate the 6K2 is a host-specific determinant for long-distance movement and exemplify that mutations that arise during viral propagation represent a mechanisms by which viruses can evolve and adapt to different hosts

A revision of the Old World Black Nightshades (Morelloid clade of Solanum L., Solanaceae)

The Morelloid clade, also known as the black nightshades or ?Maurella? (Morella), is one of the 10 major clades within Solanum L. The pantropical clade consists of 75 currently recognised non-spiny herbaceous and suffrutescent species with simple or branched hairs with or without glandular tips, with a centre of distribution in the tropical Andes. A secondary centre of diversity is found in Africa, where a set of mainly polyploid taxa occur. A yet smaller set of species is found in Australasia and Europe, including Solanum nigrum L., the type of the genus Solanum. Due to the large number of published synonyms, combined with complex morphological variation, our understanding of species limits and diversity in the Morelloid clade has remained poor despite detailed morphological studies carried out in conjunction with breeding experiments. Here we provide the first taxonomic overview since the 19th century of the entire group in the Old World, including Africa, Asia, Australia, Europe and islands of the Pacific. Complete synonymy, morphological descriptions, distribution maps and common names and uses are provided for all 19 species occurring outside the Americas (i.e. Africa, Asia, Australia, Europe and islands of the Pacific). We treat 12 species native to the Old World, as well as 7 taxa that are putatively introduced and/or invasive in the region. The current knowledge of the origin of the polyploid species is summarised. A key to all of the species occurring in the Old World is provided, together with line drawings and colour figures to aid identification both in herbaria and in the field. Preliminary conservation assessments are provided for all species.Fil: Sarkinen, T.. University Of Edinburgh; Reino UnidoFil: Poczai, P.

MarkerMiner 1.0: a new application for phylogenetic marker development using angiosperm transcriptomes

Premise of the study: Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited. Methods and Results: We developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workflow and application for discovery of SCN loci in angiosperms. Our new tool identified as many as 1993 SCN loci from transcriptomic data sampled as part of four independent test cases representing marker development projects at different phylogenetic scales. Conclusions: MarkerMiner is an easy-to-use and effective tool for discovery of putative SCN loci. It can be run locally or via the Web, and its tabular and alignment outputs facilitate efficient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development