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

Comparative Study of \u3ci\u3eMecinus Janthiniformis\u3c/i\u3e (Coleoptera: Curculionidae) Attack and Simulated Mowing for Control of \u3ci\u3eLinaria Dalmatica\u3c/i\u3e Spp. \u3ci\u3eDalmatica\u3c/i\u3e (Plantaginaceae)

Dalmatian toadflax, Linaria dalmatica spp. dalmatica (L.) Mill. (Plantaginaceae) has invaded over one million hectares in the western United States and Canada, in habitats similar to its native range. Two field studies were conducted to examine the impact of simulated mowing or insect herbivory on L. dalmatica growth and reproduction. Simulated mowing over the duration of the study decreased L. dalmatica total biomass per square meter, significantly reduced the total number of fruits and flowers per square meter, and resulted in significantly shorter flowering stems in the simulated mowing plots than in their controls. Plants in plots attacked by Mecinus janthiniformis Toševski and Caldara (Coleoptera: Curculionidae) had significantly less biomass per square meter, significantly fewer total numbers of fruits and flowers per square meter, and significantly fewer reproductive structures per stem than plants in paired control plots over the duration of the study. Specifically, both management tactics resulted in a negative impact on this invasive plant. With repeated tissue removal or damage, a reduction in numbers of fruits and flowers per stem on both the stems subjected to simulated mowing and Mecinus-attacked stems relative to their controls suggests that long term stress effects on the plants may be similar. The results of these studies suggest that mowing may warrant further evaluation as a possible method of control in areas where M. janthiniformis release is not effective

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

Expression and trans-specific polymorphism of self-incompatibility RNases in Coffea (Rubiaceae)

Self-incompatibility (SI) is widespread in the angiosperms, but identifying the biochemical components of SI mechanisms has proven to be difficult in most lineages. Coffea (coffee; Rubiaceae) is a genus of old-world tropical understory trees in which the vast majority of diploid species utilize a mechanism of gametophytic self-incompatibility (GSI). The S-RNase GSI system was one of the first SI mechanisms to be biochemically characterized, and likely represents the ancestral Eudicot condition as evidenced by its functional characterization in both asterid (Solanaceae, Plantaginaceae) and rosid (Rosaceae) lineages. The S-RNase GSI mechanism employs the activity of class III RNase T2 proteins to terminate the growth of "self" pollen tubes. Here, we investigate the mechanism of Coffea GSI and specifically examine the potential for homology to S-RNase GSI by sequencing class III RNase T2 genes in populations of 14 African and Madagascan Coffea species and the closely related self-compatible species Psilanthus ebracteolatus. Phylogenetic analyses of these sequences aligned to a diverse sample of plant RNase T2 genes show that the Coffea genome contains at least three class III RNase T2 genes. Patterns of tissue-specific gene expression identify one of these RNase T2 genes as the putative Coffea S-RNase gene. We show that populations of SI Coffea are remarkably polymorphic for putative S-RNase alleles, and exhibit a persistent pattern of trans-specific polymorphism characteristic of all S-RNase genes previously isolated from GSI Eudicot lineages. We thus conclude that Coffea GSI is most likely homologous to the classic Eudicot S-RNase system, which was retained since the divergence of the Rubiaceae lineage from an ancient SI Eudicot ancestor, nearly 90 million years ago.United States National Science Foundation [0849186]; Society of Systematic Biologists; American Society of Plant Taxonomists; Duke University Graduate Schoolinfo:eu-repo/semantics/publishedVersio

Looking for the vector of the latest discovered geminivirus genus, Capulavirus. [P.48]

Viral metagenomics studies based on virion-associated nucleic acid extraction, sequence-independent amplification and next generation sequencing proved to be effective for discovering three highly divergent geminiviruses in South Africa, France and Finland. Although these geminiviral sequences were isolated from different continents, hemispheres and plant families, including Euphorbia caput-medusae (Euphorbiaceae), Medicago sativa (Fabaceae) and Plantago lanceolata (Plantaginaceae), they were clustered in the same phylogenetic group and were highly divergent from all the sequences classified in the seven established geminivirus genera. Based on sequence relatedness and genome organization, these new highly divergent geminivirus species were provisionally classified in a new geminivirus genus, tentatively named "Capulavirus". To estimate the epidemiological potential of these new geminiviruses but also to confirm their classification according to the criteria defined by the International Committee on Taxonomy of Viruses, including insect vector and host range, further studies were done with two capulaviruses available in our laboratory: Euphorbia caput medusae latent virus (EcmLV) from South Africa (Bernardo et al. 2013) and a capulavirus isolated from alfalfa in France provisionally named Alfalfa leaf curl virus (ALCV) according to the symptoms observed on infected plants. ALCV may cause yield losses because the infected plants exhibited stunting and distorted growth. ALCV was detected in Camargue, Provence Alpes Côte d'Azur, Languedoc Roussillon and Midi-Pyrénées. An infectious clone of EcmLV was prepared and used to determine the host range of EcmLV and test various phloem feeding insects reared in our laboratory, for vector transmission. Potentially infectious clones are presently prepared for ALCV for similar tests. In the meantime, a naturally infected alfalfa plant was transferred to a growth chamber and used as source plant for vector transmission. Potential vectors were also collected from infected alfalfa fields for testing ALCV transmission to alfalfa seedlings prepared in insect proof conditions. (Résumé d'auteur

Considerations on the two Cavanillesian types

Es discuteix el tipus nomenclatural d’Antirrhinum tenellum (Plantaginaceae) i Genista patens (Leguminosae). El nom cavanillesià Antirrhinum tenellum és tipificat a partir d’un espècimen pertanyent al material original, conservat a l’herbari de Cavanilles del Real Jardí Botànic de Madrid (MA). Es proposa esmenar la “lectotipificació” de Genista patens i es proposa l’ús del terme holòtip per designar el material disponible.The nomenclatural types of Antirrhinum tenellum (Plantaginaceae) and Genista patens (Leguminosae) are discussed. The cavanillesian name Antirrhinum tenellum is typified from an original specimen preserved in the Cavanilles’s herbarium in the Royal Botanic Garden of Madrid (MA). The previous “lectotypification” of Genista patens is commented upon, and the use of the term holotype is proposed to designate the available material

Chromosome numbers for the Italian flora: 3

In this contribution new chromosome data obtained from material collected in Italy are presented. It includes four chromosome counts for the following genera: Bellevalia (Asparagaceae), Genista (Fabaceae), Linaria (Plantaginaceae), and Teucrium (Lamiaceae)

Cytological evidence for gametophytic self-incompatibility in the genus Veronica

The self-incompatibility (SI) of 3 Middle East Veronica species (V. filiformis, V. gentianoides, V. teucrium) is studied, for the first time, by pollination and pollen tube growth experiments. Cytological observations of the self-pollen tubes within the pistils permit a conclusion about the presence of a gametophytic SI system in the first 2 species. The investigated population of the third is self-compatible and confirms the facultative trait of its self-sterility. The presence of a gametophytic SI system in 2 of them suggests the putative conservation of this SI system within the genus Veronica (Plantaginaceae) and could be related to the well-known gametophytic SI system present in the other Plantaginaceae genus, Antirrhinum