Genomic Resources for Evolutionary Studies in the Large, Diverse, Tropical Genus, Begonia

Begonia is one of the ten largest angiosperm genera with over 1,500 species found throughout the tropics. To use this group as a model for the evolution of diversity in tropical herbaceous plants, we have produced three species transcriptomes, physical genome size measures, and two backcross genetic maps. We chose to focus on two Central American species, B. conchifolia and B. plebeja, and one SE Asian species, B. venusta, allowing us to pose questions at widely different evolutionary scales within the genus. We used next generation sequencing of cDNA libraries to produce annotated transcriptome databases for each of the three species. Though Begonia is functionally diploid, transcriptome analysis suggested a genome duplication occurred at or near the base of the Begonia clade. The genetic maps were built from first generation backcrosses in both directions between B. plebeja and B. conchifolia using 105 SNP markers in genes known to regulate development that were identified from the transcriptomes and the map bulked out with 226 AFLP loci. The genetic maps had 14 distinct linkage groups each and mean marker densities of between 3. 6 and 5. 8 cM providing between 96 and 99 % genomic coverage within 10 cM. We measured genome size 1C value of 0. 60 and 0. 63 pg for B. conchifolia and B. plebeja corresponding to recombination rates of between 441 and 451 Kb per cM in the genetic maps. Altogether, these new data represent a powerful new set of molecular genetic tools for evolutionary study in the genus Begonia. © 2012 Springer Science+Business Media, LLC.Peer Reviewe

Evolutionary patterns of genome size and chromosome number variation in Begoniaceae

Cytological data resources are crucial to the study and understanding of the evolution of complex taxa. Recent research on the genus Begonia L. has provided a robust phylogenetic background for the analysis of evolutionary patterns across the group and has established that Begonia is variable in genome size and chromosome number. This paper provides an overview of the genome structural variation present in Begonia and an updated chromosome number and genome size dataset for the genus. Chromosome numbers of more than 400 species are presented and discussed within their current taxonomic and phylogenetic context. A more complete chromosome number dataset is available for Neotropical and Asian Begonia sections than for those from Africa. The distribution of chromosome numbers across phylogenetic trees supports the idea of Begonia sections as natural groups, because most variation is found between sections rather than within them. Some larger Begonia clades were found to have larger chromosome number variation. Moreover, groups with the most variable chromosome numbers belong to some of the taxonomically complex or unresolved Begonia sections. Genome size variation was found not to correlate with changes in chromosome number. It suggests that Begonia genome dynamics are caused not only by large-scale duplications, rearrangements, and changes in ploidy levels but also by changes in the repetitive fraction of the genome, which probably cause changes in chromosome size. This could potentially play an important role in species radiations.Introduction Materials and methods Data collection, phylogenetic sorting and curation Genome size estimation Results and discussion Cytological data compilation and geographical and taxonomic distribution Chromosome number variation in Begonia Genome size variation in Begonia Conclusions Acknowledgements Supplementary material Reference

RNA Interference: Its Use as Antiviral Therapy

RNA interference (RNAi) is a sequence-specific gene-silencing mechanism that has been proposed to function as a defence mechanism of eukaryotic cells against viruses and transposons. RNAi was first observed in plants in the form of a mysterious immune response to viral pathogens. But RNAi is more than just a response to exogenous genetic material. Small RNAs termed microRNA (miRNA) regulate cellular gene expression programs to control diverse steps in cell development and physiology. The discovery that exogenously delivered short interfering RNA (siRNA) can trigger RNAi in mammalian cells has made it into a powerful technique for generating genetic knock-outs. It also raises the possibility to use RNAi technology as a therapeutic tool against pathogenic viruses. Indeed, inhibition of virus replication has been reported for several human pathogens including human immunodeficiency virus, the hepatitis B and C viruses and influenza virus. We reviewed the field of antiviral RNAi research in 2003 (Haasnoot et al. 2003), but many new studies have recently been published. In this review, we present a complete listing of all antiviral strategies published up to and including December 2004. The latest developments in the RNAi field and their antiviral application are describe

Flower Development

Flowers are the most complex structures of plants. Studies of Arabidopsis thaliana, which has typical eudicot flowers, have been fundamental in advancing the structural and molecular understanding of flower development. The main processes and stages of Arabidopsis flower development are summarized to provide a framework in which to interpret the detailed molecular genetic studies of genes assigned functions during flower development and is extended to recent genomics studies uncovering the key regulatory modules involved. Computational models have been used to study the concerted action and dynamics of the gene regulatory module that underlies patterning of the Arabidopsis inflorescence meristem and specification of the primordial cell types during early stages of flower development. This includes the gene combinations that specify sepal, petal, stamen and carpel identity, and genes that interact with them. As a dynamic gene regulatory network this module has been shown to converge to stable multigenic profiles that depend upon the overall network topology and are thus robust, which can explain the canalization of flower organ determination and the overall conservation of the basic flower plan among eudicots. Comparative and evolutionary approaches derived from Arabidopsis studies pave the way to studying the molecular basis of diverse floral morphologies