Catherine A. Kidner

Spatially restricted microRNA directs leaf polarity through ARGONAUTE1.

Gene regulation by RNA interference requires the functions of the PAZ domain protein Argonaute. In plants, mutations in ARGONAUTE1 (AGO1) are associated with distinctive developmental defects that suggest a role for microRNA (miRNA) in organ polarity. Potential targets of miRNA regulation are the homeodomain/leucine zipper genes PHABULOSA (PHB) and PHAVOLUTA (PHV). These genes are expressed in a polar fashion in leaf primordia and are required for adaxial cell fate. Here we show that a 21-nucleotide miRNA that directs cleavage of PHB/PHV messenger RNA accumulates first in the embryonic meristem, and then in the abaxial domain of the developing leaf. miRNA distribution is disrupted by mutations in AGO1, indicating that AGO1 affects the regulation of miRNA. In addition, interactions between homeodomain/leucine zipper genes and an allelic series of ago1 indicate that miRNA acts as a signal to specify leaf polarity.

Signaling Sides: Adaxial–Abaxial Patterning in Leaves

Most leaves are dorsiventrally flattened and develop clearly defined upper and lower surfaces. Light capturing is the specialization of the adaxial or upper surface and the abaxial or lower surface is specialized for gas exchange (Fig. 5.1). This division into adaxial and abaxial domains is also key for the outgrowth of the leaf blade or lamina, which occurs along the boundary between the upper and lower sides. How this polarity is set up is not clear but genetic analysis in a range of species suggests that several highly conserved interlocking pathways are involved. Positional information from the meristem is reinforced by signaling through the epidermal layer as the meristem grows away from the leaf primordium. Opposing ta-siRNA and miRNA gradients help refine distinct adaxial and abaxial sides, and mutual inhibition between the genes expressed on each side stabilizes the boundary. In this review we consider how recent work in a range of species is clarifying our understanding of these processes.

The many roles of small RNAs in leaf development

Leaf development involves many complex genetic interactions, signals between adjacent cells or between more distant tissues and consequent changes in cell fate. This review describes three stages in leaf development where regulation by small RNAs have been used to modulate gene expression patterns.

Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)

Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown age of 2–10 MY, yet over 6 kb of plastid and nuclear DNA sequence data gives only poor phylogenetic resolution among species. Here we explore the use of larger-scale nuclear gene data obtained though targeted enrichment to increase phylogenetic resolution within Inga. Transcriptome data from three Inga species were used to select 264 nuclear loci for targeted enrichment and sequencing. Following quality control to remove probable paralogs from these sequence data, the final dataset comprised 259,313 bases from 194 loci for 24 accessions representing 22 Inga species and an outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci concatenated or a gene-tree/species-tree approach yielded highly resolved phylogenies. We used coalescent approaches to show that the same targeted enrichment data also have significant power to discriminate among alternative within-species population histories within the widespread species I. umbellifera. In either application, targeted enrichment simplifies the informatics challenge of identifying orthologous loci associated with de novo genome sequencing. We conclude that targeted enrichment provides the large volumes of phylogenetically-informative sequence data required to resolve relationships within recent plant species radiations, both at the species level and for within-species phylogeographic studies.

The Origin of Diversity in Begonia: Genome Dynamism, Population Processes and Phylogenetic Patterns

A. Dewitte1, A.D. Twyford2,3, D.C. Thomas2,4, C.A. Kidner2,3 and J. Van Huylenbroeck5 1KATHO Catholic University College of Southwest Flanders, Department of Health Care and Biotechnology 2Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh 3Institute of Molecular Plant Sciences, University of Edinburgh, Kings Buildings, Edinburgh 4University of Hong Kong, School of Biological Sciences, Pokfulam, Hong Kong, 5Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, 1,5Belgium 2,3United Kingdom 4PR China

Retrieval of hundreds of nuclear loci from herbarium specimens

Herbaria are unparalleled collections of biodiversity information representing the world’s flora. However, this treasure has remained largely inaccessible to genetic studies, frequently limited by the low yields of poor-quality DNA. Next-generation sequencing (NGS) has transformed every field of biological research. The different strategies for accessing genetic data using NGS are changing the direction of biodiversity research—we are no longer constrained by a relatively small number of markers for non-model organisms, by time and cost limited sample sizes, or by incomplete datasets due to recalcitrant DNA extractions or PCR amplification failure. Here we show that targeted enrichment through hybrid capture can be used to generate hundreds of kilobases of nuclear sequence data of the Neotropical genus Inga, from herbarium specimens as old as 180 years and using as little as 16 ng of degraded DNA.

Maintenance of species boundaries in a Neotropical radiation of Begonia

A major goal of evolutionary biology is to determine the mechanisms generating biodiversity. In Begonia, one of the largest plant genera (1900+ species), it has been postulated that the high number of endemic species is a by‐product of low gene flow among populations, which predisposes the group to speciation. However, this model of divergence requires that reproductive barriers accumulate rapidly among diverging species that overlap in their geographic ranges, otherwise speciation will be opposed by homogenizing gene flow in zones of secondary contact. Here, we test the outcomes of secondary contact in Begonia by genotyping multiple sympatric sites with 12 nuclear and seven plastid loci. We show that three sites of secondary contact between B. heracleifolia and B. nelumbiifolia are highly structured, mostly containing parental genotypes, with few F1 hybrids. A sympatric site between B. heracleifolia and B. sericoneura contains a higher proportion of F1s, but little evidence of introgression. The lack of later‐generation hybrids contrasts with that documented in many other plant taxa, where introgression is extensive. Our results, in conjunction with previous genetic work, show that Begonia demonstrate properties making them exceptionally prone to speciation, at multiple stages along the divergence continuum. Not only are populations weakly connected by gene flow, promoting allopatric speciation, but species often show strong reproductive barriers in secondary contact. Whether similar mechanisms contribute to diversification in other large genera remains to be tested.

Genetic differentiation and species cohesion in two widespread Central American Begonia species

Begonia is one of the ten largest plant genera, with over 1500 species. This high species richness may in part be explained by weak species cohesion, which has allowed speciation by divergence in allopatry. In this study, we investigate species cohesion in the widespread Central American Begonia heracleifolia and Begonia nelumbiifolia, by genotyping populations at microsatellite loci. We then test for post-zygotic reproductive barriers using experimental crosses, and assess whether sterility barriers are related to intraspecific changes in genome size, indicating major genome restructuring between isolated populations. Strong population substructure was found for B. heracleifolia (FST=0.364, F′ST=0.506) and B. nelumbiifolia (FST=0.277, F′ST=0.439), and Bayesian admixture analysis supports the division of most populations into discrete genetic clusters. Moderate levels of inferred selfing (B. heracleifolia s=0.40, B. nelumbiifolia s=0.62) and dispersal limitation are likely to have contributed to significant genetic differentiation (B. heracleifolia Jost’s D=0.274; B. nelumbiifolia D=0.294). Interpopulation crosses involving a divergent B. heracleifolia population with a genome size ∼10% larger than the species mean had a ∼20% reduction in pollen viability compared with other outcrosses, supporting reproductive isolation being polymorphic within the species. The population genetic data suggest that Begonia populations are only weakly connected by gene flow, allowing reproductive barriers to accumulate between the most isolated populations. This supports allopatric divergence in situ being the precursor of speciation in Begonia, and may also be a common speciation mechanism in other tropical herbaceous plant groups.

Developmental genetics of the angiosperm leaf

Abstract The leaf is the major site of photosynthesis and the prototypical organ of terrestrial plants. The past five years have seen a dramatic increase in our understanding of the genetic control of leaf development. The establishment of determinacy, the role of the meristem, the establishment of polarity, the control of cell division, vascularization and epidermal patterning have all been the subject of genetic screens and many mutants have been isolated and characterized. Many of these mutants affect floral and embryonic structures, demonstrating the inherent similarities in all lateral organs. In this review we focus on the interactions between these genes and the networks that establish pattern in lateral organs.

A complex case of simple leaves: indeterminate leaves co-express ARP and KNOX1 genes

The mutually exclusive relationship between ARP and KNOX1 genes in the shoot apical meristem and leaf primordia in simple leaved plants such as Arabidopsis has been well characterized. Overlapping expression domains of these genes in leaf primordia have been described for many compound leaved plants such as Solanum lycopersicum and Cardamine hirsuta and are regarded as a characteristic of compound leaved plants. Here, we present several datasets illustrating the co-expression of ARP and KNOX1 genes in the shoot apical meristem, leaf primordia, and developing leaves in plants with simple leaves and simple primordia. Streptocarpus plants produce unequal cotyledons due to the continued activity of a basal meristem and produce foliar leaves termed “phyllomorphs” from the groove meristem in the acaulescent species Streptocarpus rexii and leaves from a shoot apical meristem in the caulescent Streptocarpus glandulosissimus. We demonstrate that the simple leaves in both species possess a greatly extended basal meristematic activity that persists over most of the leaf’s growth. The area of basal meristem activity coincides with the co-expression domain of ARP and KNOX1 genes. We suggest that the co-expression of ARP and KNOX1 genes is not exclusive to compound leaved plants but is associated with foci of meristematic activity in leaves.