The legume family (Leguminosae) consists of approximately 17 000 species and those used as crops provide protein and carbohydrates for over 300 million people world-wide. O’Rourke et al. review how next-generation sequencing technologies and associated bioinformatic analyses have allowed individual researchers to assemble genomes, identify gene-coding regions and study gene expression patterns. To illustrate the power of next-generation sequencing in elucidating gene networks underlying biological processes, they present two example studies: an analysis of gene expression profiles in soybean oil seed development and an analysis of phosphate deficiency altering gene expression patterns to induce cluster root formation in white lupin.
Effective programmed xylogenesis is critical to the structural framework of the plant root system and its central role in the acquisition and long-distance transport of water and nutrients. Bagniewska-Zadworna et al. study the differentiation of tracheary elements (TEs) in pioneer roots of Populus trichocarpa grown in rhizotrons and find that the primary event is a burst of NO in thin-walled cells, followed by H2O2 synthesis and TUNEL-positive nuclei appearance. Subsequent events involve secondary cell wall formation and autophagy. Potential gene markers from the cinnamyl alcohol dehydrogenase (CAD) gene family that are related with secondary wall synthesis are associated with primary xylogenesis, showing clear expression in cells that undergo differentiation into TEs. The CAD genes appear to be involved in primary xylem differentiation and the formation of the cell walls in TEs before their functional maturity.
The OVATE gene encodes a nuclear-localized regulatory protein belonging to a distinct family of plant-specific proteins known as the OVATE family proteins (OFPs). Liu et al. identify 13 sequenced plant genomes in public databases that represent the major evolutionary lineages of land plants and conduct a phylogenetic analysis based on the alignment of the conserved OVATE domain. Genes for OFPs are found to be present in all the sampled land plant genomes, including the early-diverged lineages, mosses and lycophytes, and 11 subgroups of OFPs are defined in angiosperms. The results provide new insights into the evolution of the OVATE protein family and establish a solid base for future functional genomics studies on this important but poorly characterized regulatory protein family.
Submergence and de-submergence are common phenomena encountered by riparian plants as water levels fluctuate, but little is known about the role of physiological integration in the adaptation of clonal plants to such conditions. Luo et al. study Alternanthera philoxeroides (alligator weed) after 30 days of submergence and find that connections between submerged and non-submerged ramets enhance the performance of the submerged ramets, but little effect remains once the ramets have then been de-submerged for 20 days. This is due to quick recovery of growth and photosynthesis, and this combines with the benefits of physiological integration in allowing riparian clonal plants to survive submergence and spread rapidly after de-submergence.
The genus Paspalum (Poaceae) is a model to study gametophytic apomixis and its strong relation with polyploidy. Delgado et al. analyse the reproductive behaviour of natural diploid individuals of P. rufum and find that under self-pollination induction three genotypes develop seeds from both meiotic and aposporous embryo sacs, and one of them is able to complete the apomictic pathway. Cytoembryological observations reveal that all genotypes form aposporous embryo sacs, suggesting that apospory and parthenogenesis might be uncoupled. These results demonstrate variation in the functionality of apomixis components and also that genetic determinants of apomixis are not sufficient for an appreciable expression of the trait at the diploid level.
Complete legume chloroplast genomes are only available for one Papilionoid clade, and information from other lineages is thus needed to better understand this family’s atypical evolution. Martin et al. sequence the plastome of Lupinus luteus, representing the Genistoid lineage, and perform comparative analyses at the structural and sequence levels. They discover a 36-kb inversion, embedded within the already known 50-kb inversion in the large single-copy region of the Papilionoideae. This inversion occurs at the base or soon after the Genistoid emergence, and most likely resulted from a flip-flop recombination. Mutational hotspots are also identified and new potentially informative regions for phylogenetic and molecular evolutionary studies in legumes are detected.
Seagrasses are marine, flowering plants with a hydrophilous pollination strategy. Sinclair et al. study microsatellite DNA markers in order to understand the interactions between clonal structure, mating system and pollen dispersal in two seagrass meadows of Posidonia australis with contrasting local environmental conditions, one being exposed and the other being sheltered. The results show that in a system that appears to rely on chance pollination, all embryos are the result of outcrossed pollination. Pollen is thus being mixed in the water column, with local conditions having little influence on the success and pattern of pollination. Complete outcrossing suggests that post-pollination mechanisms may also be in place to prevent geitonogamous selfing.
Most of the numerous and remarkable range disjunctions across the southern oceans are probably the result of occasional long-distance dispersal, rather than of vicariance. Linder and Barker study the grass subfamily Danthonioideae, which probably reached its current global distribution by a number of long-distance dispersal events during the Neogene, and show that such dispersal is much more likely in polyploid than in diploid species. It is possible that polyploidy facilitates post-dispersal establishment, and it is postulated that the frequent occurrence of polyploidy in the grasses may thus have facilitated their long-distance dispersal, and hence contributed to the remarkable success of the family.
Seed longevity, a fundamental plant trait for ex situ conservation and persistence in the soil of many species, varies across populations and generations that experience different climates. Mondoni et al. study seeds from alpine and lowland populations of Silene vulgaris and show that seed longevity has a genetic basis but may show strong adaptive responses, which are associated with differential accumulation of mRNA via parental effects. They conclude that adaptive adjustments of seed longevity due to transgenerational plasticity may play a fundamental role for the survival and persistence of the species in the face of future environmental challenges, and that the location of regeneration may have important implications for ex situ conservation in seed banks.
Molecular approaches have been used to investigate the phylogeny of subtribe Oncidiinae, resulting in the recent re-alignment of several of its genera. Davies et al. compare the floral elaiophores (oil glands) of four species formerly assigned to Oncidium (Oncidiinae), namely Gomesa longipes, Vitekorchis excavata, Cyrtochilum meirax and florally dimorphic Oncidium heteranthum. They find that, except for C. meirax, which lacks obvious elaiophores, this structure occurs on the labellar callus, has glabrous and trichomatous regions, and comprises a single-layered, secretory epidermis lacking palisade cells, the oil being produced either by smooth endoplasmic reticulum or as plastoglobuli within elaioplasts. Subsequent stages of secretion differ little between species, with the oil traversing the cell wall and accumulating beneath the distended cuticle. Floral dimorphism has little effect on elaiophore structure.