Mapping of ionomic traits in Mimulus guttatus reveals Mo and Cd QTLs that colocalize with MOT1 homologues

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Complete Sequences of Organelle Genomes from the Medicinal Plant Rhazya Stricta (Apocynaceae) and Contrasting Patterns of Mitochondrial Genome Evolution Across Asterids

Rhazya stricta is native to arid regions in South Asia and the Middle East and is used extensively in folk medicine to treat a wide range of diseases. In addition to generating genomic resources for this medicinally important plant, analyses of the complete plastid and mitochondrial genomes and a nuclear transcriptome from Rhazya provide insights into inter-compartmental transfers between genomes and the patterns of evolution among eight asterid mitochondrial genomes. Results: The 154,841 bp plastid genome is highly conserved with gene content and order identical to the ancestral organization of angiosperms. The 548,608 bp mitochondrial genome exhibits a number of phenomena including the presence of recombinogenic repeats that generate a multipartite organization, transferred DNA from the plastid and nuclear genomes, and bidirectional DNA transfers between the mitochondrion and the nucleus. The mitochondrial genes sdh3 and rps14 have been transferred to the nucleus and have acquired targeting presequences. In the case of rps14, two copies are present in the nucleus; only one has a mitochondrial targeting presequence and may be functional. Phylogenetic analyses of both nuclear and mitochondrial copies of rps14 across angiosperms suggests Rhazya has experienced a single transfer of this gene to the nucleus, followed by a duplication event. Furthermore, the phylogenetic distribution of gene losses and the high level of sequence divergence in targeting presequences suggest multiple, independent transfers of both sdh3 and rps14 across asterids. Comparative analyses of mitochondrial genomes of eight sequenced asterids indicates a complicated evolutionary history in this large angiosperm clade with considerable diversity in genome organization and size, repeat, gene and intron content, and amount of foreign DNA from the plastid and nuclear genomes. Conclusions: Organelle genomes of Rhazya stricta provide valuable information for improving the understanding of mitochondrial genome evolution among angiosperms. The genomic data have enabled a rigorous examination of the gene transfer events. Rhazya is unique among the eight sequenced asterids in the types of events that have shaped the evolution of its mitochondrial genome. Furthermore, the organelle genomes of R. stricta provide valuable genomic resources for utilizing this important medicinal plant in biotechnology applications.King Abdulaziz UniversityIntegrative Biolog

Evolutionary processes from the perspective of flowering time diversity.

Although it is well appreciated that genetic studies of flowering time regulation have led to fundamental advances in the fields of molecular and developmental biology, the ways in which genetic studies of flowering time diversity have enriched the field of evolutionary biology have received less attention despite often being equally profound. Because flowering time is a complex, environmentally responsive trait that has critical impacts on plant fitness, crop yield, and reproductive isolation, research into the genetic architecture and molecular basis of its evolution continues to yield novel insights into our understanding of domestication, adaptation, and speciation. For instance, recent studies of flowering time variation have reconstructed how, when, and where polygenic evolution of phenotypic plasticity proceeded from standing variation and de novo mutations; shown how antagonistic pleiotropy and temporally varying selection maintain polymorphisms in natural populations; and provided important case studies of how assortative mating can evolve and facilitate speciation with gene flow. In addition, functional studies have built detailed regulatory networks for this trait in diverse taxa, leading to new knowledge about how and why developmental pathways are rewired and elaborated through evolutionary time

Multiple-line inference of selection on quantitative traits

Trait differences between species may be attributable to natural selection. However, quantifying the strength of evidence for selection acting on a particular trait is a difficult task. Here we develop a population-genetic test for selection acting on a quantitative trait which is based on multiple-line crosses. We show that using multiple lines increases both the power and the scope of selection inference. First, a test based on three or more lines detects selection with strongly increased statistical significance, and we show explicitly how the sensitivity of the test depends on the number of lines. Second, a multiple-line test allows to distinguish different lineage-specific selection scenarios. Our analytical results are complemented by extensive numerical simulations. We then apply the multiple-line test to QTL data on floral character traits in plant species of the Mimulus genus and on photoperiodic traits in different maize strains, where we find a signatures of lineage-specific selection not seen in a two-line test.Comment: 21 pages, 11 figures; to appear in Genetic

Local adaptation of two cryptic species, Lasthenia californica and Lasthenia gracilis, to distinct regions within a serpentine outcrop

Intraspecific variation providing tolerance to specific edaphic conditions may contribute to population differentiation, speciation, and species coexistence. This process is often examined using reciprocal transplant experiments of closely related species in contrasting edaphic conditions. The two cryptic species Lasthenia californica and L. gracilis occur on a serpentine outcrop in parapatry at Jasper Ridge Biological Preserve. I hypothesized that each species would demonstrate greater fitness in its home range. A reciprocal transplant experiment was conducted in the field to determine home site advantage. Seedlings from each species were planted in both home ranges and in the transition zone where both species occur. Soil was found to vary significantly by outcrop region, particularly with respect to the calcium-to-magnesium ratio. Lasthenia californica performed best in its home range, but L. gracilis demonstrated greater survival and fitness in the transition zone. These findings provided evidence of local adaptation of L. californica to the bottom of the slope where the soil calcium concentration is lower and magnesium concentration is higher, and local adaptation of L. gracilis to the transition zone and the drier top of the slope. Studies on local adaptation using reciprocal transplants are ideal tools for understanding plant evolution and provide valuable information for habitat restoration

The "Carex" fen vegetation of northern New South Wales

The floristic composition and extent of Carex-dominated fens in the New South Wales New England Tablelands Bioregion and Barrington Tops area (lat 28° 41’ S–31° 55’ S; long 151° 23’ E–152° 05’ E) together with outliers from the central west (Coonabarabran) are described from 81 full floristic survey sites. These fens contained 234 vascular plant taxa of which 27% were exotic. The fens were dominated by herbaceous vegetation (96% of taxa). Cluster analysis of cover-abundance scores of vascular plant taxa from 81 plots placed within 71 separate Carex fens revealed three alliances: 1) Carex appressa, 2) Scirpus polystachyus – Carex tereticaulis and 3) Carex gaudichaudiana and seven communities: (1) Carex appressa – Stellaria angustifolia Fen (2) Carex appressa Fen (3) Scirpus polystachyus – Carex appressa Fen (4) Carex tereticaulis Fen (5) Carex gaudichaudiana – Isachne globosa Fen (6) Carex sp. Bendemeer – Carex gaudichaudiana Fen (7) Carex gaudichaudiana – Glyceria australis Fen The distribution of alliances showed a pattern of east-west separation. The most easterly alliance shares many features with the Carex gaudichaudiana Alliance of the Monaro Region of southern NSW while the other alliances have no counterparts within the current literature. We estimate that up to 5 000 ha of fen vegetation survive in the New England Bioregion of which 90% is on grazed land and only 0.2% is within conservation reserves. Seven outstanding examples of fens remain; most are examples of Community 5, with one representing Community 6 and none representing the other five communities. Many of these are not secured, and none of those within reserves are in their ‘natural’ state. We therefore strongly encourage measures to allow closure of drains, the opening of dams, and the rehabilitation of important fens such as Bishops, Racecourse and New Country Swamps

Terzyme: a tool for identification and analysis of the plant terpenome.

BACKGROUND: Terpenoid hydrocarbons represent the largest and most ancient group of phytochemicals, such that the entire chemical library of a plant is often referred to as its 'terpenome'. Besides having numerous pharmacological properties, terpenes contribute to the scent of the rose, the flavors of cinnamon and the yellow of sunflowers. Rapidly increasing -omics datasets provide an unprecedented opportunity for terpenome detection, paving the way for automated web resources dedicated to phytochemical predictions in genomic data. RESULTS: We have developed Terzyme, a predictive algorithm for identification, classification and assignment of broad substrate unit to terpene synthase (TPS) and prenyl transferase (PT) enzymes, known to generate the enormous structural and functional diversity of terpenoid compounds across the plant kingdom. Terzyme uses sequence information, plant taxonomy and machine learning methods for predicting TPSs and PTs in genome and proteome datasets. We demonstrate a significant enrichment of the currently identified terpenome by running Terzyme on more than 40 plants. CONCLUSIONS: Terzyme is the result of a rigorous analysis of evolutionary relationships between hundreds of characterized sequences of TPSs and PTs with known specificities, followed by analysis of genome-wide gene distribution patterns, ontology based clustering and optimization of various parameters for building accurate profile Hidden Markov Models. The predictive webserver and database is freely available at http://nipgr.res.in/terzyme.html and would serve as a useful tool for deciphering the species-specific phytochemical potential of plant genomes