Population-specific selection on standing variation generated by lateral gene transfers in a grass

Evidence of eukaryote-to-eukaryote lateral gene transfer (LGT) has accumulated in recent years [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14], but the selective pressures governing the evolutionary fate of these genes within recipient species remain largely unexplored [15, 16]. Among non-parasitic plants, successful LGT has been reported between different grass species [5, 8, 11, 16, 17, 18, 19]. Here, we use the grass Alloteropsis semialata, a species that possesses multigene LGT fragments that were acquired recently from distantly related grass species [5, 11, 16], to test the hypothesis that the successful LGT conferred an advantage and were thus rapidly swept into the recipient species. Combining whole-genome and population-level RAD sequencing, we show that the multigene LGT fragments were rapidly integrated in the recipient genome, likely due to positive selection for genes encoding proteins that added novel functions. These fragments also contained physically linked hitchhiking protein-coding genes, and subsequent genomic erosion has generated gene presence-absence polymorphisms that persist in multiple geographic locations, becoming part of the standing genetic variation. Importantly, one of the hitchhiking genes underwent a secondary rapid spread in some populations. This shows that eukaryotic LGT can have a delayed impact, contributing to local adaptation and intraspecific ecological diversification. Therefore, while short-term LGT integration is mediated by positive selection on some of the transferred genes, physically linked hitchhikers can remain functional and augment the standing genetic variation with delayed adaptive consequences

Revealing the Functions of the Transketolase Enzyme Isoforms in Rhodopseudomonas palustris Using a Systems Biology Approach

BACKGROUND: Rhodopseudomonas palustris (R. palustris) is a purple non-sulfur anoxygenic phototrophic bacterium that belongs to the class of proteobacteria. It is capable of absorbing atmospheric carbon dioxide and converting it to biomass via the process of photosynthesis and the Calvin-Benson-Bassham (CBB) cycle. Transketolase is a key enzyme involved in the CBB cycle. Here, we reveal the functions of transketolase isoforms I and II in R. palustris using a systems biology approach. METHODOLOGY/PRINCIPAL FINDINGS: By measuring growth ability, we found that transketolase could enhance the autotrophic growth and biomass production of R. palustris. Microarray and real-time quantitative PCR revealed that transketolase isoforms I and II were involved in different carbon metabolic pathways. In addition, immunogold staining demonstrated that the two transketolase isoforms had different spatial localizations: transketolase I was primarily associated with the intracytoplasmic membrane (ICM) but transketolase II was mostly distributed in the cytoplasm. Comparative proteomic analysis and network construction of transketolase over-expression and negative control (NC) strains revealed that protein folding, transcriptional regulation, amino acid transport and CBB cycle-associated carbon metabolism were enriched in the transketolase I over-expressed strain. In contrast, ATP synthesis, carbohydrate transport, glycolysis-associated carbon metabolism and CBB cycle-associated carbon metabolism were enriched in the transketolase II over-expressed strain. Furthermore, ATP synthesis assays showed a significant increase in ATP synthesis in the transketolase II over-expressed strain. A PEPCK activity assay showed that PEPCK activity was higher in transketolase over-expressed strains than in the negative control strain. CONCLUSIONS/SIGNIFICANCE: Taken together, our results indicate that the two isoforms of transketolase in R. palustris could affect photoautotrophic growth through both common and divergent metabolic mechanisms

Molecular characterization of <i>Colletotrichum</i> species causing <i>Begonia</i> anthracnose in Sri Lanka

Anthracnose disease is known to affect many tropical and subtropical fruits, vegetables and also certain cut-flowers and foliage plants. The disease was known to be caused by Colletotrichum gloeosporioides or C. acutatum which are presently accepted as species complexes. The present study was conducted with the main objective of identifying Colletotrichum species causing begonia anthracnose using morphological and molecular data. Begonia is an ornamental foliage plant grown worldwide. Anthracnose symptoms appear in begonia leaves as brownish, irregular, necrotic lesions. Colletotrichum was isolated from three Begonia species showing anthracnose symptoms, collected from three Provinces of Sri Lanka. Thirty isolates were obtained in the study of which 29 formed oblong conidia and the remainder produced falcate conidia. Six randomly selected isolates forming oblong conidia and the isolate with falcate conidia were sequenced for Internal Transcribed Spacer (ITS) and β-tubulin 2 (TUB2) regions. Considering &gt;98% similarity with NCBI GenBank database for both sequences, the isolates with oblong conidia were identified as C. siamense and the isolate with falcate conidia as C. truncatum. Newly generated sequences were subjected to phylogenetic analysis with the closely related ex-type and authenticated isolates sequences. Phylogenetic analysis confirmed the species as C. siamense and C. truncatum. Koch’s postulates were performed to establish whether the fungi isolated from anthracnose lesions were actually causing anthracnose disease in Begonia leaves. This is the first report of C. siamense causing Begonia anthracnose

A checklist of plant pathogenic fungi and Oomycota in Sri Lanka

Sri Lanka is blessed with a rich ecosystem diversity, however, only a small fraction of the diverse flora and fauna in the country is known. Only around 3,000 species of fungi are currently known out of the estimated number of 25,000 species of native fungal flora of Sri Lanka. This includes the 2,000 species, belonging to 640 genera, recorded prior to 1950. The fungi studied, prior to 1950, have been well documented, as journal publications, checklists or books. In contrast, the information on Sri Lankan fungal flora, available especially after 1950, is scattered. The present `Checklist of Plant Pathogenic Fungi in Sri Lanka’ is intended to bring together all species of plant pathogenic fungi and Oomycota recorded in the country after late nineteen forties. The checklist consists of 404 species of plant pathogenic fungi and Oomycota, belonging to 110 genera and 230 species, associated with diseases of horticultural, agricultural and plantation crops and their harvested produce and forests plants in Sri Lanka