Ryegrass organelle genomes: phylogenomics and sequence evaluation
Lolium perenne L.
Plastid genome diversity
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CitationDiekmann, Kerstin.(2010) Ryegrass organelle genomes: phylogenomics and sequence evaluation. University of Dublin, Trinity College.
AbstractPerennial ryegrass (Lolium perenne L.) is the most important forage grass of temperate regions of the world. The main objective in breeding perennial ryegrass cultivars is to increase its biomass. Chloroplasts and mitochondria are two organelles of the plant cell that are actively involved in biomass production. Chloroplasts derive from cyanobacteria and are the location of photosynthesis in plant cells. Mitochondria derive from α-proteobacteria and are involved in cell respiration. Due to their evolutionary history both organelles still contain their own genome which is in general maternally inherited. The interest in chloroplast genome sequences increased in recent years because they offer a useful option for plant genetic engineering. The risk of transgene escape via pollen flow is reduced while the expression of the transgene due to the high number of chloroplast genome copies is increased (in comparison to nuclear genome transformation). Mitochondrial genomes are of special interest because they are involved in cytoplasmic male sterility. Cytoplasmic male sterility is a very important trait in plant breeding programmes because it enables the cost efficient production of hybrid seed. Additionally, both organelle genomes can be used for molecular evolution or phylogenetic studies, as well as for population genetic approaches. Therefore the major aim of this thesis was to sequence the entire chloroplast and mitochondrial genomes of L. perenne to provide sequence information for chloroplast genetic engineering approaches, insights into the mitochondrial genome of a male fertile L. perenne cultivar and to gather knowledge about sequence variation in both genomes that can be used to design new markers for phylogenetic and population genetic studies.
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Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio GenusRomano, Stefano; Fernandez-Guerra, Antonio; Reen, F. Jerry; Glockner, Frank O.; Crowley, Susan P.; O'Sullivan, Orla; Cotter, Paul D.; Adams, Claire; Dobson, Alan D. W.; O'Gara, Fergal (Frontiers Media S. A., 2016-03-30)Strains of the Pseudovibrio genus have been detected worldwide, mainly as part of bacterial communities associated with marine invertebrates, particularly sponges. This recurrent association has been considered as an indication of a symbiotic relationship between these microbes and their host. Until recently, the availability of only two genomes, belonging to closely related strains, has limited the knowledge on the genomic and physiological features of the genus to a single phylogenetic lineage. Here we present 10 newly sequenced genomes of Pseudovibrio strains isolated from marine sponges from the west coast of Ireland, and including the other two publicly available genomes we performed an extensive comparative genomic analysis. Homogeneity was apparent in terms of both the orthologous genes and the metabolic features shared amongst the 12 strains. At the genomic level, a key physiological difference observed amongst the isolates was the presence only in strain P. axinellae AD2 of genes encoding proteins involved in assimilatory nitrate reduction, which was then proved experimentally. We then focused on studying those systems known to be involved in the interactions with eukaryotic and prokaryotic cells. This analysis revealed that the genus harbors a large diversity of toxin-like proteins, secretion systems and their potential effectors. Their distribution in the genus was not always consistent with the phylogenetic relationship of the strains. Finally, our analyses identified new genomic islands encoding potential toxin-immunity systems, previously unknown in the genus. Our analyses shed new light on the Pseudovibrio genus, indicating a large diversity of both metabolic features and systems for interacting with the host. The diversity in both distribution and abundance of these systems amongst the strains underlines how metabolically and phylogenetically similar bacteria may use different strategies to interact with the host and find a niche within its microbiota. Our data suggest the presence of a sponge-specific lineage of Pseudovibrio. The reduction in genome size and the loss of some systems potentially used to successfully enter the host, leads to the hypothesis that P. axinellae strain AD2 may be a lineage that presents an ancient association with the host and that may be vertically transmitted to the progeny.
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