Stable Chloroplast: Myth or Reality?
Poster Feb 10, 2015
Shailesh Joshi and Dyfed Evans
Chloroplasts principally encode the photosynthetic machinery in Viridiplantae. It has long been accepted that in photosynthetic plants chloroplast genomic structure is uniquely stable. The first chloroplast genomes sequenced supported this view, with the only major structural rearrangements being identified between the Poales and the Poaceae. Recently, additional chloroplast genomes across all plant lineages have been sequenced. Our novel bioinformatics methodology allows whole chloroplast alignments, at the micro, gene and at macro scales. The current study includes 110 chloroplast genomes covering 280MY of plant evolution. Our results at the micro level demonstrate that short nucleotide repeats are uncommon, whereas, large scale repeats (50-300nt) are distributed throughout the genome of all lineages. However, the duplication in each event is lineage specific and is not repeated. These unique insertion and deletion events, point towards a constant chromosomal churn, which contradicts the existing perception of a stable chloroplast. At the gene level there have been specific gene losses that characterise new plant lineages as noted in the five events separating early dicots from the Poaceae. At macro levels, when plants become non-photosynthetic, we observed massive rearrangements in the chloroplast genome (eg. Petrosavia). Even when chloroplast function is essential there is a tendency for large regions to be inverted around tRNA genes (eg. Poaceae, Piper, Dioscorea.). We further noted the complete loss of the IRb region from chloroplasts in the wheat lineage.
This large scale, multigenome, study allows us to demonstrate that the chloroplast is a dynamic genome, rather than being static and stable as perceived in the traditional, erroneous view. The chloroplast is derived from an ancestral cyanobacterial genome and still retains it plasticity. This means that lineages can have profoundly different clock rates of plastid evolution. Here, we demonstrate alterations in every examined chloroplast genome, at all scales, proving that the stable chloroplast is a myth.
Genome-wide association studies (GWAS) have identified more than 100 genetic loci associated with type 2 diabetes. The majority of these are located in the intergenic or intragenic regions suggesting that the implicated variants may alter chromatin conformation. This, in turn, is likely to influence the expression of nearby or more remotely located genes to alter beta cell function. At present, however, detailed molecular and functional analyses are still lacking for most of these variants. We recently analysed one of these loci and mapped five causal variants in an islet-specific enhancer cluster within the STARD10 gene locus. Here, we aimed to understand how these causal variants influence b-cell function by alteration of the chromatin structure of enhancer clusterREAD MORE
Early life stress (ELS) is highly associated with development of psychopathology
and mood disorders in adulthood. Genetic studies have identified variation in the gene calcium voltage-gated channel subunit alpha1C (CACNA1C) to increase risk for several psychiatric disorders. This poster assessed the expression of Cacna1c following prepubertal stress.