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.
Performance of the D5000 and High Sensitivity D5000 ScreenTape Assays for the 4200 TapeStation SystemPoster
Here, we focus on quantification, sizing, and sensitivity of both D5000 ScreenTape assays.READ MORE
Applications of chemically modified synthetic guide RNA for CRISPR-Cas9 genome editingPoster
Our results indicate that MS modifications are required for experiments with co-electroporation of Cas9 mRNA and synthetic gRNA, yet have no impact on editing efficiency when delivered with lipid-based transfection reagents.READ MORE
Optimized Workflow for Single Cell Copy Number Profiling Using High Resolution Oligo CGH ArraysPoster
Here we describe GenetiSure Pre-Screen, a same day, cost-effective, analysis workflow that combines whole genome amplification (WGA) with copy number (CN) profiling using high-resolution oligo CGH microarrays.READ MORE