Abstract Detail

Comparative Genomics/Transcriptomics

Stone, Philippa [1], Lam, Vivienne [1], Darby, Hayley [1], Graham, Sean [1].

Patterns of plastid genome evolution across parasitic and mycoheterotrophic plants.

Most plants fix their carbon through photosynthesis and take up essential elements from the soil through roots. However, mycoheterotrophs obtain some or all of their fixed carbon from soil fungi, and holoparasitic plants from other plants. Loss of photosynthetic function has led to parallel gene loss in the plastid genome for most heterotrophic lineages, but this has not been fully characterized across the flowering plants in a broad phylogenetic context. Here we examine plastid genome structure and gene content in a taxonomically diverse range of heterotrophs and autotrophs in order to characterize broad commonalities and differences in patterns of gene loss and plastid genome rearrangement. Specifically, we characterized genome structure and gene content across 450 autotroph and heterotroph plastid genomes. Most heterotrophs have experienced changes in plastid genome structure: for example, about a third of species that maintain an inverted repeat (IR) region have experienced loss of colinearity compared to their autotrophic relatives, and another third have completely lost their IR. We developed a novel pipeline using BLAST and nhmmer to confirm GenBank annotations for gene presence vs. absence, which are sometimes not accurately annotated. As expected, non-photosynthetic species that have lost their photosynthetic machinery retain a core set of non-bioenergetic genes, and several have also retained full copies of rbcL and the atp genes (two classes of photosynthetic genes with secondary non-photosynthetic functions). Of the five non-bioenergetic genes expected to linger in plastid genomes (accD, clpP, trnE, ycf1 and ycf2), three genes that are involved in lipid biosynthesis (accD), protein degradation (clpP), and heme biosynthesis (trnE), have the fewest independent losses. The bifunctional gene trnE-UUC, which is also involved in translation, is retained in most species. Considering the remaining translation apparatus genes, tRNV-UAC, tRNI-GAU, and tRNK-UUU are lost most frequently, while rps15 and rps16, and rpl23 and rpl32 are also lost far more frequently than the other ribosomal protein genes. The reason for these different rates of loss in ribosomal apparatus genes is unclear.

1 - University of British Columbia, Department of Botany, 6270 University Boulevard, Vancouver, BC, Canada

Chloroplast genome

Presentation Type: Oral Paper
Number: CGT4003
Abstract ID:398
Candidate for Awards:None

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