Patterns and processes of sequence evolution: Plant organelle genomes and copia-like retrotransposons

Abstract

Gene conversion is generally considered not to occur in the plastid genome outside of the large inverted repeat regions. However, two previous reports based on the analysis of sequence similarity suggested that gene conversion occurs between the functional copy of rpl23, and a pseudogene copy, psirpl23. The evolution of rpl23 and psirpl23 can be described through models of gene lineages within species lineages based on whether one or more duplication events and/or gene conversion have occurred. Phylogenetic analysis suggests the no model is strongly corroborated. At the DNA level plastid genes appear to be conserved. An exception to this conservation is rpoC2 of rice and maize, which in comparison to other plants has an extra coding sequence that is hypervariable. A survey of 55 species from 17 families determined the extra sequence was restricted to the family Poaceae. DNA sequences of the extra sequence and adjacent flanking regions were determined for 11 species. The pattern of sequence variation suggests that slipped-strand mispairing is shaping the evolution of this region. Phylogenetic analyses based on the sequences both corroborates and contradicts several previous hypotheses regarding relationships within the Poaceae. Achlorophyllous plants are thought to lack chlorophyll and other pigments associated with photosynthesis. Chlorophyll and carentenoid pigments were determined for several putatively achlorophyllous angiosperms using high-performance liquid chromatography. Chlorophyll a was detected in all taxa except Allotropa virgata. The pattern of pigment composition demonstrates that loss of photosynthesis is independent of the loss of particular pigments generally associated with photosynthesis and that pigment loss differs between families. The phylogenetic distribution of copia-like retrotransposons, a class of transposable elements that proliferates by reverse transcription, was assessed using a polymerase chain reaction assay. Copia-like retrotransposons were identified in 64 plant species as well as the photosynthetic protist, Volvox carteri. However, no evidence was found for the presence of copia-like retrotransposons in any of the animals examined. DNA sequence analysis confirmed the identity of these sequences as copia-like reverse transcriptases. These findings demonstrate that copia-like retrotransposons are ubiquitous components of plant genomes.

Publication
PhD thesis, Harvard University, Cambridge, Massachusetts USA