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Pittman, Kimberly B. [1], Robinson, Bridget A. [1], Bryant, Curtis M. [1], Jarrell, David C. [1].

Phylogenetic analysis of matK pseudogene formation in the subtribe Aeridinae (Orchidaceae): taxonomic distribution and origin hypothesis testing..

The chloroplast locus encoding the putative RNA maturase, MATK, has been a prominent tool in molecular systematics of land plants. It is arguably the fastest evolving protein coding sequence of the chloroplast genome and is often used alone or in conjunction with various introns and spacers sequences in the analysis of inter- and intra-generic relationships. The high rate of nucleotide substitution and variation in the position of start codons that might enable complete translation of the protein has caused some to suggest that most, if not all, plants carry matK as a pseudogene. However, this disregards research that demonstrates the presence of both transcripts and proteins from this locus. In addition, while many other pseudogenes exist as truncated or deleted forms in comparison to functional copies, there is little evidence of this for matK. However, matK sequences from several related taxa in the orchid subtribe Aeridinae have frameshift deletions of 7, 8 or 10 bp mostly in the 5’ end of the gene. In addition, no inframe start codons are available for the translation of a protein of sufficient size. To explore the pseudogene's taxonomic range, taxon sampling has been greatly expanded. In addition, we have begun testing the first of several hypotheses to explain their origin. These hypothese include: 1) matK-dependent intron loss, 2) duplication of matK to another chloroplast or nuclear location, 3) functional replacement by another maturase and 4) insertional RNA editing. We have begun screening for the presence of matK-dependent introns using PCR. Primers were designed to intron flanking regions such that in cases of loss a shorter length product would be amplified. To date, all samples appear to contain tested introns but PCR optimization is necessary for successful amplification from specific samples and for certain introns. The future directions of this project will be discussed.

1 - University of Mary Washington, Biological Sciences, 1301 College Av., Jepson Science Center, Fredericksburg, VA, 22401, USA

Keywords:
Aeridinae
pseudogene
matK
intron loss.

Presentation Type: Poster
Session: 32-146
Location: Special Event Center (Cliff Lodge)
Date: Tuesday, August 3rd, 2004
Time: 12:30 PM
Abstract ID:1131