Hilu, Khidir , Moukarzel, Keenan .
MatK is a pseudogene in many angiosperms: Is it really?
Due to its high proportion of phylogenetic signal, the plastid matK gene has become one of the most utilized genomic regions in plant molecular phylogenetics. The matK gene is known for its considerably high rate of substitution at the nucleotide level, but more so at the amino acid level due to near equity in rates of mutations across the three codon positions. These high rates of substitutions, in particular the rate of amino acid substitutions, raised question on whether this group II intron maturase is a pseudogene since conserved amino acid substitution is a prerequisite for maintaining structural and functional integrity of any transcribed protein product. Some studies have explicitly noted that matK is a pseudogene because of either a lack of an apparent start codon or the presence of one or more premature stop codons that could result in a truncated protein. Further, GenBank also contains a number of matK sequences that are described as "matK-like" or "pseudogene". Using empirical data, we will address issues concerning the definition of matK open reading frame, patterns of substitutions in functional genes vs. pseudogenes, and the impact of gene functionality on phylogenetic reconstruction. Our findings question several of the published contentions regarding matK as a pseudogene.
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1 - Virginia Tech, Department of Biological Sciences, 2119 Derring Hall, Blacksburg, VA, 24061, USA
Presentation Type: Oral Paper:Papers for Sections
Location: Lindell B/Chase Park Plaza
Date: Wednesday, July 13th, 2011
Time: 8:45 AM