Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae |
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Authors: | Mary M Guisinger Timothy W Chumley Jennifer V Kuehl Jeffrey L Boore Robert K Jansen |
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Institution: | (1) DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598, USA;(2) Genome Project Solutions, 1024 Promenade Street, Hercules, CA 94547, USA;(3) University of California Berkeley, 3060 VLSB, Berkeley, CA 94720, USA;(4) Section of Integrative Biology, University of Texas, Austin, TX 78712, USA;(5) Department of Biological Sciences, Central Washington University, 400 E. University Way, Ellensburg, WA 98926, USA |
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Abstract: | Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been
a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution
has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within
Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide
substitutions. Poaceae have multiple structural rearrangements, including three inversions, three genes losses (accD, ycf1, ycf2), intron losses in two genes (clpP, rpoC1), and expansion of the inverted repeat (IR) into both large and small single-copy regions. These rearrangements are restricted
to the Poaceae, and IR expansion into the small single-copy region correlates with the phylogeny of the family. Comparisons
of 73 protein-coding genes for 47 angiosperms including nine Poaceae genera confirm that the branch leading to Poaceae has
significantly accelerated rates of change relative to other monocots and angiosperms. Furthermore, rates of sequence evolution
within grasses are lower, indicating a deceleration during diversification of the family. Overall there is a strong correlation
between accelerated rates of genomic rearrangements and nucleotide substitutions in Poaceae, a phenomenon that has been noted
recently throughout angiosperms. The cause of the correlation is unknown, but faulty DNA repair has been suggested in other
systems including bacterial and animal mitochondrial genomes. |
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