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United States Department of Agriculture

Agricultural Research Service

Research Project: AN INTEGRATED DATABASE AND BIOINFORMATICS RESOURCE FOR SMALL GRAINS

Location: Genomics and Gene Discovery

Title: Evolutionary relationship of nuclear genes encoding mitochondrial proteins across grasses

Authors
item Michalak, Monika -
item Ghavami, Farhad -
item Lazo, Gerard
item Gu, Yong
item Kianian, Shahryar -

Submitted to: Maydica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 1, 2009
Publication Date: December 23, 2009
Citation: Michalak, M.K., Ghavami, F., Lazo, G.R., Gu, Y.Q., Kianian, S.F. 2009. Evolutionary relationship of nuclear genes encoding mitochondrial proteins across grasses. Maydica. 54: 471-483

Interpretive Summary: This is a comparative genomics approach toward analyzing a key set of nuclear genes associated with mitochondrial gene function. The recent availability of genome sequences from several species makes it possible to now conduct experimental analysis of sequence information and apply it to gene function. As an example, a set of genes of known function were compared from two very different species; one from the dicotyledonous flowering plant Arabidopsis thaliana and the other from a monocotyledonous grass plant Oryza sativa. The sequence data from these model species allowed comparison to new sequence information from other upcoming sequenced grass species, including a new model species Brachypodium distachyon. The overall observations led to some interesting hypothesis to be developed based on gene presence and conservation within the species analyzed.

Technical Abstract: Comparative genome studies were done across taxa to provide a basic understanding of genome evolution regarding nuclear genes encoding for mitochondrial proteins and their conservation in grass species. Two different mitochondria-related gene sets, one from rice and another from Arabidopsis, were used in our analysis. The rice-derived gene set was analyzed using a radiation hybrid mapping approach and resulted in mapping 11 genes on chromosome 1D of wheat. The order of 11 genes was compared to rice, maize, Arabidopsis, and Brachypodium syntenic regions. The Arabidopsis set of 473 genes showed few good representatives in grass species except barley which revealed 23% Arabidopsis gene orthologs. Twenty-five genes were found conserved in both monocots and dicots underlying their significance for plant mitochondria survival. A 6.85Mb region on rice chromosome 10 revealed conserved colinearity with Brachypodium, whereas maize appeared more conserved than wheat within this region; a surprising finding since Brachypodium appears evolutionary closer to wheat. Evolutionary forces are proposed to preserve gene order of these genes in polyploids, since maize and wheat each have a history of polyploidy. Not all mitochondrial-related genes were conserved in whole genome analysis implying some importance of the conserved 6.85 Mb region in grasses. Mitochondria-related genes in grasses may resist major rearrangements or recombination or may be tied with a critical function.

Last Modified: 10/1/2014
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