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Mol Plant. 2015 Jun;8(6):885-98. doi: 10.1016/j.molp.2015.04.004. Epub 2015 Apr 18.

Genome Alignment Spanning Major Poaceae Lineages Reveals Heterogeneous Evolutionary Rates and Alters Inferred Dates for Key Evolutionary Events.

Author information

1
Plant Genome Mapping Laboratory, University of Athens, GA 30602, USA; Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China; College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China.
2
Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China; College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China.
3
Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China; College of Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China.
4
Plant Genome Mapping Laboratory, University of Athens, GA 30602, USA; Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
5
Plant Genome Mapping Laboratory, University of Athens, GA 30602, USA.
6
Plant Genome Mapping Laboratory, University of Athens, GA 30602, USA; Department of Plant Biology, University of Georgia, Athens, GA 30602, USA; Department of Crop and Soil Science, University of Georgia, Athens, GA 30602, USA; Department of Genetics, University of Georgia, Athens, GA 30602, USA. Electronic address: paterson@plantbio.uga.edu.

Abstract

Multiple comparisons among genomes can clarify their evolution, speciation, and functional innovations. To date, the genome sequences of eight grasses representing the most economically important Poaceae (grass) clades have been published, and their genomic-level comparison is an essential foundation for evolutionary, functional, and translational research. Using a formal and conservative approach, we aligned these genomes. Direct comparison of paralogous gene pairs all duplicated simultaneously reveal striking variation in evolutionary rates among whole genomes, with nucleotide substitution slowest in rice and up to 48% faster in other grasses, adding a new dimension to the value of rice as a grass model. We reconstructed ancestral genome contents for major evolutionary nodes, potentially contributing to understanding the divergence and speciation of grasses. Recent fossil evidence suggests revisions of the estimated dates of key evolutionary events, implying that the pan-grass polyploidization occurred ∼96 million years ago and could not be related to the Cretaceous-Tertiary mass extinction as previously inferred. Adjusted dating to reflect both updated fossil evidence and lineage-specific evolutionary rates suggested that maize subgenome divergence and maize-sorghum divergence were virtually simultaneous, a coincidence that would be explained if polyploidization directly contributed to speciation. This work lays a solid foundation for Poaceae translational genomics.

KEYWORDS:

evolutionary rates; genome alignment; grasses; polyploidy; whole-genome duplication

PMID:
25896453
DOI:
10.1016/j.molp.2015.04.004
[Indexed for MEDLINE]
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