期刊
MOLECULAR PLANT
卷 8, 期 6, 页码 885-898出版社
CELL PRESS
DOI: 10.1016/j.molp.2015.04.004
关键词
grasses; polyploidy; genome alignment; evolutionary rates; whole-genome duplication
资金
- China National Science Foundation [30971611, 3117022]
- Hebei New Century 100 Creative Talents Project
- Hebei-Natural Science Foundation
- Tangshan Key Laboratory Project
- Hebei 100 Talented Scholars project
- US National Science Foundation [ACI1339727, DBI 0849896, MCB-1021718]
- United Sorghum Checkoff Program
- J.S. Guggenheim Foundation
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 similar to 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.
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