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

• Published in: 分子植物：英文版 2015, Vol.8 (6), p.885-898
• Main Author: Xiyin Wa ng Jingpeng Wang Dianchuan Jin Hui Guo Tae-Ho Lee Tao Liu Andrew H. Paterson
• Format: Article
• Language: English
• Subjects: 事件; 化石证据; 基因组序列; 异质; 白垩-第三纪; 禾本科植物; 谱系; 进化速率
• ISSN: 1674-2052; 1752-9867

Multiple comparisons among genomes can clarify their evolution, speciation, and functional innova- tions. 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 Creta- ceous-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 poly- ploidization directly contributed to speciation. This work lays a solid foundation for Poaceae transla- tional genomics.