Comparative Genomics of Pineapple and Other Angiosperm Genomes
The draft pineapple genome is a remarkable resource to breeders and plant biologists. The study of the gene repertoire involved in the crassulacean acid metabolism (CAM) photosynthetic pathway enables researchers to track down genomic and regulatory changes necessary for a shift from C3 metabolism, also shedding light on the evolution of the C4 metabolism. In addition to its unique photosynthetic pathway, pineapple occupies a unique evolutionary position on the monocot tree of life, making it an ideal genome proxy for the Poales clade. The lineage of pineapple, known as the bromeliads, serve as an excellent out-group to the well-studied cereal group while retaining a less complex genome that reflects a close-to-ancestral karyotype. Herein, we take an in-depth look on the genomic comparisons both on the whole-genome level and the local scale. On the whole-genome level, we have compared pineapple against several related monocot, eudicot, and basal angiosperm genomes providing a solid framework to study the patterns of macroscale genome evolution, in order to clarify the nature and dating of recurring genome duplication events. On the local scale, we have identified significant sequence conservation outside the coding regions that have so far remained underexplored yet critical to our understanding of the unique biology and physiology of the pineapple species.
KeywordsSynteny Homology Genome evolution Polyploidy Cyber-infrastructure
We thank the Fujian provincial government for a Fujian “100 Talent Plan” award to HT. This work was supported by the National Key Research and Development Program of China (2016YFD0100305). Competing interests: the authors declare that they have no competing interests.