Explore Pant Genome Evolution and Adaptation Using Large-Scale Genomic and Transcriptomic Plantae Sequences

Symbiosis and gene (or whole genome) duplication are two major evolutionary forces that have played important roles during the origin and diversification of eukaryotes. The past decades have witnessed a remarkable explosion in sequencing technology and development of analytical tools, allowing diverse and fundamental questions to be addressed in a genome-wide scale. In photosynthetic algae and many unexplored eukaryotic microorganisms (protists), ancient or recent/ongoing (endo) symbioses, typically with intracellular symbiotic bacteria, have played a pivotal role for the evolution of the ancestor of Plantae (e.g., the evolution of plastids and mitochondria), and contributed to many extant host genomes by the horizontal spread of plastids (e.g., EGT/HGT events in euglenophytes and dinoflagellates that evolved distinct genetic and genomic characteristics). Interestingly, symbiosis events also exist in higher plants, for example, the plant-cyanobacteria and plant-rhizobia/Frankia associations that are responsible for nitrogen-fixation. The underlying genetic program(s) and evolutionary scenarios of these plant-microbe interactions are still largely elusive. On the other hand, gene duplication with modification is regarded as another significant driving force in plant evolution, as analyzed from about 100 plant genomes and the 1KP transcriptome data. The highly expanded PPR (Pentatricopeptide repeat) family, typically with 400-600 members in most angiosperms and more than 2,000 members in many bryophytes and ferns, is an excellent example. Evolution of PPRs, strongly co-evolved with RNA editing in plant organellar transcripts, are potentially required for plant terrestrialization and for the adaptive transition from a gametophyte- to a sporophyte-dominant lifestyle. Furthermore, the frequent whole-genome duplication/triplication events observed throughout the evolutionary history of flowering plants, significantly contributed to genome diversification and adaptation. In summary, large-scale genome and transcriptome sampling across a wide range of eukaryote organisms, coupled with comparative genomics and phylogenomics analyses, provide many novel insights into the entire evolutionary and adaptation history of eukaryotes.