Supporting data for "Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)"

Bamboo is one of the most important non-timber forest products worldwide. However, a chromosome-level reference genome is lacking, and the evolutionary landscape of alternative splicing (AS) in bamboo remains unclear despite emerging data and improved technologies. Here, we provide a chromosome-level de novo genome assembly of the moso bamboo (Phyllostachys edulis) using additional abundance data and different assembly strategies. The significantly improved genome is a Scaffold N50 of 79.90 Mb, approximately 243 times longer than the previous version, and 51,074 high-quality protein-coding loci with intact structures were identified using single-molecule real-time sequencing and manual verification. Moreover, we provide a comprehensive AS profile based on the identification of 266,771 uniform AS events in 25,225 AS genes by large-scale transcriptomic sequencing of 26 representative bamboo tissues using both the Illumina and PacBio sequencing platforms. Via comparison with orthologous genes in related plants, we observed dramatic evolutionary characteristics, suggesting that the AS genes are concentrated in more conserved genes that tend to accumulate higher expressed transcripts and share less specificity. Furthermore, gene family expansion, abundant AS and positive selection were identified in crucial genes involved in lignin biosynthesis, indicating that moso bamboo's specificity in being a woody plant in the grass family. These fundamental studies provide useful information for future studies performing in-depth analyses of comparative genome and AS features. Additionally, our results highlight a global perspective of AS during evolution and diversification in bamboo.