The Chromosome-Scale Genome and Methylome of Pinus Tabuliformis and the Evolution of Conifers

Abstract

Conifers dominate large parts of the world’s forest ecosystems and are the most widely planted tree species. Their huge and highly complex genomes pose great challenges for assembling a complete reference genome for various evolutionary and genomic studies. Here, we present a chromosome-scale genome assembly of Pinus tabuliformis comprising 25.4 gigabases. A total of 80,495 genes were annotated based on massive RNA-seq data from 760 biosamples. These data provides novel insights into conifer unique genomic features and adaptive evolution. We presented the first chromosome-scale methylation maps of huge conifer genome, and revealed a high concordance between TE content and methylation level, yet there was no clear correlation between TE insertion time and the methylation level. These results provide us an unprecedented opportunity to conduct evolutionary and genomics studies on its unique adaptation, developmental and secondary growth, reproductive biology, and genomics-assisted breeding.