De novo assemblies of high-quality reference transcriptomes identifies Rosaceae-common and Rosa -specific encoding genes

Abstract Roses are important plants for human beings with important economical and biological traits like continuous flowering, flower architecture, color and scent, that current model plants do not feature, thus are becoming ideal models for studying these traits. Due to high heterozygosity of rose genomes likely caused by frequent inter-species hybridization, a high-quality and well-annotated genome for Rosa plants is not available yet. Developing genetic and genomic tools with high quality has become necessary for further roses breeding and for disentangling the molecular genetic mechanisms underlying roses domestication. We here generated the high quality and comprehensive reference transcriptomes for Rosa chinensis ‘Old Blush’ (OB) and R. wichuriana ‘Basyes’ Thornless’ (BT), two roses contrasting at several important traits. These reference transcriptomes showed transcripts N50 above 2000bp. The two species shared about 23310 transcripts (N50 = 2364bp), among which about 8975 orthologs were conserved within genera of Rosa . Rosa plants shared about 5049 transcripts (Rosaceae-common) with these from Malus, Prunus, Rubus , and Fragaria . Finally, a pool of 417 transcripts unique to Rosa plants ( Rosa -specific) was identified. These Rosaceae-common and Rosa -specific transcripts should facilitate the phylogenetic analysis of Rosaceae plants and investigation of Rosa -specific traits. The data reported here should provide the fundamental genomic tools and knowledge critical for understanding the biology and domestication of roses.