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The genus  Chaenomeles  has long been considered an important ornamental, herbal and cash crop and is widely cultivated in East Asia. Traditional studies of  Chaenomeles  mainly focus on evolutionary relationships at the phenotypic level. In this study, we conducted RNA-seq on 10  Chaenomeles  germplasms supplemented with one outgroup species,  Docynia delavayi  ( D. delavayi ), on the Illumina HiSeq2500 platform. After de novo assemblies, we generated from 40,084 to 49,571 unigenes for each germplasm. After pairwise comparison of the orthologous sequences, 9,659 orthologues within the 11 germplasms were obtained, with 6,154 orthologous genes identified as single-copy genes. The phylogenetic tree was visualized to reveal evolutionary relationships for these 11 germplasms. GO and KEGG analyses were performed for these common single-copy genes to compare their functional similarities and differences. Selective pressure analysis based on 6,154 common single-copy genes revealed that 45 genes were under positive selection. Most of these genes are involved in building the plant disease defence system. A total of 292 genes containing simple sequence repeats (SSRs) were used to develop SSR markers and compare their functions in secondary metabolism pathways. Finally, 10 primers were chosen as SSR marker candidates for  Chaenomeles  germplasms by comprehensive standards. Our research provides a new methodology and reference for future related research in  Chaenomeles  and is also useful for improvement, breeding and selection projects in other related species.

Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles