Genome-wide analysis of the long noncoding RNAs and mRNAs involved in flower bud development of Eucommia ulmoides Oliver

An intricate network of genes and long noncoding RNAs (lncRNAs) involved in the floral development play pivotal roles in flower bud development. Eucommia ulmoides is a typical dioecious tree species with a long history of medicinal application in China. However, little is known regarding the function and profile of the long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) involved in sex determination and development of flower buds in E. ulmoides. Here, lncRNA and mRNA expression in male and female flower buds at the pistil and stamen differentiation stages were analyzed by RNA sequencing. A total of 562,762,194 clean reads, including 32937 lncRNAs and 26723 mRNAs, were obtained from six samples. A total of 417 and 312 differentially expressed (DE) mRNAs and lncRNAs were identified at the pistil and stamen differentiation stage, respectively. Additionally, 13 sex-biased mRNAs and 18 DE-lncRNAs were found to be involved in flowering, pollen development, reproduction, and other biological processes closely related to sex determination. Importantly, eight and 10 DE lncRNAs and mRNAs were predicted, which most likely function in the sex determination of E. ulmoides. These findings provide a valuable resource for studying floral sex organ development and provide a foundation for exploring sex determination in E. ulmoides.