Mulberry (Morus alba L.) is a perennial woody plant with significant economic benefits and ecological value. The floral character of mulberry has an important impact on the yield and quality to its fruits and leaves. However, little is known about the molecular mechanism of mulberry floral differentiation still now. The transcriptome data were obtained via Illumina HiSeq high-throughput sequencing from male and female inflorescences of the monoecious mulberry. A total of 26.21 Gb clean data were obtained, and as many as 100,177 unigenes with an average length of 821.66 bp were successfully assembled. In comparative-omics analysis, 1717 differentially expressed genes (DEGs) were identified between male and female flowers and only a quarter of the DEGs were highly expressed in female flowers. The KEGG pathway enrichment analysis revealed that DEGs were involved in glucose and lipid metabolism, hormone signal transduction, and the regulation of related transcription factors. In addition, many DEGs related to flower development and plant sex differentiation have also been detected, such as PMADS1/2, AGAMOUS, FLOWERING LOCUS T (FT), APETALA 2 (AP2), TASSELSEED2 (TS2), and ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17). Finally, the expression patterns of selected 20 DEGs were validated by q-PCR and the results showed that the transcriptome data were highly reliable. This study shows that the differentiation of male and female flowers of mulberry is affected and regulated by multiple factors, with transcription factors and hormone signals playing a key role. Briefly, the current data provide comprehensive insights into the mulberry tree’s floral differentiation as well as a bioinformatics framework for the development of molecular breeding of mulberry.

Mulberry leaves at different positions are different in photosynthetic rate, nutrient substance and feeding impact to silkworms. Here, we investigated the proteomic differences of the first (L1), sixth (L6), and twentieth (L20) mulberry leaves at different stem positions (from top to the base) using a label-free quantitative proteomics approach. L1 contained less developed photosynthetic apparatus but was more active in protein synthesis. L20 has more channel proteins and oxidoreductases relative to L6. Proteins that detected in all measured leaves were classified into three groups according to their expression patterns in L1, L6, and L20. The protein group that displayed the maximum amount in L6 has the highest possibility that function related to photosynthesis. Nine function unknown proteins belong to this group were further analyzed in the light responsive expression, evolutionary tree and sub-cellular localization analysis. Based on the results, five proteins were suggested to be involved in photosynthesis. Taken together, these results reveal the molecular details of different roles of mulberry leaves at different developmental stages and contribute to the identification of five proteins that might function related to photosynthesis.