Mulberry (Morus atropurpurea) is an economically important tree with a long history of extensive cultivation in Asia because it is the exclusive food source for the silkworm (Bombyx mori).Recently,mulberry has gained additional commercial value as a source for medicinal compounds,as animal fodder,and as landscaping trees.In the present work,the mulberry transcriptome was sequenced using Illumina paired-end sequencing technology.A total of 105 million 90-bp paired-end reads were generated,and 60,069 unigenes were assembled with an N50 of 1,219 bp.Based on a sequence similarity search with known proteins,40,121 genes were identified.Among these genes,31,548 were annotated with 55 gene ontology functional categories,7,790 had a Cluster of Orthologous Groups classification,and 23,188 mapped to 128 biological pathways in the Kyoto Encyclopedia of Genes and Genomes pathway database.In addition,10,268 microsatellites were developed and characterized as potential molecular markers.These data will accelerate the understanding of mulberry growth and development mechanisms and facilitate gene discovery and functional genomic studies in mulberry.