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Background: Bamboo occupies an important phylogenetic node in the grass family with remarkable sizes,woodiness and a striking life history.Among the bulk of the regenerated Ma bamboo (Dendrocalamus latiflorus Munro) plants which are developed from the anther,we found an interesting phenomenon that these plantlets exhibited different ploidy,most of which were dodecaploid (96/100),a few were hexaploid (3/100),and one was triploid (1/100).Significant differences in the growth among different ploidy anther-regenerated plants were intriguing.In the present study,we performed digital gene expression sequencing for the first time to produce a comparative dataset for the Ma bamboo and intend to identify whether some genes count for this.Principal Findings: In this study,we determined the genome-wide gene expression profiles of 4 primary bamboo samples by ‘second-generation’ sequencing of short cDNA tags.On average,over 3 Mb of data were generated in each four library.About 95% of the raw tags passed the filter and the clean tags in each sample ranged from 3.35 to 3.63 million,resulting in 3,283,402 clean tags in Munro_3,3,028,221 clean tags in Munro_6,3,078,729 clean tags in Munro_12,3,337,293 clean tags in Munro_10.When clean tags were mapped to the final assembled transcripts described above,it was found that the clean tags mapped to transcripts in each sample ranged from 2.3 to 2.5 million,accounting for 76.44% to 76.86%.We compared these four libraries pair-wisely so that 6 pairs of comparison were implemented.Among these comparisons,we found that 981 to 3,015 transcripts had significant changes in expression,and the total number of the differentially genes was 8,396.These differential genes are predicted to be potentially involved in growth,development,and are worthy of further investigation.To our knowledge,this is the first application of digital gene expression sequencing technology to investigate the genes responsible for the different phenotype of different ploidy Ma bamboo plants regenerated from anther.The dataset will improve our understanding of the molecular mechanisms of plant growth,develop and other biochemical processes in Ma bamboo.This resource should lay an important foundation for future genetic or genomic studies on bamboo species and will help to close a critical gap existing in grass comparative genomics and consequently allow the more efficient development of the grass system for evolutionary and functional studies of plant genes and genomes.