title: Transposable elements in Phyllostachys  pubescens (Poaceae) genome survey sequences and the full-length cDNA sequences, and their association with  simple-sequence repeats.
abstract: Phyllostachys  pubescens is a woody bamboo with the highest ecological,  economic, and cultural values of all bamboos in Asia. There is more genomic  data available for P. pubescens than for any other bamboo species,  including 2.12-Mb genome survey sequences (GSS) and 11.4-Mb full-length cDNA  sequences (FL-cDNAs) currently deposited in GenBank. Analysis of these  sequences revealed that transposable elements (TEs) are abundant, diverse and  polyphyletic in the P. pubescens genome, of which Ty3-gypsy and  Ty1-copia are the two most abundant families. Phylogenic analysis showed  that both elements probably arose before the Bambusoideae separated from the  other Poaceae subfamilies. We found evidence that the distribution of some  intragenic TEs correlated with transcript profiles, of which Mutator elements  preferred to insert in the transcripts of transcription factors. Additionally,  we found that the abundance of SSRs in TEs (4.56%) was significantly higher  than in GSS (0.098%) and in FL-cDNAs (2.60%) in P. pubescens genome, and  TA/AT and CT/AG repeats were found to be intimately associated with En/Spm and Mutator elements, respectively. Our data provide a glimpse of the structure  and evolution of P. pubescens genome, although large-scale sequencing of  the genome would be required to fully understand the architecture of the P.  pubescens genome.
authors.affiliation: The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, Zhejiang Province, P.R. China.
authors.forename: M B
authors.initials: MB
authors.lastname: Zhou
authors.forename: X M
authors.initials: XM
authors.lastname: Liu
authors.forename: D Q
authors.initials: DQ
authors.lastname: Tang
mesh_terms: D031723:Bambusa / Q000235:genetics*; D004251:DNA Transposable Elements; D018076:DNA, Complementary / Q000235:genetics*; D030541:Databases, Genetic; D019143:Evolution, Molecular; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D018895:Microsatellite Repeats; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D049490:Systems Biology / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D018076:DNA, Complementary; D014157:Transcription Factors