title: Scanning of transposable elements and analyzing expression of transposase genes of sweet potato [Ipomoea batatas].
abstract: BACKGROUND
  Transposable elements (TEs) are the most abundant genomic components in eukaryotes and affect the genome by their replications and movements to generate genetic plasticity. Sweet potato performs asexual reproduction generally and the TEs may be an important genetic factor for genome reorganization. Complete identification of TEs is essential for the study of genome evolution. However, the TEs of sweet potato are still poorly understood because of its complex hexaploid genome and difficulty in genome sequencing. The recent availability of the sweet potato transcriptome databases provides an opportunity for discovering and characterizing the expressed TEs.
  
  
  RESULTS
  We first established the integrated-transcriptome database by de novo assembling four published sweet potato transcriptome databases from three cultivars in China. Using sequence-similarity search and analysis, a total of 1,405 TEs including 883 retrotransposons and 522 DNA transposons were predicted and categorized. Depending on mapping sets of RNA-Seq raw short reads to the predicted TEs, we compared the quantities, classifications and expression activities of TEs inter- and intra-cultivars. Moreover, the differential expressions of TEs in seven tissues of Xushu 18 cultivar were analyzed by using Illumina digital gene expression (DGE) tag profiling. It was found that 417 TEs were expressed in one or more tissues and 107 in all seven tissues. Furthermore, the copy number of 11 transposase genes was determined to be 1-3 copies in the genome of sweet potato by Real-time PCR-based absolute quantification.
  
  
  CONCLUSIONS
  Our result provides a new method for TE searching on species with transcriptome sequences while lacking genome information. The searching, identification and expression analysis of TEs will provide useful TE information in sweet potato, which are valuable for the further studies of TE-mediated gene mutation and optimization in asexual reproduction. It contributes to elucidating the roles of TEs in genome evolution.
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Center for Functional Genomics and Bioinformatics, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China.
authors.forename: Lang
authors.initials: L
authors.lastname: Yan
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Center for Functional Genomics and Bioinformatics, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China.
authors.forename: Ying-Hong
authors.initials: YH
authors.lastname: Gu
authors.affiliation: Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, People's Republic of China.
authors.forename: Xiang
authors.initials: X
authors.lastname: Tao
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Center for Functional Genomics and Bioinformatics, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China.
authors.forename: Xian-Jun
authors.initials: XJ
authors.lastname: Lai
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Center for Functional Genomics and Bioinformatics, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China.
authors.forename: Yi-Zheng
authors.initials: YZ
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Center for Functional Genomics and Bioinformatics, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China.
authors.forename: Xue-Mei
authors.initials: XM
authors.lastname: Tan
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Center for Functional Genomics and Bioinformatics, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Wang
mesh_terms: D004251:DNA Transposable Elements; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D027723:Ipomoea batatas / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D011003:Ploidies; D012100:Reproduction, Asexual / Q000235:genetics; D018626:Retroelements; D059467:Transcriptome; D019895:Transposases / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D018626:Retroelements; D019895:Transposases