Abstract
BackgroundTransposable 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.Methodology/Principal FindingsWe 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/SignificanceOur 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.
Highlights
Sweet potato [Ipomoea batatas] is the world’s seventh largest food crop cultivated worldwide due to its high yield, wide adaptability and strong resistance
For annotation of the assembled transcripts, sequence-similarity search was conducted against the NCBI non-redundant (Nr) protein database through Basic Local Alignment Search Tool (BLAST) alignment [27]
A New Perspective for TEs Scanning Transposable elements may be important motors of genetic variability, they account for the majority of genome, and have the ability to generate genetic polymorphisms favoring population adaptation [38]
Summary
Sweet potato [Ipomoea batatas] is the world’s seventh largest food crop cultivated worldwide due to its high yield, wide adaptability and strong resistance. It is grown on about 9 million hectares in the world, yielding 140 million tons per year, and over 97% of the world output of sweet potato is produced from developing countries. Sweet potato belongs to the Convolvulaceae family, Ipomoea genus, Batatas section It is the only hexaploid (2n = 6x = 90) plant with a huge genome (2,200 to 3,000 Mbp) [3,4,5] and complicated genetic structure. Sweet potato performs asexual reproduction generally and the TEs may be an important genetic factor for genome reorganization.
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
