Scanning of transposable elements and analyzing expression of transposase genes of sweet potato [Ipomoea batatas].
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 reor...
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doaj-99e2eecf39c54fc2ad5de50c170caa902020-11-25T02:22:10ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0193e9089510.1371/journal.pone.0090895Scanning of transposable elements and analyzing expression of transposase genes of sweet potato [Ipomoea batatas].Lang YanYing-Hong GuXiang TaoXian-Jun LaiYi-Zheng ZhangXue-Mei TanHaiyan WangBACKGROUND: 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. METHODOLOGY/PRINCIPAL FINDINGS: 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/SIGNIFICANCE: 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.http://europepmc.org/articles/PMC3946583?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Lang Yan Ying-Hong Gu Xiang Tao Xian-Jun Lai Yi-Zheng Zhang Xue-Mei Tan Haiyan Wang |
spellingShingle |
Lang Yan Ying-Hong Gu Xiang Tao Xian-Jun Lai Yi-Zheng Zhang Xue-Mei Tan Haiyan Wang Scanning of transposable elements and analyzing expression of transposase genes of sweet potato [Ipomoea batatas]. PLoS ONE |
author_facet |
Lang Yan Ying-Hong Gu Xiang Tao Xian-Jun Lai Yi-Zheng Zhang Xue-Mei Tan Haiyan Wang |
author_sort |
Lang Yan |
title |
Scanning of transposable elements and analyzing expression of transposase genes of sweet potato [Ipomoea batatas]. |
title_short |
Scanning of transposable elements and analyzing expression of transposase genes of sweet potato [Ipomoea batatas]. |
title_full |
Scanning of transposable elements and analyzing expression of transposase genes of sweet potato [Ipomoea batatas]. |
title_fullStr |
Scanning of transposable elements and analyzing expression of transposase genes of sweet potato [Ipomoea batatas]. |
title_full_unstemmed |
Scanning of transposable elements and analyzing expression of transposase genes of sweet potato [Ipomoea batatas]. |
title_sort |
scanning of transposable elements and analyzing expression of transposase genes of sweet potato [ipomoea batatas]. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2014-01-01 |
description |
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. METHODOLOGY/PRINCIPAL FINDINGS: 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/SIGNIFICANCE: 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. |
url |
http://europepmc.org/articles/PMC3946583?pdf=render |
work_keys_str_mv |
AT langyan scanningoftransposableelementsandanalyzingexpressionoftransposasegenesofsweetpotatoipomoeabatatas AT yinghonggu scanningoftransposableelementsandanalyzingexpressionoftransposasegenesofsweetpotatoipomoeabatatas AT xiangtao scanningoftransposableelementsandanalyzingexpressionoftransposasegenesofsweetpotatoipomoeabatatas AT xianjunlai scanningoftransposableelementsandanalyzingexpressionoftransposasegenesofsweetpotatoipomoeabatatas AT yizhengzhang scanningoftransposableelementsandanalyzingexpressionoftransposasegenesofsweetpotatoipomoeabatatas AT xuemeitan scanningoftransposableelementsandanalyzingexpressionoftransposasegenesofsweetpotatoipomoeabatatas AT haiyanwang scanningoftransposableelementsandanalyzingexpressionoftransposasegenesofsweetpotatoipomoeabatatas |
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