CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species.
Recently, Cicer species have experienced increased research interest due to their economic importance, especially in genetics, genomics, and crop improvement. The Cicer arietinum, Cicer reticulatum, and Cicer echinospermum genomes have been sequenced and provide valuable resources for trait improvem...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2021-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0259540 |
| _version_ | 1828147091689439232 |
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| author | Morad M Mokhtar Alsamman M Alsamman Haytham M Abd-Elhalim Achraf El Allali |
| author_facet | Morad M Mokhtar Alsamman M Alsamman Haytham M Abd-Elhalim Achraf El Allali |
| author_sort | Morad M Mokhtar |
| collection | DOAJ |
| description | Recently, Cicer species have experienced increased research interest due to their economic importance, especially in genetics, genomics, and crop improvement. The Cicer arietinum, Cicer reticulatum, and Cicer echinospermum genomes have been sequenced and provide valuable resources for trait improvement. Since the publication of the chickpea draft genome, progress has been made in genome assembly, functional annotation, and identification of polymorphic markers. However, work is still needed to identify transposable elements (TEs) and make them available for researchers. In this paper, we present CicerSpTEdb, a comprehensive TE database for Cicer species that aims to improve our understanding of the organization and structural variations of the chickpea genome. Using structure and homology-based methods, 3942 C. echinospermum, 3579 C. reticulatum, and 2240 C. arietinum TEs were identified. Comparisons between Cicer species indicate that C. echinospermum has the highest number of LTR-RT and hAT TEs. C. reticulatum has more Mutator, PIF Harbinger, Tc1 Mariner, and CACTA TEs, while C. arietinum has the highest number of Helitron. CicerSpTEdb enables users to search and visualize TEs by location and download their results. The database will provide a powerful resource that can assist in developing TE target markers for molecular breeding and answer related biological questions. Database URL: http://cicersptedb.easyomics.org/index.php. |
| first_indexed | 2024-04-11T20:56:10Z |
| format | Article |
| id | doaj.art-139470786040441da6a79223d45f2d0c |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-11T20:56:10Z |
| publishDate | 2021-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-139470786040441da6a79223d45f2d0c2022-12-22T04:03:40ZengPublic Library of Science (PLoS)PLoS ONE1932-62032021-01-011611e025954010.1371/journal.pone.0259540CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species.Morad M MokhtarAlsamman M AlsammanHaytham M Abd-ElhalimAchraf El AllaliRecently, Cicer species have experienced increased research interest due to their economic importance, especially in genetics, genomics, and crop improvement. The Cicer arietinum, Cicer reticulatum, and Cicer echinospermum genomes have been sequenced and provide valuable resources for trait improvement. Since the publication of the chickpea draft genome, progress has been made in genome assembly, functional annotation, and identification of polymorphic markers. However, work is still needed to identify transposable elements (TEs) and make them available for researchers. In this paper, we present CicerSpTEdb, a comprehensive TE database for Cicer species that aims to improve our understanding of the organization and structural variations of the chickpea genome. Using structure and homology-based methods, 3942 C. echinospermum, 3579 C. reticulatum, and 2240 C. arietinum TEs were identified. Comparisons between Cicer species indicate that C. echinospermum has the highest number of LTR-RT and hAT TEs. C. reticulatum has more Mutator, PIF Harbinger, Tc1 Mariner, and CACTA TEs, while C. arietinum has the highest number of Helitron. CicerSpTEdb enables users to search and visualize TEs by location and download their results. The database will provide a powerful resource that can assist in developing TE target markers for molecular breeding and answer related biological questions. Database URL: http://cicersptedb.easyomics.org/index.php.https://doi.org/10.1371/journal.pone.0259540 |
| spellingShingle | Morad M Mokhtar Alsamman M Alsamman Haytham M Abd-Elhalim Achraf El Allali CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species. PLoS ONE |
| title | CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species. |
| title_full | CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species. |
| title_fullStr | CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species. |
| title_full_unstemmed | CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species. |
| title_short | CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species. |
| title_sort | cicersptedb a web based database for high resolution genome wide identification of transposable elements in cicer species |
| url | https://doi.org/10.1371/journal.pone.0259540 |
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