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...

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Autores principales:	Morad M Mokhtar, Alsamman M Alsamman, Haytham M Abd-Elhalim, Achraf El Allali
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/139470786040441da6a79223d45f2d0c
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spelling	oai:doaj.org-article:139470786040441da6a79223d45f2d0c2021-12-02T20:07:35ZCicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species.1932-620310.1371/journal.pone.0259540https://doaj.org/article/139470786040441da6a79223d45f2d0c2021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0259540https://doaj.org/toc/1932-6203Recently, 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.Morad M MokhtarAlsamman M AlsammanHaytham M Abd-ElhalimAchraf El AllaliPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 11, p e0259540 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q 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.
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.
format	article
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
title	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_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_sort	cicersptedb: a web-based database for high-resolution genome-wide identification of transposable elements in cicer species.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/139470786040441da6a79223d45f2d0c
work_keys_str_mv	AT moradmmokhtar cicersptedbawebbaseddatabaseforhighresolutiongenomewideidentificationoftransposableelementsincicerspecies AT alsammanmalsamman cicersptedbawebbaseddatabaseforhighresolutiongenomewideidentificationoftransposableelementsincicerspecies AT haythammabdelhalim cicersptedbawebbaseddatabaseforhighresolutiongenomewideidentificationoftransposableelementsincicerspecies AT achrafelallali cicersptedbawebbaseddatabaseforhighresolutiongenomewideidentificationoftransposableelementsincicerspecies
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CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species.

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