Abstract
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
Highlights
Transposable elements (TEs) are mobile DNA sequences that can move and integrate themselves in another location throughout the genome [1]
TEs identification and annotation have been formed for numerous plant genomes through extensive efforts and manual identification, e.g., Arabidopsis [80], rice [14], and maize [81]
Intact TEs are the complete structures of TEs that can transpose throughout the genome [82]
Summary
Transposable elements (TEs) are mobile DNA sequences that can move and integrate themselves in another location throughout the genome [1]. Based on the transposition systems, TEs were classified into two classes [2]. Class I is known as retrotransposons, and Class II is known as DNA transposons. Retrotransposons utilize a copy and paste system, while DNA transposons use the cut and paste systems to transpose along the genome [2].
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