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CicerSpTEdb2.0: An Upgrade of Cicer Species Transposable Elements Database

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Plant Genomic and Cytogenetic Databases

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2703))

Abstract

To meet the critical demand of LTR-RTs data-driven research, we updated the CicerSpTEdb database to version 2.0, which includes more accurate intact LTR-RT elements with annotation of internal domains. We also added the ability to BLAST against TEs of Cicer species. As a result, 3701 intact LTR-RTs were detected in the studied genomes, including 2840 Copia and 861 Gypsy elements. Of the 3701 intact LTR-RTs, 588 were in C. arietinum, including 475 Copia and 113 Gypsy. While 1373 were detected in C. reticulatum, including 1041 Copia and 332 Gypsy. Furthermore, 1740 were found in C. echinospermum, including 1324 Copia and 416 Gypsy. Based on LTR-RT clades, the analysis classified the 3701 identified intact LTR-RTs in the studied genomes as Ale (850), SIRE (740), unknown (455), Ikeros (323), Reina (290), Tork (290), Ivana (282), Tekay (197), Athila (128), TAR (99), CRM (31), and Ogre (16) elements. The newly updated CicerSpTEdb2.0 will be a valuable resource for TEs of Cicer species and their comparative genomics.

Database URL: http://cicersptedb.easyomics.org/index.php

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Acknowledgments

The authors acknowledge the African Supercomputing Center at Mohamed VI Polytechnic University for the supercomputing resources made available for conducting the research reported in this chapter.

Author information

Authors and Affiliations

  1. African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco

    Morad M. Mokhtar & Achraf El Allali

  2. Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt

    Ahmed S. Fouad

  3. Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza, Egypt

    Haytham M. Abd-Elhalim

Authors
  1. Morad M. Mokhtar
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  2. Ahmed S. Fouad
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  3. Haytham M. Abd-Elhalim
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  4. Achraf El Allali
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Corresponding author

Correspondence to Achraf El Allali .

Editor information

Editors and Affiliations

  1. Botanical Institute of Barcelona IBB (CSIC-Barcelona City Council), Barcelona, Spain

    Sònia Garcia

  2. Botanical Institute of Barcelona, IBB (CSIC-Barcelona City Council), Barcelona, Spain

    Neus Nualart

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Mokhtar, M.M., Fouad, A.S., Abd-Elhalim, H.M., El Allali, A. (2023). CicerSpTEdb2.0: An Upgrade of Cicer Species Transposable Elements Database. In: Garcia, S., Nualart, N. (eds) Plant Genomic and Cytogenetic Databases. Methods in Molecular Biology, vol 2703. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3389-2_6

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  • DOI: https://doi.org/10.1007/978-1-0716-3389-2_6

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3388-5

  • Online ISBN: 978-1-0716-3389-2

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