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

Overview

Journal Methods Mol Biol

Specialty Molecular Biology

Date 2023 Aug 30

PMID 37646938

Authors

Morad M Mokhtar

Ahmed S Fouad

Haytham M Abd-Elhalim

Achraf El Allali

Affiliations

Soon will be listed here.

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.

References

Finnegan D . Transposable elements in eukaryotes. Int Rev Cytol. 1985; 93:281-326. DOI: 10.1016/s0074-7696(08)61376-5. View

Wicker T, Sabot F, Hua-Van A, Bennetzen J, Capy P, Chalhoub B . A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 2007; 8(12):973-82. DOI: 10.1038/nrg2165. View

Bennetzen J . Transposable element contributions to plant gene and genome evolution. Plant Mol Biol. 2000; 42(1):251-69. View

Wang W, Zheng H, Fan C, Li J, Shi J, Cai Z . High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell. 2006; 18(8):1791-802. PMC: 1533979. DOI: 10.1105/tpc.106.041905. View

Lisch D . Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol. 2008; 60:43-66. DOI: 10.1146/annurev.arplant.59.032607.092744. View

Paszkowski J . Controlled activation of retrotransposition for plant breeding. Curr Opin Biotechnol. 2015; 32:200-206. DOI: 10.1016/j.copbio.2015.01.003. View

Rey O, Danchin E, Mirouze M, Loot C, Blanchet S . Adaptation to Global Change: A Transposable Element-Epigenetics Perspective. Trends Ecol Evol. 2016; 31(7):514-526. DOI: 10.1016/j.tree.2016.03.013. View

Thieme M, Lanciano S, Balzergue S, Daccord N, Mirouze M, Bucher E . Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding. Genome Biol. 2017; 18(1):134. PMC: 5501947. DOI: 10.1186/s13059-017-1265-4. View

Jukanti A, Gaur P, Gowda C, Chibbar R . Nutritional quality and health benefits of chickpea (Cicer arietinum L.): a review. Br J Nutr. 2012; 108 Suppl 1:S11-26. DOI: 10.1017/S0007114512000797. View

10.

Varshney R, Song C, Saxena R, Azam S, Yu S, Sharpe A . Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol. 2013; 31(3):240-6. DOI: 10.1038/nbt.2491. View

11.

Parween S, Nawaz K, Roy R, Pole A, Venkata Suresh B, Misra G . An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.). Sci Rep. 2015; 5:12806. PMC: 4531285. DOI: 10.1038/srep12806. View

12.

Jain M, Misra G, Patel R, Priya P, Jhanwar S, Khan A . A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). Plant J. 2013; 74(5):715-29. DOI: 10.1111/tpj.12173. View

13.

Gupta S, Nawaz K, Parween S, Roy R, Sahu K, Kumar Pole A . Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource for agronomic trait improvement. DNA Res. 2016; 24(1):1-10. PMC: 5381347. DOI: 10.1093/dnares/dsw042. View

14.

Jain M, Chevala V, Garg R . Genome-wide discovery and differential regulation of conserved and novel microRNAs in chickpea via deep sequencing. J Exp Bot. 2014; 65(20):5945-58. PMC: 4203128. DOI: 10.1093/jxb/eru333. View

15.

Gayali S, Acharya S, Lande N, Pandey A, Chakraborty S, Chakraborty N . CicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors. BMC Plant Biol. 2016; 16(1):169. PMC: 4966752. DOI: 10.1186/s12870-016-0860-y. View

16.

Singh U, Khemka N, Singh Rajkumar M, Garg R, Jain M . PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea. Nucleic Acids Res. 2017; 45(22):e183. PMC: 5727461. DOI: 10.1093/nar/gkx866. View

17.

Mokhtar M, Alsamman A, Abd-Elhalim H, El Allali A . CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species. PLoS One. 2021; 16(11):e0259540. PMC: 8584679. DOI: 10.1371/journal.pone.0259540. View

18.

Mokhtar M, El Allali A . PltRNAdb: Plant transfer RNA database. PLoS One. 2022; 17(5):e0268904. PMC: 9126412. DOI: 10.1371/journal.pone.0268904. View

19.

Szklarczyk D, Morris J, Cook H, Kuhn M, Wyder S, Simonovic M . The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res. 2016; 45(D1):D362-D368. PMC: 5210637. DOI: 10.1093/nar/gkw937. View

20.

Buels R, Yao E, Diesh C, Hayes R, Munoz-Torres M, Helt G . JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 2016; 17:66. PMC: 4830012. DOI: 10.1186/s13059-016-0924-1. View