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The landscape and structural diversity of LTR retrotransposons in Musa genome.
Mol Genet Genomics. 2017 Oct; 292(5):1051-1067.MG

Abstract

Long terminal repeat retrotransposons represent a major component of plant genomes and act as drivers of genome evolution and diversity. Musa is an important fruit crop and also used as a starchy vegetable in many countries. BAC sequence analysis by dot plot was employed to investigate the LTR retrotransposons from Musa genomes. Fifty intact LTR retrotransposons from selected Musa BACs were identified by dot plot analysis and further BLASTN searches retrieved 153 intact copies, 61 truncated, and a great number of partial copies/remnants from GenBank database. LARD-like elements were also identified with several copies dispersed among the Musa genotypes. The predominant elements were the LTR retrotransposons Copia and Gypsy, while Caulimoviridae (pararetrovirus) were rare in the Musa genome. PCR amplification of reverse transcriptase (RT) sequences revealed their abundance in almost all tested Musa accessions and their ancient nature before the divergence of Musa species. The phylogenetic analysis based on RT sequences of Musa and other retrotransposons clustered them into Gypsy, Caulimoviridae, and Copia lineages. Most of the Musa-related elements clustered in their respective groups, while some grouped with other elements indicating homologous sequences. The present work will be helpful to understand the LTR retrotransposons landscape, giving a complete picture of the nature of the elements, their structural features, annotation, and evolutionary dynamics in the Musa genome.

Authors+Show Affiliations

Molecular Cytogenetics Laboratory, Department of Biology, University of Leicester, Leicester, UK. faisalnouroz@gmail.com. Bioinformatics Laboratory, Department of Botany, Hazara University, Mansehra, Pakistan. faisalnouroz@gmail.com.Molecular Genetics Laboratory, Department of Genetics, University of Leicester, Leicester, UK.Genetics Laboratory, Department of Genetics, Hazara University, Mansehra, Pakistan.Molecular Cytogenetics Laboratory, Department of Biology, University of Leicester, Leicester, UK.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

28601922

Citation

Nouroz, Faisal, et al. "The Landscape and Structural Diversity of LTR Retrotransposons in Musa Genome." Molecular Genetics and Genomics : MGG, vol. 292, no. 5, 2017, pp. 1051-1067.
Nouroz F, Noreen S, Ahmad H, et al. The landscape and structural diversity of LTR retrotransposons in Musa genome. Mol Genet Genomics. 2017;292(5):1051-1067.
Nouroz, F., Noreen, S., Ahmad, H., & Heslop-Harrison, J. S. P. (2017). The landscape and structural diversity of LTR retrotransposons in Musa genome. Molecular Genetics and Genomics : MGG, 292(5), 1051-1067. https://doi.org/10.1007/s00438-017-1333-1
Nouroz F, et al. The Landscape and Structural Diversity of LTR Retrotransposons in Musa Genome. Mol Genet Genomics. 2017;292(5):1051-1067. PubMed PMID: 28601922.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The landscape and structural diversity of LTR retrotransposons in Musa genome. AU - Nouroz,Faisal, AU - Noreen,Shumaila, AU - Ahmad,Habib, AU - Heslop-Harrison,J S Pat, Y1 - 2017/06/10/ PY - 2016/03/09/received PY - 2017/06/07/accepted PY - 2017/6/12/pubmed PY - 2018/4/4/medline PY - 2017/6/12/entrez KW - Biodiversity KW - Copia KW - Evolution KW - Genomics KW - Gypsy KW - Musa KW - Phylogeny KW - Retrotransposons SP - 1051 EP - 1067 JF - Molecular genetics and genomics : MGG JO - Mol. Genet. Genomics VL - 292 IS - 5 N2 - Long terminal repeat retrotransposons represent a major component of plant genomes and act as drivers of genome evolution and diversity. Musa is an important fruit crop and also used as a starchy vegetable in many countries. BAC sequence analysis by dot plot was employed to investigate the LTR retrotransposons from Musa genomes. Fifty intact LTR retrotransposons from selected Musa BACs were identified by dot plot analysis and further BLASTN searches retrieved 153 intact copies, 61 truncated, and a great number of partial copies/remnants from GenBank database. LARD-like elements were also identified with several copies dispersed among the Musa genotypes. The predominant elements were the LTR retrotransposons Copia and Gypsy, while Caulimoviridae (pararetrovirus) were rare in the Musa genome. PCR amplification of reverse transcriptase (RT) sequences revealed their abundance in almost all tested Musa accessions and their ancient nature before the divergence of Musa species. The phylogenetic analysis based on RT sequences of Musa and other retrotransposons clustered them into Gypsy, Caulimoviridae, and Copia lineages. Most of the Musa-related elements clustered in their respective groups, while some grouped with other elements indicating homologous sequences. The present work will be helpful to understand the LTR retrotransposons landscape, giving a complete picture of the nature of the elements, their structural features, annotation, and evolutionary dynamics in the Musa genome. SN - 1617-4623 UR - https://www.unboundmedicine.com/medline/citation/28601922/The_landscape_and_structural_diversity_of_LTR_retrotransposons_in_Musa_genome_ L2 - https://dx.doi.org/10.1007/s00438-017-1333-1 DB - PRIME DP - Unbound Medicine ER -