Molecular Genetics and Genomics

, Volume 292, Issue 5, pp 1051–1067 | Cite as

The landscape and structural diversity of LTR retrotransposons in Musa genome

  • Faisal Nouroz
  • Shumaila Noreen
  • Habib Ahmad
  • J. S. Pat Heslop-Harrison
Original Article

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.

Keywords

Musa Retrotransposons Copia Gypsy Biodiversity Phylogeny Genomics Evolution 

Notes

Acknowledgements

The study was funded by Post quake Faculty Development Plan of Hazara University and Higher Education Commission of Pakistan. We are thankful to staff at University of Leicester, UK, who provided us technical assistance and all laboratory facilities during this work. The collection of 48 Musa genomic DNA was a gift from Professor Ashalatha (Asha) Nair, University of Kerala, India.

Compliance with ethical standards

Conflict of interest

All the authors declare no financial or other conflict of interest in publishing the manuscript.

Supplementary material

438_2017_1333_MOESM1_ESM.docx (26 kb)
Supplementary material 1 (DOCX 25 kb)

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Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  • Faisal Nouroz
    • 1
    • 2
  • Shumaila Noreen
    • 3
  • Habib Ahmad
    • 4
  • J. S. Pat Heslop-Harrison
    • 1
  1. 1.Molecular Cytogenetics Laboratory, Department of BiologyUniversity of LeicesterLeicesterUK
  2. 2.Bioinformatics Laboratory, Department of BotanyHazara UniversityMansehraPakistan
  3. 3.Molecular Genetics Laboratory, Department of GeneticsUniversity of LeicesterLeicesterUK
  4. 4.Genetics Laboratory, Department of GeneticsHazara UniversityMansehraPakistan

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