The landscape and structural diversity of LTR retrotransposons in Musa genome
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.
KeywordsMusa Retrotransposons Copia Gypsy Biodiversity Phylogeny Genomics Evolution
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.
- Du J, Tian Z, Hans CS, Laten HM, Cannon SB, Jackson SA, Shoemaker RC, Ma J (2010) Evolutionary conservation, diversity and specificity of LTR-Retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. Plant J 63:584–598. doi: 10.1111/j.1365-313X.2010.04263.x CrossRefPubMedGoogle Scholar
- Heslop-Harrison JS (2011) Genomics, banana breeding and superdomestication. In: Proceedings of the international ISHS-Pro Musa symposium on global perspectives on Asian challenges. Acta Hortic 897:55–62. doi: 10.17660/ActaHortic.2011.897.4
- Hippolyte I, Jenny C, Gardes L, Bakry F, Riyallan R, Pomies V, Cubry P, Tomekpe K, Risteruci AM, Roux N et al (2012) Foundation characteristics of edible Musa triploids revealed from allelic distribution of SSR markers. Ann Bot 109:937–951. doi: 10.1093/aob/mcs010 CrossRefPubMedPubMedCentralGoogle Scholar
- Nouroz F (2015) Large retrotransposon derivatives (LARDs) and terminal repeat retrotransposons in miniature (TRIMs) in Brassica genomes. Int J Agric Appl Sci 7:59–66Google Scholar
- Nouroz F, Noreen S, Heslop-Harrison JS (2016) Characterization and diversity of novel PIF/Harbinger DNA transposons in Brassica genomes. Pak J Bot 48(1):167–178Google Scholar
- Nouroz F, Noreen S, Heslop-Harrison JS (2017) Identification and evolutionary dynamics of CACTA DNA transposons in Brassica. Pak J Bot 49(2):789–798Google Scholar
- Pollefeys P, Sharrock S, Arnaud E (2004) Preliminary analysis of the literature on the distribution of wild Musa species using MGIS and DIVA-GIS. INIBAP, MontpellierGoogle Scholar
- Tomlinson P (1969) Anatomy of the monocotyledons. III. Commelinales-Zingiberales. Clarendon Press, Oxford, p 1969Google Scholar