Advertisement

Repetitive Sequences

  • Nagesh A. Kuravadi
  • Malali GowdaEmail author
Chapter
Part of the Compendium of Plant Genomes book series (CPG)

Abstract

Repetitive DNA sequences are an important component of eukaryotic genome. With the availability of the neem genome, it was used for identifying and classifying repetitive elements of the genome. This chapter details the analysis of transposable elements in neem that revealed the presence of 87 MB of reparative sequences in repeat families like SINEs, LINEs, and LTRs. Analysis of simple sequence repeats (SSR) was also performed that identified thousands of SSRs in each genotype. Further in silico polymorphism identification and filtration was done to shortlist polymorphic SSR’s among the neem genotypes that can be used as genetic markers in diversity studies and mapping genes.

Keywords

Repetitive DNA LINE SSR Transposable elements MISA software 

Notes

Acknowledgements

We acknowledge Genomics facility (BT/PR3481/INF/22/140/2011) at Centre for Cellular and Molecular Platforms, Bangalore for sequencing of Neem genomes. We acknowledge Pradeep H, Aarati Karaba, Manojkumar S and Annapurna for their help in NGS library preparation and sequencing. We thank Ashmita G and Divya S for their help in manual curation of SSR markers. We are grateful to Rajanna, National Botanical Garden, University of Agricultural Sciences, GKVK campus, Bangalore for his help during neem sample collection.

References

  1. Aboyoun P, Pages H, Lawrence M (2010) GenomicRanges: representation and manipulation of genomic intervals. R Package Version 1:1–25Google Scholar
  2. Biscotti MA, Olmo E, Heslop-Harrison JSP (2015) Repetitive DNA in eukaryotic genomes. SpringerGoogle Scholar
  3. Godoy JA, Jordano P (2001) Seed dispersal by animals: exact identification of source trees with endocarp DNA microsatellites. Mol Ecol 10:2275–2283CrossRefGoogle Scholar
  4. Kuravadi NA, Tiwari PB, Tanwar UK, Tripathi SK, Dhugga KS, Gill KS, Randhawa GS (2014) Identification and characterization of EST-SSR markers in cluster bean (Cyamopsis spp.). Crop Sci 54:1097–1102Google Scholar
  5. Kuravadi NA, Yenagi V, Rangiah K, Mahesh HB, Rajamani A, Shirke MD, Russiachand H, Loganathan RM, Lingu CS, Siddappa S (2015) Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree. PeerJ 3:e1066CrossRefGoogle Scholar
  6. Warnes GR, Bolker B, Lumley T (2008) gtools: Various R programming tools. R Package Version 2Google Scholar
  7. Wickham H (2010) stringr: Make it easier to work with strings. R Package Version 0.4. URL http://CRAN.R-project.org/package=stringr
  8. Zhang X, Wessler SR (2004) Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea. Proc Natl Acad Sci U S A 101:5589–5594CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Centre for Cellular and Molecular Platforms, National Centre for Biological SciencesBengaluruIndia
  2. 2.Center for Functional Genomics and Bio-Informatics, The University of TransDisciplinary and Health SciencesBengaluruIndia

Personalised recommendations