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.
KeywordsRepetitive DNA LINE SSR Transposable elements MISA software
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.
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