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Neem Genome Assembly

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

Abstract

Genome assembly refers to the process of taking a large number of short DNA sequences and putting them back together to create a representation of the original chromosomes from which the DNA originated. For assembling neem genome, we filtered the NGS raw reads from Illumina to get high-quality reads followed by assembly using Velvet assembler. Similar process was also followed to assemble Roche/454 reads using MIRA. The individual assembly from velvet and MIRA was merged using cd-hit to get the final assembly of neem genome. Transcriptome of neem was assembled from short-read data from different tissues using Trinity assembler. The reads for chloroplast and mitochondria were extracted separately by mapping genome reads to chloroplast and mitochondrial genomes of known plants. The reads were assembled separately using Velvet.

Keywords

Shotgun sequencing De novo Genome assembly MIRA Velvet 

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.

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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

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