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Comparison of Gene Families and Synteny Analysis from Neem Genome

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

Abstract

Analysis of gene families is helpful in understanding the gene evolution in species. Here we have studied the orthology of neem genes and constructed the phylogenetic tree based on the gene content in neem genome and comparing it with genes from 23 other plant species using proteinortho. The analysis shows 5832 unique genes with expression in various neem tissues. Following gene family analysis, Synteny analysis was performed which provides relative order of genes in the genome and provides information on genome structure. We aligned citrus (Citrus sinensis) and Arabidopsis genomes with neem contigs using MUMMER program. This identified 24,902 anchored neem contigs which contribute to 161 Mb (62%) of annotated neem genome covering 48% of the citrus genome. The synteny analysis showed a good synteny between neem and citrus and lowest synteny between neem and Arabidopsis.

Keywords

Synteny Ortholog MUMMER Phylogeny UPGMA 

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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