Neem Genome Annotation
Gene annotation is considered an important step in understanding the functioning of the genome. With a good genome assembly in place, gene prediction and annotation is done to understand the functional aspects of the genome. However, the process becomes more complex due to the presence of alternative splicing and other regulatory factors that affect the protein-coding genes. To make the gene prediction more accurate, we used two different gene prediction programs to identify the genes. The genome annotation was carried out by mapping the gene sequences to multiple databases to obtain gene function. Along with annotation of nuclear genes, prediction and annotation of mitochondrial and chloroplast genes have been summarized in this chapter.
KeywordsAnnotation Gene prediction Mitochondria Chloroplast Differential expression
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.