Open Access Highly Accessed Research article

A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica

Neeraja M Krishnan1, Swetansu Pattnaik12, Prachi Jain1, Prakhar Gaur1, Rakshit Choudhary1, Srividya Vaidyanathan1, Sa Deepak1, Arun K Hariharan1, PG Bharath Krishna1, Jayalakshmi Nair1, Linu Varghese1, Naveen K Valivarthi1, Kunal Dhas1, Krishna Ramaswamy1 and Binay Panda12*

Author Affiliations

1 Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bangalore, 560100, India

2 Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India

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BMC Genomics 2012, 13:464  doi:10.1186/1471-2164-13-464

Published: 9 September 2012

Additional files

Additional file 1:

Table S1. Description of sequencing read libraries used for genome and transcriptome assembly. Table S2. Classification of repeats in the neem genome. Table S3. Transcript annotations from similarity-based analyses. Table S4. Mapping neem RNA-Seq reads to other plant genomes. Table S5. Transcript mapping statistics using PASA. Table S6. Gene ontology based functional categorization of annotated transcripts. Table S7. Expression levels of genes associated with metabolism in neem compared to other plant species.

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Additional file 2:

Figure S1. kMer frequency curve. Figure S2. Frequency histograms for symmetric 4-mers. Figure S3. Genome scaffold mapping between neem and other species. Figure S4.Gene ontology based functional categorization of annotated transcripts. Figure S5. Expression density profiles of neem organ transcriptomes. Figure S6. Gene prediction statistics. Figure S7. GC-correlated expression density profiles of neem organ transcriptomes. Figure S8.AT and GC density profiles in genomes and transcriptomes of neem and other plant species.

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Additional file 3:

Text S1. Supplementary methods.

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Additional file 4:

Gene sequences from different species used to perform phylogenetic analysis.

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Additional file 5:

Phylogenetic file generated using rbcL and rbcS genes of 24-plant species.

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Additional file 6:

Phylogenetic file generated using rbcL gene of Meliaceae family members.

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