201. An Improved Genome Assembly of Azadirachta indica A. Juss
- Author
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Neeraja M. Krishnan, Saurabh Gupta, Arun K Hariharan, Binay Panda, and Prachi Jain
- Subjects
0106 biological sciences ,0301 basic medicine ,assembly ,Sequencing data ,Sequence assembly ,Computational biology ,QH426-470 ,Investigations ,01 natural sciences ,Genome ,Transcriptome ,03 medical and health sciences ,FDFT1 ,Botany ,Genetics ,SQLE ,Sequence Read Archive ,Molecular Biology ,Gene ,Genetics (clinical) ,Meliaceae ,biology ,bepress|Life Sciences|Biology ,bepress|Biology ,Azadirachta ,Short read ,biology.organism_classification ,030104 developmental biology ,bepress|Life Sciences|Bioinformatics ,mate-pair ,bepress|Bioinformatics ,010606 plant biology & botany ,PASA - Abstract
Neem (Azadirachta indica A. Juss.), an evergreen tree of the Meliaceae family, is known for its medicinal, cosmetic, pesticidal and insecticidal properties. We had previously sequenced and published the draft genome of the plant, using mainly short read sequencing data. In this report, we present an improved genome assembly generated using additional short reads from Illumina and long reads from Pacific Biosciences SMRT sequencer. We assembled short reads and error corrected long reads using Platanus, an assembler designed to perform well for heterozygous genomes. The updated genome assembly (v2.0) yielded 3- and 3.5-fold increase in N50 and N75, respectively; 2.6-fold decrease in the total number of scaffolds; 1.25-fold increase in the number of valid transcriptome alignments; 13.4-fold less mis-assembly and 1.85-fold increase in the percentage repeat, over the earlier assembly (v1.0). The current assembly also maps better to the genes known to be involved in the terpenoid biosynthesis pathway. Together, the data represents an improved assembly of the A. indica genome. The raw data described in this manuscript are submitted to the NCBI Short Read Archive under the accession numbers SRX1074131, SRX1074132, SRX1074133, and SRX1074134 (SRP013453).
- Published
- 2015