title: An Improved Genome Assembly of Azadirachta indica A. Juss.
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 a neem 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 misassembly 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 represent an improved assembly of the A. indica genome.
authors.affiliation: Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India.
authors.forename: Neeraja M
authors.initials: NM
authors.lastname: Krishnan
authors.affiliation: Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India.
authors.forename: Prachi
authors.initials: P
authors.lastname: Jain
authors.affiliation: Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India.
authors.forename: Saurabh
authors.initials: S
authors.lastname: Gupta
authors.affiliation: Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India.
authors.forename: Arun K
authors.initials: AK
authors.lastname: Hariharan
authors.affiliation: Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India Strand Life Sciences, Bangalore 560024, India binay@ganitlabs.in.
authors.forename: Binay
authors.initials: B
authors.lastname: Panda
mesh_terms: D031601:Azadirachta / Q000235:genetics* / Q000378:metabolism; D002874:Chromosome Mapping / Q000379:methods*; D018745:Genome, Plant; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing; D017422:Sequence Analysis, DNA; D013729:Terpenes / Q000378:metabolism; D059467:Transcriptome
chemical_list: D013729:Terpenes
keywords: FDFT1; PASA; SQLE; assembly; mate-pair