AZ2.0

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, resulted due to removal of mis-assembly and closure of gaps fromover 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 , under
(SRP013453).