AZ2.0

Neem (Azadirachta indica A. Juss.), an evergreen tree of the Meliaceae family, is known for its<br>medicinal, cosmetic, pesticidal and insecticidal properties. We had previously sequenced and <br>published the draft genome of the plant, using mainly short read sequencing data. In this report, we <br>present an improved genome assembly generated using additional short reads from Illumina and <br>long reads from Pacific Biosciences SMRT sequencer. We assembled short reads and error-<br>corrected long reads using Platanus, an assembler designed to perform well for heterozygous <br>genomes. The updated genome assembly (v2.0) yielded 3- and 3.5-fold increase in N50 and N75, <br>respectively; 2.6-fold decrease in the total number of scaffolds; 1.25-fold increase in the number of <br>valid transcriptome alignments; 13.4-fold less mis-assembly and 1.85-fold increase in the <br>percentage repeat, resulted due to removal of mis-assembly and closure of gaps fromover the earlier <br>assembly (v1.0). The current assembly also maps better to the genes known to be involved in the <br>terpenoid biosynthesis pathway. Together, the data represents an improved assembly of the A. <br>indica genome.<br><br>The raw data described in this manuscript are submitted to the NCBI Short Read Archive under <br>the accession numbers SRX1074131, SRX1074132, SRX1074133, and SRX1074134 , under <br>(SRP013453).