PT  - JOURNAL ARTICLE
AU  - Pierre Nouhaud
TI  - Long-read based assembly and annotation of a <em>Drosophila simulans</em> genome
AID  - 10.1101/425710
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 425710
4099  - http://biorxiv.org/content/early/2018/09/24/425710.short
4100  - http://biorxiv.org/content/early/2018/09/24/425710.full
AB  - Long-read sequencing technologies enable high-quality, contiguous genome assemblies. Here we used SMRT sequencing to assemble the genome of a Drosophila simulans strain originating from Madagascar, the ancestral range of the species. We generated 8 Gb of raw data (~50× coverage) with a mean read length of 6,410 bp, a NR50 of 9,125 bp and the longest subread at 49 kb. We benchmarked six different assemblers and merged the best two assemblies from Canu and Falcon. Our final assembly was 127.41 Mb with a N50 of 5.38 Mb and 305 contigs. We anchored more than 4 Mb of novel sequence to the major chromosome arms, and significantly improved the assembly of peri-centromeric and telomeric regions. Finally, we performed full-length transcript sequencing and used this data in conjunction with short-read RNAseq data to annotate 13,422 genes in the genome, improving the annotation in regions with complex, nested gene structures.