Sciara Genome


Sciara Genome

The Sciara genome contains 3 pairs of autosomes (chromosomes II, III and IV), two sex chromosomes (X and X'), and 2 germ line limited L chromosomes. The older estimate of 211 Mb for the size of the Sciara haploid somatic genome containing the X and three autosomes but no L chromosomes has been increased somewhat to 274 Mb (Rasch 2006). John Urban, a graduate student in the Gerbi lab at Brown, is completing the sequence of the Sciara genome and transcriptome and anticipates defending his Ph.D. thesis in the coming year. He has sequenced the Sciara genome by Illumina short reads and PacBio longer reads providing 52X coverage of the Sciara genome with an N50 of 10,125 bp and a contig N50 of ~1.2 Mb on 64 contigs. These data will be submitted for publication soon. Further refinement of the already very good sequence of the Sciara genome will be accomplished by BioNano Genomics Irys scaffolding and by use of the Oxford Nanopore Technologies MinION sequence device that provides ultra-long reads with some over 100 kb in our hands (the Gerbi lab has been selected in an international competition as a field test site for the MinION). We already have 3.7X Sciara genome coverage with the MinION and plan to expand this to 30X coverage in the coming year. With the MinION data thus far, the contig N50 size has gone up to 8.2 kb and the contig NG50 has gone up to 83 kb. These multiple sequencing strategies will provide an exceptionally fine reference genome for Sciara for use by the scientific community. John has already obtained the sequence of the transcriptome for male and female Sciara at various developmental stages and the Sciara reference genome will be annotated with these data in the next few months. We are using fluorescence in situ hybridization (FISH) to map candidate contigs (determined by copy number variation of post-amplification stage Sciara salivary gland sequence data) containing DNA puff amplicons to the Sciara salivary gland gigantic polytene chromosomes. We also are mapping the largest contings by FISH to Sciara polytene chromosomes, thus anchoring the sequence map on the chromosome map as well as validating the genome assembly.