TY - JOUR T1 - New de novo assembly of the Atlantic bottlenose dolphin (<em>Tursiops truncatus</em>) improves genome completeness and provides haplotype phasing JF - bioRxiv DO - 10.1101/376301 SP - 376301 AU - Karine A. Martinez-Viaud AU - Cindy Taylor Lawley AU - Milmer Martinez Vergara AU - Gil Ben-Zvi AU - Tammy Biniashvili AU - Kobi Baruch AU - Judy St. Leger AU - Jennie Le AU - Aparna Natarajan AU - Marlem Rivera AU - Marbie Guillergan AU - Erich Jaeger AU - Brian Steffy AU - Aleksey Zimin Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/07/24/376301.abstract N2 - High quality genomes are essential to resolve challenges in breeding, comparative biology, medicine and conservation planning. New library preparation techniques along with better assembly algorithms result in continued improvements in assemblies for non-model organisms moving them toward reference quality genomes. We report on the latest genome assembly of the Atlantic bottle nose dolphin leveraging Illumina sequencing data coupled with a combination of several library preparation techniques. These include Linked-Reads (Chromium, 10x Genomics), mate pairs, long insert paired ends and standard paired ends. Data were assembled with the commercial DeNovoMAGIC™ assembly software resulting in two assemblies, a traditional “haploid” assembly (Tur_tru_Illumina_hap_v1) that is a mosaic of the two haplotypes and a phased assembly (Tur_tru_Illumina_dip_v1) where each scaffold has sequence from a single homologous chromosome. We show that Tur_tru_Illumina_hap_v1 is more complete and accurate compared to the current best reference based on the amount and composition of sequence, the consistency of the mate pair alignments to the assembled scaffolds, and on the analysis of conserved single-copy mammalian orthologs. The phased de novo assembly Tur_tru_Illumina_dip_v1 is of the highest quality available for this species and provides the community with novel and accurate ways to explore the heterozygous nature of the dolphin genome. ER -