Abstract
High quality genomes are essential to resolve challenges in breeding, comparative biology, medicineand conservation planning. New library preparation techniques along with better assembly algorithms result in continued improvements in assemblies fornon-model organisms moving them toward reference quality genomes. We report on the latest genome assembly of the Atlanticbottlenosedolphin leveraging Illuminasequencing datacoupled with acombination of several library preparation techniques. Theseinclude Linked-Reads (Chromium, 10x Genomics), mate pairs, long insert paired ends and standard paired ends. Datawere assembled with the commercial DeNovoMAGIC ™ assembly software resulting in two assemblies, atraditional “haploid” assembly (Tur_tru_Illumina_hap_v1) that is a mosaicof the two haplotypes and aphased assembly (Tur_tru_Illumina_dip_v1) whereeach scaffold has sequence from asingle 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 availableforthis species and provides the community with noveland accurate ways to explore the heterozygous nature of the dolphin genome.
