Open AccessNewde novoassembly of the Atlantic bottlenose dolphin (Tursiops truncatus) improves genome completeness and provides haplotype phasing
Author(s) -
Karine A. Martinez-Viaud,
Cindy Lawley,
Milmer Martinez Vergara,
Gil Ben-Zvi,
Tammy Biniashvili,
Kobi Baruch,
Judy St. Leger,
Jennie Le,
Apartarajan,
Marlem Rivera,
Marbie Guillergan,
Erich B. Jaeger,
Brian Steffy,
Aleksey V. Zimin
Publication year - 2019
Publication title -
gigascience
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.947
H-Index - 54
ISSN - 2047-217X
DOI - 10.1093/gigascience/giy168
Subject(s) - genome , sequence assembly , computational biology , reference genome , biology , illumina dye sequencing , haplotype , whole genome sequencing , genomics , dna sequencing , genetics , gene , allele , gene expression , transcriptome
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 bottlenose dolphin, leveraging Illumina sequencing data coupled with a combination of several library preparation techniques. These include Linked-Reads (Chromium, 10x Genomics), mate pairs (MP), long insert paired ends, and standard paired end. 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 parental haplotypes and a phased assembly (Tur_tru_Illumina_phased_v1) where each scaffold has sequence from a single homologous chromosome. We show that Tur_tru_Illumina_hap_v1 is more complete and more accurate compared to the current best reference based on the amount and composition of sequence, the consistency of the MP alignments to the assembled scaffolds, and on the analysis of conserved single-copy mammalian orthologs. The phased de novo assembly Tur_tru_Illumina_phased_v1 is the first publicly available for this species and provides the community with novel and accurate ways to explore the heterozygous nature of the dolphin genome.