New de novo assembly of the Atlantic bottlenose dolphin (Tursiops truncatus) improves genome completeness and provides haplotype phasing

AbstractHigh 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, long insert paired ends and standard paired ends. Data were assembled with the commercial DeNovoMAGICTM 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 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_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.

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Proteomics as a metrological tool to evaluate genome annotation accuracy following de novo genome assembly: a case study using the Atlantic bottlenose dolphin (Tursiops truncatus)

10.1101/254250 ◽

2018 ◽

Cited By ~ 2

Author(s):

Benjamin A. Neely ◽

Debra L. Ellisor ◽

W. Clay Davis

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Bottlenose Dolphin ◽

Tursiops Truncatus ◽

De Novo ◽

Whole Genome ◽

High Quality ◽

Data Set ◽

Atlantic Bottlenose Dolphin ◽

Annotation Accuracy

AbstractBackgroundThe last decade has witnessed dramatic improvements in whole-genome sequencing capabilities coupled to drastically decreased costs, leading to an inundation of high-quality de novo genomes. For this reason, continued development of genome quality metrics is imperative. The current study utilized the recently updated Atlantic bottlenose dolphin (Tursiops truncatus) genome and annotation to evaluate a proteomics-based metric of genome accuracy.ResultsProteomic analysis of six tissues provided experimental confirmation of 10 402 proteins from 4 711 protein groups, almost 1/3 of the possible predicted proteins in the genome. There was an increased median molecular weight and number of identified peptides per protein using the current T. truncatus annotation versus the previous annotation. Identification of larger proteins with more identified peptides implied reduced database fragmentation and improved gene annotation accuracy. A metric is proposed, NP10, that attempts to capture this quality improvement. When using the new T. truncatus genome there was a 21 % improvement in NP10. This metric was further demonstrated by using a publicly available proteomic data set to compare human genome annotations from 2004, 2013 and 2016, which had a 33 % improvement in NP10.ConclusionsThese results demonstrate that new whole-genome sequencing techniques can rapidly generate high quality de novo genome assemblies and emphasizes the speed of advancing bioanalytical measurements in a non-model organism. Moreover, proteomics may be a useful metrological tool to benchmark genome accuracy, though there is a need for reference proteomic datasets to facilitate this utility in new de novo and existing genomes.

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