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

Karine A. Martinez-Viaud, Cindy Taylor Lawley, Milmer Martinez Vergara, Gil Ben-Zvi, Tammy Biniashvili, Kobi Baruch, Judy St. Leger, Jennie Le, Aparna Natarajan, Marlem Rivera, Marbie Guillergan, Erich Jaeger, Brian Steffy, Aleksey Zimin
doi: https://doi.org/10.1101/376301
Karine A. Martinez-Viaud
Illumina, Inc, San Diego, CA 92122, USA
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Cindy Taylor Lawley
Illumina, Inc, San Diego, CA 92122, USA
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Milmer Martinez Vergara
Plant with Purpose, San Diego, CA 92117, USA
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Gil Ben-Zvi
NRGene, Ness-Ziona, 7403649, Israel
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Tammy Biniashvili
NRGene, Ness-Ziona, 7403649, Israel
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Kobi Baruch
NRGene, Ness-Ziona, 7403649, Israel
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Judy St. Leger
SeaWorld San Diego, San Diego, CA 92109, USA
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Jennie Le
Illumina, Inc, San Diego, CA 92122, USA
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Aparna Natarajan
Illumina, Inc, San Diego, CA 92122, USA
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Marlem Rivera
Illumina, Inc, San Diego, CA 92122, USA
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Marbie Guillergan
Illumina, Inc, San Diego, CA 92122, USA
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Erich Jaeger
Illumina, Inc, San Diego, CA 92122, USA
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Brian Steffy
Illumina, Inc, San Diego, CA 92122, USA
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Aleksey Zimin
Johns Hopkins University, Baltimore, MD 21205, USA
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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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 12, 2018.
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New de novo assembly of the Atlantic bottlenose dolphin (Tursiops truncatus) improves genome completeness and provides haplotype phasing
Karine A. Martinez-Viaud, Cindy Taylor Lawley, Milmer Martinez Vergara, Gil Ben-Zvi, Tammy Biniashvili, Kobi Baruch, Judy St. Leger, Jennie Le, Aparna Natarajan, Marlem Rivera, Marbie Guillergan, Erich Jaeger, Brian Steffy, Aleksey Zimin
bioRxiv 376301; doi: https://doi.org/10.1101/376301
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New de novo assembly of the Atlantic bottlenose dolphin (Tursiops truncatus) improves genome completeness and provides haplotype phasing
Karine A. Martinez-Viaud, Cindy Taylor Lawley, Milmer Martinez Vergara, Gil Ben-Zvi, Tammy Biniashvili, Kobi Baruch, Judy St. Leger, Jennie Le, Aparna Natarajan, Marlem Rivera, Marbie Guillergan, Erich Jaeger, Brian Steffy, Aleksey Zimin
bioRxiv 376301; doi: https://doi.org/10.1101/376301

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