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.

中文翻译：

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大西洋宽吻海豚（Tursiops truncatus）的新从头组装提高了基因组完整性并提供单倍型定相。

高质量的基因组对于解决育种、比较生物学、医学和保护规划方面的挑战至关重要。新的文库制备技术以及更好的组装算法导致非模型生物组装的持续改进，使它们朝着参考质量的基因组方向发展。我们利用 Illumina 测序数据并结合多种文库制备技术，报告了大西洋宽吻海豚的最新基因组组装。其中包括 Linked-Reads（Chromium、10x Genomics）、配对 (MP)、长插入配对末端和标准配对末端。使用商业 DeNovoMAGIC 组装软件组装数据，产生两个组装体，一个传统的“单倍体”组装体 (Tur_tru_Illumina_hap_v1)，它是两个亲本单倍型的镶嵌体，另一个是定相组装体 (Tur_tru_Illumina_phased_v1)，其中每个支架都具有来自单个同源染色体的序列。我们基于序列的数量和组成、MP 比对与组装支架的一致性以及对保守单拷贝哺乳动物直系同源物的分析，表明与当前最佳参考相比，Tur_tru_Illumina_hap_v1 更完整、更准确。分阶段从头组装 Tur_tru_Illumina_phased_v1 是该物种的第一个公开可用的，为社区提供了探索海豚基因组杂合性质的新颖而准确的方法。