Draft genome of a porcupinefish, <i>Diodon Holocanthus</i>

Xu, Mengyang; Su, Xiaoshan; Zhang, Mengqi; Li, Ming; Huang, Xiaoyun; Fan, Guangyi; Liu, Xin; Zhang, He

doi:10.1101/775387

Cited by 1 publication

(1 citation statement)

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“…The utilization of SLR, such as stLFR 7,10 , has obtained a series of successes in haplotyping 10,[29][30][31][32][33] , structural variation detection [33][34][35][36] and de novo genome assembly [37][38][39][40][41][42][43] . Its achievements are established on the efficient clustering of short reads with longrange barcode information.…”

Section: Pagementioning

confidence: 99%

Haplotype-Resolved Assembly for Synthetic Long Reads Using a Trio-Binning Strategy

Xu¹,

Guo

et al. 2020

Preprint

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The accuracy and completeness of genome haplotyping are crucial for characterizing the relationship between human disease susceptibility and genetic variations, especially for the heterozygous variations. However, most of current variations are unphased genotypes, and the construction of long-range haplotypes remains challenging. We introduced a de novo haplotype-resolved assembly tool, HAST that exports two haplotypes of a diploid species for synthetic long reads with trio binning.It generates parental distinguishing k-mer libraries, partitions reads from the offspring according to the unique markers, and individually assembles them to resolve the haplotyping problem. Based on the stLFR co-barcoding data of an Asian as well as his parental massive parallel sequencing data, we utilized HAST to recover both haplotypes with a scaffold N50 of >11 Mb and an assembly accuracy of 99.99995% (Q63). The complete and accurate employment of long-range haplotyping information provided sub-chromosome level phase blocks (N50 ~13 Mb) with 99.6% precision and 94.1% recall on average. We suggest that the accurate and efficient approach accomplishes the regeneration of the haplotype chromosomes with trio binning, thus promoting the determination of haplotype phase, the heterosis of crossbreeding, and the formation of autopolyploid and allopolyploid.Page 3 haplotyping at its source. However, it is technically impractical for most species.Another strategy refers to the whole-chromosome isolation, for instance, chromosome sorting 6 , which is not applicable to large sample size due to its time-consuming and labor-intensive procedure. Haplotyping information can also be straightforwardly obtained from the sequencing of fragmented or whole DNA molecules. This approach requires long-range information to reconstruct the haplotypes from the biological or physical markers or overlapping relations of the segmented homologous chromosomes, including synthetic long reads (SLR, such as MGI stLFR co-barcoding reads and 10X genomics linked reads) 7-10 , single-molecule long reads (Pacific Biosciences (PacBio) or Oxford Nanopore (ONT) long reads) 11, 12 , Hi-C 13, 14 and optical mapping (Bionano) 15 . In practice the long-range information is employed to recover diploid or polyploid genomes with read-mapping-based, or de novo assemblybased methods.Currently, to attribute the successive genotypes to an arbitrary haplotype, sequencing reads are generally mapped to the reference genomes and then the alignment information recovers the heterozygous genotypes at each polymorphic site 16,17 .Nevertheless, the read-mapping-based methods are hampered by the lack of perfect reference sequence and the inability to detect large structural variations. Long reads 18, 19 or SLR 7,8,20 can extend the phase blocks to ~1Mb, but it is still complex to span regions of low heterozygous density or gaps in the reference. Assembly-based methods usually generate longer phase blocks across homozygous regions of the

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