Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

Cheng, Haoyu; Concepcion, Gregory T.; Feng, Xiaowen; Zhang, Haowen; Li, Heng

doi:10.1038/s41592-020-01056-5

Cited by 2,939 publications

(1,828 citation statements)

References 35 publications

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“…Many more MHC genomic haplotype sequences need to be added to those already generated by Horton et al (2008), Lam et al (2015), and Norman et al (2017) for better informed comparative genomics, population studies, disease associations, and genetic manipulations such as knock-in and knock-out in regulatory and functional studies. The advancement of new sequencing strategies (Cheng et al, 2021;Ebert et al, 2021;Human Genome Structural Variation Consortium et al, 2021) might allow these types of analyses to be extended to many more fully phased HLA haplotypes in the future. Such work will lead to a better understanding of the role of TEs and the different DNA processes involved in the evolution of the human MHC haplotypes, IBD segments, and their association with autoimmune disorders and other disease traits.…”

Section: Discussionmentioning

confidence: 99%

Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region

2021

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The major histocompatibility complex (MHC) on chromosome 6p21 is one of the most single-nucleotide polymorphism (SNP)-dense regions of the human genome and a prime model for the study and understanding of conserved sequence polymorphisms and structural diversity of ancestral haplotypes/conserved extended haplotypes. This study aimed to follow up on a previous analysis of the MHC class I region by using the same set of 95 MHC haplotype sequences downloaded from a publicly available BioProject database at the National Center for Biotechnology Information to identify and characterize the polymorphic human leukocyte antigen (HLA)-class II genes, the MTCO3P1 pseudogene alleles, the indels of transposable elements as haplotypic lineage markers, and SNP-density crossover (XO) loci at haplotype junctions in DNA sequence alignments of different haplotypes across the extended class II region (∼1 Mb) from the telomeric PRRT1 gene in class III to the COL11A2 gene at the centromeric end of class II. We identified 42 haplotypic indels (20 Alu, 7 SVA, 13 LTR or MERs, and 2 indels composed of a mosaic of different transposable elements) linked to particular HLA-class II alleles. Comparative sequence analyses of 136 haplotype pairs revealed 98 unique XO sites between SNP-poor and SNP-rich genomic segments with considerable haplotype shuffling located in the proximity of putative recombination hotspots. The majority of XO sites occurred across various regions including in the vicinity of MTCO3P1 between HLA-DQB1 and HLA-DQB3, between HLA-DQB2 and HLA-DOB, between DOB and TAP2, and between HLA-DOA and HLA-DPA1, where most XOs were within a HERVK22 sequence. We also determined the genomic positions of the PRDM9-recombination suppression sequence motif ATCCATG/CATGGAT and the PRDM9 recombination activation partial binding motif CCTCCCCT/AGGGGAG in the class II region of the human reference genome (NC_ 000006) relative to published meiotic recombination positions. Both the recombination and anti-recombination PRDM9 binding motifs were widely distributed throughout the class II genomic regions with 50% or more found within repeat elements; the anti-recombination motifs were found mostly in L1 fragmented repeats. This study shows substantial haplotype shuffling between different polymorphic blocks and confirms the presence of numerous putative ancestral recombination sites across the class II region between various HLA class II genes.

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Section: Discussionmentioning

confidence: 99%

Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region

2021

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“…The CHM13 genome was assembled from PacBio HiFi data using HiCanu 5 as previously described 5 . The HG00733 genome was assembled from PacBio HiFi data (Supplementary Table 3 ) using hifiasm 6 (v.0.7). The chimpanzee, orangutan and macaque genomes were assembled from PacBio HiFi data (Supplementary Table 5 ) using HiCanu 5 (v.2.0).…”

Section: Methodsmentioning

confidence: 99%

The structure, function and evolution of a complete human chromosome 8

Logsdon

Vollger

Hsieh

et al. 2021

Nature

273

278

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The complete assembly of each human chromosome is essential for understanding human biology and evolution1,2. Here we use complementary long-read sequencing technologies to complete the linear assembly of human chromosome 8. Our assembly resolves the sequence of five previously long-standing gaps, including a 2.08-Mb centromeric α-satellite array, a 644-kb copy number polymorphism in the β-defensin gene cluster that is important for disease risk, and an 863-kb variable number tandem repeat at chromosome 8q21.2 that can function as a neocentromere. We show that the centromeric α-satellite array is generally methylated except for a 73-kb hypomethylated region of diverse higher-order α-satellites enriched with CENP-A nucleosomes, consistent with the location of the kinetochore. In addition, we confirm the overall organization and methylation pattern of the centromere in a diploid human genome. Using a dual long-read sequencing approach, we complete high-quality draft assemblies of the orthologous centromere from chromosome 8 in chimpanzee, orangutan and macaque to reconstruct its evolutionary history. Comparative and phylogenetic analyses show that the higher-order α-satellite structure evolved in the great ape ancestor with a layered symmetry, in which more ancient higher-order repeats locate peripherally to monomeric α-satellites. We estimate that the mutation rate of centromeric satellite DNA is accelerated by more than 2.2-fold compared to the unique portions of the genome, and this acceleration extends into the flanking sequence.

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“…Several long-read assembly tools were compared: FALCON (falcon-kit v1.8.0) (Falcon, RRID:SCR_016089 ) [ 17 ], Flye (v2.9.1-b1676) (Flye, RRID:SCR_017016 ) [ 18 ], HiCanu (v2.1) [ 19 ], Hifiasm (v0.12-r304) [ 20 ], IPA (v1.1.2) [ 21 ], and wtdbg2 v2.5 (WTDBG, RRID:SCR_017225 ) [ 22 ]. The command lines and statistics of preliminary assemblies are provided in Supplementary File S1 .…”

Section: Methodsmentioning

confidence: 99%

Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola)

et al. 2021

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Background Genome sequencing of all known eukaryotes on Earth promises unprecedented advances in biological sciences and in biodiversity-related applied fields such as environmental management and natural product research. Advances in long-read DNA sequencing make it feasible to generate high-quality genomes for many non–genetic model species. However, long-read sequencing today relies on sizable quantities of high-quality, high molecular weight DNA, which is mostly obtained from fresh tissues. This is a challenge for biodiversity genomics of most metazoan species, which are tiny and need to be preserved immediately after collection. Here we present de novo genomes of 2 species of submillimeter Collembola. For each, we prepared the sequencing library from high molecular weight DNA extracted from a single specimen and using a novel ultra-low input protocol from Pacific Biosciences. This protocol requires a DNA input of only 5 ng, permitted by a whole-genome amplification step. Results The 2 assembled genomes have N50 values >5.5 and 8.5 Mb, respectively, and both contain ∼96% of BUSCO genes. Thus, they are highly contiguous and complete. The genomes are supported by an integrative taxonomy approach including placement in a genome-based phylogeny of Collembola and designation of a neotype for 1 of the species. Higher heterozygosity values are recorded in the more mobile species. Both species are devoid of the biosynthetic pathway for β-lactam antibiotics known in several Collembola, confirming the tight correlation of antibiotic synthesis with the species way of life. Conclusions It is now possible to generate high-quality genomes from single specimens of minute, field-preserved metazoans, exceeding the minimum contig N50 (1 Mb) required by the Earth BioGenome Project.

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Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

Cited by 2,939 publications

References 35 publications

Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region

Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region

The structure, function and evolution of a complete human chromosome 8

Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola)

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