Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data

Zhang, Xingtan; Zhang, Shengcheng; Zhao, Qian; Ming, Ray; Tang, Haibao

doi:10.1038/s41477-019-0487-8

Cited by 403 publications

(344 citation statements)

References 48 publications

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“…Tools such as "HapCut" can leverage this distance information to recover long, high coverage accurate haplotypes [17,18]. The linked read sequencing and Hi-C technologies have been used for generating long phased haplotypes [19,20].…”

Section: Introductionmentioning

confidence: 99%

A Comparison between Hi-C and 10X Genomics Linked Read Sequencing for Whole Genome Phasing in Hanwoo Cattle

Srikanth

Park

Lim

et al. 2020

Genes

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Until recently, genome-scale phasing was limited due to the short read sizes of sequence data. Though the use of long-read sequencing can overcome this limitation, they require extensive error correction. The emergence of technologies such as 10X genomics linked read sequencing and Hi-C which uses short-read sequencers along with library preparation protocols that facilitates long-read assemblies have greatly reduced the complexities of genome scale phasing. Moreover, it is possible to accurately assemble phased genome of individual samples using these methods. Therefore, in this study, we compared three phasing strategies which included two sample preparation methods along with the Long Ranger pipeline of 10X genomics and HapCut2 software, namely 10X-LG, 10X-HapCut2, and HiC-HapCut2 and assessed their performance and accuracy. We found that the 10X-LG had the best phasing performance amongst the method analyzed. They had the highest phasing rate (89.6%), longest adjusted N50 (1.24 Mb), and lowest switch error rate (0.07%). Moreover, the phasing accuracy and yield of the 10X-LG stayed over 90% for distances up to 4 Mb and 550 Kb respectively, which were considerably higher than 10X-HapCut2 and Hi-C Hapcut2. The results of this study will serve as a good reference for future benchmarking studies and also for reference-based imputation in Hanwoo.

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Section: Introductionmentioning

confidence: 99%

A Comparison between Hi-C and 10X Genomics Linked Read Sequencing for Whole Genome Phasing in Hanwoo Cattle

Srikanth

Park

Lim

et al. 2020

Genes

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“…To avoid these problems, it is a common strategy to inbreed or to generate double-haploid genotypes to enable the assembly of homozygous genomes. More recent alternatives include chromosome sorting 3 , Hi-C 4,5 and Strand-seq 6 to either separate the chromosomes before sequencing or to generate additional information that discriminates between the two haplotypes and thereby reconstructs the sequence of both haplotypes separately. Another elegant method, trio binning, is based on the separation of whole-genome sequencing reads into haplotype-specific read sets before assembly using the genomic differences between the parental genomes 2 .…”

mentioning

confidence: 99%

Chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes

Campoy

Sun

Goel

et al. 2020

Preprint

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Generating haplotype-resolved, chromosome-level assemblies of heterozygous genomes remains challenging. To address this, we developed gamete binning, a method based on single-cell sequencing of hundreds of haploid gamete genomes, which enables the separation of conventional long sequencing reads into two haplotype-specific read sets. After independently assembling the reads of each haplotype, the contigs are scaffolded to chromosome-level using a genetic map derived from the recombination patterns within the same gamete genomes. As a proof-of-concept, we assembled the two genomes of a diploid apricot tree supported by the analysis of 445 pollen genomes. Both assemblies (N50: 25.5 and 25.8 Mb) featured a haplotyping precision of >99% and were accurately scaffolded to chromosome-level as reflected by high levels of synteny to closely-related species. These two assemblies allowed for first insights into haplotype diversity of apricot and enabled the identification of non-allelic crossover events introducing severe chromosomal anomalies in 1.6% of the pollen genomes.

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“…Briefly, abnormal Hi‐C contacts were detected within each contig and mis‐joined conformations triggered contig splitting to form a set of Hi‐C corrected contigs. The corrected contigs were further processed using the ALLHiC assembler (Zhang, Zhang, Zhao, Ming, & Tang, 2019) with the diploid scaffolding model. Hi‐C reads were uniquely mapped into the corrected contigs, and reads within 500 bp flanking regions of restriction enzyme sites (MboI) were retained for further analysis.…”

Section: Methodsmentioning

confidence: 99%

A chromosome‐scale genome assembly of Antheraea pernyi (Saturniidae, Lepidoptera)

Duan

Liu

et al. 2020

Molecular Ecology Resources

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Antheraea pernyi is a semi‐domesticated lepidopteran insect species valuable to the silk industry, human health, and ecological tourism. Owing to its economic influence and developmental properties, it serves as an ideal model for investigating divergence of the Bombycoidea super family. However, studies on the karyotype evolution and functional genomics of A. pernyi are limited by scarce genomic resource. Here, we applied PacBio sequencing and chromosome structure capture technique to assemble the first high‐quality A. pernyi genome from a single male individual. The genome is 720.67 Mb long with 49 chromosomes and a 13.77‐Mb scaffold N50. Approximately 441.75 Mb, accounting for 60.74% of the genome, was identified as repeats. The genome comprises 21,431 protein‐coding genes, 85.22% of which were functionally annotated. Comparative genomics analysis suggested that A. pernyi diverged from its common ancestor with A. yamamai ~30.3 million years ago, and that chromosome fission contributed to the increased chromosome number. The genome assembled in this work will not only facilitate future research on A. pernyi and related species but also help to progress comparative genomics analyses in Lepidoptera.

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Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data

Cited by 403 publications

References 48 publications

A Comparison between Hi-C and 10X Genomics Linked Read Sequencing for Whole Genome Phasing in Hanwoo Cattle

A Comparison between Hi-C and 10X Genomics Linked Read Sequencing for Whole Genome Phasing in Hanwoo Cattle

Chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes

A chromosome‐scale genome assembly of Antheraea pernyi (Saturniidae, Lepidoptera)

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