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

Campoy, José Antonio; Sun, Hequan; Goel, Manish; Jiao, Wen-Biao; Folz-Donahue, Kat; Kukat, Christian; Rubio, M.; Ruiz, David; Huettel, Bruno; Schneeberger, Korbinian

doi:10.1101/2020.04.24.060046

Cited by 9 publications

(16 citation statements)

References 79 publications

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“…BAM, VCF file processing and sequencing depth analysis were performed using samtools 34 and bedtools 35 . PacBio sequence reads were assembled using hifiasm 18 , and genome annotation was performed following a previous pipeline 8 . Structural variations were identified using SyRI 36 based on minimap2 genome alignments.…”

Section: Methodsmentioning

confidence: 99%

Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

Sun

Jiao

Krause

et al. 2021

Preprint

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Potato is the third most important food crop in the world. Despite its social and economic importance, the autotetraploid genome of cultivated potato has not been assembled yet. The distinct reconstruction all of four haplotypes remained an unsolved challenge. Here, we report the 3.1 Gb haplotype-resolved, chromosome-scale assembly of the autotetraploid potato cultivar, Otava. We assembled the genome with high-quality long reads coupled with single-cell sequencing of 717 pollen genomes and chromosome conformation capture data at a haplotyping precision of 99.6%. Unexpectedly, we found that almost 50% of the tetraploid genome were identical-by-descent with at least one of the other haplotypes. This high level of inbreeding contrasted with the extreme level of structural rearrangements encompassing nearly 20% of the genome. Overall, we annotated 148,577 gene models, where only 54% of the genes were present in all four haplotypes with an average of 3.2 copies per gene. Our work showcases how accurate assemblies of complex and partially inbred autotetraploid genomes can be generated. The newly established resource gives novel insights in the breeding history of autotetraploid potato and has the potential to change the future of genomics-assisted potato breeding.

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Section: Methodsmentioning

confidence: 99%

Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

Sun

Jiao

Krause

et al. 2021

Preprint

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“…Trio binning is a promising route for resolving haplotypes especially in interspecific F1 hybrids, however is limited by access to parents and offspring, which is not possible for many species. An alternative based on similar principles, is that of gamete binning, which uses single‐cell sequencing of gametes to inform partitioning of reads into distinct haplotype sets for subsequent assembly (Campoy et al, 2020).…”

Section: Biological Challengesmentioning

confidence: 99%

The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes

Whibley

Kelley

Narum

2021

Molecular Ecology Resources

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The quality of genome assemblies has improved rapidly in recent years due to continual advances in sequencing technology, assembly approaches, and quality control. In the field of molecular ecology, this has led to the development of exceptional quality genome assemblies that will be important long‐term resources for broader studies into ecological, conservation, evolutionary, and population genomics of naturally occurring species. Moreover, the extent to which a single reference genome represents the diversity within a species varies: pan‐genomes will become increasingly important ecological genomics resources, particularly in systems found to have considerable presence‐absence variation in their functional content. Here, we highlight advances in technology that have raised the bar for genome assembly and provide guidance on standards to achieve exceptional quality reference genomes. Key recommendations include the following: (a) Genome assemblies should include long‐read sequencing except in rare cases where it is effectively impossible to acquire adequately preserved samples needed for high molecular weight DNA standards. (b) At least one scaffolding approach should be included with genome assembly such as Hi‐C or optical mapping. (c) Genome assemblies should be carefully evaluated, this may involve utilising short read data for genome polishing, error correction, k‐mer analyses, and estimating the percent of reads that map back to an assembly. Finally, a genome assembly is most valuable if all data and methods are made publicly available and the utility of a genome for further studies is verified through examples. While these recommendations are based on current technology, we anticipate that future advances will push the field further and the molecular ecology community should continue to adopt new approaches that attain the highest quality genome assemblies.

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“…Single gamete sequencing was demonstrated to be a powerful method to phase genomes, dissect meiotic crossover (CO) patterns or even investigate haploid diversities (Wang et al ., 2012; Lu et al ., 2012b; Hou et al ., 2013; Kirkness et al ., 2013; Li et al ., 2015; Luo et al ., 2019; Nkhoma et al ., 2020). Moreover, the combination of single gamete sequencing with BAC clones or long reads sequencing can be applied for haplotype assembly (Shi et al ., 2019; Campoy et al ., 2020) and this can be streamlined using the R package Hapi (Li et al ., 2018). Another recently developed method combining linked‐read sequencing with pooled pollens used only one DNA library to perform CO detection and haplotype phasing (Sun et al ., 2019).…”

Section: Introductionmentioning

confidence: 99%

A phased genome based on single sperm sequencing reveals crossover pattern and complex relatedness in tea plants

et al. 2020

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SUMMARYFor diploid organisms that are highly heterozygous, a phased haploid genome can greatly aid in functional genomic, population genetic and breeding studies. Based on the genome sequencing of 135 single sperm cells of the elite tea cultivar ‘Fudingdabai’, we herein phased the genome of Camellia sinensis, one of the most popular beverage crops worldwide. High‐resolution genetic and recombination maps of Fudingdabai were constructed, which revealed that crossover (CO) positions were frequently located in the 5′ and 3′ ends of annotated genes, while CO distributions across the genome were random. The low CO frequency in tea can be explained by strong CO interference, and CO simulation revealed the proportion of interference insensitive CO ranged from 5.2% to 11.7%. We furthermore developed a method to infer the relatedness between tea accessions and detected complex kinship and genetic signatures of 106 tea accessions. Among them, 59 accessions were closely related with Fudingdabai and 31 of them were first‐degree relatives. We additionally identified genes displaying allele specific expression patterns between the two haplotypes of Fudingdabai and genes displaying significantly differential expression levels between Fudingdabai and other haplotypes. These results lay the foundation for further investigation of genetic and epigenetic factors underpinning the regulation of gene expression and provide insights into the evolution of tea plants as well as a valuable genetic resource for future breeding efforts.

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

Cited by 9 publications

References 79 publications

Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes

A phased genome based on single sperm sequencing reveals crossover pattern and complex relatedness in tea plants

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