Phased Genome Assembly Research Articles

A fully phased, chromosome-scale genome of sugar beet line FC309 enables the discovery of Fusarium yellows resistance QTL.

Sugar beet (Beta vulgaris L.) is a global source for table sugar and animal fodder. Here we report a highly contiguous, haplotype phased genome assembly and annotation for sugar beet line FC309. Both assembled haplomes for FC309 represent the largest and most contiguous assembled beet genomes reported to date, as well as gene annotations sets that capture over 1500 additional protein-coding loci compared to prior beet genome annotations. These new genomic resources were used to identify novel quantitative trait loci (QTL) for Fusarium yellows resistance from the FC309 genetic background using an F2 mapping-by-sequencing approach. The highest QTL signals were detected on Chromosome 3, spanning approximately 10Mbp in both haplomes. A parallel transcriptome profiling experiment identified candidate genes within the Chromosome 3 QTL with plausible roles in disease response, including NBS-LRR genes with expression trends supporting a role in resistance. Investigation of genetic variants in these candidate genes found one major disease resistance protein containing high effect variants of interest. Collectively, the genomic resources for FC309 presented here be foundational tool for comparative genomics, mapping other traits in the FC309 background, and as a reference genome for other beet studies due to its contiguity, completeness, and high-quality gene annotations.

Genome assembly at chromosome scale with telomere ends for Pearlspot, Etroplus suratensis

The pearlspot, Etroplus suratensis is a climate resilient cichlid fish that exhibits unusual adaptation to salinity. The fish is able to complete full life cycle in diverse salinity habitats ranging from fresh water to marine environments. High-quality primary and phased genome assemblies were generated for pearlspot fish using PacBio HiFi and Arima HiC sequencing technologies, for the first time. The primary assembly is highly contiguous with contig N50 length of 36 Mb. The final assembly is of 1.247 Gb with N50 length of 51.57 Mb and 98% of the genome length anchored to 24 chromosomes. The genome was assessed to be 99.9% complete based on BUSCO evaluation and was predicted to contain 52.96% repeat elements. We have predicted 27,192 protein encoding genes, of which 21,580 were functionally annotated. The genome offers an invaluable resource to understand adaptation of pearlspot fish to diverse salinity habitats.

Fully phased genome assemblies and graph-based genetic variants of the olive flounder, Paralichthys olivaceus

The olive flounder, Paralichthys olivaceus, also known as the Korean halibut, is an economically important flatfish in East Asian countries. Here, we provided four fully phased genome assemblies of two different olive flounder individuals using high-fidelity long-read sequencing and their parental short-read sequencing data. We obtained 42–44 Gb of ~15-kb and ~Q30 high-fidelity long reads, and their assembly quality values were ~53. We annotated ~30 K genes, ~170-Mb repetitive sequences, and ~3 M 5-methylcytosine positions for each genome assembly, and established a graph-based draft pan-genome of the olive flounder. We identified 5 M single-nucleotide variants and 100 K structural variants with their genotype information, where ~13% of the variants were possibly fixed in the two Korean individuals. Based on our chromosome-level genome assembly, we also explored chromosome evolution in the Pleuronectiformes family, as reported earlier. Our high-quality genomic resources will contribute to future genomic selection for accelerating the breeding process of the olive flounder.

Biologically-informed killer cell immunoglobulin-like receptor gene annotation tool.

Natural killer (NK) cells are essential components of the innate immune system, with their activity significantly regulated by Killer cell Immunoglobulin-like Receptors (KIRs). The diversity and structural complexity of KIR genes present significant challenges for accurate genotyping, essential for understanding NK cell functions and their implications in health and disease. Traditional genotyping methods struggle with the variable nature of KIR genes, leading to inaccuracies that can impede immunogenetic research. These challenges extend to high-quality phased assemblies, which have been recently popularized by the Human Pangenome Consortium. This article introduces BAKIR (Biologically informed Annotator for KIR locus), a tailored computational tool designed to overcome the challenges of KIR genotyping and annotation on high-quality, phased genome assemblies. BAKIR aims to enhance the accuracy of KIR gene annotations by structuring its annotation pipeline around identifying key functional mutations, thereby improving the identification and subsequent relevance of gene and allele calls. It uses a multi-stage mapping, alignment, and variant calling process to ensure high-precision gene and allele identification, while also maintaining high recall for sequences that are significantly mutated or truncated relative to the known allele database. BAKIR has been evaluated on a subset of the HPRC assemblies, where BAKIR was able to improve many of the associated annotations and call novel variants. BAKIR is freely available on GitHub, offering ease of access and use through multiple installation methods, including pip, conda, and singularity container, and is equipped with a user-friendly command-line interface, thereby promoting its adoption in the scientific community. BAKIR is available at github.com/algo-cancer/bakir.

Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders.

Variant detection from long-read genome sequencing (lrGS) has proven to be more accurate and comprehensive than variant detection from short-read genome sequencing (srGS). However, the rate at which lrGS can increase molecular diagnostic yield for rare disease is not yet precisely characterized. We performed lrGS using Pacific Biosciences "HiFi" technology on 96 short-read-negative probands with rare diseases that were suspected to be genetic. We generated hg38-aligned variants and de novo phased genome assemblies, and subsequently annotated, filtered, and curated variants using clinical standards. New disease-relevant or potentially relevant genetic findings were identified in 16/96 (16.7%) probands, nine of which (8/96, ∼9.4%) harbored pathogenic or likely pathogenic variants. Nine probands (∼9.4%) had variants that were accurately called in both srGS and lrGS and represent changes to clinical interpretation, mostly from recently published gene-disease associations. Seven cases included variants that were only correctly interpreted in lrGS, including copy-number variants (CNVs), an inversion, a mobile element insertion, two low-complexity repeat expansions, and a 1 bp deletion. While evidence for each of these variants is, in retrospect, visible in srGS, they were either not called within srGS data, were represented by calls with incorrect sizes or structures, or failed quality control and filtration. Thus, while reanalysis of older srGS data clearly increases diagnostic yield, we find that lrGS allows for substantial additional yield (7/96, 7.3%) beyond srGS. We anticipate that as lrGS analysis improves, and as lrGS data sets grow allowing for better variant-frequency annotation, the additional lrGS-only rare disease yield will grow over time.

Biologically-informed Killer cell immunoglobulin-like receptor (KIR) gene annotation tool.

Natural killer (NK) cells are essential components of the innate immune system, with their activity significantly regulated by Killer cell Immunoglobulin-like Receptors (KIRs). The diversity and structural complexity of KIR genes present significant challenges for accurate genotyping, essential for understanding NK cell functions and their implications in health and disease. Traditional genotyping methods struggle with the variable nature of KIR genes, leading to inaccuracies that can impede immunogenetic research. These challenges extend to high-quality phased assemblies, which have been recently popularized by the Human Pangenome Consortium. This paper introduces BAKIR (Biologically-informed Annotator for KIR locus), a tailored computational tool designed to overcome the challenges of KIR genotyping and annotation on high-quality, phased genome assemblies. BAKIR aims to enhance the accuracy of KIR gene annotations by structuring its annotation pipeline around identifying key functional mutations, thereby improving the identification and subsequent relevance of gene and allele calls. It uses a multi-stage mapping, alignment, and variant calling process to ensure high-precision gene and allele identification, while also maintaining high recall for sequences that are significantly mutated or truncated relative to the known allele database. BAKIR has been evaluated on a subset of the HPRC assemblies, where BAKIR was able to improve many of the associated annotations and call novel variants. BAKIR is freely available on GitHub, offering ease of access and use through multiple installation methods, including pip, conda, and singularity container, and is equipped with a user-friendly command-line interface, thereby promoting its adoption in the scientific community.

Genome analysis of the esca-associated Basidiomycetes Fomitiporia mediterranea, Fomitiporia polymorpha, Inonotus vitis, and Tropicoporus texanus reveals virulence factor repertoires characteristic of white-rot fungi.

Some Basidiomycete fungi are important plant pathogens, and certain species have been associated with the grapevine trunk disease esca. We present the genomes of 4 species associated with esca: Fomitiporia mediterranea, Fomitiporia polymorpha, Tropicoporus texanus, and Inonotus vitis. We generated high-quality phased genome assemblies using long-read sequencing. The genomic and functional comparisons identified potential virulence factors, suggesting their roles in disease development. Similar to other white-rot fungi known for their ability to degrade lignocellulosic substrates, these 4 genomes encoded a variety of lignin peroxidases and carbohydrate-active enzymes (CAZymes) such as CBM1, AA9, and AA2. The analysis of gene family expansion and contraction revealed dynamic evolutionary patterns, particularly in genes related to secondary metabolite production, plant cell wall decomposition, and xenobiotic degradation. The availability of these genomes will serve as a reference for further studies of diversity and evolution of virulence factors and their roles in esca symptoms and host resistance.

A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree.

Using five complementary short- and long-read sequencing technologies, we phased and assembled >95% of each diploid human genome in a four-generation, 28-member family (CEPH 1463) allowing us to systematically assess de novo mutations (DNMs) and recombination. From this family, we estimate an average of 192 DNMs per generation, including 75.5 de novo single-nucleotide variants (SNVs), 7.4 non-tandem repeat indels, 79.6 de novo indels or structural variants (SVs) originating from tandem repeats, 7.7 centromeric de novo SVs and SNVs, and 12.4 de novo Y chromosome events per generation. STRs and VNTRs are the most mutable with 32 loci exhibiting recurrent mutation through the generations. We accurately assemble 288 centromeres and six Y chromosomes across the generations, documenting de novo SVs, and demonstrate that the DNM rate varies by an order of magnitude depending on repeat content, length, and sequence identity. We show a strong paternal bias (75-81%) for all forms of germline DNM, yet we estimate that 17% of de novo SNVs are postzygotic in origin with no paternal bias. We place all this variation in the context of a high-resolution recombination map (~3.5 kbp breakpoint resolution). We observe a strong maternal recombination bias (1.36 maternal:paternal ratio) with a consistent reduction in the number of crossovers with increasing paternal (r=0.85) and maternal (r=0.65) age. However, we observe no correlation between meiotic crossover locations and de novo SVs, arguing against non-allelic homologous recombination as a predominant mechanism. The use of multiple orthogonal technologies, near-telomere-to-telomere phased genome assemblies, and a multi-generation family to assess transmission has created the most comprehensive, publicly available "truth set" of all classes of genomic variants. The resource can be used to test and benchmark new algorithms and technologies to understand the most fundamental processes underlying human genetic variation.

The first high-quality genome assembly and annotation of Lantana camara, an important ornamental plant and a major invasive species

This study presents the first annotated, haplotype-resolved, chromosome-scale genome of Lantana camara, a flowering shrub native to Central America and known for its dual role as an ornamental plant and an invasive species. Despite its widespread cultivation and ecological impact, the lack of a high-quality genome has hindered the investigation of traits of both ornamental and invasive. This research bridges the gap in genomic resources for L. camara, which is crucial for both ornamental breeding programs and invasive species management. Whole-genome and transcriptome sequencing were utilized to elucidate the genetic complexity of a diploid L. camara breeding line UF-T48. The genome was assembled de novo using HiFi and Hi-C reads, resulting in two phased genome assemblies with high Benchmarking Universal Single-Copy Orthologs (BUSCO) scores of 97.7%, indicating their quality. All 22 chromosomes were assembled with pseudochromosomes averaging 117 Mb. The assemblies revealed 29 telomeres and an extensive presence of repetitive sequences, primarily long terminal repeat transposable elements. The genome annotation identified 83,775 protein-coding genes, with 83% functionally annotated. In particular, the study mapped 42 anthocyanin and carotenoid candidate gene clusters and 12 herbicide target genes to the assembly, identifying 38 genes spread across the genome that are integral to flower color development and 53 genes for herbicide targeting in L. camara. This comprehensive genomic study not only enhances the understanding of L. camara’s genetic makeup but also sets a precedent for genomic research in the Verbenaceae family, offering a foundation for future studies in plant genetics, conservation, and breeding.

The phased Solanum okadae genome and Petota pangenome analysis of 23 other potato wild relatives and hybrids

Potato is an important crop in the genus Solanum section Petota. Potatoes are susceptible to multiple abiotic and biotic stresses and have undergone constant improvement through breeding programs worldwide. Introgression of wild relatives from section Petota with potato is used as a strategy to enhance the diversity of potato germplasm. The current dataset contributes a phased genome assembly for diploid S. okadae, and short read sequences and de novo assemblies for the genomes of 16 additional wild diploid species in section Petota that were noted for stress resistance and were of interest to potato breeders. Genome sequence data for three additional genomes representing polyploid hybrids with cultivated potato, and an additional genome from non-tuberizing S. etuberosum, which is outside of section Petota, were also included. High quality short reads assemblies were achieved with genome sizes ranging from 575 to 795 Mbp and annotations were performed utilizing transcriptome sequence data. Genomes were compared for presence/absence of genes and phylogenetic analyses were carried out using plastome and nuclear sequences.

Phased assembly of neo-sex chromosomes reveals extensive Y degeneration and rapid genome evolution in Rumex hastatulus.

Y chromosomes are thought to undergo progressive degeneration due to stepwise loss of recombination and subsequent reduction in selection efficiency. However, the timescales and evolutionary forces driving degeneration remain unclear. To investigate the evolution of sex chromosomes on multiple timescales, we generated a high-quality phased genome assembly of the massive older (<10MYA) and neo (<200,000 years) sex chromosomes in the XYY cytotype of the dioecious plant Rumex hastatulus and a hermaphroditic outgroup R. salicifolius. Our assemblies, supported by fluorescence in situ hybridization, confirmed that the neo-sex chromosomes were formed by two key events: an X-autosome fusion and a reciprocal translocation between the homologous autosome and the Y chromosome. The enormous sex-linked regions of the X (296 MB) and two Y chromosomes (503 MB) both evolved from large repeat-rich genomic regions with low recombination; however, the complete loss of recombination on the Y still led to over 30% gene loss and major rearrangements. In the older sex-linked region, there has been a significant increase in transposable element abundance, even into and near genes. In the neo sex-linked regions, we observed evidence of extensive rearrangements without gene degeneration and loss. Overall, we inferred significant degeneration during the first 10 million years of Y chromosome evolution but not on very short timescales. Our results indicate that even when sex chromosomes emerge from repetitive regions of already-low recombination, the complete loss of recombination on the Y chromosome still leads to a substantial increase in repetitive element content and gene degeneration.

A phased genome assembly of a Colombian Trypanosoma cruzi TcI strain and the evolution of gene families

Chagas is an endemic disease in tropical regions of Latin America, caused by the parasite Trypanosoma cruzi. High intraspecies variability and genome complexity have been challenges to assemble high quality genomes needed for studies in evolution, population genomics, diagnosis and drug development. Here we present a chromosome-level phased assembly of a TcI T. cruzi strain (Dm25). While 29 chromosomes show a large collinearity with the assembly of the Brazil A4 strain, three chromosomes show both large heterozygosity and large divergence, compared to previous assemblies of TcI T. cruzi strains. Nucleotide and protein evolution statistics indicate that T. cruzi Marinkellei separated before the diversification of T. cruzi in the known DTUs. Interchromosomal paralogs of dispersed gene families and histones appeared before but at the same time have a more strict purifying selection, compared to other repeat families. Previously unreported large tandem arrays of protein kinases and histones were identified in this assembly. Over one million variants obtained from Illumina reads aligned to the primary assembly clearly separate the main DTUs. We expect that this new assembly will be a valuable resource for further studies on evolution and functional genomics of Trypanosomatids.

Phased genome assemblies reveal haplotype-specific genetic load in the critically endangered Chinese Bahaba (Teleostei, Sciaenidae).

While haplotype-specific genetic load shapes the evolutionary trajectory of natural and captive populations, mixed-haplotype assembly and genotyping hindered its characterization in diploids. Herein, we produced two phased genome assemblies of the critically endangered fish Chinese Bahaba (Bahaba taipingensis, Sciaenidae, Teleostei) and resequenced 20 whole genomes to quantify population genetic load at a haplotype level. We identified frame-shifting variants as the most deleterious type, followed by mutations in the 5'-UTR, 3'-UTR and missense mutations at conserved amino acids. Phased haplotypes revealed gene deletions and high-impact deleterious variants. We estimated ~1.12% of genes missing or interrupted per haplotype, with a significant overlap of disrupted genes (30.35%) between haplotype sets. Relative proportions of deleterious variant categories differed significantly between haplotypes. Simulations suggested that purifying selection struggled to purge slightly deleterious genetic load in captive breeding compared to genotyping interventions, and that higher inter-haplotypic variance of genetic load predicted more efficient purging by artificial selection. Combining the knowledge of haplotype-resolved genetic load with predictive modelling will be immensely useful for understanding the evolution of deleterious variants and guiding conservation planning.

Chromosome-level phased genome assembly of "Antonovka" identified candidate apple scab-resistance genes highly homologous to HcrVf2 and HcrVf1 on linkage group 1.

Apple scab, a fungal disease caused by Venturia inaequalis, leads to losses in both yield and fruit quality of apples (Malus domestica Borkh.). Most commercial apple cultivars, including those containing the well-characterized Rvi6-scab-resistance locus on linkage group (LG) 1, are susceptible to scab. HcrVf2 and HcrVf1 are considered the main paralogs of the Rvi6 locus. The major apple scab-resistance loci Vhc1 in "Honeycrisp" and Rvi17 in "Antonovka," were identified in close proximity to HcrVf2. In this study, we used long-read sequencing and in silico gene sequence characterization to identify candidate resistance genes homologous to HcrVf2 and HcrVf1 in Honeycrisp and Antonovka. Previously published chromosome-scale phased assembly of Honeycrisp and a newly assembled phased genome of Antonovka 172670-B were used to identify HcrVf2 and HcrVf1 homologs spanning Vhc1 and Rvi17 loci. In combination with 8 available Malus assemblies, 43 and 46 DNA sequences highly homologous to HcrVf2 and HcrVf1, respectively, were identified on LG 1 and 6, with identity and coverage ranging between 87-95 and 81-95%, respectively. Among these homologs, 2 candidate genes in Antonovka and Honeycrisp haplome A are located in close physical proximity to the scab-resistance marker Ch-Vf1 on LG 1. They showed the highest identity and coverage (95%) of HcrVf2 and only minor changes in the protein motifs. They were identical by state between each other, but not with HcrVf2. This study offers novel genomic resources and insights into the Vhc1 and Rvi17 loci on LG 1 and identifies candidate genes for further resistance characterization.

High quality de novo genome assembly of the non-conventional yeast Kazachstania bulderi describes a potential low pH production host for biorefineries

Kazachstania bulderi is a non-conventional yeast species able to grow efficiently on glucose and δ-gluconolactone at low pH. These unique traits make K. bulderi an ideal candidate for use in sustainable biotechnology processes including low pH fermentations and the production of green chemicals including organic acids. To accelerate strain development with this species, detailed information of its genetics is needed. Here, by employing long read sequencing we report a high-quality phased genome assembly for three strains of K. bulderi species, including the type strain. The sequences were assembled into 12 chromosomes with a total length of 14 Mb, and the genome was fully annotated at structural and functional levels, including allelic and structural variants, ribosomal array and mating type locus. This high-quality reference genome provides a resource to advance our fundamental knowledge of biotechnologically relevant non-conventional yeasts and to support the development of genetic tools for manipulating such strains towards their use as production hosts in biotechnological processes.

A high-quality, phased genome assembly of broomcorn millet reveals the features of its subgenome evolution and 3D chromatin organization

A high-quality, phased genome assembly of broomcorn millet reveals the features of its subgenome evolution and 3D chromatin organization

PROGRESS IN SEQUENCING OF THE COMPLETE HAPLOTYPE-RESOLVED DIPLOID GENOMES OF PLANTS

Now most of the genomes of higher organisms are assembled for haploid set of chromosomes, in which DNA fragments from paired chromosomes from different parents alternate in the mosaic order. In this regard, such assemblies are more logical to consider as quasi-genomes, since they do not provide accurate information about the relationship between genotype and phenotype. A new level of genome assembly is haplotype-resolved diploid genomes of higher organisms, including plants and their polyploid forms that have undergone cytological and functional diploidization. Given the importance of such genome assemblies, a large number of corresponding computer programs have been developed that allow phased genome assembly and analysis. To date, haplotype-resolved diploid genomes have been assembled for more than 60 species of plants. Among them are various agricultural plants, ornamental plants, fruit trees and shrubs, forest trees, medicinal plants and others. For the most part, they are represented by diploid plants, but there are also triploids, auto- and allo-tetraploids, hexaploids and even octaploids. The sizes of the assembled genomes also vary greatly - from 135 million bp to 21.6 billion bp. In many articles it is note that phased genome assembly helped to more accurately determine individual important characteristics of the studied plants, including origin, evolution, domestication, yield, resistance to diseases and pests, as well as better understanding of metabolic pathways and mechanisms of heterosis.

Phased Genome Assemblies.

The ultimate goal of de novo assembly of reads sequenced from a diploid individual is the separate reconstruction of the sequences corresponding to the two copies of each chromosome. Unfortunately, the allele linkage information needed to perform phased genome assemblies has been difficult to generate. Hence, most current genome assemblies are a haploid mixture of the two underlying chromosome copies present in the sequenced individual. Sequencing technologies providing long (20kb) and accurate reads are the basis to generate phased genome assemblies. This chapter provides a brief overview of the main milestones in traditional genome assembly, focusing on the bioinformatic techniques developed to generate haplotype information from different specialized protocols. Using these techniques as a knowledge background, the chapter reviews the current algorithms to generate phased assemblies from long reads with low error rates. Current techniques perform haplotype-aware error correction steps to increase the quality of the raw reads. In addition, variations on the traditional overlap-layout-consensus (OLC) graph have been developed in an effort to eliminate edges between reads sequenced from different chromosome copies. This allows for large presence-absence variants between the chromosome copies to be taken into account. The development of these algorithms, along with the improved sequencing technologies has been crucial to finish chromosome-level assemblies of complex genomes.

A multi-omics framework reveals strawberry flavor genes and their regulatory elements.

Flavor is essential to consumer preference of foods and is an increasing focus of plant breeding programs. In fruit crops, identifying genes underlying volatile organic compounds has great promise to accelerate flavor improvement, but polyploidy and heterozygosity in many species have slowed progress. Here we use octoploid cultivated strawberry to demonstrate how genomic heterozygosity, transcriptomic intricacy and fruit metabolomic diversity can be treated as strengths and leveraged to uncover fruit flavor genes and their regulatory elements. Multi-omics datasets were generated including an expression quantitative trait loci map with 196 diverse breeding lines, haplotype-phased genomes of a highly-flavored breeding selection, a genome-wide structural variant map using five haplotypes, and volatile genome-wide association study (GWAS) with &gt; 300 individuals. Overlaying regulatory elements, structural variants and GWAS-linked allele-specific expression of numerous genes to variation in volatile compounds important to flavor. In one example, the functional role of anthranilate synthase alpha subunit 1 in methyl anthranilate biosynthesis was supported via fruit transient gene expression assays. These results demonstrate a framework for flavor gene discovery in fruit crops and a pathway to molecular breeding of cultivars with complex and desirable flavor.

Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity

Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity, including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome, which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function, complicating breeder’s efforts to reduce genetic load. The StCDF1 locus controls maturity, and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.