Biology subjects

Genomics

Explore bioRxiv genomics preprints on sequencing, gene expression and genetic variation. Read source abstracts and verify methods in the manuscript; preprints are not peer reviewed.

Follow this topic with RSS

At least 433 records · Page 24Linked to original sources

bioRxiv2019

Draft genome sequence of the Solanum aethiopicum provides insights into disease resistance, drought tolerance and the evolution of the genome

BackgroundS. aethiopicum is a close relative to S. melongena and has been routinely used to improve disease resistance in S. melongena. However, these efforts have been greatly limited by the lack of a reference genome and the clear understanding of the genes involved during biotic and abiotic stress response. ResultsWe present here a draft genome assembly of S. aethiopicum of 1.02 Gb in size, which is predominantly occupied by repetitive sequences (76.2%), particularly long terminal repeat elements. We annotated 37,681 gene models including 34,905 protein-coding genes. We observed an expansion of resistance genes through two rounds of amplification of LTR-Rs, occurred around 1.25 and 3.5 million years ago, respectively. The expansion also occurred in gene families related to drought tolerance. A number of 14,995,740 SNPs are identified by re-sequencing 65 S. aethiopicum genotypes including "Gilo" and "Shum" accessions, 41,046 of which are closely linked to resistance genes. The domestication and demographic history analysis reveals selection of genes involved in drought tolerance in both "Gilo" and "Shum" groups. A pan-genome of S. aethiopicum with a total of 36,250 protein-coding genes was assembled, of which 1,345 genes are missing in the reference genome. ConclusionsOverall, the genome sequence of S. aethiopicum increases our understanding of the genomic mechanisms of its extraordinary disease resistance and drought tolerance. The SNPs identified are available for potential use by breeders. The information provided here will greatly accelerate the selection and breeding of the African eggplant as well as other crops within the Solanaceae family.

genomics↗

bioRxiv2019

Whole genome sequencing and comparative genomic analysis reveal novel allelic variations unique to a purple colored rice landrace (Oryza sativa ssp. indica cv. Purpleputtu)

Purpleputtu (Oryza sativa ssp. indica cv. Purpleputtu) is a unique rice landrace from southern India that exhibits predominantly purple color. This study reports the underlying genetic complexity of the trait and associated domestication and de-domestication processes during its coevolution with present day cultivars. Along-with genome level allelic variations in the entire gene repertoire associated with purple, red coloration of grain and other plant parts. Comparative genomic analysis of the whole genome sequence of Purpleputtu (PP) revels total of 3,200,951 variants including 67,774 unique variations were observed in PP when compared with 108 rice genomes. Multiple sequence alignment uncovered a 14bp deletion in Rc (Red colored, a transcription factor of bHLH class) locus of PP, a key regulatory gene of anthocyanin biosynthetic pathway. Interestingly, this deletion in Rc gene is a characteristic feature of the present-day white pericarped rice cultivars. Phylogenetic analysis of Rc locus revealed a distinct clade showing proximity to the progenitor species rufipogon and nivara. In addition, PP genome exhibits a well conserved a 4.5Mbp region on chromosome 5 that harbors several loci associated with domestication of rice. Further, PP showed 1,387 unique SNPs compared to 3,024 lines of rice (SNP-Seek database). The results indicate that PP genome is rich in allelic diversity and can serve as an excellent resource for rice breeding for a variety of agronomically important traits such as disease resistance, enhanced nutritional values, stress tolerance and protection from harmful UV-B rays.

genomics↗

bioRxiv2019

Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies

Genomic resources for the domestic dog have improved with the widespread adoption of a 173k SNP array platform and updated reference genome. SNP arrays of this density are sufficient for detecting genetic associations within breeds but are underpowered for finding associations across multiple breeds or in mixed-breed dogs, where linkage disequilibrium rapidly decays between markers, even though such studies would hold particular promise for mapping complex diseases and traits. Here we introduce an imputation reference panel, consisting of 365 diverse, whole-genome sequenced dogs and wolves, which increases the number of markers that can be queried in genome-wide association studies approximately 130-fold. Using previously genotyped dogs, we show the utility of this reference panel in identifying novel associations and fine-mapping for canine body size and blood phenotypes, even when causal loci are not in strong linkage disequilibrium with any single array marker. This reference panel resource will improve future genome-wide association studies for canine complex diseases and other phenotypes. Author SummaryComplex traits are controlled by more than one gene and as such are difficult to map. For complex trait mapping in the domestic dog, researchers use the current array of 173,000 variants, with only minimal success. Here, we use a method called imputation to increase the number of variants - from 173,000 to 24 million - that can be queried in canine association studies. We use sequence data from the whole genomes of 365 dogs and wolves to accurately predict variants, in a separate cohort of dogs, that are not present on the array. Using dog body size, we show that the increase in variants results in an increase in mapping power, through the identification of new associations and the narrowing of regions of interest. This imputation panel is particularly important because of its usefulness in improving complex trait mapping in the dog, which has significant implications for discovery of variants in humans with similar diseases.

genomics↗

bioRxiv2019

Matching whole genomes to rare genetic disorders: Identification of potential causative variants using phenotype-weighted knowledge in the CAGI SickKids5 clinical genomes challenge

Precise identification of causative variants from whole-genome sequencing data, including both coding and non-coding variants, is challenging. The CAGI5 SickKids clinical genome challenge provided an opportunity to assess our ability to extract such information. Participants in the challenge were required to match each of 24 whole-genome sequences to the correct phenotypic profile and to identify the disease class of each genome. These are all rare disease cases that have resisted genetic diagnosis in a state-of-the-art pipeline. The patients have a range of eye, neurological, and connective-tissue disorders. We used a gene-centric approach to address this problem, assigning each gene a multi-phenotype-matching score. Mutations in the top scoring genes for each phenotype profile were ranked on a six-point scale of pathogenicity probability, resulting in an approximately equal number of top ranked coding and non-coding candidate variants overall. We were able to assign the correct disease class for 12 cases and the correct genome to a clinical profile for five cases. The challenge assessor found genes in three of these five cases as likely appropriate. In the post-submission phase, after careful screening of the genes in the correct genome we identified additional potential diagnostic variants, a high proportion of which are non-coding.

genomics↗

bioRxiv2019

Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era

Cactus, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequence. We describe progressive extensions to Cactus that enable reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We show that Cactus is capable of scaling to hundreds of genomes and beyond by describing results from an alignment of over 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment yet created. Further, we show improvements in orthology resolution leading to downstream improvements in annotation.

genomics↗

bioRxiv2026

High-quality genome assemblies of diploid Bromus species enhance understanding of genome complexity and uncover large DNA satellite structures.

Genus Bromus includes important cool-season forage grasses, but large genome sizes and complex ploidy hinder genomic studies. Here we carried out long read sequencing of two diploid genomes, Bromus riparius and Bromus squarrosus, generating highly contiguous assemblies with contig N50 values of 294.76 Mb and 98.78 Mb, respectively. These assemblies uncovered high-order centromeric repeats and two unique large sub-telomeric repeats on chromosome 5 and 7. Repeat expansion in Bromus appears relatively recent compared to speciation events ([~]9.75 million years ago); yet strong synteny persists across species. Transposable elements such as Angela, SIRE, Athila, CRM, and Retand were identified as major contributors to genome expansion in related Bromus species. Population structure analysis resolved six major subpopulations, with wild relatives exhibiting a higher genetic divergence than cultivated types. Hybrid bromegrass lines showed a higher proportion of genomic contribution from B. inermis than B. riparius. Together, these genomic resources provide a foundation for investigating traits of interest and advancing bromegrass breeding.

genomics↗

bioRxiv2026

The 3D Genome of Gigaspora margarita Unveils Stable Chromatin and Nucleolar Organization and Symbiont-Dependent Genome Dynamics

Arbuscular mycorrhizal fungi (AMF) are widespread plant symbionts that enhance nutrient acquisition and influence ecosystem productivity. Previous chromosome-level assemblies of a model species revealed a two-compartment genome architecture (active A and repressed B chromatin compartments), yet its conservation across evolutionarily distant AMF lineages remains unresolved. Here, we present a chromosome-scale and 3D genome assembly of Gigaspora margarita isolate BEG34--the largest and most repeat-rich AMF genome to date--alongside that of its obligate endobacterium, Candidatus Glomerobacter gigasporarum (CaGg), using PacBio HiFi and Hi-C sequencing. The G. margarita genome comprises 43 chromosomes (792 Mb) organized into stable A/B compartments and Topologically Associating Domains structures, irrespective of the presence of endobacteria. We uncover 21 divergent rDNA operons distributed across six chromosomes and show that these physically interact, suggesting conserved nucleolar organization. We also reveal that the CaGg genome is tripartite and mobilome-rich, encoding prophages, an orphan CRISPR array, and complete pathways for many novel and essential cofactors, including heme, which may enhance host bioenergetics. We also find that the endobacteriums presence regulates transposable elements in G. margarita. These findings reveal conserved principles of chromatin architecture in AMF symbionts and highlight the tight molecular interplay between fungal hosts and their endosymbionts, offering new insights into genome evolution and symbiotic adaptation.

genomics↗

bioRxiv2026

Pan-genome and multi-omics analyses reveal the genomic basis of symbiotic evolution in the mycoheterotrophic medicinal orchid Gastrodia elata

Mycoheterotrophy represents an extreme evolutionary strategy in which plants abandon photosynthesis and become obligately dependent on fungal partners for carbon and nutrients. Gastrodia elata, a medicinal orchid forming long-term symbioses with Armillaria and Mycena, provides a compelling system to investigate the genomic basis of obligate plant-fungus mutualism. Here, we generate a chromosome-level genome assembly (1.09 Gb) of a dark-red G. elata accession and construct a pan-genome from 12 Gastrodia accessions to dissect the evolutionary consequences of mycoheterotrophy. Phylogenomic analyses reveal pervasive hybridization across cultivated germplasm and demonstrate that tuber morphology more accurately reflects intraspecific relationships than stem color, challenging the traditional color-based taxonomy. Comparative genomic analyses reveal a pronounced degeneration of photosynthetic capacity. We detect no intact nuclear-encoded rbcS loci, which would preclude assembly of the Rubisco holoenzyme and thus canonical Calvin-Benson carbon fixation. Notably, a subset of photosynthesis-related genes is retained and transcriptionally active, suggesting their co-option into non-photosynthetic regulatory roles. Despite millions of years of intimate association with fungal partners, we detect no evidence of fungal-derived horizontal gene transfer based on a multi-step phylogenomic validation pipeline, indicating that G. elata-fungus mutualism is sustained through metabolic exchange rather than genetic integration. We further identify the Gastrodia antifungal protein (GAFP) gene family as a key molecular innovation underlying symbiotic homeostasis. The recently derived Class 1 GAFP lineage exhibits distinct domain architecture, tandem expansion, and elevated expression, consistent with enhanced regulation of fungal overgrowth. Finally, we delineate a specialized nutrient-acquisition framework adapted to obligate heterotrophy, in which fungal trehalose hydrolysis supplies hexose carbon via an expanded sugar transporter protein (STP) repertoire, while organic nitrogen is assimilated through amino acid and oligopeptide transporters coupled with urease-mediated conversion, compensating for the loss of nitrate uptake and reduction pathways. Together, these results establish a pan-genomic blueprint for symbiotic adaptation and reductive genome evolution in G. elata.

genomics↗

bioRxiv2026

Assessment of Oxford Nanopore whole genome sequencing for large-scale genomic characterisation of Staphylococcus aureus

Whole-genome sequencing (WGS) is increasingly being utilised in microbial diagnostics, surveillance, and research. In this paper we assess the performance of one leading long-read sequencing technology, Oxford Nanopore Technology (ONT), on 836 Staphylococcus aureus bacteraemia isolates. We compare the results to that of a leading short-read sequencing technology, Illumina. All isolates were sequenced using ONT MinION Mk1B and Illumina HiSeq or MiSeq. Libraries were prepared according to manufacturers instructions. Preprocessing and downstream bioinformatic analyses were performed using a combination of in-house pipelines and publicly available software tools. The average base substitution error rate in ONT assemblies was low but varied between sequence types, possibly due to lineage-specific methylation patterns. Multi locus sequence typing was similar between the technologies, while ONT assemblies allowed for better spa typing than Illumina assemblies. The reported detection rate was similar between ONT and Illumina assemblies for most virulence- and AMR-associated genes and variants. For 42 (22.2%) of 189 genes/variants, the two technologies disagreed in gene detection in 5 isolates or more, and in 39 (20.6.%) of these the highest detection rate was found with ONT. Discrepancies were mainly associated with low GC content, multiple repetitive segments, and small plasmids. Polishing of ONT data resulted in minor changes in gene/variant calling. Our study supports the use of ONT WGS for bacterial population genomic studies on a large collection of S. aureus isolates. While assembly of ONT reads may be affected by its own methodological limitations, it was superior to Illumina assemblies in detection of potentially clinically relevant genes and variants at a low read error rate. Understanding the advantages and limitations of WGS technologies is essential before undertaking studies involving such methods on large sets of bacteria. Author summaryIn this paper, we present a practical assessment of one important whole genome sequencing (WGS) method, Oxford Nanopore Technology (ONT), and compare its performance in bacterial population genomics to that of WGS with Illumina technology. Our goal was to investigate the usefulness of ONT in studies aiming to identify clinically relevant bacterial characteristics in large collections of bacteria, such as genotype-phenotype studies. We sequenced a large set of clinical S. aureus isolates from episodes of bloodstream infections using both ONT and Illumina technologies and performed analyses with widely used software and bioinformatic pipelines. We have elucidated inherent strengths and limitations of ONT and Illumina sequencing and report some of the practical consequences of these on bacterial typing and detection of clinically relevant genes. With this study, we present one of the most comprehensive assessments of long-read sequencing technology for the genomic characterisation of clinical bacterial isolates, and the findings provide guidance for researchers considering WGS in large-scale bacterial genomics.

genomics↗

bioRxiv2026

Genomic insights into polyketide toxin synthesis and algal symbiosis using high-quality genome sequences of the early divergent hexacorallian genus Palythoa (Cnidaria, Zoantharia)

Palytoxin, first isolated from Palythoa toxica, is among the most potent marine toxins known. Despite decades of biochemical investigation, genetic bases underlying its potential biosynthesis in Palythoa remain unresolved. Here we present four high-quality genome assemblies of Palythoa species, including Palythoa cf. toxica, and integrate these with a chromosome-scale genome assembly of P. caribaeorum. Performing comparative genomic analyses, we screened for candidate genes potentially involved in palytoxin biosynthesis and examined patterns of genome evolution. Unexpectedly, we identified only two classes of ketosynthase (KS) domain-containing genes in Palythoa: fatty acid synthases (FAS) and bacterial-like polyketide synthases (PKSs). Contrasting other anthozoans, animal FAS-like PKS (AFPK) genes common to all Palythoa species were not detected. We found no evidence for lineage-specific expansion of PKS genes unique to Palythoa, suggesting that if palytoxin/palytoxin-like molecule biosynthesis is host-encoded, it may involve functional modification or co-opting pre-existing FAS and/or bacterial-like PKS pathways. Comparative analyses revealed expansions of gene families associated with transport and binding functions in Palythoa, potentially reflecting molecular adaptations linked to their sand-incorporating body structure. We identified TPT1 and CLEC4A as rapidly evolving genes in multiple Palythoa species, consistent with possible roles in growth regulation and host-microbe interactions. Additionally, comparison between azooxanthellate and zooxanthellate species revealed mutations within conserved protein domains of LePin, which has been implicated in cnidarian endosymbiosis, suggesting lineage-specific modifications associated with symbiotic state. This study establishes a foundation for zoantharian genomic research, provides insights into lineage-specific genomic signatures, and advances molecular and evolutionary biological knowledge of this ecologically important group.

genomics↗

bioRxiv2026

Genomic basis of rapid urban evolution revealed by the subgenome-resolved genome of octoploid Oxalis corniculata

Urbanization is a major driver of contemporary evolution, yet the genomic basis of urban adaptation remains poorly understood, particularly in non-model plants with complex polyploid genomes. Here, we investigate the genetic mechanisms underlying leaf color variation in the octoploid Oxalis corniculata, a phenotype associated with heat tolerance in urban environments. By integrating high-fidelity long-read sequencing and chromosome conformation capture, we generated the subgenome-resolved, chromosome-scale genome assemblies for both red- and green-leaved lines, resolving four distinct subgenomes. LTR insertion timing revealed a two-step hybridization history that established this octoploid genome within the last 1 million years. Leveraging a nationwide citizen science initiative, we collected and analyzed over 1,700 samples across a broad geographic range. We identified a major locus on one subgenome underlying this variation and implicate a coding-sequence repeat-length polymorphism in a MYB transcription factor as the candidate causal variant. This simple sequence repeat likely acts as a molecular "tuning knob" for rapid adaptation to urban heat islands. This study provides a new baseline for evolutionary ecological genomics in plants and highlights the power of integrating advanced genomics with public participation to forecast evolutionary responses in an increasingly urbanized world.

genomics↗

bioRxiv2026

Genome-wide mapping of persistent long-range correlation in the complete telomere-to-telomere human reference genome

Long-range correlations (LRCs) in DNA sequences have been reported for decades, but their interpretation has been limited by incomplete representation of repetitive and structurally complex regions in earlier human genome assemblies. Here, we use the complete telomere-to-telomere (T2T) human reference genome to systematically map LRC structure across all human chromosomes. Most chromosomes exhibited persistent long-range dependence (LRD), with chromosome-specific scaling intervals spanning kilobase to megabase scales and wavelet Hurst exponents consistently above the uncorrelated expectation of 0.5. Spatially resolved Hurst landscapes revealed that this signal is not uniformly distributed along chromosomes, but instead reflects a heterogeneous genomic mosaic. For the purine-pyrimidine encoding, chromosomes 9, 15, X, and Y showed complex fluctuation profiles not adequately summarized by a single scaling exponent; multifractal detrended fluctuation analysis (MF-DFA) confirmed broad, q-dependent multiscaling consistent with multifractal behavior in these chromosomes, consistent with heterogeneous contributions from satellite-rich and structurally distinct sequence compartments. Surrogate analyses further showed that the observed correlations exceed expectations from base composition alone and are not fully explained by local sequence structure preserved in block-shuffled controls. However, short-memory Autoregressive Moving-Average (ARMA) surrogates reproduced the observed H range in a subset of chromosomes, indicating that the strength of evidence for LRD is chromosome-dependent. Together, these results demonstrate that LRC is a widespread but spatially heterogeneous property of the complete human genome. The T2T assembly reveals that previously unresolved repetitive and satellite-rich regions are strongly associated with chromosome-scale and local scaling variation, providing a framework for future studies of genome evolution, chromatin structure, recombination, structural variation, and genomic instability.

genomics↗

bioRxiv2026

Hidden in the genomic bycatch: insights into genome reorganization and population structure of the parasitic nematode Contortylenchus reversus

Insect-parasitic nematodes are widespread and often significantly reduce host fitness, yet we know surprisingly little about most species. Contortylenchus reversus is a hemocoel-inhabiting parasitic nematode that infects Dendroctonus bark beetles, notably impacting host mobility and fecundity. We first detail a chromosome-scale genome assembly of C. reversus, recovered serendipitously from a sequencing project targeting a host (Dendroctonus ponderosae). We assembled the 79.4 Mb genome into nine linkage groups and, through transcriptome-aided annotation, identified 11,244 protein-coding genes. Synteny comparisons with the only relatives for which there are complete assemblies reveal extensive chromosomal rearrangements and extreme loss of gene collinearity suggesting these insect-parasitic nematodes may have exceptionally malleable genomes. Using this genome assembly and repurposed reduced-representation genomic data from 707 D. ponderosae individuals, we investigated infection frequencies and population structure, identifying infection rates ranging from 0% to 50% across 18 geographically widespread collection sites. Population structure of C. reversus appears broadly concordant with the structure of the host beetle, suggesting a shared evolutionary history, while genetic variation (nucleotide diversity) in the parasitic nematode is highly reduced in comparison to its host. These results offer insights into its population genetics, host associations, and the evolutionary dynamics of a nematode-beetle interaction and highlight how genomic bycatch can reveal previously hidden details about an important species in a complex community.

genomics↗

bioRxiv2026

A telomere-to-telomere genome of Manilkara zapota (Chiku) reveals the repeat-mediated genome evolution

Manilkara zapota (Chiku) is a tropical fruit tree in the Sapotaceae family. In this study, we assembled the first Telomere-to-telomere (T2T) genome assembly of M. zapota, spanning 1.6 Gb with high contiguity (N50 = 134 Mb). Comparative analysis revealed a very recent divergence and a shared WGD among Sapotaceae members. A newly constructed Ancestral Sapotaceae Karyotype (ASK) suggests a fusion-dominated chromosome structure in the family. The genome exhibits lineage-specific proliferation of transposable elements (TEs) accompanied by a recent burst of LTR-Gypsy elements (~0.09 mya). Genome-wide methylation profiling revealed elevated CpG and CHG methylation levels and age-dependent reinforcement of TE silencing, suggesting strong epigenetic regulation that stabilises the repeat-rich genome while maintaining gene expression. Collectively, these findings advance our understanding of repeat-rich genome evolution in plants and provide a valuable framework for genomic-assisted breeding in M. zapota.

genomics↗

bioRxiv2026

Genome-wide mapping of endogenous topoisomerase cleavage complexes reveals TOP1 at the interface of DNA topological regulation and genome instability

Topoisomerase cleavage complexes (TOPcc) are covalent protein-DNA intermediates formed transiently during topoisomerase catalysis and constitute a major class of DNA-protein crosslinks in human cells, yet their endogenous genomic distributions remain difficult to resolve. Here, we developed protein-DNA adduct immunoprecipitation followed by sequencing (pDAIP-seq), a highly sensitive method for detecting endogenous TOPcc that enables their genome-wide profiling under normal physiological conditions without stabilization by topoisomerase poisons. Using pDAIP-seq, we found that camptothecin treatment, required by existing TOP1cc profiling methods, not only increased TOP1cc abundance but also substantially altered its genomic distribution. Endogenous TOP1cc were globally reduced upon transcriptional suppression and increased upon TOP2A depletion, supporting TOP1cc regulation by the maintenance of genome-wide DNA topological homeostasis. Interestingly, both the regional distribution and nucleotide-scale positioning of TOP1cc, including the positions of TOP1 catalytic cleavage sites, were largely specified by local DNA sequence context. By extending pDAIP-seq to capture transient covalent protein-DNA intermediates involved in DNA repair, including TDP1-, PARP1-, and KU70-DNA adducts, we further identified endogenous TOP1cc as a potential major source of spontaneous DNA breaks in human cells. Finally, pDAIP-seq also enabled genome-wide mapping of TOP2cc, TOP3cc, and SPO11-DNA covalent intermediates in mouse testis undergoing programmed meiotic DNA cleavage. Together, these findings establish pDAIP-seq as a broadly applicable method for the mapping of covalent protein-DNA intermediates and reveal endogenous TOP1cc as a key intermediate between DNA topological regulation and human genome instability.

genomics↗

bioRxiv2017

The Sorghum bicolor reference genome: improved assembly and annotations, a transcriptome atlas, and signatures of genome organization

2Sorghum bicolor is a drought tolerant C4 grass used for production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (~800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34,211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp. Sub-telomeric repeats with characteristics of Tandem Repeats In Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of the reference genome sequence to 56 resequenced genomes from diverse sorghum genotypes identified ~7.4M SNPs and 1.8M indels. Large scale variant features in euchromatin were identified with periodicities of ~25 kbp. An RNA transcriptome atlas of gene expression was constructed from 47 samples derived from growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement.

plant biology↗

bioRxiv2017

Genome Wide Association Analyses Based On Broadly Different Specifications For Prior Distributions, Genomic Windows, And Estimation Methods

A popular strategy (EMMAX) for genome wide association (GWA) analysis fits all marker effects as classical random effects (i.e., Gaussian prior) by which association for the specific marker of interest is inferred by treating its effect as fixed. It seems more statistically coherent to specify all markers as sharing the same prior distribution, whether it is Gaussian, heavy-tailed (BayesA), or has variable selection specifications based on a mixture of, say, two Gaussian distributions (SSVS). Furthermore, all such GWA inference should be formally based on posterior probabilities or test statistics as we present here, rather than merely being based on point estimates. We compared these three broad categories of priors within a simulation study to investigate the effects of different degrees of skewness for quantitative trait loci (QTL) effects and numbers of QTL using 43,266 SNP marker genotypes from 922 Duroc-Pietrain F2 cross pigs. Genomic regions were based either on single SNP associations, on non-overlapping windows of various fixed sizes (0.5 to 3 Mb) or on adaptively determined windows that cluster the genome into blocks based on linkage disequilibrium (LD). We found that SSVS and BayesA lead to the best receiver operating curve properties in almost all cases. We also evaluated approximate marginal a posteriori (MAP) approaches to BayesA and SSVS as potential computationally feasible alternatives; however, MAP inferences were not promising, particularly due to their sensitivity to starting values. We determined that it is advantageous to use variable selection specifications based on adaptively constructed genomic window lengths for GWA studies.\n\nSUMMARYGenome wide association (GWA) analyses strategies have been improved by simultaneously fitting all marker effects when inferring upon any single marker effect, with the most popular distributional assumption being normality. Using data generated from 43,266 genotypes on 922 Duroc-Pietrain F2 cross pigs, we demonstrate that GWA studies could particularly benefit from more flexible heavy-tailed or variable selection distributional assumptions. Furthermore, these associations should not just be based on single markers or even genomic windows of markers of fixed physical distances (0.5 - 3.0 Mb) but based on adaptively determined genomic windows using linkage disequilibrium information.

genetics↗

bioRxiv2020

GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline

In recent years, there has been a significant increase in whole genome sequencing data of individual genomes produced by research projects as well as direct to consumer service providers. While many of these sources provide their users with an interpretation of the data, there is a lack of free, open tools for generating reports exploring the data in an easy to understand manner. GenomeChronicler was developed as part of the Personal Genome Project UK (PGP-UK) to address this need. PGP-UK provides genomic, transcriptomic, epigenomic and self-reported phenotypic data under an open-access model with full ethical approval. As a result, the reports generated by GenomeChronicler are intended for research purposes only and include information relating to potentially beneficial and potentially harmful variants, but without clinical curation. GenomeChronicler can be used with data from whole genome or whole exome sequencing, producing a genome report containing information on variant statistics, ancestry and known associated phenotypic traits. Example reports are available from the PGP-UK data page (personalgenomes.org.uk/data). The objective of this method is to leverage existing resources to find known phenotypes associated with the genotypes detected in each sample. The provided trait data is based primarily upon information available in SNPedia, but also collates data from ClinVar, GETevidence and gnomAD to provide additional details on potential health implications, presence of genotype in other PGP participants and population frequency of each genotype. The analysis can be run in a self-contained environment without requiring internet access, making it a good choice for cases where privacy is essential or desired: any third party project can embed GenomeChronicler within their off-line safe-haven environments. GenomeChronicler can be run for one sample at a time, or in parallel making use of the Nextflow workflow manager. The source code is available from GitHub (https://github.com/PGP-UK/GenomeChronicler), container recipes are available for Docker and Singularity, as well as a pre-built container from SingularityHub (https://singularity-hub.org/collections/3664) enabling easy deployment in a variety of settings. Users without access to computational resources to run GenomeChronicler can access the software from the Lifebit CloudOS platform (https://lifebit.ai/cloudos) enabling the production of reports and variant calls from raw sequencing data in a scalable fashion.

bioinformatics↗