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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 Read source abstracts and verify methods in the manuscript; preprints are not peer reviewed.

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bioRxiv2019

Mitochondrial genomes of Columbicola feather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice

Most animals have a conserved mitochondrial genome structure composed of a single chromosome. However, some organisms have their mitochondrial genes separated on several smaller circular or linear chromosomes. Highly fragmented circular chromosomes (\"minicircles\") are especially prevalent in parasitic lice (Insecta: Phthiraptera), with 16 species known to have between 9 and 20 mitochondrial minicircles per genome. All of these species belong to the same clade (mammalian lice), suggesting a single origin of drastic fragmentation. Nevertheless, other work indicates a lesser degree of fragmentation (2-3 chromosomes/genome) is present in some avian feather lice (Ischnocera: Philopteridae). In this study, we tested for minicircles in four species of the feather louse genus Columbicola (Philopteridae). Using whole genome shotgun sequence data, we applied three different bioinformatic approaches for assembling the Columbicola mitochondrial genome. We further confirmed these approaches by assembling the mitochondrial genome of Pediculus humanus from shotgun sequencing reads, a species known to have minicircles. All three methods indicated Columbicola spp. genomes are highly fragmented into 15-17 minicircles between 1,119 and 3,173 bp in length, with 1-4 genes per minicircle. Subsequent annotation of the minicircles indicated that tRNA arrangements of minicircles varied substantially between species. These mitochondrial minicircles for species of Columbicola represent the first feather lice (Philopteridae) for which minicircles have been found in a full mitochondrial genome assembly. Combined with recent phylogenetic studies of parasitic lice, our results provide strong evidence that highly fragmented mitochondrial genomes, which are otherwise rare across the Tree of Life, evolved multiple times within parasitic lice.

evolutionary biology↗

bioRxiv2019

Genomic loci susceptible to systematic sequencing bias in clinical whole genomes

Accurate massively parallel sequencing (MPS) of genetic variants is key to many areas of science and medicine, such as cataloguing population genetic variation and diagnosing genetic diseases. Certain genomic positions can be prone to higher rates of systematic sequencing and alignment bias that limit accuracy, resulting in false positive variant calls. Current standard practices to differentiate between loci that can and cannot be sequenced with high confidence utilise consensus between different sequencing methods as a proxy for sequencing confidence. These practices have significant limitations and alternative methods are required to overcome these. We have developed a novel statistical method based on summarising sequenced reads from whole genome clinical samples and cataloguing them in "Incremental Databases" that maintain individual confidentiality. Allele statistics were catalogued for each genomic position that consistently showed systematic biases with the corresponding MPS sequencing pipeline. We found systematic biases present at [~]1-3% of the human autosomal genome across five patient cohorts. We identified which genomic regions were more or less prone to systematic biases, including large homopolymer flanks (odds ratio=23.29-33.69) and the NIST high confidence genomic regions (odds ratio=0.154-0.191). We confirmed our predictions on a gold-standard reference genome and showed that these systematic biases can lead to suspect variant calls within clinical panels. Our results recommend increased caution to address systematic biases in whole genome sequencing and alignment. This study provides the implementation of a simple statistical approach to enhance quality control of clinically sequenced samples by flagging variants at suspect loci for further analysis or exclusion.

bioinformatics↗

bioRxiv2019

Genome Complexity Browser: estimation and visualization of prokaryote genome variability

MotivationComparative genomics studies may be used to acquire new knowledge about chromosomal architecture - the rules to combine a set of genes in a genome of a living organism. Hundreds of thousands of prokaryote genomes were sequenced and assembled. Still, there is a lack of computational tools able to compare hundreds of genomes simultaneously, i.e. to find hotspots of genome rearrangements and horizontal gene transfer or to analyze which part of an operon is conservative and which is variable.\n\nResultsWe developed Genomic Complexity Browser (GCB), a tool that allows to visualize gene contexts in a graph form and evaluate genome variability of different parts of a prokaryotic chromosome. We introduce a measure called complexity, which is an indirect measure of genome variability. Intraspecies and interspecies comparisons reveal that regions with high complexity tend to be located in a similar context in different strains and species. While many of such hot spots are associated with prophages and pathogenicity islands, some of them lack these determinants and mechanisms that govern their dynamics are to be elucidated.\n\nAvailabilityGCB is freely available as a web server at http://gcb.rcpcm.org and as a stand-alone application at https://github.com/DNKonanov/GCB\n\nContactparaslonic@gmail.com

bioinformatics↗

bioRxiv2019

Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy

We recently introduced the Genome Taxonomy Database (GTDB), a phylogenetically consistent, genome-based taxonomy providing rank normalized classifications for nearly 150,000 genomes from domain to genus. However, nearly 40% of the genomes used to infer the GTDB reference tree lack a species name, reflecting the large number of genomes in public repositories without complete taxonomic assignments. Here we address this limitation by proposing 24,706 species clusters which encompass all publicly available bacterial and archaeal genomes when using commonly accepted average nucleotide identity (ANI) criteria for circumscribing species. In contrast to previous ANI studies, we selected a single representative genome to serve as the nomenclatural type for circumscribing each species with type strains used where available. We complemented the 8,792 species clusters with validly or effectively published names with 15,914 de novo species clusters in order to assign placeholder names to the growing number of genomes from uncultivated species. This provides the first complete domain to species taxonomic framework which will improve communication of scientific results.

microbiology↗

bioRxiv2025

CGAS (Chloroplast Genome Analysis Suite): An Automated Python Pipeline for Comprehensive Comparative Chloroplast Genomics

BackgroundChloroplast genome analysis underpins plant phylogenetics, comparative genomics, and molecular marker development. Although high-quality chloroplast genomes are now routinely generated, downstream comparative analyses still rely on fragmented toolchains requiring separate tools for annotation, codon analysis, and SNP detection, extensive manual curation, and ad hoc scripting, which limit reproducibility and scalability. ResultsWe present the Chloroplast Genome Analysis Suite (CGAS), an automated Python-based pipeline designed as a comprehensive solution for comparative chloroplast genomics. CGAS integrates nine core analytical modules into a single, reproducible workflow operating directly on annotated GenBank files and pre-aligned FASTA datasets. The pipeline performs automated gene content analysis, publication-ready gene table generation, chloroplast structural characterization (LSC/SSC/IR boundaries and GC content), codon usage and amino acid composition analyses enabling batch processing of 10-50+ genomes, SNP detection with transition/transversion statistics, intron feature characterization, simple sequence repeat identification, and nucleotide diversity profiling. Unlike existing tools, CGAS emphasizes biologically informed handling of edge cases, including trans-spliced genes (e.g., rps12), IR-mediated gene duplication, and annotation artifacts. All outputs are generated in standardized, publication-ready Excel and Word formats with timestamped provenance. ConclusionsCGAS provides a unified, automated, and biologically robust framework for comparative chloroplast genome analysis. By minimizing manual intervention and emphasizing batch processing, the suite substantially accelerates methodologically consistent analyses. The pipeline is openly available at https://github.com/abdullah30/Chloroplast-Genome-Analysis-Suite-CGAS and readily extensible, supporting its adoption as a standardized analytical backend for chloroplast comparative genomics.

bioinformatics↗

bioRxiv2025

GenoME: a MoE-based generative model for individualized, multimodal prediction and perturbation of genomic profiles

The non-coding genome operates through a complex, multiscale regulatory system where regulated gene expressions are closely associated with cell-type-specific histone modifications, transcription factor binding and 3D conformation. Developing computational models that can integrate these patterns to predict and interpret the regulatory system remains challenging. Here, we present GenoME, a Mixture of Experts (MoE)-based generative model that uses DNA sequence and cell-type-specific ATAC-seq signals to predict a unified genomic profile encompassing epigenomics, transcriptomics, and chromatin architecture at base-pair to kilobase resolutions. GenoME enables multiscale predictions for held-out genomic regions and, critically, generalizes to predict the full regulatory landscape of unseen or individualized cell types from a single ATAC-seq input. We equip GenoME with an in silico perturbation framework that accurately forecasts the multimodal consequences of genetic perturbations and identifies functional enhancer-promoter connections, outperforming specialized models like Activity-by-Contact. These predictions can also be used to decipher the transcription factor grammar of cell-type-specific enhancers. GenoME thus provides a versatile, all-in-one platform for generative modeling, cross-cell-type generalization, and causal mechanistic investigation of the multiscale regulatory genome.

bioinformatics↗

bioRxiv2026

Creating bacterial genomic diversity through large-scale reconfigurations reveals phenotype robustness to organizational genome change

The ability to generate genomic diversity expands opportunities for understanding and engineering biology. Here, we demonstrate on-demand generation of diversity in bacterial genome configurations and its application to probing physiology under altered genome organization. We engineered the fast-growing bacterium Vibrio natriegens to enable large-scale stochastic duplications, translocations, inversions, and deletions, producing populations with a wide range of genome arrangements. We investigated phenotypic robustness to genome reconfigurations and found that distinct genome organizations can support stable physiology, indicating that bacteria may tolerate chromosomal alterations more readily than previously appreciated. Our work provides a framework for advancing the understanding and engineering of bacterial genomes and suggests that genome reconfigurations may contribute to phenogenetic drift, allowing for evolutionary exploration while preserving phenotype.

synthetic biology↗

bioRxiv2026

Track Hub Quickload Translator: Convert Track Hub or Quickload data for viewing in the UCSC Genome Browser or the Integrated Genome Browser

Summary: Genome browsers are essential for understanding genomic data in detail but use incompatible data repository formats and access protocols, limiting their use. We present a new web application Hub Facade that translates the Track Hub format used by the UCSC Genome Browser into the Quickload format used by the Integrated Genome Browser (IGB), and vice versa. We used the Facade's translation capability to write a single-page web application for IGB users to search and add UCSC-curated Hubs to IGB for exploration and visual analysis. We created a new IGB App (GenArk Genomes) that uses the Facade to automate importing genome assemblies from GenArk, a Hub-based repository with nearly 50,000 genomes hosted by the UCSC Genome Browser team. An example use case investigating alternative splicing of human gene MEOX1 shows how using both browsers to view the same data via the Hub Facade promotes understanding and discovery. Availability and Implementation: Hub Facade is free, open-source software deployed at translate.bioviz.org. Code is available from git repositories at [bitbucket.org|github.com]/lorainelab/hub-facade. The use case is available as Supplemental File 1.

bioinformatics↗

bioRxiv2026

Genome-resolved surveillance of African Klebsiella oxytoca species complex genomes reveals resistome-mobilome and biosynthetic gene cluster diversity

The Klebsiella oxytoca species complex (KoSC) comprises taxonomically diverse commensals and opportunistic pathogens, but its genomic diversity remains poorly characterized across Africa. We curated publicly available African KoSC data through raw-read and public-assembly routes and analyzed 163 African genomes together with 282 global comparators. Pangenome, phylogenomic, sequence-typing, surface-locus, antimicrobial-resistance, plasmid-replicon, mobile-element, biosynthetic-gene-cluster, and virulence-component analyses were integrated. The African collection comprised K. michiganensis (112/163), K. oxytoca (36/163), K. pasteurii (8/163), and K. grimontii (7/163) from 13 countries. The African pangenome contained 4,286 core, 4,505 shell, and 18,066 cloud gene families. Official PubMLST sequence types were assigned to 129/163 genomes. Four core/intrinsic antimicrobial-resistance-associated loci (ompA, oqxA, oqxB, and blaOXY) occurred in all genomes, whereas acquired resistance determinants were heterogeneous. Intact til biosynthetic gene clusters occurred in 55/163 genomes and intact leup clusters in 103/163. leup was concentrated in K. michiganensis (102/112), whereas intact til was frequent in K. oxytoca (26/36), K. pasteurii (7/8), and K. grimontii (7/7). Klebsiella-focused Virulence Factor Database screening detected at least one curated component in 112/163 genomes, but no complete curated factor; three K. michiganensis genomes carried complete mrkABCDF structural-operon candidates. These data define an African genome-resolved baseline for KoSC diversity and identify species-structured biosynthetic loci alongside heterogeneous resistance and mobilome profiles.

microbiology↗

bioRxiv2026

Ancestral genomic stasis and coordinated genome erosion underlies asymmetric acarine diversification

Mites and ticks (Acari) constitute one of the most species-rich and ecologically diverse arachnid radiations, yet their interrelationships and genomic mechanisms underlying their diversification remain poorly resolved. Here, we reconstructed the evolutionary relationships and trajectory of Parasitiformes using phylogenetics and comparative genomics to test the phylogenetic signal in rare genomic changes. Maximum likelihood and macrosynteny analysis revealed multiple shared chromosomal fusion-with-mixing events that unite Opilioacaridae and Ixodida as sister taxa, with Mesostigmata as a derived sister clade, overturning the prior basal placement of Opilioacaridae as a slowly evolving "living fossil" lineage. We show that major parasitiform lineages diversified through asymmetric, large-scale genome and regulatory rewiring. Opilioacaridae genome retains ancestral chelicerate genomic features, including an intact, contiguous Hox gene cluster, high repetitive-element content, and a conserved microRNA repertoire, all shared with Ixodida. By contrast, the hyperdiverse Mesostigmata shows marked genome compaction, with shortened introns, disrupted and fragmented Hox clusters, and widespread loss of microRNA families, despite retention of developmentally essential miRNAs. Comparative analysis of gene-family evolution further identifies lineage-specific expansions in Ixodida associated with blood feeding and immune evasion, alongside independent, convergent expansion of cuticle-protein gene families in ectoparasitic Mesostigmata. These findings demonstrate that contrasting modes of genome evolution, long-term structural stasis versus rapid compaction, together with convergent gene-family expansion linked to independent origins of parasitism, can coexist within a single arachnid radiation, offering new insight into the molecular basis of developmental regulatory evolution and adaptive diversification in Acari.

evolutionary biology↗

bioRxiv2026

Phased Chromosome-level Genome and Organellar Assemblies of Castilleja foliolosa Provide Vital Resource for Orobanchaceae Genomics

Castilleja (Orobanchaceae) is a diverse, facultatively hemiparasitic plant genus characterized by a complex evolutionary history of reticulate evolution and significant taxonomic ambiguity. High-quality genomic resources have historically been limited, hindering robust macro-evolutionary and macro-ecological inquiries. Here, we present the first high-quality, phased, chromosome-level reference genome for the diploid species Castilleja foliolosa. Utilizing a hybrid assembly strategy, we integrated long-read PacBio HiFi sequencing with Omni-C proximity ligation data to generate a highly contiguous nuclear assembly, complemented by reconstructed mitochondrial and chloroplastic genomes. The primary nuclear haplotype spans approximately 510 Mbp, containing 39,417 predicted genes and a substantial repetitive landscape covering ~66% of the genome. Our organellar assemblies reveal notable structural complexity: the chloroplast maintains heteroplasmy via two primary structural haplotypes, while the 611 kbp mitogenome adopts a circular master topology existing in two isomeric forms. Comparative genomic analyses demonstrate a largely conserved chromosomal architecture relative to the closely related Pedicularis cranolopha, punctuated by the presence of lineage-specific genes. Functional enrichment of Castilleja-specific orthogroups identifies a consistent association with telomere maintenance, DNA integration, and zinc ion binding, likely stemming from the substantial repeat content. This reference genome provides a robust framework for dissecting the genomic drivers of taxonomic diversification and adaptation within the Orobanchaceae family. This resource significantly enhances our capacity to untangle reticulate evolutionary patterns, offering a definitive foundation for future comparative studies of genome evolution in the Orobanchaceae lineage of parasitic plants.

plant biology↗

bioRxiv2026

Leveraging genomes and metagenome-assembled genomes unveils novel diversity and transmission between public transport and clinical settings in Acinetobacter

The molecular epidemiology of Acinetobacter, which is almost exclusively culture-dependent, has centered mainly on clinical isolates of A. baumannii. Yet, this overlooks sources not amenable to microbial culture and many non-A. baumannii species. Here, by analysing metagenomic projects from public transport systems worldwide, we show that metagenome-assembled genomes (MAGs) are highly relevant for assessing the unrecognized diversity of Acinetobacter. We recovered 839 Acinetobacter MAGs, with 269 being high-quality MAGs. The high-quality MAGs were across more than 20 well-defined Acinetobacter species; however, five species (A. nosocomilalis, A. ursingii, A. radioresistens, A. schindleri, and A. variabilis) had the most MAGs. Pangenome and phylogenetic diversity analyses of 685 genomes plus the 269 high-quality MAGs from those 5 species showed that MAGs are an important source of both lineage and gene diversity. Also, FST analyses and genome phylogenies show that for some species there is no genetic differentiation between MAGs and clinical isolates, implying transmission between hospitals and public transport settings. In addition to finding the antibiotic resistance genes (ARGs) in MAGs, we implemented an ad hoc strategy (leveraging the use of genomes) to recover considerably more ARGs. PCoA and PERMANOVA analyses show that, whereas in A. nosocomialis and A. ursingii, the ARG profiles of MAGs and clinical genomes are different, in A. radioresistens and A. schindleri, the ARG profiles are not different. Finally, some clinically important ARGs, such as sul1 and sul2, aadA, and blaOXA23, were found in all or some of the 5 species. Our study shows how combining MAGs and regular genomes is a powerful strategy for better appraising the genomic diversity (including the resistome) of Acinetobacter. On a broader level, our study showcases the importance of MAGs for genomic surveillance of man-made environments with clear public health implications.

microbiology↗

bioRxiv2026

VenusGenome: Genome-Aware Masked Autoencoding for Microbial Genome Representation Learning

Genomic-context models have shown that contextualizing protein embeddings can improve predictions of microbial function. We observe that a gene's protein embedding is partially predictable from the embeddings of neighboring genes in the genome, motivating high-ratio masking that requires reconstruction from sparser genomic context. Genomic modeling must also distinguish biological relationships from assembly conventions, since the ordering of separate contigs does not imply adjacency and strand labels depend on the reference orientation. We therefore introduce VenusGenome, a gene-resolution masked autoencoder that combines visible-only encoding with genome-aware attention incorporating contig boundaries, relative strand orientations, and gene positions. We pretrain this model on a curated corpus of over 1.7 million microbial genome assemblies from isolate and metagenomic sources, using frozen protein embeddings as gene-level inputs. Across genome-level phenotype prediction and gene-level tasks, the resulting frozen representations achieve the highest mean performance among the evaluated models on nine of eleven primary metrics. An exploratory gene-input perturbation analysis further links representation sensitivity to experimentally measured fitness defects. Ablations support the contribution of genome-aware attention and show the benefits of masked autoencoding over BERT-style masked modeling, with further gains from higher masking ratios.

bioinformatics↗

bioRxiv2014

Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing

Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we perform genome-wide CNV analysis in 12 diversified chicken genomes based on whole genome sequencing. A total of 9,025 CNV regions (CNVRs) covering 100.1 Mb and representing 9.6% of the chicken genome are identified, ranging in size from 1.1 to 268.8 kb with an average of 11.1 kb. Sequencing-based predictions are confirmed at high validation rate by two independent approaches, including array comparative genomic hybridization (aCGH) and quantitative PCR (qPCR). The Pearson?s correlation values between sequencing and aCGH results range from 0.395 to 0.740, and qPCR experiments reveal a positive validation rate of 91.71% and a false negative rate of 22.43%. In total, 2,188 predicted CNVRs (24.2%) span 2,182 RefSeq genes (36.8%) associated with specific biological functions. Besides two previously accepted copy number variable genes EDN3 and PRLR, we also find some promising genes with potential in phenotypic variants. FZD6 and LIMS1, two genes related to diseases susceptibility and resistance are covered by CNVRs. Highly duplicated SOCS2 may lead to higher bone mineral density. Entire or partial duplication of some genes like POPDC3 and LBFABP may have great economic importance in poultry breeding. Our results based on extensive genetic diversity provide the first individualized chicken CNV map and genome-wide gene copy number estimates and warrant future CNV association studies for important traits of chickens.

Genomics↗

bioRxiv2016

Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification

Translating genomic technologies into healthcare applications for the malaria parasite Plasmodium falciparum has been limited by the technical and logistical difficulties of obtaining high quality clinical samples from the field. Sampling by dried blood spot (DBS) finger-pricks can be performed safely and efficiently with minimal resource and storage requirements compared with venous blood (VB). Here, we evaluate the use of selective whole genome amplification (sWGA) to sequence the P. falciparum genome from clinical DBS samples, and compare the results to current methods using leucodepleted VB. Parasite DNA with high (> 95%) human DNA contamination was selectively amplified by Phi29 polymerase using short oligonucleotide probes of 8-12 mers as primers. These primers were selected on the basis of their differential frequency of binding the desired (P. falciparum DNA) and contaminating (human) genomes. Using sWGA method, we sequenced clinical samples from 156 malaria patients, including 120 paired samples for head-to-head comparison of DBS and leucodepleted VB. Greater than 18-fold enrichment of P. falciparum DNA was achieved from DBS extracts. The parasitaemia threshold to achieve >5x coverage for 50% of the genome was 0.03% (40 parasites per 200 white blood cells). Over 99% SNP concordance between VB and DBS samples was achieved after excluding missing calls. The sWGA methods described here provide a reliable and scalable way of generating P. falciparum genome sequence data from DBS samples. Our data indicate that it will be possible to get good quality sequence data on most if not all drug resistance loci from the majority of symptomatic malaria patients. This technique overcomes a major limiting factor in P. falciparum genome sequencing from field samples, and paves the way for large-scale epidemiological applications.

Genomics↗

bioRxiv2017

Genome-Wide Association Study And Genomic Predictions For Resistance Against Piscirickettsia salmonis In Coho Salmon (Oncorhynchus kisutch) Using ddRAD Sequencing

Piscirickettsia salmonis is one of the main infectious diseases affecting coho salmon (Oncorhynchus kisutch) farming. Current treatments have been ineffective for the control of the disease. Genetic improvement for P. salmonis resistance has been proposed as a feasible alternative for the control of this infectious disease in farmed fish. Genotyping by sequencing (GBS) strategies allow genotyping hundreds of individuals with thousands of single nucleotide polymorphisms (SNPs), which can be used to perform genome wide association studies (GWAS) and predict genetic values using genome-wide information. We used double-digest restriction-site associated DNA (ddRAD) sequencing to dissect the genetic architecture of resistance against P. salmonis in a farmed coho salmon population and identify molecular markers associated with the trait. We also evaluated genomic selection (GS) models in order to determine the potential to accelerate the genetic improvement of this trait by means of using genome-wide molecular information. 764 individuals from 33 full-sib families (17 highly resistant and 16 highly susceptible) which were experimentally challenged against P. salmonis were sequenced using ddRAD sequencing. A total of 4,174 SNP markers were identified in the population. These markers were used to perform a GWAS and testing genomic selection models. One SNP related with iron availability was genome-wide significantly associated with resistance to P. salmonis defined as day of death. Genomic selection models showed similar accuracies and predictive abilities than traditional pedigree-based best linear unbiased prediction (PBLUP) method.

genomics↗

bioRxiv2017

Improved de novo Genome Assembly: Synthetic long read sequencing combined with optical mapping produce a high quality mammalian genome at relatively low cost

Current short-read methods have come to dominate genome sequencing because they are cost-effective, rapid, and accurate. However, short reads are most applicable when data can be aligned to a known reference. Two new methods for de novo assembly are linked-reads and restriction-site labeled optical maps. We combined commercial applications of these technologies for genome assembly of an endangered mammal, the Hawaiian Monk seal.\n\nWe show that the linked-reads produced with 10X Genomics Chromium chemistry and assembled with Supernova v1.1 software produced scaffolds with an N50 of 22.23 Mbp with the longest individual scaffold of 84.06 Mbp. When combined with Bionano Genomics optical maps using Bionano RefAligner, the scaffold N50 increased to 29.65 Mbp for a total of 170 hybrid scaffolds, the longest of which was 84.78 Mbp. These results were 161X and 215X, respectively, improved over DISCOVAR de novo assemblies. The quality of the scaffolds was assessed using conserved synteny analysis of both the DNA sequence and predicted seal proteins relative to the genomes of humans and other species. We found large blocks of conserved synteny suggesting that the hybrid scaffolds were high quality. An inversion in one scaffold complementary to human chromosome 6 was found and confirmed by optical maps.\n\nThe complementarity of linked-reads and optical maps is likely to make the production of high quality genomes more routine and economical and, by doing so, significantly improve our understanding of comparative genome biology.

genomics↗

bioRxiv2017

De-novo assembly of zucchini genome reveals a whole genome duplication associated with the origin of the Cucurbita genus

The Cucurbita genus (squashes, pumpkins, gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata. In this study, we present a high-quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb, 34,240 gene models, includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules, that represent 81.4% of the assembly, and it is integrated with a genetic map of 7,718 SNPs. Despite its small genome size three independent evidences support that the C. pepo genome is the result of a Whole Genome Duplication: the topology of the gene family phylogenies, the karyotype organization, and the distribution of 4DTv distances. Additionally, 40 transcriptomes of 12 species of the genus were assembled and analyzed together with all the other published genomes of the Cucurbitaceae family. The duplication was detected in all the Cucurbita species analyzed, including C. maxima and C. moschata, but not in the more distant cucurbits belonging to the Cucumis and Citrullus genera, and it is likely to have happened 30 {+/-} 4 Mya in the ancestral species that gave rise to the genus.

genomics↗