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 Read source abstracts and verify methods in the manuscript; preprints are not peer reviewed.

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bioRxiv2022

Using large-scale whole-genome sequence data for single-step genomic predictions in maternal and terminal pig lines

BackgroundWhole-genome sequence (WGS) data harbor causative variants that may not be present in the regular SNP chip data. The objective of this study was to investigate the impact of using preselected variants from WGS for single-step genomic predictions in maternal and terminal pig lines with up to 1.8k sequenced and 104k imputed sequenced animals per line. MethodsTwo maternal and four terminal lines were investigated for eight and seven traits, respectively. The number of sequenced animals ranged from 1,365 to 1,491 in maternal lines and 381 to 1,865 in terminal lines. Imputation occurred within each line, and the number of animals imputed to sequence ranged from 66k to 76k in maternal lines and 29k to 104k in terminal lines. Two preselected SNP sets were generated based on genome-wide association study (GWAS). Top40k included the SNP with the lowest p-value in each of 40k genomic windows; ChipPlusSign included significant variants integrated into the regular porcine SNP chip. Single-step genomic predictions with equal or different SNP variances using those SNP sets were compared to the regular porcine SNP chip. ResultsIn maternal lines, ChipPlusSign, and Top40k showed, on average, 0.62%, and 4.9% increased accuracy compared to the regular porcine SNP chip. The greatest changes were for fertility traits with Top40k, where the initial accuracy based on the SNP chip was low. However, for terminal lines, Top40k resulted in a loss of accuracy of 1% on average. Only ChipPlusSign provided a positive, albeit small, gain (0.85%). Assigning different variances for SNP slightly improved accuracies when using variances obtained from BayesR; however, the increase was inconsistent across the lines and traits. ConclusionsThe benefit of using sequence data depends on the line, size of the genotyped population, and how the WGS variants are preselected. When WGS is available on hundreds of thousands of animals, the advantage of sequence data is present but limited in maternal and terminal pig lines.

genomics↗

bioRxiv2022

Localized assembly for long reads enables genome-wide analysis of repetitive regions at single-base resolution in human genomes

BackgroundLong-read sequencing technologies have the potential to overcome the limitations of short reads and provide a comprehensive picture of the human genome. However, it remains hard to characterize repetitive sequences by reconstructing genomic structures at high resolution solely from long reads. Here, we developed a localized assembly method (LoMA) that constructs highly accurate consensus sequences (CSs) from long reads. MethodsWe first developed LoMA, by combining minimap2, MAFFT, and our algorithm, which classifies diploid haplotypes based on structural variants and constructs CSs. Using this tool, we analyzed two human samples (NA18943 and NA19240) sequenced with the Oxford Nanopore sequencer. We defined target regions in each genome based on mapping patterns and then constructed a high-quality catalog of the human insertion solely from the long-read data. ResultsThe assessment of LoMA showed high accuracy of CSs (error rate < 0.3%) compared with raw data (error rate > 8%) and superiority to the previous study. The genome-wide analysis of NA18943 and NA19240 identified 5,516 and 6,542 insertions ({zeta} 100 bp) respectively. Most insertions ([~]80%) were derived from the tandem repeat and transposable elements. We also detected processed pseudogenes, insertions in transposable elements, and long insertions (> 10 kbp). Further, our analysis suggested that short tandem duplications were association with gene expression and transposons. ConclusionsOur analysis showed that LoMA constructs high-quality sequences from long reads with substantial errors. This study revealed the true structures of insertions with high accuracy and inferred mechanisms for the insertions. Our approach contributes to the future human genome studies. LoMA is available at our GitHub page: https://github.com/kolikem/loma.

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bioRxiv2023

De novo genome assembly and comparative genomics for a colonial ascidian

Ascidians have the potential to reveal fundamental biological insights related to coloniality, regeneration, immune function, and the evolution of these traits. This study implements a hybrid assembly technique to produce a genome assembly and annotation for the botryllid ascidian, Botrylloides violaceus. A hybrid genome assembly was produced using Illumina, Inc. short and Oxford Nanopore Technologies long-read sequencing technologies. The resulting assembly is comprised of 831 contigs, has a total length of 121 Mbp, N50 of 1 Mbp and a BUSCO score of 96.1%. Genome annotation identified 13K protein-coding genes. Comparative genomic analysis with other tunicates reveals patterns of conservation and divergence within orthologous gene families even among closely related species. Characterization of the Wnt gene family, encoding signaling ligands involved in development and regeneration, reveals conserved patterns of subfamily presence and gene copy number among botryllids. This supports the use of genomic data from non-model organisms in the investigation of biological phenomena.

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bioRxiv2023

Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet's whelk

Next-generation sequencing technologies, such as Nanopore MinION, Illumina Hiseq and Novaseq, and PacBio Sequel II, hold immense potential for advancing genomic research on non-model organisms, including the vast majority of marine species. However, application of these technologies to marine invertebrate species is often impeded by challenges in extracting and purifying their genomic DNA due to high polysaccharide content and other secondary metabolites. In this study, we help resolve this issue by developing and testing DNA extraction protocols for Kellets whelk (Kelletia kelletii), a subtidal gastropod with ecological and commercial importance, by comparing four DNA extraction methods commonly used in marine invertebrate studies. We identified an optimized protocol that balances efficiency, cost, and DNA extraction quality; the Salting out protocol. We validated the protocol using an independent set of tissue samples, then applied it to extract high-molecular-weight (HMW) DNA from over three thousand Kellets whelk tissue samples. The protocol demonstrated scalability and, with added clean-up, suitability for RAD-seq, GT-seq, as well as whole genome sequencing using both long read (ONT MinION) and short read (Illumina Novaseq) sequencing platforms. Our findings offer a robust and versatile DNA extraction and clean-up protocol for supporting genomic research efforts on non-model marine organisms, to help mediate the under-representation of invertebrates in genomic studies.

genomics↗

bioRxiv2023

Genome report: Whole genome sequence and annotation of Penstemon davidsonii

Penstemon is the most speciose flowering plant genus endemic to North America. Penstemon species diverse morphology and adaptation to various environments have made them a valuable model system for studying evolution, but the absence of publicly available reference genomes limits possible research directions. Here we report the first reference genome assembly and annotation for Penstemon davidsonii. Using PacBio long-read sequencing and Hi-C scaffolding technology, we constructed a de novo reference genome of 437,568,744 bases, with a contig N50 of 40 Mb and L50 of 5. The annotation includes 18,199 gene models, and both the genome and transcriptome assembly contain over 95% complete eudicot BUSCOs. This genome assembly will serve as a valuable reference for studying the evolutionary history and genetic diversity of the Penstemon genus.

genomics↗

bioRxiv2023

Interactive visualization of whole eukaryote genome alignments using NCBI's Comparative Genome Viewer (CGV)

We report a new visualization tool for analysis of whole genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) (https://ncbi.nlm.nih.gov/genome/cgv/). CGV visualizes pairwise same-species and cross-species alignments provided by NCBI using assembly alignment algorithms developed by us and others. Researchers can examine the alignments between the two assemblies using two alternate views: a chromosome ideogram- based view or a 2D genome dotplot. Whole genome alignment views expose large structural differences spanning chromosomes, such as inversions or translocations. Users can also navigate to regions of interest, where they can detect and analyze smaller-scale deletions and rearrangements within specific chromosome or gene regions. RefSeq or user-provided gene annotation is displayed in the ideogram view where available. CGV currently provides approximately 700 alignments from over 300 animal, plant, and fungal species. CGV and related NCBI viewers are undergoing active development to further meet needs of the research community in comparative genome visualization.

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bioRxiv2024

Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe

Genomic resources are important for evaluating genetic diversity and supporting conservation efforts. The garden dormouse (Eliomys quercinus) is a small rodent that has experienced one of the most severe modern population declines in Europe. We present a high-quality haplotype-resolved reference genome for the garden dormouse, and combine comprehensive short and long-read transcriptomics datasets with homology-based methods to generate a highly complete gene annotation. Demographic history analysis of the genome revealed a sharp population decline since the last interglacial, indicating an association between colder climates and population declines prior to anthropogenic influence. Using our genome and genetic data from 100 individuals, largely sampled in a citizen-science project across the contemporary range, we conducted the first population genomic analysis for this species. We found clear evidence for population structure across the species core Central European range. Notably, our data shows that the Alpine population, characterized by strong differentiation and reduced genetic diversity, is reproductively isolated from other regions and likely represents a differentiated evolutionary significant unit (ESU). The predominantly declining Eastern European populations also show signs of recent isolation, a pattern consistent with a range expansion from Western to Eastern Europe during the Holocene, leaving relict populations now facing local extinction. Overall, our findings suggest that garden dormouse conservation may be enhanced in Europe through designation of ESUs.

genomics↗

bioRxiv2024

Genetic Dissection of Heat Stress Tolerance in Soybean through Genome-Wide Association Studies and the Use of Genomic Prediction to Enhance Breeding Applications

Rising temperatures and associated heat stress pose an increasing threat to soybean [Glycine max L. (Merr.)] productivity. Due to a limited choice of mitigation strategies, the primary arsenal in crop protection comes from improved genetic stress tolerance. Despite this current and looming threat to soybean production, limited studies have examined the genetics of heat stress tolerance. There is a need to conduct large-scale germplasm screening and genetic studies, including genome-wide association mapping and genomic prediction, to identify genomic regions and useful markers associated with heat tolerance traits that can be utilized in soybean breeding programs. We screened a diverse panel of 450 soybean accessions from MG 0-IV to dissect the genetic architecture of physiological and growth-related traits under optimal and heat stress temperatures and study trait relationships and predictive ability. The genetic architecture information of the response to heat revealed in this study provides insights into the genetics of heat stress tolerance. Thirty-seven significant SNPs were detected, with 20 unique SNPs detected in optimal, 16 detected in heat stress, and a single SNP detected for a heat tolerance index. Only one significant SNP was identified across temperature treatments indicating a genetic divergence in soybean responses to temperature. The genomic prediction worked well for biomass traits, but physiological traits associated with heat stress had poor model accuracy. Through our phenotyping efforts, we identified heat tolerant soybean accessions. The identification of heat tolerant accessions and significant SNPs are useful in heat tolerant variety development through marker-assisted and genomic selection. Core ideasO_LISoybean exhibit phenotypic diversity in response to heat stress. C_LIO_LILarge scale phenotypic screening identified heat tolerant accessions. C_LIO_LIPreviously unreported QTL and SNP associated with biomass and physiological parameters under heat stress are reported. C_LIO_LIGenomic prediction shows promise in abiotic stress breeding applications. C_LI

genomics↗

bioRxiv2024

First genome assembly of the order Strepsiptera using PacBio HiFi reads reveals a miniature genome

Twisted-wing insects (Strepsiptera) are an enigmatic order of parasites with unusual life histories and striking sexual dimorphism. Males emerge from hosts as free-living winged adults, while females from most species remain as endoparasites that retain larval traits. Due to scarce genomic data and phylogenetic controversies, Strepsiptera was only recently placed as the closest living relative to beetles (Coleoptera). Here, we report the first PacBio HiFi genome assembly of the strepsipteran Xenos peckii (Xenidae). This de novo assembly size is 72.1 Mb, with a BUSCO score of 87.4%, N50 of 7.3 Mb, 23.4% GC content and 38.41% repeat content. We identified 8 contigs that contain > 75% of the assembly and reflect the haploid chromosome number reported from karyotypic data, and 3 contigs that exhibit sex chromosome coverage patterns. Additionally, the mitochondrial genome is 16,111 bp long and has 34 genes. This long-read assembly for Strepsiptera reveals a miniature genome and provides a unique tool to understand complex genome evolution associated with a parasitic lifestyle and extreme sexual dimorphism.

genomics↗

bioRxiv2024

A chromosome-level genome assembly of Dracaena cambodiana and comparative genomics analysis highlights the distinct biological features of two resource species of dragon's blood

This study reports a chromosome-level genome for Dracaena cambodiana, one of two typical dracaena species in China. This work will help to deepen the understanding of the dracaena species and the conservation and development of plant resources. The final assembly consisted of 54 scaffolds, spanning 1.08 Gb, with a scaffold N50 size of 52.29 Mb, encoded 36860 predicted protein-coding genes. A total of 1,064,810,157 bp of genome sequences were located on 20 chromosomes (2n = 40), accounting for 98.46%. We investigate the possible mechanisms of the longevity of dracaena, the longest-lived plant in the world, which involve DNA repair and post-translational modification. We also performed comparative genomic analysis of the previously assembled genome of Dracaena cochinchinesis with this genome, and found that the two involved interaction of plant-pathogen interaction and ubiquitin mediated proteolysis, which may reveal why Dracaena has environmental adaptability and longevity characteristics.

genomics↗

bioRxiv2024

Complete Reference Genome and Pangenome Expand Biologically Relevant Information for Genome-Wide DNA Methylation Analysis Using Short-Read Sequencing and Array Data

BackgroundThe new complete telomere-to-telomere human genome assembly, T2T-CHM13, and the first draft of the human pangenome reference provide unique opportunities to update the reference genome for epigenetics investigations and clinical research. However, it is largely unclear how these reference genome updates may impact DNA methylation (DNAm) analysis. ResultsCompared to the previous GRCh38 assembly, we found an average increase of 7.4% (range 5.4%-9.9% across samples and sequencing methods) in the number of CpGs genome-wide using T2T-CHM13 with data from four commonly used short-read sequencing DNAm profiling methods. The increase in number of CpGs facilitated discovery of 88 new differentially methylated CpGs within cancer driver genes in an epigenome-wide association study (EWAS) of colon cancer. Further, by aligning probe sequences from the commonly used and recently released Illumina DNAm arrays to T2T-CHM13 and GRCh38, we showed the enhanced utility of T2T-CHM13 for evaluation of potential probe cross-reactivity (i.e., where probes match multiple regions) and mismatch (i.e., where probes do not perfectly match the target region), resulting in the identification of new and more reproducible sets of unambiguous probes (i.e., probes uniquely mapping to the target region) (HM450K, n = 430,719; EPIC, n = 777,491; EPICv2, n = 859,216). In EWASs of 24 cancer types, an average of 945 additional differentially methylated CpG sites were identified in the new unambiguous probe set rather than in the GRCh38-based unambiguous probe set, with enrichments in cancer driver genes and cancer signaling pathways. Moreover, the pangenome called 4.5% more CpGs on average in short-read sequencing data than T2T-CHM13 and identified cross-population and population-specific unambiguous probes in DNAm arrays, owing to its improved representation of genetic diversity. These additional CpGs were overlapped with the promoters and gene bodies of various biologically and medically relevant genes and pangenome-based unambiguous probes can potentially facilitate the discovery of DNAm alterations in more than 200 cancer driver genes in each cancer type. ConclusionsUse of T2T-CHM13 and pangenome references can benefit epigenome-wide association studies by including CpGs previously unobserved in short-read sequencing data and by improving the identification of unambiguous probes for DNAm arrays, thus expanding biologically relevant information. This study highlights the practical applications of T2T-CHM13 and pangenome for genome biology and provides a basis for expansion of epigenetics investigations.

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bioRxiv2025

A high-quality reference genome and comparative genomics of the widely-farmed bandedcricket (Gryllodes sigillatus) identifies selective breeding targets

Farmed insects have gained attention as an alternative, sustainable source of protein with a lower carbon footprint than traditional livestock. We present a high-quality reference genome for one of the most commonly farmed insects, the banded cricket Gryllodes sigillatus. In addition to its agricultural importance, G. sigillatus is also a model in behavioural and evolutionary ecology research on reproduction and mating systems. We report comparative genomic analyses that clarify the banded crickets evolutionary history, identify gene family expansions and contractions unique to this lineage, associate these with agriculturally important traits, and identify targets for genome-assisted breeding efforts. The high-quality G. sigillatus genome assembly plus accompanying comparative genomic analyses serve as foundational resources for both applied and basic research on insect farming and behavioural biology, enabling researchers to pinpoint trait-associated genetic variants, unravel functional pathways governing those phenotypes, and accelerate selective breeding efforts to increase the efficacy of large-scale insect farming operations.

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bioRxiv2025

The telomere-to-telomere genome and lifestyle transcriptome profiling of Discula destructiva Redlin provide modern molecular and genomic context to a historical epidemic

Fungal pathogens have dramatically altered forests worldwide, yet the mechanisms underlying their virulence remain poorly understood. From the 1970s to the early 2000s, dogwood anthracnose, caused by Discula destructiva Redlin, devastated flowering and Pacific dogwoods (Cornus florida L. and C. nuttallii Aud., respectively). Despite the impacts of D. destructiva and other phytopathogens on forest ecosystems, genomic resources remain limited, hindering efforts to understand pathogenicity. The goal of this study was to evaluate the historical D. destructiva epidemic through a modern genomics lens by uncovering virulence- associated genes that likely contributed to its rapid spread across native dogwoods. We therefore utilized PacBio HiFi and Proximo Hi-C sequencing to assemble the first telomere-to-telomere, chromosome-scale genome for D. destructiva isolate AS111. The resulting 46.655 Mb assembly comprised eight chromosomes with an overall BUSCO completeness of 97.64%. We also identified 10,373 predicted gene models with an overall BUSCO completeness of 96.45%. To investigate gene expression across distinct life cycle phases, reproductive (sporulating) and vegetative (nonsporulating), we conducted RNA sequencing and identified 240 differentially expressed genes (padj < 0.05). GO enrichment revealed 162 upregulated genes during sporulation linked to plant cell wall degradation and sugar metabolism, whereas 78 downregulated genes were linked to electron carrier activity and redox balance. Among these 240 genes, 117 genes had predicted protein sequences that were also identified as a candidate virulence factor, including signal peptides, carbohydrate-active enzymes (CAZymes), and effectors, highlighting the role of sporulation-associated gene expression in D. destructiva virulence. Together, these findings suggest that the reproductive phase primes D. destructiva for host invasion and ecological persistence, which may influence its success as a forest pathogen. Author SummaryForest pathogens threaten ecosystems worldwide and cause extensive ecological and economic damage. Since the 1970s, native dogwood populations in North America have been devastated by dogwood anthracnose, caused by the exotic fungal pathogen Discula destructiva. Discula destructiva is just one of many destructive fungal pathogens in the order Diaporthales, which includes other noteworthy pathogens that cause chestnut blight (Cryphonectria parasitica) and butternut canker (Ophiognomonia clavigignenti-juglandacearum). Despite the widespread impact of fungal diseases, little is known about the genetic factors that drive their spread and severity. To help address this gap, we generated the first telomere-to-telomere, chromosome- scale genome assembly of D. destructiva and analyzed gene expression across distinct life cycle phases: reproductive (sporulating) and vegetative (nonsporulating) growth. Our findings revealed key sporulation-associated genes and virulence factors that may facilitate host infection and underscore the importance of sporulation in the pathogenicity of D. destructiva. These insights improve our understanding of the mechanisms that drive disease development, influence how fungal pathogens such as D. destructiva establish and persist in forest ecosystems, and provide a foundation for future comparative genomics among other devastating pathogens in Diaporthales.

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bioRxiv2025

Dynamics of complex genomic regions in giant genomes: MHC evolution in newts

Major Histocompatibility Complex (MHC) molecules are central to vertebrate adaptive immunity and MHC genes serve are key models in evolutionary genomics, offering insight into birth-and-death evolution, gene duplication, and the maintenance of genetic diversity. However, the organization and evolution of the MHC in species with giant genomes, such as salamanders, remain poorly understood. Here, we use comparative genomics, ontogenetic, tissue expression and polymorphism data across seven newt species to investigate MHC evolution in this group. Contrary to earlier suggestions of a massively expanded MHC in salamanders, we find that the core MHC region remains relatively compact, demonstrating that genome gigantism does not scale proportionally in this region. Our finding also challenges the model of coevolution between a single classical MHC-Ia gene and antigen processing genes (APGs), revealing instead several polymorphic and highly expressed putative MHC-Ia located at varying distances from the APGs. MHC-I genes exhibit lineage-specific duplications and signs of concerted evolution, resulting in poorly resolved phylogenies. In contrast, MHC-II genes are more conserved and exhibit extensive trans-species polymorphism. Expression and polymorphism patterns identify putative nonclassical MHC-Ib genes, likely repeatedly derived from MHC-Ia genes--paralleling patterns seen in mammals, but contrasting with the situation in fish and Xenopus frogs. In all seven species, some MHC-Ib genes show high relative expression during the larval stage but not at adulthood, suggesting a role in larval immunity. Our results underscore the importance of salamanders for understanding the evolution of complex regions in giant genomes and the architecture of the tetrapod MHC.

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bioRxiv2017

A new standard for crustacean genomes: the highly contiguous, annotated genome assembly of the clam shrimp Eulimnadia texana reveals HOX gene order and identifies the sex chromosome

Vernal pool clam shrimp (Eulimnadia texana) are a promising model system due to their ease of lab culture, short generation time, modest sized genome, a somewhat rare stable androdioecious sex determination system, and a requirement to reproduce via desiccated diapaused eggs. We generated a highly contiguous genome assembly using 46X of PacBio long read data and 216X of Illumina short reads, and annotated using Illumina RNAseq obtained from adult males or hermaphrodites. 85% of the 120Mb genome is contained in the largest 8 contigs, the smallest of which is 4.6Mb. The assembly contains 98% of transcripts predicted via RNAseq. This assembly is qualitatively different from scaffolded Illumina assemblies: it is produced from long reads that contain sequence data along their entire length, and is thus gap free. The contiguity of the assembly allows us to order the HOX genes within the genome, identifying two loci that contain HOX gene orthologs, and which approximately maintain the order observed in other arthropods. We identified a partial duplication of the Antennapedia gene adjacent to the few genes homologous to the Bithorax locus. Because the sex chromosome of an androdioecious species is of special interest, we used existing allozyme and microsatellite markers to identify the E. texana sex chromosome, and find that it comprises nearly half of the genome of this species. Linkage patterns indicate that recombination is extremely rare and perhaps absent in hermaphrodites, and as a result the location of the sex determining locus will be difficult to refine using recombination mapping.

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bioRxiv2018

Genome-wide enhancer - gene regulatory maps in two vertebrate genomes

The spatiotemporal expression of genes is controlled by enhancer sequences that bind transcription factors. Identifying the target genes of enhancers remains difficult because enhancers regulate gene expression over long genomic distances. To address this, we used an evolutionary approach to build two genome-wide maps of enhancer-gene associations in the human and zebrafish genomes. Enhancers were identified using sequence conservation, and linked to their predicted target genes using PEGASUS, a bioinformatics method that relies on evolutionary conservation of synteny. The analysis of these maps revealed that the number of enhancers linked to a gene correlate with its expression breadth. Comparison of both maps identified hundreds of vertebrate ancestral regulatory relationships from which we could determine that enhancer-gene distances scale with genome size despite strong positional conservation. The two maps represent a resource for further studies, including the prioritisation of sequence variants in whole genome sequence of patients affected by genetic diseases.

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bioRxiv2018

Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data

The Wheat@URGI portal (https://wheat-urgi.versailles.inra.fr) has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.

bioinformatics↗

bioRxiv2018

De Novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole genome duplication

For over a thousand years throughout Asia, the common goldfish (Carassius auratus) was raised for both food and as an ornamental pet. Selective breeding over more than 500 years has created a wide array of body and pigmentation variation particularly valued by ornamental fish enthusiasts. As a very close relative of the common carp (Cyprinus carpio), goldfish shares the recent genome duplication that occurred approximately 14-16 million years ago (mya) in their common ancestor. The combination of centuries of breeding and a wide array of interesting body morphologies is an exciting opportunity to link genotype to phenotype as well as understanding the dynamics of genome evolution and speciation. Here we generated a high-quality draft sequence of a \"Wakin\" goldfish using 71X PacBio long-reads. We identified 70,324 coding genes and more than 11,000 non-coding transcripts. We found that the two sub-genomes in goldfish retained extensive synteny and collinearity between goldfish and zebrafish. However, \"ohnologous\" genes were lost quickly after the carp whole-genome duplication, and the expression of 30% of the retained duplicated gene diverged significantly across seven tissues sampled. Loss of sequence identity and/or exons determined the divergence of the expression across all tissues, while loss of conserved, non-coding elements determined expression variance between different tissues. This draft assembly also provides an important resource for comparative genomics with the very commonly used zebrafish model (Danio rerio), and for understanding the underlying genetic causes of goldfish variants.

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