SEARCH · bioRxiv Science

Results for “genomics”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,045 records · Page 58Linked to original sources

bioRxiv2023

Plant genome evolution in the genus Eucalyptus driven by structural rearrangements that promote sequence divergence

Genomes have a highly organised architecture (non-random organisation of functional and non-functional genetic elements within chromosomes) that is essential for many biological functions, particularly, gene expression and reproduction. Despite the need to conserve genome architecture, a surprisingly high level of structural variation has been observed within species. As species separate and diverge, genome architecture also diverges, becoming increasingly poorly conserved as divergence time increases. However, within plant genomes, the processes of genome architecture divergence are not well described. Here we use long-read sequencing and de novo assembly of 33 phylogenetically diverse, wild and naturally evolving Eucalyptus species, covering 1-50 million years of diverging genome evolution to measure genome architectural conservation and describe architectural divergence. The investigation of these genomes revealed that following lineage divergence genome architecture is highly fragmented by rearrangements. As genomes continue to diverge, the accumulation of mutations and subsequent divergence beyond recognition of rearrangements becomes the primary driver of genome divergence. The loss of syntenic regions also contribute to genome divergence, but at a slower pace than rearrangements. We hypothesise that duplications and translocations are potentially the greatest contributors to Eucalyptus genome divergence.

genomics↗

bioRxiv2023

Study on genetic differentiation of Schistosome japonicum intermediate hosts Oncomelania hupensis robertsoni in hilly regions of China: using the complete mitochondrial genome

ObjectiveOncomelania hupensis robertsoni is the only intermediate host of Schistosoma japonicum in western China, its genetic differentiation directly impacts the susceptibility of Schistosoma japonicum. This study aimed to sequence the complete mitochondrial genome of Oncomelania hupensis robertsoni Yunnan strain and analyze the genetic differentiation of Oncomelania hupensis robertsoni in hilly regions of China. MethodsSamples were from 14 administrative villages in Yunnan Province of China, with 30 Oncomelania hupensis per village, and the complete mitochondrial genome was sequenced. Additional, we retrieved 14 other region Oncomelania hupensis of complete mitochondrial sequences from GenBank, and a comprehensive analysis of the genetic differentiation of Oncomelania hupensis robertsoni was conducted by constructing phylogenetic trees, calculating genetic distances, and analyzing homogeneity. ResultsA total of 26 complete mitochondrial sequences were determined. The length of genome ranged from 15,181 to 15,187 bp, and the base composition of the genome was A+T (67.5%) and G+C content (32.5%). This genome encoded 37 genes, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a non-coding region rich in A+T. Using the Philippines genotypes as outgroup, the phylogenetic trees and homology analysis confirmed the existence of two distinct phylogroups, Oncomelania hupensis robertsoni and the remaining 9 provincial genotypes. Oncomelania hupensis robertsoni is subdivided into Oncomelania hupensis robertsoni Yunnan strain and Sichuan strain, with a genetic distance of 0.0834. Oncomelania hupensis robertsoni Yunnan strain is subdivided into two subbranches, "Yunnan North" and "Yunnan South", with a genetic distance of 0.0216, and the samples exhibited over 97% homology. ConclusionOncomelania hupensis robertsoni Yunnan strain exhibits a higher level of genetic homology and clear north-south differentiation, the distribution characteristics were closely associated with watershed distribution. This work reported the first mitochondrial genome of Oncomelania hupensis robertsoni Yunnan strain, which could be used as an important reference genome for Oncomelania hupensis, and also provide a theoretical basis for explaining the distribution pattern of Oncomelania hupensis robertsoni and control of schistosomiasis. Author SummaryOncomelania hupensis (O. hupensis) is the only intermediate host of Schistosoma japonicum (S. japonicum), O. hupensis residing in different geographical regions display morphological differences and genetic variations, along with varying susceptibility to S. japonicum. In this study, we sequenced 26 complete mitochondrial genome of O. hupensis robertsoni Yunnan strain (O. h. r. Yunnan strain), the length of genome ranged from 15,181 to 15,187 bp, and the base composition of the genome was A+T (67.5%) and G+C content (32.5%). This genome encoded 37 genes, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a non-coding region rich in A+T. Additional, we retrieved 14 other region O. hupensis of complete mitochondrial sequences from GenBank. The phylogenetic trees and homology analysis confirmed that O. hupensis robertsoni is subdivided into Yunnan strain and Sichuan strain, and O. h. r. Yunnan strain is subdivided into two subbranches, "Yunnan North" and "Yunnan South", the samples exhibited over 97% homology. This work reported the first mitochondrial genome of O. h. r. Yunnan strain, which could be used as an important reference genome for O. hupensis, and also provide a molecular biology-based theoretical foundation for understanding the genetic differentiation of O. hupensis.

genomics↗

bioRxiv2024

Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles

Environmental viruses (primarily bacteriophages) are widely recognized as playing an important role in ecosystem homeostasis through the infection of host cells. However, the majority of environmental viruses are still unknown as their mosaic structure and frequent mutations in their sequences hinder genome construction in current metagenomics. To enable the large-scale acquisition of environmental viral genomes, we developed a new single-viral genome sequencing platform with microfluidic-generated gel beads. Amplification of individual DNA viral genomes in mass-produced gel beads allows high-throughput genome sequencing compared to conventional single-virus genomics. The sequencing analysis of river water samples yielded 1431 diverse viral single-amplified genomes, while viral metagenomics recovered 100 viral metagenome-assembled genomes at the comparable sequence depth. The 99.5% of viral single-amplified genomes were determined novel at the species level, most of which could not be recovered by a metagenomic assembly. The large-scale acquisition of diverse viral genomes identified protein clusters commonly detected in different viral strains, allowing the gene transfer to be tracked. Moreover, comparative genomics within the same viral species revealed that the profiles of various methyltransferase subtypes were diverse, suggesting an enhanced escape from host bacterial internal defense mechanisms. Our use of gel bead-based single-virus genomics will contribute to exploring the nature of viruses by accelerating the accumulation of draft genomes of environmental DNA viruses.

genomics↗

bioRxiv2024

De novo genome assembly for an endangered lemur using portable nanopore sequencing in rural Madagascar

As one of the most threatened mammalian taxa, lemurs of Madagascar are facing unprecedented anthropogenic pressures. To address conservation imperatives such as this, researchers have increasingly relied on conservation genomics to identify populations of particular concern. However, many of these genomic approaches necessitate high-quality genomes. While the advent of next generation sequencing technologies and the resulting reduction of associated costs have led to the proliferation of genomic data and high-quality reference genomes, global discrepancies in genomic sequencing capabilities often result in biological samples from biodiverse host countries being exported to facilities in the Global North, creating inequalities in access and training within genomic research. Here, we present the first reference genome for the endangered red-fronted brown lemur (Eulemur rufifrons) from sequencing efforts conducted entirely within the host country using portable Oxford Nanopore sequencing. Using an archived E. rufifrons specimen, we conducted long-read, nanopore sequencing at the Centre ValBio Research Station near Ranomafana National Park, in rural Madagascar, generating over 750 Gb of sequencing data from 10 MinION flow cells. Exclusively using this long-read data, we assembled 2.21 gigabase, 20,330-contig nuclear assembly with an N50 of 98.9 Mb and a 17,108 bp mitogenome. The nuclear assembly had 31x average coverage and was comparable in completeness to other primate reference genomes, with a 95.47% BUSCO completeness score for primate-specific genes. As the first reference genome for E. rufifrons and the only annotated genome available for the speciose Eulemur genus, this resource will prove vital for conservation genomic studies while our efforts exhibit the potential of this protocol to address research inequalities and build genomic capacity.

genomics↗

bioRxiv2024

Repeat-rich regions cause false positive detection of NUMTs - a case study in amphibians using an improved cane toad reference genome

Mitochondrial DNA (mtDNA) has been widely used in genetics research for decades. Contamination from nuclear DNA of mitochondrial origin (NUMT) can confound studies of phylogenetic relationships and mtDNA heteroplasmy. Homology searches with mtDNA are widely used to detect NUMTs in the nuclear genome. Nevertheless, false positive detection of NUMTs is common when handling repeat-rich sequences, whilst fragmented genomes might result in missing true NUMTs. In this study, we investigated different NUMT detection methods and how the quality of the genome assembly affects them. We presented an improved nuclear genome assembly (aRhiMar1.3) of the invasive cane toad (Rhinella marina) with additional long-read Nanopore and 10x linked-read sequencing. The final assembly was 3.47 Gb in length with 91.3% of tetrapod universal single-copy orthologs (n=5,310), indicating the gene-containing regions were well assembled. We used three complementary methods (NUMTFinder, dinumt and PALMER) to study the NUMT landscape of the cane toad genome. All three methods yielded consistent results, showing very few NUMTs in the cane toad genome. Furthermore, we expanded NUMT detection analyses to other amphibians and confirmed a weak relationship between genome size and the number of NUMTs present in the nuclear genome. Amphibians are repeat-rich, and we show that the number of NUMTs found in highly repetitive genomes is prone to inflation when using homology-based detection without filters. Together, this study provides an exemplar of how to robustly identify NUMTs in complex genomes when confounding effects on mtDNA analyses are a concern. SignificanceThis study uses an updated cane toad nuclear genome assembly and multiple NUMT detection methods to confirm a lack of NUMTs that might confound the use of mtDNA as a population genetic marker in the cane toad. We provide an exemplar study for NUMT detection accounting for genome assembly quality and composition, and highlight the risks of using BLASTN-based approaches in highly repetitive nuclear genomes.

genomics↗

bioRxiv2024

The first de novo HiFi genome assemblies for three clownfish-hosting sea anemone species (Anthozoa: Actiniaria)

The symbiosis between clownfish and giant tropical sea anemones (Order Actiniaria) is one of the most iconic on the planet. Distributed on tropical reefs, 28 species of clownfishes form obligate mutualistic relationships with 10 nominal species of venomous sea anemones. Our understanding of the symbiosis is limited by the fact that most research has been focused on the clownfishes. Chromosome scale reference genomes are available for all clownfish species, yet there are no published reference genomes for the host sea anemones. Recent studies have shown that the clownfish-hosting sea anemones belong to three distinct clades of sea anemones that have evolved symbiosis with clownfishes independently. Here we present the first high quality long read assemblies for three species of clownfish hosting sea anemones belonging to each of these clades: Entacmaea quadricolor, Stichodactyla haddoni, Radianthus doreensis. PacBio HiFi sequencing yielded 1,597,562, 3,101,773, and 1,918,148 million reads for E. quadricolor, S. haddoni, and R. doreensis, respectively. All three assemblies were highly contiguous and complete with N50 values above 4Mb and BUSCO completeness above 95% on the Metazoa dataset. Genome structural annotation with BRAKER3 predicted 20,454, 18,948 and 17,056 protein coding genes in E. quadricolor, S. haddoni and R. doreeensis genome, respectively. These new resources will form the basis of comparative genomic analyses that will allow us to deepen our understanding of this mutualism from the host perspective. SignificanceChromosome-scale genomes are available for all 28 clownfish species yet there are no high-quality reference genomes published for the clownfish-hosting sea anemones. The lack of genomic resources impedes our ability to understand evolution of this iconic symbiosis from the host perspective. The clownfish-hosting sea anemones belong to three clades of sea anemones that have evolved mutualism with clownfish independently. Here we assembled the first high-quality long-read genomes for three species of host sea anemones each belonging to a different host clade: Entacmaea quadricolor, Stichodactyla haddoni, Radianthus doreensis. These resources will enable in depth comparative genomics of clownfish-hosting sea anemones providing a critical perspective for understanding how the symbiosis has evolved. Finally, these reference genomes present a significant increase in the number of high-quality long-read genome assemblies for sea anemones (11 currently published) and double the number of high-quality reference genomes for the sea anemone superfamily Actinoidea.

genomics↗

bioRxiv2025

Ancestral and recent bursts of transposition shaped the massive genomes of plant pathogenic rust fungi

BackgroundTransposable elements (TEs) play a crucial role in genome evolution, influencing gene regulation, diversity, and genome architecture. Rust fungi of the order Pucciniales (Subphylum Pucciniomycotina) are the largest group of obligate biotrophic plant pathogens and harbor some of the largest and most TE-rich genomes - up to 1.2Gb - compared to other fungi. This global genomic expansion contrasts with the smaller genomes and minimal mobilome found in other Pucciniomycotina species. Despite the availability of high-quality genome assemblies, our understanding of TE dynamics in Pucciniales remains limited due to inconsistent and incomplete TE annotations. ResultsWe analyzed the mobilomes of 12 Pucciniomycotina species, producing a manually curated TE library for each genome. In Pucciniales, TEs occupy 47-92% of the genome, whereas 2-36% of TEs are detected in other Pucciniomycotina genomes. The comparison of gene and TE repertoires indicates that TEs, particularly LTR-retrotransposons and TIR-DNA transposons, are the primary contributors to the genome expansion of the Pucciniales. We reconstructed the proliferation histories of TEs in the Pucciniales, combining sequence similarity, clustering, and molecular clock approaches. We highlight recent and ancient TE invasions with some LTR-Gypsy elements predating the divergence of Pucciniomycotina ([~]176 Mya), while most TE accumulation in Pucciniales occurred within the last 50 Mya. However, the TE invasions in the Pucciniales genomes do not seem to result from specific deficiencies in known TE-control mechanisms. ConclusionOur findings uncover extensive TE proliferation in Pucciniales, predominantly driven by LTR-Gypsy expansions. The retention of ancestral TEs and the consistently TE-rich genomes observed in Pucciniales highlight TE proliferation as an ancestral genomic feature in rust fungi.

genomics↗

bioRxiv2025

Two telomere-to-telomere, gap-free genome assemblies and comparisons revealed the conserved key genes associated with sugar accumulation in Rubus genus

For the first time, we assembled two highly continuous, completely gap-free reference genomes of the Rubus subgenus: Rubus hirsutus Thunb. Penglei (XMM) and Rubus eustephanos Focke ex Diels Dahongpao (DHP), which are widely distributed in southern China with similar phenotypic traits (Figures 1A, 1B, and Figure S1), yet ripe fruits display distinct sugar accumulation levels (Table S1), making them ideal candidates for investigating the mechanisms underlying sugar accumulation in the Rubus genus. The XMM (213.53 Mb, 28,204 genes) and DHP (218.26 Mb, 28,569 genes) genomes exhibit close evolutionary relationships, diverging approximately 3.21 Mya. Comparative genomics identified extensive synteny, interspecific structural variations (translocations, inversions, segmental duplications), and presence/absence variation (PAV). Using Hi-C interaction heatmaps and Sanger sequencing, we validated interspecific structural inversions. Additionally, we identified a sugar transporter gene (MFS1), which is present in XMM but absent in DHP. Combined analysis of the gene family expansion/contraction and transcriptome identified two conserved key genes (RhSTP13 and RhSTP7) associated with sugar accumulation in Rubus genus and displayed distinct roles through transient expression assay. To facilitate functional genomics study, we also established a comprehensive Rubus database, RubusDB, a freely accessible repository consolidating all genomic, transcriptomic and phenotypic data of Rubus genus. These findings provide a foundational framework for elucidating the genetic basis of sugar accumulation, genome diversification, and trait improvement in Rubus species. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=170 SRC="FIGDIR/small/646780v2_fig1.gif" ALT="Figure 1"> View larger version (72K): org.highwire.dtl.DTLVardef@1baca20org.highwire.dtl.DTLVardef@2c01eaorg.highwire.dtl.DTLVardef@131dc00org.highwire.dtl.DTLVardef@62a04f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFIGURE 1.C_FLOATNO Phenotypic characterization, de novo genome assemblies, variation, and evolution of Rubus hirsutus Thunb. Penglei (XMM) and Rubus eustephanos Focke ex Diels Dahongpao (DHP). (A) Illustration of XMM whole plants, stem, flower bud and flower, respectively. (B) Illustration of DHP whole plants, stem, flower bud and flower, respectively. (C) The chromosome karyotype analysis of XMM. Bar = 10 {micro}m. (D) Circular diagram of XMM and DHP reference genomes. (a) Chromosomes are represented by centromeres (dark red) and telomeres (blue); (b) CEN18 density; (c) CEN17 density; (d) Gene density; (e) TE density; (f) PAV density; (g) SNP density; (h) Collinear lines at the center of diagram highlight homoeologous chromosomes relationships and non-homoeologous regions. (E) Genomic alignments between XMM and DHP. Inversions, duplications and translocations are marked with orange, blue and green ribbons, respectively. (F) Identification of large inversions in chromosome 7 between XMM and DHP. The three heatmaps show the chromatin interaction matrix, including mapping Hi-C data of DHP against DHP genome (left), mapping Hi-C data of DHP against XMM genome (middle) and mapping Hi-C data of XMM against XMM genome (right). The lower panel illustrates gene alignments between XMM and DHP. (G) Synteny, structural rearrangements, monomer, and identity distribution in the 16-20 Mbp region of chromosome 6 between XMM and DHP. (H) Local genome synteny of chromosome 5, with a structural variation that is present only in XMM. The PAV region includes a gene related to sugar transporter (MFS1, XMM05G025540). (I) Gene-level matchings of MFS genes in the PAVs region between XMM and DHP. (J) Phylogenetic relationships and divergence times between raspberries and other Rosaceae species. The black numbers close to the divergence nodes indicate the divergence times and the red bars represent the 95% confidence intervals. The red and black numbers indicate expanded and contracted ortholog groups at the corresponding node. Scale bar corresponds to 10 Mya. C_FIG

genomics↗

bioRxiv2025

A Chromosome-Scale Genome of Nanomia septata Reveals Extensive Rearrangement But No Clear Driver of the Unique Colony-Level Organization of Siphonophores

Siphonophores (Cnidaria:Hydrozoa) are pelagic colonial marine invertebrates with many highly specialized bodies (zooids) within a single colony. Their unique biology and ecological importance have made them of particular interest. Recent work revealed siphonophore genomes to be larger than in most other cnidarians. To investigate siphonophores genome biology and develop resources for future studies, we sequenced the genome of a single Nanomia septata to chromosome scale. The haploid genome is 1.5GB across 8 chromosomes, a reduction relative to the 15 chromosomes seen in closely related hydrozoan genomes, and is highly rearranged, consistent with multiple mixing events. Genome expansion occurred through intergenic repeat expansion, with protein-coding genes shorter than in most cnidarians. We found no genomic features clearly associated with siphonophores exceptional colony-level complexity. Gene families that play critical roles in cnidarian development have not expanded, and gene proximity was not generally correlated to their expression across zooids, except in male gonophores. To contextualize these observations, we genome sequenced 20 additional Nanomia specimens across the globe and mapped them to our chromosome-scale reference. Population genomic analyses support three previously recognized species of Nanomia, and at least one additional undescribed species. Overlapping geographic distribution of some Nanomia species suggest reproductive isolation in sympatry. Phylogenetic analyses of genome size indicate Nanomia septata and Nanomia cara have similarly large genomes between 1.5-1.7GB, while Nanomia bijuga and an undescribed species show a secondary reduction to 0.7GB. These results highlight how genomic factors have shaped colony organization and genome diversity within Nanomia.

genomics↗

bioRxiv2025

Genome Dynamics and Chromosome Structural Variations in Histoplasma ohiense, a fungal pathogen of humans

Histoplasma is a clinically important but understudied genus of thermally dimorphic human fungal pathogens. Histoplasma species normally transition between a multicellular sporulating hyphal form in the soil and a unicellular pathogenic yeast form in a mammalian host. Little is known about genome plasticity of Histoplasma, which we address in this study with the ultimate goal of increasing our understanding of its pathogenicity. This study addresses the Histoplasma genome and its plasticity to further our understanding Histoplasmas ability to cause severe disease. Here we present the first telomere-to-telomere genome assemblies for Histoplasma ohiense. To analyze genome alterations between isolates, we develop an analysis tool to identify genome discontinuities relative to a reference genome. We utilize this analysis to interrogate the genome of laboratory strains and natural Histoplasma isolates and discover that the previously published reference genome does not completely match the chromosome structure of the majority of isolates, instead harboring reciprocal chromosome translocations. We identify the telomere-to-telomere Histoplasma ohiense reference genome that is most representative of clinical isolates. Additionally, to determine the rate of Histoplasma genomic changes, we sequence 46 passaged isolates and calculate the mutation rate to be 2.6 x10-10 SNP/base/doubling--the first such measurement to our knowledge within the order Onygenales, which encompasses several critical fungal pathogens. Finally, we sequence populations of cells to assess genome stability over the course of a month under both yeast and hyphal growth conditions. Interestingly, we observe that transposon signal is not static over time and instead increases during growth in both the yeast and hyphal forms as well as through morphologic transitions, suggesting an increase in transposon copy number. Taken together, this work highlights the plasticity of the Histoplasma genome and presents a comprehensive genome assembly that is representative of Histoplasma ohiense natural isolates.

genomics↗

bioRxiv2025

Tracing genome size dynamics in sharks and rays with inclusive sequence analysis by the Squalomix Consortium

Genomes have maintained stable sets of protein-coding genes during evolution, while chromosome organization and genome size vary drastically. Changes in genome size are often attributed to variable amounts of repetitive sequences, including transposable elements. However, it remains poorly understood how such changes were accommodated while maintaining other genomic components. Elasmobranchs, including sharks, rays, and skates, exhibit high among-species variation of genome size and high within-species variation of chromosome length, offering a unique study system to address the question. In this study, we present the first whole genome sequences of the whitebelly skate with remarkably small genome size among elasmobranchs (2.2 Gb), and the red stingray. These chromosome-scale assemblies enabled the assessment of genomic compositions including centromeres and non-coding elements, which revealed notable profiles of tRNA loci and unbiased intragenomic distribution of transposons in elasmobranch genomes. Comparative analyses across these species revealed a shared genomic architecture characterized by correlations of intergenic and intronic sequence lengths with chromosome sizes, with repetitive element accumulation in elongated regions. We analyzed tandemly duplicated genes with high copy number variability. This genome-wide survey revealed the tendency for more frequent tandem gene duplications along with genome size expansion. We document the batoid HoxC cluster in the red stingray genome, which has undergone extensive repetitive element invasion and co-localizes with the HoxB cluster on a sex chromosome. Our study demonstrates an inclusive analysis encompassing both coding and non-coding regions, adaptable to more species in the taxon and a basis for molecular-level understanding on phenotypic diversity of elasmobranchs.

genomics↗

bioRxiv2018

The Genome of the Human Pathogen Candida albicans is Shaped by Mutation and Cryptic Sexual Recombination

The opportunistic fungal pathogen Candida albicans lacks a conventional sexual program and is thought to evolve, at least primarily, through the clonal acquisition of genetic changes. Here, we performed an analysis of heterozygous diploid genomes from 21 clinical isolates to determine the natural evolutionary processes acting on the C. albicans genome. Consistent with a model of inheritance by descent, most single nucleotide polymorphisms (SNPs) were shared between closely related strains. However, strain-specific SNPs and insertions/deletions (indels) were distributed non-randomly across the genome. For example, base substitution rates were higher in the immediate vicinity of indels, and heterozygous regions of the genome contained significantly more strain-specific polymorphisms than homozygous regions. Loss of heterozygosity (LOH) events also contributed substantially to genotypic variation, with most long-tract LOH events extending to the ends of the chromosomes suggestive of repair via break-induced replication. Importantly, some isolates contained highly mosaic genomes and failed to cluster closely with other isolates within their assigned clades. Mosaicism is consistent with strains having experienced inter-clade recombination during their evolutionary history and a detailed examination of nuclear and mitochondrial genomes revealed striking examples of recombination. Together, our analyses reveal that both (para)sexual recombination and mitotic mutational processes drive evolution of this important pathogen in nature. To further facilitate the study of genome differences we also introduce an online platform, SNPMap, to examine SNP patterns in sequenced C. albicans genomes.\n\nAUTHOR SUMMARYMutations introduce variation into the genome upon which selection can act. Defining the nature of these changes is critical for determining species evolution, as well as for understanding the genetic changes driving important cellular processes such as carcinogenesis. The fungus Candida albicans is a heterozygous diploid species that is both a frequent commensal organism and a prevalent opportunistic pathogen. Prevailing theory is that C. albicans evolves primarily through the gradual build-up of mutations, and a pressing question is whether sexual or parasexual processes also operate within natural populations. Here, we determine the evolutionary patterns of genetic change that have accompanied species evolution in nature by examining genomic differences between clinical isolates. We establish that the C. albicans genome evolves by a combination of base-substitution mutations, insertions/deletion events, and both short-tract and long-tract loss of heterozygosity (LOH) events. These mutations are unevenly distributed across the genome, and reveal that non-coding regions and heterozygous regions are evolving more quickly than coding regions and homozygous regions, respectively. Furthermore, we provide evidence that genetic exchange has occurred between isolates, establishing that sexual or parasexual processes have transpired in C. albicans populations and contribute to the diversity of both nuclear and mitochondrial genomes.

genomics↗

bioRxiv2018

Multi-species mosaicism of evolutionary origins of genomic loci harboring 59,732 human-specific regulatory sequences reflects a complex continuous speciation process of the human lineage

Nearly sixty thousand genomic regions harboring various types of candidate human-specific regulatory sequences (HSRS) have been identified using high-resolution sequencing technologies and methodologically diverse comparative analyses of human and non-human primates reference genomes. Here, the systematic analysis of evolutionary origins of 59,732 genomic loci harboring candidate HSRS has been performed to identify genomic sequences that were either inherited from extinct common ancestors (ECAs) or created de novo in human genomes after the split of human and chimpanzee lineages. Present analyses revealed thousands of HSRS that appear inherited from ECAs yet bypassed genomes of our closest evolutionary relatives, Chimpanzee and Bonobo, presumably due to the incomplete lineage sorting and/or species-specific loss or regulatory DNA. The bypassing pattern is particularly prominent for HSRS putatively associated with development and functions of human brain. Significant fractions of retrotransposon-derived loci that are transcriptionally-active in human dorsolateral prefrontal cortex are highly conserved in genomes of Gorilla, Orangutan, Gibbon, and Rhesus (1,688; 1,371; 1,148; and 1,045 loci, respectively), yet they are absent in genomes of both Chimpanzee and Bonobo. These observations were independently corroborated by common evolutionary patterns of 248 insertions sites of African ape-specific retrovirus PtERV1 (45.9%; p = 1.03E-44) intersecting genomic regions harboring 442 HSRS, which are enriched for HSRS that have been associated with human-specific (HS) changes of gene expression in cerebral organoid models of brain development. A prominent majority of genomic regions harboring HS mutations associated with HS gene expression changes during brain development is highly conserved in Chimpanzee, Bonobo, and Gorilla genomes. Among nonhuman primates (NHP), most significant fractions of candidate HSRS associated with HS gene expression changes in both excitatory neurons (347 loci; 67%) and radial glia (683 loci; 72%) are highly conserved in the Gorilla genome. Present analyses revealed that Modern Humans captured unique combinations of regulatory sequences, divergent subsets of which are highly conserved in distinct species of six NHP separated by 30 million years of evolution. Concurrently, this unique-to-human mosaic of genomic regulatory patterns inherited from ECAs was supplemented with 12,486 created de novo HSRS. Evidence of multispecies evolutionary origins of HSRS support the model of complex continuous speciation process during evolution of Great Apes that is not likely to occur as an instantaneous event.

genomics↗

bioRxiv2019

An Improved Genome Assembly of the European Aspen Populus tremula

Aspen (Populus tremula L.) is a widely distributed keystone species and a model system for forest tree genomics, with extensive resources developed for population genetics and genomics. Here we present an updated resource comprising a chromosome-scale assembly of P. tremula and population genetics and genomics data integrated into the PlantGenIE.org web resource. We demonstrate use of the diverse data types included to explore the genetic basis of natural variation in leaf size and shape as examples of traits with complex genetic architecture. We present a chromosome-scale genome assembly generated using long-read sequencing, optical and high-density genetic maps containing 39,894 annotated genes with functional annotations for 73,765 transcripts from 37,184 gene loci. We conducted whole-genome resequencing of the Ume[a] Aspen (UmAsp) collection comprising 227 aspen individuals. We utilised the assembly, the UmAsp re-sequencing data and existing whole genome re-sequencing data from the Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections to perform genome-wide association analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) for leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq) and identified genomic regions of accessible chromatin and subset SNPs to these regions, which improved the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples and quantified their expression in an updated co-expression network (AspLeaf, available in PlantGenIE.org), which we further used to explore the functions of candidate genes identified from the GWAS. We examined synteny to the reference P. trichocarpa assembly and identified P. tremula-specific regions. Analysis of whole-genome duplication indicated differential substitution rates for the two Populus species, indicating more rapid evolution in P. tremula. A GWAS of 26 leaf physiognomy traits and all SNPs in each of the three aspen collections found significant associations for only two traits in ScotAsp collection and one in UmAsp, whereas subsetting SNPs to those in open chromatin regions revealed associations for a further four traits among all three aspen collections. The significant SNPs were associated with genes annotated for developmental and growth functions, which represent candidates for further study. Of particular interest was a 177-kbp region of chromosome 9 harbouring SNPs associated with multiple leaf phenotypes in ScotAsp, with the set of SNPs in linkage disequilibrium explaining 24 to 30 % of the phenotypic variation in leaf indent depth variation. We have incorporated the assembly, population genetics, genomics and leaf physiognomy GWAS data into the PlantGenIE.org web resource, including updating existing genomics data to the new genome version. This enables easy exploration and visualisation of the genomics data and exploration of GWAS results. We provide all raw and processed data used for the presented analyses to facilitate reuse in future studies.

genomics↗

bioRxiv2019

Found in Space: Nanopore long reads enable the first complete genome assembly of a Malaysian Vibrio parahaemolyticus isolate bearing the pVa plasmid associated with acute hepatopancreatic necrosis disease

BackgroundVibrio parahaemolyticus MVP1 was isolated from a Malaysian aquaculture farm affected with shrimp acute hepatopancreatic necrosis disease (AHPND). Its genome was previously sequenced on the Illumina MiSeq platform and assembled de novo producing a relatively fragmented assembly. Despite identifying the binary toxin genes in the MVP1 draft genome that were linked to AHPND, the toxin genes were localized on a very small contig precluding proper analysis of gene neighbourhood. MethodsThe genome of Vibrio parahaemolyticus MVP1 was sequenced on the Nanopore MinION device to obtain long reads that can span longer repeats and improve genome contiguity. De novo genome assembly was subsequently performed using long-read only assembler (Flye) followed by genome polishing as well as hybrid assembler (Unicycler). ResultsLong-read only assembly produced three complete circular MVP1 contigs consisting of chromosome 1, chromosome 2 and the pVa plasmid that pirABvp binary toxin genes. Polishing of the long read assembly with Illumina short reads was necessary to remove indel errors. The complete assembly of the pVa plasmid could not be achieved using Illumina reads due to the presence of identical repetitive elements flanking the binary toxin genes leading to multiple contigs. Whereas these regions were fully spanned by the Nanopore long reads resulting in a single contig. In addition, alignment of Illumina reads to the complete genome assembly indicated there is sequencing bias as read depth was lowest in low-GC genomic regions. Comparative genomic analysis revealed the presence of a gene cluster coding for additional insecticidal toxins in chromosome 2 of MVP1 that may further contribute to host pathogenesis pending functional validation. Scanning of all publicly available V. parahaemolyticus genomes revealed the presence of a single AinS-family quorum-sensing system in this species that can be targeted for future microbial management. ConclusionsWe generated the first chromosome-scale genome assembly of a Malaysian pirABVp-bearing V. parahaemolyticus isolate. Structural variations identified from comparative genomic analysis provide new insights into the genomic features of V. parahaemolyticus MVP1 that may be associated with host colonization and pathogenicity.

genomics↗

bioRxiv2025

Decoding Prokaryotic Whole Genomes with a Product-Contextualized Large Language Model

Genomes encode the instructions for life, yet their interpretation requires models capable of capturing long-range genome-wide functional context at scale. Existing genomic foundation models have primarily focused on sequence-level representations, providing powerful tools for biological prediction while leaving complementary opportunities for function-level genome modeling. Here, we present GenSyntax, a function-level genome representation learning framework that models prokaryotic genomes as ordered sequences of gene-product descriptors. By treating gene products as semantic units, GenSyntax transforms annotated replicons into interpretable "genetic paragraphs" that capture genome-wide functional context. We trained GenSyntax on 49,250 annotated prokaryotic genomes and evaluated its ability across genome-scale tasks, including plasmid host prediction, gene-product disambiguation, genome contig ordering and gene essentiality prediction. Compared with general-purpose large language models and representative genomic foundation models, GenSyntax achieved competitive performance across multiple benchmarks, with independent external evaluations supporting its generalization beyond the original training datasets. GenSyntax embeddings also captured signals associated with microbial phenotypes, and gene essentiality predictions enabled exploratory design of minimal genomes. Together with the lightweight GenSyntax-Tiny model, GenSyntax provides a complementary, post-annotation framework for function-level analysis of prokaryotic genomes.

genomics↗

bioRxiv2026

Sequencing, Chromosome-scale Assembly, and Annotation of the Genome of the Halophilic Nanoflagellate Halocafeteria seosinensis

Compared with bacterial and archaeal extremophiles, single-celled eukaryotes living in extreme habitats are understudied and underrepresented in genomic databases. An exception is the obligately halophilic stramenopile Halocafeteria seosinensis strain EHF34. A transcriptome-focused analysis of this extremophilic protists revealed the importance of organic osmolyte regulation and transport in its adaptation to hypersaline environments. However, genomic resources for H. seosinensis are currently limited to a highly fragmented assembly generated by short-read sequencing, which has hindered further investigation of the genome biology and evolution of this fascinating organism. Here, we used long-read Oxford Nanopore sequencing to generate a highly contiguous, chromosome-scale genome assembly for H. seosinensis. The assembly is 38.8 megabase pairs (Mbp) in size and contains 60 nuclear contigs, making it the most contiguous genome for a member of the order Bicosoecida. Approximately 19% of the genome is comprised of transposable elements. Of the 11,684 predicted protein-coding genes, many appear to be associated with DNA mobility-related functions, and several may be linked to adaptation to a hypersaline environment. Analysis of the H. seosinensis long-read genome assembly presented herein will facilitate our understanding of the ways in which protists have adapted to extreme environments. SignificanceHalocafeteria seosinensis is an extremophilic protist adapted to hypersaline environments. Previous analyses of a transcriptome and short-read draft genome assembly for this organism provided insights into the molecular mechanisms underlying osmotic regulation, which facilitate its adaptation to high-salt conditions. However, the lack of contiguity and quality of the draft assembly prevented the characterization of complex genomic regions, including transposable elements and viral insertions, as well as genomic comparisons with related species. Here we present a highly contiguous, chromosome-scale genome assembly for H. seosinensis that enables accurate gene prediction, detailed analysis of repeat content, and comparative genomic analysis. This long-read genome assembly will serve as a valuable resource for studying one of the few tractable halophilic protists sequenced to date.

genomics↗

bioRxiv2017

Specific Virus-Host Genome Interactions Revealed By Tethered Chromosome Conformation Capture

Viruses have evolved a variety of mechanisms to interact with host cells for their adaptive benefits, including subverting host immune responses and hijacking host DNA replication/transcription machineries [1-3]. Although interactions between viral and host proteins have been studied extensively, little is known about how the vial genome may interact with the host genome and how such interactions could affect the activities of both the virus and the host cell. Since the three-dimensional organization of a genome can have significant impact on genomic activities such as transcription and replication, we hypothesize that such structure-based regulation of genomic functions also applies to viral genomes depending on their association with host genomic regions and their spatial locations inside the nucleus. Here, we used Tethered Chromosome Conformation Capture (TCC) to investigate viral-host genome interactions between the adenovirus and human lung fibroblast cells. We found viral-host genome interactions were enriched in certain active chromatin regions and chromatin domains marked by H3K27me3. The contacts by viral DNA seems to impact the structure and function of the host genome, leading to remodeling of the fibroblast epigenome. Our study represents the first comprehensive analysis of viral-host interactions at the genome structure level, revealing unexpectedly specific virus-host genome interactions. The non-random nature of such interactions indicates a deliberate but poorly understood mechanism for targeting of host DNA by foreign genomes.

microbiology↗