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Genomics

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bioRxiv2019

Complete genome sequence and annotation of the laboratory reference strain Shigella flexneri serovar 5a M90T and genome-wide transcription start site determination

BackgroundShigella is a Gram-negative facultative intracellular bacterium that causes bacillary dysentery in humans. Shigella invades cells of the colonic mucosa owing to its virulence plasmid-encoded Type 3 Secretion System (T3SS), and multiplies in the target cell cytosol. Although the laboratory reference strain S. flexneri serotype 5a M90T has been extensively used to understand the molecular mechanisms of pathogenesis, its complete genome sequence is not available, thereby greatly limiting studies employing high-throughput sequencing and systems biology approaches.\n\nResultsWe have sequenced, assembled, annotated and manually curated the full genome of S. flexneri 5a M90T. This yielded two complete circular contigs, the chromosome and the virulence plasmid (pWR100). To obtain the genome sequence, we have employed long-read PacBio DNA sequencing followed by polishing with Illumina RNA-seq data. This provides a new pipeline to prepare gapless, highly accurate genome sequences. Furthermore, we have performed genome-wide analysis of transcriptional start sites and determined the length of 5 untranslated regions (5-UTRs) at typical culture conditions for the inoculum of in vitro infection experiments. We identified 6,723 primary TSS (pTSS) and 7,328 secondary TSS (sTSS). The S. flexneri 5a M90T annotated genome sequence and the transcriptional start sites are integrated into RegulonDB (http://regulondb.ccg.unam.mx) and RSAT (http://embnet.ccg.unam.mx/rsat/) to use its analysis tools in S. flexneri 5a M90T genome.\n\nConclusionsWe provide the first complete genome for S. flexneri serotype 5a, specifically the laboratory reference strain M90T. Our work opens the possibility of employing S. flexneri M90T in high-quality systems biology studies such as transcriptomic and differential expression analyses or in genome evolution studies. Moreover, the catalogue of TSS that we report here can be used in molecular pathogenesis studies as a resource to know which genes are transcribed before infection of host cells. The genome sequence, together with the analysis of transcriptional start sites, is also a valuable tool for precise genetic manipulation of S. flexneri 5a M90T. The hybrid pipeline that we report here combining genome sequencing with long-reads technology and polishing with RNAseq data defines a powerful strategy for genome assembly, polishing and annotation in any type of organism.

microbiology↗

bioRxiv2026

BGX: A Comprehensive Pipeline for Genomic Insight into Bioactivity Prediction, Genomic Surveillance, and Novel Biosynthetic Gene Cluster Assessment

The increasing availability of genomic and metagenomic data has created significant opportunities to explore microbial diversity, biosynthetic potential and functional traits. However, comprehensive and comparative genome analysis often requires integrating multiple independent tools, making large-scale studies challenging to implement and manage. Here, we present Bacterial Genome eXplorer (BGX), an integrated and scalable pipeline that streamlines large-scale genome analysis and exploration of biosynthetic potential. BGX integrates different analytical tools into six major stages: (i) genome retrieval and assembly, (ii) genome quality assessment, (iii) antimicrobial resistance (AMR) gene profiling, (iv) annotating Biosynthetic gene clusters (BGCs) and novelty assessment, (v) bioactivity predictions, and (vi) clustering and networking analysis. In addition, BGX provides a user-friendly interactive interface to facilitate data exploration and interpretation. We demonstrated the versatility and scalability of BGX through large-scale analysis of two independent datasets: 248 genomes from the One Day One Genome (ODOG) initiative and 153 publicly available genomes from NCBI. This analysis enabled the comprehensive characterisation of genome quality, AMR determinants, biosynthetic potential and candidate bioactive metabolites across two datasets. BGX is distributed as a Docker container that simplifies installation, enables reproducible data processing, and supports pipeline execution across different computational environments. The modular and reproducible architecture of the BGX pipeline provides an effective framework for large-scale genome mining, genomic surveillance, and accelerates the discovery and prioritisation of novel secondary metabolites. BGX is now accessible at https://bgx.nabi.res.in

bioinformatics↗

bioRxiv2016

A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus

The Drosophila Genome Nexus is a population genomic resource that provides D. melanogaster genomes from multiple sources. To facilitate comparisons across data sets, genomes are aligned using a common reference alignment pipeline which involves two rounds of mapping. Regions of residual heterozygosity, identity-by-descent, and recent population admixture are annotated to enable data filtering based on the users needs. Here, we present a significant expansion of the Drosophila Genome Nexus, which brings the current data object to a total of 1,122 wild-derived genomes. New additions include 306 previously unpublished genomes from inbred lines representing six population samples in Egypt, Ethiopia, France, and South Africa, along with another 193 genomes added from recently-published data sets. We also provide an aligned D. simulans genome to facilitate divergence comparisons. This improved resource will broaden the range of population genomic questions that can addressed from multi-population allele frequencies and haplotypes in this model species. The larger set of genomes will also enhance the discovery of functionally relevant natural variation that exists within and between populations.

Genomics↗

bioRxiv2020

Transposon- and genome dynamics in the fungal genus Neurospora: insights from nearly gapless genome assemblies

BackgroundA large portion of nuclear DNA is composed of transposable element (TE) sequences, whose transposition is controlled by diverse host defense strategies in order to maintain genomic integrity. One such strategy is the fungal-specific Repeat-Induced Point (RIP) mutation that hyper-mutates repetitive DNA sequences. While RIP is found across Fungi, it has been shown to vary in efficiency. To date, detailed information on the TE landscapes and associated RIP patterns exist only in a few species belonging to highly divergent lineages. ResultWe investigated 18 nearly gapless genome assemblies of ten Neurospora species, which diverged from a common ancestor about 7 MYA, to determine genome-wide TE distribution and their associated RIP patterns. We showed that the TE contents between 8.7-18.9% covary with genome sizes that range between 37.8-43.9 Mb. Degraded copies of Long Terminal Repeat (LTR) retrotransposons were abundant among the identified TEs, and these are distributed across the genome at varying frequencies. In all investigated genomes, TE sequences had signs of numerous C-to-T substitutions, suggesting that RIP occurred in all species. RIP signatures in all genomes correlated with TE-dense regions. ConclusionsEssentially gapless genome assemblies allowed us to identify TEs in Neurospora genomes, and reveal that TEs contribute to genome size variation in this group. Our study suggests that TEs and RIP are highly correlated in Neurospora, and hence, the pattern of interaction is conserved over the investigated evolutionary timescale. We show that RIP signatures can be used to facilitate the identification of TE-rich region in the genome.

genomics↗

bioRxiv2021

Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT

The cost of sequencing the genome is dropping at a much faster rate compared to assembling and finishing the genome. The use of lightly sampled genomes (genome-skims) could be transformative for genomic ecology, and results using k-mers have shown the advantage of this approach in identification and phylogenetic placement of eukaryotic species. Here, we revisit the basic question of estimating genomic parameters such as genome length, coverage, and repeat structure, focusing specifically on estimating the k-mer repeat spectrum. We show using a mix of theoretical and empirical analysis that there are fundamental limitations to estimating the k-mer spectra due to ill-conditioned systems, and that has implications for other genomic parameters. We get around this problem using a novel constrained optimization approach (Spline Linear Programming), where the constraints are learned empirically. On reads simulated at 1X coverage from 66 genomes, our method, REPeat SPECTra Estimation (RESPECT), had < 1.5% error in length estimation compared to 34% error previously achieved. In shotgun sequenced read samples with contaminants, RESPECT length estimates had median error 4%, in contrast to other methods that had median error 80%. Together, the results suggest that low-pass genomic sequencing can yield reliable estimates of the length and repeat content of the genome. The RESPECT software will be publicly available at https://github.com/shahab-sarmashghi/RESPECT.git

genomics↗

bioRxiv2021

Genomic insights into longan evolution from a chromosome-level genome assembly and population analysis of longan accessions

Longan (Dimocarpus longan) is a subtropical fruit best known for its nutritious fruit and regarded as a precious tonic and traditional medicine since ancient times. High-quality chromosome-scale genome assembly is valuable for functional genomic study and genetic improvement of longan. Here, we report a chromosome-level reference genome sequence for longan cultivar JDB with an assembled genome of 455.5 Mb in size anchored to fifteen chromosomes, representing a significant improvement of contiguity (contig N50=12.1 Mb, scaffold N50= 29.5 Mb) over a previous draft assembly. A total of 40,420 protein-coding genes were predicted in D. longan genome. Synteny analysis suggests longan shares the widespread gamma event with core eudicots, but has no other whole genome duplications. Comparative genomics showed that D. longan genome experienced significant expansions of gene families related to phenylpropanoid biosynthesis and UDP-glucosyltransferase. Deep genome sequencing analysis of longan cultivars identified longan biogeography as a major contributing factor for genetic diversity, and revealed a clear population admixture and introgression among cultivars of different geographic origins, postulating a likely migration trajectory of longan overall confirmed by existing historical records. Finally, genome-wide association studies (GWAS) of longan cultivars identified quantitative trait loci (QTL) for six different fruit quality traits and revealed a shared QTL containing three genes for total soluble solid and seed weight. The chromosome-level reference genome assembly, annotation and population genetic resource for D. longan will facilitate the molecular studies and breeding of desirable longan cultivars in the future.

genomics↗

bioRxiv2023

Hagfish genome illuminates vertebrate whole genome duplications and their evolutionary consequences

Whole genome duplications (WGDs) are major events that drastically reshape genome architecture and are causally associated with organismal innovations and radiations1. The 2R Hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution2, 3. However, the veracity and timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved4-6 and whether these WGD events underlie vertebrate phenotypic diversification remains elusive7. Here we present the genome of the inshore hagfish, Eptatretus burgeri. Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and the 2R event occurred in the gnathostome stem-lineage in the late Cambrian after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced two additional, independent genome duplications (herein CR1 and CR2). Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only after the 2R event, questioning the general expectation that WGDs lead to leaps of morphological complexity7.

genomics↗

bioRxiv2023

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

A global genome database of all of Earths species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all [~]1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.

genomics↗

bioRxiv2023

A Small Genome Amidst the Giants: Evidence of Genome Reduction in a Small Tubulinid Free-Living Amoeba

This study investigates the genomic characteristics of Echinamoeba silvestris, a small-sized amoeba within the Tubulinea clade of the Amoebozoa supergroup. Despite Tubulineas significance in various fields, genomic data for this clade have been scarce. E. silvestris presents the smallest free-living amoeba genome within Tubulinea and Amoebozoa to date. Comparative analysis reveals intriguing parallels with parasitic lineages in terms of genome size and predicted gene numbers, emphasizing the need to understand the consequences of reduced genomes in free-living amoebae. Functional categorization of predicted genes in E. silvestris shows similar percentages of ortholog groups to other amoebae in various categories, but a distinctive feature is the extensive gene contraction in orphan (ORFan) genes and those involved in biological processes. Notably, among the few genes that underwent expansion, none are related to cellular components, suggesting adaptive processes that streamline biological processes and cellular components for efficiency and energy conservation. The investigation delves into genomic structural evidence, including gene content and repetitive elements, illuminating the distinctive genomic traits of E. silvestris and providing reinforcement for its compact genome size. Overall, this research underscores the diversity within Tubulinea, highlights knowledge gaps in Amoebozoa genomics, and positions E. silvestris as a valuable addition to genomic datasets, prompting further exploration of complexities in Amoebozoa diversity and genome evolution.

genomics↗

bioRxiv2024

A chromosome-scale genome assembly of Timorese crabgrass (Digitaria radicosa): a useful genomic resource for the Poaceae

Timorese crabgrass (Digitaria radicosa) is a grass species commonly found in Southeast Asia and Oceania. Digitaria species have high intraspecific and interspecific genetic and phenotypic diversity, suggesting their potential usefulness as a genetic resource. However, as the only high-quality reference genome available is for a tetraploid Digitaria species, a reference genome of the diploid species D. radicosa would be a useful resource for genomic studies of Digitaria and Poaceae plants. Here, we present a chromosome-level genome assembly of D. radicosa and describe its genetic characteristics; we also illustrate its usefulness as a genomic resource for Poaceae. We constructed a 441.6 Mb draft assembly consisting of 61 scaffolds with an N50 scaffold length of 41.5 Mb, using PacBio HiFi long reads. Thirty scaffolds, encompassing 440.8 Mb, were anchored to nine pseudochromosomes. We predicted 26,577 protein-coding genes, reaching a BUSCO score of 96.5%. To demonstrate the usefulness of the D. radicosa reference genome, we investigated the evolution of Digitaria species and the genetic diversity of Japanese Digitaria plants based on our new reference genome. We also defined the syntenic blocks between D. radicosa and Poaceae crops and the diverse distribution of representative resistance genes in D. radicosa. The D. radicosa reference genome presented here should help elucidate the genetic relatedness of Digitaria species and the genetic diversity of Digitaria plants. In addition, the D. radicosa genome will be an important genomic resource for Poaceae genomics and crop breeding.

genomics↗

bioRxiv2024

Dispensable genome and segmental duplications drive the genome plasticity in Fusarium solani

Fusarium solani is a species complex encompassing a large phylogenetic clade with diverse members occupying varied habitats. We recently reported a unique opportunistic F. solani associated with unusual dark galls in sugarbeet. We assembled the chromosome-level genome of the F. solani sugarbeet isolate strain SB1 using Oxford Nanopore and Hi-C sequencing. SB1 has a large genome (59.38 Mb) organized into 15 chromosomes. The genome expansion is due to the high repeats and massive segmental duplications within its three potentially accessory chromosomes. These chromosomes are absent in the closest reference genome with chromosome-level assembly, F. vanettenii 77-13-4. The extensive segmental duplications between the two SB1 chromosomes suggest that this isolate may have doubled its accessory genes. Further comparison of the F. solani strain SB1 genome demonstrates inversions and syntenic regions to an accessory chromosome of F. vanettenii 77-13-4. The pan-genome of 12 publicly available F. solani isolates nearly reached gene saturation, with few new genes discovered after the addition of the last genome. Based on orthogroups and average nucleotide identity, F. solani is not grouped by lifestyle or origin. The pan-genome analysis further revealed the enrichment of several enzymes-coding genes within the dispensable (accessory + unique genes) genome, such as hydrolases, transferases, oxidoreductases, lyases, ligases, isomerase, and dehydrogenase. The evidence presented here suggests that genome plasticity, genetic diversity, and adaptive traits in Fusarium solani are driven by the dispensable genome with significant contributions from segmental duplications.

genomics↗

bioRxiv2025

Phylogenomic synteny analysis tracks conserved ancient polyploid-derived triplicated genomic blocks across Asteraceae genomes

The Asteraceae (Compositae) is the largest flowering plant family, ubiquitous in most terrestrial communities, and morphologically hyper-diverse. An ancient whole genome triplication (paleo-hexaploidization) occurred at approximately the same time as the evolutionary innovation and adaptive radiation of the family during the middle Eocene. Despite its importance, the genomic contents arising from this triplication have yet to be tracked in context of the Asteraceae genome evolution. We applied a synteny oriented phylogenomic analysis of 21 Asterales genomes and to study the paleo-hexaploidization and its consequences to gene, trait, and genome evolution. We identified 15 ancestral linkage groups (ALGs) that date back to the common diploid ancestor of all Asteraceae. Each of these groups was triplicated, resulting in 45 genomic blocks (3x15), which serve as the foundation for cross-family analyses. We demonstrate the complex evolutionary dynamics of the 45 genomic blocks across the Asteraceae phylogeny. We found that modern genomes are genetic mosaics of three progenitor genomes by extensive genomic exchange, chromosomal shuffling and gene fractionation. 157 genes retained three paleo-hexaploid derived syntenic paralogs across most Asteraceae species. Transcription factors (TFs) and auxin-related genes are significantly overrepresented in the conserved triplets, and expression of the paleo-hexaploidy paralogs is spatiotemporally differentiated. These genes are involved in the development of floral capitulum, a remarkable morphological innovation of the family. The discovery of conserved triplicated genes can direct further study to understand the evolutionary innovation, and the synteny-phylogenomic framework and ALGs provide a comparative framework to characterize newly sequenced Asteraceae genomes.

genomics↗

bioRxiv2025

Comparative genomics reveals multipartite genomes undergoing loss in the fungal endosymbiotic genus Mycetohabitans

Endosymbiotic bacteria extensively impact phenotypes of their eukaryotic hosts, while experiencing dramatic changes to their own genome as they become more host-restricted in lifestyle. Understanding the trajectory of such a genome has largely been done through study of animal-associated bacteria, especially insect endosymbionts. Yet, endofungal bacteria provide another natural experimental model for investigating how microbial genomes change when living inside of a host cell. Mycetohabitans spp. are culturable bacterial endosymbionts of the Mucoromycota fungus Rhizopus microsporus. To investigate the genome dynamics resulting from the endohyphal nature of this emerging model genus, we long-read sequenced and assembled new complete genomes to combine with previous assemblies, creating a global dataset of 28 complete Mycetohabitans genomes. All genomes were between 3.3 and 3.9 Mbp in size and were multipartite, structured into two conserved replicons with some strains having an additional plasmid. Based on evolutionary rate and gene content analysis of the different replicons, we termed the two major ones a chromosome and chromid. The differential presence of a third, mobilome-rich plasmid in some strains and the proliferation of transposable elements provide putative mechanisms for recombination or gene loss. The conservation of intact prophage and putative toxin-antitoxin systems, and extensive enrichment of secondary metabolite clusters in the Mycetohabitans genomes highlight the dynamic nature of this reducing genome. With fungal-bacterial symbioses becoming increasingly apparent phenomena, lessons learned from this symbiosis will inform our understanding of bacterial adaptation to novel hosts, and the process of microbe-microbe coevolution. SIGNIFICANCEGenomes change when organisms become closely associated, as bacterial partners undergo less opportunities for genetic exchange and become more reliant on their hosts. Our pangenome analysis of the endofungal genus Mycetohabitans shows a snapshot of evolution where the bacteria are moving from a facultative towards an obligate relationship with their host fungi. We find that Mycetohabitans genomes are marked by transposable elements, pseudogenes, a large biosynthetic repertoire, and novel bacteriophage. We provide a genomic resource to match publicly accessible strains for future work on endosymbiotic genetics and evolution.

genomics↗

bioRxiv2018

Comparative Genomics and Genome Evolution in Birds-of-paradise

BackgroundThe diverse array of phenotypes and lekking behaviors in birds-of-paradise have long excited scientists and laymen alike. Remarkably, almost nothing is known about the genomics underlying this iconic radiation. Currently, there are 41 recognized species of birds-of-paradise, most of which live on the islands of New Guinea. In this study we sequenced genomes of representatives from all five major clades recognized within the birds-of-paradise family (Paradisaeidae). Our aim was to characterize genomic changes that may have been important for the evolution of the groups extensive phenotypic diversity.\n\nResultsWe sequenced three de novo genomes and re-sequenced two additional genomes representing all major clades within the birds-of-paradise. We found genes important for coloration, morphology and feather development to be under positive selection. GO enrichment of positively selected genes on the branch leading to the birds-of-paradise shows an enrichment for collagen, glycogen synthesis and regulation, eye development and other categories. In the core birds-of-paradise, we found GO categories for startle response (response to predators) and olfactory receptor activity to be enriched among the gene families expanding significantly faster compared to the other birds in our study. Furthermore, we found novel families of retrovirus-like retrotransposons active in all three de novo genomes since the early diversification of the birds-of-paradise group, which could have potentially played a role in the evolution of this fascinating group of birds.\n\nConclusionHere we provide a first glimpse into the genomic changes underlying the evolution of birds-of-paradise. Our aim was to use comparative genomics to study to what degree the genomic landscape of birds-of-paradise deviates from other closely related passerine birds. Given the extreme phenotypic diversity in this family, our prediction was that genomes should be able to reveal features important for the evolution of this amazing radiation. Overall, we found a strong signal for evolution on mechanisms important for coloration, morphology, sensory systems, as well as genome structure.

genomics↗

bioRxiv2018

Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires

Essential features of cancer tissue cellular heterogeneity such as negatively selected genome topologies, sub-clonal mutation patterns and genome replication states can only effectively be studied by sequencing single-cell genomes at scale and high fidelity. Using an amplification-free single-cell genome sequencing approach implemented on commodity hardware (DLP+) coupled with a cloud-based computational platform, we define a resource of 40,000 single-cell genomes characterized by their genome states, across a wide range of tissue types and conditions. We show that shallow sequencing across thousands of genomes permits reconstruction of clonal genomes to single nucleotide resolution through aggregation analysis of cells sharing higher order genome structure. From large-scale population analysis over thousands of cells, we identify rare cells exhibiting mitotic mis-segregation of whole chromosomes. We observe that tissue derived scWGS libraries exhibit lower rates of whole chromosome anueploidy than cell lines, and loss of p53 results in a shift in event type, but not overall prevalence in breast epithelium. Finally, we demonstrate that the replication states of genomes can be identified, allowing the number and proportion of replicating cells, as well as the chromosomal pattern of replication to be unambiguously identified in single-cell genome sequencing experiments. The combined annotated resource and approach provide a re-implementable large scale platform for studying lineages and tissue heterogeneity.

genomics↗

bioRxiv2019

The genome and mRNA transcriptome of the cosmopolitan calanoid copepod Acartia tonsa Dana improve the understanding of copepod genome size evolution

Members of the crustacean subclass Copepoda are likely the most abundant metazoans worldwide. Pelagic marine species are critical in converting planktonic microalgae to animal biomass, supporting oceanic food webs. Despite their abundance and ecological importance, only five copepod genomes are publicly available, owing to a number of factors including large genome size, repetitiveness, GC-content, and small animal size. Here, we report the sixth representative copepod genome and the first genome and transcriptome from the calanoid copepod species Acartia tonsa Dana, which is among the most numerous mesozooplankton in boreal coastal and estuarine waters. The ecology, physiology and behavior of A. tonsa has been studied extensively. The genetic resources contributed in this work will allow researchers to link experimental results to molecular mechanisms. From PCRfree WGS and mRNA Illumina data, we assemble the largest copepod genome to date. We estimate A. tonsa has a total genome size of 2.5 Gb including repetitive elements we could not resolve. The non-repetitive fraction of the genome assembly is estimated to be 566Mb. Our DNA sequencing-based analyses suggest there is a 14-fold difference in genome size between the six members of Copepoda with available genomic information through NCBI. This finding complements nucleus staining genome size estimations, where 100-fold difference has been reported within 70 species. We briefly analyze the repeat structure in the existing copepod WGS datasets. The information presented here confirms the evolution of genome size in Copepoda and expands the scope for evolutionary inferences in Copepoda by providing several levels of genetic information from a key planktonic crustacean species.

genomics↗

bioRxiv2025

The first chromosome-scale Dugesia genomes shed light on structural rearrangements and genome size evolution in flatworms

AbstractHigh-quality, chromosome-scale genomes are crucial for understanding biological processes, yet many metazoan lineages, including most Lophotrochozoa, remain underrepresented in genome databases. Among these, planarians (Platyhelminthes, Tricladida), particularly Dugesia, are a globally distributed and phenotypically diverse group that has become an important model in evolutionary biology, notably for investigating the genetic effects of agametic asexuality. However, the lack of chromosome-scale assemblies has limited progress. Here, we present the first chromosome-scale genomes of four Western Mediterranean Dugesia species, displaying the first intra- and intergeneric comparisons. Comparison with the regeneration model organism Schmidtea mediterranea, rejects a whole-genome duplication as the cause of differences in chromosomal number and genome size between genera. Instead, Dugesia shows extensive lineage-specific and differential expansions of DNA transposable elements, likely contributing to genome size variation during diversification. Despite differences in the dynamics of structural genome rearrangements observed between genera, both groups lack the conservation of ancestral metazoan linkage groups, supporting the idea that genome structural instability is a key feature of flatworm genome evolution. Our newly generated genomic resources and findings offer vital insights into the genetic basis of diversification and establish Dugesia as a valuable model for studying metazoan genome dynamics, including the evolution of alternative reproductive systems.

genomics↗

bioRxiv2026

Hookworm genomic diversity and population structure from accessible sample types: A validated approach to generate genome-wide polymorphism datasets from individual third-stage larvae

Hookworm infection is a neglected tropical disease affecting hundreds of thousands of people annually in the tropics and sub-tropics. Population genomic approaches have the potential to improve our understanding of hookworm infection dynamics and control efficacy. Here, we validate an approach to generate genome-wide polymorphism datasets from accessible sample types in the zoonotic hookworm (Ancylostoma ceylanicum) then apply the validated approach in the human hookworm (Necator americanus) to compare laboratory- and field-derived samples. We first present an optimized method for purifying nucleic acid from individual third-stage hookworm larvae (L3s). We then measure the accuracy of variant call datasets generated through whole genome amplification (WGA) and next-generation sequencing (NGS). We demonstrate that WGA via multiple displacement amplification (MDA) introduces predictable biases that are exacerbated by low inputs and poor sample preservation but show that with sufficient input mass ([≥]0.1ng) we are still able to produce highly accurate variant call datasets from nucleic acid concentrations that reflect those of individual L3s. Using our validated approach, we infer laboratory- and field-collected samples of N. americanus as distinct populations, with higher levels of heterozygosity and nucleotide diversity identified in field-collected samples, suggesting signatures of inbreeding and/or drift are detectable in laboratory specimens within several years of initiation of infection. We also show that, despite expected reductions in heterozygosity, laboratory samples still possess numerous heterozygous sites, and we demonstrate that a reference genome generated from an adult worm from an early laboratory passage performs well for variant calling in both laboratory- and field-derived samples. Moving forward, our optimized method for nucleic acid purification can be broadly applied to generate input for any amplification-based approach where sequencing individual hookworm L3s, rather than a pool of specimens, is preferred. Our validated population genomics workflow can be used to characterize structure and connectivity of hookworm populations in endemic communities, with the goal of leveraging these insights to improve our approach to hookworm treatment and control. AUTHOR SUMMARYInfection with the human hookworm, Necator americanus, is a significant cause of morbidity in the global south. Population genomic techniques have the potential to improve our understanding of hookworm infection and control. However, third-stage larvae, or L3, which are the hookworm life-cycle stage we routinely have access to when screening infected people, are less than a millimeter long, and this small size makes generating genomic datasets from individual worms difficult. Here, we introduce an optimized approach for purifying DNA from individual L3s and validate its use with whole genome amplification (WGA) for population genomics. We found that WGA from L3s produces sequencing datasets that are biased in their breadth and depth of coverage across the hookworm genome. But by ensuring a minimum threshold for the mass of DNA input to WGA and setting strict criteria for variant filtration, these biases can be overcome to produce highly accurate variant calls genome-wide. We then use this approach to demonstrate reduced genetic diversity in a recently established laboratory hookworm strain as compared to field-collected samples. Our study outlines a specimen-through-analysis workflow that can be used with accessible sample types to measure population structure and diversity of hookworms in endemic communities.

genomics↗