bioRxiv Science⌕ Search

Biology subjects

Blaxter, M.

Publications and source records attributed to Blaxter, M..

At least 19 recordsLinked to original sources

An atlas of eukaryotic centromere architecture reveals recurrent evolutionary dynamics

Centromeres evolved at the root of eukaryotes to segregate chromosomes during cell division. Despite their ancient origin, centromeric DNA sequences evolve rapidly and adopt diverse architectures, including point centromeres, satellite arrays, transposon clusters, and holocentrics. To analyse centromere evolution at a broad scale, we characterised architectures across 325 diverse Darwin Tree of Life genome assemblies. Centromere architecture is evolutionarily labile, and similar configurations arise independently across divergent lineages. In plants and animals, we modelled centromere evolution as a recurrent cycle, in which satellite- and transposon-based architectures interconvert, with independent origins of holocentricity. We curated >23 million satellite repeats comprising 263 families from 165 species. Despite sequence divergence between satellite families, higher order repeats are prevalent, indicating constraint on repeat architecture rather than primary sequence. Satellite arrays are heavily invaded by diverse transposon families, consistent with convergent adaptation to the centromeric niche. In 89 species, transposons themselves constitute the primary centromere structure. We observed centrophilic transposons forming tandem arrays, suggesting mechanisms for satellite regeneration. Our sample includes five independent origins of holocentricity in plants and animals, which vary in association with periodic satellite arrays. We propose that genetic instability, centrophilic transposition, and transmission distortion promote recurrent centromere architectural interconversions during evolution.

genomics↗

Massive programmed DNA elimination during embryogenesis in the trioecious nematode Auanema rhodense

In animals, the germline is usually set aside early in development and its genome is protected to ensure faithful transmission of genetic information to future generations. Genetic alterations in somatic cells are not inherited by progeny, and the somatic genome does not have to be protected from change in the same way. In some species, programmed DNA elimination (PDE) results in the directed loss of genetic material from somatic cells. Here, we report extreme PDE in Auanema rhodense, a free-living nematode with a remarkable, trioecious life history and unusual patterns of sex chromosome inheritance. We find that nearly two thirds of the A. rhodense germline genome is eliminated from somatic cells, with DNA lost from chromosome ends as well as within chromosomes, resulting in fragmentation of the seven germline chromosomes into fourteen somatic chromosomes. Most eliminated DNA comprises multi-megabase tandem repeat blocks. Eliminated DNA on the X chromosome harbours germline-restricted repeats that are distinct from those on the autosomes. The eliminated DNA includes many highly-repeated non-coding RNA loci but few protein-coding genes. Elimination sites are strongly associated with a palindromic sequence motif that likely directs DNA breakage and new telomere repeat array addition. Cytologically, PDE begins at the 12-cell stage of embryogenesis, is synchronous across all chromosomes, and is characterised by the formation of transient micronucleus-like bodies. Together, these findings reveal unusually extensive PDE in a free-living nematode and raise the possibility that germline-restricted repeat architecture may contribute to the atypical sex chromosome inheritance observed in Auanema.

genomics↗

Ecological genomics of a novel host-parasitoid arms-race in nature

Novel antagonistic interactions between species are expected to drive especially rapid coevolution. However, little is known about the genomic basis of such coevolution in nature because novel inter-specific interactions are rarely observed. Here, we study two species that recently came into first contact in Hawaii, the parasitoid fly Ormia ochracea and its cricket host Teleogryllus oceanicus. The fly locates crickets acoustically using their song, and parasitism usually results in host death. In response, protective male-silencing mutations have rapidly spread through cricket populations over the last [~]25 years, imposing novel selective pressure on flies. By integrating population genomic analyses of 358 re-sequenced flies with field surveys of selection imposed by host adaptations, we discover genomic signatures of recent selective sweeps driven by host adaptations, indicative of escalating arms-race dynamics. This evolutionary response is occurring despite severely depleted genetic variation after bottlenecks in Hawaiian fly populations. Comparative analyses suggest that the genomic substrate of modern-day, rapid counter-adaptation in O. ochracea has been under positive selection on intermediate and long-term timescales across parasitoid flies. Our findings thus support predictions of influential arms race coevolution models and illustrate the current and ancient genomic bases of counteradaptation in nature.

evolutionary biology↗

The Vertebrate Genomes Project Phase I: A global reference genome resource

The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all [~]70,000 extant vertebrate species1. Organized in four phases, it progressively targets all vertebrate orders, families, genera, and eventually all species. Here we present the completion of VGP Phase I, delivering reference genomes for [~]95% of vertebrate orders, along with additional lineages within those orders, totaling 816 species and 1.6 trillion base pairs of main haplotype sequence. These genomes were assembled and annotated over an 8-year period (2018-2026) of rapid advances in genome sequencing, assembly, and annotation methods2-4, alongside the growth of associated consortium initiatives and international collaborations5-9. They represent some of the highest-quality vertebrate genomes currently available, and most have become the primary reference for their respective species in public databases. Comparative analyses across a subset of 579 species when we reached a threshold of 85% of orders allowed us to reconstruct the genome of the last common ancestor of all vertebrates 500 million years ago, identify diverse modes of sex chromosome evolution, reveal clade-specific three-dimensional genome architecture, discover methylated epigenetic landscapes across vertebrates, and provide a framework for studying gene and pseudogene evolution, immune loci, cancer-associated genes, and other trait-associated loci. Approximately a quarter of this subset are listed as Vulnerable to Critically Endangered by the IUCN Red List of Threatened Species, and have enabled more advanced genomic investigations of extinction risk. VGP Phase I delivers a reference backbone for vertebrate genomics, enabling discoveries that would otherwise remain out of reach across evolution, conservation, and medicine. Talking pointsO_LIThe flagship paper of VGP Phase I C_LIO_LIThe highest quality collection of genomes within the eukaryotic domain of life C_LIO_LIEvolution of genome sequencing technology quality throughout VGP Phase I C_LIO_LIA driver project that has been a model for multiple large-scale, high-quality reference genome projects C_LIO_LIReleases all currently unpublished genomes in Phase I from scientific study embargoes C_LIO_LIMultiple biological discoveries across the vertebrate tree of life C_LI

genomics↗

Hybridisation and herbivory fuel Amazonian tree radiations

Tropical rainforests, and Amazonia in particular, contain more tree species than anywhere else, most of which arose through rapid evolutionary radiations 1-3. Rapid radiations are often catalysed by ecological opportunity 4-6, which in rainforest trees is presented by intense insect herbivore pressure, spurring the evolution of novel plant defence chemistry to escape it 7. However, we do not understand how long-lived trees can adapt quickly enough to keep pace with rapidly-evolving insect herbivores. Here we show that hybridisation in rainforest trees, which was considered rare, allows exchange of gene clusters used in chemical defence against herbivore attack, facilitating rapid adaptation and diversification. Using genome sequencing for 461 individuals from the genus Inga, a characteristic Amazonian tree radiation, we find that regional tree communities form syngameons - networks of closely related, co-occurring species connected by gene flow. Integrating these genomes with herbivore abundance data from the same communities across the tropical Americas, we show that herbivore compositional turnover coincides with local, recurrent interspecific transfer of defence gene clusters that are retained by balancing selection, consistent with fluctuating selective pressure imposed by shifting herbivore communities. Together, our results demonstrate that hybridisation allows long-lived tropical trees to rapidly evolve chemical defences, fuelling adaptation to the relentless insect herbivory that structures the worlds most species-rich forests.

evolutionary biology↗

Chromosome-level genome assembly and annotation of the parthenogenetic nematode Acrobeloides nanus

Acrobeloides nanus is a species of widely distributed bacteria-feeding nematodes belonging to the family Cephalobidae. It reproduces parthenogenetically, making it a valuable system for studying the consequences of obligate asexuality, and exhibits early developmental processes that differ significantly from the model organism Caenorhabditis elegans. Additionally, the species has demonstrated remarkable resistance in extreme conditions, surviving near-complete desiccation through anhydrobiosis. This new chromosome-level genome assembly provides a high-quality reference to study these traits. Combining Nanopore, amplified PacBio HiFi, and Hi-C sequencing, we generated a chromosome-level assembly spanning 188.9 Mb over six chromosomes. The genome features a 48.1% repeat content, dominated by Mutator-like elements, and contains 24,912 predicted genes. Structural analysis reveals the conservation of ancestral nematode linkage groups. This resource significantly improves upon previous fragmented assemblies, offering a new framework for identifying genomic adaptations in the family Cephalobidae.

genomics↗

Rapid chromosomal evolution and oligocentromeric drive in sedges and rushes

The chromosomes of most eukaryotes have a single centromere, a specialised region involved in chromosome partitioning to daughter cells. Inter-chromosomal rearrangement risks generating chromosomes with two centromeres or none, disrupting segregation. Holocentric chromosomes, with centromere function distributed along the chromosome, are hypothesised to better tolerate inter-chromosomal rearrangement. However, evidence linking centromere organisation to rearrangement rate has been lacking. Sedges and rushes (Cyperaceae and Juncaceae) are specifically polycentric: they have several satellite-based centromeres per chromosome, whereas centromere location in "asatellitic" holocentrics is solely defined epigenetically. Using 36 chromosome-level genomes, we quantify extraordinary rearrangement rates and annotate candidate polycentromeres. Under our polycentromeric drive model, we expected satellite sequence, polycentromere architecture, and karyotype to evolve to exploit biased segregation during asymmetric meiosis. We find satellite turnover but also deep sequence conservation. Polycentromeric organisation seems constrained by chromosome size, and rearrangements are more stable when chromosomes have fewer polycentromeres, despite breakpoint regions being enriched for polycentromeres. Notably, we find putative monocentromeres in Carex myosuroides, which would be the first evidence for reversion to monocentricity in eukaryotes, and no identifiable polycentromeres in Cyperus rotundus, possibly a transition to asatellitic holocentricity. Overall, we demonstrate that this clade is powerful for linking centromere organisation to genome evolution.

genomics↗

Transposable Element Diversification and the Evolution of Peltigerales Lichen Symbionts

Lichens are composite organisms formed through the symbiotic association between fungi, algae and/or bacteria. Multiple independent origins of the lichenized lifestyle have been reported in both fungal and algal lineages, but the molecular mechanisms and evolution underpinning these symbiotic relationships remain largely unknown. In this study, we performed long-read metagenomic sequencing on 11 Peltigerales lichen species to characterize the genomic content of lichen symbionts via metagenome assembled genomes (MAGs). Peltigerales genomes generated in this work represent the largest Lecanoromycetes genome sequenced to date, driven by high transposable element content. Transposable elements (TEs) are known to drive genome evolution in other symbioses but have been underexplored in lichen symbionts due technological limitations. Transcriptomics revealed that many genes associated with adaptations to the lichenized lifestyle are associated with TEs suggesting that they may play a key role in the evolution of lichenization.

genomics↗

Panagrolaimus einhardi sp. nov. and two sisters of fortune

Identifying nematodes to the species level is known to be complicated due to their morphological plasticity and limited number of taxonomically important characters. This is especially apparent in the genus Panagrolaimus, which comprises many cryptic species that are morphologically difficult to distinguish but differ genetically. These roundworms are particularly notable for their adaptation to extreme environments that are inhospitable to many other forms of life. Traditional morphological identification methods often fail at distinguishing genetically divergent populations due to high morphological plasticity in Panagrolaimus, limiting the efficacy of species discovery. High-quality genome assemblies overcome these challenges, offering a comprehensive blueprint of an organisms genetic structure that can be used for species identification. The analysis of ultra-conserved elements across multiple loci harvested from genome assemblies provides robust phylogenetic resolution. In this study, we integrate genome sequencing, ultra-conserved element analysis, and morphological assessment to identify and describe three novel species: Panagrolaimus einhardi sp. nov., formerly Panagrolaimus sp. ES5 from Germany; Panagrolaimus shuimeiren sp. nov. from the Namib Desert; and Panagrolaimus nebliphilus sp. nov. from the Atacama Desert. P. einhardi sp. nov. is named after Prof. Einhard Schierenberg, a renowned expert in roundworm development and cherished member of the nematode community, who isolated this species himself. All three species originate from different geographical locations, and their respective identification are supported by high-quality genome assemblies from either PacBio HiFi or Oxford Nanopore long-read data. The P. einhardi sp. nov. genome was scaffolded using Hi-C technology, which resulted in a 116 Mb collapsed assembly composed of 44 scaffolds (N50: 28 Mb). P. shuimeiren sp. nov. has an assembly size of 69 Mb with 49 scaffolds and a N50 of 13 Mb. P. nebliphilus sp. nov. assembly is 70 Mb with 24 scaffolds (N50: 13 Mb). The capacity of Panagrolaimus to adapt to extreme environments is driving research into their survival mechanisms, requiring comprehensive genomic resources. By combining morphology and genomics, we can gain a more comprehensive understanding of the rich biological diversity in lineages with numerous cryptic species, such as the Panagrolaimidae, thereby clarifying relationships where morphological data alone are ambiguous or confounded.

zoology↗

Somatic and germline mutational processes across the tree of life

The characterisation of mutational processes active in somatic and germline cells in vivo has predominantly focused on human cancers1,2, normal tissues3-5 and model organisms6-8. Beyond mammals9, little is known about mutational processes across the tree of life. We developed himut (high-fidelity mutation), an algorithm to identify somatic mutations from circular consensus long-read sequencing data, deploying it on 708 samples from 661 species from Britain and Ireland10. The spectra of somatic mutations, categorised by mutation type and local sequence context, showed considerable between-species divergence but within-species similarity. From normalised spectra across the dataset, we extracted 95 distinct patterns, or signatures, of somatic mutations, together with 18 signatures of germline mutational processes. Only two of the somatic signatures resembled mutational signatures extracted from human cancers1,2. Of the somatic signatures, 22 had significant clustering within the taxonomic classification, with some distributed across an entire kingdom or phylum, while others were restricted to a single family or species. Three somatic signatures were found only in water-dwelling species, with one distributed across multiple clades that might suggest it derives from a water-borne mutagen. Of germline signatures, eight were found in multiple species, showed significant clustering by taxonomic classification and had counterpart somatic signatures with matching mutational spectrum and species distribution. Thus, there is considerably greater diversity of mutational processes across the tree of life than found in human samples, likely reflecting either cell-intrinsic biological processes or environmental exposures (or both) operative within distinct clades.

genomics↗

Tangerine: a Starship-like element in the genomes of Xanthoria lichen-forming fungi

Lichens are symbiotic associations between filamentous fungi and photosynthetic micro-organisms, such as green algae and/or cyanobacteria, that result in a single anatomically-complex structure that can thrive in environments inhospitable to most organisms, including arctic tundra, high mountains, and deserts. Recent evidence suggests that lichens may be even more complex than previously appreciated, containing multiple microbial constituents, but how genomes of the principal fungal symbiont (which provides the majority of biomass in lichen tissue) have been shaped during evolution is largely unexplored. Recently, giant transposable elements called Starships have been found in many genomes of filamentous fungi, but to which extent they occur in lichen-forming fungi is not known. In this report, we describe a Starship element from the lichen fungus Xanthoria parietina. This element, named Tangerine, contains several genes that have signatures of horizontal gene transfer from non-lichen-forming fungi, most likely from black yeasts of the Chaetothyriales, that are often lichen-associated. Repetitive sequences carried by Tangerine, and found in other sites in Xanthoria genomes, are affected by repeat-induced point mutation (RIP), a mechanism of genome defense against transposable elements, consistent with fungal sexual reproduction which always precedes new lichen formation by Xanthoria. Tangerines "captain" belongs to a newly defined family of tyrosine recombinases specific to lichen-forming Lecanoromycetes. Several other captain clades have signatures of horizontal gene transfer between distantly related lichen-forming fungi and non-mycobiont lichen-associated fungi. We speculate that Starships may play a significant, yet hitherto unrecognized role, in lichen genome evolution and provide a roadmap for further investigation.

genomics↗

Programmed DNA elimination was present in the last common ancestor of Caenorhabditis nematodes

In most organisms, all cells inherit the same genome, and many mechanisms exist to preserve its integrity across cell divisions. Programmed DNA elimination (PDE), the targeted removal of specific genomic regions from somatic cell lineages during early embryogenesis, is a striking exception. Since its discovery in parasitic nematodes over a century ago, PDE has been observed in diverse eukaryotes, including ciliates, arthropods, and vertebrates. However, the mechanisms, functions, and evolutionary origins of PDE remain poorly understood. Here, we describe the discovery of PDE in three species of the free-living nematode genus Caenorhabditis. Multiple genomic regions are precisely eliminated from somatic cells during early embryogenesis, resulting in chromosome fragmentation and the loss of key germline genes. The sites of elimination are strongly associated with conserved sequence motifs that likely direct DNA breakage. Comparative analyses indicate that PDE was present in the last common ancestor of Caenorhabditis and subsequently lost early during the evolution of many species, including C. elegans. The presence of PDE in the ancestors of one of biologys most important model organisms, together with recent discoveries in other eukaryotic lineages, reveals PDE to be a far more widespread and significant feature of evolution and development than previously recognised.

evolutionary biology↗

Retrocopy formation and domestication shape genome evolution in sloths and other xenarthrans

Xenarthrans, comprising sloths, anteaters, and armadillos, represent one of the most morphologically and physiologically specialised mammalian clades, yet the genomic basis of their adaptations remains poorly understood. Here, we present chromosome-level genomes for the two-toed sloth (Choloepus didactylus) and the southern anteater (Tamandua tetradactyla), and investigate how retrotransposon-mediated gene duplications (retrocopies) have shaped xenarthran genome evolution. Comparative analyses revealed that xenarthran genomes harbor the highest number of retrocopies reported among mammals, with lineage-specific insertion dynamics. Anteater and armadillo genomes contain older LINE1 repertoires and species-specific older retrocopy insertions. In contrast, sloths retain both an abundance of young LINE1s and thousands of young retrocopies, alongside a large shared set that originated from an evolutionary burst of retroduplication in the branch leading to their last common ancestor ([~]30 Mya). In C. didactylus, approximately 50% of retrocopies are expressed, compared with 24% in Dasypus novemcinctus. Evolutionary analyses identified 38 retrocopies with strong hallmarks of domestication in C. didactylus. Many of these retrocopies derive from parental genes involved in mitochondrial and metabolic processes, suggesting a genomic mechanism underlying the physiological specialisations of sloths. Altogether, our findings identify retrotransposition as a major contributor to the genomic architecture of Xenarthra and highlight retrocopy origination as a mechanism for generating lineage-specific novelty and distinctive biological specialisations.

genomics↗

Comparative transcriptomics reveals an extracellular worm argonaute as an ancestral regulator of LTR retrotransposons.

Safeguarding the genome from non-self elements is essential for reproduction, development, and ageing. One of the major threats to genome integrity is Transposable Elements (TEs), which can be post-transcriptionally silenced through small RNAs (sRNAs) and argonaute proteins. Recent work suggests TE-derived sRNAs may also act as virulence factors in host-pathogen interactions. During infection, the intestinal parasite Heligmosomoides bakeri secretes a single argonaute protein (exWAGO) and a wide variety of TE-derived sRNAs. Although exWAGO is highly expressed, conserved, and secreted by parasitic nematodes, its function and sRNA guide preference remain unclear. Using comparative transcriptomics of the sRNAs bound to exWAGO within parasites of rodents, livestock and humans, and its orthologs in C. elegans, we found that exWAGO is capable of loading sRNAs produced from all classes of TEs in addition to some protein-coding and non-coding transcripts. However, our results suggest that the ancestral endogenous function of exWAGO was likely linked to LTR retrotransposon regulation. To understand how this relates to potential extracellular functions of exWAGO we also examined the sRNAs bound to exWAGO secreted by H. bakeri in both vesicular and non-vesicular forms. Extracellular exWAGO preferentially loads sRNA guides derived from non-autonomous and fragmented LTRs, suggesting the existence of adaptable reservoirs of regulatory sRNAs with potential roles in cross-species RNA communication. Together, our results show that exWAGO is part of an evolutionarily conserved pathway for LTR retrotransposon regulation, while preferentially utilising degenerated elements as sources of secreted sRNAs.

genomics↗

Emergence and stabilisation of a neo-Y chromosome in nematode species with rare males

How do sex chromosomes evolve in the transition to asexuality? So far, species that depart from canonical sexual reproduction - for example, parthenogens with rare sex, or species where the paternal genome is set aside - have been found to carry either no sex chromosomes, or sex chromosomes but no male-specific sex chromosome (i. e., no Y). Here we reveal that, in Mesorhabditis nematodes, a new Y chromosome emerged once, from sexual ancestors, in species that have transitioned into an unconventional mode of reproduction called autopseudogamy. In this reproductive system, females produce clonal females plus rare ([~]10%) males that are needed for fertilisation, but that do not contribute to the female genome. Analysing the Y chromosomes of two autopseudogamous species, we found high levels of degeneration, most likely due to loss of recombination, and two additional conserved features: i) they accumulated male-beneficial genes, and ii) they display a strong fertilisation drive, in that mainly Y-bearing sperm fertilise female oocytes. Both features are likely evolutionarily favourable in the context of autopseudogamy. Our results suggest that male-specific chromosomes can still be maintained in systems with rare, and possibly genetically useless, males.

evolutionary biology↗

Forty New Genomes Shed Light on Sexual Reproduction and the Origin of Tetraploidy in Microsporidia

Microsporidia are single-celled, obligately intracellular parasites with growing public health, agricultural, and economic importance. Despite this, Microsporidia remain relatively enigmatic, with many aspects of their biology and evolution unexplored. Key questions include whether Microsporidia undergo sexual reproduction, and the nature of the relationship between tetraploid and diploid lineages. While few high-quality microsporidian genomes currently exist to help answer such questions, large-scale biodiversity genomics initiatives, such as the Darwin Tree of Life project, can generate high-quality genome assemblies for microsporidian parasites when sequencing infected host species. Here, we present 40 new microsporidian genome assemblies from infected arthropod hosts that were sequenced to create reference genomes. Out of the 40, 32 are complete genomes, eight of which are chromosome-level, and eight are partial microsporidian genomes. We characterised 14 of these as polyploid and five as diploid. We found that tetraploid genome haplotypes are consistent with autopolyploidy, in that they coalesce more recently than species, and that they likely recombine. Within some genomes, we found large-scale rearrangements between the homeologous genomes. We also observed a high rate of rearrangement between genomes from different microsporidian groups, and a striking tolerance for segmental duplications. Analysis of chromatin conformation capture (Hi-C) data indicated that tetraploid genomes are likely organised into two diploid compartments, similar to dikaryotic cells in fungi, with evidence of recombination within and between compartments. Together, our results provide evidence for the existence of a sexual cycle in Microsporidia, and suggest a model for the microsporidian lifecycle that mirrors fungal reproduction.

genomics↗

Genome evolution in parthenogenetic nematodes shaped by chromosome rearrangements and rare sex

In contrast to their dioecious relatives, members of the parthenogenetic Diploscapter nematode genus harbour their entire genome within a single pair of highly heterozygous chromosomes. To examine how this unusual karyotype relates to the evolution of parthenogenesis, we generated chromosome-level assemblies for two species in this clade: Diploscapter pachys and Diploscapter coronatus. Sequence comparisons revealed that the two genomes are colinear across their entirety, and that multiple ancestral chromosome fusions and extensive genomic rearrangements preceded the divergence of these two species. The presence of shortened telomeres and extended subtelomeric repeats suggests that the fusions arose from defects in telomere function in the lineage. Our analysis also identified an introgression event after divergence of the two species, suggesting that their parthenogenetic lifestyle may have been punctuated by rare sexual reproduction. These findings shed new light on how telomere loss, chromatin architecture, and reproductive strategies interconnect in shaping chromosome evolution.

genomics↗

On the path to reference genomes for all biodiversity: lessons learned and laboratory protocols created in the Sanger Tree of Life core laboratory over the first 2000 species

Since its inception in 2019, the Tree of Life programme at the Wellcome Sanger Institute has released high-quality, chromosomally-resolved reference genome assemblies for over 2000 species. Tree of Life has at its core multiple teams, each of which are responsible for key components of the genome engine. One of these teams is the Tree of Life core laboratory, which is responsible for processing tissues across a wide range of species into high quality, high molecular weight DNA and intact RNA, and preparing tissues for Hi-C. Here, we detail the different workflows we have developed to successfully process a wide variety of species, covering plants, fungi, chordates, protists, arthropods, meiofauna and other metazoa. We summarise our success rates and describe how to best apply and combine the suite of current protocols, which are all publicly available at protocols.io.

molecular biology↗