Biology subjects

Baril, T.

Publications and source records attributed to Baril, T..

11 recordsLinked to original sources

bioRxiv2026

Comparative analyses reveal rapid turnover and emergence of transitory 3D genome architectures in the fungal kingdom

The three-dimensional architecture of genomes plays major roles in biological processes such as gene expression and DNA replication. The architecture of genomes has evolved substantially with distinct 3D genome shapes being identified in different lineages. The factors driving the evolution of genome architectures have primarily been assessed in animals and plants, yet large parts of the tree of life remain poorly explored. Fungi offer excellent models to assess the evolution of 3D genome architecture in a phylogenetic context given rapid genome size changes and chromosomal sequence turnover. Here, we analyzed chromosome conformation data (Hi-C) of 55 fungal species with completely assembled genomes. We identified ten species with Rabl, one species with chromosome territories and ten with a novel, intermediate chromosomal architecture, where centromeres and telomeres are at opposites in the nucleus (Rabl-like) but with a distinct 3D organization. This "bean" shape likely evolved several times independently. The discovery of a genome with a chromosome territories conformation was unexpected, as this was thought to be associated with condensin II subunits in the animal kingdom. We investigated whether 3D conformations correlated with genome size and repeat content using phylogenetic independent contrasts, however we found no genomic feature to be significantly associated with changes in genome architecture. Overall, we report the first large-scale comparison of 3D genome architecture in the fungal kingdom and identify a novel "bean" configuration. SignificanceThree-dimensional genome architecture strongly influences gene regulation, yet little is known about 3D genome architecture in an organismal group that has adapted to nearly all ecosystems on our planet, Fungi. We reconstructed 3D genome architectures from 55 fungal species covering three different phyla and demonstrate that most species do not conform to the existing definitions of 3D architectures. We identified the first case of Chromosome Territories in the Fungal Kingdom and a previously undescribed organization that we label "bean-shaped", and show that some fungal species do not conform to the canonical 3D-architecture categories of the animal and plant kingdoms. The diversity of genome architectures observed in the study could reflect the diverse gene regulatory mechanisms known from Fungi and marks the beginning of mapping out 3D genome organizations in this diverse clade. Further research in this area will uncover the diverse strategies employed by Fungi in light of their rapid adaptation.

evolutionary biology↗

bioRxiv2026

Transposable elements underlie chromosomal fusions and fissions in a highly species-rich group of butterflies

Chromosomal fusions and fissions reshape karyotypes, recombination landscapes and patterns of speciation, yet the molecular mechanisms underlying their formation remain poorly understood. Comparing 37 chromosome-level Erebia genomes, a butterfly genus with exceptionally high rates of chromosomal rearrangements, we identify more than 250 fusion and fission events and characterise over one hundred breakpoints. Breakpoints and homologous regions in the most closely related species with the unfused chromosomal state are significantly enriched for repetitive elements, particularly R1-like LINE retrotransposons. This provides evidence for the implication of a specific LINE family in inter-chromosomal rearrangements that promote species diversification. R1-like elements at breakpoints are longer than copies in other genomic regions, consistent with ectopic recombination requiring sufficient sequence length and similarity. However, the burst of rearrangements in the youngest and most species-rich Erebia clade does not coincide with increased R1-like activity, indicating that repeat dynamics does not solely account for the elevated rates of fusion and fission. Indeed, we detect lineage-specific gains and losses of genes involved in DNA repair and chromatin organisation that coincide with this burst, suggesting a genomic context that facilitates chromosomal fusions and fissions. Our findings refine the role of repetitive elements in inter-chromosomal rearrangements, identify a candidate substrate for ectopic recombination in Lepidoptera, and establish a framework for understanding how karyotypic diversity arises.

evolutionary biology↗

bioRxiv2024

Genomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants

The naturally selected fungal crop (Leucoagaricus gongylophorus) farmed by leafcutter ants shows striking parallels with artificially selected plant crops domesticated by humans (e.g., polyploidy, engorged nutritional rewards, dependence on cultivation). To date, poorly resolved L. gongylophorus genomes based on short-read sequencing have constrained hypotheses about how millions of years under cultivation by ants shaped the fungal crop genome and potentially drove domestication. We use PacBio HiFi sequencing of L. gongylophorus from the leafcutter ant Atta colombica to identify 18 putatively novel biosynthetic gene clusters that likely cemented life as a cultivar (e.g., plant fragment degradation, ant-farmer communication, antimicrobial defense). Comparative analyses with cultivated and free-living fungi showed genomic signatures of stepwise domestication transitions: 1) free-living to ant-cultivated: loss of genes conferring stress response and detoxification, 2) hyphal food to engorged nutritional rewards: expansions of genes governing cellular homeostasis, carbohydrate metabolism, and siderophore biosynthesis, and 3) detrital provisioning to freshly cut plant fragments: gene expansions promoting cell wall biosynthesis, fatty acid metabolism, and DNA repair. Comparisons across L. gongylophorus fungi farmed by three leafcutter ant species highlight genomic signatures of exclusively vertical clonal propagation and widespread transposable element activity. These results show how natural selection can shape domesticated cultivar genomes towards long-term ecological resilience of farming systems that have thrived across millennia.

evolutionary biology↗

bioRxiv2024

The sensory shark: high-quality phenotypic, genomic and transcriptomic data for the small spotted catshark Scyliorhinus canicula reveal the molecular bases of sensory organ evolution in jawed vertebrates

Cartilaginous fishes (chimaeras and elasmobranchs -sharks, skates and rays) hold a key phylogenetic position to explore the origin and diversifications of jawed vertebrates. Here, we report and integrate reference genomic, transcriptomic and morphological data in the small-spotted catshark Scyliorhinus canicula to shed light on the evolution of sensory organs. We first characterise general aspects of the catshark genome, confirming the high conservation of genome organisation across cartilaginous fishes, and investigate population genomic signatures. Taking advantage of a dense sampling of transcriptomic data, we also identify gene signatures for all major organs, including chondrichthyan specializations, and evaluate expression diversifications between paralogs within major gene families involved in sensory functions. Finally, we combine these data with 3D synchrotron imaging and in situ gene expression analyses to explore chondrichthyan-specific traits and more general evolutionary trends of sensory systems. This approach brings to light, among others, novel markers of the ampullae of Lorenzini electro-sensory cells, a duplication hotspot for crystallin genes conserved in jawed vertebrates, and a new metazoan clade of the Transient-receptor potential (TRP) family. These resources and results, obtained in an experimentally tractable chondrichthyan model, open new avenues to integrate multiomics analyses for the study of elasmobranchs and jawed vertebrates.

evolutionary biology↗

bioRxiv2022

The origin of a new chromosome in gerbils

Chromosome-scale genome assemblies based on ultra-long read sequencing technologies are able to illuminate previously intractable aspects of genome biology such as fine-scale centromere structure and large-scale variation in genome features such as heterochromatin, GC content, recombination rate, and gene content. We present here a new chromosome-scale genome of the Mongolian gerbil (Meriones unguiculatus) which includes the complete sequence of all centromeres. Gerbil centromeres are composed of four different repeats of length 6pb, 37bp, 127bp, or 1747bp which occur in simple alternating arrays and span 1-6Mb. Gerbil genomes have both an extensive set of GC-rich genes and chromosomes strikingly enriched for constitutive heterochromatin. We sought to determine if there was a link between these two phenomena and found that the two heterochromatic chromosomes of the Mongolian gerbil have distinct underpinnings: Chromosome 5 has a large block of intra-arm heterochromatin as the result of a massive expansion of centromeric repeats, while chromosome 13 is comprised of extremely large (>150kb) repeated sequences. In addition to characterizing centromeres, our results demonstrate the importance of including karyotypic features such as chromosome number and the locations of centromeres in the interpretation of genome sequence data, and highlight novel patterns involved in the evolution of chromosomes.

genomics↗

bioRxiv2022

The genome sequence of the scarce swallowtail, Iphiclides podalirius

The scarce swallowtail, Iphiclides podalirius (Linnaeus, 1758), is a species of butterfly in the family Papilionidae. Here we present a chromosome-level genome assembly for I. podalirius as well as gene and transposable element annotations. We estimate heterozygosity within different partitions of the genome and find a negative correlation between chromosome length and heterozygosity at fourfold-degenerate sites. This high quality genome assembly, the first for any species in the tribe Leptocircini, will be a valuable resource for population genomics in the genus Iphiclides and comparative genomics more generally.

evolutionary biology↗

bioRxiv2021

The genome sequence of the lesser marbled fritillary, Brenthis ino, and evidence for a segregating neo-Z chromosome

The lesser marbled fritillary, Brenthis ino (Rottemburg, 1775), is a species of Palearctic butterfly. Male B. ino individuals have been reported to have between 12 and 14 pairs of chromosomes, a much reduced chromosome number than is typical in butterflies. Here we present a chromosome-level genome assembly for B. ino, as well as gene and transposable element annotations. The assembly is 411.8 Mb in span with contig and scaffold N50s of 9.6 and 29.5 Mb respectively. We also show evidence that the male individual from which we generated HiC data was heterozygous for a neo-Z chromosome, consistent with inheriting 14 chromosomes from one parent and 13 from the other. This genome assembly will be a valuable resource for studying chromosome evolution in Lepidoptera, as well as for comparative and population genomics more generally.

evolutionary biology↗

bioRxiv2021

Broadscale evolutionary analysis of eukaryotic DDE transposons

DDE transposons are widespread selfish genetic elements, often comprising a large proportion of eukaryotic genomic content. DDE transposons have also made important contributions to varied host functions during eukaryotic evolution, and their transposases may be the most abundant and ubiquitous genes in nature. Yet much remains unknown about their basic biology. We employ a broadscale screen of DDE transposase diversity to characterise major evolutionary patterns for all 19 DDE transposon superfamilies. We identify considerable variation in DDE transposon superfamily size, and find a dominant association with animal hosts. While few DDE transposon superfamilies specialise in plants or fungi, the four largest superfamilies contain major plant-associated clades, at least partially underlying their relative success. We recover a pattern of host conservation among DDE transposon lineages, punctuated by occasional horizontal transfer to distantly related hosts. Host range and horizontal transfer are strongly positively correlated with DDE transposon superfamily size, arguing against variation in the capacity for generalism. We find that rates of horizontal transfer decrease sharply with increasing levels of host taxonomy, supporting the existence of host-associated barriers to DDE transposon spread. Overall, despite their relatively simple genetic structure, our results imply that trade-offs in host adaptation are important in defining DDE transposon-host relationships and evolution. In addition, our study provides a phylogenetic framework to facilitate the identification and further analysis of DDE transposons.

genomics↗

bioRxiv2020

Horseshoe crab genomes reveal the evolutionary fates of genes and microRNAs after three rounds (3R) of whole genome duplication

Whole genome duplication (WGD) has occurred in relatively few sexually reproducing invertebrates. Consequently, the WGD that occurred in the common ancestor of horseshoe crabs ~135 million years ago provides a rare opportunity to decipher the evolutionary consequences of a duplicated invertebrate genome. Here, we present a high-quality genome assembly for the mangrove horseshoe crab Carcinoscorpius rotundicauda (1.7Gb, N50 = 90.2Mb, with 89.8% sequences anchored to 16 pseudomolecules, 2n = 32), and a resequenced genome of the tri-spine horseshoe crab Tachypleus tridentatus (1.7Gb, N50 = 109.7Mb). Analyses of gene families, microRNAs, and synteny show that horseshoe crabs have undergone three rounds (3R) of WGD, and that these WGD events are shared with spiders. Comparison of the genomes of C. rotundicauda and T. tridentatus populations from several geographic locations further elucidates the diverse fates of both coding and noncoding genes. Together, the present study represents a cornerstone for a better understanding of the consequences of invertebrate WGD events on evolutionary fates of genes and microRNAs at individual and population levels, and highlights the genetic diversity with practical values for breeding programs and conservation of horseshoe crabs.

evolutionary biology↗

bioRxiv2020

Chromosomal-level reference genome of the incense tree Aquilaria sinensis

Trees in the genus Aquilaria (Thymelaeaceae) are known as lign aloes, and are native to the forests of southeast Asia. Lign aloes produce agarwood as an antimicrobial defence. Agarwood has a long history of cultural and medicinal use, and is of considerable commercial value. However, due to habitat destruction and over collection, lign aloes are threatened in the wild. We present a chromosomal-level assembly for Aquilaria sinensis, a lign aloe endemic to China known as the incense tree, based on Illumina short-read, 10X Genomics linked-read, and Hi-C sequencing data. Our 783.8Mbp A. sinensis genome assembly is of high physical contiguity, with a scaffold N50 of 87.6Mbp, and high completeness, with a 95.8% BUSCO score for eudicotyledon genes. We include 17 transcriptomes from various plant tissues, providing a total of 35,965 gene models. We reveal the first complete set of genes involved in sesquiterpenoid production, plant defence, and agarwood production for the genus Aquilaria, including genes involved in the biosynthesis of sesquiterpenoids via the mevalonic acid (MVA), 1-deoxy-D-xylulose-5-phosphate (DXP), and methylerythritol phosphate (MEP) pathways. We perform a detailed repeat content analysis, revealing that transposable elements account for [~]61% of the genome, with major contributions from gypsy-like and copia-like LTR retroelements. We also provide a comparative analysis of repeat content across sequenced species in the order Malvales. Our study reveals the first chromosomal-level genome assembly for a tree in the genus Aquilaria and provides an unprecedented opportunity to address a variety of applied, genomic and evolutionary questions in the Thymelaeaceae more widely.

genomics↗

bioRxiv2020

Millipede genomes reveal unique adaptation of genes and microRNAs during myriapod evolution

The Myriapoda including millipedes and centipedes is of major importance in terrestrial ecology and nutrient recycling. Here, we sequenced and assembled two chromosomal-scale genomes of millipedes Helicorthomorpha holstii (182 Mb, N50 18.11 Mb mainly on 8 pseudomolecules) and Trigoniulus corallinus (449 Mb, N50 26.78 Mb mainly on 15 pseudomolecules). Unique defense systems, genomic features, and patterns of gene regulation in millipedes, not observed in other arthropods, are revealed. Millipedes possesses a unique ozadene defensive gland unlike the venomous forcipules in centipedes. Sets of genes associated with anti-microbial activity are identified with proteomics, suggesting that the ozadene gland is not primarily an antipredator adaptation (at least in T. corallinus). Macro-synteny analyses revealed highly conserved genomic blocks between centipede and the two millipedes. Tight Hox and the first loose ecdysozoan ParaHox homeobox clusters are identified, and a myriapod-specific genomic rearrangement including Hox3 is also observed. The Argonaute proteins for loading small RNAs are duplicated in both millipedes, but unlike insects, an argonaute duplicate has become a pseudogene. Evidence of post-transcriptional modification in small RNAs, including species-specific microRNA arm switching that provide differential gene regulation is also obtained. Millipede genomes reveal a series of unique genomic adaptations and microRNA regulation mechanisms have occurred in this major lineage of arthropod diversity. Collectively, the two millipede genomes shed new light on this fascinating but poorly understood branch of life, with a highly unusual body plan and novel adaptations to their environment.

evolutionary biology↗