Biology subjects

Georges, A.

Publications and source records attributed to Georges, A..

At least 19 recordsLinked to original sources

bioRxiv2026

DNA methylation regulates a key sex differentiation gene in Pogona vitticeps, a dragon lizard with sex reversal

During embryonic development bipotential gonads differentiate into either testes or ovaries under the direction of mutually exclusive gene networks. DNA methylation has been shown to regulate gene expression and to play a role in many developmental processes. This includes sex differentiation in which DNA methylation is linked to control of key sex genes. Whether DNA methylation regulates sexual differentiation in species where environmental influences such as temperature are involved is less clear. We conducted a genome-wide study in embryonic gonads of the central bearded dragon (Pogona vitticeps), a lizard with temperature induced sex reversal, and compared DNA methylation patterns to gene expression profiles at a stage of early sex differentiation. Overall, sex reversed ZZf females were found to have lower global methylation than both canonical sexes, ZZm males and ZWf females. We found that the expression of a key gene in sex differentiation, Amh, is regulated via DNA methylation. Amh is a driver of testis differentiation and is repressed in genetically determined females, as well as in temperature sex-reversed females, by hypermethylation around its transcription start site. Although the trigger of ovary determination is different in both groups of females, one by genetic complement and one by a temperature signal, downstream regulation of gene expression converges and seems to follow similar mechanisms.

genomics↗

bioRxiv2026

Characterising differential gene expression and alternative splicing in a sex reversing skink, Bassiana duperreyi

In some reptiles, genetic and environmental sex determination interact whereby extreme incubation temperatures override genetic sex determination (GSD) to produce sex-reversed individuals. In one lizard with temperature-influenced GSD, the central bearded dragon, intron retention in the histone-modifier genes Kdm6b and Jarid2 has been implicated as a candidate signal linking temperature to sex. Equivalent intron retention is also present in two species with temperature-dependent sex determination, the red-eared slider turtle and the American alligator. The eastern three-lined skink, Bassiana duperreyi, represents another lizard with temperature induced sex reversal. It has an XY sex determination system in which low temperature incubation causes sex reversal of XX embryos to produce phenotypic males. In this study, we performed splice-aware analysis of RNA sequencing from hatchling brains of the three-lined skink. We investigated differences in alternative splicing and gene expression between the three sex conditions: XY males (XYm), XX females (XXf), and sex-reversed XX males (XXm). Sex reversal specific intron retention was observed in the gene, Ttll7, which only occurred in XXm and not in XYm or XXf. Intron retention in Ttll7 could alter the function of the encoded protein, a tubulin polyglutamylase, but its effect on sex reversal here is unknown. In addition, intron retention in the histone-modifier genes Jarid2 and Kdm6b occurred in all conditions. The presence of Kdm6b and Jarid2 intron retention in all sex conditions suggests that the pattern of intron retention in sex reversal in the eastern three-lined skink is distinct compared to the bearded dragon. We conclude that a different molecular pathway for sex reversal is induced in the three-lined skink, the details of which remain elusive.

genomics↗

bioRxiv2026

Intrinsic Population Dynamics are a Neuronal Substrate for Visual Attention

Perception results from a dynamic interplay between the feedforward processing of sensory stimuli and intrinsic neural activity 1, which is often dismissed as noise 2. To tailor perceptual processes to the organisms current needs on a continuous, moment-to-moment basis, intrinsic dynamics - rather than just being noise - have been suggested to reflect prior expectations 3,4, task demands 5, and attentional focus 6. Here, we identify a novel signature of attentive state in which intrinsic, collective neural activity modulates visuospatial attention by dynamically interacting with sensory input within the superior colliculus (SC), a midbrain hub that integrates bottom-up visual input with top-down signals 7. We show that these intrinsic dynamics organize cell activity into structured, blob-like features that are temporally and topographically localized and that rival sensory-evoked responses in strength. These features emerge as animals learn to engage in the visual detection task, and predict behavioral outcomes on a trial-by-trial basis. Although independent of sensory input or overt behavior, the features can be recruited to enhance visual responses four-fold in the attentive state, generating a "dynamic saliency map" that aligns with reaction times and behavioral outcomes. A computational model indicates that tunable blob-like features can arise from local excitatory-inhibitory interactions within the SC, and enhance sensory-evoked responses in line with observations. Together, our results identify state-dependent intrinsic population activity that interacts with sensory input to give rise to a saliency-map-like representation linked to flexible, goal-directed behavior.

neuroscience↗

bioRxiv2025

Diagnosability to inform species delimitation for the genus Emydura (Testudines: Chelidae) from northern Australia

Understanding the evolutionary history of diversifying lineages and the delineation of species remain major challenges for evolutionary biology. Here we use single nucleotide polymorphisms (SNPs) and sequence fragment presence-absence (SilicoDArT) data to combine phylogenetics and population genetics to assess species boundaries with a focus on diagnosability. We challenge current and proposed taxonomies in a genus of Australian freshwater turtles (Chelidae: Emydura) from northern Australia and southern New Guinea. In a six-step process, we combine phylogeny with the concept of diagnosability based on fixed allelic differences to select diagnosable lineages as candidate species. Four taxa are supported as diagnosable lineages, two of which we elevate to species status. The nuclear and mitochondrial phylogenies differed in important respects, which we attribute to recent or contemporary lateral transfer of mitochondria during hybridization events, deeper historical hybridization or possibly incomplete lineage sorting of the mitochondrial genome. Taxonomic decisions in cases of allopatry require subjective judgement. Our six-step strategy and the necessary (but not sufficient) criterion of diagnosability adds an additional level of objectivity before that subjectivity is applied, and so reduces the risk of taxonomic inflation that can accompany lineage approaches to species delimitation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/664252v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1b89bc8org.highwire.dtl.DTLVardef@fb892dorg.highwire.dtl.DTLVardef@1eb09a8org.highwire.dtl.DTLVardef@1c7300c_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2025

A telomere to telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps

BackgroundThe central bearded dragon (Pogona vitticeps) is widely distributed in central eastern Australia and adapts readily to captivity. Among other attributes, it is distinctive because it undergoes sex reversal from ZZ genotypic males to phenotypic females at high incubation temperatures. Here, we report an annotated telomere to telomere phased assembly of the genome of a female ZW central bearded dragon. ResultsGenome assembly length is 1.75 Gbp with a scaffold N50 of 266.2 Mbp, N90 of 28.1 Mbp, 26 gaps and 42.2% GC content. Most (99.6%) of the reference assembly is scaffolded into 6 macrochromosomes and 10 microchromosomes, including the Z and W microchromosomes, corresponding to the karyotype. The genome assembly exceeds standard recommended by the Earth Biogenome Project (6CQ40): 0.003% collapsed sequence, 0.03% false expansions, 99.8% k-mer completeness, 97.9% complete single copy BUSCO genes and an average of 93.5% of transcriptome data mappable back to the genome assembly. The mitochondrial genome (16,731 bp) and the model rDNA repeat unit (length 9.5 Kbp) were assembled. Male vertebrate sex genes Amh and Amhr2 were discovered as copies in the small non-recombining region of the Z chromosome, absent from the W chromosome. This, coupled with the prior discovery of differential Z and W transcriptional isoform composition arising from pseudoautosomal sex gene Nr5a1, suggests that complex interactions between these genes, their autosomal copies and their resultant transcription factors and intermediaries, determines sex in the bearded dragon. ConclusionThis high-quality assembly will serve as a resource to enable and accelerate research into the unusual reproductive attributes of this species and for comparative studies across the Agamidae and reptiles more generally. Species TaxonomyEukaryota; Animalia; Chordata; Reptilia; Squamata; Iguania; Agamidae; Amphibolurinae; Pogona; Pogona vitticeps (Ahl, 1926) (NCBI:txid103695). Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/651798v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1a9d5fforg.highwire.dtl.DTLVardef@1206061org.highwire.dtl.DTLVardef@97acf7org.highwire.dtl.DTLVardef@1dc939d_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

Adaptively integrated sequencing and assembly of near-complete genomes

Advances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals and plants. However, ongoing development is needed to improve accessibility, affordability, and assembly quality and completeness. Cornetto is a new strategy in which we use programmable selective nanopore sequencing to focus LRS data production onto the unsolved regions of a nascent assembly. This improves assembly quality and streamlines the process, both for humans and non-human vertebrates. Cornetto enables us to generate highly complete diploid human genome assemblies using only nanopore LRS data, surpassing the quality of previous efforts at a fraction of the cost. Cornetto enables genome assembly from challenging sample types like human saliva. Finally, we obtain accurate assemblies for clinically-relevant repetitive loci at the extremes of the genome, demonstrating valid approaches for genetic diagnosis in facioscapulohumeral muscular dystrophy (FSHD) and MUC1-autosomal dominant tubulointerstitial kidney disease (MUC1-ADTKD).

genomics↗

bioRxiv2024

A genome assembly and annotation for the Australian alpine skink Bassiana duperreyi using long-read technologies

The eastern three-lined skink (Bassiana duperreyi) inhabits the Australian high country in the southwest of the continent including Tasmania. It is an oviparous species that is distinctive because it undergoes sex reversal (from XX genotypic females to phenotypic males) at low incubation temperatures. We present a chromosome-scale genome assembly of a Bassiana duperreyi XY male individual, constructed using a combination of PacBio HiFi and ONT long reads scaffolded using Illumina HiC data. The genome assembly length is 1.57 Gb with a scaffold N50 of 222 Mbp, N90 of 26 Mbp, 200 gaps and 43.10% GC content. Most (95%) of the assembly is scaffolded into 6 macrochromosomes, 8 microchromosomes and the X chromosome, corresponding to the karyotype. Fragmented Y chromosome scaffolds (n=11 > 1 Mbp) were identified using Y-specific contigs generated by genome subtraction. We identified two novel alpha-satellite repeats of 187 bp and 199 bp in the putative centromeres that did not form higher order repeats. The genome assembly exceeds the standard recommended by the Earth Biogenome Project; 0.02% false expansions, 99.63% kmer completeness, 94.66% complete single copy BUSCO genes and an average 98.42% of transcriptome data mappable to the genome assembly. The mitochondrial genome (17,506 bp) and the model rDNA repeat unit (15,154 bp) were assembled. The B. duperreyi genome assembly has one of the highest completeness levels for a skink and will provide a resource for research focused on sex determination and thermolabile sex reversal, as an oviparous foundation species for studies of the evolution of viviparity, and for other comparative genomics studies of the Scincidae. Species TaxonomyEukaryota; Animalia; Chordata; Reptilia; Squamata; Scincidae; Lygosominae; Eugongylini; Bassiana (=Acritoscincus); Bassiana duperreyi (Gray, 1838) (NCBI: txid316450).

genomics↗

bioRxiv2024

ZNF827 pleiotropic cardiovascular risk locus involves regulation by Nuclear factor-1

IntroductionSCAD (spontaneous coronary artery dissection) is a form of myocardial infarction that disproportionately affects young women. SCAD is caused by the formation of a hematoma within coronary artery wall, resulting in its blockage. Sixteen SCAD susceptibility loci are currently known, including ZNF827 gene locus on chromosome 4. Several common genetic variations within ZNF827 are also linked to coronary artery disease (CAD), systolic blood pressure (SBP), and ascending aortic diameter. The molecular processes driving these genetic connections, however, are unknown. MethodsWe performed fine-mapping and genetic colocalization analysis at ZNF827 locus on multiple GWAS signals and quantitative expression traits. We explored the regulatory function of sequences of interest using a luciferase reporter system in rat smooth muscle cells. We used siRNA to knockdown the expression of gene and assessed transcriptomic changes through bulk RNA-Seq. ResultsThe genetic association signals for SCAD, CAD, blood pressure, and aorta dimensions could all be explained by a single causal variant. We identified rs13128814 as the most likely causative variant. This variant overlaps epigenetic regulatory markers specifically active in vascular SMCs and fibroblasts. A 1kb region containing the SCAD-risk allele (A) of rs13128814 variant had a transcriptional activation impact, while the protective allele (G) had no effect. In silico predictions found nuclear factor 1 (NF1) transcription factors preferentially bind to the A allele of rs13128814. We found that overexpressing NFIA (Nuclear Factor 1 A-Type) activated transcription in this area. SCAD association and ZNF827 eQTL colocalization in various vascular tissues suggested the latter as a plausible target gene in this locus. Knockdown of ZNF827 in iPSC-derived SMCs and fibroblasts, followed by RNA-seq, identified a large number of dysregulated genes, including multiple genes involved in cardiovascular disease. ConclusionOur findings in ZNF827 locus support the hypothesis that the rs13128814 variant, which may affect the binding of NF1 family transcription factors and cause ZNF827 expression to be deregulated, is the molecular mechanism underpinning the relationship of the ZNF827 locus with numerous cardiovascular disorders. ZNF827 acts as a regulator of gene expression in vascular SMCs and fibroblasts. Further investigation of ZNF827 function in vascular tissue will be required to understand the implications of its dysregulation on cardiovascular physiopathology.

cell biology↗

bioRxiv2023

Both phenotypic and genotypic sex influence sex chromosome dosage compensation in a sex reversing lizard

BackgroundLizards have sex determination systems that can differ between even closely related species. These include XY and ZW systems, and thermolabile systems where genes and temperature interact to determine sex. The eastern three-lined skink (Bassiana duperreyi) has a differentiated XY sex determination system, in which low temperature incubation during development can cause female to male sex reversal, producing XX males. This provides a unique opportunity to investigate how genotype and sexual phenotype affect dosage compensation. ResultsHere, we present a draft genome assembly of the Eastern three-lined skink generated from nanopore sequencing. We also generated transcriptomes from brain and heart tissue of normal adult males and females, along with brain tissue of sex-reversed XX males. We observed partial dosage compensation between XX females and XY males in both brain and heart, with median gene expression from the X in normal males being 0.7 times that of normal females. In brain of sex reversed XX males the median X chromosome output matched that of the normal XX female level, and not that of normal XY males. ConclusionsPartial dosage compensation in the Eastern three-lined skink is similar to several other species of lizard. However, here for the first time we describe dosage compensation in a lizard with natural sex reversal, and show that in sex reversed individuals dosage compensation of the X chromosome follows genotypic sex and not phenotypic sex.

genomics↗

bioRxiv2023

Regulatory mechanisms in multiple vascular diseases locus LRP1 involve repression by SNAIL and extracellular matrix remodeling

BackgroundGenome-wide association studies (GWAS) implicate common genetic variations in the low-density lipoprotein receptor-related protein 1 locus (LRP1) in risk for multiple vascular diseases and traits. However, the underlying biological mechanisms are unknown. MethodsFine mapping analyses included Bayesian colocalization to identify the most likely causal variant. Human induced pluripotent stem cells (iPSC) were genome-edited using CRISPR-Cas9 to delete or modify candidate enhancer regions, and generate LRP1 knockout cell lines (KO). Cells were differentiated into smooth muscle cells (SMCs) through a mesodermal lineage. Transcription regulation was assessed using luciferase reporter assay, transcription factor knockdown and chromatin immunoprecipitation. Phenotype changes in cells were conducted using cellular assays, bulk RNA-sequencing and mass spectrometry. ResultsMulti-trait co-localization analyses pointed at rs11172113 as the most likely causal variant in LRP1 for fibromuscular dysplasia, migraine, pulse pressure and pulmonary function trait. We found rs11172113-T allele to associate with higher LRP1 expression. Genomic deletion in iPSC-derived SMCs supported rs11172113 to locate in an enhancer region regulating LRP1 expression. We found transcription factors MECP2 and SNAIL to repress LRP1 expression through an allele-specific mechanism, involving SNAIL interaction with disease risk allele. LRP1 KO decreased iPSC-derived SMCs proliferation and migration. Differentially expressed genes were enriched for collagen-containing extracellular matrix, connective tissue and lung development. LRP1 KO showed potentiated canonical TGF-{beta} signaling through enhanced phosphorylation of SMAD2/3. Analyses of protein content of decellularized extracts indicated partial extracellular matrix (ECM) remodeling involving enhanced secretion of CYR61, a known LRP1 ligand involved in vascular integrity and TIMP3, implicated in extracellular matrix maintenance and also known to interact with LRP1. ConclusionsOur findings support allele specific LRP1 gene repression by the endothelial-to-mesenchymal transition regulator SNAIL. We propose decreased LRP1 expression in SMCs to remodel the ECM enhanced by TGF- {beta} as a potential mechanism of this pleiotropic locus for vascular diseases. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=193 HEIGHT=200 SRC="FIGDIR/small/539992v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@11926a8org.highwire.dtl.DTLVardef@390a37org.highwire.dtl.DTLVardef@cdad4dorg.highwire.dtl.DTLVardef@12cbf92_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

Distances and their visualization in studies of spatial-temporal genetic variation using single nucleotide polymorphisms (SNPs)

O_LIDistance measures are widely used for examining genetic structure in datasets that comprise many individuals scored for a very large number of attributes. Genotype datasets composed of single nucleotide polymorphisms (SNPs) typically contain bi-allelic scores for tens of thousands if not hundreds of thousands of loci. C_LIO_LIWe examine the application of distance measures to SNP genotypes and sequence tag presence-absences (SilicoDArT) and use real datasets and simulated data to illustrate pitfalls in the application of genetic distances and their visualization. C_LIO_LIEuclidean Distance is the metric of choice in many distance studies. However, other measures may be preferable because of their underlying models of divergence, population demographic history and linkage disequilibrium, because it is desirable to down-weight joint absences, or because of other characteristics specific to the data or analyses. Distance measures for SNP genotype data that depend on the arbitrary choice of reference and alternate alleles (e.g. Bray-Curtis distance) should not be used. Careful consideration should be given to which state is scored zero when applying binary distance measures to sequence tag presence-absences (e.g. Jaccard distance). C_LIO_LIMissing values that arise in the SNP discovery process can cause displacement of affected individuals from their natural groupings and artificial inflation of confidence envelopes, leading to potential misinterpretation. Filtering on missing values then imputing those that remain avoids distortion in visual representations. Failure of a distance measure to conform to metric and Euclidean properties is important but only likely to create unacceptable outcomes in extreme cases. Lack of randomness in the selection of individuals (e.g. inclusion of sibs) and lack of independence of both individuals and loci (e.g. polymorphic haploblocks), can lead to substantial and otherwise inexplicable distortions of the visual representations and again, potential misinterpretation. C_LI

bioinformatics↗

bioRxiv2022

Genomic, transcriptomic and proteomic depiction of iPSC-derived smooth muscle cells as emerging cellular models for arterial diseases

BackgroundVascular smooth muscle cells (VSMCs) plasticity is a central mechanism in cardiovascular health and disease. We aimed at providing deep cellular phenotyping, epigenomic and proteomic depiction of SMCs derived from induced pluripotent stem cells (iPSCs) and evaluating their potential as cellular models in the context of complex genetic arterial diseases. MethodsWe differentiated 3 human iPSC lines using either RepSox (R-SMCs) or PDGF-BB and TGF-{beta} (TP-SMCs), during the second half of a 24-days-long protocol. In addition to cellular assays, we performed RNA-Seq and assay for transposase accessible chromatin (ATAC)-Seq at 6 time-points of differentiation. The extracellular matrix content (matrisome) generated by iPSCs derived SMCs was analyzed using mass spectrometry. ResultsBoth iPSCs differentiation protocols generated SMCs with positive expression of SMC markers. TP-SMCs exhibited greater capacity of proliferation, migration and lower calcium release in response to contractile stimuli compared to R-SMCs. RNA-Seq data showed that genes involved in the contractile function of arteries were highly expressed in R-SMCs compared to TP-SMCs or primary SMCs. Matrisome analyses supported an overexpression of proteins involved in wound repair in TP-SMCs and a higher secretion of basal membrane constituents by R-SMCs. Open chromatin regions of R-SMCs and TP-SMCs were significantly enriched for variants associated with coronary artery disease and blood pressure, while only TP-SMCs were enriched for variants associated with peripheral artery disease. ConclusionsOur study portrayed two iPSCs derived SMCs models presenting complementary cellular phenotypes of high relevance to SMC plasticity. In combination with genome-editing tools, our data supports high relevance of the use of these cellular models to the study of complex regulatory mechanisms at genetic risk loci involved in several arterial diseases. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=179 HEIGHT=200 SRC="FIGDIR/small/490058v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@1f1002corg.highwire.dtl.DTLVardef@1426fa7org.highwire.dtl.DTLVardef@b05b56org.highwire.dtl.DTLVardef@3c6e88_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2022

dartR v2: an accessible genetic analysis platform for conservation, ecology, and agriculture

O_LIInnumerable approaches to analyse genetic data are now available to guide conservation, ecological and agricultural projects. However, streamlined and accessible tools are needed to bring these approaches within reach of a broader user base. dartR was released in 2018 to lessen the intrinsic complexity of analysing single nucleotide polymorphisms (SNPs) and dominant markers (presence/absence of amplified sequence tags) by providing user-friendly data quality control and marker selection functions. dartR users have grown steadily since its release and provided valuable feedback on their interaction with the package allowing us to enhance dartR capabilities. C_LIO_LIHere, we present Version 2 of dartR. In this iteration, we substantially increased the number of available functions from 45 to 144. In addition to improved functionality, we focused on enhancing the user experience by extending plot customisation, function standardisation, increasing user support and function speed. dartR provides functions for various stages in analysing genetic data, from data manipulation to reporting. C_LIO_LIdartR provides many functions for importing, exporting and linking to other packages, to provide an easy-to-navigate conduit between data generation and analysis options already available via other packages. We also implemented simulation functions whose results can be analysed seamlessly with several other dartR functions. C_LIO_LIAs more methods and approaches mature to inform conservation, we envision that accessible platforms to analyse genetic data will play a crucial role in translating science into practice. C_LI

genomics↗

bioRxiv2021

Diversity of reptile sex chromosome evolution revealed by cytogenetic and linked-read sequencing

Reptile sex determination is attracting much attention because the great diversity of sex-determination and dosage compensation mechanisms permits us to approach fundamental questions about sex chromosome turnover and evolution. However, reptile sex chromosome variation remains largely uncharacterized and no reptile master sex determination genes have yet been identified. Here we describe a powerful and cost-effective "chromosomics" approach, combining probes generated from the microdissected sex chromosomes with transcriptome sequencing to explore this diversity in non-model Australian reptiles with heteromorphic or cryptic sex chromosomes. We tested the pipeline on a turtle, a gecko, and a worm-lizard, and we also identified sequences located on sex chromosomes in a monitor lizard using linked-read sequencing. Genes identified on sex chromosomes were compared to the chicken genome to identify homologous regions among the four species. We identified candidate sex determining genes within these regions, including conserved vertebrate sex-determining genes pdgfa, pdgfra amh and wt1, and demonstrated their testis or ovary-specific expression. All four species showed gene-by-gene rather than chromosome-wide dosage compensation. Our results imply that reptile sex chromosomes originated by independent acquisition of sex-determining genes on different autosomes, as well as translocations between different ancestral macro- and micro-chromosomes. We discuss the evolutionary drivers of the slow differentiation, but rapid turnover, of reptile sex chromosomes.

genomics↗

bioRxiv2021

Draft genomes of a male and female Australian jacky dragon (Amphibolurus muricatus)

Australia is remarkable for its lizard diversity, with very high endemicity because of continental-scale diversification and adaptive radiation during prolonged isolation. We here employed stLFR linked-read technology to generate male and female draft genomes of the jacky dragon Amphibolurus muricatus, an Australian dragon lizard (family Agamidae; the agamids). The assemblies are 1.8 Gb in size and have a repeat content (39%) and GC content (42%) similar to other dragon lizards. The longest scaffold was 39.7 Mb (female) and 9.6 Mb (male), with corresponding scaffold N50 values of 6.8 Mb and 1.6 Mb. The BUSCO (Sauropsida database) completeness percentages were 90.2% and 88.8% respectively. Phylogenetic comparisons show that Australian and Asian agamids split from a common ancestor about 80 million years ago, while the Australian genera Amphibolurus, Pogona, and the basal Intellagama split [~]37 million years ago. The draft A. muricatus assemblies will be a valuable resource for understanding lizard sex determination and the evolution and conservation of Australian dragon lizards.

genomics↗

bioRxiv2021

Developmental dynamics of sex reprogramming by high incubation temperatures in a dragon lizard

In some vertebrate species, gene-environment interactions can determine sex, driving bipotential gonads to differentiate into either ovaries or testes. In the central bearded dragon (Pogona vitticeps), the genetic influence of sex chromosomes (ZZ/ZW) can be overridden by high incubation temperatures, causing ZZ male to female sex reversal. Previous research showed ovotestes, a rare gonadal phenotype with traits of both sexes, develop during sex reversal, leading to the hypothesis that sex reversal relies on high temperature feminisation to outcompete the male genetic cue. To test this, we conducted temperature switching experiments at key developmental stages, and analysed the effect on gonadal phenotypes using histology and transcriptomics. We found sexual fate is more strongly influenced by the ZZ genotype than temperature. Any exposure to low temperatures (28{degrees}C) caused testes differentiation, whereas sex reversal required longer exposure to high temperatures. We revealed ovotestes exist along a spectrum of female-ness to male-ness at the transcriptional level. We found inter-individual variation in gene expression changes following temperature switches, suggesting both genetic sensitivity to, and the timing and duration of the temperature cue influences sex reversal. These findings bring new insights to the mechanisms underlying sex reversal, improving our understanding of thermosensitive sex systems in vertebrates.

developmental biology↗

bioRxiv2021

Microchromosomes are building blocks of bird, reptile and mammal chromosomes

Microchromosomes, once considered unimportant shreds of the chicken genome, are gene rich elements with a high GC content and few transposable elements. Their origin has been debated for decades. We used cytological and whole genome sequence comparisons, and chromosome conformation capture, to trace their origin and fate in genomes of reptiles, birds and mammals. We find that microchromosomes as well as macrochromosomes are highly conserved across birds, and share synteny with single small chromosomes of the chordate amphioxus, attesting to their origin as elements of an ancient animal genome. Turtles and squamates (snakes and lizards) share different subsets of ancestral microchromosomes, having independently lost microchromosomes by fusion with other microchromosomes or macrochromosomes. Patterns of fusions were quite different in different lineages. Cytological observations show that microchromosomes in all lineages are spatially separated into a central compartment at interphase and during mitosis and meiosis. This reflects higher interaction between microchromosomes than with macrochromosomes, as observed by chromosome conformation capture, and suggests some functional coherence. In highly rearranged genomes fused microchromosomes retain most ancestral characteristics, but these may erode over evolutionary time; surprisingly de novo microchromosomes have rapidly adopted high interaction. Some chromosomes of early branching monotreme mammals align to several bird microchromosomes, suggesting multiple microchromosome fusions in a mammalian ancestor. Subsequently multiple rearrangements fueled the extraordinary karyotypic diversity of therian mammals. Thus microchromosomes, far from being aberrant genetic elements, represent fundamental building blocks of amniote chromosomes, and it is mammals, rather than reptiles, that are atypical. Significance StatementGenomes of birds and reptiles, but not mammals, consist of a few large chromosomes and many tiny microchromosomes. Once considered unimportant shreds of the genome, microchromosomes are gene rich and highly conserved among bird and reptiles, and share homology with one or more of the tiny chromosomes of an invertebrate that diverged from the vertebrate lineage 684 million years ago. Microchromosomes interact strongly and crowd together at the centre of cells, suggesting functional coherence. Many microchromosomes have been lost independently in turtles, snakes and lizards as they have fused with each other, or with larger chromosomes. In mammals they have completely disappeared, yet some chromosomes of the basal platypus line up with several microchromosomes, suggesting that they are the building blocks of the atypically variable chromosomes of mammals.

genomics↗

bioRxiv2021

Phylogenetic study of thermophilic genera Anoxybacillus, Geobacillus, Parageobacillus, and proposal of a new classification Quasigeobacillus gen. nov.

A phylogenetic study of Anoxybacillus, Geobacillus and Parageobacillus was performed using publicly available whole genome sequences. A total of 113 genomes were selected for phylogenomic metrics including calculation of Average Nucleotide Identity (ANI) and Average Amino acid Identity (AAI), and a maximum likelihood tree was built from alignment of a set of 662 orthologous core genes. The combined results from the core gene tree and ANI and AAI dendrograms show that the genomes split into two main clades, clade I containing all Geobacillus, all Parageobacillus and some species of Anoxybacillus, and clade II, containing the majority of Anoxybacillus species. Clade I is further partitioned into three clades, consisting separately of Geobacillus, Parageobacillus, and a third clade which we suggest should be elevated to a new genus Quasigeobacillus gen. nov. Two species of Anoxybacillus showed inconsistent positioning among the trees produced by differing methods and could not be clearly resolved into any of the three existing genera or the new genus. This research shows the importance of considering closely related genera together when studying phylogeny or assigning genomic affinities.

microbiology↗