Biology subjects

Leite, D. J.

Publications and source records attributed to Leite, D. J..

12 recordsLinked to original sources

bioRxiv2026

Lost and found: beer belly is a novel, ancient regulator of animal development

Single-cell RNA sequencing (scRNA-seq) can provide new insights into the regulation of developmental processes by revealing unknown or overlooked genes. We identified a novel gene called beer belly (bebe) as a marker of a segment addition zone (SAZ) associated cell cluster in a single-cell atlas of the spider Parasteatoda tepidariorum. Here we show that bebe is an ancient toolkit gene encoding a previously uncharacterised protein predicted to be secreted, which likely plays an important role in the development of most animal phyla. However, we could not identify a bebe ortholog in any mammal or holometabolous insect, suggesting it has been lost in these lineages and explaining why it has been overlooked to date. Knock-down of bebe expression in P. tepidariorum demonstrates that it regulates SAZ size and consequently segment size by interacting with Wnt8. Our findings also suggest that bebe may regulate segmentation in other invertebrates and play additional developmental roles in bilaterian and non-bilaterian animals, likely ancestrally, through modulation of Wnt signalling. This study emphasises the promise of applying single-cell sequencing across a diverse range of species to better understand the regulation of development beyond candidate genes from traditional models, allowing us to better characterise the animal developmental toolkit and its evolution.

developmental biology↗

bioRxiv2024

Assessing the impact of whole genome duplication on gene expression and regulation during arachnid development

Whole genome duplication (WGD) generates new genetic material that can contribute to the evolution of the regulation of developmental processes and phenotypic diversification. A WGD occurred in an ancestor of arachnopulmonates (spiders, scorpions, and their relatives), which provides an important independent comparison to WGDs in other animal lineages like those in vertebrates and horseshoe crabs. After WGD, arachnopulmonates retained many duplicated copies (ohnologues) of developmental genes including clusters of homeobox genes, many of which have been inferred to have undergone subfunctionalisation. However, there has been little systematic analysis of gene regulatory sequences and comparison of the expression of ohnologues versus their single-copy orthologues between arachnids. Here we compare the regions of accessible chromatin and gene expression of ohnologues and single-copy genes during three embryonic stages between an arachnopulmonate arachnid, the spider Parasteatoda tepidariorum, and a non-arachnopulmonate arachnid, the harvestman Phalangium opilio. We found that the expression of each spider ohnologue was lower than their single-copy orthologues in the harvestman providing evidence for subfunctionalisation. However, this was not reflected in a reduction in peaks of accessible chromatin because both spider ohnologues and single-copy genes had more peaks than the harvestman genes. We also found peaks of open chromatin that increased in the late stage associated with activation of genes expressed later during embryogenesis in both species. Taken together, our study provides the first genome-wide comparison of gene regulatory sequences and gene expression in arachnids and thus provides new insights into the impact of the arachnopulmonate WGD. Significance statementThe comparison of independent WGD events is essential to understanding their evolutionary outcomes. Here we examine gene expression and chromatin accessibility during the development of two arachnids, one of which underwent an ancient WGD. Our data provide the first direct comparison of the regulation of ohnologues and single-copy genes in arachnids.

genomics↗

bioRxiv2023

Development and patterning of a highly versatile visual system in spiders

Visual systems provide a key interface between organisms and their surroundings, and have evolved in many forms to perform diverse functions across the animal kingdom. Spiders exhibit a range of visual abilities and ecologies, the diversity of which is underpinned by a highly versatile, modular visual system architecture. This typically includes eight eyes of two developmentally distinct types, but the number, size, location, and function of the eyes can vary dramatically between lineages. Previous studies of visual system development in spiders have confirmed that many components of the retinal determination gene (RDG) network are conserved with other arthropods, but so far, comparative studies among spiders are lacking. We characterised visual system development in eight species of spiders representing a range of morphologies, visual ecologies, and phylogenetic positions, to determine how these diverse configurations are formed, and how they might evolve. Combining synchrotron radiation tomography, transcriptomics, in situ hybridisation, and selection analyses, we characterise the repertoires and expression of key RDGs in relation to adult morphology. We identify key molecular players, timepoints, and developmental events that may contribute to adult diversity, in particular the molecular and developmental underpinnings of eye size, number, position, and identity across spiders.

developmental biology↗

bioRxiv2023

Evolution of the spider homeobox gene repertoire by tandem and whole genome duplication

Gene duplication generates new genetic material that can contribute to the evolution of gene regulatory networks and phenotypes. Duplicated genes can undergo subfunctionalisation to partition ancestral functions and/or neofunctionalisation to assume a new function. We previously found there had been a whole genome duplication (WGD) in an ancestor of arachnopulmonates, the lineage including spiders and scorpions but excluding other arachnids like mites, ticks, and harvestmen. This WGD was evidenced by many duplicated homeobox genes, including two Hox clusters, in spiders. However, it was unclear which homeobox paralogues originated by WGD versus smaller-scale events such as tandem duplications. Understanding this is key to determining the contribution of the WGD to arachnopulmonate genome evolution. Here we characterised the distribution of duplicated homeobox genes across eight chromosome-level spider genomes. We found that most duplicated homeobox genes in spiders are consistent with an origin by WGD. We also found two copies of conserved homeobox gene clusters, including the Hox, NK, HRO, Irx, and SINE clusters, in all eight species. Consistently, we observed one copy of each cluster was degenerated in terms of gene content and organisation while the other remained more intact. Focussing on the NK cluster, we found evidence for regulatory subfunctionalisation between the duplicated NK genes in the spider Parasteatoda tepidariorum compared to their single-copy orthologues in the harvestman Phalangium opilio. Our study provides new insights into the relative contributions of multiple modes of duplication to the homeobox gene repertoire during the evolution of spiders and the function of NK genes.

evolutionary biology↗

bioRxiv2023

Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories

Pelagic larval stages are widespread across animals, yet it is unclear if larvae were present in the last common ancestor of animals or whether they evolved multiple times due to common selective pressures. Many marine larvae are at least superficially similar, they are small, swim through beating of ciliated bands and sense the environment with an apical organ structure. To understand these similarities, we have generated single cell atlases for marine larvae from two animal phyla and have compared their cell types. We found clear similarities among ciliary band cells and neurons of the apical organ in the two larvae pointing to possible homology of these structures suggesting a single origin of larvae within the clade analysed here (Lophotrochozoa). We also find several clade specific innovations in each larva, including distinct myocytes and shell gland cells in the oyster larva. Oyster shell gland cells express many novel genes which have made previous gene age estimates for trochophore larvae too young.

evolutionary biology↗

bioRxiv2022

Genome assembly of the polyclad flatworm Prostheceraeus crozieri

Polyclad flatworms are widely thought to be one of the least derived of the flatworm classes and, as such, are well placed to investigate evolutionary and developmental features such as spiral cleavage and larval diversification lost in other platyhelminths. Prostheceraeus crozieri, formerly Maritigrella crozieri, is an emerging model polyclad flatworm that already has some useful transcriptome data but, to date, no sequenced genome. We have used high molecular weight DNA extraction and long read PacBio sequencing to assemble the highly repetitive (67.9%) P. crozieri genome (2.07 Gb). We have annotated 43,325 genes, with 89.7% BUSCO completeness. Perhaps reflecting its large genome, introns were considerably larger than other free-living flatworms, but evidence of abundant transposable elements suggests genome expansion has been principally via transposable elements activity. This genome resource will be of great use for future developmental and phylogenomic research.

genomics↗

bioRxiv2022

The slow evolving genome of the xenacoelomorph worm Xenoturbella bocki

The evolutionary origins of Bilateria remain enigmatic. One of the more enduring proposals highlights similarities between a cnidarian-like planula larva and simple acoel-like flatworms. This idea is based in part on the view of the Xenacoelomorpha as an outgroup to all other bilaterians which are themselves designated the Nephrozoa (protostomes and deuterostomes). Genome data can help to elucidate phylogenetic relationships and provide important comparative data. Here we assemble and analyse the genome of the simple, marine xenacoelomorph Xenoturbella bocki, a key species for our understanding of early bilaterian and deuterostome evolution. Our highly contiguous genome assembly of X. bocki has a size of [~]111 Mbp in 18 chromosome like scaffolds, with repeat content and intron, exon and intergenic space comparable to other bilaterian invertebrates. We find X. bocki to have a similar number of genes to other bilaterians and to have retained ancestral metazoan synteny. Key bilaterian signalling pathways are also largely complete and most bilaterian miRNAs are present. We conclude that X. bocki has a complex genome typical of bilaterians, in contrast to the apparent simplicity of its body plan. Overall, our data do not provide evidence supporting the idea that Xenacoelomorpha are a primitively simple outgroup to other bilaterians and gene presence/absence data support a relationship with Ambulacraria.

evolutionary biology↗

bioRxiv2022

An atlas of spider development at single-cell resolution provides new insights into arthropod embryogenesis

Spiders are a diverse order of chelicerates that diverged from other arthropods over 500 million years ago. Research on spider embryogenesis, particular studies using the common house spider Parasteatoda tepidariorum, has made important contributions to understanding the evolution of animal development, including axis formation, segmentation, and patterning. However, we lack knowledge about the cells that build spider embryos, their gene expression profiles and fate. Single-cell transcriptomic analyses have been revolutionary in describing these complex landscapes of cellular genetics in a range of animals. Therefore, we carried out single-cell RNA sequencing of P. tepidariorum embryos at stages 7, 8 and 9, which encompass the establishment and patterning of the body plan, and initial differentiation of many tissues and organs. We identified 20 cell clusters, from 18.5k cells, which were marked by many developmental toolkit genes, as well as a plethora of genes not previously investigated. There were differences in the cell cycle transcriptional signatures, suggestive of different proliferation dynamics, which related to distinctions between endodermal and some mesodermal clusters, compared with ectodermal clusters. We found many Hox genes were markers of cell clusters, and Hox gene ohnologs often were present in different clusters. This provided additional evidence of sub- and/or neo-functionalisation of these important developmental genes after the whole genome duplication in the arachnopulmonate ancestor (spiders, scorpions, and allies). We also examined the spatial expression of marker genes for each cluster to generate a comprehensive cell atlas of these embryonic stages. This revealed new insights into the cellular basis and genetic regulation of head patterning, hematopoiesis, limb development, gut development, and posterior segmentation. This atlas will serve as a platform for future analysis of spider cell specification and fate, and studying the evolution of these processes among animals at cellular resolution.

developmental biology↗

bioRxiv2020

Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria.

The bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia and Deuterostomia. Protostomia contains the Ecdysozoa and the Lophotrochozoa; Deuterostomia contains the Chordata and the Xenambulacraria (Hemichordata, Echinodermata and Xenacoelomorpha). Their names refer to a supposed distinct origin of the mouth (stoma) in the two clades, but these groups have been differentiated by other embryological characters including embryonic cleavage patterns and different ways of forming their mesoderm and coeloms. Deuterostome monophyly is not consistently supported by recent studies. Here we compare support for Protostomia and Deuterostomia using five recently published, phylogenomic datasets. Protostomia is always strongly supported, especially by longer and higher quality genes. Support for Deuterostomia is always equivocal and barely higher than support for paraphyletic alternatives. Conditions that can cause tree reconstruction errors - inadequate models, short internal branch, faster evolving genes, and unequal branch lengths - correlate with statistical support for monophyletic deuterostomes. Simulation experiments show that support for Deuterostomia could be explained by systematic error. A survey of molecular characters supposedly diagnostic of deuterostomes shows many are not valid synapomorphies. The branch between bilaterian and deuterostome common ancestors, if real, is very short. This finding fits with growing evidence suggesting the common ancestor of all Bilateria had many deuterostome characteristics. This finding has important implications for our understanding of early animal evolution and for the interpretation of some enigmatic Cambrian fossils such as vetulicolians and banffiids.

evolutionary biology↗

bioRxiv2018

A SoxB gene acts as an anterior gap gene and regulates posterior segment addition in the spider Parasteatoda tepidariorum

The Sox gene family encode a set of highly conserved HMG domain transcription factors that regulate many key processes during metazoan embryogenesis. In insects, the SoxB gene Dichaete is the only Sox gene known to be involved in embryonic segmentation. To determine if similar mechanisms are used in other arthropods, we investigated the role of Sox genes during segmentation in the spider Parasteatoda tepidariorum. While Dichaete does not appear to be involved in spider segmentation, RNAi knockdown of the closely related Sox21b-1 gene results in a gap like phenotype in the developing prosoma and also perturbs the sequential addition of opisthosomal segments. We show that this is in part due to a role for Sox21b-1 in regulating the expression of Wnt8 and influencing Delta-Notch signalling during the formation of the segment addition zone. Thus, we have found that two different mechanisms for segmentation in a non-mandibulate arthropod are regulated by a Group B Sox gene. Our work provides new insights into the function of an important and conserved gene family across arthropods, and the evolution of the regulation of segmentation in these animals.

developmental biology↗

bioRxiv2017

Duplication and divergence of Sox genes in spiders

BackgroundThe Sox family of transcription factors are present and conserved in the genomes of all metazoans examined to data and are known to play important developmental roles in vertebrates and insects. However, outside the commonly studied Drosophila model little is known about the extent or conservation of the Sox family in other arthropod species. Here we characterise the Sox family in two chelicerate species, the spiders Parasteatoda tepidariorum and Stegodyphus mimosarum, which have experienced a whole genome duplication (WGD) in their evolutionary history.\n\nResultsWe find that virtually all of the duplicate Sox genes have been retained in these spiders after the WGD. Analysis of the expression of Sox genes in P. tepidariorum embryos indicates that it is likely that some of these genes have neofunctionalised after duplication. Our expression analysis also strengthens the view that an orthologue of vertebrate Group B1 genes, SoxNeuro, is implicated in the earliest events of CNS specification in both vertebrates and invertebrates. In addition, a gene in the Dichaete/Sox21b class is dynamically expressed in the spider segment addition zone, suggestive of an ancient regulatory mechanism controlling arthropod segmentation as recently suggested for flies and beetles. Together with the recent analysis of Sox gene expression in the embryos of other arthropods, our findings are also indicative of conserved functions for some of these genes, including a role for SoxC and SoxD genes in CNS development, SoxF in limb development and a tantalising suggestion that SoxE genes may be involved in gonadogenesis across the metazoa.\n\nConclusionsOur study provides a new chelicerate perspective to understanding the evolution and function of Sox genes and how the retention of duplicates of such important tool-box genes after WGD has contributed to different aspects of spider embryogenesis. Future characterisation of the function of these genes in spiders will help us to better understand the evolution of the regulation of important developmental processes in arthropods and other metazoans including neurogenesis and segmentation.

evolutionary biology↗

bioRxiv2017

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neofunctionalization and/or subfunctionalization since their duplication, and therefore may have contributed to the diversification of spiders and other pulmonate arachnids.

genomics↗