Biology subjects

Hejnol, A.

Publications and source records attributed to Hejnol, A..

30 records · Page 2Linked to original sources

bioRxiv2020

Conservative route to extreme genome compaction in a miniature annelid

The causes and consequences of genome reduction in animals are unclear, because our understanding of this process mostly relies on lineages with often exceptionally high rates of evolution. Here, we decode the compact 73.8 Mb genome of Dimorphilus gyrociliatus, a meiobenthic segmented worm. The D. gyrociliatus genome retains traits classically associated with larger and slower-evolving genomes, such as an ordered, intact Hox cluster, a generally conserved developmental toolkit, and traces of ancestral bilaterian linkage. Unlike some other animals with small genomes, the analysis of the D. gyrociliatus epigenome revealed canonical features of genome regulation, excluding the presence of operons and trans-splicing. Instead, the gene dense D. gyrociliatus genome presents a divergent Myc pathway, a key physiological regulator of growth, proliferation, and genome stability in animals. Altogether, our results uncover a conservative route to genome compaction in annelids, reminiscent of that observed in the vertebrate Takifugu rubripes.

genomics↗

bioRxiv2019

Hox gene expression during the development of the phoronid Phoronopsis harmeri

BackgroundPhoronida is a small group of marine worm-like suspension feeders, which together with brachiopods and bryozoans form the clade Lophophorata. Although their development is well studied on the morphological level, data regarding gene expression during this process are scarce and restricted to the analysis of relatively few transcription factors. Here we present a description of the expression patterns of Hox genes during the embryonic and larval development of the phoronid Phoronopsis harmeri.\n\nResultsWe identified sequences of 8 Hox genes in the transcriptome of P. harmeri and determined their expression pattern during embryonic and larval development using whole mount in situ hybridization. We found that none of the Hox genes is expressed during embryonic development. Instead their expression is initiated in the later developmental stages, when the larval body is already formed. The Hox genes are expressed in the metasomal sac, posterior mesoderm and junction between midgut and hindgut - structures that represent rudiments of the adult worm, which emerges through the process of drastic metamorphosis. Additionally, two Hox genes are expressed in the posterior telotroch, which develops in the later larval stages.\n\nConclusionsThe lack of Hox gene expression during early development of P. harmeri indicates that the larval body develops without positional information of the Hox patterning system. Such phenomenon might be a consequence of the evolutionary intercalation of the larval form into an ancestral, direct life cycle of phoronids. Accordingly, the specific actinotrocha larva found only in Phoronida, would represent an evolutionary novelty, for which an alternative molecular mechanism of antrerior-posterior patterning was recruited. Another explanation of the observed Hox gene expression is that the actinotrocha represents a \"head larva\", which is composed of the most anterior body region that is devoid of Hox gene expression. This implies that the Hox patterning system is used for the positional information of the trunk rudiments and is, therefore, delayed to the later larval stages. Future investigation on head-specific genes expression is needed to test this hypothesis.

developmental biology↗

bioRxiv2019

Molecular patterning during the development of Phoronopsis harmeri reveals similarities to rhynchonelliform brachiopods

BackgroundAnswering the question how conserved patterning systems are across evolutionary lineages requires a broad taxon sampling. Phoronid development has previously been studied using fate mapping and morphogenesis, yet molecular descriptions are missing. Here we report the expression patterns of the evolutionarily conserved anterior (otx, gsc, six3/6, nk2.1), posterior (cdx, bra) and endomesodermal (foxA, gata4/5/6, twist) markers in the phoronid Phoronopsis harmeri.\n\nResultsThe transcription factors foxA, gata4/5/6 and cdx show conserved expression in patterning the development and regionalization of the phoronid embryonic gut, with foxA expressed in the presumptive foregut, gata4/5/6 demarcating the midgut and cdx confined to the hindgut. Surprisingly, brachyury, an evolutionary conserved transcription factor often associated with gastrulation movements and patterning of the mouth and hindgut, seems to be unrelated with gastrulation and mouth patterning in phoronids. Furthermore, six3/6, a well-conserved anterior marker, shows a remarkably dynamic expression, demarcating not only the apical organ and the oral ectoderm, but also clusters of cells of the developing midgut and the anterior mesoderm, similar to what has been reported for brachiopods, bryozoans and some deuterostome Bilateria.\n\nConclusionsOur comparison of gene expression patterns with other studied Bilateria reveals that the timing of axis determination and cell fate distribution of the phoronid shows highest similarities to rhynchonelliform brachiopods. Despite these similarities, the phoronid P. harmeri shows also particularities in its development, which hint to divergences in the arrangement of gene regulatory networks responsible for germ layer formation and axis specification.

developmental biology↗

bioRxiv2019

Morphology of the nervous system of monogonont rotifer Epiphanes senta with focus on sexual dimorphism between feeding females and dwarfed males

BackgroundMonogononta is a large clade of rotifers comprised of diverse morphological forms found in a wide range of ecological habitats. Most of the monogonont species display a cyclical parthenogenesis, where generations of asexually reproducing females are interspaced by mixis events when sexual reproduction occurs between mictic females and dwarfed, haploid males. The morphology of monogonont feeding females is relatively well described, however data on male anatomy are very limited. Thus far, male musculature of only two species has been described with confocal laser scanning microscopy (CLSM) and it remained unknown how dwarfism influences neuroanatomy of males.\n\nResultsHere, we provide a CLSM-based description of the nervous system of both sexes of Epiphanes senta, a freshwater monogonont rotifer. The general nervous system architecture is similar between males and females and shows same level of complexity. However, the nervous system in males is more compact and lacks its stomatogastric part.\n\nConclusionComparison of the neuroanatomy between male and normal-sized feeding females provides better understanding of the nature of male dwarfism in Monogononta. We propose that dwarfism of monogonont non-feeding males is a specific case of progenesis as they, due to their inability to feed, retain a juvenile body size. Reduction of the stomatogastric nervous system in the males correlates with the loss of entire digestive tract and associated morphological structures.

zoology↗

bioRxiv2019

A nemertean excitatory peptide/CCHamide regulates ciliary swimming in the larvae of Lineus longissimus

BackgroundThe trochozoan excitatory peptide (EP) and its ortholog, the arthropod CCHamide, are neuropeptides that are only investigated in very few animal species. Previous studies on different trochozoan species focused on their physiological effect in adult specimens, demonstrating a myo-excitatory effect, often on tissues of the digestive system. The function of EP in the planktonic larvae of trochozoans has not yet been studied.\n\nResultsWe surveyed transcriptomes from species of various spiralian (Orthonectia, Nemertea, Brachiopoda, Entoprocta, Rotifera) and ecdysozoan taxa (Tardigrada, Onychophora, Priapulida, Loricifera, Nematomorpha) to investigate the evolution of EPs/CCHamides in protostomes. We found that the EPs of several pilidiophoran nemerteans show a characteristic difference in their C-terminus. Deorphanization of a pilidiophoran EP receptor showed, that the two isoforms of the nemertean Lineus longissimus EP activate a single receptor. We investigated the expression of EP in L. longissimus larvae and juveniles with customized antibodies and found that EP-positive nerves in larvae project from the apical organ to the ciliary band and that EP is expressed more broadly in juveniles in the neuropil and the prominent longitudinal nerve cords. While exposing juvenile L. longissimus specimens to synthetic excitatory peptides did not show any obvious effect, exposure of larvae to either of the two EPs increased the beat frequency of their locomotory cilia and shifted their vertical swimming distribution in a water column upwards.\n\nConclusionOur results show that EP/CCHamide peptides are broadly conserved in protostomes. We show that the EP increases the ciliary beat frequency of L. longissimus larvae, which shifts their vertical distribution in a water column upwards. Endogenous EP may be released at the ciliary band from the projections of apical organ EP-positive neurons to regulate ciliary beating. A locomotory function of EP in L. longissimus larvae, compared to the association of EP/CCHamides with the digestive system in other animals suggests a dynamic integration of orthologous neuropeptides into different functions during evolution.

neuroscience↗

bioRxiv2018

Evolutionary implications of the first microRNA- and piRNA complement of Lepidodermella squamata (Gastrotricha)

Gastrotrichs - hairy bellies - are microscopic free-living animals inhabiting marine and freshwater habitats. Based on morphological and early molecular analyses, gastrotrichs were placed close to nematodes, but recent phylogenomic analyses have suggested their close relationship to flatworms (Platyhelminthes) within Spiralia. Small non-coding RNA data on e.g. microRNAs (miRNAs) and PIWI-interacting RNAs (piRNA) may help to resolve this long-standing question. MiRNAs are short post-transcriptional gene regulators that together with piRNAs play key roles in development. In a multi-omics approach we here used small-RNA sequencing, available transcriptome and genomic data to unravel the miRNA-and piRNA complements along with the RNAi protein machinery of Lepidodermella squamata (Gastrotricha, Chaetonotida). We identified 52 miRNA genes representing 35 highly conserved miRNA families specific to Eumetazoa, Bilateria, Protostomia, and Spiralia, respectively, with overall high similarities to platyhelminth miRNA complements. In addition, we found four large piRNA clusters that also resemble flatworm piRNAs but not those earlier described for nematodes. Congruently, transcriptomic annotation revealed that the Lepidodermella protein machinery is highly similar to flatworms, too. Taken together, miRNA, piRNA and protein data support a close relationship of gastrotrichs and flatworms.

evolutionary biology↗

bioRxiv2018

Hox gene expression in postmetamorphic juveniles of the brachiopod Terebratalia transversa

BackgroundHox genes encode a family of homeodomain containing transcription factors that are clustered together on chromosomes of many Bilateria. Some bilaterian lineages express these genes during embryogenesis in spatial and/or temporal order according to their arrangement in the cluster, a phenomenon referred to as collinearity. Expression of Hox genes is well studied during embryonic and larval development of numerous species; however, relatively few studies focus on the comparison of pre- and postmetamorphic expression of Hox genes in animals with biphasic life cycle. Recently, the expression of Hox genes was described for embryos and larvae of Terebratalia transversa, a rhynchonelliformean brachiopod, which possesses distinct metamorphosis from planktonic larvae to sessile juvenile. During premetamorphic development, T. transversa does not exhibit spatial collinearity and several of its Hox genes are recruited for the morphogenesis of novel structures. In our study we determined expression of Hox genes in post-metamorphic juveniles of T. transversa in order to examine metamorphosis-related changes of expression patterns and to test if Hox genes are expressed in the spatially collinear way in the postmetamorphic juveniles.\n\nResultsHox genes are expressed in a spatially non-collinear manner in juveniles, generally showing similar patterns as ones observed in competent larvae: genes labial and Post1 are expressed in chaetae-related structures, sex comb reduced in the shell forming epithelium, whereas Lox5 and Lox4 in dorso-posterior epidermis. After metamorphosis expression of genes proboscipedia, Hox3, Deformed and Antennapedia becomes restricted to, respectively, shell musculature, prospective hinge rudiments, and pedicle musculature and epidermis.\n\nConclusionsAll developmental stages of T. transversa, including postmetamorphic juveniles, exhibit a spatial non-collinear Hox genes expression with only minor changes observed between pre- and postmetamorphic stages. Our results are concordant with morphological observation that metamorphosis in rhynchonelliformean brachiopods, despite being rapid, is rather gradual. The most drastic changes in Hox genes expression patterns observed during metamorphosis could be explained by the inversion of the mantle lobe, which relocates some of the more posterior larval structures into the anterior edge of the juveniles. Cooption of Hox genes for the morphogenesis of novel structures is even more pronounced in post-metamorphic brachiopods when compared to larvae.

developmental biology↗

bioRxiv2018

Changes in the neuropeptide complement correlate with nervous system architectures in xenacoelomorphs

Neuropeptides are essential neurosecretory signaling molecules common in protostomes and deuterostomes (together Nephrozoa). Not much, however, is known about the neuropeptide complement of the sister group Xenacoelomorpha. This group is comprised of the three clades Xenoturbella, Nemertodermatida, and Acoela, which differ strongly in their nervous system anatomy. In order to reconstruct the ancestral bilaterian neuropeptide complement and gain insights into neuropeptide evolution within Xenacoelomorpha, we analyzed transcriptomes of 13 acoels, nemertodermatids, and Xenoturbella species. Together with motif searches, similarity searches, mass spectrometry and phylogenetic analyses of neuropeptide precursors and neuropeptide receptors, we reconstruct the xenacoelomorph neuropeptide complement. Our comparison of xenacoelomorph GPCRs with cnidarian and nephrozoan neuropeptide receptors shows that the neuropeptide signaling diversified into at least 20 ancestral peptidergic systems in the lineage to Bilateria. We find that Xenoturbella species possess many of the ancestral bilaterian peptidergic systems and only a few clade-specific neuropeptides. Nemertodermatids seem to have nearly the complete complement of ancestral bilaterian systems and several novel neuropeptides. Acoels show an extensive loss of conserved bilaterian systems, but gained the highest number of novel and group-specific neuropeptides. While it is difficult to correlate the emergence of the bilaterian neuropeptide complement with the evolution of centralized nervous systems, we find a correlation between nervous system novelties and the expansion of taxon-specific neuropeptides in Xenacoelomorpha.

evolutionary biology↗

bioRxiv2017

Excretion Through Digestive Tissues Predates The Evolution Of Excretory Organs

Most bilaterian animals excrete toxic metabolites through specialized organs, such as nephridia and kidneys, which share morphological and functional correspondences. In contrast, the excretory mechanisms in non-nephrozoans are largely unknown, and therefore the reconstruction of ancestral excretory mechanisms is problematic. Here, we investigated the excretory mode of members of the Xenacoelomorpha, the sister group to Nephrozoa, and Cnidaria, the sister group to Bilateria. By combining gene expression, inhibitor experiments and exposure to varying environmental ammonia conditions we show that both, Xenacoelomorpha and Cnidaria, are able to excrete across digestive-associated tissues. Based on these results we propose that digestive-associated tissues functioned as excretory sites before the evolution of specialized organs in nephrozoans. We conclude that diffusion was likely the ancestral mode of excretion, whilst the emergence of a compact, multiple-layered bilaterian body plan necessitated the evolution of active transport excretory mechanisms that was later recruited into the specialized excretory organs.

evolutionary biology↗

bioRxiv2017

A safer, urea-based in situ hybridization method improves detection of gene expression in diverse animal species

In situ hybridization is a widely employed technique allowing spatial visualization of gene expression in fixed specimens. It has proven to be essential to our understanding of biological processes, including developmental regulation. In situ protocols are today routine in numerous laboratories, and although details might change, they all include a hybridization step, where specific antisense RNA or DNA probes anneal to the target nucleic acids strand. This step, in general, is carried out at high temperatures and in a denaturing solution, the hybridization buffer, commonly containing 50% (v/v) formamide. An important drawback is that hot formamide poses a significant health risk and so must be handled with great care.\n\nWe were prompted to test alternative hybridization solutions for in situ detection of gene expression in the medusa of the hydrozoan Clytia hemisphaerica, where traditional protocols caused extensive deterioration of the morphology and texture during hybridization, hindering observation and interpretation of results. Inspired by optimized protocols for Northern and Southern blot analysis, we substituted the 50% formamide with an equal volume of 8 M urea solution in the hybridization buffer. The new protocol yielded better morphologies and consistency of tissues, and also notably improved the resolution of the signal, allowing more precise localization of gene expression, as well as reduced staining at non-specific sites. Given the improved results using a less toxic hybridization solution, we tested the urea protocol on a number of other metazoans: two brachiopod species (Novocrania anomala and Terebratalia transversa) and the worm Priapulus caudatus, obtaining a similar reduction of aspecific probe binding. Overall, substitution of formamide by urea in in situ hybridization offers safer alternative protocols, potentially useful in research, medical and teaching contexts. We encourage other workers to test this approach on their study organisms, and hope that they will also obtain better sample preservation, more precise expression patterns and fewer problems due to aspecific staining, as we report here for Clytia medusae and Novocrania and Terebratalia developing larvae.

developmental biology↗

bioRxiv2017

An ancient FMRFamide-related peptide-receptor pair induces defense behavior in a brachiopod larva

Animals show different behaviors that can consist of various spatially or temporally separated sub-reactions. Even less complex organisms, like ciliated larvae that display important behaviors (e.g. metamorphosis, defense, feeding), need to coordinate coherent sub-reactions with their simple nervous system. These behaviors can be triggered by neuropeptides, which are short signaling peptides. Despite the high diversity of neuropeptides in animals, and although their immunoreactivity is widely used in morphological studies of animal nervous systems (e.g. FMRFamide), their function and role in trochozoan larval behavior has so far only been tested in a few cases. When mechanically disturbed, the planktonic larvae of the brachiopod Terebratalia transversa protrude their stiff and pointy chaetae in a defensive manner and sink down slowly: a startle reaction that is known from different chaetous trochozoan larvae. We found that both of these reactions can be induced simultaneously by the FMRFamide-related neuropeptide FLRFamide. We deorphanized the Terebratalia FLRFamide receptor and found its expression spatially separated in the apical lobe at the prototroch of the larvae and in the trunk musculature, which correlates with the tissues that are responsible to perform the two sub-reactions. A behavioral assay showed a decreasing efficiency of modified peptides in triggering this behavior, which correlates with the decreasing efficiency of activating the FLRFamide receptor in transfected CHO-K1 cells. Immunohistochemistry and in situ hybridization show FLRFamidergic neurons in the apical lobe as well as next to the trunk musculature. Our results show that the single neuropeptide FLRFamide can specifically induce the two coherent sub-reactions of the T. transversa startle behavior.

neuroscience↗

bioRxiv2017

Pairwise comparisons are problematic when analyzing functional genomic data across species

AbstractThere is considerable interest in comparing functional genomic data across species. One goal of such work is to provide an integrated understanding of genome and phenotype evolution. Most comparative functional genomic studies have relied on multiple pairwise comparisons between species, an approach that does not incorporate information about the evolutionary relationships among species. The statistical problems that arise from not considering these relationships can lead pairwise approaches to the wrong conclusions, and are a missed opportunity to learn about biology that can only be understood in an explicit phylogenetic context. Here we examine two recently published studies that compare gene expression across species with pairwise methods, and find reason to question the original conclusions of both. One study interpreted pairwise comparisons of gene expression as support for the ortholog conjecture, the hypothesis that orthologs tend to be more similar than paralogs. The other study interpreted pairwise comparisons of embryonic gene expression across distantly related animals as evidence for a distinct evolutionary process that gave rise to phyla. In each study, distinct patterns of pairwise similarity among species were originally interpreted as evidence of particular evolutionary processes, but instead we find they reflect species relationships. These reanalyses concretely demonstrate the inadequacy of pairwise comparisons for analyzing functional genomic data across species. It will be critical to adopt phylogenetic comparative methods in future functional genomic work. Fortunately, phylogenetic comparative biology is also a rapidly advancing field with many methods that can be directly applied to functional genomic data.\n\nSignificanceComparisons of genome function between species are providing important insight into the evolutionary origins of diversity. Here we demonstrate that comparative functional genomics studies can come to the wrong conclusions if they do not take the relationships of species into account and instead rely on pairwise comparisons between species, as is common practice. We re-examined two previously published studies and found problems with pairwise comparisons that draw both their original conclusions into question. One study had found support for the ortholog conjecture and the other had concluded that the evolution of gene expression was different between animal phyla than within them. Our results demonstrate that to answer evolutionary questions about genome function, it is critical to consider evolutionary relationships.

genomics↗