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Vellutini BC, Martín-Durán JM, Børve A, Hejnol A. Combinatorial Wnt signaling landscape during brachiopod anteroposterior patterning. BMC Biol 2024; 22:212. [PMID: 39300453 PMCID: PMC11414264 DOI: 10.1186/s12915-024-01988-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 08/19/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND Wnt signaling pathways play crucial roles in animal development. They establish embryonic axes, specify cell fates, and regulate tissue morphogenesis from the early embryo to organogenesis. It is becoming increasingly recognized that these distinct developmental outcomes depend upon dynamic interactions between multiple ligands, receptors, antagonists, and other pathway modulators, consolidating the view that a combinatorial "code" controls the output of Wnt signaling. However, due to the lack of comprehensive analyses of Wnt components in several animal groups, it remains unclear if specific combinations always give rise to specific outcomes, and if these combinatorial patterns are conserved throughout evolution. RESULTS In this work, we investigate the combinatorial expression of Wnt signaling components during the axial patterning of the brachiopod Terebratalia transversa. We find that T. transversa has a conserved repertoire of ligands, receptors, and antagonists. These genes are expressed throughout embryogenesis but undergo significant upregulation during axial elongation. At this stage, Frizzled domains occupy broad regions across the body while Wnt domains are narrower and distributed in partially overlapping patches; antagonists are mostly restricted to the anterior end. Based on their combinatorial expression, we identify a series of unique transcriptional subregions along the anteroposterior axis that coincide with the different morphological subdivisions of the brachiopod larval body. When comparing these data across the animal phylogeny, we find that the expression of Frizzled genes is relatively conserved, whereas the expression of Wnt genes is more variable. CONCLUSIONS Our results suggest that the differential activation of Wnt signaling pathways may play a role in regionalizing the anteroposterior axis of brachiopod larvae. More generally, our analyses suggest that changes in the receptor context of Wnt ligands may act as a mechanism for the evolution and diversification of the metazoan body axis.
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Affiliation(s)
- Bruno C Vellutini
- Michael Sars Centre, University of Bergen, Thormøhlensgate 55, 5008, Bergen, Norway.
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany.
| | - José M Martín-Durán
- Michael Sars Centre, University of Bergen, Thormøhlensgate 55, 5008, Bergen, Norway
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, Fogg Building, London, E1 4NS, UK
| | - Aina Børve
- Michael Sars Centre, University of Bergen, Thormøhlensgate 55, 5008, Bergen, Norway
- Department of Biological Sciences, Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008, Bergen, Norway
| | - Andreas Hejnol
- Michael Sars Centre, University of Bergen, Thormøhlensgate 55, 5008, Bergen, Norway.
- Department of Biological Sciences, Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008, Bergen, Norway.
- Institute of Zoology and Evolutionary Research, Friedrich Schiller University Jena, Erbertstraße 1, 07743, Jena, Germany.
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2
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Gąsiorowski L. Phoronida-A small clade with a big role in understanding the evolution of lophophorates. Evol Dev 2024; 26:e12437. [PMID: 37119003 DOI: 10.1111/ede.12437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 04/30/2023]
Abstract
Phoronids, together with brachiopods and bryozoans, form the animal clade Lophophorata. Modern lophophorates are quite diverse-some can biomineralize while others are soft-bodied, they could be either solitary or colonial, and they develop through various eccentric larval stages that undergo different types of metamorphoses. The diversity of this clade is further enriched by numerous extinct fossil lineages with their own distinct body plans and life histories. In this review, I discuss how data on phoronid development, genetics, and morphology can inform our understanding of lophophorate evolution. The actinotrocha larvae of phoronids is a well documented example of intercalation of the new larval body plan, which can be used to study how new life stages emerge in animals with biphasic life cycle. The genomic and embryonic data from phoronids, in concert with studies of the fossil lophophorates, allow the more precise reconstruction of the evolution of lophophorate biomineralization. Finally, the regenerative and asexual abilities of phoronids can shed new light on the evolution of coloniality in lophophorates. As evident from those examples, Phoronida occupies a central role in the discussion of the evolution of lophophorate body plans and life histories.
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Affiliation(s)
- Ludwik Gąsiorowski
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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3
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Tian S, Asano Y, Banerjee TD, Wee JLQ, Lamb A, Wang Y, Murugesan SN, Ui-Tei K, Wittkopp PJ, Monteiro A. A micro-RNA is the effector gene of a classic evolutionary hotspot locus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579741. [PMID: 38659873 PMCID: PMC11042203 DOI: 10.1101/2024.02.09.579741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
In Lepidoptera (butterflies and moths), the genomic region around the gene cortex is a 'hotspot' locus, repeatedly used to generate intraspecific melanic wing color polymorphisms across 100-million-years of evolution. However, the identity of the effector gene regulating melanic wing color within this locus remains unknown. Here, we show that none of the four candidate protein-coding genes within this locus, including cortex, serve as major effectors. Instead, a micro-RNA (miRNA), mir-193, serves as the major effector across three deeply diverged lineages of butterflies, and its function is conserved in Drosophila. In Lepidoptera, mir-193 is derived from a gigantic long non-coding RNA, ivory, and it functions by directly repressing multiple pigmentation genes. We show that a miRNA can drive repeated instances of adaptive evolution in animals.
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Affiliation(s)
- Shen Tian
- Department of Biological Sciences, Faculty of Science, National University of Singapore; Singapore, 117543, Singapore
| | - Yoshimasa Asano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo; Tokyo, 113-0033, Japan
| | - Tirtha Das Banerjee
- Department of Biological Sciences, Faculty of Science, National University of Singapore; Singapore, 117543, Singapore
| | - Jocelyn Liang Qi Wee
- Department of Biological Sciences, Faculty of Science, National University of Singapore; Singapore, 117543, Singapore
| | - Abigail Lamb
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Science, and the Arts, The University of Michigan; Ann Arbor, MI 48109-1085, USA
| | - Yehan Wang
- Department of Biological Sciences, Faculty of Science, National University of Singapore; Singapore, 117543, Singapore
| | - Suriya Narayanan Murugesan
- Department of Biological Sciences, Faculty of Science, National University of Singapore; Singapore, 117543, Singapore
| | - Kumiko Ui-Tei
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo; Tokyo, 113-0033, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo; Chiba, 277-8561, Japan
| | - Patricia J. Wittkopp
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Science, and the Arts, The University of Michigan; Ann Arbor, MI 48109-1085, USA
- Department of Ecology and Evolutionary Biology, College of Literature, Science, and the Arts, The University of Michigan; Ann Arbor, MI 48109-1085, USA
| | - Antónia Monteiro
- Department of Biological Sciences, Faculty of Science, National University of Singapore; Singapore, 117543, Singapore
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4
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Saadi AJ, de Oliveira AL, Kocot KM, Schwaha T. Genomic and transcriptomic survey of bryozoan Hox and ParaHox genes with emphasis on phylactolaemate bryozoans. BMC Genomics 2023; 24:711. [PMID: 38001438 PMCID: PMC10675955 DOI: 10.1186/s12864-023-09826-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/22/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Bryozoans are mostly sessile aquatic colonial invertebrates belonging to the clade Lophotrochozoa, which unites many protostome bilaterian phyla such as molluscs, annelids and brachiopods. While Hox and ParaHox genes have been extensively studied in various lophotrochozoan lineages, investigations on Hox and ParaHox gene complements in bryozoans are scarce. RESULTS Herein, we present the most comprehensive survey of Hox and ParaHox gene complements in bryozoans using four genomes and 35 transcriptomes representing all bryozoan clades: Cheilostomata, Ctenostomata, Cyclostomata and Phylactolaemata. Using similarity searches, phylogenetic analyses and detailed manual curation, we have identified five Hox genes in bryozoans (pb, Dfd, Lox5, Lox4 and Post2) and one ParaHox gene (Cdx). Interestingly, we observed lineage-specific duplication of certain Hox and ParaHox genes (Dfd, Lox5 and Cdx) in some bryozoan lineages. CONCLUSIONS The bryozoan Hox cluster does not retain the ancestral lophotrochozoan condition but appears relatively simple (includes only five genes) and broken into two genomic regions, characterized by the loss and duplication of serval genes. Importantly, bryozoans share the lack of two Hox genes (Post1 and Scr) with their proposed sister-taxon, Phoronida, which suggests that those genes were missing in the most common ancestor of bryozoans and phoronids.
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Affiliation(s)
- Ahmed J Saadi
- Department of Evolutionary Biology, Unit for Integrative Zoology, University of Vienna, Schlachthausgasse 43, Vienna, A-1030, Austria.
| | - André Luiz de Oliveira
- Department of Symbiosis, Max-Planck-Institute for Marine Microbiology, Celsiustraße,1, D-28359, Bremen, Germany
| | - Kevin M Kocot
- Department of Biological Sciences and Alabama Museum of Natural History, University of Alabama, Tuscaloosa, Alabama, 35487, USA
| | - Thomas Schwaha
- Department of Evolutionary Biology, Unit for Integrative Zoology, University of Vienna, Schlachthausgasse 43, Vienna, A-1030, Austria
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Schuster KJ, Christiaen L. The Chordate Origins of Heart Regeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558507. [PMID: 37781597 PMCID: PMC10541106 DOI: 10.1101/2023.09.19.558507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The human heart is infamous for not healing after infarction in adults, prompting biomedical interest in species that can regenerate damaged hearts. In such animals as zebrafish and neonatal mice, cardiac repair relies on remaining heart tissue supporting cardiomyocyte proliferation. Natural de novo cardiogenesis in post-embryonic stages thus remains elusive. Here we show that the tunicate Ciona, an ascidian among the closest living relatives to the vertebrates, can survive complete chemogenetic ablation of the heart and loss of cardiac function, and recover both cardiac tissue and contractility. As in vertebrates, Ciona heart regeneration relies on Bone Morphogenetic Protein (BMP) signaling-dependent proliferation of cardiomyocytes, providing insights into the evolutionary origins of regenerative cardiogenesis in chordates. Remarkably, prospective lineage tracing by photoconversion of the fluorescent protein Kaede suggested that new cardiomyocytes can emerge from endodermal lineages in post-metamorphic animals, providing an unprecedented case of regenerative de novo cardiogenesis. Finally, while embryos cannot compensate for early losses of the cardiogenic lineage, forming heartless juveniles, developing animals gain their regenerative ability during metamorphosis, uncovering a fundamental transition between deterministic embryogenesis and regulative post-embryonic development.
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Affiliation(s)
- Keaton J Schuster
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
- Michael Sars Centre, University of Bergen, Bergen, Norway
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6
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Freitas ÍN, Dourado AV, da Silva Matos SG, de Souza SS, da Luz TM, Rodrigues ASDL, Guimarães ATB, Mubarak NM, Rahman MM, Arias AH, Malafaia G. Short-term exposure of the mayfly larvae (Cloeon dipterum, Ephemeroptera: Baetidae) to SARS-CoV-2-derived peptides and other emerging pollutants: A new threat for the aquatic environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157813. [PMID: 35931160 PMCID: PMC9345649 DOI: 10.1016/j.scitotenv.2022.157813] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/26/2022] [Accepted: 07/31/2022] [Indexed: 05/09/2023]
Abstract
The input of SARS-CoV-2 or its fragments into freshwater ecosystems (via domestic or hospital sewage) has raised concerns about its possible impacts on aquatic organisms. Thus, using mayfly larvae [Cloeon dipterum (L.), Ephemeroptera: Baetidae] as a model system, we aimed to evaluate the possible effects of the combined short exposure of SARS-CoV-2-derived peptides (named PSPD-2001, PSPD-2002, and PSPD-2003 - at 266.2 ng/L) with multiple emerging pollutants at ambient concentrations. After six days of exposure, we observed higher mortality of larvae exposed to SARS-CoV-2-derived peptides (alone or in combination with the pollutant mix) and a lower-body condition index than those unexposed larvae. In the "PSPD" and "Mix+PSPD" groups, the activity of superoxide dismutase, catalase, DPPH radical scavenging activity, and the total thiol levels were also lower than in the "control" group. In addition, we evidenced the induction of nitrosative stress (inferred by increased nitrite production) and reduced acetylcholinesterase activity by SARS-CoV-2-derived peptides. On the other hand, malondialdehyde levels in larvae exposed to treatments were significantly lower than in unexposed larvae. The values of the integrated biomarker response index and the principal component analysis (PCA) results confirmed the similarity between the responses of animals exposed to SARS-CoV-2-derived peptides (alone and in combination with the pollutant mix). Although viral peptides did not intensify the effects of the pollutant mix, our study sheds light on the potential ecotoxicological risk associated with the spread of the new coronavirus in aquatic environments. Therefore, we recommend exploring this topic in other organisms and experimental contexts.
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Affiliation(s)
- Ítalo Nascimento Freitas
- Laboratory of Toxicology Applied to the Environment, Goiano Federal Institute, Urutaí, GO, Brazil; Post-Graduation Program in Conservation of Cerrado Natural Resources, Goiano Federal Institute, Urutaí, GO, Brazil
| | - Amanda Vieira Dourado
- Laboratory of Toxicology Applied to the Environment, Goiano Federal Institute, Urutaí, GO, Brazil
| | | | - Sindoval Silva de Souza
- Post-Graduation Program in Biotechnology and Biodiversity, Federal University of Goiás, Goiânia, GO, Brazil
| | - Thiarlen Marinho da Luz
- Laboratory of Toxicology Applied to the Environment, Goiano Federal Institute, Urutaí, GO, Brazil; Post-Graduation Program in Conservation of Cerrado Natural Resources, Goiano Federal Institute, Urutaí, GO, Brazil
| | | | | | - Nabisab Mujawar Mubarak
- Petroleum and Chemical Engineering, Faculty of Engineering, Universiti Teknologi Brunei, Bandar Seri Begawan BE1410, Brunei Darussalam
| | - Md Mostafizur Rahman
- Laboratory of Environmental Health and Ecotoxicology, Department of Environmental Sciences, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Andrés Hugo Arias
- Instituto Argentino de Oceanografía (IADO), Universidad Nacional del Sur (UNS)-CONICET, Florida 8000, Complejo CCT CONICET Bahía Blanca, Bahía Blanca, Argentina
| | - Guilherme Malafaia
- Laboratory of Toxicology Applied to the Environment, Goiano Federal Institute, Urutaí, GO, Brazil; Post-Graduation Program in Conservation of Cerrado Natural Resources, Goiano Federal Institute, Urutaí, GO, Brazil; Petroleum and Chemical Engineering, Faculty of Engineering, Universiti Teknologi Brunei, Bandar Seri Begawan BE1410, Brunei Darussalam; Post-Graduation Program in Ecology, Conservation, and Biodiversity, Federal University of Uberlândia, Uberlândia, MG, Brazil.
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7
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Brachiopod and mollusc biomineralisation is a conserved process that was lost in the phoronid-bryozoan stem lineage. EvoDevo 2022; 13:17. [PMID: 36123753 PMCID: PMC9484238 DOI: 10.1186/s13227-022-00202-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Brachiopods and molluscs are lophotrochozoans with hard external shells which are often believed to have evolved convergently. While palaeontological data indicate that both groups are descended from biomineralising Cambrian ancestors, the closest relatives of brachiopods, phoronids and bryozoans, are mineralised to a much lower extent and are comparatively poorly represented in the Palaeozoic fossil record. Although brachiopod and mollusc shells are structurally analogous, genomic and proteomic evidence indicates that their formation involves a complement of conserved, orthologous genes. Here, we study a set of genes comprised of 3 homeodomain transcription factors, one signalling molecule and 6 structural proteins which are implicated in mollusc and brachiopod shell formation, search for their orthologs in transcriptomes or genomes of brachiopods, phoronids and bryozoans, and present expression patterns of 8 of the genes in postmetamorphic juveniles of the rhynchonelliform brachiopod T. transversa. RESULTS Transcriptome and genome searches for the 10 target genes in the brachiopods Terebratalia transversa, Lingula anatina, Novocrania anomala, the bryozoans Bugula neritina and Membranipora membranacea, and the phoronids Phoronis australis and Phoronopsis harmeri resulted in the recovery of orthologs of the majority of the genes in all taxa. While the full complement of genes was present in all brachiopods with a single exception in L. anatina, a bloc of four genes could consistently not be retrieved from bryozoans and phoronids. The genes engrailed, distal-less, ferritin, perlucin, sp1 and sp2 were shown to be expressed in the biomineralising mantle margin of T. transversa juveniles. CONCLUSIONS The gene expression patterns we recovered indicate that while mineralised shells in brachiopods and molluscs are structurally analogous, their formation builds on a homologous process that involves a conserved complement of orthologous genes. Losses of some of the genes related to biomineralisation in bryozoans and phoronids indicate that loss of the capacity to form mineralised structures occurred already in the phoronid-bryozoan stem group and supports the idea that mineralised skeletons evolved secondarily in some of the bryozoan subclades.
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8
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Wei M, Qin Z, Kong D, Liu D, Zheng Q, Bai S, Zhang Z, Ma Y. Echiuran Hox genes provide new insights into the correspondence between Hox subcluster organization and collinearity pattern. Proc Biol Sci 2022; 289:20220705. [PMID: 36264643 PMCID: PMC9449475 DOI: 10.1098/rspb.2022.0705] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 07/29/2022] [Indexed: 09/16/2023] Open
Abstract
In many bilaterians, Hox genes are generally clustered along the chromosomes and expressed in spatial and temporal order. In vertebrates, the expression of Hox genes follows a whole-cluster spatio-temporal collinearity (WSTC) pattern, whereas in some invertebrates the expression of Hox genes exhibits a subcluster-level spatio-temporal collinearity pattern. In bilaterians, the diversity of collinearity patterns and the cause of collinearity differences in Hox gene expression remain poorly understood. Here, we investigate genomic organization and expression pattern of Hox genes in the echiuran worm Urechis unicinctus (Annelida, Echiura). Urechis unicinctus has a split cluster with four subclusters divided by non-Hox genes: first subcluster (Hox1 and Hox2), second subcluster (Hox3), third subcluster (Hox4, Hox5, Lox5, Antp and Lox4), fourth subcluster (Lox2 and Post2). The expression of U. unicinctus Hox genes shows a subcluster-based whole-cluster spatio-temporal collinearity (S-WSTC) pattern: the anterior-most genes in each subcluster are activated in a spatially and temporally colinear manner (reminiscent of WSTC), with the subsequent genes in each subcluster then being very similar to their respective anterior-most subcluster gene. Combining genomic organization and expression profiles of Hox genes in different invertebrate lineages, we propose that the spatio-temporal collinearity of invertebrate Hox is subcluster-based.
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Affiliation(s)
- Maokai Wei
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Zhenkui Qin
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Dexu Kong
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Danwen Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Qiaojun Zheng
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Shumiao Bai
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, People's Republic of China
| | - Yubin Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, People's Republic of China
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9
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Orús-Alcalde A, Lu TM, Børve A, Hejnol A. The evolution of the metazoan Toll receptor family and its expression during protostome development. BMC Ecol Evol 2021; 21:208. [PMID: 34809567 PMCID: PMC8609888 DOI: 10.1186/s12862-021-01927-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 10/21/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Toll-like receptors (TLRs) play a crucial role in immunity and development. They contain leucine-rich repeat domains, one transmembrane domain, and one Toll/IL-1 receptor domain. TLRs have been classified into V-type/scc and P-type/mcc TLRs, based on differences in the leucine-rich repeat domain region. Although TLRs are widespread in animals, detailed phylogenetic studies of this gene family are lacking. Here we aim to uncover TLR evolution by conducting a survey and a phylogenetic analysis in species across Bilateria. To discriminate between their role in development and immunity we furthermore analyzed stage-specific transcriptomes of the ecdysozoans Priapulus caudatus and Hypsibius exemplaris, and the spiralians Crassostrea gigas and Terebratalia transversa. RESULTS We detected a low number of TLRs in ecdysozoan species, and multiple independent radiations within the Spiralia. V-type/scc and P-type/mcc type-receptors are present in cnidarians, protostomes and deuterostomes, and therefore they emerged early in TLR evolution, followed by a loss in xenacoelomorphs. Our phylogenetic analysis shows that TLRs cluster into three major clades: clade α is present in cnidarians, ecdysozoans, and spiralians; clade β in deuterostomes, ecdysozoans, and spiralians; and clade γ is only found in spiralians. Our stage-specific transcriptome and in situ hybridization analyses show that TLRs are expressed during development in all species analyzed, which indicates a broad role of TLRs during animal development. CONCLUSIONS Our findings suggest that a clade α TLR gene (TLR-Ca) and a clade β/γ TLR gene (TLR-Cβ/γ) were already present in the cnidarian-bilaterian common ancestor. However, although TLR-Ca was conserved in cnidarians, TLR-Cβ/γ was lost during the early evolution of these taxa. Moreover, TLR-Cβ/γ duplicated to generate TLR-Cβ and TLR-Cγ in the lineage to the last common protostome-deuterostome ancestor. TLR-Ca, TLR-Cβ and TLR-Cγ further expanded generating the three major TLR clades. While all three clades radiated in several spiralian lineages, specific TLRs clades have been presumably lost in other lineages. Furthermore, the expression of the majority of these genes during protostome ontogeny suggests a likely role in development.
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Affiliation(s)
- Andrea Orús-Alcalde
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Tsai-Ming Lu
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Aina Børve
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway.
- Department of Biological Sciences, University of Bergen, Bergen, Norway.
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10
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Gąsiorowski L, Børve A, Cherneva IA, Orús-Alcalde A, Hejnol A. Molecular and morphological analysis of the developing nemertean brain indicates convergent evolution of complex brains in Spiralia. BMC Biol 2021; 19:175. [PMID: 34452633 PMCID: PMC8400761 DOI: 10.1186/s12915-021-01113-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/30/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The brain anatomy in the clade Spiralia can vary from simple, commissural brains (e.g., gastrotrichs, rotifers) to rather complex, partitioned structures (e.g., in cephalopods and annelids). How often and in which lineages complex brains evolved still remains unclear. Nemerteans are a clade of worm-like spiralians, which possess a complex central nervous system (CNS) with a prominent brain, and elaborated chemosensory and neuroglandular cerebral organs, which have been previously suggested as homologs to the annelid mushroom bodies. To understand the developmental and evolutionary origins of the complex brain in nemerteans and spiralians in general, we investigated details of the neuroanatomy and gene expression in the brain and cerebral organs of the juveniles of nemertean Lineus ruber. RESULTS In the juveniles, the CNS is already composed of all major elements present in the adults, including the brain, paired longitudinal lateral nerve cords, and an unpaired dorsal nerve cord, which suggests that further neural development is mostly related with increase in the size but not in complexity. The ultrastructure of the juvenile cerebral organ revealed that it is composed of several distinct cell types present also in the adults. The 12 transcription factors commonly used as brain cell type markers in bilaterians show region-specific expression in the nemertean brain and divide the entire organ into several molecularly distinct areas, partially overlapping with the morphological compartments. Additionally, several of the mushroom body-specific genes are expressed in the developing cerebral organs. CONCLUSIONS The dissimilar expression of molecular brain markers between L. ruber and the annelid Platynereis dumerilii indicates that the complex brains present in those two species evolved convergently by independent expansions of non-homologous regions of a simpler brain present in their last common ancestor. Although the same genes are expressed in mushroom bodies and cerebral organs, their spatial expression within organs shows apparent differences between annelids and nemerteans, indicating convergent recruitment of the same genes into patterning of non-homologous organs or hint toward a more complicated evolutionary process, in which conserved and novel cell types contribute to the non-homologous structures.
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Affiliation(s)
| | - Aina Børve
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Irina A Cherneva
- Biological Faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | | | - Andreas Hejnol
- Department of Biological Sciences, University of Bergen, Bergen, Norway.
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11
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Molecular evidence for a single origin of ultrafiltration-based excretory organs. Curr Biol 2021; 31:3629-3638.e2. [PMID: 34166606 DOI: 10.1016/j.cub.2021.05.057] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/14/2021] [Accepted: 05/26/2021] [Indexed: 01/14/2023]
Abstract
Excretion is an essential physiological process, carried out by all living organisms, regardless of their size or complexity.1-3 Both protostomes (e.g., flies and flatworms) and deuterostomes (e.g., humans and sea urchins) possess specialized excretory organs serving that purpose. Those organs exhibit an astonishing diversity, ranging from units composed of just few distinct cells (e.g., protonephridia) to complex structures, built by millions of cells of multiple types with divergent morphology and function (e.g., vertebrate kidneys).4,5 Although some molecular similarities between the development of kidneys of vertebrates and the regeneration of the protonephridia of flatworms have been reported,6,7 the molecular underpinnings of the development of excretory organs have never been systematically studied in a comparative context.4 Here, we show that a set of transcription factors (eya, six1/2, pou3, sall, lhx1/5, and osr) and structural proteins (nephrin, kirre, and zo1) is expressed in the excretory organs of a phoronid, brachiopod, annelid, onychophoran, priapulid, and hemichordate that represent major protostome lineages and non-vertebrate deuterostomes. We demonstrate that the molecular similarity observed in the vertebrate kidney and flatworm protonephridia6,7 is also seen in the developing excretory organs of those animals. Our results show that all types of ultrafiltration-based excretory organs are patterned by a conserved set of developmental genes, an observation that supports their homology. We propose that the last common ancestor of protostomes and deuterostomes already possessed an ultrafiltration-based organ that later gave rise to the vast diversity of extant excretory organs, including both proto- and metanephridia.
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12
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Sevigny JL, Norenburg JL, Leasi F. A Bioinformatics Tutorial for Comparative Development Genomics in Diverse Meiofauna. Methods Mol Biol 2021; 2219:289-305. [PMID: 33074549 DOI: 10.1007/978-1-0716-0974-3_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Miniaturization, which is a common feature in animals, is particularly manifest in meiofauna-animals sharing peculiar phenotypic features that evolved as adaptations to the highly specialized aquatic interstitial habitat. While revealing much about the extreme phyletic diversity of meiofauna, the genome structure of meiofaunal species could also characterize the phenotype of ancestral states as well as explain the origin and evolution of miniaturization. Here, we present a practical bioinformatics tutorial for genome assembly, genome comparison, and characterization of Hox clusters in meiofaunal species.
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Affiliation(s)
- Joseph L Sevigny
- Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Jon L Norenburg
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | - Francesca Leasi
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN, USA.
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13
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Abstract
In many animals the head develops early, most of the body axis later. A larva composed mostly of the developing front end therefore can attain mobility and feeding earlier in development. Fossils, functional morphology, and inferred homologies indicate that feeding head larvae existed by the Early Cambrian in members of three major clades of animals: ecdysozoans, lophotrochozoans, and deuterostomes. Some of these early larval feeding mechanisms were also those of juveniles and adults (the lophophore of brachiopod larvae and possibly the ciliary band of the dipleurula of hemichordates and echinoderms); some were derived from structures that previously had other functions (appendages of the nauplius). Trochophores that swim with a preoral band of cilia, the prototroch, originated before divergence of annelids and molluscs, but evidence of larval growth and thus a prototrochal role in feeding is lacking for molluscs until the Ordovician. Feeding larvae that definitely originated much later, as in insects, teleost fish, and amphibians, develop all or nearly all of what will become the adult body axis before they begin feeding. On present evidence, head larvae, including feeding head larvae, evolved multiple times early in the evolution of bilaterian animals and never since.
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Affiliation(s)
- Richard R. Strathmann
- Friday Harbor Laboratories, 620 University Road, Friday Harbor, WA 98250, USA
- Friday Harbor Laboratories, 620 University Road, Friday Harbor, WA 98250, USA
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14
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Young AP, Jackson DJ, Wyeth RC. A technical review and guide to RNA fluorescence in situ hybridization. PeerJ 2020; 8:e8806. [PMID: 32219032 PMCID: PMC7085896 DOI: 10.7717/peerj.8806] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/25/2020] [Indexed: 12/20/2022] Open
Abstract
RNA-fluorescence in situ hybridization (FISH) is a powerful tool to visualize target messenger RNA transcripts in cultured cells, tissue sections or whole-mount preparations. As the technique has been developed over time, an ever-increasing number of divergent protocols have been published. There is now a broad selection of options available to facilitate proper tissue preparation, hybridization, and post-hybridization background removal to achieve optimal results. Here we review the technical aspects of RNA-FISH, examining the most common methods associated with different sample types including cytological preparations and whole-mounts. We discuss the application of commonly used reagents for tissue preparation, hybridization, and post-hybridization washing and provide explanations of the functional roles for each reagent. We also discuss the available probe types and necessary controls to accurately visualize gene expression. Finally, we review the most recent advances in FISH technology that facilitate both highly multiplexed experiments and signal amplification for individual targets. Taken together, this information will guide the methods development process for investigators that seek to perform FISH in organisms that lack documented or optimized protocols.
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Affiliation(s)
- Alexander P Young
- Department of Biology, St. Francis Xavier University, Antigonish, NS, Canada
| | - Daniel J Jackson
- Department of Geobiology, Georg-August Universität Göttingen, Göttingen, Germany
| | - Russell C Wyeth
- Department of Biology, St. Francis Xavier University, Antigonish, NS, Canada
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15
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Gąsiorowski L, Hejnol A. Hox gene expression during development of the phoronid Phoronopsis harmeri. EvoDevo 2020; 11:2. [PMID: 32064072 PMCID: PMC7011278 DOI: 10.1186/s13227-020-0148-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
Background Phoronida 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. Results We identified sequences of eight Hox genes in the transcriptome of Ph. 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. In the investigated initial larval stages the Hox genes are expressed in the non-collinear manner in the posterior body of the larvae: in the telotroch and the structures that represent rudiments of the adult worm. Additionally, we found that certain head-specific transcription factors are expressed in the oral hood, apical organ, preoral coelom, digestive system and developing larval tentacles, anterior to the Hox-expressing territories. Conclusions The lack of Hox gene expression during early development of Ph. harmeri indicates that the larval body develops without positional information from the Hox patterning system. Such phenomenon might be a consequence of the evolutionary intercalation of the larval form into an ancestral life cycle of phoronids. The observed Hox gene expression can also be a consequence of the actinotrocha representing a “head larva”, which is composed of the most anterior body region that is devoid of Hox gene expression. Such interpretation is further supported by the expression of head-specific transcription factors. 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. We propose that a new body form was intercalated to the phoronid life cycle by precocious development of the anterior structures or by delayed development of the trunk rudiment in the ancestral phoronid larva.
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Affiliation(s)
- Ludwik Gąsiorowski
- 1Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway.,2Department of Biological Sciences, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway
| | - Andreas Hejnol
- 1Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway.,2Department of Biological Sciences, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway
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