1
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Guynes K, Sarre LA, Carrillo-Baltodano AM, Davies BE, Xu L, Liang Y, Martín-Zamora FM, Hurd PJ, de Mendoza A, Martín-Durán JM. Annelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across Bilateria. Genome Biol 2024; 25:204. [PMID: 39090757 PMCID: PMC11292947 DOI: 10.1186/s13059-024-03346-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: 01/17/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND DNA methylation in the form of 5-methylcytosine (5mC) is the most abundant base modification in animals. However, 5mC levels vary widely across taxa. While vertebrate genomes are hypermethylated, in most invertebrates, 5mC concentrates on constantly and highly transcribed genes (gene body methylation; GbM) and, in some species, on transposable elements (TEs), a pattern known as "mosaic". Yet, the role and developmental dynamics of 5mC and how these explain interspecies differences in DNA methylation patterns remain poorly understood, especially in Spiralia, a large clade of invertebrates comprising nearly half of the animal phyla. RESULTS Here, we generate base-resolution methylomes for three species with distinct genomic features and phylogenetic positions in Annelida, a major spiralian phylum. All possible 5mC patterns occur in annelids, from typical invertebrate intermediate levels in a mosaic distribution to hypermethylation and methylation loss. GbM is common to annelids with 5mC, and methylation differences across species are explained by taxon-specific transcriptional dynamics or the presence of intronic TEs. Notably, the link between GbM and transcription decays during development, alongside a gradual and global, age-dependent demethylation in adult stages. Additionally, reducing 5mC levels with cytidine analogs during early development impairs normal embryogenesis and reactivates TEs in the annelid Owenia fusiformis. CONCLUSIONS Our study indicates that global epigenetic erosion during development and aging is an ancestral feature of bilateral animals. However, the tight link between transcription and gene body methylation is likely more important in early embryonic stages, and 5mC-mediated TE silencing probably emerged convergently across animal lineages.
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Affiliation(s)
- Kero Guynes
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, 1030, Austria
| | - Luke A Sarre
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Allan M Carrillo-Baltodano
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Billie E Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Lan Xu
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Yan Liang
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
- Altos Labs, Cambridge, UK
| | - Paul J Hurd
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Alex de Mendoza
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
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2
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Liang Y, Carrillo-Baltodano AM, Martín-Durán JM. Emerging trends in the study of spiralian larvae. Evol Dev 2024; 26:e12459. [PMID: 37787615 DOI: 10.1111/ede.12459] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 10/04/2023]
Abstract
Many animals undergo indirect development, where their embryogenesis produces an intermediate life stage, or larva, that is often free-living and later metamorphoses into an adult. As their adult counterparts, larvae can have unique and diverse morphologies and occupy various ecological niches. Given their broad phylogenetic distribution, larvae have been central to hypotheses about animal evolution. However, the evolution of these intermediate forms and the developmental mechanisms diversifying animal life cycles are still debated. This review focuses on Spiralia, a large and diverse clade of bilaterally symmetrical animals with a fascinating array of larval forms, most notably the archetypical trochophore larva. We explore how classic research and modern advances have improved our understanding of spiralian larvae, their development, and evolution. Specifically, we examine three morphological features of spiralian larvae: the anterior neural system, the ciliary bands, and the posterior hyposphere. The combination of molecular and developmental evidence with modern high-throughput techniques, such as comparative genomics, single-cell transcriptomics, and epigenomics, is a promising strategy that will lead to new testable hypotheses about the mechanisms behind the evolution of larvae and life cycles in Spiralia and animals in general. We predict that the increasing number of available genomes for Spiralia and the optimization of genome-wide and single-cell approaches will unlock the study of many emerging spiralian taxa, transforming our views of the evolution of this animal group and their larvae.
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Affiliation(s)
- Yan Liang
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
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3
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Mutemi KN, Simakov O, Pan L, Santangeli L, Null RW, Handberg-Thorsager M, Vellutini BC, Larsson T, Savage EL, Lopez MO, Hercog R, Provaznik J, Ordoñez-Rueda D, Azevedo N, Gazave E, Vervoort M, Tomancak P, Tan W, Winkler S, Benes V, Hui J, Helm C, Özpolat BD, Arendt D. A genome resource for the marine annelid Platynereis dumerilii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600153. [PMID: 38948846 PMCID: PMC11213123 DOI: 10.1101/2024.06.21.600153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The marine annelid Platynereis dumerilii is a model organism used in many research areas including evolution and development, neurobiology, ecology and regeneration. Here we present the genomes of P. dumerilii and of the closely related P. massiliensis and P. megalops, to facilitate comparative genomic approaches and help explore Platynereis biology. We used long-read sequencing technology and chromosomal-conformation capture along with extensive transcriptomic resources to obtain and annotate a draft genome assembly of ~1.47 Gbp for P. dumerilii, of which more than half represent repeat elements. We predict around 29,000 protein-coding genes, with relatively large intron sizes, over 38,000 non-coding genes, and 580 miRNA loci. We further explore the high genetic variation (~3% heterozygosity) within the Platynereis species complex. Gene ontology reveals the most variable loci to be associated with pigmentation, development and immunity. The current work sets the stage for further development of Platynereis genomic resources.
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Affiliation(s)
- Kevin Nzumbi Mutemi
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Oleg Simakov
- Department for Neurosciences and Developmental Biology, University of Vienna, Austria
| | - Leslie Pan
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Luca Santangeli
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Ryan W. Null
- Current: Department of Biology, Washington University in Saint Louis, MO, USA 63139 Previous: Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA. 02543. USA
| | - Mette Handberg-Thorsager
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | | | - Tomas Larsson
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. Current: Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Emily L. Savage
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Current: Centre for Organismal Studies, University of Heidelberg, Heidelberg
| | - Mireia Osuna Lopez
- European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Rajna Hercog
- European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany - not at EMBL anymore, do not know current address
| | - Jan Provaznik
- European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Diana Ordoñez-Rueda
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Nayara Azevedo
- European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany. - not at EMBL anymore, do not know current address
| | - Eve Gazave
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Michel Vervoort
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France. - deceased
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Wenhua Tan
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Vladimir Benes
- EMBL, Genomics Core Facility, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Jerome Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Conrad Helm
- Animal Evolution and Biodiversity, University of Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany
| | - B. Duygu Özpolat
- Current: Department of Biology, Washington University in Saint Louis, MO, USA 63139 Previous: Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA. 02543. USA
| | - Detlev Arendt
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Centre for Organismal Studies (COS) University of Heidelberg, 69120 Heidelberg, Germany
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4
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Lin CY, Marlétaz F, Pérez-Posada A, Martínez-García PM, Schloissnig S, Peluso P, Conception GT, Bump P, Chen YC, Chou C, Lin CY, Fan TP, Tsai CT, Gómez Skarmeta JL, Tena JJ, Lowe CJ, Rank DR, Rokhsar DS, Yu JK, Su YH. Chromosome-level genome assemblies of 2 hemichordates provide new insights into deuterostome origin and chromosome evolution. PLoS Biol 2024; 22:e3002661. [PMID: 38829909 PMCID: PMC11175523 DOI: 10.1371/journal.pbio.3002661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/13/2024] [Accepted: 05/03/2024] [Indexed: 06/05/2024] Open
Abstract
Deuterostomes are a monophyletic group of animals that includes Hemichordata, Echinodermata (together called Ambulacraria), and Chordata. The diversity of deuterostome body plans has made it challenging to reconstruct their ancestral condition and to decipher the genetic changes that drove the diversification of deuterostome lineages. Here, we generate chromosome-level genome assemblies of 2 hemichordate species, Ptychodera flava and Schizocardium californicum, and use comparative genomic approaches to infer the chromosomal architecture of the deuterostome common ancestor and delineate lineage-specific chromosomal modifications. We show that hemichordate chromosomes (1N = 23) exhibit remarkable chromosome-scale macrosynteny when compared to other deuterostomes and can be derived from 24 deuterostome ancestral linkage groups (ALGs). These deuterostome ALGs in turn match previously inferred bilaterian ALGs, consistent with a relatively short transition from the last common bilaterian ancestor to the origin of deuterostomes. Based on this deuterostome ALG complement, we deduced chromosomal rearrangement events that occurred in different lineages. For example, a fusion-with-mixing event produced an Ambulacraria-specific ALG that subsequently split into 2 chromosomes in extant hemichordates, while this homologous ALG further fused with another chromosome in sea urchins. Orthologous genes distributed in these rearranged chromosomes are enriched for functions in various developmental processes. We found that the deeply conserved Hox clusters are located in highly rearranged chromosomes and that maintenance of the clusters are likely due to lower densities of transposable elements within the clusters. We also provide evidence that the deuterostome-specific pharyngeal gene cluster was established via the combination of 3 pre-assembled microsyntenic blocks. We suggest that since chromosomal rearrangement events and formation of new gene clusters may change the regulatory controls of developmental genes, these events may have contributed to the evolution of diverse body plans among deuterostomes.
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Affiliation(s)
- Che-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Ferdinand Marlétaz
- Center for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Alberto Pérez-Posada
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Pedro Manuel Martínez-García
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | | | - Paul Peluso
- Pacific Biosciences, Menlo Park, California, United States of America
| | | | - Paul Bump
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, California, United States of America
| | - Yi-Chih Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Cindy Chou
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Ching-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Tzu-Pei Fan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Chang-Tai Tsai
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - José Luis Gómez Skarmeta
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Juan J. Tena
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Christopher J. Lowe
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, California, United States of America
- Chan-Zuckerberg Biohub, San Francisco, California, United States of America
| | - David R. Rank
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Daniel S. Rokhsar
- Chan-Zuckerberg Biohub, San Francisco, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- Molecular Genetics Unit, Okinawa Institute for Science and Technology, Onna, Japan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
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5
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Gajda Ł, Daszkowska-Golec A, Świątek P. Discovery and characterization of the α-amylases cDNAs from Enchytraeus albidus shed light on the evolution of "Enchytraeus-Eisenia type" Amy homologs in Annelida. Biochimie 2024; 221:38-59. [PMID: 38242278 DOI: 10.1016/j.biochi.2024.01.008] [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: 05/17/2023] [Revised: 12/02/2023] [Accepted: 01/13/2024] [Indexed: 01/21/2024]
Abstract
Although enchytraeids have gained popularity in scientific research, fundamental questions regarding their feeding ecology and biology remain largely unexplored. This study investigates α-amylases, major digestive enzymes responsible for hydrolyzing starch and similar polysaccharides into sugars, in Enchytraeus albidus. Genetic data related to α-amylases is currently lacking for the family Enchytraeidae but also for the entire Annelida. To detect and identify coding sequences of the expressed α-amylase genes in COI-monohaplotype culture (PL-A strain) of E. albidus, we used classical "gene fishing" and transcriptomic approaches. We also compared coding sequence variants of α-amylase retrieved from transcriptomic data related to freeze-tolerant strains. Our results reveal that E. albidus possesses two distinct α-amylase genes (Amy I and Amy II) that are homologs to earthworm Eisenia fetida Ef-Amy genes. Different strains of E. albidus possess distinctive alleles of α-amylases with unique SNP patterns specific to a particular strain. Unlike Amy II, Amy I seems to be a highly polymorphic and multicopy gene. The domain architecture of the putative Amy proteins was found the same as for classical animal α-amylases with ABC-domains. A characteristic feature of Amy II is the lack of GHGA motif in the flexible loop region, similarly to many insect amylases. We identified "Enchytraeus-Eisenia type" α-amylase homologs in other clitellates and polychaetes, indicating the ancestral origin of Amy I/II proteins in Annelida. This study provides the first insight into the endogenous non-proteolytic digestive enzyme genes in potworms, discusses the evolution of Amy α-amylases in Annelida, and explores phylogenetic implications.
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Affiliation(s)
- Łukasz Gajda
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland.
| | - Agata Daszkowska-Golec
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland
| | - Piotr Świątek
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007, Katowice, Poland
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6
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Defourneaux É, Herranz M, Armenteros M, Sørensen MV, Norenburg JL, Park T, Worsaae K. Circumtropical distribution and cryptic species of the meiofaunal enteropneust Meioglossus (Harrimaniidae, Hemichordata). Sci Rep 2024; 14:9296. [PMID: 38654022 DOI: 10.1038/s41598-024-57591-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
Hemichordata has always played a central role in evolutionary studies of Chordata due to their close phylogenetic affinity and shared morphological characteristics. Hemichordates had no meiofaunal representatives until the surprising discovery of a microscopic, paedomorphic enteropneust Meioglossus psammophilus (Harrimaniidae, Hemichordata) from the Caribbean in 2012. No additional species have been described since, questioning the broader distribution and significance of this genus. However, being less than a millimeter long and superficially resembling an early juvenile acorn worm, Meioglossus may easily be overlooked in both macrofauna and meiofauna surveys. We here present the discovery of 11 additional populations of Meioglossus from shallow subtropical and tropical coralline sands of the Caribbean Sea, Red Sea, Indian Ocean, and East China Sea. These geographically separated populations show identical morphology but differ genetically. Our phylogenetic reconstructions include four gene markers and support the monophyly of Meioglossus. Species delineation analyses revealed eight new cryptic species, which we herein describe using DNA taxonomy. This study reveals a broad circumtropical distribution, supporting the validity and ecological importance of this enigmatic meiobenthic genus. The high cryptic diversity and apparent morphological stasis of Meioglossus may exemplify a potentially common evolutionary 'dead-end' scenario, where groups with highly miniaturized and simplified body plan lose their ability to diversify morphologically.
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Affiliation(s)
- Éloïse Defourneaux
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100, Copenhagen, Denmark
| | - Maria Herranz
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100, Copenhagen, Denmark
- Area of Biodiversity and Conservation, Superior School of Experimental Science and Technology (ESCET), Rey Juan Carlos University, C/ Tulipán S/N, 28933, Mostoles, Madrid, Spain
| | - Maickel Armenteros
- Unidad Académica Mazatlán, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Joel Montes Camarena S/N, 82040, Mazatlán, México
| | - Martin V Sørensen
- Natural History Museum Denmark, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Jon L Norenburg
- Smithsonian National Museum of Natural History, Washington, DC, USA
| | - Taeseo Park
- Species Diversity Research Division, National Institute of Biological Resources, Hwangyeong-Ro 42, Incheon, 22689, South Korea
| | - Katrine Worsaae
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100, Copenhagen, Denmark.
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7
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Worsaae K, Rouan A, Seaver E, Miyamoto N, Tilic E. Postembryonic development and male paedomorphosis in Osedax (Siboglinidae, Annelida). Front Neurosci 2024; 18:1369274. [PMID: 38562300 PMCID: PMC10984269 DOI: 10.3389/fnins.2024.1369274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 01/31/2024] [Indexed: 04/04/2024] Open
Abstract
Most species of the bone-devouring marine annelid, Osedax, display distinct sexual dimorphism with macroscopic sedentary females rooted in bones and free-living microscopic dwarf males. The paedomorphic male resembles the non-feeding metatrochophore larva in size, presence of eight pairs of chaetae, and a head ciliation potentially representing a residual prototroch. The male development may thus uniquely reiterate and validate the theoretical heterochrony process "progenesis", which suggests that an accelerated sexual maturation and early arrest of somatic growth can lead to a miniaturized and paedomorphic adult. In this study, we describe the postembryonic larval and juvenile organogenesis of Osedax japonicus to test for a potential synchronous arrest of somatic growth during male development. Five postembryonic stages could be distinguished, resembling day one to five in the larval development at 10°C: (0D) first cleavage of fertilized eggs (embryos undergo unequal spiral cleavage), (1D) pre-trochophore, with apical organ, (2D) early trochophore, + prototroch, brain, circumesophageal connectives and subesophageal commissure, (3D) trochophore, + telotroch, four ventral nerves, (4D) early metatrochophore, + protonephridia, dorsal and terminal sensory organs, (5D) metatrochophore, + two ventral paratrochs, mid-ventral nerve, posterior trunk commissure, two dorsal nerves; competent for metamorphosis. The larval development largely mirrors that of other lecithotrophic annelid larvae but does not show continuous chaetogenesis or full gut development. Additionally, O. japonicus larvae exhibit an unpaired, mid-dorsal, sensory organ. Female individuals shed their larval traits during metamorphosis and continue organogenesis (including circulatory system) and extensive growth for 2-3 weeks before developing oocytes. In contrast, males develop sperm within a day of metamorphosis and display a synchronous metamorphic arrest in neural and muscular development, retaining a large portion of larval features post metamorphosis. Our findings hereby substantiate male miniaturization in Osedax to be the outcome of an early and synchronous offset of somatic development, fitting the theoretical process "progenesis". This may be the first compelling morpho-developmental exemplification of a progenetic origin of a microscopic body plan. The presented morphological staging system will further serve as a framework for future examination of molecular patterns and pathways determining Osedax development.
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Affiliation(s)
- Katrine Worsaae
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alice Rouan
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Elaine Seaver
- The Whitney Laboratory for Marine Bioscience, University of Florida, Gainesville, FL, United States
| | - Norio Miyamoto
- X-STAR, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Ekin Tilic
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Department of Marine Zoology, Senckenberg Research Institute and Natural History Museum, Frankfurt, Germany
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8
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Legras M, Ghisleni G, Regnard L, Dias M, Soilihi R, Celmar E, Balavoine G. Fast cycling culture of the annelid model Platynereis dumerilii. PLoS One 2023; 18:e0295290. [PMID: 38127889 PMCID: PMC10735030 DOI: 10.1371/journal.pone.0295290] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023] Open
Abstract
Platynereis dumerilii, a marine annelid, is a model animal that has gained popularity in various fields such as developmental biology, biological rhythms, nervous system organization and physiology, behaviour, reproductive biology, and epigenetic regulation. The transparency of P. dumerilii tissues at all developmental stages makes it easy to perform live microscopic imaging of all cell types. In addition, the slow-evolving genome of P. dumerilii and its phylogenetic position as a representative of the vast branch of Lophotrochozoans add to its evolutionary significance. Although P. dumerilii is amenable to transgenesis and CRISPR-Cas9 knockouts, its relatively long and indefinite life cycle, as well as its semelparous reproduction have been hindrances to its adoption as a reverse genetics model. To overcome this limitation, an adapted culturing method has been developed allowing much faster life cycling, with median reproductive age at 13-14 weeks instead of 25-35 weeks using the traditional protocol. A low worm density in boxes and a strictly controlled feeding regime are important factors for the rapid growth and health of the worms. This culture method has several advantages, such as being much more compact, not requiring air bubbling or an artificial moonlight regime for synchronized sexual maturation and necessitating only limited water change. A full protocol for worm care and handling is provided.
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Affiliation(s)
- Mathieu Legras
- Université de Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Giulia Ghisleni
- Université de Paris Cité, CNRS, Institut Jacques Monod, Paris, France
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Léna Regnard
- Université de Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Manon Dias
- Université de Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Rabouant Soilihi
- Université de Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Enzo Celmar
- Université de Paris Cité, CNRS, Institut Jacques Monod, Paris, France
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9
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Thalén F, Köhne CG, Bleidorn C. Patchwork: Alignment-Based Retrieval and Concatenation of Phylogenetic Markers from Genomic Data. Genome Biol Evol 2023; 15:evad227. [PMID: 38085033 PMCID: PMC10735302 DOI: 10.1093/gbe/evad227] [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] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Low-coverage whole-genome sequencing (also known as "genome skimming") is becoming an increasingly affordable approach to large-scale phylogenetic analyses. While already routinely used to recover organellar genomes, genome skimming is rather rarely utilized for recovering single-copy nuclear markers. One reason might be that only few tools exist to work with this data type within a phylogenomic context, especially to deal with fragmented genome assemblies. We here present a new software tool called Patchwork for mining phylogenetic markers from highly fragmented short-read assemblies as well as directly from sequence reads. Patchwork is an alignment-based tool that utilizes the sequence aligner DIAMOND and is written in the programming language Julia. Homologous regions are obtained via a sequence similarity search, followed by a "hit stitching" phase, in which adjacent or overlapping regions are merged into a single unit. The novel sliding window algorithm trims away any noncoding regions from the resulting sequence. We demonstrate the utility of Patchwork by recovering near-universal single-copy orthologs within a benchmarking study, and we additionally assess the performance of Patchwork in comparison with other programs. We find that Patchwork allows for accurate retrieval of (putatively) single-copy genes from genome skimming data sets at different sequencing depths with high computational speed, outperforming existing software targeting similar tasks. Patchwork is released under the GNU General Public License version 3. Installation instructions, additional documentation, and the source code itself are all available via GitHub at https://github.com/fethalen/Patchwork.
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Affiliation(s)
- Felix Thalén
- Department for Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Göttingen 37073, Germany
- Cardio-CARE AG, Medizincampus Davos, Davos Wolfgang 7265, Switzerland
| | - Clara G Köhne
- Department for Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Göttingen 37073, Germany
| | - Christoph Bleidorn
- Department for Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Göttingen 37073, Germany
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10
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Kobayashi G. Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA). PeerJ 2023; 11:e16446. [PMID: 38047014 PMCID: PMC10693233 DOI: 10.7717/peerj.16446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/21/2023] [Indexed: 12/05/2023] Open
Abstract
Background The mitochondrial genomes (mitogenomes) of metazoans generally include the same set of protein-coding genes, which ensures the homology of mitochondrial genes between species. The mitochondrial genes are often used as reference data for species identification based on genetic data (DNA barcoding). The need for such reference data has been increasing due to the application of environmental DNA (eDNA) analysis for environmental assessments. Recently, the number of publicly available sequence reads obtained with next-generation sequencing (NGS) has been increasing in the public database (the NCBI Sequence Read Archive, SRA). Such freely available NGS reads would be promising sources for assembling mitochondrial protein-coding genes (mPCGs) of organisms whose mitochondrial genes are not available in GenBank. The present study aimed to assemble annelid mPCGs from raw data deposited in the SRA. Methods The recent progress in the classification of Annelida was briefly introduced. In the present study, the mPCGs of 32 annelid species of 19 families in clitellates and allies in Sedentaria (echiurans and polychaetes) were newly assembled from the reads deposited in the SRA. Assembly was performed with a recently published pipeline mitoRNA, which includes cycles of Bowtie2 mapping and Trinity assembly. Assembled mPCGs were deposited in GenBank as Third Party Data (TPA) data. A phylogenetic tree was reconstructed with maximum likelihood (ML) analysis, together with other mPCGs deposited in GenBank. Results and Discussion mPCG assembly was largely successful except for Travisia forbesii; only four genes were detected from the assembled contigs of the species probably due to the reads targeting its parasite. Most genes were largely successfully obtained, whereas atp8, nad2, and nad4l were only successful in 22-24 species. The high nucleotide substitution rates of these genes might be relevant to the failure in the assembly although nad6, which showed a similarly high substitution rate, was successfully assembled. Although the phylogenetic positions of several lineages were not resolved in the present study, the phylogenetic relationships of some polychaetes and leeches that were not inferred by transcriptomes were well resolved probably due to a more dense taxon sampling than previous phylogenetic analyses based on transcriptomes. Although NGS data are generally better sources for resolving phylogenetic relationships of both higher and lower classifications, there are ensuring needs for specific loci of the mitochondrial genes for analyses that do not require high resolutions, such as DNA barcoding, eDNA, and phylogenetic analysis among lower taxa. Assembly from publicly available NGS reads would help design specific primers for the mitochondrial gene sequences of species, whose mitochondrial genes are hard to amplify by Sanger sequencing using universal primers.
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Affiliation(s)
- Genki Kobayashi
- Research Center for Creative Partnerships, Ishinomaki Senshu University, Ishinomaki, Miyagi, Japan
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11
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Martín-Zamora FM, Davies BE, Donnellan RD, Guynes K, Martín-Durán JM. Functional genomics in Spiralia. Brief Funct Genomics 2023; 22:487-497. [PMID: 37981859 PMCID: PMC10658182 DOI: 10.1093/bfgp/elad036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/12/2023] [Accepted: 07/25/2023] [Indexed: 11/21/2023] Open
Abstract
Our understanding of the mechanisms that modulate gene expression in animals is strongly biased by studying a handful of model species that mainly belong to three groups: Insecta, Nematoda and Vertebrata. However, over half of the animal phyla belong to Spiralia, a morphologically and ecologically diverse animal clade with many species of economic and biomedical importance. Therefore, investigating genome regulation in this group is central to uncovering ancestral and derived features in genome functioning in animals, which can also be of significant societal impact. Here, we focus on five aspects of gene expression regulation to review our current knowledge of functional genomics in Spiralia. Although some fields, such as single-cell transcriptomics, are becoming more common, the study of chromatin accessibility, DNA methylation, histone post-translational modifications and genome architecture are still in their infancy. Recent efforts to generate chromosome-scale reference genome assemblies for greater species diversity and optimise state-of-the-art approaches for emerging spiralian research systems will address the existing knowledge gaps in functional genomics in this animal group.
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Affiliation(s)
- Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Billie E Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Rory D Donnellan
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Kero Guynes
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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12
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Liao IJY, Lu TM, Chen ME, Luo YJ. Spiralian genomics and the evolution of animal genome architecture. Brief Funct Genomics 2023; 22:498-508. [PMID: 37507111 DOI: 10.1093/bfgp/elad029] [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: 05/05/2023] [Revised: 06/27/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Recent developments in sequencing technologies have greatly improved our knowledge of phylogenetic relationships and genomic architectures throughout the tree of life. Spiralia, a diverse clade within Protostomia, is essential for understanding the evolutionary history of parasitism, gene conversion, nervous systems and animal body plans. In this review, we focus on the current hypotheses of spiralian phylogeny and investigate the impact of long-read sequencing on the quality of genome assemblies. We examine chromosome-level assemblies to highlight key genomic features that have driven spiralian evolution, including karyotype, synteny and the Hox gene organization. In addition, we show how chromosome rearrangement has influenced spiralian genomic structures. Although spiralian genomes have undergone substantial changes, they exhibit both conserved and lineage-specific features. We recommend increasing sequencing efforts and expanding functional genomics research to deepen insights into spiralian biology.
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13
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Rogers TF, Simakov O. Emerging questions on the mechanisms and dynamics of 3D genome evolution in spiralians. Brief Funct Genomics 2023; 22:533-542. [PMID: 37815133 PMCID: PMC10658181 DOI: 10.1093/bfgp/elad043] [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: 04/29/2023] [Revised: 08/17/2023] [Accepted: 09/12/2023] [Indexed: 10/11/2023] Open
Abstract
Information on how 3D genome topology emerged in animal evolution, how stable it is during development, its role in the evolution of phenotypic novelties and how exactly it affects gene expression is highly debated. So far, data to address these questions are lacking with the exception of a few key model species. Several gene regulatory mechanisms have been proposed, including scenarios where genome topology has little to no impact on gene expression, and vice versa. The ancient and diverse clade of spiralians may provide a crucial testing ground for such mechanisms. Sprialians have followed distinct evolutionary trajectories, with some clades experiencing genome expansions and/or large-scale genome rearrangements, and others undergoing genome contraction, substantially impacting their size and organisation. These changes have been associated with many phenotypic innovations in this clade. In this review, we describe how emerging genome topology data, along with functional tools, allow for testing these scenarios and discuss their predicted outcomes.
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Affiliation(s)
- Thea F Rogers
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
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14
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Fourreau CJL, Kise H, Santander MD, Pirro S, Maronna MM, Poliseno A, Santos ME, Reimer JD. Genome sizes and repeatome evolution in zoantharians (Cnidaria: Hexacorallia: Zoantharia). PeerJ 2023; 11:e16188. [PMID: 37868064 PMCID: PMC10586311 DOI: 10.7717/peerj.16188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/06/2023] [Indexed: 10/24/2023] Open
Abstract
Across eukaryotes, large variations of genome sizes have been observed even between closely related species. Transposable elements as part of the repeated DNA have been proposed and confirmed as one of the most important contributors to genome size variation. However, the evolutionary implications of genome size variation and transposable element dynamics are not well understood. Together with phenotypic traits, they are commonly referred to as the "C-value enigma". The order Zoantharia are benthic cnidarians found from intertidal zones to the deep sea, and some species are particularly abundant in coral reefs. Despite their high ecological relevance, zoantharians have yet to be largely studied from the genomic point of view. This study aims at investigating the role of the repeatome (total content of repeated elements) in genome size variations across the order Zoantharia. To this end, whole-genomes of 32 zoantharian species representing five families were sequenced. Genome sizes were estimated and the abundances of different repeat classes were assessed. In addition, the repeat overlap between species was assessed by a sequence clustering method. The genome sizes in the dataset varied up to 2.4 fold magnitude. Significant correlations between genome size, repeated DNA content and transposable elements, respectively (Pearson's correlation test R2 = 0.47, p = 0.0016; R2 = 0.22, p = 0.05) were found, suggesting their involvement in the dynamics of genome expansion and reduction. In all species, long interspersed nuclear elements and DNA transposons were the most abundant identified elements. These transposable elements also appeared to have had a recent expansion event. This was in contrast to the comparative clustering analysis which revealed species-specific patterns of satellite elements' amplification. In summary, the genome sizes of zoantharians likely result from the complex dynamics of repeated elements. Finally, the majority of repeated elements (up to 70%) could not be annotated to a known repeat class, highlighting the need to further investigate non-model cnidarian genomes. More research is needed to understand how repeated DNA dynamics relate to zoantharian evolution and their biology.
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Affiliation(s)
- Chloé Julie Loïs Fourreau
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Hiroki Kise
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- AIST Tsukuba Central, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Mylena Daiana Santander
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Stacy Pirro
- Iridian Genomes, Bethesda, United States of America
| | - Maximiliano M. Maronna
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Faculdade de Ciências, Universidade Estadual Paulista (UNESP), Bauru, Brazil
| | - Angelo Poliseno
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Maria E.A. Santos
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, United States of America
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15
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Ramos-Llorens M, Hontoria F, Navarro JC, Ferrier DEK, Monroig Ó. Functionally diverse front-end desaturases are widespread in the phylum Annelida. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159377. [PMID: 37517549 DOI: 10.1016/j.bbalip.2023.159377] [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: 06/02/2023] [Revised: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
Aquatic single-cell organisms have long been believed to be unique primary producers of omega-3 long-chain (≥C20) polyunsaturated fatty acids (ω3 LC-PUFA). Multiple invertebrates including annelids have been discovered to possess methyl-end desaturases enabling key steps in the de novo synthesis of ω3 LC-PUFA, and thus potentially contributing to their production in the ocean. Along methyl-end desaturases, the repertoire and function of further LC-PUFA biosynthesising enzymes is largely missing in Annelida. In this study we examined the front-end desaturase gene repertoire across the phylum Annelida, from Polychaeta and Clitellata, major classes of annelids comprising most annelid diversity. We further characterised the functions of the encoded enzymes in selected representative species by using a heterologous expression system based in yeast, demonstrating that functions of Annelida front-end desaturases have highly diversified during their expansion in both terrestrial and aquatic ecosystems. We concluded that annelids possess at least two front-end desaturases with Δ5 and Δ6Δ8 desaturase regioselectivities, enabling all the desaturation reactions required to convert the C18 precursors into the physiologically relevant LC-PUFA such as eicosapentaenoic and arachidonic acids, but not docosahexaenoic acid. Such a gene complement is conserved across the different taxonomic groups within Annelida.
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Affiliation(s)
- Marc Ramos-Llorens
- Instituto de Acuicultura Torre de la Sal (IATS), CSIC, 12595 Ribera de Cabanes, Castellón, Spain
| | - Francisco Hontoria
- Instituto de Acuicultura Torre de la Sal (IATS), CSIC, 12595 Ribera de Cabanes, Castellón, Spain
| | - Juan C Navarro
- Instituto de Acuicultura Torre de la Sal (IATS), CSIC, 12595 Ribera de Cabanes, Castellón, Spain
| | - David E K Ferrier
- The Scottish Oceans Institute, School of Biology, University of St. Andrews, St Andrews, Fife KY16 8LB, UK
| | - Óscar Monroig
- Instituto de Acuicultura Torre de la Sal (IATS), CSIC, 12595 Ribera de Cabanes, Castellón, Spain.
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16
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Schuster HC, Hirth F. Phylogenetic tracing of midbrain-specific regulatory sequences suggests single origin of eubilaterian brains. SCIENCE ADVANCES 2023; 9:eade8259. [PMID: 37224241 PMCID: PMC10208574 DOI: 10.1126/sciadv.ade8259] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 04/18/2023] [Indexed: 05/26/2023]
Abstract
Conserved cis-regulatory elements (CREs) control Engrailed-, Pax2-, and dachshund-related gene expression networks directing the formation and function of corresponding midbrain circuits in arthropods and vertebrates. Polarized outgroup analyses of 31 sequenced metazoan genomes representing all animal clades reveal the emergence of Pax2- and dachshund-related CRE-like sequences in anthozoan Cnidaria. The full complement, including Engrailed-related CRE-like sequences, is only detectable in spiralians, ecdysozoans, and chordates that have a brain; they exhibit comparable genomic locations and extensive nucleotide identities that reveal the presence of a conserved core domain, all of which are absent in non-neural genes and, together, distinguish them from randomly assembled sequences. Their presence concurs with a genetic boundary separating the rostral from caudal nervous systems, demonstrated for the metameric brains of annelids, arthropods, and chordates and the asegmental cycloneuralian and urochordate brain. These findings suggest that gene regulatory networks for midbrain circuit formation evolved within the lineage that led to the common ancestor of protostomes and deuterostomes.
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Affiliation(s)
- Helen C. Schuster
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, and Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
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17
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Moggioli G, Panossian B, Sun Y, Thiel D, Martín-Zamora FM, Tran M, Clifford AM, Goffredi SK, Rimskaya-Korsakova N, Jékely G, Tresguerres M, Qian PY, Qiu JW, Rouse GW, Henry LM, Martín-Durán JM. Distinct genomic routes underlie transitions to specialised symbiotic lifestyles in deep-sea annelid worms. Nat Commun 2023; 14:2814. [PMID: 37198188 DOI: 10.1038/s41467-023-38521-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 05/03/2023] [Indexed: 05/19/2023] Open
Abstract
Bacterial symbioses allow annelids to colonise extreme ecological niches, such as hydrothermal vents and whale falls. Yet, the genetic principles sustaining these symbioses remain unclear. Here, we show that different genomic adaptations underpin the symbioses of phylogenetically related annelids with distinct nutritional strategies. Genome compaction and extensive gene losses distinguish the heterotrophic symbiosis of the bone-eating worm Osedax frankpressi from the chemoautotrophic symbiosis of deep-sea Vestimentifera. Osedax's endosymbionts complement many of the host's metabolic deficiencies, including the loss of pathways to recycle nitrogen and synthesise some amino acids. Osedax's endosymbionts possess the glyoxylate cycle, which could allow more efficient catabolism of bone-derived nutrients and the production of carbohydrates from fatty acids. Unlike in most Vestimentifera, innate immunity genes are reduced in O. frankpressi, which, however, has an expansion of matrix metalloproteases to digest collagen. Our study supports that distinct nutritional interactions influence host genome evolution differently in highly specialised symbioses.
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Affiliation(s)
- Giacomo Moggioli
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Balig Panossian
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Yanan Sun
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Daniel Thiel
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Martin Tran
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Alexander M Clifford
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Nadezhda Rimskaya-Korsakova
- Friedrich Schiller University Jena, Faculty of Biological Sciences, Institute of Zoology and Evolutionary Research, Erbertstr. 1, 07743, Jena, Germany
| | - Gáspár Jékely
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Martin Tresguerres
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Pei-Yuan Qian
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lee M Henry
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
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18
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Degnan BM, Degnan SM. How larvae and life cycles evolve. Trends Genet 2023:S0168-9525(23)00086-0. [PMID: 37024335 DOI: 10.1016/j.tig.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 03/28/2023] [Indexed: 04/08/2023]
Abstract
Marine larvae have factored heavily in pursuits to understand the origin and evolution of animal life cycles. Recent comparisons of gene expression and chromatin state in different species of sea urchin and annelid show how evolutionary changes in embryonic gene regulation can lead to markedly different larval forms.
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Affiliation(s)
- Bernard M Degnan
- School of Biological Sciences and Centre for Marine Science, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Sandie M Degnan
- School of Biological Sciences and Centre for Marine Science, University of Queensland, Brisbane, QLD 4072, Australia
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19
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Martín-Zamora FM, Liang Y, Guynes K, Carrillo-Baltodano AM, Davies BE, Donnellan RD, Tan Y, Moggioli G, Seudre O, Tran M, Mortimer K, Luscombe NM, Hejnol A, Marlétaz F, Martín-Durán JM. Annelid functional genomics reveal the origins of bilaterian life cycles. Nature 2023; 615:105-110. [PMID: 36697830 PMCID: PMC9977687 DOI: 10.1038/s41586-022-05636-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 12/07/2022] [Indexed: 01/26/2023]
Abstract
Indirect development with an intermediate larva exists in all major animal lineages1, which makes larvae central to most scenarios of animal evolution2-11. Yet how larvae evolved remains disputed. Here we show that temporal shifts (that is, heterochronies) in trunk formation underpin the diversification of larvae and bilaterian life cycles. We performed chromosome-scale genome sequencing in the annelid Owenia fusiformis with transcriptomic and epigenomic profiling during the life cycles of this and two other annelids. We found that trunk development is deferred to pre-metamorphic stages in the feeding larva of O. fusiformis but starts after gastrulation in the non-feeding larva with gradual metamorphosis of Capitella teleta and the direct developing embryo of Dimorphilus gyrociliatus. Accordingly, the embryos of O. fusiformis develop first into an enlarged anterior domain that forms larval tissues and the adult head12. Notably, this also occurs in the so-called 'head larvae' of other bilaterians13-17, with which the O. fusiformis larva shows extensive transcriptomic similarities. Together, our findings suggest that the temporal decoupling of head and trunk formation, as maximally observed in head larvae, facilitated larval evolution in Bilateria. This diverges from prevailing scenarios that propose either co-option9,10 or innovation11 of gene regulatory programmes to explain larva and adult origins.
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Affiliation(s)
| | - Yan Liang
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Kero Guynes
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - Billie E Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Rory D Donnellan
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Yongkai Tan
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Giacomo Moggioli
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Océane Seudre
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Martin Tran
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - Kate Mortimer
- Department of Natural Sciences, Amgueddfa Cymru-Museum Wales, Cardiff, UK
| | - Nicholas M Luscombe
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Andreas Hejnol
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Institute of Zoology and Evolutionary Research, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Ferdinand Marlétaz
- Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
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20
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Ballentine WM, Dorgan KM. Locomotory Palp Function in Interstitial Annelids. THE BIOLOGICAL BULLETIN 2023; 244:51-62. [PMID: 37167622 DOI: 10.1086/724580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
AbstractThe interstitial environment of marine sediments is a complex network of voids and pores that is inhabited by a diverse and abundant fauna. Animals living within these interstitial spaces show widespread functional adaptations to this environment and have developed many strategies for moving and navigating through small spaces. Interstitial annelids demonstrate a remarkable level of morphologic diversity, and some possess dexterous, filiform palps (tentacle-like appendages common across Annelida). The function(s) of these palps in interstitial spaces has not been closely examined, and we propose that they serve a sensory role in the navigation of interstitial spaces. We investigated the locomotory function of long, dexterous palps in three families of interstitial annelids to determine their role in interstitial navigation. We observed two species of protodrilids (Protodrilidae), Pharyngocirrus eroticus (Saccocirridae), and Protodorvillea recuperata (Dorvilleidae), as they moved through two transparent sand analogs: cyolite and glass beads. All four species of annelids consistently used their palps to probe the interstitial environment while locomoting, and the distance probed with their palps was greater than the distance traveled with their heads, indicating a sensory form of palp-based navigation. The functionality of palps as sensory organs in the interstitial environment raises interesting questions about interstitial navigation and how fauna without appendages map their surroundings. The discovery of this previously undocumented function was possible only through the direct observation of interstitial behavior and emphasizes the importance of developing new techniques to study these animals in more natural habitats.
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21
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Seudre O, Martín-Zamora FM, Rapisarda V, Luqman I, Carrillo-Baltodano AM, Martín-Durán JM. The Fox Gene Repertoire in the Annelid Owenia fusiformis Reveals Multiple Expansions of the foxQ2 Class in Spiralia. Genome Biol Evol 2022; 14:evac139. [PMID: 36099507 PMCID: PMC9539403 DOI: 10.1093/gbe/evac139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
Fox genes are a large and conserved family of transcription factors involved in many key biological processes, including embryogenesis and body patterning. Although the role of Fox genes has been studied in an array of model systems, comprehensive comparative studies in Spiralia-a large clade of invertebrate animals including molluscs and annelids-are scarce but much needed to better understand the evolutionary history of this gene family. Here, we reconstruct and functionally characterize the Fox gene complement in the annelid Owenia fusiformis, a slow evolving species and member of the sister group to all remaining annelids. The genome of O. fusiformis contains at least a single ortholog for 20 of the 22 Fox gene classes that are ancestral to Bilateria, including an ortholog of the recently discovered foxT class. Temporal and spatial expression dynamics reveal a conserved role of Fox genes in gut formation, mesoderm patterning, and apical organ and cilia formation in Annelida and Spiralia. Moreover, we uncover an ancestral expansion of foxQ2 genes in Spiralia, represented by 11 paralogs in O. fusiformis. Notably, although all foxQ2 copies have apical expression in O. fusiformis, they show variable spatial domains and staggered temporal activation, which suggest cooperation and sub-functionalization among foxQ2 genes for the development of apical fates in this annelid. Altogether, our study informs the evolution and developmental roles of Fox genes in Annelida and Spiralia generally, providing the basis to explore how regulatory changes in Fox gene expression might have contributed to developmental and morphological diversification in Spiralia.
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Affiliation(s)
- Océane Seudre
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Valentina Rapisarda
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Imran Luqman
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Allan M Carrillo-Baltodano
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
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22
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Drábková M, Kocot KM, Halanych KM, Oakley TH, Moroz LL, Cannon JT, Kuris A, Garcia-Vedrenne AE, Pankey MS, Ellis EA, Varney R, Štefka J, Zrzavý J. Different phylogenomic methods support monophyly of enigmatic 'Mesozoa' (Dicyemida + Orthonectida, Lophotrochozoa). Proc Biol Sci 2022; 289:20220683. [PMID: 35858055 PMCID: PMC9257288 DOI: 10.1098/rspb.2022.0683] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Dicyemids and orthonectids were traditionally classified in a group called Mesozoa, but their placement in a single clade has been contested and their position(s) within Metazoa is uncertain. Here, we assembled a comprehensive matrix of Lophotrochozoa (Metazoa) and investigated the position of Dicyemida (= Rhombozoa) and Orthonectida, employing multiple phylogenomic approaches. We sequenced seven new transcriptomes and one draft genome from dicyemids (Dicyema, Dicyemennea) and two transcriptomes from orthonectids (Rhopalura). Using these and published data, we assembled and analysed contamination-filtered datasets with up to 987 genes. Our results recover Mesozoa monophyletic and as a close relative of Platyhelminthes or Gnathifera. Because of the tendency of the long-branch mesozoans to group with other long-branch taxa in our analyses, we explored the impact of approaches purported to help alleviate long-branch attraction (e.g. taxon removal, coalescent inference, gene targeting). None of these were able to break the association of Orthonectida with Dicyemida in the maximum-likelihood trees. Contrastingly, the Bayesian analysis and site-specific frequency model in maximum-likelihood did not recover a monophyletic Mesozoa (but only when using a specific 50 gene matrix). The classic hypothesis on monophyletic Mesozoa is possibly reborn and should be further tested.
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Affiliation(s)
- Marie Drábková
- Department of Parasitology, University of South Bohemia, České Budějovice 37005, Czech Republic,Laboratory of Molecular Ecology and Evolution, Institute of Parasitology, Biology Centre CAS, České Budějovice 37005, Czech Republic
| | - Kevin M. Kocot
- Department of Biological Sciences, The University of Alabama, Campus Box 870344, Tuscaloosa, AL 35487, USA
| | - Kenneth M. Halanych
- The Centre for Marine Science, University of North Carolina, Wilmington, 57000 Marvin K. Moss Lane, Wilmington, NC 28409, USA
| | - Todd H. Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Leonid L. Moroz
- Department of Neuroscience, and the Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Boulevard, St Augustine, FL 32080, USA
| | - Johanna T. Cannon
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Armand Kuris
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ana Elisa Garcia-Vedrenne
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - M. Sabrina Pankey
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Emily A. Ellis
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Rebecca Varney
- Department of Biological Sciences, The University of Alabama, Campus Box 870344, Tuscaloosa, AL 35487, USA,Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Jan Štefka
- Department of Parasitology, University of South Bohemia, České Budějovice 37005, Czech Republic,Laboratory of Molecular Ecology and Evolution, Institute of Parasitology, Biology Centre CAS, České Budějovice 37005, Czech Republic
| | - Jan Zrzavý
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice 37005, Czech Republic
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23
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Koch TL, Ramiro IBL, Flórez Salcedo P, Engholm E, Jensen KJ, Chase K, Olivera BM, Bjørn-Yoshimoto WE, Safavi-Hemami H. Reconstructing the Origins of the Somatostatin and Allatostatin-C Signaling Systems Using the Accelerated Evolution of Biodiverse Cone Snail Toxins. Mol Biol Evol 2022; 39:msac075. [PMID: 35383850 PMCID: PMC9048919 DOI: 10.1093/molbev/msac075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Somatostatin and its related peptides (SSRPs) form an important family of hormones with diverse physiological roles. The ubiquitous presence of SSRPs in vertebrates and several invertebrate deuterostomes suggests an ancient origin of the SSRP signaling system. However, the existence of SSRP genes outside of deuterostomes has not been established, and the evolutionary history of this signaling system remains poorly understood. Our recent discovery of SSRP-like toxins (consomatins) in venomous marine cone snails (Conus) suggested the presence of a related signaling system in mollusks and potentially other protostomes. Here, we identify the molluscan SSRP-like signaling gene that gave rise to the consomatin family. Following recruitment into venom, consomatin genes experienced strong positive selection and repeated gene duplications resulting in the formation of a hyperdiverse family of venom peptides. Intriguingly, the largest number of consomatins was found in worm-hunting species (>400 sequences), indicating a homologous system in annelids, another large protostome phylum. Consistent with this, comprehensive sequence mining enabled the identification of SSRP-like sequences (and their corresponding orphan receptor) in annelids and several other protostome phyla. These results established the existence of SSRP-like peptides in many major branches of bilaterians and challenge the prevailing hypothesis that deuterostome SSRPs and protostome allatostatin-C are orthologous peptide families. Finally, having a large set of predator-prey SSRP sequences available, we show that although the cone snail's signaling SSRP-like genes are under purifying selection, the venom consomatin genes experience rapid directional selection to target receptors in a changing mix of prey.
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Affiliation(s)
- Thomas Lund Koch
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen-N 2200, Denmark
| | - Iris Bea L. Ramiro
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen-N 2200, Denmark
| | | | - Ebbe Engholm
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen-N 2200, Denmark
- Department of Chemistry, University of Copenhagen, Frederiksberg 1871, Denmark
| | - Knud Jørgen Jensen
- Department of Chemistry, University of Copenhagen, Frederiksberg 1871, Denmark
| | - Kevin Chase
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Baldomero M. Olivera
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Helena Safavi-Hemami
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen-N 2200, Denmark
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
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24
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Seaver EC. Sifting through the mud: A tale of building the annelid Capitella teleta for EvoDevo studies. Curr Top Dev Biol 2022; 147:401-432. [PMID: 35337457 DOI: 10.1016/bs.ctdb.2021.12.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Over the last few decades, the annelid Capitella teleta has been used increasingly as a study system for investigations of development and regeneration. Its favorable properties include an ability to continuously maintain a laboratory culture, availability of a sequenced genome, a stereotypic cleavage program of early development, substantial regeneration abilities, and established experimental and functional genomics techniques. With this review I tell of my adventure of establishing the Capitella teleta as an emerging model and share examples of a few of the contributions our work has made to the fields of evo-devo and developmental biology. I highlight examples of conservation in developmental programs as well as surprising deviations from existing paradigms that highlight the importance of leveraging biological diversity to shift thinking in the field. The story for each study system is unique, and every animal has its own advantages and disadvantages as an experimental system. Just like most progress in science, it takes strategy, hard work and determination to develop tools and resources for a less studied animal, but luck and serendipity also play a role. I include a few narratives to personalize the science, share details of the story that are not included in typical publications, and provide perspective for investigators who are interested in developing their own study organism.
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Affiliation(s)
- Elaine C Seaver
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, United States.
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25
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Kobayashi G, Itoh H, Kojima S. Mitogenome of a stink worm (Annelida: Travisiidae) includes degenerate group II intron that is also found in five congeneric species. Sci Rep 2022; 12:4449. [PMID: 35292662 PMCID: PMC8924214 DOI: 10.1038/s41598-022-08103-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/25/2022] [Indexed: 12/05/2022] Open
Abstract
Mitogenomes are useful for inferring phylogenetic relationships between organisms. Although the mitogenomes of Annelida, one of the most morphologically and ecologically diverse metazoan groups have been well sequenced, those of several families remain unexamined. This study determined the first mitogenome from the family Travisiidae (Travisia sanrikuensis), analyzed its mitogenomic features, and reconstructed a phylogeny of Sedentaria. The monophyly of the Terebellida + Arenicolida + Travisiidae clade is supported by molecular phylogenetic analysis. The placement of Travisiidae is unclear because of the lack of mitogenomes from closely related lineages. An unexpected intron appeared within the cox1 gene of T. sanrikuensis and in the same positions of five undescribed Travisia spp. Although the introns are shorter (790–1386 bp) than other group II introns, they can be considered degenerate group II introns due to type II intron maturase open reading frames, found in two of the examined species, and motifs characteristic of group II introns. This is likely the first known case in metazoans where mitochondrial group II introns obtained by a common ancestor are conserved in several descendants. Insufficient evolutionary time for intron loss in Travisiidae, or undetermined mechanisms may have helped maintain the degenerate introns.
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Affiliation(s)
- Genki Kobayashi
- Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, 459 Shirahama, Nishimuro, Wakayama, 649-2211, Japan.
| | - Hajime Itoh
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Shigeaki Kojima
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
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26
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Purschke G, Vodopyanov S, Baller A, von Palubitzki T, Bartolomaeus T, Beckers P. Ultrastructure of cerebral eyes in Oweniidae and Chaetopteridae (Annelida) - implications for the evolution of eyes in Annelida. ZOOLOGICAL LETTERS 2022; 8:3. [PMID: 35078543 PMCID: PMC8787891 DOI: 10.1186/s40851-022-00188-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/23/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Recent phylogenomic studies have revealed a robust, new hypothesis of annelid phylogeny. Most surprisingly, a few early branching lineages formed a basal grade, whereas the majority of taxa were categorized as monophyletic Pleistoannelida. Members of these basal groups show a comparatively simple organization lacking certain characters regarded to be annelid specific. Thus, the evolution of organ systems and the characteristics probably present in the last common annelid ancestor require reevaluation. With respect to light-sensitive organs, a pair of simple larval eyes is regarded as being present in their last common ancestor. However, the evolutionary origin and structure of adult eyes remain obscure. Typically, adult eyes are multicellular pigment cups or pinhole eyes with or without a lens comprising rhabdomeric photoreceptor cells (PRCs) and pigmented supportive cells (PSCs) in converse design. However, in the most basal lineages, eyes are only present in a few taxa, and thus far, their ultrastructure is unknown. RESULTS Ultrastructural investigations of members of Oweniidae and Chaetopteridae reveal a corresponding design of adult cerebral eyes and PRCs. The eyes in species of these groups are simple pigment spot eyes, either forming a flat patch or embedded in a tube-like invagination. They are part of the epidermis and comprise two cell types, PSCs and rhabdomeric PRCs. Both cell types bear microvilli and one more or less reduced cilium. However, the PRCs showed only a moderate increase in the apical membrane surface in the form of irregularly arranged microvilli intermingling with those of the PSCs; a densely arranged brush border of rhabdomeric microvilli was absent. Additionally, both cell types show certain characteristics elsewhere observable in typical epidermal supportive cells. CONCLUSIONS These findings shed new light on the evolutionary history of adult eyes in Annelida. Most likely, the adult eye of the annelid stem species was a pair of simple pigment spot eyes with only slightly specialized PSCs and PRCs being an integrative part of the epidermis. As is the case for the nuchal organs, typical pigment cup adult eyes presumably evolved later in the annelid phylogeny, namely, in the stem lineages of Amphinomida and Pleistoannelida.
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Affiliation(s)
- Günter Purschke
- Zoology and Developmental Biology, Department of Biology and Chemistry, Osnabrück University, Osnabrück, Germany.
| | - Stepan Vodopyanov
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Anjilie Baller
- Zoology and Developmental Biology, Department of Biology and Chemistry, Osnabrück University, Osnabrück, Germany
- Present address: Department of Biology, Faculty II, University of Vechta, Vechta, Germany
| | - Tim von Palubitzki
- Zoology and Developmental Biology, Department of Biology and Chemistry, Osnabrück University, Osnabrück, Germany
| | - Thomas Bartolomaeus
- Institute of Evolutionary Biology and Ecology, University of Bonn, Bonn, Germany
| | - Patrick Beckers
- Institute of Evolutionary Biology and Ecology, University of Bonn, Bonn, Germany
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27
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Zakas C, Harry ND, Scholl EH, Rockman MV. The genome of the poecilogonous annelid Streblospio benedicti. Genome Biol Evol 2022; 14:6515305. [PMID: 35078222 PMCID: PMC8872972 DOI: 10.1093/gbe/evac008] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Streblospio benedicti is a common marine annelid that has become an important model for developmental evolution. It is the only known example of poecilogony (where two distinct developmental modes occur within a single species) that is due to a heritable difference in egg size. The dimorphic developmental programs and life-histories exhibited in this species depend on differences within the genome, making it an optimal model for understanding the genomic basis of developmental divergence. Studies using S. benedicti have begun to uncover the genetic and genomic principles that underlie developmental uncoupling, but until now they have been limited by the lack of availability of genomic tools. Here we present an annotated chromosomal-level genome assembly of S. benedicti generated from a combination of Illumina reads, Nanopore long reads, Chicago and Hi-C chromatin interaction sequencing, and a genetic map from experimental crosses. At 701.4 Mb, the S. benedicti genome is the largest annelid genome to date that has been assembled to chromosomal scaffolds. The complete genome of S. benedicti is valuable for functional genomic analyses of development and evolution, as well as phylogenetic comparison within the annelida and the Lophotrochozoa. Despite having two developmental modes, there is no evidence of genome duplication or substantial gene number expansions. Instead, lineage specific repeats account for much of the expansion of this genome compared to other annelids.
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Affiliation(s)
- Christina Zakas
- Department of Genetics, North Carolina State University, Raleigh, NC, USA
| | - Nathan D Harry
- Department of Genetics, North Carolina State University, Raleigh, NC, USA
| | - Elizabeth H Scholl
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Matthew V Rockman
- Department of Biology and Center for Genomics & Systems Biology, New York University, New York, NY, USA
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28
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Fofanova E, Mayorova TD, Voronezhskaya EE. Dinophiliformia early neurogenesis suggests the evolution of conservative neural structures across the Annelida phylogenetic tree. PeerJ 2021; 9:e12386. [PMID: 34966573 PMCID: PMC8667735 DOI: 10.7717/peerj.12386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/04/2021] [Indexed: 11/27/2022] Open
Abstract
Despite the increasing data concerning the structure of the adult nervous system in various Lophotrochozoa groups, the early events during the neurogenesis of rare and unique groups need clarification. Annelida are a diverse clade of Lophotrochozoa, and their representatives demonstrate a variety of body plans, lifestyles, and life cycles. Comparative data about the early development are available for Errantia, Sedentaria, Sipuncula, and Palaeoannelida; however, our knowledge of Dinophiliformia is currently scarce. Representatives of Dinophiliformia are small interstitial worms combining unique morphological features of different Lophotrochozoan taxa and expressing paedomorphic traits. We describe in detail the early neurogenesis of two related species: Dimorphilus gyrociliatus and Dinophilus vorticoides, from the appearance of first nerve cells until the formation of an adult body plan. In both species, the first cells were detected at the anterior and posterior regions at the early trochophore stage and demonstrated positive reactions with pan-neuronal marker anti-acetylated tubulin only. Long fibers of early cells grow towards each other and form longitudinal bundles along which differentiating neurons later appear and send their processes. We propose that these early cells serve as pioneer neurons, forming a layout of the adult nervous system. The early anterior cell of D. vorticoides is transient and present during the short embryonic period, while early anterior and posterior cells in D. gyrociliatus are maintained throughout the whole lifespan of the species. During development, the growing processes of early cells form compact brain neuropile, paired ventral and lateral longitudinal bundles; unpaired medial longitudinal bundle; and commissures in the ventral hyposphere. Specific 5-HT- and FMRFa-immunopositive neurons differentiate adjacent to the ventral bundles and brain neuropile in the middle trochophore and late trochophore stages, i.e. after the main structures of the nervous system have already been established. Processes of 5-HT- and FMRFa-positive cells constitute a small proportion of the tubulin-immunopositive brain neuropile, ventral cords, and commissures in all developmental stages. No 5-HT- and FMRFa-positive cells similar to apical sensory cells of other Lophotrochozoa were detected. We conclude that: (i) like in Errantia and Sedentaria, Dinophiliformia neurogenesis starts from the peripheral cells, whose processes prefigure the forming adult nervous system, (ii) Dinophiliformia early cells are negative to 5-HT and FMRFa antibodies like Sedentaria pioneer cells.
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Affiliation(s)
- Elizaveta Fofanova
- Department of Comparative and Developmental Physiology, Koltzov Institute of Developmental Biology RAS, Moscow, Russia
| | - Tatiana D Mayorova
- Department of Comparative and Developmental Physiology, Koltzov Institute of Developmental Biology RAS, Moscow, Russia.,Laboratory of Neurobiology, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA
| | - Elena E Voronezhskaya
- Department of Comparative and Developmental Physiology, Koltzov Institute of Developmental Biology RAS, Moscow, Russia
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29
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Chavarria RA, Game M, Arbelaez B, Ramnarine C, Snow ZK, Smith FW. Extensive loss of Wnt genes in Tardigrada. BMC Ecol Evol 2021; 21:223. [PMID: 34961481 PMCID: PMC8711157 DOI: 10.1186/s12862-021-01954-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/09/2021] [Indexed: 11/28/2022] Open
Abstract
Background Wnt genes code for ligands that activate signaling pathways during development in Metazoa. Through the canonical Wnt (cWnt) signaling pathway, these genes regulate important processes in bilaterian development, such as establishing the anteroposterior axis and posterior growth. In Arthropoda, Wnt ligands also regulate segment polarity, and outgrowth and patterning of developing appendages. Arthropods are part of a lineage called Panarthropoda that includes Onychophora and Tardigrada. Previous studies revealed potential roles of Wnt genes in regulating posterior growth, segment polarity, and growth and patterning of legs in Onychophora. Unlike most other panarthropods, tardigrades lack posterior growth, but retain segmentation and appendages. Here, we investigated Wnt genes in tardigrades to gain insight into potential roles that these genes play during development of the highly compact and miniaturized tardigrade body plan. Results We analyzed published genomes for two representatives of Tardigrada, Hypsibius exemplaris and Ramazzottius varieornatus. We identified single orthologs of Wnt4, Wnt5, Wnt9, Wnt11, and WntA, as well as two Wnt16 paralogs in both tardigrade genomes. We only found a Wnt2 ortholog in H. exemplaris. We could not identify orthologs of Wnt1, Wnt6, Wnt7, Wnt8, or Wnt10. We identified most other components of cWnt signaling in both tardigrade genomes. However, we were unable to identify an ortholog of arrow/Lrp5/6, a gene that codes for a Frizzled co-receptor of Wnt ligands. Additionally, we found that some other animals that have lost several Wnt genes and are secondarily miniaturized, like tardigrades, are also missing an ortholog of arrow/Lrp5/6. We analyzed the embryonic expression patterns of Wnt genes in H. exemplaris during developmental stages that span the establishment of the AP axis through segmentation and leg development. We detected expression of all Wnt genes in H. exemplaris besides one of the Wnt16 paralogs. During embryo elongation, expression of several Wnt genes was restricted to the posterior pole or a region between the anterior and posterior poles. Wnt genes were expressed in distinct patterns during segmentation and development of legs in H. exemplaris, rather than in broadly overlapping patterns. Conclusions Our results indicate that Wnt signaling has been highly modified in Tardigrada. While most components of cWnt signaling are conserved in tardigrades, we conclude that tardigrades have lost Wnt1, Wnt6, Wnt7, Wnt8, and Wnt10, along with arrow/Lrp5/6. Our expression data may indicate a conserved role of Wnt genes in specifying posterior identities during establishment of the AP axis. However, the loss of several Wnt genes and the distinct expression patterns of Wnt genes during segmentation and leg development may indicate that combinatorial interactions among Wnt genes are less important during tardigrade development compared to many other animals. Based on our results, and comparisons to previous studies, we speculate that the loss of several Wnt genes in Tardigrada may be related to a reduced number of cells and simplified development that accompanied miniaturization and anatomical simplification in this lineage. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01954-y.
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Affiliation(s)
- Raul A Chavarria
- Biology Department, University of North Florida, Jacksonville, FL, USA
| | - Mandy Game
- Biology Department, University of North Florida, Jacksonville, FL, USA
| | - Briana Arbelaez
- Biology Department, University of North Florida, Jacksonville, FL, USA
| | - Chloe Ramnarine
- Biology Department, University of North Florida, Jacksonville, FL, USA
| | - Zachary K Snow
- Biology Department, University of North Florida, Jacksonville, FL, USA
| | - Frank W Smith
- Biology Department, University of North Florida, Jacksonville, FL, USA.
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30
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de Oliveira AL, Mitchell J, Girguis P, Bright M. Novel insights on obligate symbiont lifestyle and adaptation to chemosynthetic environment as revealed by the giant tubeworm genome. Mol Biol Evol 2021; 39:6454105. [PMID: 34893862 PMCID: PMC8789280 DOI: 10.1093/molbev/msab347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The mutualism between the giant tubeworm Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone has been extensively researched over the past 40 years. However, the lack of the host whole genome information has impeded the full comprehension of the genotype/phenotype interface in Riftia. Here we described the high-quality draft genome of Riftia, its complete mitogenome, and tissue-specific transcriptomic data. The Riftia genome presents signs of reductive evolution, with gene family contractions exceeding expansions. Expanded gene families are related to sulphur metabolism, detoxification, anti-oxidative stress, oxygen transport, immune system, and lysosomal digestion, reflecting evolutionary adaptations to the vent environment and endosymbiosis. Despite the derived body plan, the developmental gene repertoire in the gutless tubeworm is extremely conserved with the presence of a near intact and complete Hox cluster. Gene expression analyses establishes that the trophosome is a multi-functional organ marked by intracellular digestion of endosymbionts, storage of excretory products and haematopoietic functions. Overall, the plume and gonad tissues both in contact to the environment harbour highly expressed genes involved with cell cycle, programmed cell death, and immunity indicating a high cell turnover and defence mechanisms against pathogens. We posit that the innate immune system plays a more prominent role into the establishment of the symbiosis during the infection in the larval stage, rather than maintaining the symbiostasis in the trophosome. This genome bridges four decades of physiological research in Riftia, whilst simultaneously provides new insights into the development, whole organism functions and evolution in the giant tubeworm.
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Affiliation(s)
| | - Jessica Mitchell
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Peter Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Monika Bright
- Department of Functional and Evolutionary Ecology, University of Vienna, Austria
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Tilic E, Stiller J, Campos E, Pleijel F, Rouse GW. Phylogenomics resolves ambiguous relationships within Aciculata (Errantia, Annelida). Mol Phylogenet Evol 2021; 166:107339. [PMID: 34751138 DOI: 10.1016/j.ympev.2021.107339] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/23/2021] [Accepted: 10/27/2021] [Indexed: 10/20/2022]
Abstract
Aciculata (Eunicida + Phyllodocida) is among the largest clades of annelids, comprising almost half of the known diversity of all marine annelids. Despite the group's large size and biological importance, most phylogenomic studies on Annelida to date have had a limited sampling of this clade. The phylogenetic placement of many clades within Phyllodocida in particular has remained poorly understood. To resolve the relationships within Aciculata we conducted a large-scale phylogenomic analysis based on 24 transcriptomes (13 new), chosen to represent many family-ranked taxa that have never been included in a broad phylogenomic study. Our sampling also includes several enigmatic taxa with challenging phylogenetic placement, such as Histriobdella, Struwela, Lacydonia, Pilargis and the holopelagic worms Lopadorrhynchus, Travisiopsis and Tomopteris. Our robust phylogeny allows us to name and place some of these problematic clades and has significant implications on the systematics of the group. Within Eunicida we reinstate the names Eunicoidea and Oenonoidea. Within Phyllodocida we delineate Phyllodociformia, Glyceriformia, Nereidiformia, Nephtyiformia and Aphroditiformia. Phyllodociformia now includes: Lacydonia, Typhloscolecidae, Lopadorrhynchidae and Phyllodocidae. Nephtyiformia includes Nephtyidae and Pilargidae. We also broaden the delineation of Glyceriformia to include Sphaerodoridae, Tomopteridae and Glyceroidea (Glyceridae + Goniadidae). Furthermore, our study demonstrates and explores how conflicting, yet highly supported topologies can result from confounding signals in gene trees.
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Affiliation(s)
- Ekin Tilic
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA; Institute of Evolutionary Biology and Animal Ecology, University of Bonn, Germany; Marine Biological Section, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.
| | - Josefin Stiller
- Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Ernesto Campos
- Facultad de Ciencias, Universidad Autónoma de Baja California. Ensenada, Baja California, México
| | - Fredrik Pleijel
- Department of Marine Sciences, University of Gothenburg, Tjärnö, Sweden
| | - Greg W Rouse
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA.
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Thiel D, Guerra LAY, Franz-Wachtel M, Hejnol A, Jékely G. Nemertean, brachiopod and phoronid neuropeptidomics reveals ancestral spiralian signalling systems. Mol Biol Evol 2021; 38:4847-4866. [PMID: 34272863 PMCID: PMC8557429 DOI: 10.1093/molbev/msab211] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Neuropeptides are diverse signaling molecules in animals commonly acting through G-protein coupled receptors (GPCRs). Neuropeptides and their receptors underwent extensive diversification in bilaterians and the relationships of many peptide–receptor systems have been clarified. However, we lack a detailed picture of neuropeptide evolution in lophotrochozoans as in-depth studies only exist for mollusks and annelids. Here, we analyze peptidergic systems in Nemertea, Brachiopoda, and Phoronida. We screened transcriptomes from 13 nemertean, 6 brachiopod, and 4 phoronid species for proneuropeptides and neuropeptide GPCRs. With mass spectrometry from the nemertean Lineus longissimus, we validated several predicted peptides and identified novel ones. Molecular phylogeny combined with peptide-sequence and gene-structure comparisons allowed us to comprehensively map spiralian neuropeptide evolution. We found most mollusk and annelid peptidergic systems also in nemerteans, brachiopods, and phoronids. We uncovered previously hidden relationships including the orthologies of spiralian CCWamides to arthropod agatoxin-like peptides and of mollusk APGWamides to RGWamides from annelids, with ortholog systems in nemerteans, brachiopods, and phoronids. We found that pleurin neuropeptides previously only found in mollusks are also present in nemerteans and brachiopods. We also identified cases of gene family duplications and losses. These include a protostome-specific expansion of RFamide/Wamide signaling, a spiralian expansion of GnRH-related peptides, and duplications of vasopressin/oxytocin before the divergence of brachiopods, phoronids, and nemerteans. This analysis expands our knowledge of peptidergic signaling in spiralians and other protostomes. Our annotated data set of nearly 1,300 proneuropeptide sequences and 600 GPCRs presents a useful resource for further studies of neuropeptide signaling.
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Affiliation(s)
- Daniel Thiel
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, UK.,Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | | | - Mirita Franz-Wachtel
- Eberhard Karls Universität Tübingen, Interfaculty Institute for Cell Biology, Tübingen, Germany
| | - Andreas Hejnol
- Department of Biological Sciences, University of Bergen, Bergen, 5006, Norway
| | - Gáspár Jékely
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, UK
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Sun Y, Sun J, Yang Y, Lan Y, Ip JCH, Wong WC, Kwan YH, Zhang Y, Han Z, Qiu JW, Qian PY. Genomic signatures supporting the symbiosis and formation of chitinous tube in the deep-sea tubeworm Paraescarpia echinospica. Mol Biol Evol 2021; 38:4116-4134. [PMID: 34255082 PMCID: PMC8476170 DOI: 10.1093/molbev/msab203] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Vestimentiferan tubeworms are iconic animals that present as large habitat-forming chitinized tube bushes in deep-sea chemosynthetic ecosystems. They are gutless and depend entirely on their endosymbiotic sulfide-oxidizing chemoautotrophic bacteria for nutrition. Information on the genomes of several siboglinid endosymbionts has improved our understanding of their nutritional supplies. However, the interactions between tubeworms and their endosymbionts remain largely unclear due to a paucity of host genomes. Here, we report the chromosome-level genome of the vestimentiferan tubeworm Paraescarpia echinospica. We found that the genome has been remodeled to facilitate symbiosis through the expansion of gene families related to substrate transfer and innate immunity, suppression of apoptosis, regulation of lysosomal digestion, and protection against oxidative stress. Furthermore, the genome encodes a programmed cell death pathway that potentially controls the endosymbiont population. Our integrated genomic, transcriptomic, and proteomic analyses uncovered matrix proteins required for the formation of the chitinous tube and revealed gene family expansion and co-option as evolutionary mechanisms driving the acquisition of this unique supporting structure for deep-sea tubeworms. Overall, our study provides novel insights into the host’s support system that has enabled tubeworms to establish symbiosis, thrive in deep-sea hot vents and cold seeps, and produce the unique chitinous tubes in the deep sea.
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Affiliation(s)
- Yanan Sun
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jin Sun
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yi Yang
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yi Lan
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jack Chi-Ho Ip
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Wai Chuen Wong
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yick Hang Kwan
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yanjie Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Zhuang Han
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- Corresponding authors: E-mails: ;
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Corresponding authors: E-mails: ;
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Structural and Functional Characterization of the FGF Signaling Pathway in Regeneration of the Polychaete Worm Alitta virens (Annelida, Errantia). Genes (Basel) 2021; 12:genes12060788. [PMID: 34063978 PMCID: PMC8224027 DOI: 10.3390/genes12060788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/16/2022] Open
Abstract
Epimorphic regeneration of lost body segments is a widespread phenomenon across annelids. However, the molecular inducers of the cell sources for this reparative morphogenesis have not been identified. In this study, we focused on the role of fibroblast growth factor (FGF) signaling in the posterior regeneration of Alitta virens. For the first time, we showed an early activation of FGF ligands and receptor expression in an annelid regenerating after amputation. The expression patterns indicate that the entire regenerative bud is competent to FGFs, whose activity precedes the initiation of cell proliferation. The critical requirement of FGF signaling, especially at early stages, is also supported by inhibitor treatments followed by proliferation assay, demonstrating that induction of blastemal cells depends on FGFs. Our results show that FGF signaling pathway is a key player in regenerative response, while the FGF-positive wound epithelium, ventral nerve cord and some mesodermal cells around the gut could be the inducing tissues. This mechanism resembles reparative regeneration of vertebrate appendages suggesting such a response to the injury may be ancestral for all bilaterians.
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Carrillo-Baltodano AM, Seudre O, Guynes K, Martín-Durán JM. Early embryogenesis and organogenesis in the annelid Owenia fusiformis. EvoDevo 2021; 12:5. [PMID: 33971947 PMCID: PMC8111721 DOI: 10.1186/s13227-021-00176-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/23/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Annelids are a diverse group of segmented worms within Spiralia, whose embryos exhibit spiral cleavage and a variety of larval forms. While most modern embryological studies focus on species with unequal spiral cleavage nested in Pleistoannelida (Sedentaria + Errantia), a few recent studies looked into Owenia fusiformis, a member of the sister group to all remaining annelids and thus a key lineage to understand annelid and spiralian evolution and development. However, the timing of early cleavage and detailed morphogenetic events leading to the formation of the idiosyncratic mitraria larva of O. fusiformis remain largely unexplored. RESULTS Owenia fusiformis undergoes equal spiral cleavage where the first quartet of animal micromeres are slightly larger than the vegetal macromeres. Cleavage results in a coeloblastula approximately 5 h post-fertilization (hpf) at 19 °C. Gastrulation occurs via invagination and completes 4 h later, with putative mesodermal precursors and the chaetoblasts appearing 10 hpf at the dorso-posterior side. Soon after, at 11 hpf, the apical tuft emerges, followed by the first neurons (as revealed by the expression of elav1 and synaptotagmin-1) in the apical organ and the prototroch by 13 hpf. Muscles connecting the chaetal sac to various larval tissues develop around 18 hpf and by the time the mitraria is fully formed at 22 hpf, there are FMRFamide+ neurons in the apical organ and prototroch, the latter forming a prototrochal ring. As the mitraria feeds, it grows in size and the prototroch expands through active proliferation. The larva becomes competent after ~ 3 weeks post-fertilization at 15 °C, when a conspicuous juvenile rudiment has formed ventrally. CONCLUSIONS Owenia fusiformis embryogenesis is similar to that of other equal spiral cleaving annelids, supporting that equal cleavage is associated with the formation of a coeloblastula, gastrulation via invagination, and a feeding trochophore-like larva in Annelida. The nervous system of the mitraria larva forms earlier and is more elaborated than previously recognized and develops from anterior to posterior, which is likely an ancestral condition to Annelida. Altogether, our study identifies the major developmental events during O. fusiformis ontogeny, defining a conceptual framework for future investigations.
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Affiliation(s)
| | - Océane Seudre
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Kero Guynes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - José María Martín-Durán
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
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The Early Branching Group of Orbiniida Sensu Struck et al., 2015: Parergodrilidae and Orbiniidae. DIVERSITY 2021. [DOI: 10.3390/d13010029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This review addresses the state of the art of the systematics and the improvements in the biology, ecology and species diversity of the two annelid taxa Parergodrilidae and Orbiniidae, the early branching group of Orbiniida sensu Struck et al., 2015 according to molecular studies. An effort to identify gaps of knowledge is given to understand the distribution, dispersal and the diversity Parergodrilidae and Orbiniidae hold, as well as to give several directions for future research. Parergodrilidae is a taxon of interstitial annelids constituted by the terrestrial Parergodrilus heideri (monotypic genus up to date), reported throughout Europe but also in Korea and North America, and the genus Stygocapitella, which includes eleven species from the upper shore of sandy beaches distributed along Europe and other regions of the world. Orbiniidae contains more than 200 described species spread over 20 valid genera, varying in size from a few millimeters up to 30 cm, distributed globally and living in a wide variety of soft bottoms. Improving the knowledge on these two sister-taxa is crucial for the understanding of the evolution to interstitial forms by progenesis in Annelida.
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