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Short S, Green Etxabe A, Robinson A, Spurgeon D, Kille P. The genome sequence of the red compost earthworm, Lumbricus rubellus (Hoffmeister, 1843). Wellcome Open Res 2023; 8:354. [PMID: 38618197 PMCID: PMC11015115 DOI: 10.12688/wellcomeopenres.19834.1] [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] [Accepted: 08/02/2023] [Indexed: 04/16/2024] Open
Abstract
We present a genome assembly from an individual Lumbricus rubellus (the red compost earthworm; Annelida; Clitellata; Haplotaxida; Lumbricidae). The genome sequence is 787.5 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.81 kilobases in length. Gene annotation of this assembly on Ensembl identified 33,426 protein coding genes.
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Affiliation(s)
- Stephen Short
- UK Centre for Ecology & Hydrology, Wallingford, England, UK
| | | | - Alex Robinson
- UK Centre for Ecology & Hydrology, Wallingford, England, UK
| | - David Spurgeon
- UK Centre for Ecology & Hydrology, Wallingford, England, UK
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2
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Abstract
Regeneration, the ability to restore body parts after an injury or an amputation, is a widespread property in the animal kingdom. This chapter describes methods used to study this fascinating process in the annelid Platynereis dumerilii. During most of its life, this segmented worm is able to regenerate upon amputation the posterior part of its body, including its pygidium (terminal non-segmented body region bearing the anus) and a subterminal posterior growth zone which contains stem cells required for the formation of new segments. Detailed description of Platynereis worm culture and how to obtain large quantity of regenerating worms is provided. We also describe the staging system that we established and three important methods to study regeneration: whole mount in situ hybridization to study gene expression, 5-ethynyl-2'-deoxyuridine (EdU) labeling to characterize cell proliferation, and use of pharmacological treatments to establish putative roles of defined signaling pathways and processes.
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Affiliation(s)
- Michel Vervoort
- CNRS, Institut Jacques Monod, UMR 7592, Université de Paris, Paris Cedex, France
| | - Eve Gazave
- CNRS, Institut Jacques Monod, UMR 7592, Université de Paris, Paris Cedex, France.
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3
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Seaver EC, de Jong DM. Regeneration in the Segmented Annelid Capitella teleta. Genes (Basel) 2021; 12:genes12111769. [PMID: 34828375 PMCID: PMC8623021 DOI: 10.3390/genes12111769] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/22/2021] [Accepted: 10/28/2021] [Indexed: 12/30/2022] Open
Abstract
The segmented worms, or annelids, are a clade within the Lophotrochozoa, one of the three bilaterian superclades. Annelids have long been models for regeneration studies due to their impressive regenerative abilities. Furthermore, the group exhibits variation in adult regeneration abilities with some species able to replace anterior segments, posterior segments, both or neither. Successful regeneration includes regrowth of complex organ systems, including the centralized nervous system, gut, musculature, nephridia and gonads. Here, regenerative capabilities of the annelid Capitella teleta are reviewed. C. teleta exhibits robust posterior regeneration and benefits from having an available sequenced genome and functional genomic tools available to study the molecular and cellular control of the regeneration response. The highly stereotypic developmental program of C. teleta provides opportunities to study adult regeneration and generate robust comparisons between development and regeneration.
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4
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Wiggans M, Pearson BJ. One stem cell program to rule them all? FEBS J 2020; 288:3394-3406. [PMID: 33063917 DOI: 10.1111/febs.15598] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/17/2020] [Accepted: 10/12/2020] [Indexed: 12/23/2022]
Abstract
Many species of animals have stem cells that they maintain throughout their lives, which suggests that stem cells are an ancestral feature of all animals. From this, we take the viewpoint that cells with the biological properties of 'stemness'-self-renewal and multipotency-may share ancestral genetic circuitry. However, in practice is it very difficult to identify and compare stemness gene signatures across diverse animals and large evolutionary distances? First, it is critical to experimentally demonstrate self-renewal and potency. Second, genomic methods must be used to determine specific gene expression in stem cell types compared with non-stem cell types to determine stem cell gene enrichment. Third, gene homology must be mapped between diverse animals across large evolutionary distances. Finally, conserved genes that fulfill these criteria must be tested for role in stem cell function. It is our viewpoint that by comparing stem cell-specific gene signatures across evolution, ancestral programs of stemness can be uncovered, and ultimately, the dysregulation of stemness programs drives the state of cancer stem cells.
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Affiliation(s)
- Mallory Wiggans
- Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, ON, Canada
| | - Bret J Pearson
- Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, ON, Canada.,Ontario Institute for Cancer Research, Toronto, ON, Canada
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5
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Han YH, Ryu KB, Medina Jiménez BI, Kim J, Lee HY, Cho SJ. Muscular Development in Urechis unicinctus (Echiura, Annelida). Int J Mol Sci 2020; 21:ijms21072306. [PMID: 32225111 PMCID: PMC7178014 DOI: 10.3390/ijms21072306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 12/27/2022] Open
Abstract
Echiura is one of the most intriguing major subgroups of phylum Annelida because, unlike most other annelids, echiuran adults lack metameric body segmentation. Urechis unicinctus lives in U-shape burrows of soft sediments. Little is known about the molecular mechanisms underlying the development of U. unicinctus. Herein, we overviewed the developmental process from zygote to juvenile U. unicinctus using immunohistochemistry and F-actin staining for the nervous and muscular systems, respectively. Through F-actin staining, we found that muscle fibers began to form in the trochophore phase and that muscles for feeding were produced first. Subsequently, in the segmentation larval stage, the transversal muscle was formed in the shape of a ring in an anterior-to-posterior direction with segment formation, as well as a ventromedian muscle for the formation of a ventral nerve cord. After that, many muscle fibers were produced along the entire body and formed the worm-shaped larva. Finally, we investigated the spatiotemporal expression of Uun_st-mhc, Uun_troponin I, Uun_calponin, and Uun_twist genes found in U. unicinctus. During embryonic development, the striated and smooth muscle genes were co-expressed in the same region. However, the adult body wall muscles showed differential gene expression of each muscle layer. The results of this study will provide the basis for the understanding of muscle differentiation in Echiura.
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Affiliation(s)
- Yong-Hee Han
- School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 28644, Korea; (Y.-H.H.); (K.-B.R.); (B.I.M.J.)
| | - Kyoung-Bin Ryu
- School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 28644, Korea; (Y.-H.H.); (K.-B.R.); (B.I.M.J.)
| | - Brenda I. Medina Jiménez
- School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 28644, Korea; (Y.-H.H.); (K.-B.R.); (B.I.M.J.)
- Department of Earth Sciences, Paleobiology, Uppsala University, Villavägen 16, 75236 Uppsala, Sweden
| | - Jung Kim
- Department of Molecular and Cell Biology, University of California, 539 LSA, Berkeley, CA 94720-3200, USA;
| | - Hae-Youn Lee
- School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 28644, Korea; (Y.-H.H.); (K.-B.R.); (B.I.M.J.)
- Correspondence: (H.-Y.L.); (S.-J.C.); Tel.: +82-43-261-2294 (S.-J.C.)
| | - Sung-Jin Cho
- School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 28644, Korea; (Y.-H.H.); (K.-B.R.); (B.I.M.J.)
- Correspondence: (H.-Y.L.); (S.-J.C.); Tel.: +82-43-261-2294 (S.-J.C.)
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6
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Kuo DH, Lai YT. On the origin of leeches by evolution of development. Dev Growth Differ 2018; 61:43-57. [PMID: 30393850 DOI: 10.1111/dgd.12573] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 12/19/2022]
Abstract
Leeches are a unique group of annelids arising from an ancestor that would be characterized as a freshwater oligochaete worm. Comparative biology of the oligochaetes and the leeches reveals that body plan changes in the oligochaete-to-leech transition probably occurred by addition or modification of the terminal steps in embryonic development and that they were likely driven by a change in the feeding behavior in the ancestor of leeches. In this review article, developmental changes that are associated with the evolution of several leech-specific traits are discussed. These include (1) the evolution of suckers, (2) the loss of chaetae, (3) the loss of septa, and (4) a fixed number of segments. An altered developmental fate of the teloblast is further proposed to be a key factor contributing to the fixation of the segment number, and the evolutionary change in teloblast development may also account for the loss of the ability to regenerate the lost body segments in the leech.
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Affiliation(s)
- Dian-Han Kuo
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yi-Te Lai
- Department of Life Science, National Taiwan University, Taipei, Taiwan
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7
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Tomioka S, Kakui K, Kajihara H. Molecular Phylogeny of the Family Capitellidae (Annelida). Zoolog Sci 2018; 35:436-445. [PMID: 30298787 DOI: 10.2108/zs180009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Capitellids have emerged as monophyletic in most but not all recent molecular phylogenies, indicating that more extensive taxon sampling is necessary. In addition, monophyly of most or all capitellid genera was questionable, as some diagnostic characters vary ontogenetically within individuals. We tested the monophyly of Capitellidae and eight capitellid genera using phylogenetic analyses of combined 18S, 28S, H3, and COI gene sequences from 36 putative capitellid species. In our trees, Capitellidae formed a monophyletic sister group to Echiura, and Capitella was also monophyletic, separated by a long branch from other capitellids. Well-supported clades each containing representatives of different genera, or containing a subset of species within a genus, indicated that Barantolla, Heteromastus, and Notomastus are likely not monophyletic. We mapped three morphological characters traditionally used to define capitellid genera (head width relative to width of first segment, number of thoracic segments, and number of segments with capillary chaetae) onto our tree. While Capitella showed unique character states, states in the other genera were decidedly not phylogenetically informative. Morphology-based capitellid taxonomy will require a fine-scale reevaluation of character states and detection of new characters.
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Affiliation(s)
- Shinri Tomioka
- 1 Rishiri Town Museum, Senhoshi, Rishiri Is., Hokkaido 097-0311, Japan
| | - Keiichi Kakui
- 2 Department of Biological Sciences, Faculty of Science, Hokkaido University, N10 W8, Sapporo, Hokkaido 060-0810, Japan
| | - Hiroshi Kajihara
- 2 Department of Biological Sciences, Faculty of Science, Hokkaido University, N10 W8, Sapporo, Hokkaido 060-0810, Japan
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8
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Barton-Owen TB, Szabó R, Somorjai IML, Ferrier DEK. A Revised Spiralian Homeobox Gene Classification Incorporating New Polychaete Transcriptomes Reveals a Diverse TALE Class and a Divergent Hox Gene. Genome Biol Evol 2018; 10:2151-2167. [PMID: 29986009 PMCID: PMC6118893 DOI: 10.1093/gbe/evy144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2018] [Indexed: 11/13/2022] Open
Abstract
The diversity of mechanisms and capacity for regeneration across the Metazoa present an intriguing challenge in evolutionary biology, impacting on the burgeoning field of regenerative medicine. Broad taxonomic sampling is essential to improve our understanding of regeneration, and studies outside of the traditional model organisms have proved extremely informative. Within the historically understudied Spiralia, the Annelida have an impressive variety of tractable regenerative systems. The biomeralizing, blastema-less regeneration of the head appendage (operculum) of the serpulid polychaete keelworm Spirobranchus (formerly Pomatoceros) lamarcki is one such system. To profile potential regulatory mechanisms, we classified the homeobox gene content of opercular regeneration transcriptomes. As a result of retrieving several difficult-to-classify homeobox sequences, we performed an extensive search and phylogenetic analysis of the TALE and PRD-class homeobox gene content of a broad selection of lophotrochozoan genomes. These analyses contribute to our increasing understanding of the diversity, taxonomic extent, rapid evolution, and radical flexibility of these recently discovered homeobox gene radiations. Our expansion and integration of previous nomenclature systems helps to clarify their cryptic orthology. We also describe an unusual divergent S. lamarcki Antp gene, a previously unclassified lophotrochozoan orphan gene family (Lopx), and a number of novel Nk class orphan genes. The expression and potential involvement of many of these lineage- and clade-restricted homeobox genes in S. lamarcki operculum regeneration provides an example of diversity in regenerative mechanisms, as well as significantly improving our understanding of homeobox gene evolution.
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Affiliation(s)
- Thomas B Barton-Owen
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St. Andrews, United Kingdom
- The Biomedical Sciences Research Complex, School of Biology, University of St. Andrews, United Kingdom
| | - Réka Szabó
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St. Andrews, United Kingdom
| | - Ildiko M L Somorjai
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St. Andrews, United Kingdom
- The Biomedical Sciences Research Complex, School of Biology, University of St. Andrews, United Kingdom
| | - David E K Ferrier
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St. Andrews, United Kingdom
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9
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Thiruketheeswaran P, Thomalla P, Krüger E, Hinssen H, D'Haese J. Four paralog gelsolin genes are differentially expressed in the earthworm Lumbricus terrestris. Comp Biochem Physiol B Biochem Mol Biol 2017; 208-209:58-67. [PMID: 28400331 DOI: 10.1016/j.cbpb.2017.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 04/04/2017] [Accepted: 04/06/2017] [Indexed: 11/25/2022]
Abstract
We have identified and characterized four distinct variants of the gelsolin-related protein (EWAM P1-P4) in the earthworm L. terrestris. All of these proteins biochemically qualify as gelsolins since they sever actin filaments in a calcium dependent manner. P1, P2 and P3 are present in the Lumbricus body wall muscle whereas in the gizzard muscle P3 and P4 were found. P1-P4 are encoded by four paralog genes and are differentially expressed in various muscle cell tissues. While the genes for P1 and P2 contain one intron, there was no intron in both P3 and P4 genes. The coding sequences consist of 1104bp (368 amino acids) for P1/P4 and 1101bp (367 amino acids) for P2/P3. Corresponding genes were confirmed by northern blot analysis which revealed three (calculated lengths: 3100, 2300 and 2100 nucleotides) and two (calculated lengths: 2300 and 1700 nucleotides) mRNA transcripts in the body wall and the gizzard, respectively. EWAM mRNA was localized by fluorescence in situ hybridization in the body wall and the gizzard muscle. P1 mRNA was detected in the inner proximal layers of both the circular and longitudinal muscle of the body wall whereas in the gizzard no significant staining was observed for P1. P2-P4 mRNAs were abundant in the outer distal layers of both the circular and the longitudinal muscles of both body wall and gizzard. The differential expression of four paralog gelsolin genes suggests a functional adaptation of different muscle cells with respect to actin filament turnover and modulation of its polymer state.
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Affiliation(s)
- Prasath Thiruketheeswaran
- Institute for Cell Biology, Department Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Paul Thomalla
- Institute for Cell Biology, Department Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Evelyn Krüger
- Institute for Cell Biology, Department Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Horst Hinssen
- Biochemical Cell Biology, Faculty of Biology, University of Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany
| | - Jochen D'Haese
- Institute for Cell Biology, Department Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany.
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10
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Boilly B, Boilly‐Marer Y, Bely AE. Regulation of dorso-ventral polarity by the nerve cord during annelid regeneration: A review of experimental evidence. REGENERATION (OXFORD, ENGLAND) 2017; 4:54-68. [PMID: 28616245 PMCID: PMC5469730 DOI: 10.1002/reg2.78] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/06/2017] [Accepted: 04/07/2017] [Indexed: 12/14/2022]
Abstract
An important goal for understanding regeneration is determining how polarity is conferred to the regenerate. Here we review findings in two groups of polychaete annelids that implicate the ventral nerve cord in assigning dorso-ventral polarity, and specifically ventral identity, to the regenerate. In nereids, surgical manipulations indicate that parapodia develop where dorsal and ventral body wall territories contact. Without a nerve cord at the wound site, the regenerate differentiates no evident polarity (with no parapodia) and only dorsal identity, while with two nerve cords the regenerate develops a twinned dorso-ventral axis (with four parapodia per segment instead of the normal two). In sabellids, a striking natural dorso-ventral inversion in parapodial morphology occurs along the body axis and this inversion is morphologically correlated with the position of the nerve cord. Parapodial inversion also occurs in segments in which the nerve cord has been removed, even without any segment amputation. Together, these data strongly support a role for the nerve cord in annelid dorso-ventral pattern regulation, with the nerve cord conferring ventral identity.
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Affiliation(s)
- Bénoni Boilly
- UFR de BiologieUniversité de Lille59655 Villeneuve d'AscqFrance
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11
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Koenig KM, Sun P, Meyer E, Gross JM. Eye development and photoreceptor differentiation in the cephalopod Doryteuthis pealeii. Development 2016; 143:3168-81. [PMID: 27510978 DOI: 10.1242/dev.134254] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 07/25/2016] [Indexed: 12/11/2022]
Abstract
Photoreception is a ubiquitous sensory ability found across the Metazoa, and photoreceptive organs are intricate and diverse in their structure. Although the morphology of the compound eye in Drosophila and the single-chambered eye in vertebrates have elaborated independently, the amount of conservation within the 'eye' gene regulatory network remains controversial, with few taxa studied. To better understand the evolution of photoreceptive organs, we established the cephalopod Doryteuthis pealeii as a lophotrochozoan model for eye development. Utilizing histological, transcriptomic and molecular assays, we characterize eye formation in Doryteuthis pealeii Through lineage tracing and gene expression analyses, we demonstrate that cells expressing Pax and Six genes incorporate into the lens, cornea and iris, and the eye placode is the sole source of retinal tissue. Functional assays demonstrate that Notch signaling is required for photoreceptor cell differentiation and retinal organization. This comparative approach places the canon of eye research in traditional models into perspective, highlighting complexity as a result of both conserved and convergent mechanisms.
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Affiliation(s)
- Kristen M Koenig
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Peter Sun
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Eli Meyer
- Department of Zoology, Oregon State University, Cordley Hall 3029, Corvallis, OR 97331, USA
| | - Jeffrey M Gross
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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12
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Özpolat BD, Bely AE. Developmental and molecular biology of annelid regeneration: a comparative review of recent studies. Curr Opin Genet Dev 2016; 40:144-153. [PMID: 27505269 DOI: 10.1016/j.gde.2016.07.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 11/29/2022]
Abstract
Studies of annelid regeneration have greatly increased in frequency in recent years, providing new insights into the developmental basis and evolution of regeneration. In this review, we summarize recent findings related to regeneration in annelids, focusing on molecular and developmental studies of epimorphic (blastema-based) regeneration, morphallactic (tissue-remodeling based) regeneration, and development and regeneration of putative stem cells of the posterior growth zone and germline. Regeneration is being investigated in a broad range of annelids spanning the phylum, and comparing findings among species reveals both widely conserved features that may be ancestral for the phylum as well as features that are variable across the group.
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Affiliation(s)
- B Duygu Özpolat
- Department of Biology, University of Maryland, College Park, MD, USA.
| | - Alexandra E Bely
- Department of Biology, University of Maryland, College Park, MD, USA.
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14
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Moubayidin L, Østergaard L. Symmetry matters. THE NEW PHYTOLOGIST 2015; 207:985-990. [PMID: 26086581 DOI: 10.1111/nph.13526] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 03/26/2015] [Indexed: 06/04/2023]
Abstract
985 I. 985 II. 986 III. 987 IV. 988 V. 989 989 References 989 SUMMARY: The development of multicellular organisms depends on correct establishment of symmetry both at the whole-body scale and within individual tissues and organs. Setting up planes of symmetry must rely on communication between cells that are located at a distance from each other within the organism, presumably via mobile morphogenic signals. Although symmetry in nature has fascinated scientists for centuries, it is only now that molecular data to unravel mechanisms of symmetry establishment are beginning to emerge. As an example we describe the genetic and hormonal interactions leading to an unusual bilateral-to-radial symmetry transition of an organ in order to promote reproduction.
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Affiliation(s)
- Laila Moubayidin
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Lars Østergaard
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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15
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Hariharan IK, Wake DB, Wake MH. Indeterminate Growth: Could It Represent the Ancestral Condition? Cold Spring Harb Perspect Biol 2015. [PMID: 26216720 DOI: 10.1101/cshperspect.a019174] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Although we are used to the idea that many organisms stop growing when they reach a predictable size, in many taxa, growth occurs throughout the life of an organism, a phenomenon referred to as indeterminate growth. Our comparative analysis suggests that indeterminate growth may indeed represent the ancestral condition, whereas the permanent arrest of growth may be a more derived state. Consistent with this idea, in diverse taxa, the basal branches show indeterminate growth, whereas more derived branches arrest their growth. Importantly, in some closely related taxa, the termination of growth has evolved in mechanistically distinct ways. Also, even within a single organism, different organs can differ with respect to whether they terminate their growth or not. Finally, the study of tooth development indicates that, even at the level of a single tissue, multiple determinate patterns of growth can evolve from an ancestral one that is indeterminate.
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Affiliation(s)
- Iswar K Hariharan
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - David B Wake
- Department of Integrative Biology, University of California, Berkeley, California 94720
| | - Marvalee H Wake
- Department of Integrative Biology, University of California, Berkeley, California 94720
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16
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High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin. Nat Biotechnol 2015; 33:503-9. [PMID: 25867922 DOI: 10.1038/nbt.3209] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 03/13/2015] [Indexed: 01/12/2023]
Abstract
Understanding cell type identity in a multicellular organism requires the integration of gene expression profiles from individual cells with their spatial location in a particular tissue. Current technologies allow whole-transcriptome sequencing of spatially identified cells but lack the throughput needed to characterize complex tissues. Here we present a high-throughput method to identify the spatial origin of cells assayed by single-cell RNA-sequencing within a tissue of interest. Our approach is based on comparing complete, specificity-weighted mRNA profiles of a cell with positional gene expression profiles derived from a gene expression atlas. We show that this method allocates cells to precise locations in the brain of the marine annelid Platynereis dumerilii with a success rate of 81%. Our method is applicable to any system that has a reference gene expression database of sufficiently high resolution.
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17
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Biscotti MA, Canapa A, Forconi M, Barucca M. HoxandParaHoxgenes: A review on molluscs. Genesis 2014; 52:935-45. [DOI: 10.1002/dvg.22839] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 11/10/2014] [Accepted: 11/11/2014] [Indexed: 01/28/2023]
Affiliation(s)
- Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; Ancona Italy
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; Ancona Italy
| | - Mariko Forconi
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; Ancona Italy
| | - Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; Ancona Italy
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Gazave E, Guillou A, Balavoine G. History of a prolific family: the Hes/Hey-related genes of the annelid Platynereis. EvoDevo 2014; 5:29. [PMID: 25250171 PMCID: PMC4172395 DOI: 10.1186/2041-9139-5-29] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 07/30/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The Hes superfamily or Hes/Hey-related genes encompass a variety of metazoan-specific bHLH genes, with somewhat fuzzy phylogenetic relationships. Hes superfamily members are involved in a variety of major developmental mechanisms in metazoans, notably in neurogenesis and segmentation processes, in which they often act as direct effector genes of the Notch signaling pathway. RESULTS We have investigated the molecular and functional evolution of the Hes superfamily in metazoans using the lophotrochozoan Platynereis dumerilii as model. Our phylogenetic analyses of more than 200 Metazoan Hes/Hey-related genes revealed the presence of five families, three of them (Hes, Hey and Helt) being pan-metazoan. Those families were likely composed of a unique representative in the last common metazoan ancestor. The evolution of the Hes family was shaped by many independent lineage specific tandem duplication events. The expression patterns of 13 of the 15 Hes/Hey-related genes in Platynereis indicate a broad functional diversification. Nevertheless, a majority of these genes are involved in two crucial developmental processes in annelids: neurogenesis and segmentation, resembling functions highlighted in other animal models. CONCLUSIONS Combining phylogenetic and expression data, our study suggests an unusual evolutionary history for the Hes superfamily. An ancestral multifunctional annelid Hes gene may have undergone multiples rounds of duplication-degeneration-complementation processes in the lineage leading to Platynereis, each gene copies ensuring their maintenance in the genome by subfunctionalisation. Similar but independent waves of duplications are at the origin of the multiplicity of Hes genes in other metazoan lineages.
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Affiliation(s)
- Eve Gazave
- Institut Jacques Monod, CNRS, UMR 7592, CNRS/Université Paris Diderot-Paris 7, 15 rue H. Brion, Paris cedex 13 75205, France
| | - Aurélien Guillou
- Institut Jacques Monod, CNRS, UMR 7592, CNRS/Université Paris Diderot-Paris 7, 15 rue H. Brion, Paris cedex 13 75205, France
| | - Guillaume Balavoine
- Institut Jacques Monod, CNRS, UMR 7592, CNRS/Université Paris Diderot-Paris 7, 15 rue H. Brion, Paris cedex 13 75205, France
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Posterior elongation in the annelid Platynereis dumerilii involves stem cells molecularly related to primordial germ cells. Dev Biol 2013; 382:246-67. [DOI: 10.1016/j.ydbio.2013.07.013] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 06/28/2013] [Accepted: 07/15/2013] [Indexed: 12/22/2022]
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