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Kuo DH, Szczupak L, Weisblat DA, Portiansky EL, Winchell CJ, Lee JR, Tsai FY. Transgenesis enables mapping of segmental ganglia in the leech Helobdella austinensis. J Exp Biol 2024; 227:jeb247419. [PMID: 38940760 DOI: 10.1242/jeb.247419] [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: 01/26/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024]
Abstract
The analysis of how neural circuits function in individuals and change during evolution is simplified by the existence of neurons identified as homologous within and across species. Invertebrates, including leeches, have been used for these purposes in part because their nervous systems comprise a high proportion of identified neurons, but technical limitations make it challenging to assess the full extent to which assumptions of stereotypy hold true. Here, we introduce Minos plasmid-mediated transgenesis as a tool for introducing transgenes into the embryos of the leech Helobdella austinensis (Spiralia; Lophotrochozoa; Annelida; Clitellata; Hirudinida; Glossiphoniidae). We identified an enhancer driving pan-neuronal expression of markers, including histone2B:mCherry, which allowed us to enumerate neurons in segmental ganglia. Unexpectedly, we found that the segmental ganglia of adult transgenic H. austinensis contain fewer and more variable numbers of neurons than in previously examined leech species.
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Affiliation(s)
- Dian-Han Kuo
- Department of Life Science, National Taiwan University, Taipei, Taiwan116
- Museum of Zoology, National Taiwan University, Taipei, Taiwan106
| | - Lidia Szczupak
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBYNE UBA-CONICET, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - David A Weisblat
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Enrique L Portiansky
- Laboratory of Image Analysis, School of Veterinary Sciences, National University of La Plata, CONICET, B1900 La Plata, Argentina
| | - Christopher J Winchell
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Jun-Ru Lee
- Department of Life Science, National Taiwan University, Taipei, Taiwan116
| | - Fu-Yu Tsai
- Department of Life Science, National Taiwan University, Taipei, Taiwan116
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2
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Wudarski J, Aliabadi S, Gulia-Nuss M. Arthropod promoters for genetic control of disease vectors. Trends Parasitol 2024; 40:619-632. [PMID: 38824066 PMCID: PMC11223965 DOI: 10.1016/j.pt.2024.04.011] [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: 02/16/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 06/03/2024]
Abstract
Vector-borne diseases (VBDs) impose devastating effects on human health and a heavy financial burden. Malaria, Lyme disease, and dengue fever are just a few examples of VBDs that cause severe illnesses. The current strategies to control VBDs consist mainly of environmental modification and chemical use, and to a small extent, genetic approaches. The genetic approaches, including transgenesis/genome modification and gene-drive technologies, provide the basis for developing new tools for VBD prevention by suppressing vector populations or reducing their capacity to transmit pathogens. The regulatory elements such as promoters are required for a robust sex-, tissue-, and stage-specific transgene expression. As discussed in this review, information on the regulatory elements is available for mosquito vectors but is scant for other vectors.
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Affiliation(s)
- Jakub Wudarski
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - Simindokht Aliabadi
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - Monika Gulia-Nuss
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA.
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3
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Mouton S, Mougel A, Ustyantsev K, Dissous C, Melnyk O, Berezikov E, Vicogne J. Optimized protocols for RNA interference in Macrostomum lignano. G3 (BETHESDA, MD.) 2024; 14:jkae037. [PMID: 38421640 PMCID: PMC11075559 DOI: 10.1093/g3journal/jkae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024]
Abstract
Macrostomum lignano, a marine free-living flatworm, has emerged as a potent invertebrate model in developmental biology for studying stem cells, germline, and regeneration processes. In recent years, many tools have been developed to manipulate this worm and to facilitate genetic modification. RNA interference is currently the most accessible and direct technique to investigate gene functions. It is obtained by soaking worms in artificial seawater containing dsRNA targeting the gene of interest. Although easy to perform, the original protocol calls for daily exchange of dsRNA solutions, usually until phenotypes are observed, which is both time- and cost-consuming. In this work, we have evaluated alternative dsRNA delivery techniques, such as electroporation and osmotic shock, to facilitate the experiments with improved time and cost efficiency. During our investigation to optimize RNAi, we demonstrated that, in the absence of diatoms, regular single soaking in artificial seawater containing dsRNA directly produced in bacteria or synthesized in vitro is, in most cases, sufficient to induce a potent gene knockdown for several days with a single soaking step. Therefore, this new and highly simplified method allows a very significant reduction of dsRNA consumption and lab work. In addition, it enables performing experiments on a larger number of worms at minimal cost.
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Affiliation(s)
- Stijn Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9700AD, The Netherlands
| | - Alexandra Mougel
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Kirill Ustyantsev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9700AD, The Netherlands
| | - Colette Dissous
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Oleg Melnyk
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9700AD, The Netherlands
| | - Jérôme Vicogne
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
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4
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Cīrulis A, Nordén AK, Churcher AM, Ramm SA, Zadesenets KS, Abbott JK. Sex-limited experimental evolution drives transcriptomic divergence in a hermaphrodite. Genome Biol Evol 2024; 16:evad235. [PMID: 38155579 PMCID: PMC10786194 DOI: 10.1093/gbe/evad235] [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: 02/22/2023] [Revised: 12/12/2023] [Accepted: 12/23/2023] [Indexed: 12/30/2023] Open
Abstract
The evolution of gonochorism from hermaphroditism is linked with the formation of sex chromosomes, as well as the evolution of sex-biased and sex-specific gene expression to allow both sexes to reach their fitness optimum. There is evidence that sexual selection drives the evolution of male-biased gene expression in particular. However, previous research in this area in animals comes from either theoretical models or comparative studies of already old sex chromosomes. We therefore investigated changes in gene expression under 3 different selection regimes for the simultaneous hermaphrodite Macrostomum lignano subjected to sex-limited experimental evolution (i.e. selection for fitness via eggs, sperm, or a control regime allowing both). After 21 and 22 generations of selection for male-specific or female-specific fitness, we characterized changes in whole-organism gene expression. We found that female-selected lines had changed the most in their gene expression. Although annotation for this species is limited, gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses suggest that metabolic changes (e.g. biosynthesis of amino acids and carbon metabolism) are an important adaptive component. As predicted, we found that the expression of genes previously identified as testis-biased candidates tended to be downregulated in the female-selected lines. We did not find any significant expression differences for previously identified candidates of other sex-specific organs, but this may simply reflect that few transcripts have been characterized in this way. In conclusion, our experiment suggests that changes in testis-biased gene expression are important in the early evolution of sex chromosomes and gonochorism.
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Affiliation(s)
- Aivars Cīrulis
- Department of Biology, Lund University, 223 62 Lund, Sweden
- Laboratory of Microbiology and Pathology, Institute of Food Safety, Animal Health and Environment “BIOR,”Riga LV-1076, Latvia
- Faculty of Biology, University of Latvia, Riga LV-1004, Latvia
| | - Anna K Nordén
- Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Allison M Churcher
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden, Umeå University, 901 87 Umeå, Sweden
| | - Steven A Ramm
- Department of Evolutionary Biology, Bielefeld University, 33615 Bielefeld, Germany
- UMR 6553 ECOBIO, Université de Rennes, 35042 Rennes, France
| | - Kira S Zadesenets
- Department of Molecular Genetics, Cell Biology and Bionformatics, The Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russian Federation
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5
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Zadesenets KS, Ershov NI, Bondar NP, Rubtsov NB. Unraveling the Unusual Subgenomic Organization in the Neopolyploid Free-Living Flatworm Macrostomum lignano. Mol Biol Evol 2023; 40:msad250. [PMID: 37979163 PMCID: PMC10733133 DOI: 10.1093/molbev/msad250] [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: 06/20/2023] [Revised: 09/21/2023] [Accepted: 11/14/2023] [Indexed: 11/20/2023] Open
Abstract
Whole genome duplication (WGD) is an evolutionary event resulting in a redundancy of genetic material. Different mechanisms of WGD, allo- or autopolyploidization, lead to distinct evolutionary trajectories of newly formed polyploids. Genome studies on such species are important for understanding the early stages of genome evolution. However, assembling neopolyploid is a challenging task due to the presence of 2 homologous (or homeologous) chromosome sets and therefore the existence of the extended paralogous regions in its genome. Post-WGD evolution of polyploids includes cytogenetic diploidization leading to the formation of species, whose polyploid origin might be hidden by disomic inheritance. Earlier we uncovered the hidden polyploid origin of the free-living flatworms of the genus Macrostomum (Macrostomum lignano, M. janickei, and M. mirumnovem). Cytogenetic diploidization in these species is accompanied by intensive chromosomal rearrangements including chromosomes fusions. In this study, we unravel the M. lignano genome organization through generation and sequencing of 2 sublines of the commonly used inbred line of M. lignano (called DV1) differing only in a copy number of the largest chromosome (MLI1). Using nontrivial assembly free comparative analysis of their genomes, we deciphered DNA sequences belonging to MLI1 and validated them by sequencing the pool of microdissected MLI1. Here we presented the uncommon mechanism of genome rediplodization of M. lignano, which consists of (i) presence of 3 subgenomes, which emerged via formation of large fused chromosomes and its variants, and (ii) sustaining their heterozygosity through inter- and intrachromosomal rearrangements.
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Affiliation(s)
- Kira S Zadesenets
- Department of Molecular Genetics, Cell Biology and Bionformatics, The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Nikita I Ershov
- Department of Molecular Genetics, Cell Biology and Bionformatics, The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Natalia P Bondar
- Department of Molecular Genetics, Cell Biology and Bionformatics, The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nikolai B Rubtsov
- Department of Molecular Genetics, Cell Biology and Bionformatics, The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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6
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Brand JN. Support for a radiation of free-living flatworms in the African Great Lakes region and the description of five new Macrostomum species. Front Zool 2023; 20:31. [PMID: 37670326 PMCID: PMC10478486 DOI: 10.1186/s12983-023-00509-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/14/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND The African Great Lakes have long been recognized as an excellent location to study speciation. Most famously, cichlid fishes have radiated in Lake Tanganyika and subsequently spread into Lake Malawi and Lake Victoria, where they again radiated. Other taxa have diversified in these lakes, such as catfish, ostracods, gastropods, and Monegenean gill parasites of cichlids. However, these radiations have received less attention, and the process leading to their speciation in this unique region remains to be further explored. Here I present evidence that suggests a radiation of Macrostomum flatworms has occurred in the African Great Lakes region, offering a good opportunity for such investigations. RESULTS Recent field work has revealed a monophyletic clade of 16 Macrostomum flatworms that have, to date, only been collected from Lake Tanganyika. Additionally, a species collected from Lake Malawi was found nested within this clade. Molecular phylogenetic analysis, largely based on transcriptome data, suggests that this clade underwent rapid speciation, possibly due to a large habitat diversity in the lake. I also observed significant differences in the sperm morphology of these flatworms compared to those of species found outside Lake Tanganyika and Lake Malawi. These included the elongation of an anterior structure, a reduction in the size of the lateral sperm bristles, and changes in relative proportions. I propose functional hypotheses for these changes in sperm design, and formally describe Macrostomum gracilistylum sp. nov from Lake Malawi and its sister species Macrostomum crassum sp. nov., Macrostomum pellitum sp. nov., Macrostomum longispermatum sp. nov., and Macrostomum schäreri sp. nov., from Lake Tanganyika. CONCLUSIONS The available evidence is consistent with the hypothesis that Macrostomum flatworms have radiated in Lake Tanganyika and subsequently spread to Lake Malawi. However, whether this represents a bona fide adaptive radiation still needs to be determined. Therefore, the African Great Lakes are promising targets for further research into flatworm diversity and speciation.
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Affiliation(s)
- Jeremias N Brand
- Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland.
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Science, Am Fassberg 11, 37077, Göttingen, Germany.
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7
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Wiberg RAW, Brand JN, Viktorin G, Mitchell JO, Beisel C, Schärer L. Genome assemblies of the simultaneously hermaphroditic flatworms Macrostomum cliftonense and Macrostomum hystrix. G3 (BETHESDA, MD.) 2023; 13:jkad149. [PMID: 37398989 PMCID: PMC10468722 DOI: 10.1093/g3journal/jkad149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/05/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023]
Abstract
The free-living, simultaneously hermaphroditic flatworms of the genus Macrostomum are increasingly used as model systems in various contexts. In particular, Macrostomum lignano, the only species of this group with a published genome assembly, has emerged as a model for the study of regeneration, reproduction, and stem-cell function. However, challenges have emerged due to M. lignano being a hidden polyploid, having recently undergone whole-genome duplication and chromosome fusion events. This complex genome architecture presents a significant roadblock to the application of many modern genetic tools. Hence, additional genomic resources for this genus are needed. Here, we present such resources for Macrostomum cliftonense and Macrostomum hystrix, which represent the contrasting mating behaviors of reciprocal copulation and hypodermic insemination found in the genus. We use a combination of PacBio long-read sequencing and Illumina shot-gun sequencing, along with several RNA-Seq data sets, to assemble and annotate highly contiguous genomes for both species. The assemblies span ∼227 and ∼220 Mb and are represented by 399 and 42 contigs for M. cliftonense and M. hystrix, respectively. Furthermore, high BUSCO completeness (∼84-85%), low BUSCO duplication rates (8.3-6.2%), and low k-mer multiplicity indicate that these assemblies do not suffer from the same assembly ambiguities of the M. lignano genome assembly, which can be attributed to the complex karyology of this species. We also show that these resources, in combination with the prior resources from M. lignano, offer an excellent foundation for comparative genomic research in this group of organisms.
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Affiliation(s)
- R Axel W Wiberg
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel 4051, Switzerland
| | - Jeremias N Brand
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel 4051, Switzerland
| | - Gudrun Viktorin
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel 4051, Switzerland
| | - Jack O Mitchell
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel 4051, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Lukas Schärer
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel 4051, Switzerland
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8
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Ma Y, He J, Sieber M, von Frieling J, Bruchhaus I, Baines JF, Bickmeyer U, Roeder T. The microbiome of the marine flatworm Macrostomum lignano provides fitness advantages and exhibits circadian rhythmicity. Commun Biol 2023; 6:289. [PMID: 36934156 PMCID: PMC10024726 DOI: 10.1038/s42003-023-04671-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 03/07/2023] [Indexed: 03/20/2023] Open
Abstract
The close association between animals and their associated microbiota is usually beneficial for both partners. Here, we used a simple marine model invertebrate, the flatworm Macrostomum lignano, to characterize the host-microbiota interaction in detail. This analysis revealed that the different developmental stages each harbor a specific microbiota. Studies with gnotobiotic animals clarified the physiological significance of the microbiota. While no fitness benefits were mediated by the microbiota when food was freely available, animals with microbiota showed significantly increased fitness with a reduced food supply. The microbiota of M. lignano shows circadian rhythmicity, affecting both the total bacterial load and the behavior of specific taxa. Moreover, the presence of the worm influences the composition of the bacterial consortia in the environment. In summary, the Macrostomum-microbiota system described here can serve as a general model for host-microbe interactions in marine invertebrates.
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Affiliation(s)
- Yuanyuan Ma
- Kiel University, Zoological Institute, Molecular Physiology, Kiel, Germany
| | - Jinru He
- Kiel University, Zoological Institute, Cell and Developmental Biology, Kiel, Germany
| | - Michael Sieber
- Max-Planck Institute for Evolutionary Biology, Dept. Evolutionary Theory, Plön, Germany
| | - Jakob von Frieling
- Kiel University, Zoological Institute, Molecular Physiology, Kiel, Germany
| | - Iris Bruchhaus
- Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - John F Baines
- Kiel University, Medical Faculty, Institute for Experimental Medicine, Kiel, Germany
- Max-Planck Institute for Evolutionary Biology, Group Evolutionary Medicine, Plön, Germany
| | - Ulf Bickmeyer
- Alfred-Wegener-Institute, Biosciences, Ecological Chemistry, Bremerhaven, Germany
| | - Thomas Roeder
- Kiel University, Zoological Institute, Molecular Physiology, Kiel, Germany.
- German Center for Lung Research (DZL), Airway Research Center North, Kiel, Germany.
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McClain ML, Nowotarski SH. Serial block-face scanning electron microscopy of Schmidtea mediterranea. Methods Cell Biol 2023; 177:213-240. [PMID: 37451768 DOI: 10.1016/bs.mcb.2023.01.013] [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] [Indexed: 02/27/2023]
Abstract
The flatworm planarian, Schmidtea mediterranea (Smed) is a master at regenerating and rebuilding whole animals from fragments. A full understanding of Smed's regenerative capabilities requires a high-resolution characterization of organs, tissues, and the adult stem cells necessary for regeneration in their native environment. Here, we describe a serial block face scanning electron microscopy (SBF-SEM) protocol, optimized for Smed specifically, for visualizing the ultrastructure of membranes and condensed chromosomes in this model organism.
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Affiliation(s)
| | - Stephanie H Nowotarski
- Stowers Institute for Medical Research, Kansas City, MO, United States; Howard Hughes Medical Institute, Chevy Chase, MD, United States.
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Lei K, Zhang W, Chen J, McKinney SA, Ross EJ, Lee HC, Sánchez Alvarado A. Pluripotency retention and exogenous mRNA introduction in planarian stem cells in culture. iScience 2023; 26:106001. [PMID: 36866042 PMCID: PMC9971864 DOI: 10.1016/j.isci.2023.106001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/31/2022] [Accepted: 01/13/2023] [Indexed: 01/21/2023] Open
Abstract
Planarians possess naturally occurring pluripotent adult somatic stem cells (neoblasts) required for homeostasis and whole-body regeneration. However, no reliable neoblast culture methods are currently available, hindering mechanistic studies of pluripotency and the development of transgenic tools. We report robust methods for neoblast culture and delivery of exogenous mRNAs. We identify optimal culture media for the short-term maintenance of neoblasts in vitro and show via transplantation that cultured stem cells retain pluripotency for two days. We developed a procedure that significantly improves neoblast yield and purity by modifying standard flow cytometry methods. These methods enable the introduction and expression of exogenous mRNAs in neoblasts, overcoming a key hurdle impeding the application of transgenics in planarians. The advances in cell culture reported here create new opportunities for mechanistic studies of planarian adult stem cell pluripotency, and provide a systematic framework to develop cell culture techniques in other emerging research organisms.
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Affiliation(s)
- Kai Lei
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Wenya Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Jiajia Chen
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Sean A. McKinney
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Eric J. Ross
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Heng-Chi Lee
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Alejandro Sánchez Alvarado
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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11
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Martinez P, Ustyantsev K, Biryukov M, Mouton S, Glasenburg L, Sprecher SG, Bailly X, Berezikov E. Genome assembly of the acoel flatworm Symsagittifera roscoffensis, a model for research on body plan evolution and photosymbiosis. G3 (BETHESDA, MD.) 2023; 13:jkac336. [PMID: 36542495 PMCID: PMC9911081 DOI: 10.1093/g3journal/jkac336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Symsagittifera roscoffensis is a well-known member of the order Acoela that lives in symbiosis with the algae Tetraselmis convolutae during its adult stage. Its natural habitat is the eastern coast of the Atlantic, where at specific locations thousands of individuals can be found, mostly, lying in large pools on the surface of sand at low tide. As a member of the Acoela it has been thought as a proxy for ancestral bilaterian animals; however, its phylogenetic position remains still debated. In order to understand the basic structural characteristics of the acoel genome, we sequenced and assembled the genome of aposymbiotic species S. roscoffensis. The size of this genome was measured to be in the range of 910-940 Mb. Sequencing of the genome was performed using PacBio Hi-Fi technology. Hi-C and RNA-seq data were also generated to scaffold and annotate it. The resulting assembly is 1.1 Gb large (covering 118% of the estimated genome size) and highly continuous, with N50 scaffold size of 1.04 Mb. The repetitive fraction of the genome is 61%, of which 85% (half of the genome) are LTR retrotransposons. Genome-guided transcriptome assembly identified 34,493 genes, of which 29,351 are protein coding (BUSCO score 97.6%), and 30.2% of genes are spliced leader trans-spliced. The completeness of this genome suggests that it can be used extensively to characterize gene families and conduct accurate phylogenomic reconstructions.
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Affiliation(s)
- Pedro Martinez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona 08193, Spain
| | - Kirill Ustyantsev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen 9700AD, The Netherlands
| | - Mikhail Biryukov
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Stijn Mouton
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen 9700AD, The Netherlands
| | - Liza Glasenburg
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen 9700AD, The Netherlands
| | - Simon G Sprecher
- Department of Biology, University of Fribourg, Chemin du Musee 10, 1700 Fribourg, Switzerland
| | - Xavier Bailly
- Station Biologique de Roscoff, Multicellular Marine Models (M3) team, FR2424, CNRS/Sorbonne Université—Place Georges Teissier, 29680 Roscoff, France
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen 9700AD, The Netherlands
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12
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Wiberg RAW, Viktorin G, Schärer L. Mating strategy predicts gene presence/absence patterns in a genus of simultaneously hermaphroditic flatworms. Evolution 2022; 76:3054-3066. [PMID: 36199200 PMCID: PMC10092323 DOI: 10.1111/evo.14635] [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: 05/16/2022] [Accepted: 09/28/2022] [Indexed: 01/22/2023]
Abstract
Gene repertoire turnover is a characteristic of genome evolution. However, we lack well-replicated analyses of presence/absence patterns associated with different selection contexts. Here, we study ∼100 transcriptome assemblies across Macrostomum, a genus of simultaneously hermaphroditic flatworms exhibiting multiple convergent shifts in mating strategy and associated reproductive morphologies. Many species mate reciprocally, with partners donating and receiving sperm at the same time. Other species convergently evolved to mate by hypodermic injection of sperm into the partner. We find that for orthologous transcripts annotated as expressed in the body region containing the testes, sequences from hypodermically inseminating species diverge more rapidly from the model species, Macrostomum lignano, and have a lower probability of being observed in other species. For other annotation categories, simpler models with a constant rate of similarity decay with increasing genetic distance from M. lignano match the observed patterns well. Thus, faster rates of sequence evolution for hypodermically inseminating species in testis-region genes result in higher rates of homology detection failure, yielding a signal of rapid evolution in sequence presence/absence patterns. Our results highlight the utility of considering appropriate null models for unobserved genes, as well as associating patterns of gene presence/absence with replicated evolutionary events in a phylogenetic context.
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Affiliation(s)
- R Axel W Wiberg
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, CH-4051, Switzerland.,Evolutionary Biology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, SE-75236, Sweden
| | - Gudrun Viktorin
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, CH-4051, Switzerland
| | - Lukas Schärer
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, CH-4051, Switzerland
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13
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Biryukov M, Dmitrieva A, Vavilova V, Ustyantsev K, Bazarova E, Sukhikh I, Berezikov E, Blinov A. Mlig-SKP1 Gene Is Required for Spermatogenesis in the Flatworm Macrostomum lignano. Int J Mol Sci 2022; 23:ijms232315110. [PMID: 36499445 PMCID: PMC9740662 DOI: 10.3390/ijms232315110] [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: 11/02/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022] Open
Abstract
In a free-living flatworm, Macrostomum lignano, an S-phase kinase-associated protein 1 (SKP1) homologous gene was identified as enriched in proliferating cells, suggesting that it can function in the regulation of stem cells or germline cells since these are the only two types of proliferating cells in flatworms. SKP1 is a conserved protein that plays a role in ubiquitination processes as a part of the Skp1-Cullin 1-F-box (SCF) ubiquitin ligase complex. However, the exact role of Mlig-SKP1 in M. lignano was not established. Here, we demonstrate that Mlig-SKP1 is neither involved in stem cell regulation during homeostasis, nor in regeneration, but is required for spermatogenesis. Mlig-SKP1(RNAi) animals have increased testes size and decreased fertility as a result of the aberrant maturation of sperm cells. Our findings reinforce the role of ubiquitination pathways in germ cell regulation and demonstrate the conserved role of SKP1 in spermatogenesis.
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Affiliation(s)
- Mikhail Biryukov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - Anastasia Dmitrieva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - Valeriya Vavilova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - Kirill Ustyantsev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9700AD Groningen, The Netherlands
| | - Erzhena Bazarova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - Igor Sukhikh
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9700AD Groningen, The Netherlands
| | - Alexandr Blinov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Science, 630090 Novosibirsk, Russia
- Correspondence:
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14
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Sukhikh IS, Biryukov MY, Blinov AG. Transgenesis in Worms: Candidates for an Ideal Model. Mol Biol 2022. [DOI: 10.1134/s0026893322060176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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15
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Leite DJ, Piovani L, Telford MJ. Genome assembly of the polyclad flatworm Prostheceraeus crozieri. Genome Biol Evol 2022; 14:6678951. [PMID: 36040059 PMCID: PMC9469890 DOI: 10.1093/gbe/evac133] [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] [Accepted: 08/25/2022] [Indexed: 11/24/2022] Open
Abstract
Polyclad flatworms are widely thought to be one of the least derived of the flatworm classes and, as such, are well placed to investigate evolutionary and developmental features such as spiral cleavage and larval diversification lost in other platyhelminths. Prostheceraeus crozieri, (formerly Maritigrella crozieri), is an emerging model polyclad flatworm that already has some useful transcriptome data but, to date, no sequenced genome. We have used high molecular weight DNA extraction and long-read PacBio sequencing to assemble the highly repetitive (67.9%) P. crozieri genome (2.07 Gb). We have annotated 43,325 genes, with 89.7% BUSCO completeness. Perhaps reflecting its large genome, introns were considerably larger than other free-living flatworms, but evidence of abundant transposable elements suggests genome expansion has been principally via transposable elements activity. This genome resource will be of great use for future developmental and phylogenomic research.
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Affiliation(s)
- Daniel J Leite
- Department of Biosciences, Durham University, Durham DH1 3LE, UK.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Laura Piovani
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
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16
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A World of Viruses Nested within Parasites: Unraveling Viral Diversity within Parasitic Flatworms (Platyhelminthes). Microbiol Spectr 2022; 10:e0013822. [PMID: 35536058 PMCID: PMC9241645 DOI: 10.1128/spectrum.00138-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Because parasites have an inextricable relationship with their host, they have the potential to serve as viral reservoirs or facilitate virus host shifts. And yet, little is known about viruses infecting parasitic hosts except for blood-feeding arthropods that are well-known vectors of zoonotic viruses. Herein, we uncovered viruses of flatworms (phylum Platyhelminthes, group Neodermata) that specialize in parasitizing vertebrates and their ancestral free-living relatives. We discovered 115 novel viral sequences, including 1 in Macrostomorpha, 5 in Polycladida, 44 in Tricladida, 1 in Monogenea, 15 in Cestoda, and 49 in Trematoda, through data mining. The majority of newly identified viruses constitute novel families or genera. Phylogenetic analyses show that the virome of flatworms changed dramatically during the transition of neodermatans to a parasitic lifestyle. Most Neodermata viruses seem to codiversify with their host, with the exception of rhabdoviruses, which may switch hosts more often, based on phylogenetic relationships. Neodermata rhabdoviruses also have a position ancestral to vertebrate-associated rhabdo viruses, including lyssaviruses, suggesting that vertebrate-associated rhabdoviruses emerged from a flatworm rhabdovirus in a parasitized host. This study reveals an extensive diversity of viruses in Platyhelminthes and highlights the need to evaluate the role of viral infection in flatworm-associated diseases. IMPORTANCE Little is known about the diversity of parasite-associated viruses and how these viruses may impact parasite fitness, parasite-host interactions, and virus evolution. The discovery of over a hundred viruses associated with a range of free-living and parasitic flatworms, including parasites of economic and clinical relevance, allowed us to compare the viromes of flatworms with contrasting lifestyles. The results suggest that flatworms acquired novel viruses after their transition to a parasitic lifestyle and highlight the possibility that they acquired viruses from their hosts and vice versa. An interesting example is the discovery of flatworm rhabdoviruses that have a position ancestral to rabies viruses and other vertebrate-associated rhabdoviruses, demonstrating that flatworm-associated viruses have emerged in a vertebrate host at least once in history. Therefore, parasitic flatworms may play a role in virus diversity and emergence. The roles that parasite-infecting viruses play in parasite-associated diseases remain to be investigated.
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17
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Brand JN, Harmon LJ, Schärer L. Frequent origins of traumatic insemination involve convergent shifts in sperm and genital morphology. Evol Lett 2022; 6:63-82. [PMID: 35127138 PMCID: PMC8802240 DOI: 10.1002/evl3.268] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/18/2022] Open
Abstract
Traumatic insemination is a mating behavior during which the (sperm) donor uses a traumatic intromittent organ to inject an ejaculate through the epidermis of the (sperm) recipient, thereby frequently circumventing the female genitalia. Traumatic insemination occurs widely across animals, but the frequency of its evolution, the intermediate stages via which it originates, and the morphological changes that such shifts involve remain poorly understood. Based on observations in 145 species of the free-living flatworm genus Macrostomum, we identify at least nine independent evolutionary origins of traumatic insemination from reciprocal copulation, but no clear indication of reversals. These origins involve convergent shifts in multivariate morphospace of male and female reproductive traits, suggesting that traumatic insemination has a canalizing effect on morphology. We also observed sperm in both the sperm receiving organ and within the body tissue of two species. These species had intermediate trait values indicating that traumatic insemination evolves through initial internal wounding during copulation. Finally, signatures of male-female coevolution of genitalia across the genus indicate that sexual selection and sexual conflict drive the evolution of traumatic insemination, because it allows donors to bypass postcopulatory control mechanisms of recipients.
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Affiliation(s)
- Jeremias N. Brand
- Department of Environmental Sciences, Zoological InstituteUniversity of BaselBaselCH‐4051Switzerland
- Department of Tissue Dynamics and RegenerationMax Planck Institute for Biophysical ChemistryGöttingenDE‐37077Germany
| | - Luke J. Harmon
- Department of Biological SciencesUniversity of IdahoMoscowIdaho83843
| | - Lukas Schärer
- Department of Environmental Sciences, Zoological InstituteUniversity of BaselBaselCH‐4051Switzerland
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18
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Wudarski J, Ustyantsev K, Reinoite F, Berezikov E. Random Integration Transgenesis in a Free-Living Regenerative Flatworm Macrostomum lignano. Methods Mol Biol 2022; 2450:493-508. [PMID: 35359325 PMCID: PMC9761508 DOI: 10.1007/978-1-0716-2172-1_26] [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] [Indexed: 06/14/2023]
Abstract
Regeneration-capable flatworms are highly informative research models to study the mechanisms of stem cell regulation, regeneration, and tissue patterning. Transgenesis is a powerful research tool for investigating gene function, but until recently, a transgenesis method was missing in flatworms, hampering their wider adoption in biomedical research. Here we describe a detailed protocol to create stable transgenic lines of the flatworm M. lignano using random integration of DNA constructs through microinjection into single-cell stage embryos.
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Affiliation(s)
- Jakub Wudarski
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Filipa Reinoite
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
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19
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Ustyantsev KV, Vavilova VY, Blinov AG, Berezikov EV. Macrostomum lignano as a model to study the genetics and genomics of parasitic flatworms. Vavilovskii Zhurnal Genet Selektsii 2021; 25:108-116. [PMID: 34901708 PMCID: PMC8629357 DOI: 10.18699/vj21.013] [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: 10/17/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 12/02/2022] Open
Abstract
Hundreds of millions of people worldwide are infected by various species of parasitic flatworms. Without
treatment, acute and chronical infections frequently lead to the development of severe pathologies and even death.
Emerging data on a decreasing efficiency of some important anthelmintic compounds and the emergence of resistance to them force the search for alternative drugs. Parasitic flatworms have complex life cycles, are laborious and
expensive in culturing, and have a range of anatomic and physiological adaptations that complicate the application
of standard molecular-biological methods. On the other hand, free-living flatworm species, evolutionarily close to
parasitic flatworms, do not have the abovementioned difficulties, which makes them potential alternative models
to search for and study homologous genes. In this review, we describe the use of the basal free-living flatworm
Macrostomum lignano as such a model. M. lignano has a number of convenient biological and experimental properties, such as fast reproduction, easy and non-expensive laboratory culturing, optical body transparency, obligatory
sexual reproduction, annotated genome and transcriptome assemblies, and the availability of modern molecular
methods, including transgenesis, gene knockdown by RNA interference, and in situ hybridization. All this makes
M. lignano amenable to the most modern approaches of forward and reverse genetics, such as transposon insertional mutagenesis and methods of targeted genome editing by the CRISPR/Cas9 system. Due to the availability of
an increasing number of genome and transcriptome assemblies of different parasitic flatworm species, new knowledge generated by studying M. lignano can be easily translated to parasitic flatworms with the help of modern
bioinformatic methods of comparative genomics and transcriptomics. In support of this, we provide the results of
our bioinformatics search and analysis of genes homologous between M. lignano and parasitic flatworms, which
predicts a list of promising gene targets for subsequent research.
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Affiliation(s)
- K V Ustyantsev
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V Yu Vavilova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A G Blinov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E V Berezikov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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20
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Ustyantsev KV, Berezikov EV. Computational analysis of spliced leader trans-splicing in the regenerative flatworm Macrostomum lignano reveals its prevalence in conserved and stem cell related genes. Vavilovskii Zhurnal Genet Selektsii 2021; 25:101-107. [PMID: 34901707 PMCID: PMC8629364 DOI: 10.18699/vj21.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 11/28/2022] Open
Abstract
In eukaryotes, trans-splicing is a process of nuclear pre-mRNA maturation where two different RNA molecules are joined together by the spliceosomal machinery utilizing mechanisms similar to cis-splicing. In diverse taxa of
lower eukaryotes, spliced leader (SL) trans-splicing is the most frequent type of trans-splicing, when the same sequence
derived from short small nuclear RNA molecules, called SL RNAs, is attached to the 5’ ends of different non-processed
pre-mRNAs. One of the functions of SL trans-splicing is processing polycistronic pre-mRNA molecules transcribed from
operons, when several genes are transcribed as one pre-mRNA molecule. However, only a fraction of trans-spliced
genes reside in operons, suggesting that SL trans-splicing must also have some other, less understood functions. Regenerative flatworms are informative model organisms which hold the keys to understand the mechanism of stem
cell regulation and specialization during regeneration and homeostasis. Their ability to regenerate is fueled by the
division and differentiation of the adult somatic stem cell population called neoblasts. Macrostomum lignano is a flatworm model organism where substantial technological advances have been achieved in recent years, including the
development of transgenesis. Although a large fraction of genes in M. lignano were estimated to be SL trans-spliced,
SL trans-splicing was not studied in detail in M. lignano before. Here, we performed the first comprehensive study of
SL trans-splicing in M. lignano. By reanalyzing the existing genome and transcriptome data of M. lignano, we estimate
that 30 % of its genes are SL trans-spliced, 15 % are organized in operons, and almost 40 % are both SL trans-spliced
and in operons. We annotated and characterized the sequence of SL RNA and characterized conserved cis- and SL transsplicing motifs. Finally, we found that a majority of SL trans-spliced genes are evolutionarily conserved and significantly
over-represented in neoblast-specific genes. Our findings suggest an important role of SL trans-splicing in the regulation and maintenance of neoblasts in M. lignano.
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Affiliation(s)
- K V Ustyantsev
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E V Berezikov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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21
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Wiberg RAW, Brand JN, Schärer L. Faster Rates of Molecular Sequence Evolution in Reproduction-Related Genes and in Species with Hypodermic Sperm Morphologies. Mol Biol Evol 2021; 38:5685-5703. [PMID: 34534329 PMCID: PMC8662610 DOI: 10.1093/molbev/msab276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Sexual selection drives the evolution of many striking behaviors and morphologies and should leave signatures of selection at loci underlying these phenotypes. However, although loci thought to be under sexual selection often evolve rapidly, few studies have contrasted rates of molecular sequence evolution at such loci across lineages with different sexual selection contexts. Furthermore, work has focused on separate sexed animals, neglecting alternative sexual systems. We investigate rates of molecular sequence evolution in hermaphroditic flatworms of the genus Macrostomum. Specifically, we compare species that exhibit contrasting sperm morphologies, strongly associated with multiple convergent shifts in the mating strategy, reflecting different sexual selection contexts. Species donating and receiving sperm in every mating have sperm with bristles, likely to prevent sperm removal. Meanwhile, species that hypodermically inject sperm lack bristles, potentially as an adaptation to the environment experienced by hypodermic sperm. Combining functional annotations from the model, Macrostomum lignano, with transcriptomes from 93 congeners, we find genus-wide faster sequence evolution in reproduction-related versus ubiquitously expressed genes, consistent with stronger sexual selection on the former. Additionally, species with hypodermic sperm morphologies had elevated molecular sequence evolution, regardless of a gene's functional annotation. These genome-wide patterns suggest reduced selection efficiency following shifts to hypodermic mating, possibly due to higher selfing rates in these species. Moreover, we find little evidence for convergent amino acid changes across species. Our work not only shows that reproduction-related genes evolve rapidly also in hermaphroditic animals, but also that well-replicated contrasts of different sexual selection contexts can reveal underappreciated genome-wide effects.
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Affiliation(s)
- R Axel W Wiberg
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Jeremias N Brand
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Lukas Schärer
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
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22
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Transgenesis in the acoel worm Hofstenia miamia. Dev Cell 2021; 56:3160-3170.e4. [PMID: 34752780 DOI: 10.1016/j.devcel.2021.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 07/20/2021] [Accepted: 10/12/2021] [Indexed: 12/27/2022]
Abstract
The acoel worm Hofstenia miamia, which can replace tissue lost to injury via differentiation of a population of stem cells, has emerged as a new research organism for studying regeneration. To enhance the depth of mechanistic studies in this system, we devised a protocol for microinjection into embryonic cells that resulted in stable transgene integration into the genome and generated animals with tissue-specific fluorescent transgene expression in epidermis, gut, and muscle. We demonstrate that transgenic Hofstenia are amenable to the isolation of specific cell types, investigations of regeneration, tracking of photoconverted molecules, and live imaging. Further, our stable transgenic lines revealed insights into the biology of Hofstenia, including a high-resolution three-dimensional view of cell morphology and the organization of muscle as a cellular scaffold for other tissues. Our work positions Hofstenia as a powerful system with multiple toolkits for mechanistic investigations of development, whole-body regeneration, and stem cell biology.
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23
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Rinkevich B, Ballarin L, Martinez P, Somorjai I, Ben-Hamo O, Borisenko I, Berezikov E, Ereskovsky A, Gazave E, Khnykin D, Manni L, Petukhova O, Rosner A, Röttinger E, Spagnuolo A, Sugni M, Tiozzo S, Hobmayer B. A pan-metazoan concept for adult stem cells: the wobbling Penrose landscape. Biol Rev Camb Philos Soc 2021; 97:299-325. [PMID: 34617397 PMCID: PMC9292022 DOI: 10.1111/brv.12801] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022]
Abstract
Adult stem cells (ASCs) in vertebrates and model invertebrates (e.g. Drosophila melanogaster) are typically long‐lived, lineage‐restricted, clonogenic and quiescent cells with somatic descendants and tissue/organ‐restricted activities. Such ASCs are mostly rare, morphologically undifferentiated, and undergo asymmetric cell division. Characterized by ‘stemness’ gene expression, they can regulate tissue/organ homeostasis, repair and regeneration. By contrast, analysis of other animal phyla shows that ASCs emerge at different life stages, present both differentiated and undifferentiated phenotypes, and may possess amoeboid movement. Usually pluri/totipotent, they may express germ‐cell markers, but often lack germ‐line sequestering, and typically do not reside in discrete niches. ASCs may constitute up to 40% of animal cells, and participate in a range of biological phenomena, from whole‐body regeneration, dormancy, and agametic asexual reproduction, to indeterminate growth. They are considered legitimate units of selection. Conceptualizing this divergence, we present an alternative stemness metaphor to the Waddington landscape: the ‘wobbling Penrose’ landscape. Here, totipotent ASCs adopt ascending/descending courses of an ‘Escherian stairwell’, in a lifelong totipotency pathway. ASCs may also travel along lower stemness echelons to reach fully differentiated states. However, from any starting state, cells can change their stemness status, underscoring their dynamic cellular potencies. Thus, vertebrate ASCs may reflect just one metazoan ASC archetype.
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Affiliation(s)
- Baruch Rinkevich
- Israel Oceanographic & Limnological Research, National Institute of Oceanography, POB 9753, Tel Shikmona, Haifa, 3109701, Israel
| | - Loriano Ballarin
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35121, Italy
| | - Pedro Martinez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain.,Institut Català de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, 08010, Spain
| | - Ildiko Somorjai
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9ST, Scotland, UK
| | - Oshrat Ben-Hamo
- Israel Oceanographic & Limnological Research, National Institute of Oceanography, POB 9753, Tel Shikmona, Haifa, 3109701, Israel
| | - Ilya Borisenko
- Department of Embryology, Faculty of Biology, Saint-Petersburg State University, University Embankment, 7/9, Saint-Petersburg, 199034, Russia
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Alexander Ereskovsky
- Department of Embryology, Faculty of Biology, Saint-Petersburg State University, University Embankment, 7/9, Saint-Petersburg, 199034, Russia.,Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE), Aix Marseille University, CNRS, IRD, Avignon University, Jardin du Pharo, 58 Boulevard Charles Livon, Marseille, 13007, France.,Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Ulitsa Vavilova, 26, Moscow, 119334, Russia
| | - Eve Gazave
- Université de Paris, CNRS, Institut Jacques Monod, Paris, F-75006, France
| | - Denis Khnykin
- Department of Pathology, Oslo University Hospital, Bygg 19, Gaustad Sykehus, Sognsvannsveien 21, Oslo, 0188, Norway
| | - Lucia Manni
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35121, Italy
| | - Olga Petukhova
- Collection of Vertebrate Cell Cultures, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
| | - Amalia Rosner
- Israel Oceanographic & Limnological Research, National Institute of Oceanography, POB 9753, Tel Shikmona, Haifa, 3109701, Israel
| | - Eric Röttinger
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, 06107, France.,Université Côte d'Azur, Federative Research Institute - Marine Resources (IFR MARRES), 28 Avenue de Valrose, Nice, 06103, France
| | - Antonietta Spagnuolo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
| | - Michela Sugni
- Department of Environmental Science and Policy (ESP), Università degli Studi di Milano, Via Celoria 26, Milan, 20133, Italy
| | - Stefano Tiozzo
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06234 Villefranche-sur-Mer, Villefranche sur Mer, Cedex, France
| | - Bert Hobmayer
- Institute of Zoology and Center for Molecular Biosciences, University of Innsbruck, Technikerstr, Innsbruck, 256020, Austria
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24
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Large-scale phylogenomics of the genus Macrostomum (Platyhelminthes) reveals cryptic diversity and novel sexual traits. Mol Phylogenet Evol 2021; 166:107296. [PMID: 34438051 DOI: 10.1016/j.ympev.2021.107296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/01/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023]
Abstract
Free-living flatworms of the genus Macrostomum are small and transparent animals, representing attractive study organisms for a broad range of topics in evolutionary, developmental, and molecular biology. The genus includes the model organism M. lignano for which extensive molecular resources are available, and recently there is a growing interest in extending work to additional species in the genus. These endeavours are currently hindered because, even though >200 Macrostomum species have been taxonomically described, molecular phylogenetic information and geographic sampling remain limited. We report on a global sampling campaign aimed at increasing taxon sampling and geographic representation of the genus. Specifically, we use extensive transcriptome and single-locus data to generate phylogenomic hypotheses including 145 species. Across different phylogenetic methods and alignments used, we identify several consistent clades, while their exact grouping is less clear, possibly due to a radiation early in Macrostomum evolution. Moreover, we uncover a large undescribed diversity, with 94 of the studied species likely being new to science, and we identify multiple novel morphological traits. Furthermore, we identify cryptic speciation in a taxonomically challenging assemblage of species, suggesting that the use of molecular markers is a prerequisite for future work, and we describe the distribution of putative synapomorphies and suggest taxonomic revisions based on our finding. Our large-scale phylogenomic dataset now provides a robust foundation for comparative analyses of morphological, behavioural and molecular evolution in this genus.
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25
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Wu W, LoVerde PT. Identification and evolution of nuclear receptors in Platyhelminths. PLoS One 2021; 16:e0250750. [PMID: 34388160 PMCID: PMC8363021 DOI: 10.1371/journal.pone.0250750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/18/2021] [Indexed: 11/24/2022] Open
Abstract
Since the first complete set of Platyhelminth nuclear receptors (NRs) from Schistosoma mansoni were identified a decade ago, more flatworm genome data is available to identify their NR complement and to analyze the evolutionary relationship of Platyhelminth NRs. NRs are important transcriptional modulators that regulate development, differentiation and reproduction of animals. In this study, NRs are identified in genome databases of thirty-three species including in all Platyhelminth classes (Rhabditophora, Monogenea, Cestoda and Trematoda). Phylogenetic analysis shows that NRs in Platyhelminths follow two different evolutionary lineages: 1) NRs in a free-living freshwater flatworm (Schmidtea mediterranea) and all parasitic flatworms share the same evolutionary lineage with extensive gene loss. 2) NRs in a free-living intertidal zone flatworm (Macrostomum lignano) follow a different evolutionary lineage with a feature of multiple gene duplication and gene divergence. The DNA binding domain (DBD) is the most conserved region in NRs which contains two C4-type zinc finger motifs. A novel zinc finger motif is identified in parasitic flatworm NRs: the second zinc finger of parasitic Platyhelminth HR96b possesses a CHC2 motif which is not found in NRs of all other animals studied to date. In this study, novel NRs (members of NR subfamily 3 and 6) are identified in flatworms, this result demonstrates that members of all six classical NR subfamilies are present in the Platyhelminth phylum. NR gene duplication, loss and divergence in Platyhelminths are analyzed along with the evolutionary relationship of Platyhelminth NRs.
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Affiliation(s)
- Wenjie Wu
- Departments of Biochemistry and Structural Biology and Pathology and Laboratory Medicine, University of Texas Health Sciences Center, San Antonio, Texas, United States of America
| | - Philip T. LoVerde
- Departments of Biochemistry and Structural Biology and Pathology and Laboratory Medicine, University of Texas Health Sciences Center, San Antonio, Texas, United States of America
- * E-mail:
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Ustyantsev K, Wudarski J, Sukhikh I, Reinoite F, Mouton S, Berezikov E. Proof of principle for piggyBac-mediated transgenesis in the flatworm Macrostomum lignano. Genetics 2021; 218:6276877. [PMID: 33999134 PMCID: PMC8717057 DOI: 10.1093/genetics/iyab076] [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: 04/08/2021] [Accepted: 05/06/2021] [Indexed: 12/03/2022] Open
Abstract
Regeneration-capable flatworms are informative research models to study the mechanisms of stem cell regulation, regeneration, and tissue patterning. The free-living flatworm Macrostomum lignano is currently the only flatworm where stable transgenesis is available, and as such it offers a powerful experimental platform to address questions that were previously difficult to answer. The published transgenesis approach relies on random integration of DNA constructs into the genome. Despite its efficiency, there is room and need for further improvement and diversification of transgenesis methods in M. lignano. Transposon-mediated transgenesis is an alternative approach, enabling easy mapping of the integration sites and the possibility of insertional mutagenesis studies. Here, we report for the first time that transposon-mediated transgenesis using piggyBac can be performed in M. lignano to create stable transgenic lines with single-copy transgene insertions.
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Affiliation(s)
- Kirill Ustyantsev
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - Jakub Wudarski
- Laboratory of Biological Diversity, National Institute for Basic Biology, Okazaki 444-8585 Aichi, Japan
| | - Igor Sukhikh
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - Filipa Reinoite
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, 9700AD, The Netherlands
| | - Stijn Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, 9700AD, The Netherlands
| | - Eugene Berezikov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, 9700AD, The Netherlands
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Marie‐Orleach L, Vellnow N, Schärer L. The repeatable opportunity for selection differs between pre- and postcopulatory fitness components. Evol Lett 2021; 5:101-114. [PMID: 33552539 PMCID: PMC7857279 DOI: 10.1002/evl3.210] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/21/2020] [Accepted: 11/25/2020] [Indexed: 11/29/2022] Open
Abstract
In species with multiple mating, intense sexual selection may occur both before and after copulation. However, comparing the strength of pre- and postcopulatory selection is challenging, because (i) postcopulatory processes are generally difficult to observe and (ii) the often-used opportunity for selection (I) metric contains both deterministic and stochastic components. Here, we quantified pre- and postcopulatory male fitness components of the simultaneously hermaphroditic flatworm, Macrostomum lignano. We did this by tracking fluorescent sperm-using transgenics-through the transparent body of sperm recipients, enabling to observe postcopulatory processes in vivo. Moreover, we sequentially exposed focal worms to three independent mating groups, and in each assessed their mating success, sperm-transfer efficiency, sperm fertilizing efficiency, and partner fecundity. Based on these multiple measures, we could, for each fitness component, combine the variance (I) with the repeatability (R) in individual success to assess the amount of repeatable variance in individual success-a measure we call the repeatable opportunity for selection (IR ). We found higher repeatable opportunity for selection in sperm-transfer efficiency and sperm fertilizing efficiency compared to mating success, which clearly suggests that postcopulatory selection is stronger than precopulatory selection. Our study demonstrates that the opportunity for selection contains a repeatable deterministic component, which can be assessed and disentangled from the often large stochastic component, to provide a better estimate of the strength of selection.
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Affiliation(s)
- Lucas Marie‐Orleach
- Department of Environmental Sciences, Zoological InstituteUniversity of BaselBasel4051Switzerland
- School of Biology, Centre for Biological DiversityUniversity of St AndrewsSt AndrewsKY16 9THUnited Kingdom
- Natural History MuseumUniversity of OsloOslo0318Norway
- CNRS, ECOBIO (Écosystèmes, Biodiversité, Évolution) – UMR 6553Université de Rennes 1Rennes35000France
| | - Nikolas Vellnow
- Department of Environmental Sciences, Zoological InstituteUniversity of BaselBasel4051Switzerland
- Evolutionary BiologyBielefeld UniversityBielefeldDE‐33615Germany
| | - Lukas Schärer
- Department of Environmental Sciences, Zoological InstituteUniversity of BaselBasel4051Switzerland
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TIM29 is required for enhanced stem cell activity during regeneration in the flatworm Macrostomum lignano. Sci Rep 2021; 11:1166. [PMID: 33441924 PMCID: PMC7806878 DOI: 10.1038/s41598-020-80682-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/10/2020] [Indexed: 01/29/2023] Open
Abstract
TIM29 is a mitochondrial inner membrane protein that interacts with the protein import complex TIM22. TIM29 was shown to stabilize the TIM22 complex but its biological function remains largely unknown. Until recently, it was classified as one of the Domain of Unknown Function (DUF) genes, with a conserved protein domain DUF2366 of unclear function. Since characterizing DUF genes can provide novel biological insight, we used previously established transcriptional profiles of the germline and stem cells of the flatworm Macrostomum lignano to probe conserved DUFs for their potential role in germline biology, stem cell function, regeneration, and development. Here, we demonstrate that DUF2366/TIM29 knockdown in M. lignano has very limited effect during the normal homeostatic condition but prevents worms from adapting to a highly proliferative state required for regeneration.
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29
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Singh P, Ballmer DN, Laubscher M, Schärer L. Successful mating and hybridisation in two closely related flatworm species despite significant differences in reproductive morphology and behaviour. Sci Rep 2020; 10:12830. [PMID: 32732887 PMCID: PMC7393371 DOI: 10.1038/s41598-020-69767-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/20/2020] [Indexed: 12/16/2022] Open
Abstract
Reproductive traits are some of the fastest diverging characters and can serve as reproductive barriers. The free-living flatworm Macrostomum lignano, and its congener M. janickei are closely related, but differ substantially in their male intromittent organ (stylet) morphology. Here, we examine whether these morphological differences are accompanied by differences in behavioural traits, and whether these could represent barriers to successful mating and hybridization between the two species. Our data shows that the two species differ in many aspects of their mating behaviour. Despite these differences, the species mate readily with each other in heterospecific pairings. Although both species have similar fecundity in conspecific pairings, the heterospecific pairings revealed clear postmating barriers, as few heterospecific pairings produced F1 hybrids. These hybrids had a stylet morphology that was intermediate between that of the parental species, and they were fertile. Finally, using a mate choice experiment, we show that the nearly two-fold higher mating rate of M. lignano caused it to mate more with conspecifics, leading to assortative mating, while M. janickei ended up mating more with heterospecifics. Thus, while the two species can hybridize, the mating rate differences could possibly lead to higher fitness costs for M. janickei compared to M. lignano.
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Affiliation(s)
- Pragya Singh
- Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
| | - Daniel N Ballmer
- Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.,Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Max Laubscher
- Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Lukas Schärer
- Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
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Brand JN, Wiberg RAW, Pjeta R, Bertemes P, Beisel C, Ladurner P, Schärer L. RNA-Seq of three free-living flatworm species suggests rapid evolution of reproduction-related genes. BMC Genomics 2020; 21:462. [PMID: 32631219 PMCID: PMC7336406 DOI: 10.1186/s12864-020-06862-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 06/22/2020] [Indexed: 01/03/2023] Open
Abstract
Background The genus Macrostomum consists of small free-living flatworms and contains Macrostomum lignano, which has been used in investigations of ageing, stem cell biology, bioadhesion, karyology, and sexual selection in hermaphrodites. Two types of mating behaviour occur within this genus. Some species, including M. lignano, mate via reciprocal copulation, where, in a single mating, both partners insert their male copulatory organ into the female storage organ and simultaneously donate and receive sperm. Other species mate via hypodermic insemination, where worms use a needle-like copulatory organ to inject sperm into the tissue of the partner. These contrasting mating behaviours are associated with striking differences in sperm and copulatory organ morphology. Here we expand the genomic resources within the genus to representatives of both behaviour types and investigate whether genes vary in their rate of evolution depending on their putative function. Results We present de novo assembled transcriptomes of three Macrostomum species, namely M. hystrix, a close relative of M. lignano that mates via hypodermic insemination, M. spirale, a more distantly related species that mates via reciprocal copulation, and finally M. pusillum, which represents a clade that is only distantly related to the other three species and also mates via hypodermic insemination. We infer 23,764 sets of homologous genes and annotate them using experimental evidence from M. lignano. Across the genus, we identify 521 gene families with conserved patterns of differential expression between juvenile vs. adult worms and 185 gene families with a putative expression in the testes that are restricted to the two reciprocally mating species. Further, we show that homologs of putative reproduction-related genes have a higher protein divergence across the four species than genes lacking such annotations and that they are more difficult to identify across the four species, indicating that these genes evolve more rapidly, while genes involved in neoblast function are more conserved. Conclusions This study improves the genus Macrostomum as a model system, by providing resources for the targeted investigation of gene function in a broad range of species. And we, for the first time, show that reproduction-related genes evolve at an accelerated rate in flatworms.
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Affiliation(s)
- Jeremias N Brand
- Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
| | - R Axel W Wiberg
- Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Robert Pjeta
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Philip Bertemes
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Peter Ladurner
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Lukas Schärer
- Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
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31
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Weber M, Patlar B, Ramm SA. Effects of two seminal fluid transcripts on post-mating behaviour in the simultaneously hermaphroditic flatworm Macrostomum lignano. J Evol Biol 2020; 33:714-726. [PMID: 32064699 DOI: 10.1111/jeb.13606] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/29/2020] [Accepted: 02/06/2020] [Indexed: 12/12/2022]
Abstract
The seminal fluid proteins (SFPs) transferred to mating partners along with sperm often play crucial roles in mediating post-mating sexual selection. One way in which sperm donors can maximize their own reproductive success is by modifying the partner's (sperm recipient's) post-copulatory behaviour to prevent or delay re-mating, thereby decreasing the likelihood or intensity of sperm competition. Here, we adopted a quantitative genetic approach combining gene expression and behavioural data to identify candidates that could mediate such a response in the simultaneously hermaphroditic flatworm Macrostomum lignano. We identified two putative SFPs-Mlig-pro46 and Mlig-pro63-linked to both mating frequency and 'suck' frequency, a distinctive behaviour, in which, upon ejaculate receipt, the worm places its pharynx over its female genital opening and apparently attempts to remove the received ejaculate. We, therefore, performed a manipulative experiment using RNA interference-induced knockdown to ask how the loss of Mlig-pro46 and Mlig-pro63 expression, singly and in combination, affects mating frequency, partner suck propensity and sperm competitive ability. None of the knockdown treatments impacted strongly on the mating frequency or sperm competitive ability, but knockdown of Mlig-pro63 resulted in a significantly decreased suck propensity of mating partners. This suggests that Mlig-pro63 may normally act as a cue in the ejaculate to trigger recipient suck behaviour and-given that other proteins in the ejaculate have the opposite effect-could be one component of an ongoing arms race between donors and recipients over the control of ejaculate fate. However, the adaptive significance of Mlig-pro46 and Mlig-pro63 from a donor perspective remains enigmatic.
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Affiliation(s)
- Michael Weber
- Department of Evolutionary Biology, Bielefeld University, Bielefeld, Germany
| | - Bahar Patlar
- Department of Evolutionary Biology, Bielefeld University, Bielefeld, Germany
| | - Steven A Ramm
- Department of Evolutionary Biology, Bielefeld University, Bielefeld, Germany
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32
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Wudarski J, Egger B, Ramm SA, Schärer L, Ladurner P, Zadesenets KS, Rubtsov NB, Mouton S, Berezikov E. The free-living flatworm Macrostomum lignano. EvoDevo 2020; 11:5. [PMID: 32158530 PMCID: PMC7053086 DOI: 10.1186/s13227-020-00150-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/12/2020] [Indexed: 01/20/2023] Open
Abstract
Macrostomum lignano is a free-living flatworm that is emerging as an attractive experimental animal for research on a broad range of biological questions. One feature setting it apart from other flatworms is the successful establishment of transgenesis methods, facilitated by a steady supply of eggs in the form of single-cell zygotes that can be readily manipulated. This, in combination with the transparency of the animal and its small size, creates practical advantages for imaging and fluorescence-activated cell sorting in studies related to stem cell biology and regeneration. M. lignano can regenerate most of its body parts, including the germline, thanks to the neoblasts, which represent the flatworm stem cell system. Interestingly, neoblasts seem to have a high capacity of cellular maintenance, as M. lignano can survive up to 210 Gy of γ-irradiation, and partially offset the negative consequence of ageing. As a non-self-fertilizing simultaneous hermaphrodite that reproduces in a sexual manner, M. lignano is also used to study sexual selection and other evolutionary aspects of sexual reproduction. Work over the past several years has led to the development of molecular resources and tools, including high-quality genome and transcriptome assemblies, transcriptional profiling of the germline and somatic neoblasts, gene knockdown, and in situ hybridization. The increasingly detailed characterization of this animal has also resulted in novel research questions, such as bio-adhesion based on its adhesion-release glands and genome evolution due to its recent whole-genome duplication.![]()
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Affiliation(s)
- Jakub Wudarski
- 1European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands
| | - Bernhard Egger
- 2Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Steven A Ramm
- 3Department of Evolutionary Biology, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Lukas Schärer
- 4Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Peter Ladurner
- 2Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Kira S Zadesenets
- 5The Federal Research Center Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
| | - Nikolay B Rubtsov
- 5The Federal Research Center Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
| | - Stijn Mouton
- 1European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands
| | - Eugene Berezikov
- 1European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands.,5The Federal Research Center Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
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Patlar B, Weber M, Temizyürek T, Ramm SA. Seminal Fluid-Mediated Manipulation of Post-mating Behavior in a Simultaneous Hermaphrodite. Curr Biol 2020; 30:143-149.e4. [DOI: 10.1016/j.cub.2019.11.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 09/25/2019] [Accepted: 11/05/2019] [Indexed: 10/25/2022]
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Schärer L, Brand JN, Singh P, Zadesenets KS, Stelzer C, Viktorin G. A phylogenetically informed search for an alternative
Macrostomum
model species, with notes on taxonomy, mating behavior, karyology, and genome size. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12344] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Lukas Schärer
- Evolutionary Biology Zoological Institute University of Basel Basel Switzerland
| | - Jeremias N. Brand
- Evolutionary Biology Zoological Institute University of Basel Basel Switzerland
| | - Pragya Singh
- Evolutionary Biology Zoological Institute University of Basel Basel Switzerland
| | - Kira S. Zadesenets
- The Federal Research Center Institute of Cytology and Genetics SB RAS Novosibirsk Russia
| | | | - Gudrun Viktorin
- Evolutionary Biology Zoological Institute University of Basel Basel Switzerland
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Weber M, Giannakara A, Ramm SA. Seminal fluid-mediated fitness effects in the simultaneously hermaphroditic flatworm Macrostomum lignano. Ecol Evol 2019; 9:13889-13901. [PMID: 31938489 PMCID: PMC6953679 DOI: 10.1002/ece3.5825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 11/08/2022] Open
Abstract
As a class, seminal fluid proteins are expected to exert strong effects on mating partners due to the selection pressures of sperm competition and sexual conflict. But because of the complexity of this secretion, linking specific proteins to downstream effects on own fitness-via manipulating the reproductive behavior, physiology, and ultimately the sperm utilization of mating partners-is not straightforward. Here, we adopted a systematic gene knockdown approach to screen for seminal fluid-mediated fitness effects in the simultaneously hermaphroditic flatworm Macrostomum lignano. We focused on 18 transcripts in M. lignano seminal fluid, testing how their RNA interference-induced knockdown impacted on three aspects of donor (male) reproductive success: (a) fertility (offspring production of the partner); (b) defensive sperm competitive ability, P 1; and (c) offensive sperm competitive ability, P 2. In general, the knockdown of most individual transcripts appeared to have only a minor impact on male reproductive success, though we found evidence that the knockdown of up to five different transcripts impacted on fertility; the knockdown of two other transcripts resulted in reduced P 2; and knockdown of a further transcript actually increased P 2. We thus identify a number of candidate seminal fluid transcripts that appear to modulate offspring production and sperm competitiveness in M. lignano. That only a minority of transcripts exhibit such a pattern likely reflects both the difficulty of accurately estimating sperm competitiveness and the functional redundancy of seminal fluid.
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Affiliation(s)
- Michael Weber
- Department of Evolutionary BiologyBielefeld UniversityBielefeldGermany
| | - Athina Giannakara
- Department of Evolutionary BiologyBielefeld UniversityBielefeldGermany
| | - Steven A. Ramm
- Department of Evolutionary BiologyBielefeld UniversityBielefeldGermany
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36
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Azlan A, Halim MA, Azzam G. Genome-wide identification and characterization of long intergenic noncoding RNAs in the regenerative flatworm Macrostomum lignano. Genomics 2019; 112:1273-1281. [PMID: 31381967 DOI: 10.1016/j.ygeno.2019.07.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 07/16/2019] [Accepted: 07/30/2019] [Indexed: 01/03/2023]
Abstract
The free-living flatworm Macrostoma lignano (M. lignano) is an emerging model organism for aging and regeneration research. Long intergenic non-coding RNAs (lincRNAs) have important roles in many biological processes such as aging, stem cell maintenance and differentiation. However, to date, there is no systematic identification of lincRNAs in M. lignano. By using public RNA-seq data, we identified a total of 2547 lincRNA transcripts in M. lignano genome. We discovered that M. lignano lincRNAs shared many characteristics with other species such as shorter in length, lower GC content, and lower in expression compared to protein-coding genes. Unlike protein-coding genes, M. lignano lincRNAs showed higher tendency to be expressed in temporal and region-specific fashion. Additionally, co-expression network analysis and functional enrichment suggest that M. lignano lincRNAs have potential roles in regeneration. This study will provide important resources and pave the way for investigations on non-coding genes involved in aging and regeneration.
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Affiliation(s)
- Azali Azlan
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia; USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, 11800 Penang, Malaysia.
| | - Mardani Abdul Halim
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia; USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Ghows Azzam
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia; USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, 11800 Penang, Malaysia.
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37
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Ramm SA, Lengerer B, Arbore R, Pjeta R, Wunderer J, Giannakara A, Berezikov E, Ladurner P, Schärer L. Sex allocation plasticity on a transcriptome scale: Socially sensitive gene expression in a simultaneous hermaphrodite. Mol Ecol 2019; 28:2321-2341. [PMID: 30891857 DOI: 10.1111/mec.15077] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 03/04/2019] [Accepted: 03/11/2019] [Indexed: 12/11/2022]
Abstract
Phenotypic plasticity can enable organisms to produce optimal phenotypes in multiple environments. A crucial life history trait that is often highly plastic is sex allocation, which in simultaneous hermaphrodites describes the relative investment into the male versus female sex functions. Theory predicts-and morphological evidence supports-that greater investment into the male function is favoured with increasing group size, due to the increasing importance of sperm competition for male reproductive success. Here, we performed a genome-wide gene expression assay to test for such sex allocation plasticity in a model simultaneous hermaphrodite, the free-living flatworm Macrostomum lignano. Based on RNA-Seq data from 16 biological replicates spanning four different group size treatments, we demonstrate that at least 10% of the >75,000 investigated transcripts in M. lignano are differentially expressed according to the social environment, rising to >30% of putative gonad-specific transcripts (spermatogenesis and oogenesis candidates) and tail-specific transcripts (seminal fluid candidates). This transcriptional response closely corresponds to the expected shift away from female and towards male reproductive investment with increasing sperm competition level. Using whole-mount in situ hybridization, we then confirm that many plastic transcripts exhibit the expected organ-specific expression, and RNA interference of selected testis- and ovary-specific candidates establishes that these indeed function in gametogenesis pathways. We conclude that a large proportion of sex-specific transcripts in M. lignano are differentially expressed according to the prevailing ecological conditions and that these are functionally relevant to key reproductive phenotypes. Our study thus begins to bridge organismal and molecular perspectives on sex allocation plasticity.
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Affiliation(s)
- Steven A Ramm
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany.,Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland
| | - Birgit Lengerer
- Institute of Zoology & CMBI, University of Innsbruck, Innsbruck, Austria
| | - Roberto Arbore
- Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland
| | - Robert Pjeta
- Institute of Zoology & CMBI, University of Innsbruck, Innsbruck, Austria
| | - Julia Wunderer
- Institute of Zoology & CMBI, University of Innsbruck, Innsbruck, Austria
| | | | - Eugene Berezikov
- ERIBA, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter Ladurner
- Institute of Zoology & CMBI, University of Innsbruck, Innsbruck, Austria
| | - Lukas Schärer
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany
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Patlar B, Weber M, Ramm SA. Genetic and environmental variation in transcriptional expression of seminal fluid proteins. Heredity (Edinb) 2019; 122:595-611. [PMID: 30356222 PMCID: PMC6461930 DOI: 10.1038/s41437-018-0160-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 08/29/2018] [Accepted: 09/18/2018] [Indexed: 12/31/2022] Open
Abstract
Seminal fluid proteins (SFPs) are crucial mediators of sexual selection and sexual conflict. Recent studies have chiefly focused on environmentally induced plasticity as one source of variation in SFP expression, particularly in response to differing sperm competition levels. However, understanding the evolution of a trait in heterogenous environments requires estimates of both environmental and genetic sources of variation, as well as their interaction. Therefore, we investigated how environment (specifically mating group size, a good predictor of sperm competition intensity), genotype and genotype-by-environment interactions affect seminal fluid expression. To do so, we reared 12 inbred lines of a simultaneously hermaphroditic flatworm Macrostomum lignano in groups of either two or eight worms and measured the expression levels of 58 putative SFP transcripts. We then examined the source of variation in the expression of each transcript individually and for multivariate axes extracted from a principal component analysis. We found that mating group size did not affect expression levels according to the single transcript analyses, nor did it affect the first principal component (presumably representing overall investment in seminal fluid production). However, mating group size did affect the relative expression of different transcripts captured by the second principal component (presumably reflecting variation in seminal fluid composition). Most transcripts were genetically variable in their expression level and several exhibited genotype-by-environment interactions; relative composition also showed high genetic variation. Collectively, our results reveal the tightly integrated nature of the seminal fluid transcriptome and provide new insights into the quantitative genetic basis of seminal fluid investment and composition.
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Affiliation(s)
- Bahar Patlar
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany.
| | - Michael Weber
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany
| | - Steven A Ramm
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany
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Mouton S, Wudarski J, Grudniewska M, Berezikov E. The regenerative flatworm Macrostomum lignano, a model organism with high experimental potential. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2019; 62:551-558. [PMID: 29938766 DOI: 10.1387/ijdb.180077eb] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Understanding the process of regeneration has been one of the longstanding scientific aims, from a fundamental biological perspective, as well as within the applied context of regenerative medicine. Because regeneration competence varies greatly between organisms, it is essential to investigate different experimental animals. The free-living marine flatworm Macrostomum lignano is a rising model organism for this type of research, and its power stems from a unique set of biological properties combined with amenability to experimental manipulation. The biological properties of interest include production of single-cell fertilized eggs, a transparent body, small size, short generation time, ease of culture, the presence of a pluripotent stem cell population, and a large regeneration competence. These features sparked the development of molecular tools and resources for this animal, including high-quality genome and transcriptome assemblies, gene knockdown, in situ hybridization, and transgenesis. Importantly, M. lignano is currently the only flatworm species for which transgenesis methods are established. This review summarizes biological features of M. lignano and recent technological advances towards experimentation with this animal. In addition, we discuss the experimental potential of this model organism for different research questions related to regeneration and stem cell biology.
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Affiliation(s)
- Stijn Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Wunderer J, Lengerer B, Pjeta R, Bertemes P, Kremser L, Lindner H, Ederth T, Hess MW, Stock D, Salvenmoser W, Ladurner P. A mechanism for temporary bioadhesion. Proc Natl Acad Sci U S A 2019; 116:4297-4306. [PMID: 30782790 PMCID: PMC6410801 DOI: 10.1073/pnas.1814230116] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The flatworm Macrostomum lignano features a duo-gland adhesive system that allows it to repeatedly attach to and release from substrates in seawater within a minute. However, little is known about the molecules involved in this temporary adhesion. In this study, we show that the attachment of M. lignano relies on the secretion of two large adhesive proteins, M. lignano adhesion protein 1 (Mlig-ap1) and Mlig-ap2. We revealed that both proteins are expressed in the adhesive gland cells and that their distribution within the adhesive footprints was spatially restricted. RNA interference knockdown experiments demonstrated the essential function of these two proteins in flatworm adhesion. Negatively charged modified sugars in the surrounding water inhibited flatworm attachment, while positively charged molecules impeded detachment. In addition, we found that M. lignano could not adhere to strongly hydrated surfaces. We propose an attachment-release model where Mlig-ap2 attaches to the substrate and Mlig-ap1 exhibits a cohesive function. A small negatively charged molecule is secreted that interferes with Mlig-ap1, inducing detachment. These findings are of relevance for fundamental adhesion science and efforts to mitigate biofouling. Further, this model of flatworm temporary adhesion may serve as the starting point for the development of synthetic reversible adhesion systems for medicinal and industrial applications.
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Affiliation(s)
- Julia Wunderer
- Institute of Zoology, University of Innsbruck, 6020 Innsbruck, Austria
- Center of Molecular Bioscience Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria
| | - Birgit Lengerer
- Institute of Zoology, University of Innsbruck, 6020 Innsbruck, Austria
- Center of Molecular Bioscience Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria
- Biology of Marine Organisms and Biomimetics, Research Institute for Biosciences, University of Mons, 7000 Mons, Belgium
| | - Robert Pjeta
- Institute of Zoology, University of Innsbruck, 6020 Innsbruck, Austria
- Center of Molecular Bioscience Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria
| | - Philip Bertemes
- Institute of Zoology, University of Innsbruck, 6020 Innsbruck, Austria
- Center of Molecular Bioscience Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - Thomas Ederth
- Division of Molecular Physics, Department of Physics, Chemistry and Biology, Linköping University, 58183 Linköping, Sweden
| | - Michael W Hess
- Division of Histology and Embryology, Innsbruck Medical University, 6020 Innsbruck, Austria
| | - David Stock
- Institute for Material Technology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Willi Salvenmoser
- Institute of Zoology, University of Innsbruck, 6020 Innsbruck, Austria
- Center of Molecular Bioscience Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria
| | - Peter Ladurner
- Institute of Zoology, University of Innsbruck, 6020 Innsbruck, Austria;
- Center of Molecular Bioscience Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria
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Wudarski J, Ustyantsev K, Glazenburg L, Berezikov E. Influence of temperature on development, reproduction and regeneration in the flatworm model organism, Macrostomum lignano. ZOOLOGICAL LETTERS 2019; 5:7. [PMID: 30805201 PMCID: PMC6371448 DOI: 10.1186/s40851-019-0122-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The free-living marine flatworm Macrostomum lignano is a powerful model organism for use in studying mechanisms of regeneration and stem cell regulation due to its combination of biological and experimental properties, including the availability of transgenesis methods, which is unique among flatworm models. However, due to its relatively recent introduction in research, many aspects of this animal's biology remain unknown. One such question is the influence of culture temperature on Macrostomum biology. RESULTS We systematically investigated how different culture temperatures affect development time, reproduction rate, regeneration, heat shock response, and gene knockdown efficiency by RNA interference (RNAi) in M. lignano. We used marker transgenic lines to accurately measure the regeneration endpoint, and to establish the stress response threshold for temperature shock. We found that compared to the culture temperature of 20 °C commonly used for M. lignano, temperatures of 25 °C-30 °C substantially increase the speed of development and regeneration, lead to faster manifestation of RNAi phenotypes, and increase reproduction rate without detectable negative consequences for the animal, while temperatures above 30 °C elicit a heat shock response. CONCLUSIONS We show that altering temperature conditions can be used to reduce the time required to establish M. lignano cultures, perform RNAi experiments, store important lines, and optimize microinjection procedures for transgenesis. These findings will help to optimize the design of experiments in M. lignano, and thus facilitate future research using this model organism.
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Affiliation(s)
- Jakub Wudarski
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
| | - Kirill Ustyantsev
- Institute of Cytology and Genetics, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia
| | - Lisa Glazenburg
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
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Establishment of Transgenesis in the Demosponge Suberites domuncula. Genetics 2018; 210:435-443. [PMID: 30143594 PMCID: PMC6216596 DOI: 10.1534/genetics.118.301121] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/27/2018] [Indexed: 12/20/2022] Open
Abstract
Sponges (Porifera) represent one of the most basally branching animal clades with key relevance for evolutionary studies, stem cell biology, and development. Despite a long history of sponges as experimental model systems, however, functional molecular studies are still very difficult to perform in these animals. Here, we report the establishment of transgenic technology as a basic and versatile experimental tool for sponge research. We demonstrate that slice explants of the demosponge Suberites domuncula regenerate functional sponge tissue and can be cultured for extended periods of time, providing easy experimental access under controlled conditions. We further show that an engineered expression construct driving the enhanced green fluorescence protein (egfp) gene under control of the Suberites domuncula β-actin locus can be transfected into such tissue cultures, and that faithfully spliced transcripts are produced from such transfected DNA. Finally, by combining fluorescence-activated cell sorting (FACS) with quantitative PCR, we validate that transfected cells can be specifically reisolated from tissue based on their fluorescence. Although the number of detected enhanced green fluorescent protein (EGFP)-expressing cells is still limited, our approach represents the first successful introduction and expression of exogenous DNA in a sponge. These results represent a significant advance for the use of transgenic technology in a cornerstone phylum, for instance for the use in lineage tracing experiments.
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Mouton S, Grudniewska M, Glazenburg L, Guryev V, Berezikov E. Resilience to aging in the regeneration-capable flatworm Macrostomum lignano. Aging Cell 2018; 17:e12739. [PMID: 29488325 PMCID: PMC5946080 DOI: 10.1111/acel.12739] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2018] [Indexed: 12/15/2022] Open
Abstract
Animals show a large variability of lifespan, ranging from short-lived as Caenorhabditis elegans to immortal as Hydra. A fascinating case is flatworms, in which reversal of aging by regeneration is proposed, yet conclusive evidence for this rejuvenation-by-regeneration hypothesis is lacking. We tested this hypothesis by inducing regeneration in the sexual free-living flatworm Macrostomum lignano. We studied survival, fertility, morphology, and gene expression as a function of age. Here, we report that after regeneration, genes expressed in the germline are upregulated at all ages, but no signs of rejuvenation are observed. Instead, the animal appears to be substantially longer lived than previously appreciated, and genes expressed in stem cells are upregulated with age, while germline genes are downregulated. Remarkably, several genes with known beneficial effects on lifespan when overexpressed in mice and C. elegans are naturally upregulated with age in M. lignano, suggesting that molecular mechanism for offsetting negative consequences of aging has evolved in this animal. We therefore propose that M. lignano represents a novel powerful model for molecular studies of aging attenuation, and the identified aging gene expression patterns provide a valuable resource for further exploration of anti-aging strategies.
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Affiliation(s)
- Stijn Mouton
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Magda Grudniewska
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Lisa Glazenburg
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
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Weber M, Wunderer J, Lengerer B, Pjeta R, Rodrigues M, Schärer L, Ladurner P, Ramm SA. A targeted in situ hybridization screen identifies putative seminal fluid proteins in a simultaneously hermaphroditic flatworm. BMC Evol Biol 2018; 18:81. [PMID: 29848299 PMCID: PMC5977470 DOI: 10.1186/s12862-018-1187-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/30/2018] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Along with sperm, in many taxa ejaculates also contain large numbers of seminal fluid proteins (SFPs). SFPs and sperm are transferred to the mating partner, where they are thought to play key roles in mediating post-mating sexual selection. They modulate the partner's behavior and physiology in ways that influence the reproductive success of both partners, thus potentially leading to sexual conflict. Despite the presumed general functional and evolutionary significance of SFPs, their identification and characterization has to date focused on just a few animal groups, predominantly insects and mammals. Moreover, until now seminal fluid profiling has mainly focused on species with separate sexes. Here we report a comprehensive screen for putative SFPs in the simultaneously hermaphroditic flatworm Macrostomum lignano. RESULTS Based on existing transcriptomic data, we selected 150 transcripts known to be (a) predominantly expressed in the tail region of the worms, where the seminal fluid-producing prostate gland cells are located, and (b) differentially expressed in social environments differing in sperm competition level, strongly implying that they represent a phenotypically plastic aspect of male reproductive allocation in this species. For these SFP candidates, we then performed whole-mount in situ hybridization (ISH) experiments to characterize tissue-specific expression. In total, we identified 98 transcripts that exhibited prostate-specific expression, 76 of which we found to be expressed exclusively in the prostate gland cells; additional sites of expression for the remaining 22 included the testis or other gland cells. Bioinformatics analyses of the prostate-limited candidates revealed that at least 64 are predicted to be secretory proteins, making these especially strong candidates to be SFPs that are transferred during copulation. CONCLUSIONS Our study represents a first comprehensive analysis using a combination of transcriptomic and ISH screen data to identify SFPs based on transcript expression in seminal fluid-producing tissues. We thereby extend the range of taxa for which seminal fluid has been characterized to a flatworm species with a sequenced genome and for which several methods such as antibody staining, transgenesis and RNA interference have been established. Our data provide a basis for testing the functional and evolutionary significance of SFPs.
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Affiliation(s)
- Michael Weber
- Evolutionary Biology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany
| | - Julia Wunderer
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Birgit Lengerer
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Robert Pjeta
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Marcelo Rodrigues
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Current address: School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne, England NE1 7RU UK
| | - Lukas Schärer
- Evolutionary Biology, Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Peter Ladurner
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Steven A. Ramm
- Evolutionary Biology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany
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Dattani A, Sridhar D, Aziz Aboobaker A. Planarian flatworms as a new model system for understanding the epigenetic regulation of stem cell pluripotency and differentiation. Semin Cell Dev Biol 2018; 87:79-94. [PMID: 29694837 DOI: 10.1016/j.semcdb.2018.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/21/2018] [Indexed: 12/11/2022]
Abstract
Planarian flatworms possess pluripotent stem cells (neoblasts) that are able to differentiate into all cell types that constitute the adult body plan. Consequently, planarians possess remarkable regenerative capabilities. Transcriptomic studies have revealed that gene expression is coordinated to maintain neoblast pluripotency, and ensure correct lineage specification during differentiation. But as yet they have not revealed how this regulation of expression is controlled. In this review, we propose that planarians represent a unique and effective system to study the epigenetic regulation of these processes in an in vivo context. We consolidate evidence suggesting that although DNA methylation is likely present in some flatworm lineages, it does not regulate neoblast function in Schmidtea mediterranea. A number of phenotypic studies have documented the role of histone modification and chromatin remodelling complexes in regulating distinct neoblast processes, and we focus on four important examples of planarian epigenetic regulators: Nucleosome Remodeling Deacetylase (NuRD) complex, Polycomb Repressive Complex (PRC), the SET1/MLL methyltransferases, and the nuclear PIWI/piRNA complex. Given the recent advent of ChIP-seq in planarians, we propose future avenues of research that will identify the genomic targets of these complexes allowing for a clearer picture of how neoblast processes are coordinated at the epigenetic level. These insights into neoblast biology may be directly relevant to mammalian stem cells and disease. The unique biology of planarians will also allow us to investigate how extracellular signals feed into epigenetic regulatory networks to govern concerted neoblast responses during regenerative polarity, tissue patterning, and remodelling.
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Affiliation(s)
- Anish Dattani
- Department of Zoology, South Parks Road, University of Oxford, OX1 3PS, UK.
| | - Divya Sridhar
- Department of Zoology, South Parks Road, University of Oxford, OX1 3PS, UK
| | - A Aziz Aboobaker
- Department of Zoology, South Parks Road, University of Oxford, OX1 3PS, UK.
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46
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Grudniewska M, Mouton S, Grelling M, Wolters AHG, Kuipers J, Giepmans BNG, Berezikov E. A novel flatworm-specific gene implicated in reproduction in Macrostomum lignano. Sci Rep 2018; 8:3192. [PMID: 29453392 PMCID: PMC5816591 DOI: 10.1038/s41598-018-21107-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/30/2018] [Indexed: 12/20/2022] Open
Abstract
Free-living flatworms, such as the planarian Schmidtea mediterranea, are extensively used as model organisms to study stem cells and regeneration. The majority of flatworm studies so far focused on broadly conserved genes. However, investigating what makes these animals different is equally informative for understanding its biology and might have biomedical value. We re-analyzed the neoblast and germline transcriptional signatures of the flatworm M. lignano using an improved transcriptome assembly and show that germline-enriched genes have a high fraction of flatworm-specific genes. We further identified the Mlig-sperm1 gene as a member of a novel gene family conserved only in free-living flatworms and essential for producing healthy spermatozoa. In addition, we established a whole-animal electron microscopy atlas (nanotomy) to visualize the ultrastructure of the testes in wild type worms, but also as a reference platform for different ultrastructural studies in M. lignano. This work demonstrates that investigation of flatworm-specific genes is crucial for understanding flatworm biology and establishes a basis for such future research in M. lignano.
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Affiliation(s)
- Magda Grudniewska
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
| | - Stijn Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
| | - Margriet Grelling
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
| | - Anouk H G Wolters
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
| | - Jeroen Kuipers
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands.
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