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Sumner JT, Andrasz CL, Johnson CA, Wax S, Anderson P, Keeling EL, Davidson JM. De novo genome assembly and comparative genomics for the colonial ascidian Botrylloides violaceus. G3 (BETHESDA, MD.) 2023; 13:jkad181. [PMID: 37555394 PMCID: PMC10542563 DOI: 10.1093/g3journal/jkad181] [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: 01/25/2023] [Revised: 01/25/2023] [Accepted: 07/12/2023] [Indexed: 08/10/2023]
Abstract
Ascidians have the potential to reveal fundamental biological insights related to coloniality, regeneration, immune function, and the evolution of these traits. This study implements a hybrid assembly technique to produce a genome assembly and annotation for the botryllid ascidian, Botrylloides violaceus. A hybrid genome assembly was produced using Illumina, Inc. short and Oxford Nanopore Technologies long-read sequencing technologies. The resulting assembly is comprised of 831 contigs, has a total length of 121 Mbp, N50 of 1 Mbp, and a BUSCO score of 96.1%. Genome annotation identified 13 K protein-coding genes. Comparative genomic analysis with other tunicates reveals patterns of conservation and divergence within orthologous gene families even among closely related species. Characterization of the Wnt gene family, encoding signaling ligands involved in development and regeneration, reveals conserved patterns of subfamily presence and gene copy number among botryllids. This supports the use of genomic data from nonmodel organisms in the investigation of biological phenomena.
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Affiliation(s)
- Jack T Sumner
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Cassidy L Andrasz
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Christine A Johnson
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Sarah Wax
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Paul Anderson
- Department of Computer Science and Software Engineering, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Elena L Keeling
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Jean M Davidson
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
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Tiozzo S, Schneider I. Editorial: Emerging research organisms in regenerative biology. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.1127607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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Ricci L, Salmon B, Olivier C, Andreoni-Pham R, Chaurasia A, Alié A, Tiozzo S. The Onset of Whole-Body Regeneration in Botryllus schlosseri: Morphological and Molecular Characterization. Front Cell Dev Biol 2022; 10:843775. [PMID: 35237607 PMCID: PMC8882763 DOI: 10.3389/fcell.2022.843775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 01/19/2022] [Indexed: 11/24/2022] Open
Abstract
Colonial tunicates are the only chordates that regularly regenerate a fully functional whole body as part of their asexual life cycle, starting from specific epithelia and/or mesenchymal cells. In addition, in some species, whole-body regeneration (WBR) can also be triggered by extensive injuries, which deplete most of their tissues and organs and leave behind only small fragments of their body. In this manuscript, we characterized the onset of WBR in Botryllus schlosseri, one colonial tunicate long used as a laboratory model. We first analyzed the transcriptomic response to a WBR-triggering injury. Then, through morphological characterization, in vivo observations via time-lapse, vital dyes, and cell transplant assays, we started to reconstruct the dynamics of the cells triggering regeneration, highlighting an interplay between mesenchymal and epithelial cells. The dynamics described here suggest that WBR in B. schlosseri is initiated by extravascular tissue fragments derived from the injured individuals rather than particular populations of blood-borne cells, as has been described in closely related species. The morphological and molecular datasets here reported provide the background for future mechanistic studies of the WBR ontogenesis in B. schlosseri and allow to compare it with other regenerative processes occurring in other tunicate species and possibly independently evolved.
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Affiliation(s)
- Lorenzo Ricci
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), CNRS, Sorbonne University, Paris, France
- Institute for Research on Cancer and Aging in Nice (IRCAN), CNRS, INSERM, Université Côte d’Azur, Nice, France
| | - Bastien Salmon
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), CNRS, Sorbonne University, Paris, France
| | - Caroline Olivier
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), CNRS, Sorbonne University, Paris, France
| | - Rita Andreoni-Pham
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), CNRS, Sorbonne University, Paris, France
- Institute for Research on Cancer and Aging in Nice (IRCAN), CNRS, INSERM, Université Côte d’Azur, Nice, France
| | - Ankita Chaurasia
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), CNRS, Sorbonne University, Paris, France
| | - Alexandre Alié
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), CNRS, Sorbonne University, Paris, France
| | - Stefano Tiozzo
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), CNRS, Sorbonne University, Paris, France
- *Correspondence: Stefano Tiozzo,
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