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Anselmi C, Fuller GK, Stolfi A, Groves AK, Manni L. Sensory cells in tunicates: insights into mechanoreceptor evolution. Front Cell Dev Biol 2024; 12:1359207. [PMID: 38550380 PMCID: PMC10973136 DOI: 10.3389/fcell.2024.1359207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Tunicates, the sister group of vertebrates, offer a unique perspective for evolutionary developmental studies (Evo-Devo) due to their simple anatomical organization. Moreover, the separation of tunicates from vertebrates predated the vertebrate-specific genome duplications. As adults, they include both sessile and pelagic species, with very limited mobility requirements related mainly to water filtration. In sessile species, larvae exhibit simple swimming behaviors that are required for the selection of a suitable substrate on which to metamorphose. Despite their apparent simplicity, tunicates display a variety of mechanoreceptor structures involving both primary and secondary sensory cells (i.e., coronal sensory cells). This review encapsulates two decades of research on tunicate mechanoreception focusing on the coronal organ's sensory cells as prime candidates for understanding the evolution of vertebrate hair cells of the inner ear and the lateral line organ. The review spans anatomical, cellular and molecular levels emphasizing both similarity and differences between tunicate and vertebrate mechanoreception strategies. The evolutionary significance of mechanoreception is discussed within the broader context of Evo-Devo studies, shedding light on the intricate pathways that have shaped the sensory system in chordates.
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Affiliation(s)
- Chiara Anselmi
- Hopkins Marine Station, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Pacific Grove, CA, United States
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, United States
| | - Gwynna K. Fuller
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Andrew K. Groves
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Lucia Manni
- Dipartimento di Biologia, Università degli Studi di Padova, Padova, Italy
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2
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Daric V, Lanoizelet M, Mayeur H, Leblond C, Darras S. Genomic Resources and Annotations for a Colonial Ascidian, the Light-Bulb Sea Squirt Clavelina lepadiformis. Genome Biol Evol 2024; 16:evae038. [PMID: 38441487 PMCID: PMC10950049 DOI: 10.1093/gbe/evae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
Ascidian embryos have been studied since the birth of experimental embryology at the end of the 19th century. They represent textbook examples of mosaic development characterized by a fast development with very few cells and invariant cleavage patterns and lineages. Ascidians belong to tunicates, the vertebrate sister group, and their study is essential to shed light on the emergence of vertebrates. Importantly, deciphering developmental gene regulatory networks has been carried out mostly in two of the three ascidian orders, Phlebobranchia and Stolidobranchia. To infer ancestral developmental programs in ascidians, it is thus essential to carry out molecular embryology in the third ascidian order, the Aplousobranchia. Here, we present genomic resources for the colonial aplousobranch Clavelina lepadiformis: a transcriptome produced from various embryonic stages, and an annotated genome. The assembly consists of 184 contigs making a total of 233.6 Mb with a N50 of 8.5 Mb and a L50 of 11. The 32,318 predicted genes capture 96.3% of BUSCO orthologs. We further show that these resources are suitable to study developmental gene expression and regulation in a comparative framework within ascidians. Additionally, they will prove valuable for evolutionary and ecological studies.
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Affiliation(s)
- Vladimir Daric
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), F-66650 Banyuls/Mer, France
| | - Maxence Lanoizelet
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), F-66650 Banyuls/Mer, France
| | - Hélène Mayeur
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), F-66650 Banyuls/Mer, France
| | - Cécile Leblond
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), F-66650 Banyuls/Mer, France
| | - Sébastien Darras
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), F-66650 Banyuls/Mer, France
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3
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Johnson CJ, Razy-Krajka F, Zeng F, Piekarz KM, Biliya S, Rothbächer U, Stolfi A. Specification of distinct cell types in a sensory-adhesive organ important for metamorphosis in tunicate larvae. PLoS Biol 2024; 22:e3002555. [PMID: 38478577 PMCID: PMC10962819 DOI: 10.1371/journal.pbio.3002555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 03/25/2024] [Accepted: 02/21/2024] [Indexed: 03/22/2024] Open
Abstract
The papillae of tunicate larvae contribute sensory, adhesive, and metamorphosis-regulating functions that are crucial for the biphasic lifestyle of these marine, non-vertebrate chordates. We have identified additional molecular markers for at least 5 distinct cell types in the papillae of the model tunicate Ciona, allowing us to further study the development of these organs. Using tissue-specific CRISPR/Cas9-mediated mutagenesis and other molecular perturbations, we reveal the roles of key transcription factors and signaling pathways that are important for patterning the papilla territory into a highly organized array of different cell types and shapes. We further test the contributions of different transcription factors and cell types to the production of the adhesive glue that allows for larval attachment during settlement, and to the processes of tail retraction and body rotation during metamorphosis. With this study, we continue working towards connecting gene regulation to cellular functions that control the developmental transition between the motile larva and sessile adult of Ciona.
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Affiliation(s)
- Christopher J Johnson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Florian Razy-Krajka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Fan Zeng
- Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Katarzyna M Piekarz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Shweta Biliya
- Molecular Evolution Core, Petit H. Parker Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Ute Rothbächer
- Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
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4
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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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5
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Nanglu K, Lerosey-Aubril R, Weaver JC, Ortega-Hernández J. A mid-Cambrian tunicate and the deep origin of the ascidiacean body plan. Nat Commun 2023; 14:3832. [PMID: 37414759 PMCID: PMC10325964 DOI: 10.1038/s41467-023-39012-4] [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: 09/06/2022] [Accepted: 05/25/2023] [Indexed: 07/08/2023] Open
Abstract
Tunicates are an evolutionarily significant subphylum of marine chordates, with their phylogenetic position as the sister-group to Vertebrata making them key to unraveling our own deep time origin. Tunicates greatly vary with regards to morphology, ecology, and life cycle, but little is known about the early evolution of the group, e.g. whether their last common ancestor lived freely in the water column or attached to the seafloor. Additionally, tunicates have a poor fossil record, which includes only one taxon with preserved soft-tissues. Here we describe Megasiphon thylakos nov., a 500-million-year-old tunicate from the Marjum Formation of Utah, which features a barrel-shaped body with two long siphons and prominent longitudinal muscles. The ascidiacean-like body of this new species suggests two alternative hypotheses for early tunicate evolution. The most likely scenario posits M. thylakos belongs to stem-group Tunicata, suggesting that a biphasic life cycle, with a planktonic larva and a sessile epibenthic adult, is ancestral for this entire subphylum. Alternatively, a position within the crown-group indicates that the divergence between appendicularians and all other tunicates occurred 50 million years earlier than currently estimated based on molecular clocks. Ultimately, M. thylakos demonstrates that fundamental components of the modern tunicate body plan were already established shortly after the Cambrian Explosion.
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Affiliation(s)
- Karma Nanglu
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Rudy Lerosey-Aubril
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - James C Weaver
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, 02138, USA
| | - Javier Ortega-Hernández
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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Smith G, Manzano-Marín A, Reyes-Prieto M, Antunes CSR, Ashworth V, Goselle ON, Jan AAA, Moya A, Latorre A, Perotti MA, Braig HR. Human follicular mites: Ectoparasites becoming symbionts. Mol Biol Evol 2022; 39:msac125. [PMID: 35724423 PMCID: PMC9218549 DOI: 10.1093/molbev/msac125] [Citation(s) in RCA: 2] [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: 10/11/2021] [Revised: 05/23/2022] [Accepted: 05/31/2022] [Indexed: 12/13/2022] Open
Abstract
Most humans carry mites in the hair follicles of their skin for their entire lives. Follicular mites are the only metazoans tha continuously live on humans. We propose that Demodex folliculorum (Acari) represents a transitional stage from a host-injuring obligate parasite to an obligate symbiont. Here, we describe the profound impact of this transition on the genome and physiology of the mite. Genome sequencing revealed that the permanent host association of D. folliculorum led to an extensive genome reduction through relaxed selection and genetic drift, resulting in the smallest number of protein-coding genes yet identified among panarthropods. Confocal microscopy revealed that this gene loss coincided with an extreme reduction in the number of cells. Single uninucleate muscle cells are sufficient to operate each of the three segments that form each walking leg. While it has been assumed that the reduction of the cell number in parasites starts early in development, we identified a greater total number of cells in the last developmental stage (nymph) than in the terminal adult stage, suggesting that reduction starts at the adult or ultimate stage of development. This is the first evolutionary step in an arthropod species adopting a reductive, parasitic or endosymbiotic lifestyle. Somatic nuclei show underreplication at the diploid stage. Novel eye structures or photoreceptors as well as a unique human host melatonin-guided day/night rhythm are proposed for the first time. The loss of DNA repair genes coupled with extreme endogamy might have set this mite species on an evolutionary dead-end trajectory.
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Affiliation(s)
- Gilbert Smith
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
| | - Alejandro Manzano-Marín
- Centre for Microbiology and Environmental Systems Science (CMESS), University of Vienna, Vienna, Austria
| | - Mariana Reyes-Prieto
- Institute of Integrative Systems Biology (I2Sysbio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Foundation for the Promotion of Health and Biomedical Research of the Valencian Community (FISABIO), València, Spain
| | | | - Victoria Ashworth
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
| | - Obed Nanjul Goselle
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
| | | | - Andrés Moya
- Institute of Integrative Systems Biology (I2Sysbio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Foundation for the Promotion of Health and Biomedical Research of the Valencian Community (FISABIO), València, Spain
- Center for Networked Biomedical Research in Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - Amparo Latorre
- Institute of Integrative Systems Biology (I2Sysbio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Foundation for the Promotion of Health and Biomedical Research of the Valencian Community (FISABIO), València, Spain
- Center for Networked Biomedical Research in Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - M Alejandra Perotti
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Henk R Braig
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
- Institute and Museum of Natural Sciences, National University of San Juan, San Juan, Argentina
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7
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Morphological Study and 3D Reconstruction of the Larva of the Ascidian Halocynthia roretzi. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2021. [DOI: 10.3390/jmse10010011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The swimming larva represents the dispersal phase of ascidians, marine invertebrates belonging to tunicates. Due to its adhesive papillae, the larva searches the substrate, adheres to it, and undergoes metamorphosis, thereby becoming a sessile filter feeding animal. The larva anatomy has been described in detail in a few species, revealing a different degree of adult structure differentiation, called adultation. In the solitary ascidian Halocynthia roretzi, a species reared for commercial purposes, embryogenesis has been described in detail, but information on the larval anatomy is still lacking. Here, we describe it using a comparative approach, utilizing 3D reconstruction, as well as histological/TEM observations, with attention to its papillae. The larva is comparable to those of other solitary ascidians, such as Ciona intestinalis. However, it displays a higher level of adultation for the presence of the atrium, opened outside by means of the atrial siphon, and the peribranchial chambers. It does not reach the level of complexity of the larva of Botryllus schlosseri, a phylogenetically close colonial ascidian. Our study reveals that the papillae of H. roretzi, previously described as simple and conform, exhibit dynamic changes during settlement. This opens up new considerations on papillae morphology and evolution and deserves to be further investigated.
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Parra-Rincón E, Velandia-Huerto CA, Gittenberger A, Fallmann J, Gatter T, Brown FD, Stadler PF, Bermúdez-Santana CI. The Genome of the "Sea Vomit" Didemnum vexillum. Life (Basel) 2021; 11:life11121377. [PMID: 34947908 PMCID: PMC8704543 DOI: 10.3390/life11121377] [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: 09/03/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 11/25/2022] Open
Abstract
Tunicates are the sister group of vertebrates and thus occupy a key position for investigations into vertebrate innovations as well as into the consequences of the vertebrate-specific genome duplications. Nevertheless, tunicate genomes have not been studied extensively in the past, and comparative studies of tunicate genomes have remained scarce. The carpet sea squirt Didemnum vexillum, commonly known as “sea vomit”, is a colonial tunicate considered an invasive species with substantial ecological and economical risk. We report the assembly of the D. vexillum genome using a hybrid approach that combines 28.5 Gb Illumina and 12.35 Gb of PacBio data. The new hybrid scaffolded assembly has a total size of 517.55 Mb that increases contig length about eightfold compared to previous, Illumina-only assembly. As a consequence of an unusually high genetic diversity of the colonies and the moderate length of the PacBio reads, presumably caused by the unusually acidic milieu of the tunic, the assembly is highly fragmented (L50 = 25,284, N50 = 6539). It is sufficient, however, for comprehensive annotations of both protein-coding genes and non-coding RNAs. Despite its shortcomings, the draft assembly of the “sea vomit” genome provides a valuable resource for comparative tunicate genomics and for the study of the specific properties of colonial ascidians.
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Affiliation(s)
- Ernesto Parra-Rincón
- Biology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C 111321, Colombia; (E.P.-R.); (P.F.S.)
| | - Cristian A. Velandia-Huerto
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany; (J.F.); (T.G.)
- Correspondence: (C.A.V.-H.); (C.I.B.-S.)
| | - Adriaan Gittenberger
- GiMaRIS, Rijksstraatweg 75, 2171 AK Sassenheim, The Netherlands;
- Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany; (J.F.); (T.G.)
| | - Thomas Gatter
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany; (J.F.); (T.G.)
| | - Federico D. Brown
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, Rua do Matão, Tr. 14 no. 101, São Paulo 05508-090, Brazil;
- Centro de Biologia Marinha, Universidade de São Paulo, Rod. Manuel Hypólito do Rego km. 131.5, São Sebastião 11612-109, Brazil
| | - Peter F. Stadler
- Biology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C 111321, Colombia; (E.P.-R.); (P.F.S.)
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany; (J.F.); (T.G.)
- Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria
- Santa Fe Institute, Santa Fe, NM 87506, USA
| | - Clara I. Bermúdez-Santana
- Biology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C 111321, Colombia; (E.P.-R.); (P.F.S.)
- Correspondence: (C.A.V.-H.); (C.I.B.-S.)
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9
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Fodor ACA, Powers MM, Andrykovich K, Liu J, Lowe EK, Brown CT, Di Gregorio A, Stolfi A, Swalla BJ. The Degenerate Tale of Ascidian Tails. Integr Comp Biol 2021; 61:358-369. [PMID: 33881514 PMCID: PMC10452958 DOI: 10.1093/icb/icab022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Ascidians are invertebrate chordates, with swimming chordate tadpole larvae that have distinct heads and tails. The head contains the small brain, sensory organs, including the ocellus (light) and otolith (gravity) and the presumptive endoderm, while the tail has a notochord surrounded by muscle cells and a dorsal nerve cord. One of the chordate features is a post-anal tail. Ascidian tadpoles are nonfeeding, and their tails are critical for larval locomotion. After hatching the larvae swim up toward light and are carried by the tide and ocean currents. When competent to settle, ascidian tadpole larvae swim down, away from light, to settle and metamorphose into a sessile adult. Tunicates are classified as chordates because of their chordate tadpole larvae; in contrast, the sessile adult has a U-shaped gut and very derived body plan, looking nothing like a chordate. There is one group of ascidians, the Molgulidae, where many species are known to have tailless larvae. The Swalla Lab has been studying the evolution of tailless ascidian larvae in this clade for over 30 years and has shown that tailless larvae have evolved independently several times in this clade. Comparison of the genomes of two closely related species, the tailed Molgula oculata and tailless Molgula occulta reveals much synteny, but there have been multiple insertions and deletions that have disrupted larval genes in the tailless species. Genomics and transcriptomics have previously shown that there are pseudogenes expressed in the tailless embryos, suggesting that the partial rescue of tailed features in their hybrid larvae is due to the expression of intact genes from the tailed parent. Yet surprisingly, we find that the notochord gene regulatory network is mostly intact in the tailless M. occulta, although the notochord does not converge and extend and remains as an aggregate of cells we call the "notoball." We expect that eventually many of the larval gene networks will become evolutionarily lost in tailless ascidians and the larval body plan abandoned, with eggs developing directly into an adult. Here we review the current evolutionary and developmental evidence on how the molgulids lost their tails.
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Affiliation(s)
- Alexander C A Fodor
- Biology Department, University of Washington, Seattle, WA 98195, USA
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA 98250, USA
| | - Megan M Powers
- Biology Department, University of Washington, Seattle, WA 98195, USA
| | - Kristin Andrykovich
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA 98250, USA
| | - Jiatai Liu
- Biology Department, University of Washington, Seattle, WA 98195, USA
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA 98250, USA
| | - Elijah K Lowe
- Biology Department, University of Washington, Seattle, WA 98195, USA
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA 98250, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Station Biologique de Roscoff, 29680 Roscoff, France
| | - C Titus Brown
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA 98250, USA
- Station Biologique de Roscoff, 29680 Roscoff, France
- Population Health and Reproduction, UC Davis School of Veterinary Medicine, Davis, CA 95616, USA
| | - Anna Di Gregorio
- Department of Molecular Pathobiology, NYU College of Dentistry, New York, NY 10010, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Station Biologique de Roscoff, 29680 Roscoff, France
| | - Billie J Swalla
- Biology Department, University of Washington, Seattle, WA 98195, USA
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA 98250, USA
- Station Biologique de Roscoff, 29680 Roscoff, France
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10
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Zhang J, Wei J, Yu H, Dong B. Genome-Wide Identification, Comparison, and Expression Analysis of Transcription Factors in Ascidian Styela clava. Int J Mol Sci 2021; 22:4317. [PMID: 33919240 PMCID: PMC8122590 DOI: 10.3390/ijms22094317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/09/2021] [Accepted: 04/06/2021] [Indexed: 11/29/2022] Open
Abstract
Tunicates include diverse species, as they are model animals for evolutionary developmental biology study. The embryonic development of tunicates is known to be extensively regulated by transcription factors (TFs). Styela clava, the globally distributed invasive tunicate, exhibits a strong capacity for environmental adaptation. However, the TFs were not systematically identified and analyzed. In this study, we reported 553 TFs categorized into 60 families from S. clava, based on the whole genome data. Comparison of TFs analysis among the tunicate species revealed that the gene number in the zinc finger superfamily displayed the most significant discrepancy, indicating this family was under the highly evolutionary selection and might be related to species differentiation and environmental adaptation. The greatest number of TFs was discovered in the Cys2His2-type zinc finger protein (zf-C2H2) family in S. clava. From the point of temporal view, more than half the TFs were expressed at the early embryonic stage. The expression correlation analysis revealed the existence of a transition for TFs expression from early embryogenesis to the later larval development in S. clava. Eight Hox genes were identified to be located on one chromosome, exhibiting different arrangement and expression patterns, compared to Ciona robusta (C. intestinalis type A). In addition, a total of 23 forkhead box (fox) genes were identified in S. clava, and their expression profiles referred to their potential roles in neurodevelopment and sensory organ development. Our data, thus, provides crucial clues to the potential functions of TFs in development and environmental adaptation in the leathery sea squirt.
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Affiliation(s)
- Jin Zhang
- Sars-Fang Centre, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (J.Z.); (J.W.)
| | - Jiankai Wei
- Sars-Fang Centre, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (J.Z.); (J.W.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Haiyan Yu
- Sars-Fang Centre, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (J.Z.); (J.W.)
| | - Bo Dong
- Sars-Fang Centre, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (J.Z.); (J.W.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
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Medina-Feliciano JG, Pirro S, García-Arrarás JE, Mashanov V, Ryan JF. Draft Genome of the Sea Cucumber Holothuria glaberrima, a Model for the Study of Regeneration. FRONTIERS IN MARINE SCIENCE 2021; 8:603410. [PMID: 38741925 PMCID: PMC11090492 DOI: 10.3389/fmars.2021.603410] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Regeneration is one of the most fascinating and yet least understood biological processes. Echinoderms, one of the closest related invertebrate groups to humans, can contribute to our understanding of the genetic basis of regenerative processes. Among echinoderms, sea cucumbers have the ability to grow back most of their body parts following injury, including the intestine and nervous tissue. The cellular and molecular events underlying these abilities in sea cucumbers have been most extensively studied in the species Holothuria glaberrima. However, research into the regenerative abilities of this species has been impeded due to the lack of adequate genomic resources. Here, we report the first draft genome assembly of H. glaberrima and demonstrate its value for future genetic studies. Using only short sequencing reads, we assembled the genome into 89,105 scaffolds totaling 1.1 gigabases with an N50 of 25 kilobases. Our BUSCO assessment of the genome resulted in 894 (91.4%) complete and partial genes from 978 genes queried. We incorporated transcriptomic data from several different life history stages to annotate 51,415 genes in our final assembly. To demonstrate the usefulness of the genome, we fully annotated the melanotransferrin (Mtf) gene family, which have a potential role in the regeneration of the sea cucumber intestine. Using these same data, we extracted the mitochondrial genome, which showed high conservation to that of other holothuroids. Thus, these data will be a critical resource for ongoing studies of regeneration and other studies in sea cucumbers.
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Affiliation(s)
| | - Stacy Pirro
- Iridian Genomes, Inc., Bethesda, MD, United States
| | - Jose E. García-Arrarás
- Biology Department, University of Puerto Rico, Río Piedras Campus, San Juan, PR, United States
| | - Vladimir Mashanov
- Wake Forest Institute for Regenerative Medicine, Winston Salem, NC, United States
| | - Joseph F. Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, United States
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