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Jenike AE, Jenike KM, Peterson KJ, Fromm B, Halushka MK. Direct observation of the evolution of cell-type-specific microRNA expression signatures supports the hematopoietic origin model of endothelial cells. Evol Dev 2023; 25:226-239. [PMID: 37157156 PMCID: PMC10302300 DOI: 10.1111/ede.12438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/22/2023] [Accepted: 04/26/2023] [Indexed: 05/10/2023]
Abstract
The evolution of specialized cell-types is a long-standing interest of biologists, but given the deep time-scales very difficult to reconstruct or observe. microRNAs have been linked to the evolution of cellular complexity and may inform on specialization. The endothelium is a vertebrate-specific specialization of the circulatory system that enabled a critical new level of vasoregulation. The evolutionary origin of these endothelial cells is unclear. We hypothesized that Mir-126, an endothelial cell-specific microRNA may be informative. We here reconstruct the evolutionary history of Mir-126. Mir-126 likely appeared in the last common ancestor of vertebrates and tunicates, which was a species without an endothelium, within an intron of the evolutionary much older EGF Like Domain Multiple (Egfl) locus. Mir-126 has a complex evolutionary history due to duplications and losses of both the host gene and the microRNA. Taking advantage of the strong evolutionary conservation of the microRNA among Olfactores, and using RNA in situ hybridization, we localized Mir-126 in the tunicate Ciona robusta. We found exclusive expression of the mature Mir-126 in granular amebocytes, supporting a long-proposed scenario that endothelial cells arose from hemoblasts, a type of proto-endothelial amoebocyte found throughout invertebrates. This observed change of expression of Mir-126 from proto-endothelial amoebocytes in the tunicate to endothelial cells in vertebrates is the first direct observation of the evolution of a cell-type in relation to microRNA expression indicating that microRNAs can be a prerequisite of cell-type evolution.
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Affiliation(s)
- Ana E. Jenike
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
| | - Katharine M. Jenike
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
| | - Kevin J. Peterson
- Department of Biological Sciences, Dartmouth College, Hanover NH, USA
| | - Bastian Fromm
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, 9006 Tromsø, Norway
| | - Marc K. Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
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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; 11:1377. [PMID: 34947908 PMCID: PMC8704543 DOI: 10.3390/life11121377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [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.)
| | - 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.)
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Evolution and Phylogeny of MicroRNAs - Protocols, Pitfalls, and Problems. Methods Mol Biol 2021. [PMID: 34432281 DOI: 10.1007/978-1-0716-1170-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
MicroRNAs are important regulators in many eukaryotic lineages. Typical miRNAs have a length of about 22nt and are processed from precursors that form a characteristic hairpin structure. Once they appear in a genome, miRNAs are among the best-conserved elements in both animal and plant genomes. Functionally, they play an important role in particular in development. In contrast to protein-coding genes, miRNAs frequently emerge de novo. The genomes of animals and plants harbor hundreds of mutually unrelated families of homologous miRNAs that tend to be persistent throughout evolution. The evolution of their genomic miRNA complement closely correlates with important morphological innovation. In addition, miRNAs have been used as valuable characters in phylogenetic studies. An accurate and comprehensive annotation of miRNAs is required as a basis to understand their impact on phenotypic evolution. Since experimental data on miRNA expression are limited to relatively few species and are subject to unavoidable ascertainment biases, it is inevitable to complement miRNA sequencing by homology based annotation methods. This chapter reviews the state of the art workflows for homology based miRNA annotation, with an emphasis on their limitations and open problems.
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Yang L, Zhang X, Liu C, Zhang J, Dong B. MiR-92 Family Members Form a Cluster Required for Notochord Tubulogenesis in Urochordate Ciona savignyi. Genes (Basel) 2021; 12:genes12030406. [PMID: 33809016 PMCID: PMC8001136 DOI: 10.3390/genes12030406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 11/28/2022] Open
Abstract
MicroRNAs are frequently clustered in the genome and polycistronically transcribed, regulating targeted genes in diverse signaling pathways. The miR-17-92 cluster is a typical miRNA cluster, playing crucial roles in the organogenesis and homeostasis of physiological processes in vertebrates. Here, we identified three miRNAs (csa-miR-92a, csa-miR-92b, and csa-miR-92c) that belonged to the miR-92 family and formed a miRNA cluster in the genome of a urochordate marine ascidian Ciona savignyi. Except for miR-92a and miR-92b, other homologs of the vertebrate miR-17-92 cluster members could not be identified in the Ciona genome. We further found that the mature sequences of urochordate miR-92 family members were highly conserved compared with the vertebrate species. The expression pattern revealed that three miR-92 family members had consistent expression levels in adult tissues and were predominantly expressed in heart and muscle tissue. We further showed that, at the embryonic and larval stages, csa-miR-92c was expressed in the notochord of embryos during 18–31 h post fertilization (hpf) by in situ hybridization. Knockout of csa-miR-92c resulted in the disorganization of notochord cells and the block of lumen coalescence in the notochord. Fibroblast growth factor (FGF), mitogen-activated protein kinase (MAPK), and wingless/integrated (Wnt)/planar cell polarity (PCP) signaling pathways might be involved in the regulatory processes, since a large number of core genes of these pathways were the predicted target genes of the miR-92 family. Taken together, we identified a miR-92 cluster in urochordate Ciona and revealed the expression patterns and the regulatory roles of its members in organogenesis. Our results provide expression and phylogenetic data on the understanding of the miR-92 miRNA cluster’s function during evolution.
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Affiliation(s)
- Libo Yang
- Sars-Fang Centre, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (L.Y.); (X.Z.); (J.Z.)
| | - Xiaoming Zhang
- Sars-Fang Centre, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (L.Y.); (X.Z.); (J.Z.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Chengzhang Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
| | - 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; (L.Y.); (X.Z.); (J.Z.)
| | - 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; (L.Y.); (X.Z.); (J.Z.)
- 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
- Correspondence: ; Tel.: +86-532-82032732
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Dexheimer PJ, Cochella L. MicroRNAs: From Mechanism to Organism. Front Cell Dev Biol 2020; 8:409. [PMID: 32582699 PMCID: PMC7283388 DOI: 10.3389/fcell.2020.00409] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are short, regulatory RNAs that act as post-transcriptional repressors of gene expression in diverse biological contexts. The emergence of small RNA-mediated gene silencing preceded the onset of multicellularity and was followed by a drastic expansion of the miRNA repertoire in conjunction with the evolution of complexity in the plant and animal kingdoms. Along this process, miRNAs became an essential feature of animal development, as no higher metazoan lineage tolerated loss of miRNAs or their associated protein machinery. In fact, ablation of the miRNA biogenesis machinery or the effector silencing factors results in severe embryogenesis defects in every animal studied. In this review, we summarize recent mechanistic insight into miRNA biogenesis and function, while emphasizing features that have enabled multicellular organisms to harness the potential of this broad class of repressors. We first discuss how different mechanisms of regulation of miRNA biogenesis are used, not only to generate spatio-temporal specificity of miRNA production within an animal, but also to achieve the necessary levels and dynamics of expression. We then explore how evolution of the mechanism for small RNA-mediated repression resulted in a diversity of silencing complexes that cause different molecular effects on their targets. Multicellular organisms have taken advantage of this variability in the outcome of miRNA-mediated repression, with differential use in particular cell types or even distinct subcellular compartments. Finally, we present an overview of how the animal miRNA repertoire has evolved and diversified, emphasizing the emergence of miRNA families and the biological implications of miRNA sequence diversification. Overall, focusing on selected animal models and through the lens of evolution, we highlight canonical mechanisms in miRNA biology and their variations, providing updated insight that will ultimately help us understand the contribution of miRNAs to the development and physiology of multicellular organisms.
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Affiliation(s)
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
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Ferrández-Roldán A, Martí-Solans J, Cañestro C, Albalat R. Oikopleura dioica: An Emergent Chordate Model to Study the Impact of Gene Loss on the Evolution of the Mechanisms of Development. Results Probl Cell Differ 2019; 68:63-105. [PMID: 31598853 DOI: 10.1007/978-3-030-23459-1_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The urochordate Oikopleura dioica is emerging as a nonclassical animal model in the field of evolutionary developmental biology (a.k.a. evo-devo) especially attractive for investigating the impact of gene loss on the evolution of mechanisms of development. This is because this organism fulfills the requirements of an animal model (i.e., has a simple and accessible morphology, a short generation time and life span, and affordable culture in the laboratory and amenable experimental manipulation), but also because O. dioica occupies a key phylogenetic position to understand the diversification and origin of our own phylum, the chordates. During its evolution, O. dioica genome has suffered a drastic process of compaction, becoming the smallest known chordate genome, a process that has been accompanied by exacerbating amount of gene losses. Interestingly, however, despite the extensive gene losses, including entire regulatory pathways essential for the embryonic development of other chordates, O. dioica retains the typical chordate body plan. This unexpected situation led to the formulation of the so-called inverse paradox of evo-devo, that is, when a genetic diversity is able to maintain a phenotypic unity. This chapter reviews the biological features of O. dioica as a model animal, along with the current data on the evolution of its genes and genome. We pay special attention to the numerous examples of gene losses that have taken place during the evolution of this unique animal model, which is helping us to understand to which the limits of evo-devo can be pushed off.
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Affiliation(s)
- Alfonso Ferrández-Roldán
- Facultat de Biologia, Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Josep Martí-Solans
- Facultat de Biologia, Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Cristian Cañestro
- Facultat de Biologia, Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Ricard Albalat
- Facultat de Biologia, Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain.
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Zhang X, Liu X, Liu C, Wei J, Yu H, Dong B. Identification and characterization of microRNAs involved in ascidian larval metamorphosis. BMC Genomics 2018; 19:168. [PMID: 29490613 PMCID: PMC5831862 DOI: 10.1186/s12864-018-4566-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 02/22/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Metamorphosis takes place within the life cycle of most marine invertebrates. The marine ascidian is a classical model to study complex cellular processes and underlying molecular mechanisms involved in its larval metamorphosis. The detailed molecular signaling pathways remain elusive, though extracellular signal-regulated kinases (ERKs) and c-Jun N-terminal kinase (JNK) have been revealed to regulate cell migration, differentiation, and apoptosis in ascidian larval organ regression and juvenile organ development. MicroRNAs (miRNAs) are small non-coding RNAs that modulate gene expression at the post-transcriptional level. Large numbers of miRNAs have been demonstrated to be involved in many developmental and metamorphic processes. However, the identification of miRNAs in ascidian larval metamorphosis has not yet been investigated. RESULTS Totally, 106 known and 59 novel miRNAs were screened out through RNA-sequencing of three small RNA libraries from 18 to 21-h post-fertilization (hpf) tailbud embryos as well as from 42 hpf larvae (after tail regression) in Ciona savignyi. Expression profiling of miRNAs was confirmed by quantitative real-time PCR, showing that the expression levels of csa-miR-4040, csa-miR-4086, csa-miR-4055, csa-miR-4060, csa-miR-216a, csa-miR-216b, csa-miR-217, csa-miR-183, and csa-miR-92c were significantly higher in 42 hpf larvae, whereas those of csa-miR-4018a, csa-miR-4018b, and csa-miR-4000f were higher in 18 and 21 hpf embryos; then, their expression in 42 hpf larvae became significantly low. For these 12 miRNAs, whose expression levels significantly changed, we predicted their target genes through the combination of miRanda and TargetScan. This prediction analysis revealed 332 miRNA-target gene pairs that were associated with the ERK, JNK, and transforming growth factor beta signaling pathways, suggesting that the identified miRNAs are involved in the regulation of C. savignyi larval metamorphosis via controlling the expression of their target genes. Furthermore, we validated the expression of five selected miRNAs by northern blotting. Among the selected miRNAs, the expression patterns of csa-miR-4018a, csa-miR-4018b, and csa-miR-4000f were further examined by whole-mount in situ hybridization. The results showed that all three miRNAs were specifically expressed in a cell population resembling mesenchymal cells at the head and trunk part in swimming larvae but not in metamorphic larvae. Utilizing the luciferase assay, we also confirmed that miR-4000f targeted Mapk1, suggesting that the csa-miR-4018a/csa-miR-4018b/csa-miR-4000f cluster regulates larval metamorphosis through the Mapk1-mediated signaling pathway. CONCLUSIONS Totally, 165 miRNAs, including 59 novel ones, were identified from the embryos and larvae of C. savignyi. Twelve of them showed significant changes in expression before and during metamorphosis. In situ hybridization and northern blotting results revealed that three miRNAs are potentially involved in the signaling regulatory network for the migration and differentiation of mesenchymal cells in larval metamorphosis. Furthermore, the luciferase reporter assay revealed that Mapk1 is a target of csa-miR-4000f. Our results not only present a list and profile of miRNAs involved in Ciona metamorphosis but also provide informative cues to further understand their function in ascidian larval metamorphosis.
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Affiliation(s)
- Xiaoming Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Xiaozhuo Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Chengzhang Liu
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 China
| | - Jiankai Wei
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Haiyan Yu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Bo Dong
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- 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, No. 5 Yushan Road, Qingdao, 266003 People’s Republic of China
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Velandia-Huerto CA, Brown FD, Gittenberger A, Stadler PF, Bermúdez-Santana CI. Nonprotein-Coding RNAs as Regulators of Development in Tunicates. Results Probl Cell Differ 2018; 65:197-225. [PMID: 30083922 DOI: 10.1007/978-3-319-92486-1_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tunicates, or urochordates, are a group of small marine organisms that are found widely throughout the seas of the world. As most plausible sister group of the vertebrates, they are of utmost importance for a comprehensive understanding of chordate evolution; hence, they have served as model organisms for many aspects of the developmental biology. Current genomic analysis of tunicates indicates that their genomes evolved with a fast rate not only at the level of nucleotide substitutions but also in terms of genomic organization. The latter involves genome reduction, rearrangements, as well as the loss of some important coding and noncoding RNA (ncRNAs) elements and even entire genomic regions that are otherwise well conserved. These observations are largely based on evidence from comparative genomics resulting from the analysis of well-studied gene families such as the Hox genes and their noncoding elements. In this chapter, the focus lies on the ncRNA complement of tunicates, with a particular emphasis on microRNAs, which have already been studied extensively for other animal clades. MicroRNAs are known as important regulators of key genes in animal development, and they are intimately related to the increase morphological complexity in higher metazoans. Here we review the discovery, evolution, and genome organization of the miRNA repertoire, which has been drastically reduced and restructured in tunicates compared to the chordate ancestor. Known functions of microRNAs as regulators of development in tunicates are a central topic. For instance, we consider the role of miRNAs as regulators of the muscle development and their importance in the regulation of the differential expression during the oral siphon regeneration. Beyond microRNAs, we touch upon the functions of some other ncRNAs such as yellow crescent RNA, moRNAs, RMST lncRNAs, or spliced-leader (SL) RNAs, which have diverse functions associated with the embryonic development, neurogenesis, and mediation of mRNA stability in general.
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Affiliation(s)
- Cristian A Velandia-Huerto
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany.
- Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia.
| | - Federico D Brown
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratorio de Biología del Desarrollo Evolutiva, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - Adriaan Gittenberger
- Institute of Biology, Leiden University, Leiden, Netherlands
- GiMaRIS, BioScience Park Leiden, Leiden, Netherlands
- Naturalis Biodiversity Center, Leiden, Netherlands
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany
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