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Oonuma K, Kusakabe TG. The complete cell lineage and MAPK- and Otx-dependent specification of the dopaminergic cells in the Ciona brain. Development 2021; 148:269114. [PMID: 34121117 DOI: 10.1242/dev.198754] [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: 11/17/2020] [Accepted: 05/17/2021] [Indexed: 11/20/2022]
Abstract
The Ciona larva has served as a unique model for understanding the development of dopaminergic cells at single-cell resolution owing to the exceptionally small number of neurons in its brain and its fixed cell lineage during embryogenesis. A recent study suggested that the transcription factors Fer2 and Meis directly regulate the dopamine synthesis genes in Ciona, but the dopaminergic cell lineage and the gene regulatory networks that control the development of dopaminergic cells have not been fully elucidated. Here, we reveal that the dopaminergic cells in Ciona are derived from a bilateral pair of cells called a9.37 cells at the center of the neural plate. The a9.37 cells divide along the anterior-posterior axis, and all of the descendants of the posterior daughter cells differentiate into the dopaminergic cells. We show that the MAPK pathway and the transcription factor Otx are required for the expression of Fer2 in the dopaminergic cell lineage. Our findings establish the cellular and molecular framework for fully understanding the commitment to dopaminergic cells in the simple chordate brain.
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Affiliation(s)
- Kouhei Oonuma
- Institute for Integrative Neurobiology and Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan
| | - Takehiro G Kusakabe
- Institute for Integrative Neurobiology and Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan
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He X, Wu F, Zhang L, Li L, Zhang G. Comparative and evolutionary analyses reveal conservation and divergence of the notch pathway in lophotrochozoa. Sci Rep 2021; 11:11378. [PMID: 34059772 PMCID: PMC8166818 DOI: 10.1038/s41598-021-90800-8] [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] [Received: 01/19/2021] [Accepted: 05/17/2021] [Indexed: 01/03/2023] Open
Abstract
Lophotrochozoan species exhibit wide morphological diversity; however, the molecular basis underlying this diversity remains unclear. Here, we explored the evolution of Notch pathway genes across 37 metazoan species via phylogenetic and molecular evolutionary studies with emphasis on the lophotrochozoans. We displayed the components of Notch pathway in metazoans and found that Delta and Hes/Hey-related genes, as well as their functional domains, are duplicated in lophotrochozoans. Comparative transcriptomics analyses allow us to pinpoint sequence divergence of multigene families in the Notch signalling pathway. We identified the duplication mechanism of a mollusc-specific gene, Delta2, and found it displayed complementary expression throughout development. Furthermore, we found the functional diversification not only in expanded genes in the Notch pathway (Delta and Hes/Hey-related genes), but also in evolutionary conservative genes (Notch, Presenilin, and Su(H)). Together, this comprehensive study demonstrates conservation and divergence within the Notch pathway, reveals evolutionary relationships among metazoans, and provides evidence for the occurrence of developmental diversity in lophotrochozoans, as well as a basis for future gene function studies.
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Affiliation(s)
- Xin He
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fucun Wu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China.
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Linlin Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China.
| | - Li Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
| | - Guofan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
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Genome-wide identification and characterization of basic helix-loop-helix genes in nine molluscs. Gene 2021; 785:145604. [PMID: 33766707 DOI: 10.1016/j.gene.2021.145604] [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: 09/05/2020] [Revised: 03/03/2021] [Accepted: 03/17/2021] [Indexed: 11/23/2022]
Abstract
The basic helix-loop-helix (bHLH) transcription factors form a large superfamily that plays an important role in numerous physiological processes, including development and response to environmental stresses. In this study, the distribution of bHLH genes in nine molluscs was systematically investigated (including five bivalves, three gastropods and one cephalopod). Finally, 53-85 bHLH genes were identified from each genome and classified into corresponding families by using phylogenetic analysis. The results of gene structure and conserved motif analysis illustrated the hereditary conservation of bHLH transcription factors during evolution but showed low similarity in group C. Through transcription profile analysis of C. gigas and T. granosa, we found a important role of bHLH genes in responding to multiple external challenges and development; meanwhile, they also exhibited tissue-specific expression. Interestingly, we were also surprised to find different bHLH genes from the same group generally possess similar patterns expression that tends to simultaneously present high or lower expression of multiple challenges and different tissues in this study. In summary, this study lays the foundation for further investigation of the biological functions and evolution of molluscan bHLH genes.
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Cellular identity and Ca 2+ signaling activity of the non-reproductive GnRH system in the Ciona intestinalis type A (Ciona robusta) larva. Sci Rep 2020; 10:18590. [PMID: 33122709 PMCID: PMC7596717 DOI: 10.1038/s41598-020-75344-7] [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: 02/19/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022] Open
Abstract
Tunicate larvae have a non-reproductive gonadotropin-releasing hormone (GnRH) system with multiple ligands and receptor heterodimerization enabling complex regulation. In Ciona intestinalis type A larvae, one of the gnrh genes, gnrh2, is conspicuously expressed in the motor ganglion and nerve cord, which are homologous structures to the hindbrain and spinal cord, respectively, of vertebrates. The gnrh2 gene is also expressed in the proto-placodal sensory neurons, which are the proposed homologue of vertebrate olfactory neurons. Tunicate larvae occupy a non-reproductive dispersal stage, yet the role of their GnRH system remains elusive. In this study, we investigated neuronal types of gnrh2-expressing cells in Ciona larvae and visualized the activity of these cells by fluorescence imaging using a calcium sensor protein. Some cholinergic neurons and dopaminergic cells express gnrh2, suggesting that GnRH plays a role in controlling swimming behavior. However, none of the gnrh2-expressing cells overlap with glycinergic or GABAergic neurons. A role in motor control is also suggested by a relationship between the activity of gnrh2-expressing cells and tail movements. Interestingly, gnrh2-positive ependymal cells in the nerve cord, known as a kind of glia cells, actively produced Ca2+ transients, suggesting that active intercellular signaling occurs in the glia cells of the nerve cord.
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Wang Y, Wang GD, He QL, Luo ZP, Yang L, Yao Q, Chen KP. Phylogenetic analysis of achaete–scute complex genes in metazoans. Mol Genet Genomics 2020; 295:591-606. [DOI: 10.1007/s00438-020-01648-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/13/2020] [Indexed: 11/30/2022]
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Wada H, Phuangphong S, Hashimoto N, Nagai K. Establishment of the novel bivalve body plan through modification of early developmental events in mollusks. Evol Dev 2020; 22:463-470. [PMID: 32291900 DOI: 10.1111/ede.12334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mollusks have a wide variety of body plans, which develop through conserved early embryogenesis, namely spiral embryonic development and trochophore larvae. Although the comparative study of mollusks has attracted the interest of evolutionary developmental biology researchers, less attention has been paid to bivalves. In this review, we focused on the evolutionary process from single-shell ancestors to bivalves, which possess bilaterally separated shells. Our study tracing the lineage of shell field cells in bivalves did not support the old hypothesis that shell plate morphology is due to modification of the spiral cleavage pattern. Rather, we suggest that modification of the shell field induction process is the key to understanding the evolution of shell morphology. The novel body plan of bivalves cannot be established solely via separating shell plates, but rather requires the formation of additional organs, such as adductor muscles. The evolutionary biology of bivalves offers a unique view on how multiple organs evolve in a coordinated manner to establish a novel body plan.
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Affiliation(s)
- Hiroshi Wada
- School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Supanat Phuangphong
- School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Naoki Hashimoto
- Pearl Research Institute, K. Mikimoto & Co., Ltd., Shima, Mie, Japan
| | - Kiyohito Nagai
- Pearl Research Institute, K. Mikimoto & Co., Ltd., Shima, Mie, Japan
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8
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Gyoja F. Basic helix-loop-helix transcription factors in evolution: Roles in development of mesoderm and neural tissues. Genesis 2017; 55. [PMID: 28804953 DOI: 10.1002/dvg.23051] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 08/10/2017] [Accepted: 08/10/2017] [Indexed: 12/12/2022]
Abstract
Basic helix-loop-helix (bHLH) transcription factors have attracted the attention of developmental and evolutionary biologists for decades because of their conserved functions in mesodermal and neural tissue formation in both vertebrates and fruit flies. Their evolutionary history is of special interest because it will likely provide insights into developmental processes and refinement of metazoan-specific traits. This review briefly considers advances in developmental biological studies on bHLHs/HLHs. I also discuss recent genome-wide surveys and molecular phylogenetic analyses of these factors in a wide range of metazoans. I hypothesize that interactions between metazoan-specific Group A, D, and E bHLH/HLH factors enabled a sophisticated transition system from cell proliferation to differentiation in multicellular development. This control mechanism probably emerged initially to organize a multicellular animal body and was subsequently recruited to form evolutionarily novel tissues, which differentiated during a later ontogenetic phase.
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Affiliation(s)
- Fuki Gyoja
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.,Department of Biology, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada, Kobe, 658-8501, Japan
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9
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Bao Y, Xu F, Shimeld SM. Phylogenetics of Lophotrochozoan bHLH Genes and the Evolution of Lineage-Specific Gene Duplicates. Genome Biol Evol 2017; 9:869-886. [PMID: 28338988 PMCID: PMC5381572 DOI: 10.1093/gbe/evx047] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2017] [Indexed: 12/23/2022] Open
Abstract
The gain and loss of genes encoding transcription factors is of importance to understanding the evolution of gene regulatory complexity. The basic helix–loop–helix (bHLH) genes encode a large superfamily of transcription factors. We systematically classify the bHLH genes from five mollusc, two annelid and one brachiopod genomes, tracing the pattern of bHLH gene evolution across these poorly studied Phyla. In total, 56–88 bHLH genes were identified in each genome, with most identifiable as members of previously described bilaterian families, or of new families we define. Of such families only one, Mesp, appears lost by all these species. Additional duplications have also played a role in the evolution of the bHLH gene repertoire, with many new lophotrochozoan-, mollusc-, bivalve-, or gastropod-specific genes defined. Using a combination of transcriptome mining, RT-PCR, and in situ hybridization we compared the expression of several of these novel genes in tissues and embryos of the molluscs Crassostrea gigas and Patella vulgata, finding both conserved expression and evidence for neofunctionalization. We also map the positions of the genes across these genomes, identifying numerous gene linkages. Some reflect recent paralog divergence by tandem duplication, others are remnants of ancient tandem duplications dating to the lophotrochozoan or bilaterian common ancestors. These data are built into a model of the evolution of bHLH genes in molluscs, showing formidable evolutionary stasis at the family level but considerable within-family diversification by tandem gene duplication.
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Affiliation(s)
- Yongbo Bao
- Department of Zoology, University of Oxford, United Kingdom.,Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Zhejiang, China
| | - Fei Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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Fortunato SAV, Vervoort M, Adamski M, Adamska M. Conservation and divergence of bHLH genes in the calcisponge Sycon ciliatum. EvoDevo 2016; 7:23. [PMID: 27757221 PMCID: PMC5064789 DOI: 10.1186/s13227-016-0060-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/27/2016] [Indexed: 12/18/2022] Open
Abstract
Background Basic Helix-Loop-Helix (bHLH) genes encode a large family of eukaryotic transcription factors, categorized into six high-order groups: pan-eukaryotic group B involved in regulation of cell cycle, metabolism, and development; holozoan-specific groups C and F involved in development and maintenance of homeostasis; and metazoan-specific groups A, D and E including well-studied genes, such as Atonal, Twist and Hairy, with diverse developmental roles including control of morphogenesis and specification of neurons. Current scenarios of bHLH evolution in animals are mainly based on the bHLH gene set found in the genome of demosponge Amphimedon queenslandica. In this species, the majority of the 21 identified bHLH genes belong to group B, and the single group A gene is orthologous to several neurogenic bilaterian subfamilies, including atonal and neurogenin. Results Given recently discovered differences in developmental toolkit components between siliceous and calcareous sponges, we have carried out genome-wide analysis of bHLH genes in Sycon ciliatum, an emerging calcisponge model. We identified 30 bHLH genes in this species, representing 12 individual families, including four group A families not found in Amphimedon, and two larger family groupings. Notably, the families represented in Sycon are only partially overlapping with those represented in Amphimedon. Developmental expression analysis of a subset of the identified genes revealed patterns consistent with deeply conserved roles, such as specification of sensory cells by Atona-related and stem cells by Myc genes. Conclusions Our results demonstrate independent gene loss events in demosponges and calcisponges, implying a complex bHLH toolkit in the last common metazoan ancestor. Electronic supplementary material The online version of this article (doi:10.1186/s13227-016-0060-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sofia A V Fortunato
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway.,ARC Centre for Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - Michel Vervoort
- Institut Jacques Monod - CNRS, Université Paris Diderot, 75005 Paris Cedex 13, France
| | - Marcin Adamski
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway.,Research School of Biology, Australian National University, Canberra, Australia
| | - Maja Adamska
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway.,Research School of Biology, Australian National University, Canberra, Australia
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Takeuchi T, Koyanagi R, Gyoja F, Kanda M, Hisata K, Fujie M, Goto H, Yamasaki S, Nagai K, Morino Y, Miyamoto H, Endo K, Endo H, Nagasawa H, Kinoshita S, Asakawa S, Watabe S, Satoh N, Kawashima T. Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle. ZOOLOGICAL LETTERS 2016; 2:3. [PMID: 26900483 PMCID: PMC4759782 DOI: 10.1186/s40851-016-0039-2] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 02/11/2016] [Indexed: 05/12/2023]
Abstract
INTRODUCTION Bivalve molluscs have flourished in marine environments, and many species constitute important aquatic resources. Recently, whole genome sequences from two bivalves, the pearl oyster, Pinctada fucata, and the Pacific oyster, Crassostrea gigas, have been decoded, making it possible to compare genomic sequences among molluscs, and to explore general and lineage-specific genetic features and trends in bivalves. In order to improve the quality of sequence data for these purposes, we have updated the entire P. fucata genome assembly. RESULTS We present a new genome assembly of the pearl oyster, Pinctada fucata (version 2.0). To update the assembly, we conducted additional sequencing, obtaining accumulated sequence data amounting to 193× the P. fucata genome. Sequence redundancy in contigs that was caused by heterozygosity was removed in silico, which significantly improved subsequent scaffolding. Gene model version 2.0 was generated with the aid of manual gene annotations supplied by the P. fucata research community. Comparison of mollusc and other bilaterian genomes shows that gene arrangements of Hox, ParaHox, and Wnt clusters in the P. fucata genome are similar to those of other molluscs. Like the Pacific oyster, P. fucata possesses many genes involved in environmental responses and in immune defense. Phylogenetic analyses of heat shock protein70 and C1q domain-containing protein families indicate that extensive expansion of genes occurred independently in each lineage. Several gene duplication events prior to the split between the pearl oyster and the Pacific oyster are also evident. In addition, a number of tandem duplications of genes that encode shell matrix proteins are also well characterized in the P. fucata genome. CONCLUSIONS Both the Pinctada and Crassostrea lineages have expanded specific gene families in a lineage-specific manner. Frequent duplication of genes responsible for shell formation in the P. fucata genome explains the diversity of mollusc shell structures. These duplications reveal dynamic genome evolution to forge the complex physiology that enables bivalves to employ a sessile lifestyle in the intertidal zone.
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Affiliation(s)
- Takeshi Takeuchi
- />Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Ryo Koyanagi
- />DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Fuki Gyoja
- />Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Miyuki Kanda
- />DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Kanako Hisata
- />Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Manabu Fujie
- />DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Hiroki Goto
- />DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Shinichi Yamasaki
- />DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Kiyohito Nagai
- />Pearl Research Institute, Mikimoto CO. LTD, Shima, Mie 517-0403 Japan
| | - Yoshiaki Morino
- />Graduate School of Life and Environmental Science, University of Tsukuba, Ibaraki, 305-8572 Japan
| | - Hiroshi Miyamoto
- />Department of Genetic Engineering, Faculty of Biology-Oriented Science and Technology, Kinki University, 930 Nishimitani, Kinokawa, Wakayama 649-6493 Japan
| | - Kazuyoshi Endo
- />Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Hirotoshi Endo
- />Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564 Japan
| | - Hiromichi Nagasawa
- />Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 Japan
- />College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 People’s Republic of China
| | - Shigeharu Kinoshita
- />Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 Japan
| | - Shuichi Asakawa
- />Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 Japan
| | - Shugo Watabe
- />Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 Japan
- />Kitasato University School of Marine Bioscience, Sagamihara, Kanagawa 252-0373 Japan
| | - Noriyuki Satoh
- />Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Takeshi Kawashima
- />Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
- />Present Address: Graduate School of Life and Environmental Science, University of Tsukuba, Ibaraki, 305-8572 Japan
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Perea-Atienza E, Gavilán B, Chiodin M, Abril JF, Hoff KJ, Poustka AJ, Martinez P. The nervous system of Xenacoelomorpha: a genomic perspective. ACTA ACUST UNITED AC 2015; 218:618-28. [PMID: 25696825 DOI: 10.1242/jeb.110379] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Xenacoelomorpha is, most probably, a monophyletic group that includes three clades: Acoela, Nemertodermatida and Xenoturbellida. The group still has contentious phylogenetic affinities; though most authors place it as the sister group of the remaining bilaterians, some would include it as a fourth phylum within the Deuterostomia. Over the past few years, our group, along with others, has undertaken a systematic study of the microscopic anatomy of these worms; our main aim is to understand the structure and development of the nervous system. This research plan has been aided by the use of molecular/developmental tools, the most important of which has been the sequencing of the complete genomes and transcriptomes of different members of the three clades. The data obtained has been used to analyse the evolutionary history of gene families and to study their expression patterns during development, in both space and time. A major focus of our research is the origin of 'cephalized' (centralized) nervous systems. How complex brains are assembled from simpler neuronal arrays has been a matter of intense debate for at least 100 years. We are now tackling this issue using Xenacoelomorpha models. These represent an ideal system for this work because the members of the three clades have nervous systems with different degrees of cephalization; from the relatively simple sub-epithelial net of Xenoturbella to the compact brain of acoels. How this process of 'progressive' cephalization is reflected in the genomes or transcriptomes of these three groups of animals is the subject of this paper.
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Affiliation(s)
- Elena Perea-Atienza
- Departament de Genètica, Universitat de Barcelona, Av. Diagonal, 643, 08028-Barcelona, Catalonia, Spain
| | - Brenda Gavilán
- Departament de Genètica, Universitat de Barcelona, Av. Diagonal, 643, 08028-Barcelona, Catalonia, Spain
| | - Marta Chiodin
- Departament de Genètica, Universitat de Barcelona, Av. Diagonal, 643, 08028-Barcelona, Catalonia, Spain
| | - Josep F Abril
- Departament de Genètica, Universitat de Barcelona, Av. Diagonal, 643, 08028-Barcelona, Catalonia, Spain Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal, 643, 08028 Barcelona, Catalonia, Spain
| | - Katharina J Hoff
- Ernst Morith Arndt University of Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487 Greifswald, Germany
| | - Albert J Poustka
- Dahlem Centre for Genome Research and Medical Systems Biology, Evolutionary and Environmental Genomics Group, Fabeckstraße 60-62, 14195 Berlin, Germany
| | - Pedro Martinez
- Departament de Genètica, Universitat de Barcelona, Av. Diagonal, 643, 08028-Barcelona, Catalonia, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23 08010 Barcelona, Catalonia, Spain
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Gyoja F. A genome-wide survey of bHLH transcription factors in the Placozoan Trichoplax adhaerens reveals the ancient repertoire of this gene family in metazoan. Gene 2014; 542:29-37. [PMID: 24631262 DOI: 10.1016/j.gene.2014.03.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 03/07/2014] [Accepted: 03/11/2014] [Indexed: 01/04/2023]
Abstract
Basic helix-loop-helix (bHLH) transcription factors play significant roles in multiple biological processes in metazoan cells. To address the evolutionary history of this gene family, comprehensive and detailed characterization in basal metazoans is essential. Here I report a genome-wide survey of bHLH genes in the Placozoan, Trichoplax adhaerens. The present survey revealed ancient origins of two orthologous families, 48-related-1/Fer1 and ASCb, which both belong to high-order Group A. Group A factors are mainly involved in neural and mesodermal differentiation. I also identified novel members of a Group E orthologous family previously thought to be unique to Homo sapiens. These were discovered in Trichoplax, Saccoglossus kowalevskii, Euperipatoides kanangrensis, and Crassostrea gigas, but apparently are not found in Drosophila melanogaster, Caenorhabditis elegans, or Nematostella vectensis. Furthermore, as reported previously, many unclassified Group A members were observed in Trichoplax. The present study provides important information to infer the ancestral state of bHLH components in the Metazoa.
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Affiliation(s)
- Fuki Gyoja
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
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