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Klirs Y, Novosolov M, Gissi C, Garić R, Pupko T, Stach T, Huchon D. Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss. Genome Biol Evol 2024; 16:evae181. [PMID: 39162337 PMCID: PMC11384887 DOI: 10.1093/gbe/evae181] [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: 05/04/2024] [Revised: 07/19/2024] [Accepted: 08/13/2024] [Indexed: 08/21/2024] Open
Abstract
Sequencing the mitochondrial genome of the tunicate Oikopleura dioica is a challenging task due to the presence of long poly-A/T homopolymer stretches, which impair sequencing and assembly. Here, we report on the sequencing and annotation of the majority of the mitochondrial genome of O. dioica by means of combining several DNA and amplicon reads obtained by Illumina and MinIon Oxford Nanopore Technologies with public RNA sequences. We document extensive RNA editing, since all homopolymer stretches present in the mitochondrial DNA correspond to 6U-regions in the mitochondrial RNA. Out of the 13 canonical protein-coding genes, we were able to detect eight, plus an unassigned open reading frame that lacked sequence similarity to canonical mitochondrial protein-coding genes. We show that the nad3 gene has been transferred to the nucleus and acquired a mitochondria-targeting signal. In addition to two very short rRNAs, we could only identify a single tRNA (tRNA-Met), suggesting multiple losses of tRNA genes, supported by a corresponding loss of mitochondrial aminoacyl-tRNA synthetases in the nuclear genome. Based on the eight canonical protein-coding genes identified, we reconstructed maximum likelihood and Bayesian phylogenetic trees and inferred an extreme evolutionary rate of this mitochondrial genome. The phylogenetic position of appendicularians among tunicates, however, could not be accurately determined.
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Affiliation(s)
- Yael Klirs
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Maria Novosolov
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv 6997801, Israel
- Faculty of Health and Medical Sciences, GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Carmela Gissi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari 70126, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
- CoNISMa, Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma 00196, Italy
| | - Rade Garić
- Institute for Marine and Coastal Research, University of Dubrovnik, Dubrovnik 20000, Croatia
| | - Tal Pupko
- George S. Wise Faculty of Life Sciences, The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Thomas Stach
- Department of Molecular Parasitology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dorothée Huchon
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv 6997801, Israel
- The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, Tel Aviv 6997801, Israel
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Dierckxsens N, Watanabe K, Tan Y, Masunaga A, Mansfield MJ, Miao J, Luscombe NM, Plessy C. Tracing Homopolymers in Oikopleura dioica's Mitogenome. Genome Biol Evol 2024; 16:evae182. [PMID: 39162185 PMCID: PMC11384890 DOI: 10.1093/gbe/evae182] [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: 05/17/2024] [Revised: 08/05/2024] [Accepted: 08/13/2024] [Indexed: 08/21/2024] Open
Abstract
Oikopleura dioica is a planktonic tunicate (Appendicularia class) found extensively across the marine waters of the globe. The genome of a single male individual collected from Okinawa, Japan was sequenced using the single-molecule PacBio Hi-Fi method and assembled with NOVOLoci. The mitogenome is 39,268 bp long, featuring a large control region of around 22,000 bp. We annotated the proteins atp6, cob, cox1, cox2, cox3, nad1, nad4, and nad5, and found one more open reading frame that did not match any known gene. This study marks the first complete mitogenome assembly for an appendicularian, and reveals that A and T homopolymers cumulatively account for nearly half of its length. This reference sequence will be an asset for environmental DNA and phylogenetic studies.
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Affiliation(s)
- Nicolas Dierckxsens
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Kosei Watanabe
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Keio University, School of Medicine, Tokyo, Japan
| | - Yongkai Tan
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Aki Masunaga
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Michael J Mansfield
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Jiashun Miao
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Nicholas M Luscombe
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Charles Plessy
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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3
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Harry ND, Zakas C. Maternal patterns of inheritance alter transcript expression in eggs. BMC Genomics 2023; 24:191. [PMID: 37038099 PMCID: PMC10084599 DOI: 10.1186/s12864-023-09291-8] [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: 02/03/2023] [Accepted: 04/01/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Modifications to early development can lead to evolutionary diversification. The early stages of development are under maternal control, as mothers produce eggs loaded with nutrients, proteins and mRNAs that direct early embryogenesis. Maternally provided mRNAs are the only expressed genes in initial stages of development and are tightly regulated. Differences in maternal mRNA provisioning could lead to phenotypic changes in embryogenesis and ultimately evolutionary changes in development. However, the extent that maternal mRNA expression in eggs can vary is unknown for most developmental models. Here, we use a species with dimorphic development- where females make eggs and larvae of different sizes and life-history modes-to investigate the extent of variation in maternal mRNA provisioning to the egg. RESULTS We find that there is significant variation in gene expression across eggs of different development modes, and that there are both qualitative and quantitative differences in mRNA expression. We separate parental effects from allelic effects, and find that both mechanisms contribute to mRNA expression differences. We also find that offspring of intraspecific crosses differentially provision their eggs based on the parental cross direction (a parental effect), which has not been previously demonstrated in reproductive traits like oogenesis. CONCLUSION We find that maternally controlled initiation of development is functionally distinct between eggs of different sizes and maternal genotypes. Both allele-specific effects and parent-of-origin effects contribute to gene expression differences in eggs. The latter indicates an intergenerational effect where a parent's genotype can affect gene expression in an egg made by the next generation.
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Affiliation(s)
- Nathan D Harry
- Department of Biological Sciences, North Carolina State University, 112 Derieux Place, Raleigh, NC, 27607, USA
| | - Christina Zakas
- Department of Biological Sciences, North Carolina State University, 112 Derieux Place, Raleigh, NC, 27607, USA.
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4
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Onuma TA, Nishida H. Developmental biology of the larvacean Oikopleura dioica: Genome resources, functional screening, and imaging. Dev Growth Differ 2021; 64:67-82. [PMID: 34964127 DOI: 10.1111/dgd.12769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 12/01/2022]
Abstract
The larvacean Oikopleura dioica is a cosmopolitan planktonic chordate and is closely related to vertebrates. It is characterized by a tadpole-shaped morphology with notochord flanked by muscle in the tail and brain on the dorsal side, a short life cycle of five days, a compact genome of approximately 56 Mb, a simple and transparent body with a small number of cells (~4000 in functional juveniles), invariant embryonic cell lineages, and fast development that ensures complete morphogenesis and organ formation 10 h after fertilization. With these features, this marine chordate is a promising and advantageous animal model in which genetic manipulation is feasible. In this review, we introduce relevant resources and modern techniques that have been developed: (1) Genome and transcriptomes. Oikopleura dioica has the smallest genome among non-parasitic metazoans. Its genome databases have been generated using three geographically distant O. dioica populations, and several intra-species sequence differences are becoming evident; (2) Functional genetic knockdown techniques. Comprehensive screening of genes is feasible using ovarian microinjection and double-strand DNA-induced gene knockdown; and (3) Live imaging of embryos and larvae. Application of these techniques has uncovered novel aspects of development, including meiotic cell arrest, left-right patterning, epidermal cell patterning, and mouth formation involving the connection of ectoderm and endoderm sheets. Oikopleura dioca has become very useful for developmental and evolutionary studies in chordates.
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Affiliation(s)
- Takeshi A Onuma
- Graduate School of Science and Engineering, Faculty of Science, Kagoshima University, Kagoshima, Japan.,Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
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Calatayud S, Garcia-Risco M, Capdevila M, Cañestro C, Palacios Ò, Albalat R. Modular Evolution and Population Variability of Oikopleura dioica Metallothioneins. Front Cell Dev Biol 2021; 9:702688. [PMID: 34277643 PMCID: PMC8283569 DOI: 10.3389/fcell.2021.702688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/09/2021] [Indexed: 01/29/2023] Open
Abstract
Chordate Oikopleura dioica probably is the fastest evolving metazoan reported so far, and thereby, a suitable system in which to explore the limits of evolutionary processes. For this reason, and in order to gain new insights on the evolution of protein modularity, we have investigated the organization, function and evolution of multi-modular metallothionein (MT) proteins in O. dioica. MTs are a heterogeneous group of modular proteins defined by their cysteine (C)-rich domains, which confer the capacity of coordinating different transition metal ions. O. dioica has two MTs, a bi-modular OdiMT1 consisting of two domains (t-12C and 12C), and a multi-modular OdiMT2 with six t-12C/12C repeats. By means of mass spectrometry and spectroscopy of metal-protein complexes, we have shown that the 12C domain is able to autonomously bind four divalent metal ions, although the t-12C/12C pair –as it is found in OdiMT1– is the optimized unit for divalent metal binding. We have also shown a direct relationship between the number of the t-12C/12C repeats and the metal-binding capacity of the MTs, which means a stepwise mode of functional and structural evolution for OdiMT2. Finally, after analyzing four different O. dioica populations worldwide distributed, we have detected several OdiMT2 variants with changes in their number of t-12C/12C domain repeats. This finding reveals that the number of repeats fluctuates between current O. dioica populations, which provides a new perspective on the evolution of domain repeat proteins.
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Affiliation(s)
- Sara Calatayud
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Mario Garcia-Risco
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Mercè Capdevila
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Cristian Cañestro
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Òscar Palacios
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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Onuma TA, Nakanishi R, Sasakura Y, Ogasawara M. Nkx2-1 and FoxE regionalize glandular (mucus-producing) and thyroid-equivalent traits in the endostyle of the chordate Oikopleura dioica. Dev Biol 2021; 477:219-231. [PMID: 34107272 DOI: 10.1016/j.ydbio.2021.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 11/19/2022]
Abstract
The endostyle is a ventral pharyngeal organ used for internal filter feeding of basal chordates and is considered homologous to the follicular thyroid of vertebrates. It contains mucus-producing (glandular) and thyroid-equivalent regions organized along the dorsoventral (DV) axis. Although thyroid-related genes (Nkx2-1, FoxE, and thyroid peroxidase (TPO)) are known to be expressed in the endostyle, their roles in establishing regionalization within the organ have not been demonstrated. We report that Nkx2-1 and FoxE are essential for establishing DV axial identity in the endostyle of Oikopleura dioica. Genome and expression analyses showed von Willebrand factor-like (vWFL) and TPO/dual oxidase (Duox)/Nkx2-1/FoxE as orthologs of glandular and thyroid-related genes, respectively. Knockdown experiments showed that Nkx2-1 is necessary for the expression of glandular and thyroid-related genes, whereas FoxE is necessary only for thyroid-related genes. Moreover, Nkx2-1 expression is necessary for FoxE expression in larvae during organogenesis. The results demonstrate the essential roles of Nkx2-1 and FoxE in establishing regionalization in the endostyle, including (1) the Nkx2-1-dependent glandular region, and (2) the Nkx2-1/FoxE-dependent thyroid-equivalent region. DV axial regionalization may be responsible for organizing glandular and thyroid-equivalent traits of the pharynx along the DV axis.
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Affiliation(s)
- Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan.
| | - Rina Nakanishi
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, 415-0025, Japan
| | - Michio Ogasawara
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan.
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7
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Bliznina A, Masunaga A, Mansfield MJ, Tan Y, Liu AW, West C, Rustagi T, Chien HC, Kumar S, Pichon J, Plessy C, Luscombe NM. Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing. BMC Genomics 2021; 22:222. [PMID: 33781200 PMCID: PMC8008620 DOI: 10.1186/s12864-021-07512-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/05/2021] [Indexed: 11/10/2022] Open
Abstract
Background The larvacean Oikopleura dioica is an abundant tunicate plankton with the smallest (65–70 Mbp) non-parasitic, non-extremophile animal genome identified to date. Currently, there are two genomes available for the Bergen (OdB3) and Osaka (OSKA2016) O. dioica laboratory strains. Both assemblies have full genome coverage and high sequence accuracy. However, a chromosome-scale assembly has not yet been achieved. Results Here, we present a chromosome-scale genome assembly (OKI2018_I69) of the Okinawan O. dioica produced using long-read Nanopore and short-read Illumina sequencing data from a single male, combined with Hi-C chromosomal conformation capture data for scaffolding. The OKI2018_I69 assembly has a total length of 64.3 Mbp distributed among 19 scaffolds. 99% of the assembly is contained within five megabase-scale scaffolds. We found telomeres on both ends of the two largest scaffolds, which represent assemblies of two fully contiguous autosomal chromosomes. Each of the other three large scaffolds have telomeres at one end only and we propose that they correspond to sex chromosomes split into a pseudo-autosomal region and X-specific or Y-specific regions. Indeed, these five scaffolds mostly correspond to equivalent linkage groups in OdB3, suggesting overall agreement in chromosomal organization between the two populations. At a more detailed level, the OKI2018_I69 assembly possesses similar genomic features in gene content and repetitive elements reported for OdB3. The Hi-C map suggests few reciprocal interactions between chromosome arms. At the sequence level, multiple genomic features such as GC content and repetitive elements are distributed differently along the short and long arms of the same chromosome. Conclusions We show that a hybrid approach of integrating multiple sequencing technologies with chromosome conformation information results in an accurate de novo chromosome-scale assembly of O. dioica’s highly polymorphic genome. This genome assembly opens up the possibility of cross-genome comparison between O. dioica populations, as well as of studies of chromosomal evolution in this lineage. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07512-6.
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Affiliation(s)
- Aleksandra Bliznina
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
| | - Aki Masunaga
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Michael J Mansfield
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yongkai Tan
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Andrew W Liu
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Charlotte West
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Francis Crick Institute, London, UK
| | - Tanmay Rustagi
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Hsiao-Chiao Chien
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Saurabh Kumar
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Julien Pichon
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Charles Plessy
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
| | - Nicholas M Luscombe
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Francis Crick Institute, London, UK.,Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, UK
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8
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Wang K, Tomura R, Chen W, Kiyooka M, Ishizaki H, Aizu T, Minakuchi Y, Seki M, Suzuki Y, Omotezako T, Suyama R, Masunaga A, Plessy C, Luscombe NM, Dantec C, Lemaire P, Itoh T, Toyoda A, Nishida H, Onuma TA. A genome database for a Japanese population of the larvacean Oikopleura dioica. Dev Growth Differ 2020; 62:450-461. [PMID: 32677034 DOI: 10.1111/dgd.12689] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 06/10/2020] [Accepted: 06/10/2020] [Indexed: 01/01/2023]
Abstract
The larvacean Oikopleura dioica is a planktonic chordate and is a tunicate that belongs to the closest relatives to vertebrates. Its simple and transparent body, invariant embryonic cell lineages, and short life cycle of 5 days make it a promising model organism for the study of developmental biology. The genome browser OikoBase was established in 2013 using Norwegian O. dioica. However, genome information for other populations is not available, even though many researchers have studied local populations. In the present study, we sequenced using Illumina and PacBio RSII technologies the genome of O. dioica from a southwestern Japanese population that was cultured in our laboratory for 3 years. The genome of Japanese O. dioica was assembled into 576 scaffold sequences with a total length and N50 length of 56.6 and 1.5 Mb, respectively. A total of 18,743 gene models (transcript models) were predicted in the genome assembly, named OSKA2016. In addition, 19,277 non-redundant transcripts were assembled using RNA-seq data. The OSKA2016 has global sequence similarity of only 86.5% when compared with the OikoBase, highlighting the sequence difference between the two far distant O. dioica populations on the globe. The genome assembly, transcript assembly, and transcript models were incorporated into ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and BLAST searches. Mapping of reads obtained from male- or female-specific genome libraries yielded male-specific scaffolds in the OSKA2016 and revealed that over 2.6 Mb of sequence were included in the male-specific Y-region. The genome and transcriptome resources from two distinct populations will be useful datasets for developmental biology, evolutionary biology, and molecular ecology using this model organism.
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Affiliation(s)
- Kai Wang
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Ryo Tomura
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Wei Chen
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Miho Kiyooka
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hinako Ishizaki
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tomoyuki Aizu
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yohei Minakuchi
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Masahide Seki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Tatsuya Omotezako
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Ritsuko Suyama
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan
| | - Aki Masunaga
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan
| | - Charles Plessy
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan
| | - Nicholas M Luscombe
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan
| | - Christelle Dantec
- Centre de Recherches de Biochimie Macromoleculaire (CRBM), UMR5237, CNRS-Universite de Montpellier, Montpellier, France
| | - Patrick Lemaire
- Centre de Recherches de Biochimie Macromoleculaire (CRBM), UMR5237, CNRS-Universite de Montpellier, Montpellier, France
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
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9
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DeBiasse MB, Colgan WN, Harris L, Davidson B, Ryan JF. Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata. Genome Biol Evol 2020; 12:948-964. [PMID: 32211845 PMCID: PMC7337526 DOI: 10.1093/gbe/evaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2020] [Indexed: 12/21/2022] Open
Abstract
Tunicates, the closest living relatives of vertebrates, have served as a foundational model of early embryonic development for decades. Comparative studies of tunicate phylogeny and genome evolution provide a critical framework for analyzing chordate diversification and the emergence of vertebrates. Toward this goal, we sequenced the genome of Corella inflata (Ascidiacea, Phlebobranchia), so named for the capacity to brood self-fertilized embryos in a modified, "inflated" atrial chamber. Combining the new genome sequence for Co. inflata with publicly available tunicate data, we estimated a tunicate species phylogeny, reconstructed the ancestral Hox gene cluster at important nodes in the tunicate tree, and compared patterns of gene loss between Co. inflata and Ciona robusta, the prevailing tunicate model species. Our maximum-likelihood and Bayesian trees estimated from a concatenated 210-gene matrix were largely concordant and showed that Aplousobranchia was nested within a paraphyletic Phlebobranchia. We demonstrated that this relationship is not an artifact due to compositional heterogeneity, as had been suggested by previous studies. In addition, within Thaliacea, we recovered Doliolida as sister to the clade containing Salpida and Pyrosomatida. The Co. inflata genome provides increased resolution of the ancestral Hox clusters of key tunicate nodes, therefore expanding our understanding of the evolution of this cluster and its potential impact on tunicate morphological diversity. Our analyses of other gene families revealed that several cardiovascular associated genes (e.g., BMP10, SCL2A12, and PDE2a) absent from Ci. robusta, are present in Co. inflata. Taken together, our results help clarify tunicate relationships and the genomic content of key ancestral nodes within this phylogeny, providing critical insights into tunicate evolution.
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Affiliation(s)
- Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida
- Department of Biology, University of Florida, Gainesville
| | - William N Colgan
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Lincoln Harris
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Bradley Davidson
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida
- Department of Biology, University of Florida, Gainesville
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10
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A chordate species lacking Nodal utilizes calcium oscillation and Bmp for left-right patterning. Proc Natl Acad Sci U S A 2020; 117:4188-4198. [PMID: 32029598 DOI: 10.1073/pnas.1916858117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Larvaceans are chordates with a tadpole-like morphology. In contrast to most chordates of which early embryonic morphology is bilaterally symmetric and the left-right (L-R) axis is specified by the Nodal pathway later on, invariant L-R asymmetry emerges in four-cell embryos of larvaceans. The asymmetric cell arrangements exist through development of the tailbud. The tail thus twists 90° in a counterclockwise direction relative to the trunk, and the tail nerve cord localizes on the left side. Here, we demonstrate that larvacean embryos have nonconventional L-R asymmetries: 1) L- and R-cells of the two-cell embryo had remarkably asymmetric cell fates; 2) Ca2+ oscillation occurred through embryogenesis; 3) Nodal, an evolutionarily conserved left-determining gene, was absent in the genome; and 4) bone morphogenetic protein gene (Bmp) homolog Bmp.a showed right-sided expression in the tailbud and larvae. We also showed that Ca2+ oscillation is required for Bmp.a expression, and that BMP signaling suppresses ectopic expression of neural genes. These results indicate that there is a chordate species lacking Nodal that utilizes Ca2+ oscillation and Bmp.a for embryonic L-R patterning. The right-side Bmp.a expression may have arisen via cooption of conventional BMP signaling in order to restrict neural gene expression on the left side.
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Matsuo M, Onuma TA, Omotezako T, Nishida H. Protein phosphatase 2A is essential to maintain meiotic arrest, and to prevent Ca 2+ burst at spawning and eventual parthenogenesis in the larvacean Oikopleura dioica. Dev Biol 2019; 460:155-163. [PMID: 31857067 DOI: 10.1016/j.ydbio.2019.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 11/13/2019] [Accepted: 12/09/2019] [Indexed: 12/22/2022]
Abstract
Unfertilized eggs of most animals are arrested at a certain point in the meiotic cell cycles. Reinitiation of meiosis and the start of embryogenesis are triggered by fertilization. This arrest is essential for preventing parthenogenetic activation and for promoting proper initiation of development by fertilization. In the larvacean Oikopleura dioica, which is a simple model organism for studies of chordate development, the unfertilized egg is arrested at metaphase of meiosis I. We show here that protein phosphatase 2A (PP2A) is essential for maintenance of meiotic arrest after spawning of oocytes. Knockdown (KD) of the maternal PP2A catalytic subunit, which was found in functional screening of maternal factors, caused unfertilized eggs to spontaneously release polar bodies after spawning, and then start pseudo-cleavages without fertilization, namely, parthenogenesis. Parthenogenetic embryos failed to undergo proper mitosis and cytokinesis because of lack of a centrosome, which is to be brought into the egg by a sperm. Activation of the KD oocytes was triggered by possible rise of ambient and intracellular pH upon their release from the gonad into seawater at spawning. Live recording of intracellular calcium level of the KD oocytes indicated that the pH rise caused an aberrant Ca2+ burst, which mimicked the Ca2+ burst that occurs at fertilization. Then, the aberrant Ca2+ burst triggered meiosis resumption through Calcium/calmodulin-dependent protein kinase (CaMK II). Therefore, PP2A is essential for maintenance of meiotic arrest and prevention of parthenogenesis by suppressing the aberrant Ca2+ burst at spawning.
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Affiliation(s)
- Masaki Matsuo
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.
| | - Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Tatsuya Omotezako
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
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12
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Prevalence of Mutation-Prone Microhomology-Mediated End Joining in a Chordate Lacking the c-NHEJ DNA Repair Pathway. Curr Biol 2018; 28:3337-3341.e4. [PMID: 30293719 DOI: 10.1016/j.cub.2018.08.048] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/18/2018] [Accepted: 08/21/2018] [Indexed: 12/20/2022]
Abstract
Classical non-homologous end joining (c-NHEJ), a fundamental pathway that repairs double-strand breaks in DNA, is almost universal in eukaryotes and involves multiple proteins highly conserved from yeast to human [1]. The genes encoding these proteins were not detected in the genome of Oikopleura dioica, a new model system of tunicate larvaceans known for its very compact and highly rearranged genome [2-4]. After showing their absence in the genomes of six other larvacean species, the present study examined how O. dioica oocytes and embryos repair double-strand DNA breaks (DSBs), using two approaches: the injection of linearized plasmids, which resulted in their rapid end joining, and a newly established CRISPR Cas9 technique. In both cases, end joining merged short microhomologous sequences surrounding the break (mainly 4 bp long), thus inducing deletions larger than for the tunicate ascidian Ciona intestinalis and human cells. A relatively high frequency of nucleotide insertions was also observed. Finally, a survey of genomic indels supports the involvement of microhomology-mediated repair in natural conditions. Overall, O. dioica repairs DSBs as other organisms do when their c-NHEJ pathway is experimentally rendered deficient, using another mode of end joining with the same effect as alternative NHEJ (a-NHEJ) or microhomology-mediated end joining (MMEJ) [5-7]. We discuss how the exceptional loss of c-NHEJ and its replacement by a more mutation-prone mechanism may have contributed to reshaping this genome and even been advantageous under pressure for genome compaction.
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Brozovic M, Dantec C, Dardaillon J, Dauga D, Faure E, Gineste M, Louis A, Naville M, Nitta KR, Piette J, Reeves W, Scornavacca C, Simion P, Vincentelli R, Bellec M, Aicha SB, Fagotto M, Guéroult-Bellone M, Haeussler M, Jacox E, Lowe EK, Mendez M, Roberge A, Stolfi A, Yokomori R, Brown C, Cambillau C, Christiaen L, Delsuc F, Douzery E, Dumollard R, Kusakabe T, Nakai K, Nishida H, Satou Y, Swalla B, Veeman M, Volff JN, Lemaire P. ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucleic Acids Res 2018; 46:D718-D725. [PMID: 29149270 PMCID: PMC5753386 DOI: 10.1093/nar/gkx1108] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/22/2017] [Accepted: 11/09/2017] [Indexed: 12/14/2022] Open
Abstract
ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.
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Affiliation(s)
| | | | | | - Delphine Dauga
- Bioself Communication; 28 rue de la Bibliothèque, F-13001 Marseille, France
| | - Emmanuel Faure
- Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
- Team VORTEX, Institut de Recherche en Informatique de Toulouse, Universities Toulouse I and III, CNRS, INPT, ENSEEIHT; 2 rue Camichel, BP 7122, F-31071 Toulouse Cedex 7, France
| | | | - Alexandra Louis
- DYOGEN, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005, Paris, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
| | - Kazuhiro R Nitta
- IBDM, Aix-Marseille Université, CNRS, Campus de Luminy, Case 907; 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | - Jacques Piette
- CRBM, Université de Montpellier, CNRS, Montpellier, France
| | - Wendy Reeves
- Division of Biology, Kansas State University, Manhattan, Kansas
| | | | - Paul Simion
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Renaud Vincentelli
- AFMB, Aix-Marseille Université, CNRS, Campus de Luminy, Case 932, 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | | | - Sameh Ben Aicha
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
| | | | | | - Maximilian Haeussler
- Santa Cruz Genomics Institute, MS CBSE, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Edwin Jacox
- CRBM, Université de Montpellier, CNRS, Montpellier, France
| | - Elijah K Lowe
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA
| | - Mickael Mendez
- IBDM, Aix-Marseille Université, CNRS, Campus de Luminy, Case 907; 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | | | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Rui Yokomori
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo 108-8639, Japan
| | - C Titus Brown
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - Christian Cambillau
- AFMB, Aix-Marseille Université, CNRS, Campus de Luminy, Case 932, 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | - Lionel Christiaen
- New York University, Center for Developmental Genetics, Department of Biology, 1009 Silver Center, 100 Washington Square East, New York City, NY10003, USA
| | - Frédéric Delsuc
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Emmanuel Douzery
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Rémi Dumollard
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
| | - Takehiro Kusakabe
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan
| | - Kenta Nakai
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo 108-8639, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Billie Swalla
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA
- Friday Harbor Laboratories, 620 University Road, Friday Harbor, WA 98250-9299, USA
| | - Michael Veeman
- Division of Biology, Kansas State University, Manhattan, Kansas
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
| | - Patrick Lemaire
- CRBM, Université de Montpellier, CNRS, Montpellier, France
- Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
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14
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Calatayud S, Garcia-Risco M, Rojas NS, Espinosa-Sánchez L, Artime S, Palacios Ò, Cañestro C, Albalat R. Metallothioneins of the urochordate Oikopleura dioica have Cys-rich tandem repeats, large size and cadmium-binding preference. Metallomics 2018; 10:1585-1594. [DOI: 10.1039/c8mt00177d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oikopleura dioica has the longest metallothionein described so far, made of repeats generated by a modular and step-wise evolution.
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Affiliation(s)
- Sara Calatayud
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
| | - Mario Garcia-Risco
- Departament de Química
- Facultat de Ciències
- Universitat Autònoma de Barcelona
- E-08193 Cerdanyola del Vallès
- Spain
| | - Natalia S. Rojas
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
| | - Lizethe Espinosa-Sánchez
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
| | - Sebastián Artime
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
| | - Òscar Palacios
- Departament de Química
- Facultat de Ciències
- Universitat Autònoma de Barcelona
- E-08193 Cerdanyola del Vallès
- Spain
| | - Cristian Cañestro
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
| | - Ricard Albalat
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
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15
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16
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Onuma TA, Matsuo M, Nishida H. Modified whole-mount in situ hybridisation and immunohistochemistry protocols without removal of the vitelline membrane in the appendicularian Oikopleura dioica. Dev Genes Evol 2017; 227:367-374. [PMID: 28752326 DOI: 10.1007/s00427-017-0588-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/18/2017] [Indexed: 11/26/2022]
Abstract
The appendicularian Oikopleura dioica is a planktonic chordate that retains a tadpole shape throughout its life. Its simple and transparent body, invariant cell lineages, fast development and available genome and transcriptome resources make it a promising model organism for research in developmental biology. However, large-scale analysis of gene expression in O. dioica is limited owing to the laborious and time-consuming process of manual removal of the vitelline membrane, because devitellinisation of pre-hatching embryos causes failure of normal development. Therefore, in this study, modified procedures were developed for whole-mount in situ hybridisation (WISH) and immunohistochemistry (WIHC). This protocol enables rapid mRNA or protein detection without a manual devitellination step for each specimen. The critical procedure is brief treatment of the vitelline membrane of living embryos with 0.05% actinase E before fixation. Two minutes of treatment was optimal for the penetration of antisense RNA probes and antibodies through the vitelline membrane. This WISH protocol was applicable for chromogenic and fluorescent tyramide signal amplification reactions. Using the new protocol, we found eight genes with tissue-specific expression in the tail muscle, trunk epidermis, heart, pharynx, oesophagus, stomach or gill openings of developing larvae. This procedure also allowed for the detection of exogenous FLAG-tagged histone-enhanced green fluorescent protein by WIHC using anti-FLAG antibody. This study provides a useful and convenient tool for studying spatial and temporal gene expression patterns in this simple chordate model and should facilitate handling large amounts of genetic data from transcriptome-based approaches and other techniques such as treatments with chemical inhibitors.
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Affiliation(s)
- Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Osaka, Toyonaka, 560-0043, Japan.
| | | | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Osaka, Toyonaka, 560-0043, Japan
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17
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PG BL, AE M, RJ O, PH W, A B. Transcriptomic profiles of spring and summer populations of the Southern Ocean salp, Salpa thompsoni, in the Western Antarctic Peninsula region. Polar Biol 2016. [DOI: 10.1007/s00300-016-2051-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Internal and external morphology of adults of the appendicularian, Oikopleura dioica: an SEM study. Cell Tissue Res 2016; 367:213-227. [DOI: 10.1007/s00441-016-2524-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 10/04/2016] [Indexed: 10/20/2022]
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