Developmental biology of the larvacean Oikopleura dioica: Genome resources, functional screening, and imaging.
Oikopleura dioica
genome
knockdown
larvacean
live imaging
Journal
Development, growth & differentiation
ISSN: 1440-169X
Titre abrégé: Dev Growth Differ
Pays: Japan
ID NLM: 0356504
Informations de publication
Date de publication:
Jan 2022
Jan 2022
Historique:
revised:
13
12
2021
received:
17
09
2021
accepted:
13
12
2021
pubmed:
30
12
2021
medline:
3
2
2022
entrez:
29
12
2021
Statut:
ppublish
Résumé
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.
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
67-82Subventions
Organisme : Ministry of Education, Culture, Sports, Science and Technology
ID : 221S0002
Organisme : JSPS
ID : 24870019
Organisme : JSPS
ID : 26840079
Organisme : JSPS
ID : 18K06256
Organisme : JSPS
ID : 18H04763
Organisme : JSPS
ID : 20H05946
Organisme : JSPS
ID : 26650079
Organisme : JSPS
ID : 15H04377
Organisme : JSPS
ID : 16K14735
Organisme : JSPS
ID : 17KT0023
Organisme : JSPS
ID : 19H03234
Organisme : Inamori Foundation
Organisme : Kato Memorial Research Foundation
Organisme : Sumitomo Foundation
Organisme : Japan Foundation for Applied Enzymology
Informations de copyright
© 2021 Japanese Society of Developmental Biologists.
Références
Albalat, R., & Cañestro, C. (2016). Evolution by gene loss. Nature Reviews Genetics, 17(7), 379-391. https://doi.org/10.1038/nrg.2016.39
Bassham, S., & Postlethwait, J. (2000). Brachyury (T) expression in embryos of a larvacean urochordate, Oikopleura dioica, and the ancestral role of T. Developmental Biology, 220, 322-332. https://doi.org/10.1006/dbio.2000.9647
Bliznina, A., Masunaga, A., Mansfield, M. J., Tan, Y., Liu, A. W., West, C., Rustagi, T., Chien, H.-C., Kumar, S., Pichon, J., Plessy, C., & Luscombe, N. M. (2021). Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing. BMC Genomics, 22, 222. https://doi.org/10.1186/s12864-021-07512-6
Bouquet, J. M., Spriet, E., Troedsson, C., Otterå, H., Chourrout, D., & Thompson, E. M. (2009). Culture optimization for the emergent zooplanktonic model organism Oikopleura dioica. Journal of Plankton Research, 31(4), 359-370. https://doi.org/10.1093/plankt/fbn132. Epub 2009 Jan 16.
Bourlat, S. J., Juliusdottir, T., Lowe, C. J., Freeman, R., Aronowicz, J., Kirschner, M., Lander, E. S., Thorndyke, M., Nakano, H., Kohn, A. B., Heyland, A., Moroz, L. L., Copley, R. R., & Telford, M. J. (2006). Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature, 444, 85-88. https://doi.org/10.1038/nature05241
Burighel, P., Brena, C., Martinucci, G. B., & Cima, F. (2001). Gut ultrastructure of the appendicularian Oikopleura dioica (Tunicata). Invertebrate Biology, 120, 278-293. https://doi.org/10.1111/j.1744-7410.2001.tb00038.x
Cao, C., Lemaire, L. A., Wang, W., Yoon, P. H., Choi, Y. A., Parsons, L. R., Matese, J. C., Wang, W., Levine, M., & Chen, K. (2019). Comprehensive single-cell transcriptome lineages of a proto-vertebrate. Nature, 571(7765), 349-354. https://doi.org/10.1038/s41586-019-1385-y
Clarke, T., Bouquet, J., Fu, X., Kallesøe, T., Schmid, M., & Thompson, E. M. (2007). Rapidly evolving lamins in a chordate, Oikopleura dioica, with unusual nuclear architecture. Gene, 396, 159-169. https://doi.org/10.1016/j.gene.2007.03.006
Danks, G., Campsteijn, C., Parida, M., Butcher, S., Doddapaneni, H., Fu, B., Petrin, R., Metpally, R., Lenhard, B., Wincker, P., Chourrout, D., Thompson, E. M., & Manak, J. R. (2013). OikoBase: A genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica. Nucleic Acids Research, 41, 1-9. https://doi.org/10.1093/nar/gks1159
Danks, G. B., Raasholm, M., Campsteijn, C., Long, A. M., Manak, J. R., Lenhard, B., & Thompson, E. M. (2014). Trans-splicing and operons in metazoans: Translational control in maternally regulated development and recovery from growth arrest. Molecular Biology of Evolution, 32(3), 585-599. https://doi.org/10.1093/molbev/msu336
Dardaillon, J., Dauga, D., Simion, P., Faure, E., Onuma, T. A., DeBiasse, M. B., Louis, A., Nitta, K. R., Naville, M., Besnardeau, L., Reeves, W., Wang, K., Fagotto, M., Guéroult-Bellone, M., Fujiwara, S., Dumollard, R., Veeman, M., Volff, J.-N., Roest Crollius, H., … Lemaire, P. (2020). ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates. Nucleic Acids Research, 48, D668-D675.
De Robertis, E. M., & Kuroda, H. (2004). Dorsal-ventral patterning and neural induction in Xenopus embryos. Annual Review of Cell and Developmental Biology, 20, 285-308. https://doi.org/10.1146/annurev.cellbio.20.011403.154124
Delsman, H. C. (1910). Beiträge zur Entwicklungsgeschichte von Oikopleura dioica. Verh Rijksinst Onderz Zee, 3, 1-24.
Delsuc, F., Brinkmann, H., Chourrout, D., & Philippe, H. (2006). Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature, 439, 965-968. https://doi.org/10.1038/nature04336
Delsuc, F., Philippe, H., Tsagkogeorga, G., Simion, P., Tilak, M.-K., Turon, X., López-Legentil, S., Piette, J., Lemaire, P., & Douzery, E. J. P. (2018). A phylogenomic framework and timescale for comparative studies of tunicates. BMC Biology, 16, 1-14. https://doi.org/10.1186/s12915-018-0499-2
Deng, W., Henriet, S., & Chourrout, D. (2019). Prevalence of mutation-prone microhomology-mediated end joining in a chordate lacking the c-NHEJ DNA repair pathway. Current Biology, 28, 3337-3341.e4. https://doi.org/10.1016/j.cub.2018.08.048
Denoeud, F., Henriet, S., Mungpakdee, S., Aury, J.-M., Da Silva, C., Brinkmann, H., Mikhaleva, J., Olsen, L. C., Jubin, C., Cañestro, C., Bouquet, J.-M., Danks, G., Poulain, J., Campsteijn, C., Adamski, M., Cross, I., Yadetie, F., Muffato, M., Louis, A., … Chourrout, D. (2010). Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science, 330, 1381-1385. https://doi.org/10.1126/science.1194167
Fenaux, R. (1986). The house of Oikopleura dioica (Tunicata, Appendicularia): Structure and function. Zoomorphology, 106, 224-231.
Fenaux, R. (1998). Anatomy and functional morphology of the Appendicularia. In Q. Bone (Ed.), The biology of pelagic tunicates (pp. 25-34). Oxford University Press.
Ferrández-Roldán, A., Martí-Solans, J., Cañestro, C., & Albalat, R. (2019). Oikopleura dioica: An emergent chordate model to study the impact of gene loss on the evolution of the mechanisms of development. Results and Problems in Cell Differentiation, 68, 63-105. https://doi.org/10.1007/978-3-030-23459-1_
Flood, P. R. (2004). Toward photographic atlas on special taxonomic characters of oikopleurid Appendicularia (Tunicata). In: G. Gorsky, M. J. Youngbluth, & D. Deibel (Eds.), Response of marine ecosystems to global change: ecological impact of appendicularians (pp. 59-85). Editions Scientifique.
Flood, P. R., & Deibel, D. (1998). The appendicularian house. In Q. Bone (Ed.), The biology of pelagic tunicates (pp. 105-124). Oxford University Press.
Fujii, S., Nishio, T., & Nishida, H. (2008). Cleavage pattern, gastrulation, and neurulation in the appendicularian, Oikopleura dioica. Development Genes and Evolution, 218, 69-79. https://doi.org/10.1007/s00427-008-0205-4
Ganot, P., Bouquet, J. M., Kallesøe, T., & Thompson, E. M. (2007). The Oikopleura coenocyst, a unique chordate germ cell permitting rapid, extensive modulation of oocyte production. Developmental Biology, 302, 591-600. https://doi.org/10.1016/j.ydbio.2006.10.021
Ganot, P., Bouquet, J. M., & Thompson, E. M. (2006). Comparative organization of follicle, accessory cells and spawning anlagen in dynamic semelparous clutch manipulators, the urochordate Oikopleuridae. Biology of the Cells, 98, 389-401. https://doi.org/10.1042/BC20060005
Ganot, P., Kallesøe, T., Reinhardt, R., Chourrout, D., & Thompson, E. M. (2004). Spliced-leader RNA trans splicing in a Chordate, Oikopleura dioica, with a compact genome. Molecular and Cellular Biology, 24, 795-7805.
Hekimi, S., Boutis, P., & Lakowski, B. (1995). Viable maternal-effect mutations that affect the development of the nematode Caenorhabditis elegans. Genetics, 141, 1351-1364. https://doi.org/10.1093/genetics/141.4.1351
Holley, S. A., Jackson, P. D., Sasai, Y., Lu, B., De Robertis, E. M., Hoffmann, F. M., & Ferguson, E. L. (1995). A conserved system for dorsal-ventral patterning in insects and vertebrates involving sog and chordin. Nature, 376, 249-253. https://doi.org/10.1038/376249a0
Hosp, J., Sagane, Y., Danks, G., & Thompson, E. M. (2012). The evolving proteome of a complex extracellular matrix, the Oikopleura House. PLoS One, 7, e40172. https://doi.org/10.1371/journal.pone.0040172
Imai, K. S., Hino, K., Yagi, K., Satoh, N., & Satou, Y. (2005). Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: Towards a comprehensive understanding of gene networks. Development, 131(16), 4047-4058. https://doi.org/10.1242/dev.01270
Imai, K. S., Levin, M., Satoh, N., & Satou, Y. (2006). Regulatory blueprint for a chordate embryo. Science, 312, 1183-1187. https://doi.org/10.1126/science.1123404
Kawai-Toyooka, H., Kuramoto, C., Orui, K., Motoyama, K., Kikuchi, K., Kanegae, T., & Wada, M. (2004). DNA interference: A Simple and efficient gene-silencing system for high-throughput functional analysis in the fern Adiantum. Plant and Cell Physiology, 45, 1648-1657. https://doi.org/10.1093/pcp/pch186
Kemphues, K. J., Kusch, M., & Wolf, N. (1988). Maternal-effect lethal mutations on linkage group II of Caenorhabditis elegans. Genetics, 120, 977-986. https://doi.org/10.1093/genetics/120.4.977
Kishi, K., Hayashi, M., Onuma, T. A., & Nishida, H. (2017). Patterning and morphogenesis of the intricate but stereotyped oikoplastic epidermis of the appendicularian, Oikopleura dioica. Developmental Biology, 428, 245-257. https://doi.org/10.1016/j.ydbio.2017.06.008
Kishi, K., Onuma, T. A., & Nishida, H. (2014). Long-distance cell migration during larval development in the appendicularian, Oikopleura dioica. Developmental Biology, 395, 299-306. https://doi.org/10.1016/j.ydbio.2014.09.006
Liu, A. W., Tan, Y., Masunaga, A., Bliznina, A., West, C., Plessy, C., & Luscombe, N. M. (2021). H3S28P antibody staining of Okinawan Oikopleura dioica suggests the presence of three chromosomes. F1000Research, 9, 780. https://doi.org/10.12688/f1000research.25019.2
Madgwick, A., Magri, M. S., Dantec, C., Gailly, D., Fiuza, U.-M., Guignard, L., Hettinger, S., Gomez-Skarmeta, J. L., & Lemaire, P. (2019). Evolution of embryonic cis-regulatory landscapes between divergent Phallusia and Ciona ascidians. Developmental Biology, 448(2), 71-87. https://doi.org/10.1016/j.ydbio.2019.01.003
Makabe, K. W., & Nishida, H. (2012). Cytoplasmic localization and reorganization in ascidian eggs: Role of postplasmic/PEM RNAs in axis formation and fate determination. WIREs Developmental Biology, 1, 501-518. https://doi.org/10.1002/wdev.22
Martí-Solans, J., Belyaeva, O. V., Torres-Aguila, N. P., Kedishvili, N. Y., Albalat, R., & Cañestro, C. (2016). Coelimination and survival in gene network evolution: Dismantling the RA-signaling in a chordate. Molecular Biology and Evolution, 33, 2401-2416. https://doi.org/10.1093/molbev/msw118
Martí-Solans, J., Ferrández-Roldán, A., Godoy-Marín, H., Badia-Ramentol, J., Torres-Aguila, N. P., Rodríguez-Marí, A., Bouquet, J. M., Chourrout, D., Thompson, E. M., Albalat, R., & Cañestro, C. (2015). Oikopleura dioica culturing made easy: A low-cost facility for an emerging animal model in EvoDevo. Genesis, 53, 183-193.
Martí-Solans, J., Godoy-Marín, H., Diaz-Gracia, M., Onuma, T. A., Nishida, H., Albalat, R., & Cañestro, C. (2021). Massive gene loss and function shuffling in appendicularians stretch the boundaries of chordate Wnt family evolution. Frontiers in Cell and Developmental Biology, 9, 700827. https://doi.org/10.3389/fcell.2021.700827
Masunaga, A., Liu, A. W., Tan, Y., Scott, A., & Luscombe, N. M. (2020). Streamlined sampling and cultivation of the pelagic cosmopolitan larvacean, Oikopleura dioica. Journal of Visualized Experiments, 160, e61279. https://doi.org/10.3791/61279
Matsuo, M., Onuma, T., Omotezako, T., & Nishida, H. (2020). Protein phosphatase 2A is essential to maintain meiotic arrest, and to prevent Ca2+ burst at spawning and eventual parthenogenesis in the larvacean Oikopleura dioica. Developmental Biology, 460, 155-163. https://doi.org/10.1016/j.ydbio.2019.12.005
Mikhaleva, Y., Kreneisz, O., Olsen, L. C., Glover, J. C., & Chourrout, D. (2015). Modification of the larval swimming behavior in Oikopleura dioica, a chordate with a miniaturized central nervous system by dsRNA injection into fertilized eggs. Journal of Experimental Zoology, 324B, 114-127.
Mikhaleva, Y., Skinnesa, R., Sumic, S., Thompson, E. M., & Chourrout, D. (2018). Development of the house secreting epithelium, a major innovation of tunicate larvaceans, involves multiple homeodomain transcription factors. Developmental Biology, 443, 117-126. https://doi.org/10.1016/j.ydbio.2018.09.006
Mikhaleva, Y., Tolstenkov, O., & Glover, J. C. (2019). Gap junction-dependent coordination of intercellular calcium signalling in the developing appendicularian tunicate Oikopleura dioica. Developmental Biology, 450, 9-22. https://doi.org/10.1016/j.ydbio.2019.03.006
Mizutani, C. M., & Bier, E. (2008). EvoD/Vo: The origins of BMP signalling in the neuroectoderm. Nature Reviews Genetics, 9, 663-677. https://doi.org/10.1038/nrg2417
Morita, R., Onuma, T. A., Manni, L., Ohno, N., & Nishida, H. (2020). Mouth opening is mediated by separation of dorsal and ventral daughter cells of the lip precursor cells in the larvacean, Oikopleura dioica. Development Genes and Evolution, 230(5-6), 315-327. https://doi.org/10.1007/s00427-020-00667-4
Naville, M., Henriet, S., Warren, I., Sumic, S., Reeve, M., Volff, J., & Chourrout, D. (2019). Massive changes of genome size driven by expansions of non-autonomous transposable elements. Current Biology, 29, 1161-1168. https://doi.org/10.1016/j.cub.2019.01.080
Navratilova, P., Danks, G. B., Long, A., Butcher, S., Manak, J. R., & Thompson, E. M. (2017). Sex-specific chromatin landscapes in an ultra-compact chordate genome. Epigenetics and Chromatin, 10, 1-18. https://doi.org/10.1186/s13072-016-0110-4
Nishida, H. (2005). Specification of embryonic axis and mosaic development in ascidians. Devevelopmental Dynamics, 233, 1177-1193. https://doi.org/10.1002/dvdy.20469
Nishida, H. (2008). Development of the appendicularian Oikopleura dioica: Culture, genome, and cell lineages. Development Growth and Differentiation, 50, S239-S256. https://doi.org/10.1111/j.1440-169X.2008.01035.x
Nishida, H. (2012). The maternal muscle determinant in the ascidian egg. WIREs Developmental Biology, 1, 425-433. https://doi.org/10.1002/wdev.54
Nishida, H., Ohno, N., Caicci, F., & Manni, L. (2021). 3D reconstruction of structures of hatched larva and young juvenile of the larvacean Oikopleura dioica using SBF-SEM. Scientific Reports, 11, 4833. https://doi.org/10.1038/s41598-021-83706-y
Nishida, H., & Stach, T. (2014). Cell lineages and fate maps in tunicates: Conservation and modification. Zoological Science, 31, 645-652. https://doi.org/10.2108/zs140117
Nishino, A., Satou, Y., Morisawa, M., & Satoh, N. (2000). Muscle actin genes and muscle cells in the appendicularian, Oikopleura longicauda: Phylogenetic relationships among muscle tissues in the urochordates. Journal of Experimental Zoology, 288, 135-150.
Nishino, A., Satou, Y., Morisawa, M., & Satoh, N. (2001). Brachyury (T) gene expression and notochord development in Oikopleura longicauda (Appendicularia, Urochordata). Developent Genes and Evolution, 211, 219-231. https://doi.org/10.1007/s004270100141
Olovinikov, I., Chan, K., Sachidanandam, R., Newman, D. K., & Aravin, A. A. (2013). Bacterial argonaute samples he transcriptome to identify foreign DNA. Moelcular Cell, 51(5), 594-605. https://doi.org/10.1016/j.molcel.2013.08.014
Omotezako, T., Matsuo, M., Onuma, T. A., & Nishida, H. (2017). DNA interference-mediated screening of maternal factors in the chordate Oikopleura dioica. Scientific Reports, 7, 1-10. https://doi.org/10.1038/srep44226
Omotezako, T., Nishino, A., Onuma, T. A., & Nishida, H. (2013). RNA interference in the appendicularian Oikopleura dioica reveals the function of the Brachyury gene. Development Genes and Evolution, 223, 261-267. https://doi.org/10.1007/s00427-013-0438-8
Omotezako, T., Onuma, T. A., & Nishida, H. (2015). DNA interference: DNA-induced gene silencing in the appendicularian Oikopleura dioica. Proceedings of the Royal Society B: Biological Sciences, 282, 20150435.
Onuma, T. A., Hayashi, M., Gyojya, F., Kishi, K., Wang, K., & Nishida, H. (2020). A chordate species lacking Nodal utilizes calcium oscillation and Bmp for left-right patterning. Proceedings of the National Academy of Sciences of the United States of America, 117, 4188-4198.
Onuma, T. A., Isobe, M., & Nishida, H. (2017). Internal and external morphology of adults in the appendicularian, Oikopleura dioica: An SEM study. Cell and Tissue Research, 367, 213-227.
Onuma, T. A., Matsuo, M., & Nishida, H. (2017). Modified whole-mount in situ hybridisation and immunohistochemistry protocols without removal of the vitelline membrane in the appendicularian Oikopleura dioica. Development Genes and Evolution, 227, 367-374. https://doi.org/10.1007/s00427-017-0588-1
Onuma, T. A., Nakanishi, R., Sasakura, Y., & Ogasawara, M. (2021). Nkx2-1 and FoxE regionalize glandular (mucus-producing) and thyroid-equivalent traits in the endostyle of the chordate Oikopleura dioica. Developmental Biology, 230(5-6), 315-327. https://doi.org/10.1016/j.ydbio.2021.05.021
Øvrebø, J. I., Campsteijn, C., Kourtesis, I., Hausen, H., Raasholm, M., & Thompson, E. M. (2015). Functional specialization of chordate CDK1 paralogs during oogenic meiosis. Cell Cycle, 14(6), 880-893. https://doi.org/10.1080/15384101.2015.1006000
Prodon, F., Chenevert, J., Hébras, C., Dumollard, R., Faure, E., Gonzalez-Garcia, J., Nishida, H., Sardet, C., & McDougall, A. (2010). Dual mechanism controls asymmetric spindle position in ascidian germ cell precursors. Development, 137, 2011-2021. https://doi.org/10.1242/dev.047845
Ruiz, F., Vayssié, L., Klotz, C., Sperling, L., & Madeddu, L. (1998). Homology-dependent gene silencing in Paramecium. Molecular Biology of the Cell, 9(4), 931-943. https://doi.org/10.1091/mbc.9.4.931
Sagane, Y., Zech, K., Bouquet, J., Schmid, M., Bal, U., & Thompson, E. M. (2010). Functional specialization of cellulose synthase genes of prokaryotic origin in chordate larvaceans. Development, 137, 1483-1492. https://doi.org/10.1242/dev.04450
Sakuma, T., Nakade, S., Sakane, Y., Suzuki, K. T., & Yamamoto, Y. (2016). MMEJ-assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems. Nature Protocol, 11, 118-133. https://doi.org/10.1038/nprot.2015.140
Sato, R., Tanaka, Y., & Ishimaru, T. (2001). House production by Oikopleura dioica (Tunicata, Appendicularia) under laboratory conditions. Journal of Plankton Research, 23, 415-423. https://doi.org/10.1093/plankt/23.4.415
Satou, Y., Nakamura, R., Yu, D., Yoshida, R., Hamada, M., Fujie, M., Hisata, K., Takeda, H., & Satoh, N. (2019). Nearly complete genome of Ciona intestinalis Type A (C. robusta) reveals the contribution of inversion to chromosomal evolution in the genus Ciona. Genome Biology of Evolution, 11, 3144-3157.
Schüpbach, T., & Wieschaus, E. (1989). Female sterile mutations on the second chromosome of Drosophila melanogaster. I. maternal effect mutations. Genetics, 121, 101-117.
Seo, H. C., Kube, M., Edvardsen, R. B., Jensen, M. F., Beck, A., Spriet, E., Gorsky, G., Thompson, E. M., Lehrach, H., Reinhardt, R., & Chourrout, D. (2001). Miniature genome in the marine chordate Oikopleura dioica. Science, 294, 2506.
Shoguchi, E., Kawashima, T., Satou, Y., Hamaguchi, M., Sin-I, T., Kohara, Y., Putnam, N., Rokhsar, D. S., & Satoh, N. (2006). Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis. Genome Research, 16, 297-303.
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015). BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31, 3210-3212. https://doi.org/10.1093/bioinformatics/btv351
Sladitschek, H. L., Fiuza, U. M., Pavlinic, D., Benes, V., Hufnagel, L., & Neveu, P. A. (2020). MorphoSeq: Full single-cell transcriptome dynamics up to gastrulation in a chordate. Cell, 181(4), 922-935.e21. https://doi.org/10.1016/j.cell.2020.03.055
Soukup, V., Horácek, I., & Cerny, R. (2013). Development and evolution of the vertebrate primary mouth. Journal of Anatomy, 222, 79-99. https://doi.org/10.1111/j.1469-7580.2012.01540.x
Spada, F., Steen, H., Troedsson, C., Kallesøe, T., Spriet, E., Mann, M., & Thompson, E. M. (2001). Molecular patterning of the oikoplastic epithelium of the larvacean tunicate Oikopleura dioica. Journal of Biological Chemistry, 276, 20624-20632. https://doi.org/10.1074/jbc.M100438200
Stach, T., & Anselmi, C. (2015). High-precision morphology: Bifocal 4D-microscopy enables the comparison of detailed cell lineages of two chordate species separated for more than 525 million years. BMC Biology, 13, 113. https://doi.org/10.1186/s12915-015-0218-1
Stach, T., Winter, J., Bouquet, J.-M., Chourrout, D., & Schnabel, R. (2008). Embryology of a planktonic tunicate reveals traces of sessility. Proceedings of the National Academy of Sciences of the United States of America, 105, 7229-7234. https://doi.org/10.1073/pnas.0710196105
Swarts, D. C., Hegge, J. W., Hinojo, I., Shiimori, M., Ellis, M. A., Dumrongkulraksa, J., Terns, R. M., Terns, M. P., & van der Oost, J. (2015). Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA. Nucleic Acids Research, 43(10), 5120-5129. https://doi.org/10.1093/nar/gkv415
Swarts, D. C., Jore, M. M., Westra, E. R., Zhu, Y., Janssen, J. H., Snijders, A. P., Wang, Y., Patel, D. J., Berenguer, J., Brouns, S. J. J., & van der Oost, J. (2014). DNA-guided DNA interference by a prokaryotic Argonaute. Nature, 507(7491), 258-261. https://doi.org/10.1038/nature12971
Takatori, N., Oonuma, K., Nishida, H., & Saiga, H. (2015). Polarization of PI3K activity initiated by ooplasmic segregation guides nuclear migration in the mesendoderm. Developmental Cell, 35, 333-343. https://doi.org/10.1016/j.devcel.2015.10.012
Thompson, E. M., Kallesoe, T., & Spada, F. (2001). Diverse genes expressed in distinct regions of the trunk epithelium define a monolayer cellular template for construction of Oikopleurid house. Developmental Biology, 238, 260-273.
Tokuoka, M., Maeda, K., Kobayashi, K., Mochizuki, A., & Satou, Y. (2021). The gene regulatory system for specifying germ layers in early embryos of the simple chordate. Science Advances, 7(24), eabf8210. https://doi.org/10.1126/sciadv.abf8210
Tsuboi, H., Sutoh, K., & Wada, M. (2012). Epigenetic memory of DNAi associated with cytosine methylation and histone modification in fern. Plant Signaling and Behavior, 7, 1-7. https://doi.org/10.4161/psb.21974
Wang, K., Omotezako, T., Kishi, K., Nishida, H., & Onuma, T. A. (2015). Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: Novel protein-encoding genes, intra-species sequence variations, and trans-spliced RNA leader. Development Genes and Evolution, 225, 149-159. https://doi.org/10.1007/s00427-015-0502-7
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, N. M., Dantec, C., Lemaire, P., Itoh, T., Toyoda, A., Nishida, H., & Onuma, T. A. (2020). A genome database for a Japanese population of the larvacean Oikopleura dioica. Development Growth and Differentiation, 62, 450-461. https://doi.org/10.1111/dgd.12689
Žárský, V., & Tachezy, J. (2015). Evolutionary loss of peroxisomes - not limited to parasites. Biology Direct, 10, 74. https://doi.org/10.1186/s13062-015-0101-6