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3. Extreme genome scrambling in marine planktonicOikopleura dioicacryptic species

Author

Plessy, Charles, primary, Mansfield, Michael J., additional, Bliznina, Aleksandra, additional, Masunaga, Aki, additional, West, Charlotte, additional, Tan, Yongkai, additional, Liu, Andrew W., additional, Grašič, Jan, additional, del Río Pisula, María Sara, additional, Sánchez-Serna, Gaspar, additional, Fabrega-Torrus, Marc, additional, Ferrández-Roldán, Alfonso, additional, Roncalli, Vittoria, additional, Navratilova, Pavla, additional, Thompson, Eric M., additional, Onuma, Takeshi, additional, Nishida, Hiroki, additional, Cañestro, Cristian, additional, and Luscombe, Nicholas M., additional

Published
2024
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8. Extreme genome scrambling in cryptic Oikopleura dioica species

Author

Plessy, Charles, primary, Mansfield, Michael J, additional, Bliznina, Aleksandra, additional, Masunaga, Aki, additional, West, Charlotte, additional, Tan, Yongkai, additional, Liu, Andrew, additional, Grasic, Jan, additional, del Rio Pisula, Maria Sara, additional, Sanchez-Serna, Gaspar, additional, Fabrega-Torrus, Marc, additional, Ferrnandez-Roldan, Alfonso, additional, Roncalli, Vittoria, additional, Navratilova, Pavla, additional, Thompson, Eric M, additional, Onuma, Takeshi, additional, Nishida, Hiroki, additional, Canestro, Cristian, additional, and Luscombe, Nicholas M, additional

Published
2023
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9. Extreme genome scrambling in marine planktonic Oikopleura dioicacryptic species

Author

Plessy, Charles, Mansfield, Michael J., Bliznina, Aleksandra, Masunaga, Aki, West, Charlotte, Tan, Yongkai, Liu, Andrew W., Grašič, Jan, del Río Pisula, María Sara, Sánchez-Serna, Gaspar, Fabrega-Torrus, Marc, Ferrández-Roldán, Alfonso, Roncalli, Vittoria, Navratilova, Pavla, Thompson, Eric M., Onuma, Takeshi, Nishida, Hiroki, Cañestro, Cristian, and Luscombe, Nicholas M.

Abstract

Genome structural variations within species are rare. How selective constraints preserve gene order and chromosome structure is a central question in evolutionary biology that remains unsolved. Our sequencing of several genomes of the appendicularian tunicate Oikopleura dioicaaround the globe reveals extreme genome scrambling caused by thousands of chromosomal rearrangements, although showing no obvious morphological differences between these animals. The breakpoint accumulation rate is an order of magnitude higher than in ascidian tunicates, nematodes, Drosophila,or mammals. Chromosome arms and sex-specific regions appear to be the primary unit of macrosynteny conservation. At the microsyntenic level, scrambling did not preserve operon structures, suggesting an absence of selective pressure to maintain them. The uncoupling of the genome scrambling with morphological conservation in O. dioicasuggests the presence of previously unnoticed cryptic species and provides a new biological system that challenges our previous vision of speciation in which similar animals always share similar genome structures.

Published
2024
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14. The cosmopolitan appendicularian Oikopleura dioica reveals hidden genetic diversity around the globe

Author

Masunaga, Aki, primary, Mansfield, Michael J, additional, Tan, Yongkai, additional, Liu, Andrew W, additional, Bliznina, Aleksandra, additional, Barzaghi, Paolo, additional, Hodgetts, Tamara L, additional, Ferrández-Roldán, Alfonso, additional, Cañestro, Cristian, additional, Onuma, Takeshi A, additional, Plessy, Charles, additional, and Luscombe, Nicholas M, additional

Published
2022
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23. Developmental biology of the larvacean Oikopleura dioica: Genome resources, functional screening, and imaging.

Author

Onuma, Takeshi A. and Nishida, Hiroki

Subjects
*GENETIC techniques, *CELL aggregation, *ECTODERM, *ENDODERM, *DEVELOPMENTAL biology, *NOTOCHORD
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. [ABSTRACT FROM AUTHOR]

Published
2022
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28. A genome database for a Japanese population of the larvacean Oikopleura dioica

Author

Wang, Kai, primary, Tomura, Ryo, additional, Chen, Wei, additional, Kiyooka, Miho, additional, Ishizaki, Hinako, additional, Aizu, Tomoyuki, additional, Minakuchi, Yohei, additional, Seki, Masahide, additional, Suzuki, Yutaka, additional, Omotezako, Tatsuya, additional, Suyama, Ritsuko, additional, Masunaga, Aki, additional, Plessy, Charles, additional, Luscombe, Nicholas M., additional, Dantec, Christelle, additional, Lemaire, Patrick, additional, Itoh, Takehiko, additional, Toyoda, Atsushi, additional, Nishida, Hiroki, additional, and Onuma, Takeshi A., additional

Published
2020
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30. ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates

Author

Dardaillon, Justine, primary, Dauga, Delphine, additional, Simion, Paul, additional, Faure, Emmanuel, additional, Onuma, Takeshi A, additional, DeBiasse, Melissa B, additional, Louis, Alexandra, additional, Nitta, Kazuhiro R, additional, Naville, Magali, additional, Besnardeau, Lydia, additional, Reeves, Wendy, additional, Wang, Kai, additional, Fagotto, Marie, additional, Guéroult-Bellone, Marion, additional, Fujiwara, Shigeki, additional, Dumollard, Rémi, additional, Veeman, Michael, additional, Volff, Jean-Nicolas, additional, Roest Crollius, Hugues, additional, Douzery, Emmanuel, additional, Ryan, Joseph F, additional, Davidson, Bradley, additional, Nishida, Hiroki, additional, Dantec, Christelle, additional, and Lemaire, Patrick, additional

Published
2019
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37. ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates.

Author

Dardaillon, Justine, Dauga, Delphine, Simion, Paul, Faure, Emmanuel, Onuma, Takeshi A, DeBiasse, Melissa B, Louis, Alexandra, Nitta, Kazuhiro R, Naville, Magali, Besnardeau, Lydia, Reeves, Wendy, Wang, Kai, Fagotto, Marie, Guéroult-Bellone, Marion, Fujiwara, Shigeki, Dumollard, Rémi, Veeman, Michael, Volff, Jean-Nicolas, Roest Crollius, Hugues, and Douzery, Emmanuel

Published
2020
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41. Expression of hormone genes and osmoregulation in homing chum salmon: A minireview

Author

Makino, Keita, Onuma, Takeshi A., Kitahashi, Takashi, Ando, Hironori, Ban, Masatoshi, and Urano, Akihisa

Subjects
Vasotocin, 487.61, Salmon, Sex steroids, Upstream migration, Growth hormone, Prolactin
Abstract

Pacific salmon migrate from ocean through the natal river for spawning. Information on expression of genes encoding osmoregulatory hormones and migratory behavior is important for understanding of molecular events that underlie osmoregulation of homing salmon. In the present article, regulation of gene expression for osmoregulatory hormones in pre-spawning salmon was briefly reviewed with special reference to neurohypophysial hormone, vasotocin (VT), and pituitary hormones, growth hormone (GH) and prolactin (PRL). Thereafter, we introduced recent data on migratory behavior from SW to FW environment. In pre-spawning chum salmon, the hypothalamic VT mRNA levels increased in the males, while decreased in the females with loss of salinity tolerance when they were kept in SW. The amounts of GH mRNA in the pituitary decreased during ocean migration prior to entrance into FW. Hypo-osmotic stimulation by SW-to-FW transfer did not significantly affect the amount of PRL mRNA, but it was elevated in both SW and FW environments along with progress in final maturation. Behaviorally, homing chum salmon continued vertical movement between SW and FW layers in the mouth of the natal river for about 12 h prior to upstream migration. Pre-spawning chum salmon in an aquarium, which allowed fish free access to SW and FW, showed that individuals with the lower plasma testosterone (T) and higher estradiol-17β (E2) levels spent longer time in FW when compared with the SW fish. Taken together, neuroendocrine mechanisms that underlie salt and water homeostasis and migratory behavior from SW to FW may be under the control of the hypothalamus-pituitary-gonadal axis in pre-spawning salmon.

Published
2007

43. Characterization of GaAs implanted with molecular ions.

Author

Tamura, Akiyoshi and Onuma, Takeshi

Subjects
*GALLIUM arsenide, *PHOTOLUMINESCENCE, *SECONDARY ion mass spectrometry
Abstract

Presents information on a study which investigated fundamental electrical and optical characteristics of SiF[subx]- and SF[subx]- (x=1,2 and 3) implanted gallium arsenide layers. Electrical properties; Results of photoluminescence measurements carried out; Description of the secondary ion mass spectrometry conducted.

Published
1988
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44. New rapid thermal annealing for GaAs digital integrated circuits.

Author

Tamura, Akiyoshi, Uenoyama, Takeshi, Nishii, Katsunori, Inoue, Kaoru, and Onuma, Takeshi

Subjects
RAPID thermal processing, GALLIUM arsenide
Abstract

Presents a study that developed a rapid thermal annealing (RTA) method that uses gallium arsenide guard rings. Advantages of RTA; Reduction of slip lines in GaAs wafers during RTA; Dependence of annealing uniformity and activation on annealing temperature.

Published
1987
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48. Genome-wide survey of miRNAs and their evolutionary history in the ascidian, Halocynthia roretzi.

Author

Kai Wang, Dantec, Christelle, Lemaire, Patrick, Onuma, Takeshi A., and Nishida, Hiroki

Subjects
HALOCYNTHIA roretzi, MICRORNA, PLANT evolution, GENETIC translation, PLANT identification, PLANTS
Abstract

Background: miRNAs play essential roles in the modulation of cellular functions via degradation and/or translation attenuation of target mRNAs. They have been surveyed in a single ascidian genus, Ciona. Recently, an annotated draft genome sequence for a distantly related ascidian, Halocynthia roretzi, has become available, but miRNAs in H. roretzi have not been previously studied. Results: We report the prediction of 319 candidate H. roretzi miRNAs, obtained through three complementary methods. Experimental validation suggests that more than half of these candidate miRNAs are expressed during embryogenesis. The majority of predicted H. roretzi miRNAs appear specific to ascidians or tunicates, and only 32 candidates, belonging to 25 families, are widely conserved across metazoans. Conclusion: Our study presents a comprehensive identification of candidate H. roretzi miRNAs. This resource will facilitate the study of the mechanisms for miRNA-controlled gene regulatory networks during ascidian development. Further, our analysis suggests that the majority of Halocynthia miRNAs are specific to ascidian or tunicates, with only a small number of widely conserved miRNAs. This result is consistent with the general notion that animal miRNAs are less conserved between taxa than plant ones. [ABSTRACT FROM AUTHOR]

Published
2017
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