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Komoto T, Ikeo K, Yaguchi S, Yamamoto T, Sakamoto N, Awazu A. Assembly of continuous high-resolution draft genome sequence of Hemicentrotus pulcherrimus using long-read sequencing. Dev Growth Differ 2024; 66:297-304. [PMID: 38634255 DOI: 10.1111/dgd.12924] [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: 11/02/2023] [Revised: 03/13/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024]
Abstract
The update of the draft genome assembly of sea urchin, Hemicentrotus pulcherrimus, which is widely studied in East Asia as a model organism of early development, was performed using Oxford nanopore long-read sequencing. The updated assembly provided ~600-Mb genome sequences divided into 2,163 contigs with N50 = 516 kb. BUSCO completeness score and transcriptome model mapping ratio (TMMR) of the present assembly were obtained as 96.5% and 77.8%, respectively. These results were more continuous with higher resolution than those by the previous version of H. pulcherrimus draft genome, HpulGenome_v1, where the number of scaffolds = 16,251 with a total of ~100 Mb, N50 = 143 kb, BUSCO completeness score = 86.1%, and TMMR = 55.4%. The obtained genome contained 36,055 gene models that were consistent with those in other echinoderms. Additionally, two tandem repeat sequences of early histone gene locus containing 47 copies and 34 copies of all histone genes, and 185 of the homologous sequences of the interspecifically conserved region of the Ars insulator, ArsInsC, were obtained. These results provide further advance for genome-wide research of development, gene regulation, and intranuclear structural dynamics of multicellular organisms using H. pulcherrimus.
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Affiliation(s)
- Tetsushi Komoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Kazuho Ikeo
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka, Japan
| | - Shunsuke Yaguchi
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Japan
| | - Takashi Yamamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Higashi-Hiroshima, Japan
| | - Naoaki Sakamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Higashi-Hiroshima, Japan
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Higashi-Hiroshima, Japan
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Watanabe K, Yasui Y, Kurose Y, Fujii M, Yamamoto T, Sakamoto N, Awazu A. Partial exogastrulation due to apical‐basal polarity of F‐actin distribution disruption in sea urchin embryo by omeprazole. Genes Cells 2022; 27:392-408. [PMID: 35347809 PMCID: PMC9325501 DOI: 10.1111/gtc.12934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Kaichi Watanabe
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi‐Hiroshima Japan
| | - Yuhei Yasui
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi‐Hiroshima Japan
| | - Yuta Kurose
- Department of Mathematical and Life Sciences Graduate School of Science, Hiroshima University, Higashi‐Hiroshima Japan
| | - Masashi Fujii
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi‐Hiroshima Japan
| | - Takashi Yamamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi‐Hiroshima Japan
| | - Naoaki Sakamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi‐Hiroshima Japan
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi‐Hiroshima Japan
- Research Center for the Mathematics on Chromatin Live Dynamics Hiroshima University, Higashi‐Hiroshima Hiroshima Japan
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Abstract
Cardiac development is a complex developmental process that is initiated soon after gastrulation, as two sets of precardiac mesodermal precursors are symmetrically located and subsequently fused at the embryonic midline forming the cardiac straight tube. Thereafter, the cardiac straight tube invariably bends to the right, configuring the first sign of morphological left–right asymmetry and soon thereafter the atrial and ventricular chambers are formed, expanded and progressively septated. As a consequence of all these morphogenetic processes, the fetal heart acquired a four-chambered structure having distinct inlet and outlet connections and a specialized conduction system capable of directing the electrical impulse within the fully formed heart. Over the last decades, our understanding of the morphogenetic, cellular, and molecular pathways involved in cardiac development has exponentially grown. Multiples aspects of the initial discoveries during heart formation has served as guiding tools to understand the etiology of cardiac congenital anomalies and adult cardiac pathology, as well as to enlighten novels approaches to heal the damaged heart. In this review we provide an overview of the complex cellular and molecular pathways driving heart morphogenesis and how those discoveries have provided new roads into the genetic, clinical and therapeutic management of the diseased hearts.
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Yamada S, Tanaka Y, Imai KS, Saigou M, Onuma TA, Nishida H. Wavy movements of epidermis monocilia drive the neurula rotation that determines left-right asymmetry in ascidian embryos. Dev Biol 2019; 448:173-182. [PMID: 30059669 DOI: 10.1016/j.ydbio.2018.07.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/19/2018] [Accepted: 07/26/2018] [Indexed: 12/22/2022]
Abstract
Tadpole larvae of the ascidian, Halocynthia roretzi, show morphological left-right asymmetry in the brain structures and the orientation of tail bending within the vitelline membrane. Neurula embryos rotate along the anterior-posterior axis in a counterclockwise direction, and then this rotation stops when the left side of the embryo is oriented downwards. Contact of the left-side epidermis with the vitelline membrane promotes nodal gene expression in the left-side epidermis. This is a novel mechanism in which rotation of whole embryos provides the initial cue for breaking left-right symmetry. Here we show that epidermal monocilia, which appear at the neurula rotation stage, generate the driving force for rotation. A ciliary protein, Arl13b, fused with Venus YFP was used for live imaging of ciliary movements. Although overexpression of wild-type Arl13b fusion protein resulted in aberrant movements of the cilia and abrogation of neurula rotation, mutant Arl13b fusion protein, in which the GTPase and coiled-coil domains were removed, did not affect the normal ciliary movements and neurula rotation. Epidermis cilia moved in a wavy and serpentine way like sperm flagella but not in a rotational way or beating way with effective stroke and recovery stroke. They moved very slowly, at 1/7 Hz, consistent with the low angular velocity of neurula rotation (ca. 43°/min). The tips of most cilia pointed in the opposite direction of embryonic rotation. Similar motility was also observed in Ciona robusta embryos. When embryos were treated with a dynein inhibitor, Ciliobrevin D, both ciliary movements and neurula rotation were abrogated, showing that ciliary movements drive neurula rotation in Halocynthia. The drug also inhibited Ciona neurula rotation. Our observations suggest that the driving force of rotation is generated using the vitelline membrane as a substrate but not by making a water current around the embryo. It is of evolutionary interest that ascidians use ciliary movements to break embryonic left-right symmetry, like in many vertebrates. Meanwhile, ascidian embryos rotate as a whole, similar to embryos of non-vertebrate deuterostomes, such as echinoderm, hemichordate, and amphioxus, while swimming.
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Affiliation(s)
- Shiori Yamada
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yuka Tanaka
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Kaoru S Imai
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Motohiko Saigou
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
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Abstract
TGF-β family ligands function in inducing and patterning many tissues of the early vertebrate embryonic body plan. Nodal signaling is essential for the specification of mesendodermal tissues and the concurrent cellular movements of gastrulation. Bone morphogenetic protein (BMP) signaling patterns tissues along the dorsal-ventral axis and simultaneously directs the cell movements of convergence and extension. After gastrulation, a second wave of Nodal signaling breaks the symmetry between the left and right sides of the embryo. During these processes, elaborate regulatory feedback between TGF-β ligands and their antagonists direct the proper specification and patterning of embryonic tissues. In this review, we summarize the current knowledge of the function and regulation of TGF-β family signaling in these processes. Although we cover principles that are involved in the development of all vertebrate embryos, we focus specifically on three popular model organisms: the mouse Mus musculus, the African clawed frog of the genus Xenopus, and the zebrafish Danio rerio, highlighting the similarities and differences between these species.
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Affiliation(s)
- Joseph Zinski
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6058
| | - Benjamin Tajer
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6058
| | - Mary C Mullins
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6058
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Palmquist K, Davidson B. Establishment of lateral organ asymmetries in the invertebrate chordate, Ciona intestinalis. EvoDevo 2017; 8:12. [PMID: 28770040 PMCID: PMC5526266 DOI: 10.1186/s13227-017-0075-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/17/2017] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The evolutionary emergence and diversification of the chordates appear to involve dramatic changes in organ morphogenesis along the left/right axis. However, the ancestral chordate mechanism for establishing lateral asymmetry remains ambiguous. Additionally, links between the initial establishment of lateral asymmetry and subsequent asymmetries in organ morphogenesis are poorly characterized. RESULTS To explore asymmetric organ morphogenesis during chordate evolution, we have begun to characterize left/right patterning of the heart and endodermal organs in an invertebrate chordate, Ciona intestinalis. Here, we show that Ciona has a laterally asymmetric, right-sided heart. Our data indicate that cardiac lateral asymmetry requires H+/K+ ion flux, but is independent of Nodal signaling. Our pharmacological inhibitor studies show that ion flux is required for polarization of epidermal cilia and neurula rotation and suggest that ion flux functions synergistically with chorion contact to drive cardiac laterality. Live imaging analysis revealed that larval heart progenitor cells undergo a lateral shift without displaying any migratory behaviors. Furthermore, we find that this passive shift corresponds with the emergence of lateral asymmetry in the endoderm, which is also ion flux dependent. CONCLUSIONS Our data suggest that ion flux promotes laterally asymmetric morphogenesis of the larval endoderm rudiment leading to a passive, Nodal-independent shift in the position of associated heart progenitor cells. These findings help to refine hypotheses regarding ancestral chordate left/right patterning mechanisms and how they have diverged within invertebrate and vertebrate chordate lineages.
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Affiliation(s)
- Karl Palmquist
- Department of Biology, Swarthmore College, 500 College Ave., Swarthmore, PA 19081 USA
| | - Brad Davidson
- Department of Biology, Swarthmore College, 500 College Ave., Swarthmore, PA 19081 USA
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Tisler M, Wetzel F, Mantino S, Kremnyov S, Thumberger T, Schweickert A, Blum M, Vick P. Cilia are required for asymmetric nodal induction in the sea urchin embryo. BMC DEVELOPMENTAL BIOLOGY 2016; 16:28. [PMID: 27553781 PMCID: PMC4994401 DOI: 10.1186/s12861-016-0128-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 07/29/2016] [Indexed: 01/22/2023]
Abstract
Background Left-right (LR) organ asymmetries are a common feature of metazoan animals. In many cases, laterality is established by a conserved asymmetric Nodal signaling cascade during embryogenesis. In most vertebrates, asymmetric nodal induction results from a cilia-driven leftward fluid flow at the left-right organizer (LRO), a ciliated epithelium present during gastrula/neurula stages. Conservation of LRO and flow beyond the vertebrates has not been reported yet. Results Here we study sea urchin embryos, which use nodal to establish larval LR asymmetry as well. Cilia were found in the archenteron of embryos undergoing gastrulation. Expression of foxj1 and dnah9 suggested that archenteron cilia were motile. Cilia were polarized to the posterior pole of cells, a prerequisite of directed flow. High-speed videography revealed rotating cilia in the archenteron slightly before asymmetric nodal induction. Removal of cilia through brief high salt treatments resulted in aberrant patterns of nodal expression. Our data demonstrate that cilia - like in vertebrates - are required for asymmetric nodal induction in sea urchin embryos. Conclusions Based on these results we argue that the anterior archenteron represents a bona fide LRO and propose that cilia-based symmetry breakage is a synapomorphy of the deuterostomes. Electronic supplementary material The online version of this article (doi:10.1186/s12861-016-0128-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthias Tisler
- University of Hohenheim, Institute of Zoology, 70593, Stuttgart, Germany
| | - Franziska Wetzel
- University of Hohenheim, Institute of Zoology, 70593, Stuttgart, Germany
| | - Sabrina Mantino
- University of Hohenheim, Institute of Zoology, 70593, Stuttgart, Germany
| | - Stanislav Kremnyov
- Department of Embryology, Lomonosov Moscow State University, Moscow, Russia
| | - Thomas Thumberger
- University of Hohenheim, Institute of Zoology, 70593, Stuttgart, Germany.,Present Address: Centre for Organismal Studies, Im Neuenheimer Feld 230, Heidelberg University, 69120, Heidelberg, Germany
| | - Axel Schweickert
- University of Hohenheim, Institute of Zoology, 70593, Stuttgart, Germany
| | - Martin Blum
- University of Hohenheim, Institute of Zoology, 70593, Stuttgart, Germany
| | - Philipp Vick
- University of Hohenheim, Institute of Zoology, 70593, Stuttgart, Germany.
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