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Knytl M, Fornaini NR, Bergelová B, Gvoždík V, Černohorská H, Kubíčková S, Fokam EB, Evans BJ, Krylov V. Divergent subgenome evolution in the allotetraploid frog Xenopus calcaratus. Gene X 2023; 851:146974. [DOI: 10.1016/j.gene.2022.146974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
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Zattera ML, Lima L, Duarte I, de Sousa DY, Araújo OGDS, Gazoni T, Mott T, Recco-Pimentel SM, Bruschi DP. Chromosome spreading of the (TTAGGG)n repeats in the Pipa carvalhoi Miranda-Ribeiro, 1937 (Pipidae, Anura) karyotype. COMPARATIVE CYTOGENETICS 2019; 13:297-309. [PMID: 31649799 PMCID: PMC6803351 DOI: 10.3897/compcytogen.v13i3.35524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
Pipidae is a clade of Anura that diverged relatively early from other frogs in the phylogeny of the group. Pipids have a unique combination of morphological features, some of which appear to represent a mix of adaptations to aquatic life and plesiomorphic characters of Anura. The present study describes the karyotype of Pipa carvalhoi Miranda-Ribeiro, 1937, including morphology, heterochromatin distribution, and location of the NOR site. The diploid number of P. carvalhoi is 2n=20, including three metacentric pairs (1, 4, 8), two submetacentric (2 and 7), three subtelocentric (3, 5, 6), and two telocentric pairs (9 and 10). C-banding detected centromeric blocks of heterochromatin in all chromosome pairs and the NOR detected in chromosome pair 9, as confirmed by FISH using the rDNA 28S probe. The telomeric probes indicated the presence of interstitial telomeric sequences (ITSs), primarily in the centromeric region of the chromosomes, frequently associated with heterochromatin, suggesting that these repeats are a significant component of this region. The findings of the present study provide important insights for the understanding of the mechanisms of chromosomal evolution in the genus Pipa, and the diversification of the Pipidae as a whole.
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Affiliation(s)
- Michelle Louise Zattera
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-990,Curitiba, Paraná State, BrazilUniversidade Federal do ParanáCuritibaBrazil
| | - Luana Lima
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal do Alagoas (UFAL), Avenida Louriva Melo Mota S/N, 57072-900, Maceió, Alagoas State, BrazilUniversidade Federal do AlagoasMaceióBrazil
| | - Iraine Duarte
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-990,Curitiba, Paraná State, BrazilUniversidade Federal do ParanáCuritibaBrazil
| | - Deborah Yasmin de Sousa
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-990,Curitiba, Paraná State, BrazilUniversidade Federal do ParanáCuritibaBrazil
| | - Olívia Gabriela dos Santos Araújo
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista (Unesp) – Câmpus Rio Claro, Avenida 24 A 1515, Bela Vista, 13506-900, Rio Claro, São Paulo State, BrazilUniversidade Estadual PaulistaRio ClaroBrazil
| | - Thiago Gazoni
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista (Unesp) – Câmpus Rio Claro, Avenida 24 A 1515, Bela Vista, 13506-900, Rio Claro, São Paulo State, BrazilUniversidade Estadual PaulistaRio ClaroBrazil
| | - Tamí Mott
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal do Alagoas (UFAL), Avenida Louriva Melo Mota S/N, 57072-900, Maceió, Alagoas State, BrazilUniversidade Federal do AlagoasMaceióBrazil
| | - Shirlei Maria Recco-Pimentel
- Instituto de Biologia, Departamento de Biologia Estrutural e Funcional, Universidade Estadual de Campinas (UNICAMP), Avenida Bertrand Russel S/N, Barão Geraldo, 13083-865, Campinas, São Paulo State, BrazilUniversidade Estadual de CampinasCampinasBrazil
| | - Daniel Pacheco Bruschi
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-990,Curitiba, Paraná State, BrazilUniversidade Federal do ParanáCuritibaBrazil
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Schmid M, Steinlein C. Chromosome Banding in Amphibia. XXXII. The Genus Xenopus (Anura, Pipidae). Cytogenet Genome Res 2015; 145:201-17. [PMID: 26112092 DOI: 10.1159/000433481] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Mitotic chromosomes of 16 species of the frog genus Xenopus were prepared from kidney and lung cell cultures. In the chromosomes of 7 species, high-resolution replication banding patterns could be induced by treating the cultures with 5-bromodeoxyuridine (BrdU) and deoxythymidine (dT) in succession, and in 6 of these species the BrdU/dT-banded chromosomes could be arranged into karyotypes. In the 3 species of the clade with 2n = 20 and 4n = 40 chromosomes (X. tropicalis, X. epitropicalis, X. new tetraploid 1), as well as in the 3 species with 4n = 36 chromosomes (X. laevis, X. borealis, X. muelleri), the BrdU/dT-banded karyotypes show a high degree of homoeology, though differences were detected between these groups. Translocations, inversions, insertions or sex-specific replication bands were not observed. Minor replication asynchronies found between chromosomes probably involve heterochromatic regions. BrdU/dT replication banding of Xenopus chromosomes provides the landmarks necessary for the exact physical mapping of genes and repetitive sequences. FISH with an X. laevis 5S rDNA probe detected multiple hybridization sites at or near the long-arm telomeric regions in most chromosomes of X. laevis and X. borealis, whereas in X. muelleri, the 5S rDNA sequences are located exclusively at the long-arm telomeres of a single chromosome pair. Staining with the AT base pair-specific fluorochrome quinacrine mustard revealed brightly fluorescing heterochromatic regions in the majority of X. borealis chromosomes which are absent in other Xenopus species.
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Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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Kashiwagi K, Kashiwagi A, Kurabayashi A, Hanada H, Nakajima K, Okada M, Takase M, Yaoita Y. Xenopus tropicalis: an ideal experimental animal in amphibia. Exp Anim 2010; 59:395-405. [PMID: 20660986 DOI: 10.1538/expanim.59.395] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Studies using amphibians have contributed to the progress of life science including developmental biology and cell biology for more than one hundred years. Since the 1950s Xenopus laevis in particular has been used by scientists in many fields for experiments, resulting in the development of various techniques such as microsurgery on early embryos, biosynthesis of gene-encoded protein in oocytes by mRNA injection, misexpression experiments by mRNA injection into embryos, gene knockdown studies by injection of morpholino anti-sense oligonucleotide into fertilized eggs, transgenesis by the I-SceI meganuclease method, and so on. In this paper we will introduce Xenopus tropicalis as an alternative experimental animal. It has a shorter generation time and smaller diploid genome, together with whole-genome sequence data. The procedures available for Xenopus laevis can work well with Xenopus tropicalis, and embryos of both species develop at similar rates according to the developmental staging system of Nieuwkoop and Faber. Experimental systems of Xenopus tropicalis will pave the way for a new era of vertebrate genomics and genetics.
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Affiliation(s)
- Keiko Kashiwagi
- Division of Embryology and Genetics, Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashihiroshima, Japan
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Okabayashi K, Asashima M. In Vitro organogenesis using amphibian pluripotent cells. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2006; 82:197-207. [PMID: 25792783 PMCID: PMC4343058 DOI: 10.2183/pjab.82.197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Accepted: 09/12/2006] [Indexed: 06/04/2023]
Abstract
Mesoderm induction as a result of the interaction between endoderm and ectoderm is one of the most crucial events in vertebrate development. We identified activin as a strong mesoderm-inducing factor in an animal cap assay, an in vitro assay system using amphibian pluripotential cell mass. Activin induces mesodermal tisswes including most dorsal mesodermal tissue, notochord (which has important roles in neural induction, somite segmentation, and endodermal organogenesis), and its effects are concentration-dependent. Animal cap cells treated with high concentrations of activin differentiate into anterior endoderm, which can act as an organizer, or center of body patterning. We have established an in vitro induction system for 22 different organs and tissues using animal cap cells, and have isolated many organ-specific genes. With these useful methods, and analysis of newly isolated tissue- and organ-specific genes, the molecular biological "road map" for organogenesis is being established.
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Affiliation(s)
- Koji Okabayashi
- ICORP, Japan Science and Technology Agency (JST), The University of Tokyo, Tokyo,
Japan
| | - Makoto Asashima
- ICORP, Japan Science and Technology Agency (JST), The University of Tokyo, Tokyo,
Japan
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, The University of Tokyo, Tokyo,
Japan
- Recipient of Imperial Prize and Japan Academy Prize in 2001
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Haramoto Y, Tanegashima K, Onuma Y, Takahashi S, Sekizaki H, Asashima M. Xenopus tropicalis nodal-related gene 3 regulates BMP signaling: an essential role for the pro-region. Dev Biol 2004; 265:155-68. [PMID: 14697360 DOI: 10.1016/j.ydbio.2003.09.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In vertebrates, nodal-related genes are crucial for specifying mesendodermal cell fates. Six nodal-related genes have been identified in Xenopus, but only one, nodal, has been identified in the mouse. The Xenopus nodal-related gene 3 (Xnr3), however, lacks the mesoderm-inducing activity of the other five nodal-related genes in Xenopus, and can directly induce neural tissue in animal caps by antagonizing BMP signals. In this study, we isolated three clones of the Xenopus (Silurana) tropicalis nodal-related gene 3 (Xtnr3) and analyzed their function. The Xtnr3 genes show high homology to Xnr3 and have the same activity. Southern blot and genomic PCR analyses indicate that the X. tropicalis genome has duplications in the Xtnr3 gene sequences and our three clones represent separate gene loci. We also found a partial clone of Xtnr3 that coded for the N-terminal part of its pro-region. Surprisingly, this sequence also induced neural tissue by antagonizing BMP signals, and its coded protein physically associated with BMP4 mature protein. Furthermore, we showed that the pro-region of Xnr5 has the same activity. Together, these findings indicate that the pro-region of nodal-related genes acts antagonistically towards BMP signals, which identifies a novel mechanism for the inhibition of BMP signaling.
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Affiliation(s)
- Yoshikazu Haramoto
- Department of Life Sciences (Biology), The University of Tokyo, Meguro, Tokyo 153-8902, Japan
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Sekizaki H, Takahashi S, Tanegashima K, Onuma Y, Haramoto Y, Asashima M. Tracing ofXenopus tropicalis germ plasm and presumptive primordial germ cells with theXenopus tropicalis DAZ-like gene. Dev Dyn 2004; 229:367-72. [PMID: 14745962 DOI: 10.1002/dvdy.10448] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A gamete is derived initially from a presumptive primordial germ cell (pPGC) and transmits genetic potential to the next generation. Xenopus tropicalis, which is a close relative of Xenopus laevis, has a diploid genome and advantages for genetic and genomic research; however, little is known about the developmental mechanism of its germinal lineage. Here, we identified the Xenopus tropicalis DAZ-like gene (Xtdazl), which encodes RNA-binding proteins homologous to Xdazl in Xenopus laevis and examined the expression patterns of Xtdazl transcripts during embryogenesis. In this work, we showed that Xtdazl mRNA was localized in the germ plasm and was expressed from the previtellogenic oocyte to early tadpole, in testis and ovary. The same localization patterns have been reported in Xenopus laevis germ plasm and pPGCs. These results indicate that Xtdazl mRNA is the first specific marker of germ plasm and pPGCs in Xenopus tropicalis and is very useful to trace Xenopus tropicalis pPGCs, including germ plasm until the early tadpole stage.
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Affiliation(s)
- Hiroyuki Sekizaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Abstract
Polyploidy is important in the evolutionary history of plants, and it has played a crucial role in shaping the genome structures of all eukaryotes. New and rapidly improving techniques in genomics, cytogenetics and molecular ecology have resulted in a dramatic increase in publications about duplicate genes, genome rearrangements and detection of ancient duplication events. Similarly, research associated with the origins of polyploidy, its persistence in natural populations and the resulting ecological consequences is receiving more attention. Although polyploidy research has been conducted using both animal and plant systems, inferences based on cross-disciplinary comparisons have been rare. Here, I review recent developments in the field in both plants and animals, emphasizing the benefits of communication between the two groups.
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Affiliation(s)
- Barbara K Mable
- Department of Botany, University of Guelph, Guelph, Ontario, Canada N1G 2W1.
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