A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis

Xenopus laevis (XLA) is an allotetraploid species which appears to have undergone whole-genome duplication after the interspecific hybridization of 2 diploid species closely related to Silurana/Xenopus tropicalis (XTR). Previous cDNA fluorescence in situ hybridization (FISH) experiments have identified 9 sets of homoeologous chromosomes in X. laevis, in which 8 sets correspond to chromosomes 1-8 of X. tropicalis (XTR1-XTR8), and the last set corresponds to a fusion of XTR9 and XTR10. In addition, recent X. laevis genome sequencing and BAC-FISH experiments support this physiological relationship and show no gross chromosome translocation in the X. laevis karyotype. Therefore, for the benefit of both comparative cytogenetics and genome research, we here propose a new chromosome nomenclature for X. laevis based on the phylogenetic relationship and chromosome length, i.e. XLA1L, XLA1S, XLA2L, XLA2S, and so on, in which the numbering of XLA chromosomes corresponds to that in X. tropicalis and the postfixes ‘L' and ‘S' stand for ‘long' and ‘short' chromosomes in the homoeologous pairs, which can be distinguished cytologically by their relative size. The last chromosome set is named XLA9L and XLA9S, in which XLA9 corresponds to both XTR9 and XTR10, and hence, to emphasize the phylogenetic relationship to X. tropicalis, XLA9_10L and XLA9_10S are also used as synonyms.

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Evolutionary divergence in tail regeneration between Xenopus laevis and Xenopus tropicalis

Cell & Bioscience ◽

10.1186/s13578-021-00582-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Shouhong Wang ◽

Yun-Bo Shi

Keyword(s):

Xenopus Laevis ◽

Refractory Period ◽

Genetic Basis ◽

Diploid Species ◽

Xenopus Tropicalis ◽

Evolutionary Divergence ◽

Tail Regeneration ◽

Genetic Studies ◽

Spinal Cord Dorsal ◽

Organ Replacement

AbstractTissue regeneration is of fast growing importance in the development of biomedicine, particularly organ replacement therapies. Unfortunately, many human organs cannot regenerate. Anuran Xenopus laevis has been used as a model to study regeneration as many tadpole organs can regenerate. In particular, the tail, which consists of many axial and paraxial tissues, such as spinal cord, dorsal aorta and muscle, commonly present in vertebrates, can fully regenerate when amputated at late embryonic stages and most of the tadpole stages. Interestingly, between stage 45 when feeding begins to stage 47, the Xenopus laevis tail cannot regenerate after amputation. This period, termed “refractory period”, has been known for about 20 years. The underlying molecular and genetic basis is unclear in part due to the difficult to carry out genetic studies in this pseudo-tetraploid species. Here we compared tail regeneration between Xenopus laevis and the highly related diploid anuran Xenopus tropicalis and found surprisingly that Xenopus tropicalis lacks the refractory period. Further molecular and genetic studies, more feasible in this diploid species, should reveal the basis for this evolutionary divergence in tail regeneration between two related species and facilitate the understanding how tissue regenerative capacity is controlled, thus with important implications for human regenerative medicine.

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Comparative Distribution of Repetitive Sequences in the Karyotypes of Xenopus tropicalis and Xenopus laevis (Anura, Pipidae)

Genes ◽

10.3390/genes12050617 ◽

2021 ◽

Vol 12 (5) ◽

pp. 617

Author(s):

Álvaro S. Roco ◽

Thomas Liehr ◽

Adrián Ruiz-García ◽

Kateryna Guzmán ◽

Mónica Bullejos

Keyword(s):

In Situ Hybridization ◽

Xenopus Laevis ◽

Organizer Region ◽

Repetitive Sequences ◽

Nucleolus Organizer Region ◽

Nucleolus Organizer ◽

Repeated Sequences ◽

Xenopus Tropicalis ◽

Model Organisms

Xenopus laevis and its diploid relative, Xenopus tropicalis, are the most used amphibian models. Their genomes have been sequenced, and they are emerging as model organisms for research into disease mechanisms. Despite the growing knowledge on their genomes based on data obtained from massive genome sequencing, basic research on repetitive sequences in these species is lacking. This study conducted a comparative analysis of repetitive sequences in X. laevis and X. tropicalis. Genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) with Cot DNA of both species revealed a conserved enrichment of repetitive sequences at the ends of the chromosomes in these Xenopus species. The repeated sequences located on the short arm of chromosome 3 from X. tropicalis were not related to the sequences on the short arm of chromosomes 3L and 3S from X. laevis, although these chromosomes were homoeologous, indicating that these regions evolved independently in these species. Furthermore, all the other repetitive sequences in X. tropicalis and X. laevis may be species-specific, as they were not revealed in cross-species hybridizations. Painting experiments in X. laevis with chromosome 7 from X. tropicalis revealed shared sequences with the short arm of chromosome 3L. These regions could be related by the presence of the nucleolus organizer region (NOR) in both chromosomes, although the region revealed by chromosome painting in the short arm of chromosome 3L in X. laevis did not correspond to 18S + 28S rDNA sequences, as they did not colocalize. The identification of these repeated sequences is of interest as they provide an explanation to some problems already described in the genome assemblies of these species. Furthermore, the distribution of repetitive DNA in the genomes of X. laevis and X. tropicalis might be a valuable marker to assist us in understanding the genome evolution in a group characterized by numerous polyploidization events coupled with hybridizations.

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Chromosomal organization of a sequence related to LTR-like elements of Ty1-copia retrotransposons in Avena species

Genome ◽

10.1139/g99-007 ◽

1999 ◽

Vol 42 (4) ◽

pp. 706-713 ◽

Cited By ~ 10

Author(s):

Concha Linares ◽

Antonio Serna ◽

Araceli Fominaya

Keyword(s):

In Situ Hybridization ◽

Diploid Species ◽

D Genome ◽

Specific Sequence ◽

Chromosomal Organization ◽

Intergenomic Translocations ◽

A Genome ◽

Slot Blot Analysis ◽

Copia Retrotransposons

A repetitive sequence, pAs17, was isolated from Avena strigosa (As genome) and characterized. The insert was 646 bp in length and showed 54% AT content. Databank searches revealed its high homology to the long terminal repeat (LTR) sequences of the specific family of Ty1-copia retrotransposons represented by WIS2-1A and Bare. It was also found to be 70% identical to the LTR domain of the WIS2-1A retroelement of wheat and 67% identical to the Bare-1 retroelement of barley. Southern hybridizations of pAs17 to diploid (A or C genomes), tetraploid (AC genomes), and hexaploid (ACD genomes) oat species revealed that it was absent in the C diploid species. Slot-blot analysis suggested that both diploid and tetraploid oat species contained 1.3 × 104 copies, indicating that they are a component of the A-genome chromosomes. The hexaploid species contained 2.4 × 104 copies, indicating that they are a component of both A- and D-genome chromosomes. This was confirmed by fluorescent in situ hybridization analyses using pAs17, two ribosomal sequences, and a C-genome specific sequence as probes. Further, the chromosomes involved in three C-A and three C-D intergenomic translocations in Avena murphyi (AC genomes) and Avena sativa cv. Extra Klock (ACD genomes), respectively, were identified. Based on its physical distribution and Southern hybridization patterns, a parental retrotransposon represented by pAs17 appears to have been active at least once during the evolution of the A genome in species of the Avena genus.Key words: chromosomal organization, in situ hybridization, intergenomic translocations, LTR sequence, oats.

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Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut

BMC Plant Biology ◽

10.1186/s12870-021-02875-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Liuyang Fu ◽

Qian Wang ◽

Lina Li ◽

Tao Lang ◽

Junjia Guo ◽

...

Keyword(s):

In Situ Hybridization ◽

Physical Mapping ◽

Tandem Repeats ◽

Genetic Research ◽

Diploid Species ◽

Reference Sequence ◽

A Genome ◽

Genome Map ◽

Chromosomal Variants

Abstract Background Chromosomal variants play important roles in crop breeding and genetic research. The development of single-stranded oligonucleotide (oligo) probes simplifies the process of fluorescence in situ hybridization (FISH) and facilitates chromosomal identification in many species. Genome sequencing provides rich resources for the development of oligo probes. However, little progress has been made in peanut due to the lack of efficient chromosomal markers. Until now, the identification of chromosomal variants in peanut has remained a challenge. Results A total of 114 new oligo probes were developed based on the genome-wide tandem repeats (TRs) identified from the reference sequences of the peanut variety Tifrunner (AABB, 2n = 4x = 40) and the diploid species Arachis ipaensis (BB, 2n = 2x = 20). These oligo probes were classified into 28 types based on their positions and overlapping signals in chromosomes. For each type, a representative oligo was selected and modified with green fluorescein 6-carboxyfluorescein (FAM) or red fluorescein 6-carboxytetramethylrhodamine (TAMRA). Two cocktails, Multiplex #3 and Multiplex #4, were developed by pooling the fluorophore conjugated probes. Multiplex #3 included FAM-modified oligo TIF-439, oligo TIF-185-1, oligo TIF-134-3 and oligo TIF-165. Multiplex #4 included TAMRA-modified oligo Ipa-1162, oligo Ipa-1137, oligo DP-1 and oligo DP-5. Each cocktail enabled the establishment of a genome map-based karyotype after sequential FISH/genomic in situ hybridization (GISH) and in silico mapping. Furthermore, we identified 14 chromosomal variants of the peanut induced by radiation exposure. A total of 28 representative probes were further chromosomally mapped onto the new karyotype. Among the probes, eight were mapped in the secondary constrictions, intercalary and terminal regions; four were B genome-specific; one was chromosome-specific; and the remaining 15 were extensively mapped in the pericentric regions of the chromosomes. Conclusions The development of new oligo probes provides an effective set of tools which can be used to distinguish the various chromosomes of the peanut. Physical mapping by FISH reveals the genomic organization of repetitive oligos in peanut chromosomes. A genome map-based karyotype was established and used for the identification of chromosome variations in peanut following comparisons with their reference sequence positions.

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Correction to: Evolutionary divergence in tail regeneration between Xenopus laevis and Xenopus tropicalis

Cell & Bioscience ◽

10.1186/s13578-021-00615-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Shouhong Wang ◽

Yun-Bo Shi

Keyword(s):

Xenopus Laevis ◽

Xenopus Tropicalis ◽

Evolutionary Divergence ◽

Tail Regeneration

An amendment to this paper has been published and can be accessed via the original article.

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A Centromeric Tandem Repeat Family Originating From a Part of Ty3/gypsy-Retroelement in Wheat and Its Relatives

Genetics ◽

10.1093/genetics/164.2.665 ◽

2003 ◽

Vol 164 (2) ◽

pp. 665-672 ◽

Cited By ~ 4

Author(s):

Zhi-Jun Cheng ◽

Minoru Murata

Keyword(s):

In Situ Hybridization ◽

Tandem Repeats ◽

Diploid Species ◽

Upstream Region ◽

Aegilops Speltoides ◽

Repeat Family ◽

B Genome ◽

Intervening Sequences ◽

Wild Diploid Species

AbstractFrom a wild diploid species that is a relative of wheat, Aegilops speltoides, a 301-bp repeat containing 16 copies of a CAA microsatellite was isolated. Southern blot and fluorescence in situ hybridization revealed that ∼250 bp of the sequence is tandemly arrayed at the centromere regions of A- and B-genome chromosomes of common wheat and rye chromosomes. Although the DNA sequence of this 250-bp repeat showed no notable homology in the databases, the flanking or intervening sequences between the repeats showed high homologies (>82%) to two separate sequences of the gag gene and its upstream region in cereba, a Ty3/gypsy-like retroelement of Hordeum vulgare. Since the amino acid sequence deduced from the 250 bp with seven CAAs showed some similarity (∼53%) to that of the gag gene, we concluded that the 250-bp repeats had also originated from the cereba-like retroelements in diploid wheat such as Ae. speltoides and had formed tandem arrays, whereas the 300-bp repeats were dispersed as a part of cereba-like retroelements. This suggests that some tandem repeats localized at the centromeric regions of cereals and other plant species originated from parts of retrotransposons.

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Effects of freezing and activation on membrane quality and DNA damage in Xenopus tropicalis and Xenopus laevis spermatozoa

Reproduction Fertility and Development ◽

10.1071/rd16190 ◽

2017 ◽

Vol 29 (8) ◽

pp. 1556 ◽

Cited By ~ 8

Author(s):

S. Morrow ◽

J. Gosálvez ◽

C. López-Fernández ◽

F. Arroyo ◽

W. V. Holt ◽

...

Keyword(s):

Xenopus Laevis ◽

Membrane Damage ◽

Membrane Integrity ◽

Subsequent Development ◽

Xenopus Tropicalis ◽

Model Organisms ◽

Sperm Chromatin ◽

Dna Integrity ◽

Sperm Cryopreservation ◽

Sperm Plasma Membrane

There is growing concern over the effect of sperm cryopreservation on DNA integrity and the subsequent development of offspring generated from this cryopreserved material. In the present study, membrane integrity and DNA stability of Xenopus laevis and Xenopus tropicalis spermatozoa were evaluated in response to cryopreservation with or without activation, a process that happens upon exposure to water to spermatozoa of some aquatic species. A dye exclusion assay revealed that sperm plasma membrane integrity in both species decreased after freezing, more so for X. laevis than X. tropicalis spermatozoa. The sperm chromatin dispersion (SCD) test showed that for both X. tropicalis and X. laevis, activated frozen spermatozoa produced the highest levels of DNA fragmentation compared with all fresh samples and frozen non-activated samples (P < 0.05). Understanding the nature of DNA and membrane damage that occurs in cryopreserved spermatozoa from Xenopus species represents the first step in exploiting these powerful model organisms to understand the developmental consequences of fertilising with cryopreservation-damaged spermatozoa.

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Generation and Care of Xenopus laevis and Xenopus tropicalis Embryos

Methods in Molecular Biology - Xenopus ◽

10.1007/978-1-4939-8784-9_2 ◽

2018 ◽

pp. 19-32 ◽

Cited By ~ 2

Author(s):

Marcin Wlizla ◽

Sean McNamara ◽

Marko E. Horb

Keyword(s):

Xenopus Laevis ◽

Xenopus Tropicalis

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The use of double fluorescence in situ hybridization to physically map the positions of 5S rDNA genes in relation to the chromosomal location of 18S–5.8S–26S rDNA and a C genome specific DNA sequence in the genus Avena

Genome ◽

10.1139/g96-068 ◽

1996 ◽

Vol 39 (3) ◽

pp. 535-542 ◽

Cited By ~ 63

Author(s):

Concha Linares ◽

Juan González ◽

Esther Ferrer ◽

Araceli Fominaya

Keyword(s):

In Situ Hybridization ◽

Dna Sequence ◽

Diploid Species ◽

5S Rdna ◽

Rdna Genes ◽

26S Rdna ◽

A Genome ◽

Rdna Loci ◽

C Genome

A physical map of the locations of the 5S rDNA genes and their relative positions with respect to 18S–5.8S–26S rDNA genes and a C genome specific repetitive DNA sequence was produced for the chromosomes of diploid, tetraploid, and hexaploid oat species using in situ hybridization. The A genome diploid species showed two pairs of rDNA loci and two pairs of 5S loci located on both arms of one pair of satellited chromosomes. The C genome diploid species showed two major pairs and one minor pair of rDNA loci. One pair of subtelocentric chromosomes carried rDNA and 5S loci physically separated on the long arm. The tetraploid species (AACC genomes) arising from these diploid ancestors showed two pairs of rDNA loci and three pairs of 5S loci. Two pairs of rDNA loci and 2 pairs of 5S loci were arranged as in the A genome diploid species. The third pair of 5S loci was located on one pair of A–C translocated chromosomes using simultaneous in situ hybridization with 5S rDNA genes and a C genome specific repetitive DNA sequence. The hexaploid species (AACCDD genomes) showed three pairs of rDNA loci and six pairs of 5S loci. One pair of 5S loci was located on each of two pairs of C–A/D translocated chromosomes. Comparative studies of the physical arrangement of rDNA and 5S loci in polyploid oats and the putative A and C genome progenitor species suggests that A genome diploid species could be the donor of both A and D genomes of polyploid oats. Key words : oats, 5S rDNA genes, 18S–5.8S–26S rDNA genes, C genome specific repetitive DNA sequence, in situ hybridization, genome evolution.

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Genomic in situ hybridization analysis of a trigenomic hybrid involving Solanum and Lycopersicon species

Genome ◽

10.1139/g00-114 ◽

2001 ◽

Vol 44 (2) ◽

pp. 299-304 ◽

Cited By ~ 2

Author(s):

S N Haider Ali ◽

Dirk Jan Huigen ◽

M S Ramanna ◽

Evert Jacobsen ◽

Richard GF Visser

Keyword(s):

In Situ Hybridization ◽

Chromosome Doubling ◽

Genomic In Situ Hybridization ◽

Potato Genome ◽

Meiotic Chromosomes ◽

Lycopersicon Species ◽

Bridge Species ◽

Genomic Probes ◽

Homoeologous Chromosomes

A 4x potato (+) tomato fusion hybrid (2n = 4x = 48) was successfully backcrossed with a diploid Lycopersicon pennellii (2n = 2x = 24). Genomic in situ hybridization (GISH) on somatic and meiotic chromosomes confirmed that the progenies were triploids (2n = 3x = 36) and possessed three different genomes: potato, tomato, and L. pennellii. Therefore, they have been called trigenomic hybrids. Total genomic probes of both Lycopersicon species were found to hybridize mutually, whereas the potato genome was clearly differentiated. During metaphase I, bivalents were formed predominantly between tomato and L. pennellii chromosomes and the univalents of potato chromosomes were most common. Trivalents in all cases included homoeologous chromosomes of potato, tomato, and L. pennellii. However, the triploids were totally sterile as determined from extensive crossing. On chromosome doubling of triploids by shoot regeneration from callus, hexaploids (2n = 6x = 72) were obtained. Despite exhibiting clear allohexaploid behaviour by forming 36 bivalents at meiosis, these were also completely sterile like their triploid counterparts. In spite of this drawback, the prospects of chromosome pairing between potato L. pennellii and Solanum genomes does open the possibilities for bringing the two genera close.Key words: trigenomic triploids, GISH, bridge species, potato (+) tomato fusion hybrids.

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