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The schematic diagram of the distribution pattern of 5S rDNA in Amolops mantzorum. The black dots represent the results of FISH using 4 probes: the 5S rDNA coding sequences, type I NTS sequence, type II NTS sequence, and the entire type II 5S rDNA sequences, which all show the same distribution pattern.
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In an attempt to extend the knowledge of the 5S rDNA organization in anurans, the 5S rDNA sequences of Amolops mantzorum were isolated, characterized, and mapped by FISH. Two forms of 5S rDNA, type I (209 bp) and type II (about 870 bp), were found in specimens investigated from various populations. Both of them contained a 118-bp coding sequence, r...
Citations
... The sequence lengths of 5S rDNA range from 48 bp [10] to 854 bp [11] according to the copies and variations available when searching for "5S rDNA" in the Nucleotide database of the National Center for Biotechnology Information (NCBI). Furthermore, the lengths of 5S rDNA as a FISH probe in the NCBI PubMed database varied considerably, at 41-1193 bp [12,13]. ...
... With the evolution and development of the plant, 5S rDNA also underwent simultaneous changes. The length of 5S rDNA in the NCBI Nucleotide database ranged from 48 to 854 bp [10,11], while its length as a FISH probe in the PubMed database of NCBI ranged from 41 to 1193 bp [12,13,31]. This study was the first time that the 41-bp oligoprobe had been used to analyze 5S rDNA for 19 species from 13 families. ...
... Such a signal position was found in the chromosome interstitial position, distal position, proximal position, and far away from the chromosome [3,21,[25][26][27]. In this study, 5S rDNA was diverse and abundant in signal site number (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18), position (e.g., interstitial, distal, proximal position, and occasionally, outside the chromosome), and even in intensity (e.g., strong, weak, slight). These findings are consistent with previous studies of the 5S rDNA signal pattern of A. fruticose, B. formosana 'Leshan', C. campanulatus, H. mutabilis, P. nepalensis, S. oblata, two species of Berberis, two varieties of J. regia, two varieties of J. sigillata, two species of Ligustrum, two varieties of Robinia, and two varieties of Z. armatum, wild/cultural H. rhamnoides ssp. ...
This study was conducted to evaluate the 5S rDNA site number, position, and origin of signal pattern diversity in 42 plant species using fluorescence in situ hybridization. The species were selected based on the discovery of karyotype rearrangement, or because 5S rDNA had not yet been explored the species. The chromosome number varied from 14 to 160, and the chromosome length ranged from 0.63 to 6.88 μm, with 21 species having small chromosomes (<3 μm). The chromosome numbers of three species and the 5S rDNA loci of nineteen species are reported for the first time. Six 5S rDNA signal pattern types were identified. The 5S rDNA varied and was abundant in signal site numbers (2–18), positions (distal, proximal, outside of chromosome arms), and even in signal intensity. Variation in the numbers and locations of 5S rDNA was observed in 20 species, whereas an extensive stable number and location of 5S rDNA was found in 22 species. The potential origin of the signal pattern diversity was proposed and discussed. These data characterized the variability of 5S rDNA within the karyotypes of the 42 species that exhibited chromosomal rearrangements and provided anchor points for genetic physical maps.
... These results comprise the first report of 5S rDNA chromosomal location for Dendrobatidae and, in this sense, it is not possible to compare these results with similar species. However, the literature shows that, in amphibians, 5S rDNA is commonly found in a greater number of sites distributed among several chromosome pairs (Liu et al., 2017;Cholak et al., 2020). ...
Ameerega trivittata is a widely distributed dendrobatid species with colour polymorphism for which only the diploid
number, nucleolar organizer regions (NORs) and heterochromatic pattern are known. Here, we investigated the
existence of cytogenetic structure in A. trivittata populations with different morphotypes. Four morphotypes and their
geographical distributions were defined. All the individuals have 24 chromosomes and a similar heterochromatic
pattern, the same location of telomeric regions and 5S rDNA. The NOR site was coincident with the 18S rDNA in pair
9, but some individuals presented an additional site in one of the homologues of pair 11. The highest variation was
found in the microsatellite distribution patterns. Comparing the cytogenetic characters of the individuals, two groups
were detected: (1) Tabatinga (morphotype B) and Benjamin Constant (morphotype A), and (2) Presidente Figueiredo
and Tefé (morphotype C). The cytogenetic data appear to be correlated to the structure pattern of the morphotypes,
and corroborate the dispersal routes proposed in the literature. This is the first study of population cytogenetics for
the group. Our results provide a series of cytogenetic characters for A. trivittata and for Dendrobatidae for the first
time and highlight the importance of considering cytogenetics in population research.
... Finally, the sex-linked markers of eight of the nine Amolops species were successfully aligned to the genome of the sex chromosome (No. 5) of A. mantzorum, which was previously shown to be homologous among the A. mantzorum species group [40,41]. The results showed that, except for A. wuyiensis, of which only 13.8% of the sex-linked markers were successfully aligned, the majority of the sex-linked markers, ranging from 41.5% to 71.4%, were successfully mapped ( Figure S1; File S6). ...
In sharp contrast to birds and mammals, in numerous cold-blooded vertebrates, sex chromosomes have been described as homomorphic. This sex chromosome homomorphy has been suggested to result from the high turnovers often observed across deeply diverged clades. However, little is known about the tempo and mode of sex chromosome evolution among the most closely related species. Here, we examined the evolution of sex chromosome among nine species of the torrent frog genus Amolops. We analyzed male and female GBS and RAD-seq from 182 individuals and performed PCR verification for 176 individuals. We identified signatures of sex chromosomes involving two pairs of chromosomes. We found that sex-chromosome homomorphy results from both turnover and X–Y recombination in the Amolops species, which simultaneously exhibits heterogeneous evolution on homologous and non-homologous sex chromosomes. A low turnover rate of non-homologous sex chromosomes exists in these torrent frogs. The ongoing X–Y recombination in homologous sex chromosomes will act as an indispensable force in preventing sex chromosomes from differentiating.
... RNA hereditary material of ribosomes can have hundreds of homologous exons. 20 Most discrete locations often include many exons, which is especially thoroughly exemplified with immune serum globulin gene position. For instance, the murine serum immune globulin lambda light chain gene position incorporates over 140 ultraviolet genetic codes and homologous exons, of which at least 47 ultraviolet genetic codes are exons. ...
The junk DNA "pseudogenes," known as genomic fossils, are characterized by their ubiquitousness and abundance within the genomic structure. These genomics sets are recognized by the potential activity of meta-regulating the parent genes; these are transcribed into interfering RNA, consequently acting on miRNA concentration, thereby shedding light on the crosstalk of the pseudogenes' miRNA, siRNA, lncRNA/tumor therapy co-relationship. Moreover, an upcoming visualization regarding pseudogenes is under investigation, which describes the potentiality of pseudogenes as a fundamental component of cancerous evolutionary processing tools. Accordingly, here is a systematic review covering pseudobirth, pseudosignatures, and functional properties of pseudogenes, concluding that these pseudogenes are hypothetically predictive tumor therapies.
... For A. mantzorum, the subtelocentric Y (chromosome 5) was formed with a large chromosome pericentric inversion [22,23], which could easily be identified with other chromosomes under light microscopy ( Figure 1, Y chromosome microdissection). We completed Y chromosome isolation according to the protocol of Zimmer et al. (1997) [24], and DNA amplification following the protocol of Yuan et al. (2017) [25]. ...
... The chromosome heteromorphism was found in the chromosome pair 5 in males, which is composed of a subtelocentric chromosome (ST) and a metacentric chromosome (M), as can be easily identified under light microscopy. The 5S rDNA was detected in the telomeric regions of the short arms of both the X and Y homologues, clearly demonstrating that the subtelocentric Y could be reconstructed from the X chromosome by pericentric inversions [23]. The C-positive heterochromatins were observed in the middle regions of the long arm in the Y chromosome, indicating that these two originally homologous chromosomes start to differentiate [28]. ...
We used a genotyping-by-sequencing (GBS) approach to identify sex-linked markers in a torrent frog (Amolops mantzorum), using 21 male and 19 female wild-caught individuals from the same population. A total of 141 putatively sex-linked markers were screened from 1,015,964 GBS-tags via three approaches, respectively based on sex differences in allele frequencies, sex differences in heterozygosity, and sex-limited occurrence. With validations, 69 sex-linked markers were confirmed, all of which point to male heterogamety. The male specificity of eight sex markers was further verified by PCR amplifications, with a large number of additional individuals covering the whole geographic distribution of the species. Y chromosome (No. 5) was microdissected under a light microscope and amplified by whole-genome amplification, and a draft Y genome was assembled. Of the 69 sex-linked markers, 55 could be mapped to the Y chromosome assembly (i.e., 79.7%). Thus, chromosome 5 could be added as a candidate to the chromosomes that are particularly favored for recruitment in sex-determination in frogs. Three sex-linked markers that mapped onto the Y chromosome were aligned to three different promoter regions of the Rana rugosa CYP19A1 gene, which might be considered as a candidate gene for triggering sex-determination in A. mantzorum.
... Two types of repetitive DNAs, a fragment derived from the 5S rDNA type I NTS sequence (5ST1B) [Liu et al., 2017] and 7 different microsatellite motifs, were used as probes for FISH. The 5ST1B fragment, including 42 bp with the sequence 5 ′ -GCCATGC-CAAGGTGAAGAGGGATGGGAGCAGCAAAGGAGATC-3 ′ , was commercially synthesized and end-labeled with TAMRA at the 5 ′ position by Sangon Biotech Ltd. Co. (Shanghai, China). ...
In an attempt to analyze the organization of repetitive DNAs in the amphibian genome, 7 microsatellite motifs and a 5S rDNA sequence were synthesized and mapped in the karyotypes of 5 Amolops species. The results revealed nonrandom distribution of the microsatellite repeats, usually in the heterochromatic regions, as found in other organisms. These microsatellite repeats showed rapid changes among Amolops species, documenting the recent evolutionary history within this lineage. In contrast, 5S rDNA was localized in chromosomes 5 of all species, suggesting that these chromosomes are homologous within the monophyletic clade. Furthermore, the heteromorphic X and Y sex chromosomes (chromosomes 5) of A.mantzorum, had identical patterns of 5S rDNA, indicating that the subtelocentric Y resulted from a pericentric inversion. Several microsatellite repeats were found in the heteromorphic sex chromosomes, verifying the association of repetitive DNAs with sex chromosome differentiation in A. mantzorum.
Sex chromosomes are popularized as a special role in driving speciation. However, the empirical evidence from natural population processes has been limited to organisms with degenerated sex chromosomes, where hemizygosity is mainly considered to act as the driver of reproductive isolation. Here, we examined several hybrid zones of torrent frog Amolops mantzorum species complex, using an approach by mapping species-diagnostic loci onto the reference genome to compare sex-linked versus autosomal patterns of introgression. We find little support in sex-linked incompatibilities for large X-effects for these populations in hybrid zones with homomorphic sex chromosomes, due to the absence of the hemizygous effects. As expected, the large X-effects were not found in those with heteromorphic but newly evolved sex chromosomes, owing to the absence of strong genetic differences between X and Y chromosomes. The available data so far on amphibians suggest little role for sex-linked genes in speciation. The large X-effects in those with nascent sex chromosomes may not be as ubiquitous as presumed across the animal kingdom.
