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The current distribution of the fish family Siluridae (red color). Inset: Thailand map indicating the collection sites of the 13 species studied herein. 1. Belodontichthys truncates (red circle); 2. Kryptopterus bicirrhis (light pink circle); 3. Kryptopterus giminus (violet circle); 4. Kryptopterus limpok (purple circle); 5. Kryptopterus microcephalus (blue circle); 6. Micronema cheveyi (light blue circle); 7. Ompok fumidus (light green circle); 8. Ompok siluroides (green circle); 9. Phalacronotus apogon (pink circle); 10. Phalacronotus bleekeri (grey circle); 11. Silurichthys phaiosoma (yellow circle); 12. Wallago attu (orange circle); 13. Wallago micropogon (black circle); 14. Silurus aristotelis (pink circle); and 15. Silurus glanis (dark green circle). The maps were created using QGis 3.4.3, Inkscape 0.92 and Photoshop 7.0.
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The catfish family Siluridae contains 107 described species distributed in Asia, but with some distributed in Europe. In this study, karyotypes and other chromosomal characteristics of 15 species from eight genera were examined using conventional and molecular cytogenetic protocols. Our results showed the diploid number (2n) to be highly divergent...
Citations
... This suggests that many male-linked loci were false-positive loci. By contrast, large chromosomal rearrangements were often observed in teleosts, even at the same genus level [37][38][39]. Silver barb and common barbel are not at the same genus level, and intra-and interchromosomal rearrangements might result in chromosomal linkage reshuffling, whereas about half of the male-linked loci of the silver barb were informatically mapped onto common barbell chromosomes. All male-linked loci might be retained on the same linkage in the silver barb. ...
Silver barb (Barbonymus gonionotus) is among the most economically important freshwater fish species in Thailand. It ranks fourth in economic value and third in production weight for fisheries and culture in Thailand. An XX/XY sex-determination system based on gynogenesis was previously reported for this fish. In this study, the molecular basis underlying the sex-determination system was further investigated. Genome-wide single-nucleotide polymorphism data were generated for 32 captive-bred silver barb individuals, previously scored by phenotypic sex, to identify sex-linked regions associated with sex determination. Sixty-three male-linked loci, indicating putative XY chromosomes, were identified. Male-specific loci were not observed, which indicates that the putative Y chromosome is young and the sex determination region is cryptic. A homology search revealed that most male-linked loci were homologous to the Mariner/Tc1 and Gypsy transposable elements and are probably the remnants of an initial accumulation of repeats on the Y chromosome from the early stages of sex chromosome differentiation. This research provides convincing insights into the mechanism of sex determination and reveals the potential sex determination regions in silver barb. The study provides the basic data necessary for increasing the commercial value of silver barbs through genetic improvements.
... As a result, we selected a representative from each branch and compared their genomes using CGH to see if they also presented a genomic variation associated with their repetitive DNA content. This genome comparison technique has been applied to several teleost families, including the Salmonidae [64], Characidae [65], Cichlidae [66], Siluridae [67], and cyprinoids with small genome sizes, such as the Iberian Leuciscidae [68] or Carassius [69]. The remarkable chromosomal dynamism in both C. harmandi and M. chilopterus species corresponded with high dynamics in their repetitive DNA content, evidenced by a variety of non-overlapping signals revealing sequence conservation among their genomes, particularly in centromeric regions (Figure 7). ...
The representatives of cyprinid lineage 'Poropuntiinae' with 16 recognized genera and around 100 species form a significant part of Southeast Asian ichthyofauna. Cytogenetics are valuable when studying fish evolution, especially the dynamics of repetitive DNAs, such as ribosomal DNAs (5S and 18S) and microsatellites, that can vary between species. Here, karyotypes of seven 'poropuntiin' species, namely Cosmochilus harmandi, Cyclocheilichthys apogon, Hypsibarbus malcomi, H. wetmorei, Mystacoleucus chilopterus, M. ectypus, and Puntioplties proctozysron occurring in Thailand were examined using conventional and molecular cytogenetic protocols. Variable numbers of uni-and bi-armed chromosomes indicated widespread chromosome rearrangements with a stable diploid chromosome number (2n) of 50. Examination with fluorescence in situ hybridization using major and minor ribosomal probes showed that Cosmochilus harmandi, Cyclocheilichthys apogon, and Puntioplites proctozystron all had one chromosomal pair with 5S rDNA sites. However, more than two sites were found in Hypsibarbus malcolmi, H. wetmorei, Mystacoleucus chilopterus, and M. ectypus. The number of chromosomes with 18S rDNA sites varied amongst their karyotypes from one to three; additionally , comparative genomic hybridization and microsatellite patterns varied among species. Our results reinforce the trend of chromosomal evolution in cyprinifom fishes, with major chromosomal rearrangements, while conserving their 2n.
... The multiple 5S rDNA sites, due to their intensive activity and chromatin decondensation, have been proposed to act as hotspots of chromosome rearrangements (breakpoint regions for the fusion) in Loricariidae and Ancistrus [70][71][72][73][74]. However, it remains debated whether the dispersion of these ribosomal sequences in fish genomes is linked to the presence of TEs and is a byproduct of genome/chromosome re-arrangements [75]. The potential effects of the accumulation of repetitive DNA and its influence on the frequency of recombination have been shown in many fish species [e.g. ...
Ancistrus Kner, 1854, is the most diverse genus among the Ancistrini (Loricariidae) with 70 valid species showing a wide geographic distribution and great taxonomic and systematic complexity. To date, about 40 Ancistrus taxa have been karyotyped, all from Brazil and Argentina, but the statistic is uncertain because 30 of these reports deal with samples that have not yet been identified at the species level. This study provides the first cytogenetic description of the bristlenose catfish, Ancistrus clementinae Rendahl, 1937, a species endemic to Ecuador, aiming to verify whether a sex chromosome system is identifiable in the species and, if so, which, and if its differentiation is associated with the presence of repetitive sequences reported for other species of the family. We associated the karyotype analysis with the COI molecular identification of the specimens. Karyo-type analysis suggested the presence of a ♂ZZ/♀ZW1W2 sex chromosome system, never detected before in Ancistrus, with both W1W2 chromosomes enriched with heterochromatic blocks and 18S rDNA, in addition to GC-rich repeats (W2). No differences were observed between males and females in the distribution of 5S rDNA or telomeric repeats. Cytogenetic data here obtained confirm the huge karyotype diversity of Ancistrus, both in chromosome number and sex-determination systems.
... These groups of repetitive sequences have been useful as markers in comparative cytogenetic analyses, improving the understanding of mechanisms of karyotypic diversification in different groups of fish [9,10,[18][19][20][21]. Furthermore, these analyses have been efficient in evidencing mechanisms of chromosomal differentiation between species whose karyotypic constitution appears to be homogeneous, representing an important approach to the study of karyotypic diversification in these groups of organisms, as observed in different lineages of the subfamily Hypostominae [10,22,23]. ...
Pseudacanthicus is a genus of Neotropical fish with eight valid species, in addition to numerous lineages not formally identified. It occurs along the Amazon and Tocantins River basins, in Suriname and in the Guiana shield. There are no karyotypic data in the literature for species of this genus. Here, the karyotypes of three Pseudacanthicus species (P. spinosus, P. leopardus and Pseudacanthicus sp.) were comparatively analyzed by classical cytogenetics and fluorescence in situ hybridization using 18S and 5S rDNA probes, U2 snDNA and telomeric sequences. The analyzed species presented 52 chromosomes and KF = 18 m + 34 sm. Constitutive heterochromatin occurred in blocks on a few chromosomes. The 18S rDNA occurred in a single pair; interestingly, P. leopardus presented only one locus of this sequence in its diploid genome. The 5S rDNA sequence occurred in only one pair in P. leopardus, and in multiple sites in Pseudacanthicus sp. and P. spinosus. The snDNA U2 occurred in only one pair in all analyzed species. Telomeric sequences did not show interstitial sites. Although Pseudacanthicus species share the same 2n and KF, repetitive sequence analysis revealed karyotypic diversity among these species. The occurrence of DNA double-strand breaks related to fragile sites, unequal crossing over and transpositions is proposed as the mechanism of karyotypic diversification, suggesting that the conservation of the karyotypic macrostructure is only apparent in this group of fish.
... These groups of repetitive sequences have been useful as markers in comparative cytogenetic analyses, improving the understanding of mechanisms of karyotypic diversification in different groups of fish [9,10,[18][19][20][21]. Furthermore, these analyses have been efficient in evidencing mechanisms of chromosomal differentiation between species whose karyotypic constitution appears to be homogeneous, representing an important approach to the study of karyotypic diversification in these groups of organisms, as observed in different lineages of the subfamily Hypostominae [10,22,23]. ...
... What could have driven the extensive karyotype diversification observed in these populations? Although the mapping of repetitive sequences has been shown to be useful for detecting karyotypic changes during the chromosomal evolution [41,42], such analyses are still scarce among rodents. As an example, the main 96 repetitive DNA family responsible for rolling circle replication in Ctenomys was isolated and characterized [43,44]. ...
... Additionally, chromosomal mapping of eight microsatellite sequence motifs and LINE-1like retroelement was documented among the populations throughout their distribution What could have driven the extensive karyotype diversification observed in these populations? Although the mapping of repetitive sequences has been shown to be useful for detecting karyotypic changes during the chromosomal evolution [41,42], such analyses are still scarce among rodents. As an example, the main 96 repetitive DNA family responsible for rolling circle replication in Ctenomys was isolated and characterized [43,44]. ...
The Neotropical underground rodents of the genus Ctenomys (Rodentia: Ctenomyidae) comprise about 65 species, which harbor the most significant chromosomal variation among mammals (2n = 10 to 2n = 70). Among them, C. minutus stands out with 45 different cytotypes already identified, among which, seven parental ones, named A to G, are parapatrically distributed in the coastal plains of Southern Brazil. Looking for possible causes that led to such extensive karyotype diversification, we performed chromosomal mapping of different repetitive DNAs, including microsatellites and long interspersed element-1 (LINE-1) retrotransposons in the seven parental cytotypes. Although microsatellites were found mainly in the centromeric and telomeric regions of the chromosomes, different patterns occur for each cytotype, thus revealing specific features. Likewise, the LINE-1-like retrotransposons also showed a differential distribution for each cytotype, which may be linked to stochastic loss of LINE-1 in some populations. Here, microsatellite motifs (A)30, (C)30, (CA)15, (CAC)10, (CAG)10, (CGG)10, (GA)15, and (GAG)10 could be mapped to fusion of chromosomes 20/17, fission and inversion in the short arm of chromosome 2, fusion of chromosomes 23/19, and different combinations of centric and tandem fusions of chromosomes 22/24/16. These data provide evidence for a correlation between repetitive genomic content and localization of evolutionary breakpoints and highlight their direct impact in promoting chromosomal rearrangements.
... The total length of the hybrid genome, and the divided S. asotus and S. meridionalis genome are approximate to 1.54 Gb, 744.12 Mb, and 748.79 Mb, respectively (Table 1). Precisely, the total length of the anchored contigs accounted for 96.66% of the assembly, and thus the 58 scaffolds may represent the 58 chromosomes of the hybrid individual and the assembly is nearly chromosomal 41 . BUSCO assessments suggested that about 80.50% of the 3640 near-universal single-copy orthologs in Actinopterygii are duplicated in the hybrid genome, and another 17% are single-copy, and about 0.20% are fragmented and 2.30% are missing (Supplemental Figure S2). ...
Genome complexity such as heterozygosity may heavily influence its de novo assembly. Sequencing somatic cells of the F1 hybrids harboring two sets of genetic materials from both of the paternal and maternal species may avoid alleles discrimination during assembly. However, the feasibility of this strategy needs further assessments. We sequenced and assembled the genome of an F1 hybrid between Silurus asotus and S. meridionalis using the SequelII platform and Hi-C scaffolding technologies. More than 300 Gb raw data were generated, and the final assembly obtained 2344 scaffolds composed of 3017 contigs. The N50 length of scaffolds and contigs was 28.55 Mb and 7.49 Mb, respectively. Based on the mapping results of short reads generated for the paternal and maternal species, each of the 29 chromosomes originating from S. asotus and S. meridionalis was recognized. We recovered nearly 94% and 96% of the total length of S. asotus and S. meridionalis. BUSCO assessments and mapping analyses suggested that both genomes had high completeness and accuracy. Further analyses demonstrated the high collinearity between S. asotus, S. meridionalis, and the related Pelteobagrus fulvidraco. Comparison of the two genomes with that assembled only using the short reads from non-hybrid parental species detected a small portion of sequences that may be incorrectly assigned to the different species. We supposed that at least part of these situations may have resulted from mitotic recombination. The strategy of sequencing the F1 hybrid genome can recover the vast majority of the parental genomes and may improve the assembly of complex genomes.
... Thus, this genus as well as this family have the conserved NOR number as the ancestral character of the catfish. This character is quite different from silurid catfish (Ditcharoen et al., 2019). In fishes, the location of NORs in a terminal position is also considered as a primitive characteristic (Vitturi et al., 1995). ...
... This species and the genus Mystus share the most conservative patterns concerning number and position of 18S rDNA clusters. Moreover, a single pair of 18S rDNA loci was identified in several fish species, namely Channa lucius (Cioffi et al., 2015), Abudefduf genus (Getlekha et al., 2016a), Dascyllus genus (Getlekha et al., 2016b), Clarias gariepinus and C. macrocephalus (Maneechot et al., 2016), Belodontichthys truncatus, Kryptopterus limpok, K. macrocephalus, Micronema cheveyi, Ompok fumidus, Phalacronotus apogon, P. bleekeri, and Wallago attu (Ditcharoen et al., 2019). ...
... The number of 5S rDNA sequences in S. acicularis is the same as in He. spilopterus (Supiwong et al., 2014b). In addition, this distribution is the same as for other catfishes including Clarias gariepinus (Maneechot et al., 2016) and Kryptopterus geminus (Ditcharoen et al., 2019). However, it is different from Bagrids such as He. ...
The first chromosomal analysis of Salween shovelhead catfish (Sperata acicularis) was undertaken by classical cytogenetic and fluorescence in situ hybridization (FISH) techniques in the present study. Ten male and ten female fish were obtained from Salween River, Mae Hong Son Province, Northern Thailand. The mitotic chromosome preparation was directly performed from kidney tissues. Conventional Giemsa staining, Ag-NOR staining, and molecular cytogenetics techniques with FISH using 5S, 18S rDNAs, and microsatellites d(CA)15 and d(GC)15 repeats as probes were conducted. The results indicated that the diploid chromosome number of S. acicularis was 2n = 56. The fundamental number (NF) was 110 both for males and females. The karyotype is composed of 18 large metacentric, 10 large submetacentric, 14 medium metacentric, 12 medium submetacentric and 2 medium acrocentric chromosomes; sex chromosomes could not be identified. NORs localized at the subtelomeric region of the short arm of metacentric chromosome pair 3, which coincides with location of 18S rDNA probe. 5S rDNA probe signal was detected on the short arm of the metacentric chromosome pairs 5 and 8. The distribution patterns of each analysed microsatellite repeat on the chromosomes differed from each other. Microsatellite d(CA)15 repeats were highly accumulated at telomeric regions of all chromosome pairs, and throughout the chromosome in some pairs while the microsatellite d(GC)15 repeats were scattered and less accumulated in some chromosome pairs. Overall, we present the karyotype of S. acicularis providing insights into species' evolution and enabling undoubtedly species identification.
... phaiosoma (Ditcharoen et al., 2019) to 92 in Kryptopterus cryptopterus (Donsakul and Magtoon, 1996) and Kryptopterus geminus (Ditcharoen et al., 2019). It is also known that Phalacronotus is the only genus that maintains the diploid number conservation with 2n = 64 in all analyzed species, while other genera in this family display a substantial variation (Ditcharoen et al., 2019). ...
... phaiosoma (Ditcharoen et al., 2019) to 92 in Kryptopterus cryptopterus (Donsakul and Magtoon, 1996) and Kryptopterus geminus (Ditcharoen et al., 2019). It is also known that Phalacronotus is the only genus that maintains the diploid number conservation with 2n = 64 in all analyzed species, while other genera in this family display a substantial variation (Ditcharoen et al., 2019). ...
... phaiosoma (Ditcharoen et al., 2019) to 92 in Kryptopterus cryptopterus (Donsakul and Magtoon, 1996) and Kryptopterus geminus (Ditcharoen et al., 2019). It is also known that Phalacronotus is the only genus that maintains the diploid number conservation with 2n = 64 in all analyzed species, while other genera in this family display a substantial variation (Ditcharoen et al., 2019). On the mapping of highly repetitive sequences, the high 2n variation also appears to be followed by a large variation of ribosomal DNAs loci among silurid species (Ditcharoen et al., 2019). ...
The freshwater family Siluridae occurs in Eurasia and is especially speciose in South and Southeast Asia, representing an important aquaculture and fishery targets. However, despite the restricted cytogenetic data, a high diploid number variation (from 2n=40 to 92) characterizes this fish group. Considering the large genomic divergence among its species , silurid genomes have experienced an enormous diversification throughout their evolutionary history. Here, we aim to investigate the chromosomal distribution of several microsatellite repeats in 12 Siluridae species and infer about their possible roles in the karyotype evolution that occurred in this group. Our results indicate divergent patterns of microsatellite distribution and accumulation among the analyzed species. Indeed, they are especially present in significant chromosome locations, such as the centromeric and telomeric regions, precisely the ones associated with several kinds of chromosomal rearrangements. Our data provide pieces of evidence that repetitive DNAs played a direct role in fostering the chromosomal differentiation and biodiversity in this fish family.
... However, this kind of study is scarcely applied in Thai freshwater fish. Exceptions are studies in Bagrid catfishes (Supiwong et al. 2013(Supiwong et al. , 2014a, Channids (Cioffi et al. 2015), three Clarias species (Maneechot et al. 2016), Toxotes chatareus (Hamilton, 1822) , two cyprinid fishes , Asian swamp eel, Monopterus albus (Zuiew, 1793) ) and silulid catfishes (Ditcharoen et al. 2019). The present study is the first report on chromosomal characteristics in P. cochinchinensis using conventional staining, Ag-NOR banding, and FISH technique, being the basis for further study by advanced genetics and for future comparative approaches concerning systematics and evolutionary relationships of buffer-fishes. ...
Pissaparn M, Phimphan S, Chaiyasan P, Tanoamtong A, Liehr T, Suwannapoom C, Reungsing M, Supiwong W. 2020. First chromosome analysis of Thai pufferfish Pao cochinchinensis (Steindachner, 1866). Biodiversitas 21: 4309-4316. Here first analysis of chromosomes and nucleolar organizer region (NOR) pattern in pufferfish Pao cochinchinensis (Steindachner, 1866) was undertaken. Chromosomal preparations were obtained from kidney of P. cochinchinensis from Chi River basin in Thailand. Chromosomal characteristics were analyzed by Giemsa staining, Ag-NOR banding as well as fluorescence in situ hybridization (FISH) using microsatellites d(CA)15 and d(CGG)10 probes. P. cochinchinensis had 2n = 40 with the fundamental number (NF) 74, both in male and female. The karyotype exhibited 12 metacentric (m), 10 submetacentric (sm), 12 acrocentric (a) and 6 telocentric (t) chromosomes. No differentiated heteromorphic sex chromosomes were observed. NORs were located on short arms adjacent to telomere of the metacentric chromosome pair 4, which coincide with signals of d(CGG)10 probe. FISH with d(CGG)10 sequences were also displayed at the telomeres of most other chromosomes, whereas d(CA)15 repeats highly accumulated throughout almost all entire chromosomes except for centromeric regions. The results of conventional Giemsa staining presented the differentiation even the same genus. The l ocalization of NORs on one pair of chromosomes only is a common characteristic found in many fish groups as well as other vertebrates. Mapping of two distinct microsatellites demonstrated the remarkable chromosomal diversification that characterizes evolution in the genus Pao. Both, conventional and molecular cytogenetics are excellent tools to study, and better understand chromosomal evolution, as well as to uncover biodiversity among fishes.