Chromosomal Diversification in Two Species of Pimelodus (Siluriformes: Pimelodidae): Comparative Cytogenetic Mapping of Multigene Families

Cytogenetic Analysis of the Fish Genus Carassius Indicates Divergence, Fission, and Segmental Duplication as Drivers of Tandem Repeat and Microchromosome Evolution

Fishes of the genus Carassius are useful experimental vertebrate models for the study of evolutionary biology and cytogenetics. Carassius demonstrates diverse biological characteristics, such as variation in ploidy levels and chromosome numbers, and presence of microchromosomes. Those Carassius polyploids with ≥150 chromosomes have microchromosomes, but the origin of microchromosomes, especially in European populations, is unknown. We used cytogenetics to study evolution of tandem repeats (U1 and U2 small nuclear DNAs and H3 histone) and microchromosomes in Carassius from the Czech Republic. We tested the hypotheses whether the number of tandem repeats was affected by polyploidization or divergence between species and what mechanism drives evolution of microchromosomes. Tandem repeats were found in tetraploid and hexaploid Carassius gibelio, and tetraploid Carassius auratus and Carassius carassius in conserved numbers, with the exception of U1 small nuclear DNA in C. auratus. This conservation indicates reduction and/or loss in the number of copies per locus in hexaploids and may have occurred by divergence rather than polyploidization. To study the evolution of microchromosomes, we used the whole microchromosome painting probe from hexaploid C. gibelio and hybridized it to tetraploid and hexaploid C. gibelio, and tetraploid C. auratus and C. carassius. Our results revealed variation in the number of microchromosomes in hexaploids and indicated that the evolution of the Carassius karyotype is governed by macrochromosome fissions followed by segmental duplication in pericentromeric areas. These are potential mechanisms responsible for the presence of microchromosomes in Carassius hexaploids. Differential efficacy of one or both of these mechanisms in different tetraploids could ensure variability in chromosome number in polyploids in general.

U2 and U4 snDNA Comparative Chromosomal Mapping in the Neotropical Fish Genera Apareiodon and Parodon (Characiformes: Parodontidae)

Small nuclear DNA (snDNA) are valuable cytogenetic markers for comparative studies in chromosome evolution because different distribution patterns were found among species. Parodontidae, a Neotropical fish family, is known to have female heterogametic sex chromosome systems in some species. The U2 and U4 snDNA sites have been found to be involved in Z and W chromosome differentiation in Apareiodon sp., Apareiodon affinis, and Parodon hilarii. However, few studies have evaluated snDNA sites as propulsors of chromosome diversification among closely related fish species. In this study, we investigated the distribution of U2 and U4 snDNA clusters in the chromosomes of 10 populations/species belonging to Apareiodon and Parodon, aiming to identify chromosomal homeologies or diversification. In situ localization data revealed a submetacentric pair carrying the U2 snDNA site among the populations/species analyzed. Furthermore, all studied species demonstrated homeology in the location of U4 snDNA cluster in the proximal region of metacentric pair 1, besides an additional signal showing up with a divergence in Apareiodon. Comparative chromosomal mapping of U4 snDNA also helped to reinforce the proposal of the ZZ/ZW1W2 sex chromosome system origin in an A. affinis population. According to cytogenetic data, the study corroborates the diversification in Parodontidae paired species with uncertain taxonomy.

Chromosomal Diversification in Pseudacanthicus Species (Loricariidae, Hypostominae) Revealed by Comparative Mapping of Repetitive Sequences

Simple Summary

The fishes of the Loricariidae family have a huge genetic diversity, mainly involving variations in the number and shape of chromosomes. The recognition of the species genus Pseudacanthicus is complex due to the large diversity of forms and limited knowledge of their genetic diversity. In this study, the karyotypes of three Pseudacanthicus species were comparatively analyzed using classical and molecular methods. They presented the same diploid number, but with different compositions of repetitive DNA sequences. Such information can be useful for the recognition of distinct species, in addition to providing important insights into the real biodiversity of this important group of Neotropical fish.

Abstract

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.

Comparative Cytogenetic and Sequence Analysis of U Small Nuclear RNA Genes in Three Ancistrus Species (Siluriformes: Loricariidae)

Ancistrus presents a wide karyotypic diversity, resulting from numeric and structural chromosomal rearrangements. It has been proposed that some genome-specific regions containing repetitive units could organize prone-to-break DNA sites in Loricariidae, triggering chromosomal rearrangements such as Robertsonian fusions (Rb fusions), centric fissions, translocations, and inversions. The tandemly repeats of the small nuclear RNAs (snRNAs) gene families are considered good cytogenetic markers for understanding chromosomal remodeling events among closely related species, but these snRNAs have been scarcely analyzed in Ancistrus. This study presented the nucleotide sequencing and comparative in situ location of U snRNA sequences from Ancistrus aguaboensis, Ancistrus cf. multispinis, and Ancistrus sp. (2n = 50, 52, and 50, respectively), aiming to provide information about snRNA clusters in the genome and chromosome evolution in Ancistrus. U snRNA nucleotide sequences of Ancistrus presented identity to orthologous copies and folded their secondary structures correctly. In situ localization and karyotyping of the three Ancistrus species revealed clustered copies of U2 and U5 snRNA gene families to a single chromosome site, one chromosome pair bearing U1 snRNA sequence, and one main locus of U4 snRNA sequence, besides scattered signals along the chromosomes. Previous studies related the participation of the rRNA gene families in centric fusion events, contributing to chromosome rearrangements and karyotype plasticity present in Loricariidae. In this study, homeologies in U snRNA loci chromosomal locations were detected, indicating the occurrence of conserved sites of these gene families in these three Ancistrus species with 2n = 50 or 52 chromosomes.

Major and minor U small nuclear RNAs genes characterization in a neotropical fish genome: Chromosomal remodeling and repeat units dispersion in Parodontidae

In association with many proteins, small nuclear RNAs (snRNAs) organize the spliceosomes that play a significant role in processing precursor mRNAs during gene expression. According to snRNAs genic arrangements, two kinds of spliceosomes (major and minor) can be organized into eukaryotic cells. Although in situ localization of U1 and U2 snDNAs have been performed in fish karyotypes, studies with genomic characterization and functionality of U snRNAs integrated into chromosomal changes on Teleostei are still scarce. This study aimed to achieve a genomic characterization of the U snRNAs genes in Apareiodon sp. (2n = 54, ZZ/ZW), apply these data to recognize functional/defective copies, and map chromosomal changes involving snDNAs in Parodontidae species karyotype diversification. Nine snRNA multigene families (U1, U2, U4, U5, U6, U11, U12, U4atac and U6atac) arranged in putatively functional copies in the genome were analyzed. Proximal Sequence Elements (PSE) and TATA-box promoters occurrence, besides an entire transcribed region and conserved secondary structures, qualify them for spliceosome activity. In addition, several defective copies or pseudogenes were identified for the snRNAs that make up the major spliceosome. In situ localization of snDNAs in five species of Parodontidae demonstrated that U1, U2, and U4 snDNAs were involved in chromosomal location changes or units dispersion. The U snRNAs defective/pseudogenes units dispersion could be favored by the probable occurrence of active retrotransposition enzymes in the Apareiodon genome. The U2 and U4 snDNAs sites were involved in independent events in the differentiation of sex chromosomes among Parodontidae lineages. The study characterized U snRNA genes that compose major and minor spliceosomes in the Apareiodon sp. genome and proposes that their defective copies trigger chromosome differentiation and diversification events in Parodontidae.

Evolutionary insights into the genomic organization of major ribosomal DNA in ant chromosomes

The major rDNA genes are composed of tandem repeats and are part of the nucleolus organizing regions (NORs). They are highly conserved and therefore useful in understanding the evolutionary patterns of chromosomal locations. The evolutionary dynamics of the karyotype may affect the organization of rDNA genes within chromosomes. In this study, we physically mapped 18S rDNA genes in 13 Neotropical ant species from four subfamilies using fluorescence in situ hybridization. Furthermore, a survey of published rDNA cytogenetic data for 50 additional species was performed, which allowed us to detect the evolutionary patterns of these genes in ant chromosomes. Species from the Neotropical, Palearctic, and Australian regions, comprising a total of 63 species from 19 genera within six subfamilies, were analysed. Most of the species (48 out of 63) had rDNA genes restricted to a single chromosome pair in their intrachromosomal regions. The position of rDNA genes within the chromosomes appears to hinder their dispersal throughout the genome, as translocations and ectopic recombination are uncommon in intrachromosomal regions because they can generate meiotic abnormalities. Therefore, rDNA genes restricted to a single chromosome pair seem to be a plesiomorphic feature in ants, while multiple rDNA sites, observed in distinct subfamilies, may have independent origins in different genera.

Chromosome Mapping of U2 snDNA in Species of Leptodactylus (Anura, Leptodactylidae)

Small nuclear RNA (snRNA) is a class of molecules involved in the processing of pre-mRNA and in regulatory cell processes. snRNAs are always associated with a set of specific proteins. The complexes are referred to as small nuclear ribonucleoproteins, and spliceosome U RNAs are their most common snRNA components. The repetitive sequences of U snDNAs have been cytogenetically mapped in several species of Arthropoda, fishes, and mammals; however, their distribution remains unknown in amphibians. Here, we show results of FISH mapping of U2 snDNA repetitive sequences in species of the amphibian genus Leptodactylus to reveal the distribution patterns of this sequence in their karyotypes. The probe hybridized in the metacentric chromosome pair 6 in Leptodactylus fuscus, L. gracilis, L. latrans, L. chaquensis, L. petersii, L. podicipinus, and L. brevipes. A different pattern was observed in L. labyrinthicus with hybridization signals in 4 chromosome pairs. The same localization of U2 gene sequences in most of the species analyzed suggests a relatively conserved pattern and a similarity of the chromosome 6 among these species of Leptodactylus.

Karyotypic Diversification in Two Megaleporinus Species (Characiformes, Anostomidae) Inferred from In Situ Localization of Repetitive DNA Sequences

Anostomidae species have conserved diploid numbers (2n = 54), although comparative cytogenetic studies have demonstrated chromosomal rearrangements occurrence among them, especially in repetitive DNA rich regions. The location and distribution of ribosomal DNA (rDNA) and small nuclear RNAs (snRNAs) multigene families are highly dynamic in the genomes of several organisms. In this study, we in situ located the rDNA and snRNA sites in two populations of Megaleporinus obtusidens and a sample of Megaleporinus reinhardti to infer their chromosomal changes in the evolutionary lineages. Both species of Megaleporinus shared 2n = 54 chromosomes with the presence of ZZ/ZW sex chromosome system, but they diverged in relationship to the location of 5S and 45S rDNAs as well as the distribution of snRNAs sites. The characterization of the analyzed sequences revealed the presence of complete rDNA and snRNAs sequences as well as snRNAs containing transposable elements (TEs) and microsatellite repeats. After chromosomal mapping, the sequences encompassing TEs proved to be dispersed through autosomes and accumulated on sex chromosomes. The data demonstrate that intra- and interspecific chromosomal changes occurred involving the multigene family's sites in Megaleporinus karyotypes. Furthermore, we detected TE-like sequences in the differentiation of sex chromosome systems in M. obtusidens and M. reinhardti.