Is the Karyotype of Neotropical Boid Snakes Really Conserved? Cytotaxonomy, Chromosomal Rearrangements and Karyotype Organization in the Boidae Family

Karyotypic characterization of Centromochlus schultzi Rössel 1962 (Auchenipteridae, Centromochlinae) from the Xingu River basin: New inferences on chromosomal evolution in Centromochlus

Centromochlinae is a widely diverse subfamily with more than 50 species and several taxonomic conflicts due to morphological similarity between Tatia and Centromochlus species. However, cytogenetic studies on this group have been limited to only four species so far. Therefore, here we present the karyotype of Centromochlus schultzi from the Xingu River in Brazil using classic cytogenetic techniques, physical mapping of the 5S and 18S rDNAs, and telomeric sequences (TTAGGG)n. The species had 58 chromosomes, simple NORs and 18S rDNA sites. Heterochromatic regions were detected on the terminal position of most chromosomes, including pericentromeric and centromeric blocks that correspond to interstitial telomeric sites. The 5S rDNA had multiple sites, including a synteny with the 18S rDNA in the pair 24st, which is an ancestral feature for Doradidae, sister group of Auchenipteridae, but appears to be a homoplastic trait in this species. So far, C. schultzi is only the second species within Centromochlus to be karyotyped, but it has already presented characteristics with great potential to assist in future discussions on taxonomic issues in the subfamily Centromochlinae, including the first synteny between rDNAs in Auchenipteridae and also the presence of heterochromatic ITSs that could represent remnants of ancient chromosomal fusions.

Karyotype Diversification and Chromosome Rearrangements in Squamate Reptiles

Karyotype diversification represents an important, yet poorly understood, driver of evolution. Squamate reptiles are characterized by a high taxonomic diversity which is reflected at the karyotype level in terms of general structure, chromosome number and morphology, and insurgence of differentiated simple or multiple-sex-chromosome systems with either male or female heterogamety. The potential of squamate reptiles as unique model organisms in evolutionary cytogenetics has been recognised in recent years in several studies, which have provided novel insights into the chromosome evolutionary dynamics of different taxonomic groups. Here, we review and summarize the resulting complex, but promising, general picture from a systematic perspective, mapping some of the main squamate karyological characteristics onto their phylogenetic relationships. We highlight how all the major categories of balanced chromosome rearrangements contributed to the karyotype evolution in different taxonomic groups. We show that distinct karyotype evolutionary trends may occur, and coexist, with different frequencies in different clades. Finally, in light of the known squamate chromosome diversity and recent research advances, we discuss traditional and novel hypotheses on karyotype evolution and propose a scenario of circular karyotype evolution.

Cytogenetic Analysis of the Members of the Snake Genera Cylindrophis, Eryx, Python, and Tropidophis

The recent discovery of two independently evolved XX/XY sex determination systems in the snake genera Python and Boa sparked a new drive to study the evolution of sex chromosomes in poorly studied lineages of snakes, where female heterogamety was previously assumed. Therefore, we examined seven species from the genera Eryx, Cylindrophis, Python, and Tropidophis by conventional and molecular cytogenetic methods. Despite the fact that these species have similar karyotypes in terms of chromosome number and morphology, we detected variability in the distribution of heterochromatin, telomeric repeats, and rDNA loci. Heterochromatic blocks were mainly detected in the centromeric regions in all species, although accumulations were detected in pericentromeric and telomeric regions in a few macrochromosomes in several of the studied species. All species show the expected topology of telomeric repeats at the edge of all chromosomes, with the exception of Eryx muelleri, where additional accumulations were detected in the centromeres of three pairs of macrochromosomes. The rDNA loci accumulate in one pair of microchromosomes in all Eryx species and in Cylindrophis ruffus, in one macrochromosome pair in Tropidophis melanurus and in two pairs of microchromosomes in Python regius. Sex-specific differences were not detected, suggesting that these species likely have homomorphic, poorly differentiated sex chromosomes.

Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution

The distinctive biology and unique evolutionary features of snakes make them fascinating model systems to elucidate how genomes evolve and how variation at the genomic level is interlinked with phenotypic-level evolution. Similar to other eukaryotic genomes, large proportions of snake genomes contain repetitive DNA, including transposable elements (TEs) and satellite repeats. The importance of repetitive DNA and its structural and functional role in the snake genome, remain unclear. This review highlights the major types of repeats and their proportions in snake genomes, reflecting the high diversity and composition of snake repeats. We present snakes as an emerging and important model system for the study of repetitive DNA under the impact of sex and microchromosome evolution. We assemble evidence to show that certain repetitive elements in snakes are transcriptionally active and demonstrate highly dynamic lineage-specific patterns as repeat sequences. We hypothesize that particular TEs can trigger different genomic mechanisms that might contribute to driving adaptive evolution in snakes. Finally, we review emerging approaches that may be used to study the expression of repetitive elements in complex genomes, such as snakes. The specific aspects presented here will stimulate further discussion on the role of genomic repeats in shaping snake evolution.

Snake W Sex Chromosome: The Shadow of Ancestral Amniote Super-Sex Chromosome

: Heteromorphic sex chromosomes, particularly the ZZ/ZW sex chromosome system of birds and some reptiles, undergo evolutionary dynamics distinct from those of autosomes. The W sex chromosome is a unique karyological member of this heteromorphic pair, which has been extensively studied in snakes to explore the origin, evolution, and genetic diversity of amniote sex chromosomes. The snake W sex chromosome offers a fascinating model system to elucidate ancestral trajectories that have resulted in genetic divergence of amniote sex chromosomes. Although the principal mechanism driving evolution of the amniote sex chromosome remains obscure, an emerging hypothesis, supported by studies of W sex chromosomes of squamate reptiles and snakes, suggests that sex chromosomes share varied genomic blocks across several amniote lineages. This implies the possible split of an ancestral super-sex chromosome via chromosomal rearrangements. We review the major findings pertaining to sex chromosomal profiles in amniotes and discuss the evolution of an ancestral super-sex chromosome by collating recent evidence sourced mainly from the snake W sex chromosome analysis. We highlight the role of repeat-mediated sex chromosome conformation and present a genomic landscape of snake Z and W chromosomes, which reveals the relative abundance of major repeats, and identifies the expansion of certain transposable elements. The latest revolution in chromosomics, i.e., complete telomere-to-telomere assembly, offers mechanistic insights into the evolutionary origin of sex chromosomes.

Revisiting the Karyotype Evolution of Neotropical Boid Snakes: A Puzzle Mediated by Chromosomal Fissions

The Boidae family is an ancient group of snakes widely distributed across the Neotropical region, where several biogeographic events contributed towards shaping their evolution and diversification. Most species of this family have a diploid number composed of 2n = 36; however, among Booidea families, the Boidae stands out by presenting the greatest chromosomal diversity, with 2n ranging between 36 and 44 chromosomes and an undifferentiated XY sex chromosome system. Here, we applied a comparative chromosome analysis using cross-species chromosome paintings in five species representing four Boidae genera, to decipher the evolutionary dynamics of some chromosomes in these Neotropical snakes. Our study included all diploid numbers (2n = 36, 40, and 44) known for this family and our comparative chromosomal mappings point to a strong evolutionary relationship among the genera Boa, Corallus, Eunectes, and Epicrates. The results also allowed us to propose the cytogenomic diversification that had occurred in this family: a process mediated by centric fissions, including fission events of the putative and undifferentiated XY sex chromosome system in the 2n = 44 karyotype, which is critical in solving the puzzle of the karyotype evolution of boid snakes.

The Amazonian Red Side-Necked Turtle Rhinemys rufipes (Spix, 1824) (Testudines, Chelidae) Has a GSD Sex-Determining Mechanism with an Ancient XY Sex Microchromosome System

The Amazonian red side-necked turtle Rhynemis rufipes is an endemic Amazonian Chelidae species that occurs in small streams throughout Colombia and Brazil river basins. Little is known about various biological aspects of this species, including its sex determination strategies. Among chelids, the greatest karyotype diversity is found in the Neotropical species, with several 2n configurations, including cases of triploidy. Here, we investigate the karyotype of Rhinemys rufipes by applying combined conventional and molecular cytogenetic procedures. This allowed us to discover a genetic sex-determining mechanism that shares an ancestral micro XY sex chromosome system. This ancient micro XY system recruited distinct repeat motifs before it diverged from several South America and Australasian species. We propose that such a system dates back to the earliest lineages of the chelid species before the split of South America and Australasian lineages.

Landscape of snake' sex chromosomes evolution spanning 85 MYR reveals ancestry of sequences despite distinct evolutionary trajectories

Most of snakes exhibit a ZZ/ZW sex chromosome system, with different stages of degeneration. However, undifferentiated sex chromosomes and unique Y sex-linked markers, suggest that an XY system has also evolved in ancestral lineages. Comparative cytogenetic mappings revealed that several genes share ancestry among X, Y and Z chromosomes, implying that XY and ZW may have undergone transitions during serpent's evolution. In this study, we performed a comparative cytogenetic analysis to identify homologies of sex chromosomes across ancestral (Henophidia) and more recent (Caenophidia) snakes. Our analysis suggests that, despite ~ 85 myr of independent evolution, henophidians and caenophidians retained conserved synteny over much of their genomes. However, our findings allowed us to discover that ancestral and recent lineages of snakes do not share the same sex chromosome and followed distinct pathways for sex chromosomes evolution.

Interstitial Telomeric Repeats Are Rare in Turtles

Telomeres are nucleoprotein complexes protecting chromosome ends in most eukaryotic organisms. In addition to chromosome ends, telomeric-like motifs can be accumulated in centromeric, pericentromeric and intermediate (i.e., between centromeres and telomeres) positions as so-called interstitial telomeric repeats (ITRs). We mapped the distribution of (TTAGGG)_n repeats in the karyotypes of 30 species from nine families of turtles using fluorescence in situ hybridization. All examined species showed the expected terminal topology of telomeric motifs at the edges of chromosomes. We detected ITRs in only five species from three families. Combining our and literature data, we inferred seven independent origins of ITRs among turtles. ITRs occurred in turtles in centromeric positions, often in several chromosomal pairs, in a given species. Their distribution does not correspond directly to interchromosomal rearrangements. Our findings support that centromeres and non-recombining parts of sex chromosomes are very dynamic genomic regions, even in turtles, a group generally thought to be slowly evolving. However, in contrast to squamate reptiles (lizards and snakes), where ITRs were found in more than half of the examined species, and birds, the presence of ITRs is generally rare in turtles, which agrees with the expected low rates of chromosomal rearrangements and rather slow karyotype evolution in this group.

Cytogenetic Analysis Did Not Reveal Differentiated Sex Chromosomes in Ten Species of Boas and Pythons (Reptilia: Serpentes)

Homologous and differentiated ZZ/ZW sex chromosomes (or derived multiple neo-sex chromosomes) were often described in caenophidian snakes, but sex chromosomes were unknown until recently in non-caenophidian snakes. Previous studies revealed that two species of boas (Boa imperator, B. constrictor) and one species of python (Python bivittatus) independently evolved XX/XY sex chromosomes. In addition, heteromorphic ZZ/ZW sex chromosomes were recently revealed in the Madagascar boa (Acrantophis sp. cf. dumerili) and putatively also in the blind snake Myriopholis macrorhyncha. Since the evolution of sex chromosomes in non-caenophidian snakes seems to be more complex than previously thought, we examined ten species of pythons and boas representing the families Boidae, Calabariidae, Candoiidae, Charinidae, Pythonidae, and Sanziniidae by conventional and molecular cytogenetic methods, aiming to reveal their sex chromosomes. Our results show that all examined species do not possess sex-specific differences in their genomes detectable by the applied cytogenetic methods, indicating the presence of poorly differentiated sex chromosomes or even the absence of sex chromosomes. Interestingly, fluorescence in situ hybridization with telomeric repeats revealed extensive distribution of interstitial telomeric repeats in eight species, which are likely a consequence of intra-chromosomal rearrangements.

Karyoevolution of Crenicichla heckel 1840 (Cichlidae, Perciformes): a process mediated by inversions

Crenicichla (Cichliformes, Cichlidae) present a highly conserved diploid number 2n=48 with fundamental numbers varying between 52 and 62. We analyzed four species in order to investigate the role of repetitive DNA in chromosome evolution in the genus. Crenicichla johanna, Crenicichla cf. saxatilis and Crenicichla cf. regani have 2n=48 (8 m/sm and 40st/a) and FN=56, while Crenicichla sp. ‘Xingu I’ has 2n=48 (48 st/a) and FN=48. Different patterns of constitutive heterochromatin distribution were observed including pericentric, interstitial and whole arm C bands. A single chromosome bears 18S rDNA clusters in most species, except C. johanna, where population variation exists in terms of the quantity and distribution of clusters and their association with interstitial telomeric sequences. All species showed hybridization of 5S rDNA sequences in an interstitial region on an acrocentric chromosome pair. The karyotypic differences and maintenance of the diploid number supports chromosome evolution mediated by inversions in Crenicichla. The telomeric and 18S rDNA sequence association in various chromosomes of C. johanna are proposed to represent hotspots for breakage, favoring intra-chromosomal rearrangements. The results suggest that repetitive sequences can contribute to microstructural cytogenetic diversity in Crenicichla.

Summary: This paper has a great importance for understanding karyotype evolutionary dynamics in neotropical freshwater fish, focusing on repetitive DNA and the role of inversions in Crenicichla.

Evolutionary Insights of the ZW Sex Chromosomesin Snakes: A New Chapter Added by the AmazonianPuffing Snakes of the Genus Spilotes

Amazonian puffing snakes (Spilotes; Colubridae) are snakes widely distributed in the Neotropical region. However, chromosomal data are scarce in this group and, when available, are only limited to karyotype description using conventional staining. In this paper, we focused on the process of karyotype evolution and trends for sex chromosomes in two Amazonian Puffer Snakes (S. pulllatus and S. sulphureus). We performed an extensive karyotype characterization using conventional and molecular cytogenetic approaches. The karyotype of S. sulphureus (presented here for the first time) exhibits a 2n = 36, similar to that previously described in S. pullatus. Both species have highly differentiated ZZ/ZW sex chromosomes, where the W chromosome is highly heterochromatic in S. pullatus but euchromatic in S. sulphureus. Both W chromosomes are homologous between these species as revealed by cross-species comparative genomic hybridization, even with heterogeneous distributions of several repetitive sequences across their genomes, including on the Z and on the W chromosomes. Our study provides evidence that W chromosomes in these two species have shared ancestry.

Cytogenetics of two Farlowella species (Loricariidae: Loricariinae): implications on the taxonomic status of the species

ABSTRACT Farlowella is one of the most diverse genera of the Loricariinae, restricted to South America rivers. The taxonomic and phylogenetic relationships among its species are contentious and, while genetic studies would contribute to the understanding of their relationships, the only available datum refer to the karyotype description of only one species. In the present study two Amazonian species, Farlowella cf. amazonum and F. schreitmuelleri, were analyzed using conventional and molecular cytogenetic procedures. Both species had diploid chromosome number 58, but different fundamental numbers (NF) 116 and 112, respectively, indicative of chromosomal rearrangements. C-banding is almost poor, especially in F. cf. amazonum, and occurs predominantly in the centromeric and in some telomeric regions, although genome of F. schreitmuelleri possessed a much larger heterochromatin amount then those of F. cf. amazonum. The chromosomes bearing the NOR sites were likely the same for both species, corresponding to the 1st metacentric pair in F. cf. amazonum and to the 28th acrocentric in F. schreitmuelleri. The location of the 5S rDNA was species-specific marker. This study expanded the available cytogenetic data for Farlowella species and pointed the remarkable karyotype diversity among species/populations, indicating a possible species complex within genus.

Interstitial telomeric sequences in vertebrate chromosomes: Origin, function, instability and evolution

By definition, telomeric sequences are located at the very ends or terminal regions of chromosomes. However, several vertebrate species show blocks of (TTAGGG)n repeats present in non-terminal regions of chromosomes, the so-called interstitial telomeric sequences (ITSs), interstitial telomeric repeats or interstitial telomeric bands, which include those intrachromosomal telomeric-like repeats located near (pericentromeric ITSs) or within the centromere (centromeric ITSs) and those telomeric repeats located between the centromere and the telomere (i.e., truly interstitial telomeric sequences) of eukaryotic chromosomes. According with their sequence organization, localization and flanking sequences, ITSs can be classified into four types: 1) short ITSs, 2) subtelomeric ITSs, 3) fusion ITSs, and 4) heterochromatic ITSs. The first three types have been described mainly in the human genome, whereas heterochromatic ITSs have been found in several vertebrate species but not in humans. Several lines of evidence suggest that ITSs play a significant role in genome instability and evolution. This review aims to summarize our current knowledge about the origin, function, instability and evolution of these telomeric-like repeats in vertebrate chromosomes.