Chromosomal polymorphism and molecular variability in the pearly razorfish Xyrichtys novacula (Labriformes, Labridae): taxonomic and biogeographic implications

Chromosome-level assembly and annotation of the Xyrichtys novacula (Linnaeus, 1758) genome

The pearly razorfish (Xyrichtys novacula), commonly known as raor in the Balearic Islands, is a wrasse within the family Labridae. This fish species has particular biological and socio-cultural characteristics making it an ideal model organism in the fields of behavioural ecology, molecular ecology and conservation biology. In this study, we present the first annotated chromosome-level assembly for this species. Sequencing involved a combination of long reads with Oxford Nanopore Technologies, Illumina paired-end short reads (2 × 151 bp), Hi-C and RNA-seq from different tissues. The nuclear genome assembly has a scaffold N50 of 34.33 Mb, a total assembly span of 775.53 Mb and 99.63% of the sequence assembled into 24 superscaffolds, consistent with its known karyotype. Quality metrics revealed a consensus accuracy (QV) of 42.92 and gene completeness > 98%. The genome annotation resulted in 26,690 protein-coding genes and 12,737 non-coding transcripts. The coding regions encoded 39,613 unique protein products, 93% of them with assigned function. Overall, the publication of the X. novacula's reference genome will broaden the scope and impact of genomic research conducted on this iconic and colourful species.

Macroevolutionary consequences of karyotypic changes in the neotropical Serrasalmidae fishes (Ostariophysi, Characiformes) diversification

In the Neotropical region, one of the most diverse families of freshwater fishes is the monophyletic Serrasalmidae. Karyotypically, the family shows high diversity in chromosome numbers (2n = 54 to 64). However, little is discussed about whether the chromosomal changes are associated with cladogenetic events within this family. In the present study, we evaluated the role of chromosomal changes in the evolutionary diversification of Serrasalmidae. Our phylogenetic sampling included 36 species and revealed three main clades. The ancestral chromosome number reconstruction revealed the basic number 2n = 54 and a high frequency of ascending dysploid events in the most derived lineages. Our biogeographic reconstruction suggests an Amazonian origin of the family at 48-38 Mya, with independent colonization of other basins between 15 and 8 Mya. We did not find specific chromosomal changes or increased diversification rates correlated with the colonization of a new environment. On the other hand, an increase in the diversification rate was detected involving the genus Serrasalmus and Pygocentrus in the Miocene, correlated with the stasis of 2n = 60. Our data demonstrate that chromosomal rearrangements might have played an important evolutionary role in major cladogenetic events in Serrasalmidae, revealing them as a possible evolutionary driver in their diversification.

Integrating Genomic and Chromosomal Data: A Cytogenetic Study of Transancistrus santarosensis (Loricariidae: Hypostominae) with Characterization of a ZZ/ZW Sex Chromosome System

The plecos (Loricariidae) fish represent a great model for cytogenetic investigations due to their variety of karyotypes, including diploid and polyploid genomes, and different types of sex chromosomes. In this study we investigate Transancistrus santarosensis a rare loricariid endemic to Ecuador, integrating cytogenetic methods with specimens' molecular identification by mtDNA, to describe the the species karyotype. We aim to verify whether sex chromosomes are cytologically identifiable and if they are associated with the accumulation of repetitive sequences present in other species of the family. The analysis of the karyotype (2n = 54 chromosomes) excludes recent centric fusion and pericentromeric inversion and suggests the presence of a ZZ/ZW sex chromosome system at an early stage of differentiation: the W chromosome is degenerated but is not characterized by the presence of differential sex-specific repetitive DNAs. Data indicate that although T. santarosensis has retained the ancestral diploid number of Loricariidae, it accumulated heterochromatin and shows non-syntenic ribosomal genes localization, chromosomal traits considered apomorphic in the family.

Molecular cytogenetic analysis and the establishment of a cell culture in the fish species Hollandichthys multifasciatus (Eigenmann & Norris, 1900) (Characiformes, Characidae)

Hollandichthys is a fish genus of the family Characidae that was until recently considered to be monotypic, with cytogenetic, morphological, and molecular data being restricted to a few local populations. In the present study, the karyotype of a population of Hollandichthys multifasciatus was analyzed using classical and molecular cytogenetic approaches for the investigation of potential markers that could provide new perspectives on the cytotaxonomy. H. multifasciatus presented a diploid number of 2n=50 chromosomes and a karyotype formula of 8m+10sm+32st. A single pair of chromosomes presented Ag-NORs signals, which coincided with the 18S rDNA sites visualized by FISH, whilst the 5S rDNA sequences were mapped in two chromosome pairs. The distribution of the U snRNA genes was mapped on the Hollandichthys chromosomes for the first time, with the probes revealing the presence of the U1 snDNA on the chromosomes of pair 20, U2 on pairs 6 and 19, U4 on pair 16, and U6 on the chromosomes of pair 11. The results of the present study indicated karyotypic differences in comparison with the other populations of H. multifasciatus studied previously, reinforcing the need for further research to identify isolated populations or the potential existence of cryptic Hollandichthys species.

Latitudinal Cline in Chromosome Numbers of Ice Cod A. glacialis (Gadidae) from Northeast Greenland

The ice cod Arctogadus glacialis (Peters, 1872) is one of the few fish species endemic to the Arctic. With a circumpolar distribution, the species is confined to the fjords and shelves of the Arctic seas. Biological information on A. glacialis is scarce, with genomic information restricted to microsatellites. Within the frame of the TUNU-Programme: Arctic Ocean Fishes-Diversity, Adaptation and Conservation, we studied A. glacialis at the chromosomal level to explore fish diversity and evolutionary aspects. The analysis of over 50 individuals from the Northeast Greenland fjords between latitudes 71°09' N and 76°42' N revealed a remarkable intraspecific diversity epitomized by chromosome numbers spanning from 28 to 33, the occurrence of putative B chromosomes, and diversified patterns of distribution of heterochromatin and rDNAs. The number of B chromosomes followed a latitudinal gradient from 0-2 in the north to 2-5 in the south. Considering the benthic and rather stationary life history of this species, the observed chromosomal differences might have arisen independently, possibly driven and/or fostered by the dynamics of repetitive sequences, and are being fixed in relatively isolated fjord populations. The resulting latitudinal cline we observe today might have repercussions on the fate of local populations facing the ongoing climate-driven environmental changes.

Sex Chromosomes and Internal Telomeric Sequences in Dormitator latifrons (Richardson 1844) (Eleotridae: Eleotrinae): An Insight into their Origin in the Genus

The freshwater fish species Dormitator latifrons, commonly named the Pacific fat sleeper, is an important food resource in CentralSouth America, yet almost no genetic information on it is available. A cytogenetic analysis of this species was undertaken by standard and molecular techniques (chromosomal mapping of 18S rDNA, 5S rDNA, and telomeric repeats), aiming to describe the karyotype features, verify the presence of sex chromosomes described in congeneric species, and make inferences on chromosome evolution in the genus. The karyotype (2n = 46) is mainly composed of metacentric and submetacentic chromosomes, with nucleolar organizer regions (NORs) localized on the short arms of submetacentric pair 10. The presence of XX/XY sex chromosomes was observed, with the X chromosome carrying the 5S rDNA sequences. These heterochromosomes likely appeared before 1 million years ago, since they are shared with another derived Dormitator species (Dormitator maculatus) distributed in the Western Atlantic. Telomeric repeats hybridize to the terminal portions of almost all chromosomes; additional interstitial sites are present in the centromeric region, suggesting pericentromeric inversions as the main rearrangement mechanisms that has driven karyotypic evolution in the genus. The data provided here contribute to improving the cytogenetics knowledge of D. latifrons, offering basic information that could be useful in aquaculture farming of this neotropical fish.

Complete mitochondrial genome of the pearly razorfish Xyrichtys novacula: phylogenetic analysis of its placement within the Labridae family

In this paper, we report the complete mitochondrial genome (17,306 bp) of the pearly razorfish Xyrichtys novacula Linnaeus, 1758, a labrid that inhabits tropical and temperate Atlantic waters and the Mediterranean Sea. The circular double-stranded sequence contains the typical teleost gene order with 13 protein-coding genes, 22 tRNA, 2 rRNA, 1 control region, and 2 intergenic spacers between the rRNAs. Using the sequences of all protein-coding genes, we inferred the phylogeny for the Labriade family using 24 labrids and 3 outgroup species that placed X. novacula in a monophyletic group including species from the Pseudocheilines, Pseudolabrines, and Julidines.