Marine catfishes (Ariidae-Siluriformes) from the Coastal Amazon: mitochondrial DNA barcode for a recent diversification group?

Background: Ariidae species play a significant role as fishing resources in the Amazon region. However, the family's systematic classification is notably challenging, particularly regarding species delimitation within certain genera. This difficulty arises from pronounced morphological similarities among species, posing obstacles to accurate species recognition. Methods: Following morphological identification, mitochondrial markers (COI and Cytb) were employed to assess the diversity of Ariidae species in the Amazon. Results: Our sampling efforts yielded 12 species, representing 92% of the coastal Amazon region's diversity. Morphological identification findings were largely corroborated by molecular data, particularly for species within the Sciades and Bagre genera. Nonetheless, despite morphological support, Cathorops agassizii and Cathorops spixii displayed minimal genetic divergence (0.010). Similarly, Notarius quadriscutis and Notarius phrygiatus formed a single clade with no genetic divergence, indicating mitochondrial introgression. For the majority of taxa examined, both COI and Cytb demonstrated efficacy as DNA barcodes, with Cytb exhibiting greater polymorphism and resolution. Consequently, the molecular tools utilized proved highly effective for species discrimination and identification.

Genomic Anatomy of Homozygous XX Females and YY Males Reveals Early Evolutionary Trajectory of Sex-determining Gene and Sex Chromosomes in Silurus Fishes.

Sex chromosomes display remarkable diversity and variability among vertebrates. Compared with research on the X/Y and Z/W chromosomes, which have long evolutionary histories in mammals and birds, studies on the sex chromosomes at early evolutionary stages are limited. Here, we precisely assembled the genomes of homozygous XX female and YY male Lanzhou catfish (Silurus lanzhouensis) derived from an artificial gynogenetic family and a self-fertilized family, respectively. Chromosome 24 (Chr24) was identified as the sex chromosome based on resequencing data. Comparative analysis of the X and Y chromosomes showed an approximate 320 kb Y-specific region with a Y-specific duplicate of anti-Mullerian hormone type II receptor (amhr2y), which is consistent with findings in 2 other Silurus species but on different chromosomes (Chr24 of Silurus meridionalis and Chr5 of Silurus asotus). Deficiency of amhr2y resulted in male-to-female sex reversal, indicating that amhr2y plays a male-determining role in S. lanzhouensis. Phylogenetic analysis and comparative genomics revealed that the common sex-determining gene amhr2y was initially translocated to Chr24 of the Silurus ancestor along with the expansion of transposable elements. Chr24 was maintained as the sex chromosome in S. meridionalis and S. lanzhouensis, whereas a sex-determining region transition triggered sex chromosome turnover from Chr24 to Chr5 in S. asotus. Additionally, gene duplication, translocation, and degeneration were observed in the Y-specific regions of Silurus species. These findings present a clear case for the early evolutionary trajectory of sex chromosomes, including sex-determining gene origin, repeat sequence expansion, gene gathering and degeneration in sex-determining region, and sex chromosome turnover.

Construction of a Full-Length transcriptome resource for the African sharptooth catfish (Clarias gariepinus), a prototypical air-breathing Fish, based on isoform sequencing (Iso-Seq).

The African sharptooth catfish (Clarias gariepinus) assumes significance in aquaculture, given its role as a farmed freshwater species with modified gill structures functioning as an air-breathing organ (ABO). To provide a scientific basis for further elucidating the air-breathing formation mechanism and deeply utilizing the genetic resources of Clarias gariepinus, we utilized the PacBio sequencing platform to acquire a comprehensive full-length transcriptome from five juvenile developmental stages and various adult tissues, including the ABO, gills, liver, skin, and muscle. We generated 25,766,688 high-quality reads, with an average length of 2,006 bp and an N50 of 2,241 bp. Following rigorous quality control, 34,890 (97.7 %) of the high-quality isoforms were mapped to the reference genome for gene and transcript annotation, yielding 387 novel isoforms and 14,614 new isoforms. Additionally, we identified 28,582 open reading frames, 48 SNPs, 5,464 variable splices, and 6,141 variable polyadenylation sites, along with 475 long non-coding RNAs. Many DEGs were involved with low oxygen GO terms and KEGG pathways, such as response to stimulus, biological regulation and catalytic activities. Furthermore, it was found that transcription factors such as zf-C2H2, Homeobox, bHLH, and MYB could underpin the African sharptooth catfish's developmental plasticity and its capacity to adapt its morphology and function to its environment. Through the comprehensive analysis of its genomic characteristics, it was found that the African sharptooth catfish has developed a series of unique respiratory adaptive mechanisms during the evolutionary process, These results not only advances the understanding of genetic adaptations to hypoxia in Clarias fish but also provides a valuable framework for future studies aimed at improving aquaculture practices,besides provide important references and inspirations for the evolution of aquatic organisms.

Characterization of the complete mitochondrial genome of a newly discovered torrent catfish, Liobagrus geumgangensis, and their phylogenetic relationships.

BACKGROUND: A new Liobagrus fish was reported from the Korean Peninsula, but research on this taxon is lacking. Moreover, existing research on the mitogenome of the genus Liobagrus in Korea is very limited, and no studies have been conducted on structural characteristics of transfer RNA (tRNA) or gene order comparisons between taxa; instead, research has been restricted to basic phylogeny. OBJECTIVE: The complete mitochondrial genome of Liobagrus geumgangensis was analyzed for the first time. We then aimed to reconstruct the phylogenetic relationships of the genus Liobagrus and estimate the divergence time of speciation events. METHODS: We used a dissected fin clip from an adult of Liobagrus geumgangensis. Genomic DNA was extracted and analyzed with whole genome sequencing (WGS) and assembled by the NOVOPlasty method. The mitogenome sequence was annotated, and a genome map, tRNA structure, and phylogenetic tree were constructed using maximum likelihood analysis. In addition, divergence time was estimated. RESULTS: The mitochondrial genome was 16,522 bp in length and comprised 37 genes. The overall base composition was 30.5% A, 25.5% T, 28.4% C, and 15.7% G. Most tRNAs exhibited the typical clover leaf shape, except trnS1. Phylogenetic analysis revealed that Liobagrus geumgangensis clustered within a clade with four other Liobagrus species exclusive to the southern region of the Korean Peninsula. Its divergence was estimated to have occurred during the late Miocene. CONCLUSION: Characteristics of Liobagrus geumgangensis mitogenome were consistent with those of other torrent catfish species. Time scale estimation revealed distinct groupings, with some distributed across mainland Asia and others in the southern region of the Korean Peninsula. Notably, the Korean Peninsula group was identified as its own lineage, comprising entirely endemic species.

Chromosome-level genome assembly of the glass catfish ( Kryptopterus vitreolus) reveals molecular clues to its transparent phenotype.

Glass catfish ( Kryptopterus vitreolus) are notable in the aquarium trade for their highly transparent body pattern. This transparency is due to the loss of most reflective iridophores and light-absorbing melanophores in the main body, although certain black and silver pigments remain in the face and head. To date, however, the molecular mechanisms underlying this transparent phenotype remain largely unknown. To explore the genetic basis of this transparency, we constructed a chromosome-level haplotypic genome assembly for the glass catfish, encompassing 32 chromosomes and 23 344 protein-coding genes, using PacBio and Hi-C sequencing technologies and standard assembly and annotation pipelines. Analysis revealed a premature stop codon in the putative albinism-related tyrp1b gene, encoding tyrosinase-related protein 1, rendering it a nonfunctional pseudogene. Notably, a synteny comparison with over 30 other fish species identified the loss of the endothelin-3 ( edn3b) gene in the glass catfish genome. To investigate the role of edn3b, we generated edn3b -/- mutant zebrafish, which exhibited a remarkable reduction in black pigments in body surface stripes compared to wild-type zebrafish. These findings indicate that edn3b loss contributes to the transparent phenotype of the glass catfish. Our high-quality chromosome-scale genome assembly and identification of key genes provide important molecular insights into the transparent phenotype of glass catfish. These findings not only enhance our understanding of the molecular mechanisms underlying transparency in glass catfish, but also offer a valuable genetic resource for further research on pigmentation in various animal species.

Single-cell transcriptome landscape of the kidney reveals potential innate immune regulation mechanisms in hybrid yellow catfish after Aeromonas hydrophila infection.

Aeromonas hydrophila, the pathogen that is the causative agent of motile Aeromonas septicemia (MAS) disease, commonly attacks freshwater fishes, including yellow catfish (Pelteobagrus fulvidraco). Although the kidney is one of the most important organs involved in immunity in fish, its role in disease progression has not been fully elucidated. Understanding the cellular composition and innate immune regulation mechanisms of the kidney of yellow catfish is important for the treatment of MAS. In this study, single-cell RNA sequencing (scRNA-seq) was performed on the kidney of hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × Pelteobagrus vachelli ♂) after A. hydrophila infection. Nine types of kidney cells were identified using marker genes, and a transcription module of marker genes in the main immune cells of hybrid yellow catfish kidney tissue was constructed using in-situ hybridization. In addition, the single-cell transcriptome data showed that the differentially expressed genes of macrophages were primarily enriched in the Toll-like receptor and Nod-like receptor signaling pathways. The expression levels of genes involved in these pathways were upregulated in macrophages following A. hydrophila infection. Transmission electron microscopy and TUNEL analysis revealed the cellular characteristics of macrophages before and after A. hydrophila infection. These data provide empirical support for in-depth research on the role of the kidney in the innate immune response of hybrid yellow catfish.

Comparison and phylogenetic analysis of the mitochondrial genomes of Synodontis eupterus and Synodontis polli.

We aimed to distinguish Synodontis eupterus and Synodontis polli. We performed sequencing and bioinformatic analysis of their mitochondrial genomes and constructed a phylogenetic tree of Mochokidae fish using maximum likelihood and Bayesian methods based on protein-coding gene (PCG) sequences of 14 Mochokidae species. The total length of the S. eupterus mitochondrial genome was 16,579 bp, including 13 (PCGs), 22 tRNA genes, two rRNA genes, and one D-loop, with an AT-biased nucleotide composition (56.0%). The total length of the S. polli mitochondrial genome was 16,544 bp, including 13 PCGs, 22 tRNA genes, two rRNA genes, and one D-loop, with an AT-biased nucleotide composition (55.0%). In both species, except for COI, PCGs use ATG as the starting codon, the vast majority use TAG or TAA as the ending codon, and a few use incomplete codons (T - or TA -) as the ending codon. Phylogenetic analysis showed that S. eupterus and Synodontis clarias converged into one branch, S. polli and Synodontis petricola converged into one branch, Mochokiella paynei, Mochokus brevis, and nine species of the genus Synodontis converged into one branch, and M. paynei clustered with the genus Synodontis. This study lays a foundation for rebuilding a clearer Mochokidae fish classification system.

Response signatures of intestinal microbiota and gene transcription of yellow catfish (Pelteobagrus fulvidraco) to Aeromonas hydrophila infection.

Bacterial intestinal inflammation is a common disease of yellow catfish (Pelteobagrus fulvidraco) in high-density aquaculture. Understanding the interactions between host and intestinal bacteria is helpful to intestinal inflammatory disease control. Here, we constructed a model of intestinal inflammation after Aeromonas hydrophila infection in yellow catfish, and characterized variations in gene expression and microbiome in the gut through high-throughput sequencing. Furthermore, host gene-microbiome interactions were identified. Histology observation showed disordered distribution of columnar epithelial cells and decrease of goblet cells in intestine. A total of 4741 genes showed differentially expression, mostly in comparisons between 12 hpi group with each other groups respectively, including control, 24 hpi and 48 hpi groups. These genes were enriched in immune-related pathways including the IL-17 signaling pathway, triggering strong inflammatory response at the invading stage within 12 h. Subsequently, the host strengthened energy consumption by activating carbohydrate and lipid metabolism pathways to repair the intestinal mucosal immune defense line. In addition, fish with A. hydrophila infection show decreased richness of gut microbial, reduced relative abundance of probiotics including Akkermansia, and elevated pathogenic bacteria such as Plesimonas. An integrative analysis identified A. hydrophila-related genes, such as il22 and stat3, for which expression level is close associated with the shift of A. hydrophila-related bacteria relative abundance, such as Akkermansia and Cetobacterium. Aside from picturing the variations of intestine gene expression and mucosal microbiome of yellow catfish coping with A. hydrophila infection, our study probed the underlying host-microbe interactions in A. hydrophila infection induced intestinal inflammatory, providing new insights for disease control in aquaculture.

PACAP binds conserved receptors and modulates cytokine gene expression and protein secretion in trout cell lines.

Antimicrobial peptides (AMPs) are an alternative to antibiotics for treatment and prevention of infections with a lower risk of bacterial resistance. Pituitary adenylate cyclase activating polypeptide (PACAP) is an outstanding AMP with versatile effects including antimicrobial activity and modulation of immune responses. The objective of this research was to study PACAP immunomodulatory effect on rainbow trout cell lines infected with Aeromonas salmonicida. PACAP from Clarias gariepinus (PACAP1) and a modified PACAP (PACAP5) were tested. RT-qPCR results showed that il1b and il8 expression in RTgutGC was significantly downregulated while tgfb expression was upregulated after PACAP treatment. Importantly, the concentration of IL-1ß and IFN-γ increased in the conditioned media of RTS11 cells incubated with PACAP1 and exposed to A. salmonicida. There was a poor correlation between gene expression and protein concentration, suggesting a stimulation of the translation of IL-1ß protein from previously accumulated transcripts or the cleavage of accumulated IL-1ß precursor. In-silico studies of PACAP-receptor interactions showed a turn of the peptide characteristic of PACAP-PAC1 interaction, correlated with the higher number of interactions observed with this specific receptor, which is also in agreement with the higher PACAP specificity described for PAC1 compared to VPAC1 and VPACA2. Finally, the in silico analysis revealed nine amino acids related to the PACAP receptor-associated functionality.

Characteristics of the Vasa Gene in Silurus asotus and Its Expression Response to Letrozole Treatment.

The identification and expression of germ cells are important for studying sex-related mechanisms in fish. The vasa gene, encoding an ATP-dependent RNA helicase, is recognized as a molecular marker of germ cells and plays a crucial role in germ cell development. Silurus asotus, an important freshwater economic fish species in China, shows significant sex dimorphism with the female growing faster than the male. However, the molecular mechanisms underlying these sex differences especially involving in the vasa gene in this fish remain poorly understood. In this work, the vasa gene sequence of S. asotus (named as Savasa) was obtained through RT-PCR and rapid amplification of cDNA end (RACE), and its expression in embryos and tissues was analyzed using qRT-PCR and an in situ hybridization method. Letrozole (LT) treatment on the larvae fish was also conducted to investigate its influence on the gene. The results revealed that the open reading frame (ORF) of Savasa was 1989 bp, encoding 662 amino acids. The SaVasa protein contains 10 conserved domains unique to the DEAD-box protein family, showing the highest sequence identity of 95.92% with that of Silurus meridionalis. In embryos, Savasa is highly expressed from the two-cell stage to the blastula stage in early embryos, with a gradually decreasing trend from the gastrula stage to the heart-beating stage. Furthermore, Savasa was initially detected at the end of the cleavage furrow during the two-cell stage, later condensing into four symmetrical cell clusters with embryonic development. At the gastrula stage, Savasa-positive cells increased and began to migrate towards the dorsal side of the embryo. In tissues, Savasa is predominantly expressed in the ovaries, with almost no or lower expression in other detected tissues. Moreover, Savasa was expressed in phase I-V oocytes in the ovaries, as well as in spermatogonia and spermatocytes in the testis, implying a specific expression pattern of germ cells. In addition, LT significantly upregulated the expression of Savasa in a concentration-dependent manner during the key gonadal differentiation period of the fish. Notably, at 120 dph after LT treatment, Savasa expression was the lowest in the testis and ovary of the high concentration group. Collectively, findings from gene structure, protein sequence, phylogenetic analysis, RNA expression patterns, and response to LT suggest that Savasa is maternally inherited with conserved features, serving as a potential marker gene for germ cells in S.asotus, and might participate in LT-induced early embryonic development and gonadal development processes of the fish. This would provide a basis for further research on the application of germ cell markers and the molecular mechanisms of sex differences in S. asotus.

Exploitation of multiple host-derived nutrients by the yellow catfish epidermal environment facilitates Vibrio mimicus to sustain infection potency and susceptibility.

Infection with Vibrio mimicus in the Siluriformes has demonstrated a rapid and high infectivity and mortality rate, distinct from other hosts. Our earlier investigations identified necrosis, an inflammatory storm, and tissue remodeling as crucial pathological responses in yellow catfish (Pelteobagrus fulvidraco) infected with V. mimicus. The objective of this study was to further elucidate the impact linking these pathological responses within the host during V. mimicus infection. Employing metabolomics and transcriptomics, we uncovered infection-induced dense vacuolization of perimysium; Several genes related to nucleosidase and peptidase activities were significantly upregulated in the skin and muscles of infected fish. Concurrently, the translation processes of host cells were impaired. Further investigation revealed that V. mimicus completes its infection process by enhancing its metabolism, including the utilization of oligopeptides and nucleotides. The high susceptibility of yellow catfish to V. mimicus infection was associated with the composition of its body surface, which provided a microenvironment rich in various nucleotides such as dIMP, dAMP, deoxyguanosine, and ADP, in addition to several amino acids and peptides. Some of these metabolites significantly boost V. mimicus growth and motility, thus influencing its biological functions. Furthermore, we uncovered an elevated expression of gangliosides on the surface of yellow catfish, aiding V. mimicus adhesion and increasing its infection risk. Notably, we observed that the skin and muscles of yellow catfish were deficient in over 25 polyunsaturated fatty acids, such as Eicosapentaenoic acid, 12-oxo-ETE, and 13-Oxo-ODE. These substances play a role in anti-inflammatory mechanisms, possibly contributing to the immune dysregulation observed in yellow catfish. In summary, our study reveals a host immune deviation phenomenon that promotes bacterial colonization by increasing nutrient supply. It underscores the crucial factors rendering yellow catfish highly susceptible to V. mimicus, indicating that host nutritional sources not only enable the establishment and maintenance of infection within the host but also aid bacterial survival under immune pressure, ultimately completing its lifecycle.

Gap-free chromosome-level genomes of male and female spotted longbarbel catfish Hemibagrus guttatus.

Hemibagrus guttatus, also named as spotted longbarbel catfish, is an economical fish in China. However, their gender cannot be easily distinguished from their appearance, which largely impedes their artificial breeding. Therefore, we provided two gap-free chromosome-level genomes of male and female spotted longbarbel catfish by combining wtdbg2, LR_Gapcloser and TGS-GapCloser assembly approaches with Hi-C data and accurate Pacbio HiFi long-reads. We assembled 30 chromosomes without any gap. Their genome sizes are approximately 749.1 Mb and 747.8 Mb of male and female individuals. The completeness results of BUSCO evaluation show about 94.2% and 95.0%, representing a high-level of completeness of both genomes. We also obtained 35,277 and 34,571 protein-coding gene sets from male and female individuals. Both available gap-free chromosome-level genomes of H. guttatus will provide excellent references for resequencing of male and female individuals to identify accurate markers for distinguishing gender of this fish.

Molecular and SEM studies on Thaparocleidus vistulensis (Siwak, 1932) (Monopisthocotyla, Ancylodiscoididae).

Presenting new molecular and scanning electron microscope (SEM) features, this study gives additional data to the better knowledge of Thaparocleidus vistulensis (Siwak, 1932) (Monopisthocotyla, Ancylodiscoididae), a parasite of the European catfish Silurus glanis Linnaeus, 1758 (Siluriformes, Siluridae) cultured in a commercial fish farm in Hungary. In addition, notes on the early development of sclerotized anchors are also provided. The main morphological difference of T. vistulensis compared to other congeneric species is associated with the male copulatory organ, which exhibits 5-7 loops in the middle of the penis length and a long open V-shaped sclerotized accessory piece, dividing terminally into two parts, securing the terminal part of the penis tube. The present study provides for the first time molecular characterization data based on the 2694 bp long nucleotide sequence of rDNA (ITS1, 5.8S, ITS2, and flanked with partial 18S and partial 28S) submitted in GenBank with the accession number OR916383. A phylogenetic tree based on ITS1 sequences supports a well-defined clade including T. vistulensis, forming a sister group with T. siluri, a species-specific monopisthocotylan parasite to S. glanis. The morphological characterization of T. vistulensis, especially for the male copulatory organ, together with the molecular data in the present study, extends knowledge about this monopisthocotylan species and provides new information for future phylogeny studies.

Synergistic Effect of Dietary Supplementation with Sodium Butyrate, ß-Glucan and Vitamins on Growth Performance, Cortisol Level, Intestinal Microbiome and Expression of Immune-Related Genes in Juvenile African Catfish (Clarias gariepinus).

The effect of dietary supplementation with sodium butyrate, ß-glucan and vitamins (A, D3, E, K, C) on breeding indicators and immune parameters of juvenile African catfish was examined. The fish were fed with unenriched (group C) and enriched feed with a variable proportion of sodium butyrate/ß-glucan, and constant content of vitamins (W1-W3). After the experiment, blood and the middle gut were collected. The microbiome of the gut was determined using Next Generation Sequencing (NGS). Liver tissue was collected for determination of expression of immune-related genes (HSP70, IL-1ß, TNFα). W2 and W3 were characterized by the most favorable values of breeding indicators (p < 0.05). The highest blood cortisol concentration was in group C (71.25 ± 10.45 ng/mL), and significantly the lowest in W1 (46.03 ± 7.01 ng/ mL) (p < 0.05). The dominance of Cetobacterium was observed in all study groups, with the largest share in W3 (65.25%) and W1 (61.44%). Gene expression showed an increased number of HSP70 genes in W1. IL-1ß and TNFα genes peaked at W3. The W3 variant turns out to be the most beneficial supplementation, due to the improvement of breeding and immunological parameters. The data obtained can be used to create a preparation for commercial use in the breeding of this species.

Complete mitochondrial genome of critically endangered catfish Hemibagrus punctatus (Jerdon, 1849) and comparative analysis for insights into the phylogeny of hemibagrids through mitogenomic approach.

BACKGROUND: Hemibagrus punctatus (Jerdon, 1849) is a critically endangered bagrid catfish endemic to the Western Ghats of India, whose population is declining due to anthropogenic activities. The current study aims to compare the mitogenome of H. punctatus with that of other Bagrid catfishes and provide insights into their evolutionary relationships. METHODS AND RESULTS: Samples were collected from Hemmige Karnataka, India. In the present study, the mitogenome of H. punctatus was successfully assembled, and its phylogenetic relationships with other Bagridae species were studied. The total genomic DNA of samples was extracted following the phenol-chloroform isoamyl alcohol method. Samples were sequenced, and the Illumina paired-end reads were assembled to a contig length of 16,517 bp. The mitochondrial genome was annotated using MitoFish and MitoAnnotator (Iwasaki et al., 2013). A robust phylogenetic analysis employing NJ (Maximum composite likelihood) and ASAP methods supports the classification of H. punctatus within the Bagridae family, which validates the taxonomic status of this species. In conclusion, this research enriches our understanding of H. punctatus mitogenome, shedding light on its evolutionary dynamics within the Bagridae family and contributing to the broader knowledge of mitochondrial genes in the context of evolutionary biology. CONCLUSIONS: The study's findings contribute to a better understanding of the mitogenome of H. punctatus and provide insights into the evolutionary relationships within other Hemibagrids.

Questioning inbreeding: Could outbreeding affect productivity in the North African catfish in Thailand?

The North African catfish (Clarias gariepinus) is a significant species in aquaculture, which is crucial for ensuring food and nutrition security. Their high adaptability to diverse environments has led to an increase in the number of farms that are available for their production. However, long-term closed breeding adversely affects their reproductive performance, leading to a decrease in production efficiency. This is possibly caused by inbreeding depression. To investigate the root cause of this issue, the genetic diversity of captive North African catfish populations was assessed in this study. Microsatellite genotyping and mitochondrial DNA D-loop sequencing were applied to 136 catfish specimens, collected from three populations captured for breeding in Thailand. Interestingly, extremely low inbreeding coefficients were obtained within each population, and distinct genetic diversity was observed among the three populations, indicating that their genetic origins are markedly different. This suggests that outbreeding depression by genetic admixture among currently captured populations of different origins may account for the low productivity of the North African catfish in Thailand. Genetic improvement of the North African catfish populations is required by introducing new populations whose origins are clearly known. This strategy should be systematically integrated into breeding programs to establish an ideal founder stock for selective breeding.

Species boundaries of the whiptail catfish Rineloricaria (Siluriformes: Loricariidae) from the Paraíba do Sul River drainage, southeastern Brazil, with species redescriptions and description of a new species.

Species of the catfish genus Rineloricaria are common in the Paraíba do Sul River basin, in southeastern Brazil; here we present a revision of the taxonomic diversity and geographic distribution of the species of the genus inhabiting the basin, based on novel morphologic and molecular data. Five species delimitation methods based on cytochrome C oxidase subunit 1 nucleotide sequences yielded comparable molecular operational taxonomic units. The automatic barcode gap discovery, assemble species by automatic partitioning, barcode index number, and Bayesian implementation of the Poisson tree process methods supported the recognition of five evolutionary lineages. These taxonomic units were assigned to the previously described Rineloricaria nigricauda, Rineloricaria steindachneri, Rineloricaria zawadzkii, and Rineloricaria nudipectoris, and an additional undescribed species. R. zawadzkii was further divided into two intraspecific geographically structured lineages using the generalized mixed Yule coalescent delimitation method. A maximum likelihood phylogenetic analysis revealed that the five lineages from the Paraíba do Sul have closer relationships to different species from southern and southeastern Brazil (Ribeira de Iguape, Lagoa dos Patos, Uruguay, Paraguay, and Parana river basins) than to each other. Based on the analysis of lectotypes, recently collected material, and specimens from ichthyological collections, the poorly described R. nigricauda and R. steindachneri are redescribed following current descriptive standards. The undescribed species from the middle and upper Paraíba do Sul River basin is formally described. The description of a new species, along with the description of species boundaries in R. nigricauda and R. steindachneri, contributes to the knowledge of the ichthyofauna of the Paraíba do Sul River basin and adjacent coastal drainages of southeastern Brazil. An identification key for the species of Rineloricaria occurring in the Paraíba do Sul River basin is provided.

Genome-wide sequence divergence of satellite DNA could underlie meiotic failure in male hybrids of bighead catfish and North African catfish (Clarias, Clariidae).

Hybrid sterility, a hallmark of postzygotic isolation, arises from parental genome divergence disrupting meiosis. While chromosomal incompatibility is often implicated, the underlying mechanisms remain unclear. This study investigated meiotic behavior and genome-wide divergence in bighead catfish (C. macrocephalus), North African catfish (C. gariepinus), and their sterile male hybrids (important in aquaculture). Repetitive DNA analysis using bioinformatics and cytogenetics revealed significant divergence in satellite DNA (satDNA) families between parental species. Notably, one hybrid exhibited successful meiosis and spermatozoa production, suggesting potential variation in sterility expression. Our findings suggest that genome-wide satDNA divergence, rather than chromosome number differences, likely contributes to meiotic failure and male sterility in these catfish hybrids.

Mitogenomic phylogeny, biogeography, and cryptic divergence of the genus Silurus (Siluriformes: Siluridae).

The genus Silurus, an important group of catfish, exhibits heterogeneous distribution in Eurasian freshwater systems. This group includes economically important and endangered species, thereby attracting considerable scientific interest. Despite this interest, the lack of a comprehensive phylogenetic framework impedes our understanding of the mechanisms underlying the extensive diversity found within this genus. Herein, we analyzed 89 newly sequenced and 20 previously published mitochondrial genomes (mitogenomes) from 13 morphological species to reconstruct the phylogenetic relationships, biogeographic history, and species diversity of Silurus. Our phylogenetic reconstructions identified eight clades, supported by both maximum-likelihood and Bayesian inference. Sequence-based species delimitation analyses yielded multiple molecular operational taxonomic units (MOTUs) in several taxa, including the Silurus asotus complex (four MOTUs) and Silurus microdorsalis (two MOTUs), suggesting that species diversity is underestimated in the genus. A reconstructed time-calibrated tree of Silurus species provided an age estimate of the most recent common ancestor of approximately 37.61 million years ago (Ma), with divergences among clades within the genus occurring between 11.56 Ma and 29.44 Ma, and divergences among MOTUs within species occurring between 3.71 Ma and 11.56 Ma. Biogeographic reconstructions suggested that the ancestral area for the genus likely encompassed China and the Korean Peninsula, with multiple inferred dispersal events to Europe and Central and Western Asia between 21.78 Ma and 26.67 Ma and to Japan between 2.51 Ma and 18.42 Ma. Key factors such as the Eocene-Oligocene extinction event, onset and intensification of the monsoon system, and glacial cycles associated with sea-level fluctuations have likely played significant roles in shaping the evolutionary history of the genus Silurus.

The role of satellite DNAs in the chromosomal rearrangements and the evolution of the rare XY1Y2 sex system in Harttia (Siluriformes: Loricariidae).

The underlying processes behind the formation, evolution, and long-term maintenance of multiple sex chromosomes have been largely neglected. Among vertebrates, fishes represent the group with the highest diversity of multiple sex chromosome systems and, with six instances, the Neotropical fish genus Harttia stands out by presenting the most remarkable diversity. However, although the origin mechanism of their sex chromosome systems is well discussed, little is known about the importance of some repetitive DNA classes in the differentiation of multiple systems. In this work, by employing a combination of cytogenetic and genomic procedures, we evaluated the satellite DNA composition of H. carvalhoi with a focus on their role in the evolution, structure, and differentiation process of the rare XY1Y2 multiple-sex chromosome system. The genome of H. carvalhoi contains a total of 28 satellite DNA families, with the A + T content ranging between 38.1% and 68.1% and the predominant presence of long satellites. The in situ hybridization experiments detected 15 satellite DNAs with positive hybridization signals mainly on centromeric and pericentromeric regions of almost all chromosomes or clustered on a few pairs. Five of them presented clusters on X, Y1, and/or Y2 sex chromosomes which were therefore selected for comparative hybridization in the other three congeneric species. We found several conserved satellites accumulated on sex chromosomes and also in regions that were involved in chromosomal rearrangements. Our results provide a new contribution of satellitome studies in multiple sex chromosome systems in fishes and represent the first satellitome study for a Siluriformes species.