BACKGROUND: Interferon regulatory factors (IRFs) are a family of transcription factors with important functions in immunity. The genomes of most vertebrates encode ten IRF genes. IRF3 and IRF9 have key roles in interferon (IFN) induction and signaling. Most of our knowledge about the IFN pathways originates from the study of the mammalian IFN system, and the description of the corresponding avian components is not as complete. Both IRF3 and IRF9 were considered missing from the chicken genome and from the genomes of other avian species. RESULTS: Here we describe multiple avian IRF3 and IRF9 genes, all with difficult GC-rich sequence context that prevented their earlier characterization. IRF3 orthologs are narrowly distributed and are present in the avian infraclass Palaeognathae. In contrast, IRF9 orthologs were found in most avian species, with the exception of the order Galliformes. In about half of the avian orders, IRF9 was located in noncanonical chromosomal positions, indicating past translocations. Phylogenetic analysis confirmed the correct orthology of all newly described IRFs. We further performed experiments using duck IRF9, confirming its role in the IFN pathway. IRF9 knockout in duck fibroblasts decreases the induction of IFN-stimulated genes (ISGs). Full induction of ISGs in duck cells requires both an intact IRF9 and a canonical IFN-stimulated response element. Lastly, intact IRF9 is needed for IFN-mediated protection of duck cells against the vesicular stomatitis virus-induced cytopathicity. CONCLUSIONS: The identification of avian IRFs fills an important gap in our understanding of avian immunology and brings new questions related to the evolution of the IRF family.

• Keywords
• Avian genome, Gene loss, Interferon regulatory factors, Interferon signaling,
• MeSH
• Phylogeny MeSH
• Interferon Regulatory Factors * genetics   metabolism   MeSH
• Interferon Regulatory Factor-3 * genetics   metabolism   MeSH
• Interferon-Stimulated Gene Factor 3, gamma Subunit * genetics   metabolism   MeSH
• Ducks genetics   MeSH
• Chickens genetics   MeSH
• Avian Proteins * genetics   metabolism   MeSH
• Birds * genetics   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Interferon Regulatory Factors * MeSH
• Interferon Regulatory Factor-3 * MeSH
• Interferon-Stimulated Gene Factor 3, gamma Subunit * MeSH
• Avian Proteins * MeSH

Most vertebrates develop distinct females and males, where sex is determined by repeatedly evolved environmental or genetic triggers. Undifferentiated sex chromosomes and large genomes have caused major knowledge gaps in amphibians. Only a single master sex-determining gene, the dmrt1-paralogue (dm-w) of female-heterogametic clawed frogs (Xenopus; ZW♀/ZZ♂), is known across >8740 species of amphibians. In this study, by combining chromosome-scale female and male genomes of a non-model amphibian, the European green toad, Bufo(tes) viridis, with ddRAD- and whole genome pool-sequencing, we reveal a candidate master locus, governing a male-heterogametic system (XX♀/XY♂). Targeted sequencing across multiple taxa uncovered structural X/Y-variation in the 5'-regulatory region of the gene bod1l, where a Y-specific non-coding RNA (ncRNA-Y), only expressed in males, suggests that this locus initiates sex-specific differentiation. Developmental transcriptomes and RNA in-situ hybridization show timely and spatially relevant sex-specific ncRNA-Y and bod1l-gene expression in primordial gonads. This coincided with differential H3K4me-methylation in pre-granulosa/pre-Sertoli cells, pointing to a specific mechanism of amphibian sex determination.

• MeSH
• X Chromosome * genetics   MeSH
• Y Chromosome * genetics   MeSH
• Genome MeSH
• Evolution, Molecular MeSH
• RNA, Untranslated genetics   MeSH
• Amphibians genetics   MeSH
• Sex Determination Processes * genetics   MeSH
• Transcription Factors genetics   metabolism   MeSH
• Animals MeSH
• Check Tag
• Male MeSH
• Female MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• DMRT1 protein MeSH Browser
• RNA, Untranslated MeSH
• Transcription Factors MeSH

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.

• Keywords
• FISH, U1 and U2 snDNAs, chromosome painting, histone H3, polyploidy, teleost fish,
• MeSH
• Cyprinidae * MeSH
• Cytogenetic Analysis MeSH
• Polyploidy MeSH
• Segmental Duplications, Genomic * MeSH
• Tandem Repeat Sequences MeSH
• Tetraploidy MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Repetitive elements have been identified in several amphibian genomes using whole genome sequencing, but few studies have used cytogenetic mapping to visualize these elements in this vertebrate group. Here, we used fluorescence in situ hybridization and genomic data to map the U1 and U2 small nuclear RNAs and histone H3 in six species of African clawed frog (genus Xenopus), including, from subgenus Silurana, the diploid Xenopus tropicalis and its close allotetraploid relative X. calcaratus and, from subgenus Xenopus, the allotetraploid species X. pygmaeus, X. allofraseri, X. laevis, and X. muelleri. Results allowed us to qualitatively evaluate the relative roles of polyploidization and divergence in the evolution of repetitive elements because our focal species include allotetraploid species derived from two independent polyploidization events - one that is relatively young that gave rise to X. calcaratus and another that is older that gave rise to the other (older) allotetraploids. Our results demonstrated conserved loci number and position of signals in the species from subgenus Silurana; allotetraploid X. calcaratus has twice as many signals as diploid X. tropicalis. However, the content of repeats varied among the other allotetraploid species. We detected almost same number of signals in X. muelleri as in X. calcaratus and same number of signals in X. pygmaeus, X. allofraseri, X. laevis as in the diploid X. tropicalis. Overall, these results are consistent with the proposal that allopolyploidization duplicated these tandem repeats and that variation in their copy number was accumulated over time through reduction and expansion in a subset of the older allopolyploids.

• Keywords
• Allopolyploidization, Amphibians, Anura, Histone H3, In situ hybridization, snRNA,
• Publication type
• Journal Article MeSH

Sexual vs. asexual reproduction-unisexual vs. bisexual populations-diploid vs. polyploid biotypes-genetic vs. environmental sex determination: all these natural phenomena are associated with the genus of teleost fish, Carassius. This review places emphasis on two Carassius entities with completely different biological characteristics: one globally widespread and invasive Carassius gibelio, and the other C. carassius with a decreasing trend of natural occurrence. Comprehensive biological and cytogenetic knowledge of both entities, including the physical interactions between them, can help to balance the advantages of highly invasive and disadvantages of threatened species. For example, the benefits of a wide-ranged colonization can lead to the extinction of native species or be compensated by parasitic enemies and lead to equilibrium. This review emphasizes the comprehensive biology and cytogenetic knowledge and the importance of the Carassius genus as one of the most useful experimental vertebrate models for evolutionary biology and genetics. Secondly, the review points out that effective molecular cytogenetics should be used for the identification of various species, ploidy levels, and hybrids. The proposed investigation of these hallmark characteristics in Carassius may be applied in conservation efforts to sustain threatened populations in their native ranges. Furthermore, the review focuses on the consequences of the co-occurrence of native and non-native species and outlines future perspectives of Carassius research.

• Keywords
• Carassius auratus complex, asexuality, biotype, hybridization, ploidy level, sex determination, sexuality, species,
• MeSH
• Cyprinidae * MeSH
• Cytogenetic Analysis MeSH
• Cytogenetics MeSH
• Diploidy MeSH
• Ploidies MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Review MeSH

The widely distributed ray-finned fish genus Carassius is very well known due to its unique biological characteristics such as polyploidy, clonality, and/or interspecies hybridization. These biological characteristics have enabled Carassius species to be successfully widespread over relatively short period of evolutionary time. Therefore, this fish model deserves to be the center of attention in the research field. Some studies have already described the Carassius karyotype, but results are inconsistent in the number of morphological categories for individual chromosomes. We investigated three focal species: Carassius auratus, C. carassius and C. gibelio with the aim to describe their standardized diploid karyotypes, and to study their evolutionary relationships using cytogenetic tools. We measured length (q+plength) of each chromosome and calculated centromeric index (i value). We found: (i) The relationship between q+plength and i value showed higher similarity of C. auratus and C. carassius. (ii) The variability of i value within each chromosome expressed by means of the first quartile (Q1) up to the third quartile (Q3) showed higher similarity of C. carassius and C. gibelio. (iii) The fluorescent in situ hybridization (FISH) analysis revealed higher similarity of C. auratus and C. gibelio. (iv) Standardized karyotype formula described using median value (Q2) showed differentiation among all investigated species: C. auratus had 24 metacentric (m), 40 submetacentric (sm), 2 subtelocentric (st), 2 acrocentric (a) and 32 telocentric (T) chromosomes (24m+40sm+2st+2a+32T); C. carassius: 16m+34sm+8st+42T; and C. gibelio: 16m+22sm+10st+2a+50T. (v) We developed R scripts applicable for the description of standardized karyotype for any other species. The diverse results indicated unprecedented complex genomic and chromosomal architecture in the genus Carassius probably influenced by its unique biological characteristics which make the study of evolutionary relationships more difficult than it has been originally postulated.

• Keywords
• Carassius auratus, Carassius carassius, Carassius gibelio, chromosome, i value, in situ hybridization, karyogram, q/p arm ratio,
• MeSH
• Chromosomes genetics   MeSH
• Diploidy MeSH
• Phylogeny MeSH
• Genetic Variation genetics   MeSH
• Genome genetics   MeSH
• In Situ Hybridization, Fluorescence methods   MeSH
• Carps genetics   MeSH
• Goldfish genetics   MeSH
• Karyotype MeSH
• Karyotyping methods   MeSH
• Chromosome Mapping methods   MeSH
• Polyploidy MeSH
• Fishes genetics   MeSH
• Animals MeSH
• Check Tag
• Male MeSH
• Female MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH