Sex determination in the Squalius alburnoides complex: an initial characterization of sex cascade elements in the context of a hybrid polyploid genome

Production of donor-derived eggs after ovarian germ cell transplantation into the gonads of adult, germ cell-less, triploid hybrid fish†

In animals, spermatogonial transplantation in sterile adult males is widely developed; however, despite its utility, ovarian germ cell transplantation is not well developed. We previously showed that the interspecific hybrid offspring of sciaenid was a suitable model for germ cell transplantation studies as they have germ cell-less gonads. However, all these gonads have testis-like characteristics. Here, we tested whether triploidization in hybrid embryos could result in germ cell-less ovary development. Gonadal structure dimorphism and sex-specific gene expression patterns were examined in 6-month-old triploid hybrids (3nHybs). Thirty-one percent of 3nHybs had germ cell-less gonads with an ovarian cavity. cyp19a1a and foxl2, ovarian differentiation-related genes, were expressed in these gonads, whereas dmrt1 and vasa were not expressed, suggesting ovary-like germ cell-less gonad development. Some (26%) 3nHybs had testis-like germ cell-less gonads. Ovarian germ cells collected from homozygous green fluorescent protein (GFP) transgenic blue drum (BD) (Nibea mitsukurii) were transplanted into 6-month-old 3nHybs gonads via the urogenital papilla or oviduct. After 9 months, the recipients were crossed with wild type BD. Among the six 3nHyb recipients that survived, one female and one male produced fertile eggs and motile sperm carrying gfp-specific DNA sequences. Progeny tests revealed that all F1 offspring possessed gfp-specific DNA sequences, suggesting that these recipients produced only donor-derived eggs or sperm. Histological observation confirmed donor-derived gametogenesis in the 3nHyb recipients' gonads. Overall, triploidization reduces male-biased sex differentiation in germ cell-less gonads. We report, for the first time, donor-derived egg production in an animal via direct ovarian germ cell transplantation into a germ cell-less ovary.

Non-canonical expression patterns and evolutionary rates of sex-biased genes in a seasonal fish

Sex determination is a highly variable process that utilizes many different mechanisms to initiate the cascade of differentiation processes. The molecular pathways controlling sexual development are less conserved than previously assumed, and appear to require active maintenance in some species; indeed, the developmental decision of gonad phenotype in gonochoristic species is not fixed at an early developmental stage. Much of the knowledge about sex determination mechanisms was derived from research on gonochoristic, non-seasonal breeders. In this study, the transcriptome of resting adult gonads of a seasonal breeder, the endangered Iberian cyprinid fish Squalius pyrenaicus, was analyzed to assess the expression patterns and evolutionary rates of sex-biased genes that could be involved in maintenance of gonad identity as well as in sex determination. Remarkably, some crucial female genes-such as aromatase cyp19a1a, estrogen receptor esr1a, and foxl2-were expressed more abundantly in S. pyrenaicus testis than in ovaries. Moreover, contrary to the higher evolutionary rate changes observed in male-biased genes, higher d_N /d_S ratios were observed for female-biased genes than for male-biased genes in S. pyrenaicus. These results help unravel the impact of seasonality in sex determination mechanisms and the evolution of genes, and highlight the need to study fish at different gonadal maturation states to understand the function of sex-biased genes. Mol. Reprod. Dev. 83: 1102-1115, 2016. © 2016 Wiley Periodicals, Inc.

Transcriptomic Analyses Reveal Novel Genes with Sexually Dimorphic Expression in Yellow Catfish (Pelteobagrus fulvidraco) Brain

Yellow catfish (Pelteobagrus fulvidraco) is a pivotal freshwater aquaculture species in China. It shows sexual size dimorphism favoring male in growth. Whole transcriptome approach is required to get the overview of genetic toolkit for understanding the sex determination mechanism aiming at devising its monosex production. Beside gonads, the brain is also considered as a major organ for vertebrate reproduction. Transcriptomic analyses on the brain and of different developmental stages will provide the dynamic view necessary for better understanding its sex determination. In this regard, we have performed a de novo assembly of yellow catfish brain transcriptome by high throughput Illumina sequencing. A total number of 154,507 contigs were obtained with the lengths ranging from 201 to 27,822 bp and N50 of 2,101 bp, as well as 20,699 unigenes were identified. Of these unigenes, 13 and 54 unigenes were detected to be XY-specifically expressed genes (SEGs) for one and 2-year-old yellow catfish, while the corresponding numbers of XX-SEGs for those two stages were 19 and 13, respectively. Our work identifies a set of annotated genes that are candidate factors affecting sexual dimorphism as well as simple sequence repeat (SSR) and single nucleotide variation (SNV) in yellow catfish. To validate the expression patterns of the sex-related genes, we performed quantitative real-time PCR (qRT-PCR) indicating the reliability and accuracy of our analysis. The results in our study may enhance our understanding of yellow catfish sex determination and potentially help to improve the production of all-male yellow catfish for aquaculture.

Sex determination in annual fishes: Searching for the master sex-determining gene in Austrolebias charrua (Cyprinodontiformes, Rivulidae)

Evolution of sex determination and differentiation in fishes involves a broad range of sex strategies (hermaphroditism, gonochorism, unisexuality, environmental and genetic sex determination). Annual fishes inhabit temporary ponds that dry out during the dry season when adults die. The embryos exhibit an atypical developmental pattern and remain buried in the bottom mud until the next rainy season. To elucidate genomic factors involved in the sex determination in annual fish, we explored the presence of a candidate sex-specific gene related to the cascade network in Austrolebias charrua. All phylogenetic analyses showed a high posterior probability of occurrence for a clade integrated by nuclear sequences (aprox. 900 bp) from both adults (male and female), with partial cDNA fragments of A. charrua from juveniles (male) and the dsx D. melanogaster gene. The expressed fragment was detected from blastula to adulthood stages showing a sexually dimorphic expression pattern. The isolated cDNA sequence is clearly related to dsx D. melanogaster gene and might be located near the top of the sex determination cascade in this species.

Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon

Background

Sturgeons are a group of Condrostean fish with very high evolutionary, economical and conservation interest. The eggs of these living fossils represent one of the most high prized foods of animal origin. The intense fishing pressure on wild stocks to harvest caviar has caused in the last decades a dramatic decline of their distribution and abundance leading the International Union for Conservation of Nature to list them as the more endangered group of species. As a direct consequence, world-wide efforts have been made to develop sturgeon aquaculture programmes for caviar production. In this context, the characterization of the genes involved in sex determination could provide relevant information for the selective farming of the more profitable females.

Results

The 454 sequencing of two cDNA libraries from the gonads and brain of one male and one female full-sib A. naccarii, yielded 182,066 and 167,776 reads respectively, which, after strict quality control, were iterative assembled into more than 55,000 high quality ESTs. The average per-base coverage reached by assembling the two libraries was 4X. The multi-step annotation process resulted in 16% successfully annotated sequences with GO terms. We screened the transcriptome for 32 sex-related genes and highlighted 7 genes that are potentially specifically expressed, 5 in male and 2 in females, at the first life stage at which sex is histologically identifiable. In addition we identified 21,791 putative EST-linked SNPs and 5,295 SSRs.

Conclusions

This study represents the first large massive release of sturgeon transcriptome information that we organized into the public database AnaccariiBase, which is freely available at http://compgen.bio.unipd.it/anaccariibase/. This transcriptomic data represents an important source of information for further studies on sturgeon species. The hundreds of putative EST-linked molecular makers discovered in this study will be invaluable for sturgeon reintroduction and breeding programs.

Global analysis of the small RNA transcriptome in different ploidies and genomic combinations of a vertebrate complex--the Squalius alburnoides

The Squalius alburnoides complex (Steindachner) is one of the most intricate hybrid polyploid systems known in vertebrates. In this complex, the constant switch of the genome composition in consecutive generations, very frequently involving a change on the ploidy level, promotes repetitive situations of potential genomic shock. Previously in this complex, it was showed that in response to the increase in genome dosage, triploids hybrids could regulate gene expression to a diploid state. In this work we compared the small RNA profiles in the different genomic compositions interacting in the complex in order to explore the miRNA involvement in gene expression regulation of triploids. Using high-throughput arrays and sequencing technologies we were able to verify that diploid and triploid hybrids shared most of their sequences and their miRNA expression profiles were high correlated. However, an overall view indicates an up-regulation of several miRNAs in triploids and a global miRNA expression in triploids higher than the predicted from an additive model. Those results point to a participation of miRNAs in the cellular functional stability needed when the ploidy change.

Development of an in vitro system for functional studies of ovarian follicular cells in European sea bass (Dicentrarchus labrax)

The layers of follicular cells surrounding the oocyte and the interactions among them and the germ cells are critical for the successful maintenance of the ovarian functions. We have set up the isolation procedure and culture conditions of sea bass ovarian follicular cells. Their behaviour at three different physiological temperatures (25, 18 and 15 °C) was evaluated by verifying their steroidogenic capacity along time together with the expression of follicular specific genes (cyp19a1, fshr, lhr and star). These characteristics revealed this culture as a good in vitro alternative to short term in vivo studies at the level of the ovarian follicle. Moreover, to evaluate the suitability of this system for gene function studies conditions for transient transfection of plasmid DNA were optimized. Finally, the characteristics of the follicular culture were not affected by freezing and thawing cycles what facilitates the performance of experiments independently of the reproductive season. In conclusion, we have developed an in vitro homologous system that enables functional and gene expression studies and resembles the in vivo situation in the ovarian follicle.

A polymorphic microsatellite from the Squalius alburnoides complex (Osteichthyes, Cyprinidae) cloned by serendipity can be useful in genetic analysis of polyploids

A new microsatellite locus (SAS1) for Squalius alburnoides was obtained through cloning by serendipity. The possible usefulness of this new species-specific microsatellite in genetic studies of this hybrid-species complex, was explored. The polymorphism exhibited by SAS1 microsatellite is an important addition to the set of microsatellites previously used in genetic studies in S. alburnoides complex, that mostly relied in markers described for other species. Moreover, the SAS1 microsatellite could be used to identify the parental genomes of the complex, complementing other methods recently described for the same purpose..

Cytonuclear evidence for hybridogenetic reproduction in natural populations of the Australian carp gudgeon (Hypseleotris: Eleotridae)

Although most vertebrates reproduce sexually, a small number of fishes, amphibians and reptiles are known in which reproduction is asexual, i.e. without meiotic recombination. In fishes, these so-called unisexual lineages usually comprise only females and utilize co-occurring males of a related sexual species to reproduce via gynogenesis or hybridogenesis. Here, we examine patterns of microsatellite and mitochondrial DNA (mtDNA) variation in a widespread group of freshwater fishes (carp gudgeons; Hypseleotris spp.) to investigate a long-standing proposal that this group includes unisexual forms. We show that the mtDNA genome of most carp gudgeons in tributaries of the Goulburn River belongs to one of two deeply divided clades (∼10% cyt b divergence) and that nuclear variation divides the same individuals into four distinct groups. Group 1 exhibits the genotypic proportions of a random mating population and has a 1:1 sex ratio. Two other groups are extremely sex-biased (98% male, 96% female), exhibit excess heterozygosity at most loci and share at least one allele per locus with group 1. We propose that these two groups represent 'unisexual' hybridogenetic lineages and that both utilize co-occurring group 1 as sexual host. Interestingly, the fourth distinct group appears to represent hybrid offspring of the two putative hybridogenetic lineages. The propagation of clonal haploid genomes by both males and females and the ability of these clones to unite and form sexually mature diploid hybrid offspring may represent a novel mechanism that contributes to the dynamics of coexistence between hybridogenetic lineages and their sexual hosts.

The evolutionary history of the allopolyploid Squalius alburnoides (Cyprinidae) complex in the northern Iberian Peninsula

Understanding the population structure, population dynamics and processes that give rise to polyploidy and helps to maintain it is central to our knowledge of the evolution of asexual vertebrates. Previous studies revealed high genetic diversity and several reproductive pathways in the southern populations of the Squalius alburnoides hybrid complex. In contrast, lower genetic variability and the associated limited chance of introducing new genetic combinations may threaten the survival of the northern Mondego populations. We analysed the genetic diversity and structure of nine populations of S. alburnoides in the Iberian Peninsula using microsatellite loci to provide further insights on the evolutionary history of this complex. Special attention was given to the less-studied northern populations (Mondego and Douro basins). Marked population structure, a high frequency of private alleles and a high diversity of some biotypes in the Douro basin indicate that some northern populations may not be at high risk of extinction, contrary to what was expected. The genetic diversity found in the northern Douro populations contradicts the general trend of remarkable genetic impoverishment northwards that occurs in other species and regions. The results indicate the possible existence of a glacial refugium in the Rabaçal River, corroborating findings in other species of this region. Historical events seem to have affected the geographical patterns of genetic variability found among and within the northern and southern populations of this complex and contributed to different patterns of genome composition. Therefore, historical events might have a major role in the long-term persistence of some polyploid hybrid taxa.

An easier method to identify the individual genomic composition of allopolyploid complexes

A new method for the fast identification of the genomic composition of the cyprinid Squalius alburnoides is presented. The method is based on a length polymorphism detected in the beta-actin gene, which serves as the basis for the development of a semi-quantitative PCR.

Sexually dimorphic expression of dmrt1 in immature and mature Atlantic cod (Gadus morhua L.)

The Doublesex and Mab-3 related transcription factor 1 (Dmrt1) is implicated in testis development in a variety of vertebrates, including teleost fish. Atlantic cod (Gadusmorhua L.) is a promising cold-water aquaculture species, but early sexual maturation of males in particular is a major problem in today's cod farming. Molecular studies of dmrt1 were initiated to gain knowledge about the regulation of gonad development for the first time in a species of the superorder Paracanthopterygii. The predicted cod Dmrt1 of 310 amino acids contains a highly conserved DM domain, including six Cys residues probably involved in the formation of a double zinc-finger motif for DNA binding. The tissue expression analysis revealed that dmrt1 is expressed exclusively in the gonads, and the signal was localized in the germ cells in both genders by in situ hybridization. Sexually dimorphic expression of dmrt1 was documented by quantitative PCR with the highest mRNA levels in immature males corresponding to the start of spermatogenesis. Although significantly less expressed in the ovary, Dmrt1 might also play a role in oogenesis. Southern blot analysis revealed several DM domain-containing genes in the cod genome, but no sex-linked polymorphism was shown.