Discovery of Sex-Determining Genes in Portunus trituberculatus: A Comparison of Male and Female Transcriptomes During Early Developmental Stages

Portunus trituberculatus is one of the main mariculture crabs of high economic value. To identify genes involved in sex determination, we first performed sex-specific transcriptome sequencing at six larval development stages using a DNA/RNA co-extraction method. A total of 907,952,938 and 828,774,880 reads were obtained from female and male crabs, respectively. 2,379 differentially expressed genes (DEGs) were found between females and males, and were mainly enriched in DNA replication, folate biosynthesis, and retinol metabolism pathways. Furthermore, transcription patterns of genes in the sex-determining region (SD) were analyzed based on the transcriptome data, and one Dmrt gene (PtDMY) was found to be exclusively expressed in males during early developmental stages. Notably, some known sex-related genes, including IAG, Dmrt11E, DmrtB1, and DmrtC2 were significantly down-regulated after knocking down PtDMY. Our results suggested that PtDMY is involved in sex determination and may be one of the key upstream regulators of the sex determination pathway. In addition, the massive volume of transcriptome data obtained in this study provided an important basis for the systematic study of sex determination mechanisms in P. trituberculatus.

Application of SNP in Genetic Sex Identification and Effect of Estradiol on Gene Expression of Sex-Related Genes in Strongylocentrotus intermedius

Sea urchin (Strongylocentrotus intermedius) is an economically important mariculture species in Asia, and its gonads are the only edible part. The efficiency of genetic breeding in sea urchins is hampered due to the inability to distinguish gender by appearance. In this study, we first identified a sex-associated single nucleotide polymorphism (SNP) by combining type IIB endonuclease restriction site-associated DNA sequencing (2b-RAD-seq) and genome survey. Importantly, this SNP is located within spata4, a gene specifically expressed in male. Knocking down of spata4 by RNA interference (RNAi) in male individuals led to the downregulation of other conserved testis differentiation-related genes and germ cell marker genes. We also revealed that sex ratio in this validated culture population of S. intermedius is not 1:1. Moreover, after a 58-day feeding experiment with estradiol, the expression levels of several conserved genes that are related to testis differentiation, ovary differentiation, and estrogen metabolism were dynamically changed. Taken together, our results will contribute toward improving breeding efficiency, developing sex-controlled breeding, and providing a solid base for understanding sex determination mechanisms in sea urchins.

Sex-Determination Mechanisms among Populations within Cryptic Species Complex of Calotes (Squamata: Agamidae: Draconinae)

Sex-determination mechanisms and sex chromosomes are known to vary among reptile species and, in a few celebrated examples, within populations of the same species. The oriental garden lizard, Calotes versicolor, is one of the most intriguing species in this regard, exhibiting evidence of multiple sex-determination modes within a single species. One possible explanation for this unusual distribution is that in C. versicolor, different modes of sex determination are confined to a particular population or a species within a cryptic species complex. Here, we report on a population genetic analysis using SNP data from a methylation-sensitive DArT sequencing analysis and mitochondrial DNA data obtained from samples collected from six locations: three from Bangladesh and three from Thailand. Our aim was to determine whether C. versicolor is best described as a single species with multiple lineages or as multiple species, as well as if its sex-determination mechanisms vary within or between species. We present evidence that the latter possibility is the case and that C. versicolor comprises a complex of cryptic species. We also identify sex-linked markers within these species and use them to identify modes of sex determination. Overall, our results suggest that different sex-determination modes have evolved among closely related species and within populations of Agamid lizards.

The rise and fall of the ancient northern pike master sex-determining gene

The understanding of the evolution of variable sex determination mechanisms across taxa requires comparative studies among closely related species. Following the fate of a known master sex-determining gene, we traced the evolution of sex determination in an entire teleost order (Esociformes). We discovered that the northern pike (Esox lucius) master sex-determining gene originated from a 65 to 90 million-year-old gene duplication event and that it remained sex linked on undifferentiated sex chromosomes for at least 56 million years in multiple species. We identified several independent species- or population-specific sex determination transitions, including a recent loss of a Y chromosome. These findings highlight the diversity of evolutionary fates of master sex-determining genes and the importance of population demographic history in sex determination studies. We hypothesize that occasional sex reversals and genetic bottlenecks provide a non-adaptive explanation for sex determination transitions.

An Investigation of ZZ/ZW and XX/XY Sex Determination Systems in North African Catfish (Clarias gariepinus, Burchell, 1822)

An investigation of sex-specific loci may provide important insights into fish sex determination strategies. This may be useful for biotechnological purposes, for example, to produce all-male or all-female fish for commercial breeding. The North African catfish species, Clarias gariepinus, has been widely adopted for aquaculture because its superior growth and disease resistance render the species suitable for hybridization with other catfish to improve the productivity and quality of fish meat. This species has either a ZZ/ZW or XX/XY sex determination system. Here, we investigate and characterize these systems using high-throughput genome complexity reduction sequencing as Diversity Arrays Technology. This approach was effective in identifying moderately sex-linked loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA) markers in 30 perfectly sexed individuals of C. gariepinus. However, SNPs based markers were not found in this study. In total, 41 loci met the criteria for being moderately male-linked (with male vs. female ratios 80:20 and 70:30), while 25 loci were found to be moderately linked to female sex. No strictly male- or female-linked loci were detected. Seven moderately male-linked loci were partially homologous to some classes of transposable elements and three moderately male-linked loci were partially homologous to functional genes. Our data showed that the male heterogametic XX/XY sex determination system should co-exist with the ZZ/ZW system in C. gariepinus. Our finding of the co-existence of XX/XY and ZZ/ZW systems can be applied to benefit commercial breeding of this species in Thailand. This approach using moderately sex-linked loci provides a solid baseline for revealing sex determination mechanisms and identify potential sex determination regions in catfish, allowing further investigation of genetic improvements in breeding programs.

A checklist of chromosome numbers and a review of karyotype variation in Odonata of the world

The ancient insect order Odonata is divided into three suborders: Anisoptera and Zygoptera with approximately 3000 species worldwide each, and Anisozygoptera with only four extant species in the relict family Epiophlebiidae. An updated list of Odonata species studied regarding chromosome number, sex chromosome mechanism and the occurrence of m-chromosomes (= microchromosomes) is given. Karyotypes of 607 species (198 genera, 23 families), covering approximately 10% of described species, are reported: 423 species (125 genera, 8 families) of the Anisoptera, 184 species (72 genera, 14 families) of the Zygoptera, and one species of the Anisozygoptera. Among the Odonata, sex determination mechanisms in males can be of X(0), XY and X1X2Y types, and diploid chromosome numbers can vary from 6 to 41, with a clear mode at 2n = 25(60%) and two more local modes at 2n = 27(21%) and 2n = 23(13%). The karyotype 2n = 25(24A + X) is found in each of the three suborders and is the most typical (modal) in many families, including the best-covered Libellulidae, Corduliidae (Anisoptera), Lestidae, Calopterygidae, and Platycnemididae (Zygoptera). This chromosome set is considered ancestral for the Odonata in general. Chromosome rearrangements, among which fusions and fissions most likely predominated, led to independent origins of similar karyotypes within different phylogenetic lineages of the order. The karyotype 2n = 27(26A + X) prevails in Aeshnidae and Coenagrionidae, whereas the karyotype 2n = 23(22A + X) is modal in Gomphidae and Chlorocyphidae, in both pairs of families one being from the Anisoptera while the other from the Zygoptera.

A checklist of chromosome numbers and a review of karyotype variation in Odonata of the world

The ancient insect order Odonata is divided into three suborders: Anisoptera and Zygoptera with approximately 3000 species worldwide each, and Anisozygoptera with only four extant species in the relict family Epiophlebiidae. An updated list of Odonata species studied regarding chromosome number, sex chromosome mechanism and the occurrence of m-chromosomes (= microchromosomes) is given. Karyotypes of 607 species (198 genera, 23 families), covering approximately 10% of described species, are reported: 423 species (125 genera, 8 families) of the Anisoptera, 184 species (72 genera, 14 families) of the Zygoptera, and one species of the Anisozygoptera. Among the Odonata, sex determination mechanisms in males can be of X(0), XY and X1X2Y types, and diploid chromosome numbers can vary from 6 to 41, with a clear mode at 2n = 25(60%) and two more local modes at 2n = 27(21%) and 2n = 23(13%). The karyotype 2n = 25(24A + X) is found in each of the three suborders and is the most typical (modal) in many families, including the best-covered Libellulidae, Corduliidae (Anisoptera), Lestidae, Calopterygidae, and Platycnemididae (Zygoptera). This chromosome set is considered ancestral for the Odonata in general. Chromosome rearrangements, among which fusions and fissions most likely predominated, led to independent origins of similar karyotypes within different phylogenetic lineages of the order. The karyotype 2n = 27(26A + X) prevails in Aeshnidae and Coenagrionidae, whereas the karyotype 2n = 23(22A + X) is modal in Gomphidae and Chlorocyphidae, in both pairs of families one being from the Anisoptera while the other from the Zygoptera.

Multi-Tissue Transcriptome Analysis Identifies Key Sexual Development-Related Genes of the Ornate Spiny Lobster (Panulirus ornatus)

Sexual development involves the successive and overlapping processes of sex determination, sexual differentiation, and ultimately sexual maturation, enabling animals to reproduce. This provides a mechanism for enriched genetic variation which enables populations to withstand ever-changing environments, selecting for adapted individuals and driving speciation. The molecular mechanisms of sexual development display a bewildering diversity, even in closely related taxa. Many sex determination mechanisms across animals include the key family of “doublesex- and male abnormal3-related transcription factors” (Dmrts). In a few exceptional species, a single Dmrt residing on a sex chromosome acts as the master sex regulator. In this study, we provide compelling evidence for this model of sex determination in the ornate spiny lobster Panulius ornatus, concurrent with recent reports in the eastern spiny lobster Sagmariasus verreauxi. Using a multi-tissue transcriptomic database established for P. ornatus, we screened for the key factors associated with sexual development (by homology search and using previous knowledge of these factors from related species), providing an in-depth understanding of sexual development in decapods. Further research has the potential to close significant gaps in our understanding of reproductive development in this ecologically and commercially significant order.

The rise and fall of the ancient northern pike master sex determining gene

Sexual reproduction is a ubiquitous basic feature of life and genetic sex determination is thus widespread, at least among eukaryotes. Understanding the remarkable diversity of sex determination mechanisms, however, is limited by the paucity of empirical studies. Here, we traced back the evolution of sex determination in an entire clade of vertebrates and uncovered that the northern pike (Esox lucius) master sex-determining gene initiated from a 65 to 90 million-year-old gene duplication and remained sex-linked on undifferentiated sex chromosomes for at least 56 million years. Contrasting with its ancient origin, we identified several independent species- or population-specific transitions of sex determination mechanisms in this lineage, including an unexpected complete and recent Y-chromosome loss in some North American northern pike populations. These findings highlight the diversity of the evolutionary fates of master sex-determining genes and raise the importance of careful considerations of population demographic history in sex determination studies. Our study also puts forward the hypothesis that occasional sex reversals and genetic bottlenecks provide a non-adaptive explanation for sex determination transitions.

Evolutionary transition to XY sex chromosomes associated with Y-linked duplication of a male hormone gene in a terrestrial isopod

Sex chromosomes are highly variable in some taxonomic groups, but the evolutionary mechanisms underlying this diversity are not well understood. In terrestrial isopod crustaceans, interactions with Wolbachia, a vertically transmitted endosymbiont causing male-to-female sex reversal, are thought to drive rapid evolutionary turnovers in sex chromosomes. Here, we use surgical manipulations and genetic crosses, plus genome sequencing, to examine sex chromosomes in the terrestrial isopod Trachelipus rathkei. Although an earlier cytogenetics study suggested a ZZ/ZW sex chromosome system in this species, we surprisingly find that in our study population, sex is determined by an XX/XY system. Consistent with a recent evolutionary origin for this XX/XY system, the putative male-specific region of the genome is small. The genome shows evidence of sequences horizontally acquired from past Wolbachia infections, as well as evidence of Y-linked duplications of the androgenic gland hormone gene, thought to be a possible target for sex reversal by Wolbachia. Overall, these results are consistent with the hypothesis that reproductive endosymbionts such as Wolbachia can promote quick turnover of sex determination mechanisms in their hosts.