Sex-Specific Transcriptome Sequencing of Zoea I Larvae and Identification of Sex-Linked Genes Using Bulked Segregant Analysis in Pacific White Shrimp Litopenaeus vannamei

A high-density linkage map and sex-determination loci in Pacific white shrimp (Litopenaeus vannamei)

BACKGROUND

Expansion of genomic resources for the Pacific white shrimp (Litopenaeus vannamei), such as the construction of dense genetic linkage maps, is crucial for the application of genomic tools in order to improve economically relevant traits. Sexual dimorphism exists in Pacific white shrimp, and the mapping of the sex-determination region in this species may help in future reproductive applications. We have constructed male, female, and sex-averaged high-density genetic maps using a 50 K single-nucleotide polymorphism (SNP) array, followed by a genome-wide association study (GWAS) to identify genomic regions associated with sex in white shrimp.

RESULTS

The genetic map yielded 15,256 SNPs assigned to 44 linkage groups (LG). The lengths of the male, female, and sex-averaged maps were 5,741.36, 5,461.20 and 5,525.26 cM, respectively. LG18 was found to be the largest for both sexes, whereas LG44 was the shortest for males and LG31 for females. A sex-determining region was found in LG31 with 21 statistically significant SNPs. The most important SNP was previously identified as a sex-linked marker and was able to identify 99% of the males and 88% of the females. Although other significant markers had a lower ability to determine sex, putative genes were intercepted or close to them. The oplophorus-luciferin 2-monooxygenase, serine/arginine repetitive matrix protein and spermine oxidase genes were identified as candidates with possible participation in important processes of sexual differentiation in shrimp.

CONCLUSIONS

Our results provide novel genomic resources for shrimp, including a high-density linkage map and new insights into the sex-determining region in L. vannamei, which may be usefulfor future genetics and reproduction applications.

Monosex Populations of the Giant Freshwater Prawn Macrobrachium rosenbergii-From a Pre-Molecular Start to the Next Generation Era

Sexual manipulation in the giant freshwater prawn Macrobrachium rosenbergii has proven successful in generating monosex (both all-male and all-female) populations for aquaculture using a crustacean-specific endocrine gland, the androgenic gland (AG), which serves as a key masculinizing factor by producing and secreting an insulin-like AG hormone (IAG). Here, we provide a summary of the advancements from the discovery of the AG and IAG in decapods through to the development of monosex populations in M. rosenbergii. We discuss the broader sexual development pathway, which is highly divergent across decapods, and provide our future perspective on the utility of novel genetic and genomic tools in promoting refined approaches towards monosex biotechnology. Finally, the future potential benefits of deploying monosex prawn populations for environmental management are discussed.

Differentially expressed genes in the testes from early to mature development of banana shrimp (Fenneropenaeus merguiensis)

Banana shrimp (Fenneropenaeus merguiensis) is an economically important species in Thailand owing to the high value of globally exported frozen brine shrimps. However, the regulatory mechanisms governing spermatogenesis and testicular development in this species are poorly understood. High-throughput RNA sequencing was used to investigate the mechanisms and regulated genes involved in testis development using transcriptome profiling of juvenile and adult banana shrimp testes. Differentially expressed genes (DEGs) in these two libraries were identified and quantified to confirm gene expression. DEGs were found in 7,347 genes, with 4,465 upregulated and 2,882 downregulated. Some of these genes were designated as candidate genes, and six specific DEGs, including PRM1, SPATA20, Sry, SSRF, Sxl, and Tra-2c, were selected to confirm the reliability of the RNA-seq data using qPCR. Moreover, six non-DEGs were chosen based on testis-specific and regulatory genes that support a specific function in spermatogenesis and testis development in this species, including Dsx, Gfra2, IAG, Sox9, Sox13, and Sox14A. Furthermore, Sry, Sox14A, Sox14B and SPATA20 were identified in early stages (nauplius-postlarvae) of shrimp development to provide more information involving testes formation and development. The transcript data from this study could differentiate a group of genes required at the early and late stages of testis development and both sets of testis development. Therefore, this information would help in manipulating each stage of testicular development.

Sex determination mechanisms and sex control approaches in aquaculture animals

Aquaculture is one of the most efficient modes of animal protein production and plays an important role in global food security. Aquaculture animals exhibit extraordinarily diverse sexual phenotypes and underlying mechanisms, providing an ideal system to perform sex determination research, one of the important areas in life science. Moreover, sex is also one of the most valuable traits because sexual dimorphism in growth, size, and other economic characteristics commonly exist in aquaculture animals. Here, we synthesize current knowledge of sex determination mechanisms, sex chromosome evolution, reproduction strategies, and sexual dimorphism, and also review several approaches for sex control in aquaculture animals, including artificial gynogenesis, application of sex-specific or sex chromosome-linked markers, artificial sex reversal, as well as gene editing. We anticipate that better understanding of sex determination mechanisms and innovation of sex control approaches will facilitate sustainable development of aquaculture.

Allelically and Differentially Expressed Genes After Infection of Edwardsiella ictaluri in Channel Catfish as Determined by Bulk Segregant RNA-Seq

Identification of genetic markers associated with resistance against enteric septicemia of catfish (ESC) is of great interest for genetic enhancement programs of catfish. In the present study, bulk segregant RNA-Seq analysis was applied to determine differentially expressed genes and alleles after ESC infection. Here we report three genomic regions on LG1, LG12, and LG26, containing significant single-nucleotide polymorphisms (SNPs). These genomic regions aligned well with quantitative trait loci (QTL) previously identified. Within the QTL regions, eleven genes were found to be differentially regulated between phenotypic bulks. Importantly, the QTL on linkage group 1 (LG1) were found to be expressed in the liver, whereas the QTL on LG12 and LG26 were expressed in the intestine, suggesting multiple mechanisms of ESC resistance. It is apparent that apolipoproteins may be important for ESC resistance as the QTL on LG1 included the 14-kDa apolipoprotein genes that are both allelically expressed and differentially expressed between the resistant and susceptible bulks. Traf2 and NCK-interacting protein kinase (TNIK) were found in the QTL on LG12, and it was downregulated in resistant fish, suggesting the importance of NCK downregulation in ESC resistance, as previously reported. In addition, we observed divergent gene expression patterns between the liver and intestine after infection. Immune/inflammatory-related processes were overrepresented from liver DEGs, while those DEGs identified from intestine were enriched for proteolysis and wounding processes. Taken together, the BSR-Seq analysis presented here advanced the knowledge of ESC resistance, providing information of not only positions of QTL but also genes and their differential expression between resistant and susceptible fish, making it one step closer to the identification of the causal genes for ESC resistance.

Bulk segregation analysis in the NGS era: a review of its teenage years

Bulk segregation analysis (BSA) utilizes a strategy of pooling individuals with extreme phenotypes to conduct economical and rapidly linked marker screening or quantitative trait locus (QTL) mapping. With the development of next-generation sequencing (NGS) technology in the past 10 years, BSA methods and technical systems have been gradually developed and improved. At the same time, the ever-decreasing costs of sequencing accelerate NGS-based BSA application in different species, including eukaryotic yeast, grain crops, economic crops, horticultural crops, trees, aquatic animals, and insects. This paper provides a landscape of BSA methods and reviews the BSA development process in the past decade, including the sequencing method for BSA, different populations, different mapping algorithms, associated region threshold determination, and factors affecting BSA mapping. Finally, we summarize related strategies in QTL fine mapping combining BSA.

Construction of a high-density linkage map and detection of sex-specific markers in Penaeus japonicus

Penaeus japonicus is one of the most important farmed shrimp species in many countries. Sexual dimorphism is observed in P. japonicus, in which females grow faster and larger than males; therefore, a unisexual female culture of P. japonicus could improve the efficiency of productivity. However, the genetic mechanisms underlying sex determination in P. japonicus are unclear. In this study, we constructed a high-density genetic linkage map of P. japonicus using genotyping-by-sequencing (GBS) technology in a full-sib family. The final map was 3,481.98 cM in length and contained 29,757 single nucleotide polymorphisms (SNPs). These SNPs were distributed on 41 sex-averaged linkage groups, with an average inter-marker distance of 0.123 cM. One haplotype, harboring five sex-specific SNPs, was detected in linkage group 1 (LG1), and its corresponding confidence interval ranged from 211.840 to 212.592 cM. Therefore, this high-density genetic linkage map will be informative for genome assembly and marker-assisted breeding, and the sex-linked SNPs will be helpful for further studies on molecular mechanisms of sex determination and unisexual culture of P. japonicus in the future.

Sex-Biased Gene Expression and Isoform Profile of Brine Shrimp Artemia franciscana by Transcriptome Analysis

Simple Summary

The brine shrimp Artemia is a promising model organism for ZW sex determination system, but the genes related to sex determination and differentiation of Artemia have not yet been examined in detail. In this study, the first isoform-level transcriptome sequencing was performed on female and male Artemia franciscana. By using PacBio Iso-Seq and Illumina RNA-Seq technologies, we found 39 candidate sex determination genes that showed sex-biased gene expression. The male-biased expressed genes included DMRT1 and Sad genes, which had three and seven isoforms, respectively. Among these, the Sad gene is an ecdysteroid biosynthetic pathway gene associated with arthropod molting and metamorphosis. We propose the importance and the necessity of further research on genes involved in ecdysteroid biosynthesis. These results will contribute to understand sex determination and differentiation of Artemia and other crustaceans having ZW systems.

Abstract

The brine shrimp Artemia has a ZW sex determination system with ZW chromosomes in females and ZZ chromosomes in males. Artemia has been considered a promising model organism for ZW sex-determining systems, but the genes involved in sex determination and differentiation of Artemia have not yet been identified. Here, we conducted transcriptome sequencing of female and male A. franciscana using PacBio Iso-Seq and Illumina RNA-Seq techniques to identify candidate sex determination genes. Among the 42,566 transcripts obtained from Iso-Seq, 23,514 were analyzed. Of these, 2065 (8.8%) were female specific, 2513 (10.7%) were male specific, and 18,936 (80.5%) were co-expressed in females and males. Based on GO enrichment analysis and expression values, we found 10 female-biased and 29 male-biased expressed genes, including DMRT1 and Sad genes showing male-biased expression. Our results showed that DMRT1 has three isoforms with five exons, while Sad has seven isoforms with 2–11 exons. The Sad gene is involved in ecdysteroid signaling related to molting and metamorphosis in arthropods. Further studies on ecdysteroid biosynthetic genes are needed to improve our understanding of Artemia sex determination. This study will provide a valuable resource for sex determination and differentiation studies on Artemia and other crustaceans with ZW systems.

Updated Genome Assembly of Bighead Carp (Hypophthalmichthys nobilis) and Its Differences Between Male and Female on Genomic, Transcriptomic, and Methylation Level

Cyprinidae is one of the largest family in freshwater fishes, and it is most intensively cultured fish taxon of the world. However, studies about sex determination in this large family is still rear, and one of the reasons is lack of high quality and complete genome. Here, we used nanopore to sequence the genome of a male bighead carp, obtaining contig N50 = 24.25 Mb, which is one of the best assemblies in Cyprinidae. Five males and five females were re-sequenced, and a male-specific region on LG19 was confirmed. We find this region holds many male-specific markers in other Cyprinidae fishes, such as grass carp and silver carp. Transcriptome analyses of hypothalamus and pituitary tissues showed that several sex-specific differentially expressed genes were associated with steroid biosynthesis. The UCH64E gene, located in the male-specific region on LG19, showed higher expression levels in male than female tissues of bighead carp. The methyl-RAD of hypothalamus tissues between males and females indicated that the sexual methylation differences are significant in bighead carp. We also compared the methylation sites recognized using methyl-RAD and nanopore raw reads and found that approximately 73% of the methylation sites identified using methyl-RAD were within nanopore CpG sites.

Pomc Plays an Important Role in Sexual Size Dimorphism in Tilapia

Sexual dimorphism is common across the animal kingdom. Knowledge of the mechanisms of sexual size dimorphism is limited although it is important in biology and aquaculture. Tilapia is the common name for ~ 100 species of cichlid fish. Some are important aquaculture species and males outgrow females. To gain novel insights into the mechanisms underlying sexual size dimorphism, we analyzed the differences of brain transcriptomes between males and females in Mozambique tilapia and studied the function of the pro-opiomelanocortin (Pomc) gene in tilapia and zebrafish. The transcriptome analysis identified 123, 55, and 2706 sex-biased genes at 5, 30, and 90 dph (days post-hatch), respectively, indicating sexual dimorphism of gene expressions in the brain. The expression of Pomc in the tilapia brain was a female-biased at 30, 90, and 120 dph. An analysis of the DNA sequence located upstream of the tilapia Pomc transcriptional start site identified two estrogenic response elements. In vitro luciferase assay of the two elements revealed that β-estradiol significantly enhanced the expression of luciferase activity, suggesting that the expression of Pomc is mediated by estrogen. We knocked out Pomc in zebrafish using Crispr/Cas-9. The Pomc-knockout zebrafish showed faster growth and higher sensitivity to feeding as compared to the wild-type fish. Taken together, our results indicate that Pomc contributes to sexual size dimorphism and suggest that the high estrogen level in females promotes the expression of Pomc and suppresses feeding in female tilapias, which leads to the slower growth of female tilapias.

Sex Determination and Differentiation in Decapod and Cladoceran Crustaceans: An Overview of Endocrine Regulation

Mechanisms underlying sex determination and differentiation in animals are known to encompass a diverse array of molecular clues. Recent innovations in high-throughput sequencing and mass spectrometry technologies have been widely applied in non-model organisms without reference genomes. Crustaceans are no exception. They are particularly diverse among the Arthropoda and contain a wide variety of commercially important fishery species such as shrimps, lobsters and crabs (Order Decapoda), and keystone species of aquatic ecosystems such as water fleas (Order Branchiopoda). In terms of decapod sex determination and differentiation, previous approaches have attempted to elucidate their molecular components, to establish mono-sex breeding technology. Here, we overview reports describing the physiological functions of sex hormones regulating masculinization and feminization, and gene discovery by transcriptomics in decapod species. Moreover, this review summarizes the recent progresses of studies on the juvenile hormone-driven sex determination system of the branchiopod genus Daphnia, and then compares sex determination and endocrine systems between decapods and branchiopods. This review provides not only substantial insights for aquaculture research, but also the opportunity to re-organize the current and future trends of this field.