Zfy2/1 fusion gene fails to replicate Zfy1 expression pattern in fetal gonads

Discovery of sex-related genes through high-throughput transcriptome sequencing from the salmon louse Caligus rogercresseyi

Understanding the molecular underpinnings involved in the reproduction of the salmon louse is critical for designing novel strategies of pest management for this ectoparasite. However, genomic information on sex-related genes is still limited. In the present work, sex-specific gene transcription was revealed in the salmon louse Caligus rogercresseyi using high-throughput Illumina sequencing. A total of 30,191,914 and 32,292,250 high quality reads were generated for females and males, and these were de novo assembled into 32,173 and 38,177 contigs, respectively. Gene ontology analysis showed a pattern of higher expression in the female as compared to the male transcriptome. Based on our sequence analysis and known sex-related proteins, several genes putatively involved in sex differentiation, including Dmrt3, FOXL2, VASA, and FEM1, and other potentially significant candidate genes in C. rogercresseyi, were identified for the first time. In addition, the occurrence of SNPs in several differentially expressed contigs annotating for sex-related genes was found. This transcriptome dataset provides a useful resource for future functional analyses, opening new opportunities for sea lice pest control.

Transcriptome analysis of the oriental river prawn, Macrobrachium nipponense using 454 pyrosequencing for discovery of genes and markers

Background

The oriental river prawn, Macrobrachium nipponense, is an economically and nutritionally important species of the Palaemonidae family of decapod crustaceans. To date, the sequencing of its whole genome is unavailable as a non-model organism. Transcriptomic information is also scarce for this species. In this study, we performed de novo transcriptome sequencing to produce the first comprehensive expressed sequence tag (EST) dataset for M. nipponense using high-throughput sequencing technologies.

Methodology and Principal Findings

Total RNA was isolated from eyestalk, gill, heart, ovary, testis, hepatopancreas, muscle, and embryos at the cleavage, gastrula, nauplius and zoea stages. Equal quantities of RNA from each tissue and stage were pooled to construct a cDNA library. Using 454 pyrosequencing technology, we generated a total of 984,204 high quality reads (338.59Mb) with an average length of 344 bp. Clustering and assembly of these reads produced a non-redundant set of 81,411 unique sequences, comprising 42,551 contigs and 38,860 singletons. All of the unique sequences were involved in the molecular function (30,425), cellular component (44,112) and biological process (67,679) categories by GO analysis. Potential genes and their functions were predicted by KEGG pathway mapping and COG analysis. Based on our sequence analysis and published literature, many putative genes involved in sex determination, including DMRT1, FTZ-F1, FOXL2, FEM1 and other potentially important candidate genes, were identified for the first time in this prawn. Furthermore, 6,689 SSRs and 18,107 high-confidence SNPs were identified in this EST dataset.

Conclusions

The transcriptome provides an invaluable new data for a functional genomics resource and future biological research in M. nipponense. The molecular markers identified in this study will provide a material basis for future genetic linkage and quantitative trait loci analyses, and will be essential for accelerating aquaculture breeding programs with this species.

Sex-linked genes are not silenced in fetal bovine testes expressing X-inactive specific transcript (XIST)

X-inactive specific transcript (XIST), which is thought to be the central factor for the X-inactivation process in female mammals, is known to be expressed in males during spermatogenesis. Our studies have shown that XIST is not only expressed in adult bovine testis but is also expressed in fetal, newborn, and prepubertal testes long before spermatogenesis is established. To determine whether the XIST expressed in fetal testes is involved in silencing the genes on the X chromosome, we investigated the status of X-linked genes, including glucose-6-phosphate-dehydrogenase (G6PD), hypoxanthine phosphoribosyl transferase (HPRT), and X-linked zinc finger protein gene (ZFX), in fetal bovine gonads at the developmental stage, when meiosis is initiated in fetal ovaries in this species. Reverse transcription and a semiquantitative polymerase chain reaction based on the optical density of each gene-specific band relative to that of the co-amplified Quantum RNA 18S Internal Standard (Ambion, Austin, TX) showed that the XIST gene was expressed in the testes of approximately 90-day-old fetuses and was silent in all their nongonadal organs tested, although at a significantly lower level than that in fetal organs of female fetuses. Our observation that the expression of X-linked genes in the fetal testis was comparable to that in male nongonadal organs, in which X inactivation does not occur, indicates that the low level of XIST, or XIST-like RNA, expressed in the fetal bovine testis is not involved in silencing X-linked genes.