Differential gene expression in hepatopancreas of the shrimp Metapenaeus ensis during ovarian maturation

Climate change driven hyposalinity as a selective agent in the littoral mesoherbivore Idotea balthica

Climate change will include a decrease in seawater salinity in the Baltic Sea. We quantified the effects of the projected future desalination on survival of the early life stage of the littoral herbivore Idotea balthica. We collected egg-bearing Idotea from three range-margin Baltic Sea populations, we exposed half of each brood to either current (6‰) or future salinity (3.5‰). We genotyped a subsample of each brood to analyse patterns of allelic change and to identify genomic regions targeted by selection. The survival was overall reduced by hyposalinity and broods varied in response to hyposalinity implying genetic variation in tolerance, with a stronger decrease in genetic diversity in future salinity. Finally, we identified proteins with crucial roles in basic cellular functions. This study indicates that projected future northern Baltic Sea hyposalinity will not just hamper I. balthica survival, but its selective pressure may also affect genetic diversity and cell physiology.

Ovarian Transcriptome Analysis of Vitellogenic and Non-Vitellogenic Female Banana Shrimp (Fenneropenaeus merguiensis)

The banana shrimp (Fenneropenaeus merguiensis) is one of the most commercially important penaeid species in the world. Its numbers are declining in the wild, leading to a loss of broodstock for farmers of the shrimp and a need for more successful breeding programs. However, the molecular mechanism of the genes involved in this shrimp’s ovarian maturation is still unclear. Consequently, we compared transcriptomic profiles of ovarian tissue from females in both the vitellogenic stage and the non-vitellogenic stage. Using RNA-Seq technology to prepare the transcriptome libraries, a total of 12,187,412 and 11,694,326 sequencing reads were acquired from the non-vitellogenic and vitellogenic stages respectively. The analysis of the differentially expressed genes identified 1,025 which were significantly differentially expressed between the two stages, of which 694 were up-regulated and 331 down-regulated. Four genes putatively involved in the ovarian maturation pathway were chosen for validation by quantitative real-time PCR (RT-qPCR). The data from this study provided information about gene expression in ovarian tissue of the banana shrimp which could be useful for a better understanding of the regulation of this species’ reproductive cycle.

Transcriptome analysis of the differences in gene expression between testis and ovary in green mud crab (Scylla paramamosain)

Background

The green mud crab (Scylla paramamosain) is the most prevalent crustacean on the southeast coast of China. The molecular regulatory mechanism of sex determination and gonadal differentiation in this species has received considerable attention in recent years because of the huge differences—both biological and economic—between male and female crabs. In this study, next-generation sequencing technology was used to develop deep-coverage transcriptomic sequencing data for the testis and ovary of S. paramamosain.

Results

A total of 365,116 reads (testis 171,962, ovary 193,154) with an average sequence length of 285 bp were produced from testis and ovary cDNA libraries. After filtering out contaminating reads, the clean reads were assembled, producing a total of 21,791 isotigs and leaving 22,814 reads as singlets. Using the BLASTX program, 3,471 unique sequences (2,275 isotigs and 1,196 singletons) were annotated with known protein sequences from the NCBI non-redundant (Nr) protein sequence database. The Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses allowed the 224 unique sequences that were annotated with enzyme code (EC) numbers to be mapped into 174 KEGG pathways. After comparing the ovary and testis libraries, 4,021 gonad-differentially, 10,522 ovary-specifically, and 19,013 testis-specifically expressed genes were identified. Moreover, 33 ovary-specific, 14 testis-specific, and 34 gonad-differential transcripts were confirmed by semi-quantitative PCR and quantitative real-time PCR. In addition, 8,610 putative simple sequence repeats (SSRs) and 23,879 potential single nucleotide polymorphisms (SNPs) were identified.

Conclusion

This is the first large-scale RNA sequencing of S. paramamosain to be reported. We have identified many important functional genes and made a preliminary attempt to construct the regulatory network involved in the gonadal development of crustaceans. The annotated transcriptome data will provide fundamental support for future research into the reproduction biology of S. paramamosain. A large number of candidate SSRs and SNPs were detected, which could be used as genetic markers for population genetics and functional genomics in this species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-585) contains supplementary material, which is available to authorized users.

Comparative proteomic profiling during ovarian development of the shrimp Metapenaeus ensis

Two-dimensional electrophoresis and mass spectrometry were used to identify proteins that are differentially expressed during ovarian maturation in Metapenaeus ensis. 87 spots with consistently significant quantitative differences (≥ 1.5-fold for vol%) among stage I, III and V ovaries were chosen for MS/MS analysis. 45 spots were significantly matched to known proteins in the database (Mascot score >40). Half of them were down-regulated, in contrast to 9 out of 45 proteins that were up-regulated as ovarian maturation proceeded. Functionally, these identified proteins could be classified into five major groups, including cytoskeleton (11 %), metabolism (18 %), signal transduction (32 %), gene expression (14 %) and immune response (7 %). Among the differentially expressed reproduction-related proteins, the mRNA expression level of cellular retinoic acid/retinol binding protein in M. ensis (MeCRABP) during ovarian maturation was further characterized by quantitative real-time PCR. It was down-regulated during ovarian maturation. In situ hybridization further revealed that MeCRABP transcript was localized in ooplasm of previtellogenic oocytes but not in vitellogenic oocytes. These results demonstrate the application of proteomic analysis for identification of proteins involved in shrimp ovarian maturation and they provide new insights into ovarian development.

Current status of genetics and genomics of reared penaeid shrimp: information relevant to access and benefit sharing

At present, research and progress in shrimp genomics and genetics show significant developments. Shrimp genetics and genomics also show immense potential for an increased production in a way that meets shrimp culture progress goals for the third millennium. This review article aims to provide an overview of its current status and future direction, discusses questions that need focused research to address them, and summarizes areas where genetics and genomics knowledge can make a positive difference to shrimp culture sustainability. Sustainable progress of penaeid shrimps will depend upon feasible solutions for environmental, research, economic, consumer problems, proper development, and planning policy enforcement. It is recommended that increased funding for biotechnology research and progress be directed to expand worldwide commercial shrimp culture and address environmental and public health issues. For any researcher or shrimp company member who has attempted to or whom would like to thoroughly search the literature to gain a complete understanding of the current state of shrimp genetics and genomics, this publication will be an invaluable source of reference materials, some of which is reported here for the first time.

Potential roles of transglutaminase and thioredoxin in the release of gonad-stimulating factor in Penaeus monodon: implication from differential expression in the brain during ovarian maturation cycle

The synthesis of vitellogenin during ovarian maturation in crustacean is induced by gonad-stimulating factor(s) that are synthesized in the brain and thoracic ganglia. This process is negatively regulated by a gonad-inhibiting hormone (GIH) from the eyestalk. This study utilized differential-display RT-PCR technique to identify putative genes in brain and thoracic ganglia that may be involved in ovarian maturation of the black tiger shrimp, Penaeus monodon under the condition in which the expression of GIH was suppressed by GIH-specific dsRNA. After excluding redundant clones and subsequent verification by RT-PCR, 10 and 5 transcripts exhibited up-regulated and down-regulated expressions, respectively, in the GIH-dsRNA injected shrimp when compared with the Tris/NaCl injected shrimp. Among the up-regulated genes, a full sequence of thioredoxin cDNA was cloned, and nucleotide sequence analysis showed that it was highly similar to other crustacean thioredoxin. The thioredoxin gene as well as the other four genes including transglutaminase and three unknowns; U10-11, U10-15 and U13-11 that were up-regulated upon GIH-knockdown exhibited similar expression profile in the brain during ovarian maturation cycle. The highest expression level was detected in the brain of early-vitellogenic female shrimp suggesting that they are required for an initial stage of vitellogenesis. Our results posted for the first time a possible function of transglutaminase and thioredoxin in regulating the gonad-stimulating pathway in the brain of the shrimp.

Expression of sex and reproduction-related genes in Marsupenaeus japonicus

Expressed sequence tags (ESTs) were identified from reciprocal suppression subtractive hybridization cDNA libraries from Marsupenaeus japonicus (Kuruma shrimp) female and male gonads. The expression profiles of 24 of these ESTs were determined in female and male gonads and developing postlarvae by real-time quantitative reverse transcription-polymerase chain reaction. When expression was determined in gonads, six of the ESTs were expressed in ovaries only, and five of the ESTs were expressed in testes only. When expression was determined in whole individuals during postlarval development, expression of the ESTs was low and inconsistent until stage PL110 (110 days since metamorphosis from mysis stage to the first postlarval stage). At PL110, seven of the ESTs were detected in females only, and seven ESTs were detected in males only. Sex-specific expression at this developmental stage indicates that these ESTs act as important gonadal development markers and may have a role in gametogenesis.

MnHSP90 cDNA characterization and its expression during the ovary development in oriental river prawn, Macrobrachium nipponense

Heat shock protein 90 (HSP90) is not only involved in environmental stress but also plays roles in the ovary development in some vertebrates. To understand its role in crustacean, we examined the HSP90 cDNA for the first time in the ovary and hepatopancreas of the oriental river prawn, Macrobrachium nipponense and designated this protein as MnHSP90 in this study. The MnHSP90 was cloned by the methods of degenerated oligonucleotide primers and rapid amplification of the cDNA ends (RACE). Bioinformatics analysis showed that the MnHSP90 cDNA was 2,684 bp in length, containing a 126 bp 5' untranslated region (UTR), a 359 bp 3' UTR, and an open reading frame (ORF) of 2,199 bp encoding a 732-amino acid polypeptide with predicted molecular mass of 84.3 KDa. Sequence alignment showed that the MnHSP90 shared 72-79% identity with other animals. Real-time quantitative PCR (qPCR) analysis demonstrated that the MnHSP90 mRNA was ubiquitously detected in all tested tissues, with the highest expression in the thoracic ganglia, the mediate in heart, muscle and intestine, and the lowest in haemocytes and gills. The MnHSP90 mRNA levels in the hepatopancreas and ovary of M. nipponense reached a maximum at the stage III (early vitellogenic stage) and stage IV (later vitellogenic stage) ovaries, respectively, and then decreased significantly in both tissues as the ovarian development proceeded. The level of MnHSP90 expression in the hepatopancreas was higher than that in the ovary when compared with in the same ovarian developmental stage. Our results indicate that MnHSP90 is involved in ovarian development in oriental river prawn and may play a regulatory role in ovary maturation.

GTP-independent tRNA delivery to the ribosomal P-site by a novel eukaryotic translation factor

During translation, aminoacyl-tRNAs are delivered to the ribosome by specialized GTPases called translation factors. Here, we report the tRNA binding to the P-site of 40 S ribosomes by a novel GTP-independent factor eIF2D isolated from mammalian cells. The binding of tRNA(i)(Met) occurs after the AUG codon finds its position in the P-site of 40 S ribosomes, the situation that takes place during initiation complex formation on the hepatitis C virus internal ribosome entry site or on some other specific RNAs (leaderless mRNA and A-rich mRNAs with relaxed scanning dependence). Its activity in tRNA binding with 40 S subunits does not require the presence of the aminoacyl moiety. Moreover, the factor possesses the unique ability to deliver non-Met (elongator) tRNAs into the P-site of the 40 S subunit. The corresponding gene is found in all eukaryotes and includes an SUI1 domain present also in translation initiation factor eIF1. The versatility of translation initiation strategies in eukaryotes is discussed.

Identification and expression analysis of genes involved in early ovary development in diploid gynogenetic hybrids of red crucian carp x common carp

Diploid eggs of allotetraploid hybrids (red crucian carp female symbol x common carp male symbol), when activated by UV-irradiated sperm of scatter scale carp, can develop into diploid progenies without chromosome duplication treatment. Diploid progenies produce diploid eggs, which develop into diploid population by the same way. To understand the molecular mechanism underlying the production of diploid eggs by the diploid fish, we constructed a forward suppression subtractive hybridization complementary DNA (cDNA) library. The cDNAs from the ovary in proliferation phase were employed as the "tester," and those in growth phase were used as the "driver." Seventy-three cDNA clones that are specifically expressed in proliferation phase were detected by dot-blot hybridization. Sequencing analyses revealed that several of these cDNAs have high homologies to the known sequences in the NCBI database. Their encoded proteins include the protein preventing mitosis catastrophe (PMC), the signal recognition particle 9, the ATP-binding cassette transporter, the glucanase-xylanase fusion protein, and others. These genes were confirmed by reverse transcriptase-polymerase chain reaction. The expression profile of the PMC gene at different time points was analyzed by quantitative real-time polymerase chain reaction. The results indicated that the expression of this suppression subtractive hybridization-identified gene changed during the time course, corresponding with the cellular phenomenon in the ovary development. Our studies provide insights into the molecular mechanism underlying the ovary development of diploid gynogenetic fish.