Full-Length Normalization Subtractive Hybridization: A Novel Method for Generating Differentially Expressed cDNAs

Transcriptome analysis of reproductive tract tissues of male river prawn Macrobrachium americanum

BACKGROUND

The river prawn, Macrobrachium americanum (M. americanum), is one of the largest prawns of the genus in Latin America and is an amphidromous species distributed along the Pacific coast of America. This prawn has commercial value due to its size and taste, making it a good option for aquaculture production. Its culture has been attempted in ponds and concrete tanks, but no successful technique can still support commercial production. Understanding the mechanisms that regulate reproduction at the molecular level is very important. This knowledge can provide tools for manipulating transcripts, which could increase the number or size of animals in the culture. Our understanding of the mechanism that regulates the reproduction of M. americanum at the molecular level is limited.

AIM

Perform and analyze the transcriptome assembly of the testes, vas deferens, and terminal ampulla of M. americanum. to provide new molecular information about its reproduction.

METHODS AND RESULTS

The cDNA library was constructed and sequenced for each tissue to identify novel transcripts. A combined transcriptome with the three tissues was assembled using Trinity software. Unigenes were annotated using BLASTx and BLAST2GO. The transcriptome assembly generated 1,059,447 unigenes, of which 7222 genes had significant hits (e-value < 1 × 10-5) when compared against the Swiss-Prot database. Around 75 genes were related to sex determination, testis development, spermatogenesis, spermiogenesis, fertilization, maturation of testicular cells, neuropeptides, hormones, hormone receptors, and/or embryogenesis.

CONCLUSIONS

These results provide new molecular information about M. americanum reproduction, representing a reference point for further genetic studies of this species.

Full Functional Sex Reversal Achieved Through Silencing of MroDmrt11E Gene in Macrobrachium rosenbergii: Production of All-Male Monosex Freshwater Prawn

The freshwater prawn Macrobrachium rosenbergii is one kind of important economic aquaculture species and displays remarkable sexual dimorphism. The molecular mechanism of sexual differentiation in M. rosenbergii has been primarily unraveled through the research efforts of the androgenic gland and its related genes. However, the understanding of conserved genes involved in the molecular mechanism underpinning sex determination and sexual differentiation of M. rosenbergii is still fragmentary. MroDmrt11E is a member of the doublesex and mab-3-related transcription factor (Dmrt) gene family and is prominently expressed in the testis. In the present study, in vivo knockdown of MroDmrt11E at the postlarva stage in male prawn induced a complete and functional sex reversal and achieved the production of an all-male monosex population. Furthermore, a great deal of new information of upregulated and downregulated transcriptions involved in sexual differentiation of MroDmrt11E knockdown was enriched by comparative transcriptomic analysis. The effects of RNAi-mediated gene knockdown of MroDmrt11E on the differentially expressed and sex-related candidate genes, such as transformer, fruitless, feminization, insulin-like androgenic gland gene, Dmrt gene family, were primarily focused on, and their possible molecular regulatory relationships in sexual differentiation were analyzed. Meanwhile, the response of primary Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathways was investigated to expound the potential roles of MroDmrt11E in male sexual differentiation, which provided a deeper understanding of the molecular regulatory network underlying sexual differentiation of M. rosenbergii. The finding provided a novel sexual manipulation technique through silencing of Dmrt gene family for achieving a complete and functional sex reversal and offered a new insight regarding the mechanism of the Dmrt gene family in the sexual differentiation of crustaceans.

Comparative Transcriptome Analysis of Gonads for the Identification of Sex-Related Genes in Giant Freshwater Prawns (Macrobrachium Rosenbergii) Using RNA Sequencing

The giant freshwater prawn (Macrobrachium rosenbergii) exhibits sex dimorphism between the male and female individuals. To date, the molecular mechanism governing gonadal development was unclear, and limited data were available on the gonad transcriptome of M. rosenbergii. Here, we conducted comprehensive gonadal transcriptomic analysis of female (ZW), super female (WW), and male (ZZ) M. rosenbergii for gene discovery. A total of 70.33 gigabases (Gb) of sequences were generated. There were 115,338 unigenes assembled with a mean size of 1196 base pair (bp) and N50 of 2195 bp. Alignment against the National Center for Biotechnology Information (NCBI) non-redundant nucleotide/protein sequence database (NR and NT), the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, SwissProt database, Protein family (Pfam), Gene ontology (GO), and the eukaryotic orthologous group (KOG) database, 36,282 unigenes were annotated at least in one database. Comparative transcriptome analysis observed that 10,641, 16,903, and 3393 genes were significantly differentially expressed in ZW vs. ZZ, WW vs. ZZ, and WW vs. ZW samples, respectively. Enrichment analysis of differentially expressed genes (DEGs) resulted in 268, 153, and 42 significantly enriched GO terms, respectively, and a total of 56 significantly enriched KEGG pathways. Additionally, 23 putative sex-related genes, including Gtsf1, IR, HSP21, MRPINK, Mrr, and other potentially promising candidate genes were identified. Moreover, 56,241 simple sequence repeats (SSRs) were identified. Our findings provide a valuable archive for further functional analyses of sex-related genes and future discoveries of underlying molecular mechanisms of gonadal development and sex determination.

Differences in gene organization between type I and type II crustins in the morotoge shrimp, Pandalopsis japonica

Crustins are cysteine-rich cationic antimicrobial peptides (AMPs) found in decapod crustaceans. Six novel crustin genes (Paj-CrusIc, Id, Ie, If, IIb and IIc) were identified in the morotoge shrimp, Pandalopsis japonica. Deduced amino acid sequences of isolated Paj-Crus genes ranged from 99 to 178 amino acid residues (10.6-17.8 kDa). Sequence analysis of nine isolated Paj-Crus genes and 100 different crustins from various decapod crustaceans revealed that a splice site and KXXXCP motif within the WAP domain may be the main criteria for classifying type I and II crustins, suggesting that the two types of crustin genes may have been generated by different processes. We also identified three intron-less crustin I genes (Paj-Crus Id, Ie and If) for the first time, which may have been generated by gene duplication. The tissue distribution profiles showed that Paj-CrusI genes were expressed predominantly in the gill and epidermis, whereas Paj-CrusII genes were expressed ubiquitously, suggesting that the two types of crustins may play different roles in various tissues or under different physiological conditions. Differing from previous results, hemocyte-specific crustin was not isolated from Pandalopsis japonica. This study showed that both types of crustin genes (types I and II) exist in decapod crustaceans and their primary structure and expression profiles differ from each other, suggesting that they may play different biological roles. This will help to extend our knowledge of the crustacean innate immune response, which will provide important basic information of shrimp immunity against various pathogens.

Molecular insights into how a deficiency of amylose affects carbon allocation--carbohydrate and oil analyses and gene expression profiling in the seeds of a rice waxy mutant

BACKGROUND

Understanding carbon partitioning in cereal seeds is of critical importance to develop cereal crops with enhanced starch yields for food security and for producing specified end-products high in amylose, β-glucan, or fructan, such as functional foods or oils for biofuel applications. Waxy mutants of cereals have a high content of amylopectin and have been well characterized. However, the allocation of carbon to other components, such as β-glucan and oils, and the regulation of the altered carbon distribution to amylopectin in a waxy mutant are poorly understood. In this study, we used a rice mutant, GM077, with a low content of amylose to gain molecular insight into how a deficiency of amylose affects carbon allocation to other end products and to amylopectin. We used carbohydrate analysis, subtractive cDNA libraries, and qPCR to identify candidate genes potentially responsible for the changes in carbon allocation in GM077 seeds.

RESULTS

Carbohydrate analysis indicated that the content of amylose in GM077 seeds was significantly reduced, while that of amylopectin significantly rose as compared to the wild type BP034. The content of glucose, sucrose, total starch, cell-wall polysaccharides and oil were only slightly affected in the mutant as compared to the wild type. Suppression subtractive hybridization (SSH) experiments generated 116 unigenes in the mutant on the wild-type background. Among the 116 unigenes, three, AGP, ISA1 and SUSIBA2-like, were found to be directly involved in amylopectin synthesis, indicating their possible roles in redirecting carbon flux from amylose to amylopectin. A bioinformatics analysis of the putative SUSIBA2-like binding elements in the promoter regions of the upregulated genes indicated that the SUSIBA2-like transcription factor may be instrumental in promoting the carbon reallocation from amylose to amylopectin.

CONCLUSION

Analyses of carbohydrate and oil fractions and gene expression profiling on a global scale in the rice waxy mutant GM077 revealed several candidate genes implicated in the carbon reallocation response to an amylose deficiency, including genes encoding AGPase and SUSIBA2-like. We believe that AGP and SUSIBA2 are two promising targets for classical breeding and/or transgenic plant improvement to control the carbon flux between starch and other components in cereal seeds.

Molecular characterization of three crustin genes in the morotoge shrimp, Pandalopsis japonica

Crustins are among the most important antimicrobial peptides (AMPs) found in decapod crustaceans. They are small cationic AMPs (5-7 kDa) characterized by a proline-rich amino-terminal domain and a cysteine-rich carboxyl-terminal domain. Here, the first 3 crustin-like cDNAs (Pj-crus Ia, Ib, and II) were identified from the morotoge shrimp, Pandalopsis japonica. The full-length cDNAs of Pj-crus Ia, Ib, and II consisted of 1135, 580, and 700 nucleotides and encoded putative proteins containing 109, 119, and 186 amino acids residues, respectively. All 3 identified Pj-crus sequences exhibited the conserved domain organization for crustins, including a signal sequence, a cysteine-containing region, a glycine-rich region, and a whey-acidic protein (WAP) domain. Amino acid sequence comparisons and phylogenetic analysis revealed that the Pj-crus Ia and Ib belong to type I crustins (e.g., carcinin), which have been mostly identified from Brachyura and Astacidea, whereas Pj-crus II was classified as belonging to the type II crustins, which are mainly found in Dendrobranchiata. An analysis of the organization of these 3 Pj-crus genes revealed that the splicing site within the WAP domain may be an important key for classifying types I and II crustin family members. The tissue distribution profile results showed that the Pj-crus I genes were expressed in a tissue-specific manner but that the Pj-crus II gene was expressed ubiquitously, suggesting that these crustins may play different roles in various tissues or under different physiological conditions. The bacterial challenge results suggested that the Pj-crus genes may be transcriptionally influenced by different bacterial types. This comparative study of various crustin family members will help extend the knowledge on the crustacean innate immune response, which will provide important basic information for controlling shrimp immunity against various pathogens.

Determination in oocytes of the reproductive modes for the brine shrimp Artemia parthenogenetica

The brine shrimp, Artemia, reproduces either oviparously, producing encysted embryos (diapause cysts), or ovoviviparously, producing free-swimming nauplii. Environmental factors, such as photoperiod, have been applied to control the reproduction mode of Artemia, but when the determination of a reproductive mode occurs remains unknown. We analysed the differential gene expression between oocytes from oviparous and ovoviviparous Artemia reared under different photoperiods. A total of 692 qualified cDNA clones were obtained by subtractive hybridization, 327 of which matched GenBank® Nucleotide Sequence Database entries. Gene expressions of 44 cDNAs (representing 56 clones) were analysed in oocytes using real-time PCR. Among these genes, 11 (21 clones) were significantly (P<0.05) up-regulated and 7 (9 clones) down-regulated in Artemia oocytes that subsequently enter diapause. Remarkably, known diapause-related proteins such as ArHsp22 (Artemia heat-shock protein 22) and chitin-binding proteins are found to be already differentially expressed. Furthermore, RNAi (RNA interference) knockdown of a differentially expressed gene, polo-like kinase 1, in oocyte of ovoviviparous Artemia led to the production of white embryos rather than free-swimming nauplii. In summary, our results provide evidence at the molecular level that the reproductive mode of Artemia is already determined at the oocyte stage of their life cycle.