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In-depth tanscriptomic analysis on giant freshwater prawns.

ABSTRACT: Gene discovery in the Malaysian giant freshwater prawn (Macrobrachium rosenbergii) has been limited to small scale data collection, despite great interest in various research fields related to the commercial significance of this species. Next generation sequencing technologies that have been developed recently and enabled whole transcriptome sequencing (RNA-seq), have allowed generation of large scale functional genomics data sets in a shorter time than was previously possible. Using this technology, transcriptome sequencing of three tissue types: hepatopancreas, gill and muscle, has been undertaken to generate functional genomics data for M. rosenbergii at a massive scale. De novo assembly of 75-bp paired end Ilumina reads has generated 102,230 unigenes. Sequence homology search and in silico prediction have identified known and novel protein coding candidate genes (?24%), non-coding RNA, and repetitive elements in the transcriptome. Potential markers consisting of simple sequence repeats associated with known protein coding genes have been successfully identified. Using KEGG pathway enrichment, differentially expressed genes in different tissues were systematically represented. The functions of gill and hepatopancreas in the context of neuroactive regulation, metabolism, reproduction, environmental stress and disease responses are described and support relevant experimental studies conducted previously in M. rosenbergii and other crustaceans. This large scale gene discovery represents the most extensive transcriptome data for freshwater prawn. Comparison with model organisms has paved the path to address the possible conserved biological entities shared between vertebrates and crustaceans. The functional genomics resources generated from this study provide the basis for constructing hypotheses for future molecular research in the freshwater shrimp.

SUBMITTER: Mohd-Shamsudin MI

PROVIDER: S-EPMC3667022 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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In-depth tanscriptomic analysis on giant freshwater prawns.

Mohd-Shamsudin Maizatul Izzah MI Kang Yi Y Lili Zhao Z Tan Tian Tian TT Kwong Qi Bin QB Liu Hang H Zhang Guojie G Othman Rofina Yasmin RY Bhassu Subha S

PloS one 20130529 5

Gene discovery in the Malaysian giant freshwater prawn (Macrobrachium rosenbergii) has been limited to small scale data collection, despite great interest in various research fields related to the commercial significance of this species. Next generation sequencing technologies that have been developed recently and enabled whole transcriptome sequencing (RNA-seq), have allowed generation of large scale functional genomics data sets in a shorter time than was previously possible. Using this techno ...[more]

PMID: 23734171

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Project description:BackgroundAnthropogenic waste, especially microplastics, is becoming more prevalent in the environment and marine ecosystems, where it has the potential to spread through food chains and be consumed by humans. Southeast Asian countries are home to giant freshwater prawns, a common freshwater species that is eaten around the world. Microplastic pollution in river water, sediment, and commercially significant aquatic species such as fish and mollusks has been observed, yet few studies have been conducted on giant freshwater prawns in the rivers of southern Thailand, where microplastics may contaminate prawns via the food they ingest. The purpose of this research was to investigate the accumulation of anthropogenic material in the organs of river prawns (Macrobrachium rosenbergii).MethodsMicroplastics in the stomachs and intestines of giant freshwater prawns were the focus of this study. Samples were digested with 30 ml of 10% potassium hydroxide (KOH), heated for 5 min at 60 °C, and then digested at room temperature. The quantity, color, and appearance of microplastics were assessed using a stereomicroscope after 12 h. Furthermore, polymers were examined using a Fourier transform infrared spectrophotometer (FTIR). Microplastic counts were compared between sexes. A T-test was used to compare male and female microplastic counts in the stomach and intestine, and the Pearson correlation was used to compare the association between microplastic counts in the stomach and intestine and carapace length (CL), length of abdomen (LA), and body weight (BW) of male and female giant freshwater prawns. The threshold of significance was fixed at p < 0.05.ResultsBased on the study results, a total of 370 pieces of anthropogenic debris were discovered in the stomachs and intestines of both female and male prawns. The average number of microplastics per individual was 4.87 ± 0.72 in female stomachs and 3.03 ± 0.58 in male stomachs, and 1.73 ± 0.36 in female intestines and 2.70 ± 0.57 in male intestines. The majority of microplastics found in females were within the <100 µm range, while males contained microplastics in the range of 100-500 µm. Both male and female prawns contained fibers (72.70%) and fragments (27.30%). Various polymers were identified, including cotton, rayon, and polyvinyl chloride (PVC). The study also explored the relationship between carapace length, length of abdomen, body weight, stomach weight, and the number of microplastics. The findings reveal a significant association between the number of microplastics and stomach weight in male prawns (R = 0.495; p = 0.005). These findings provide alarming evidence of anthropogenic debris ingestion in prawns and raise concerns about the future effects of anthropogenic pollution on giant freshwater prawns.

Project description:Giant freshwater prawns (Macrobrachium rosenbergii) are commonly found throughout the world. The size of the male giant freshwater prawn is much larger than that of the female. Therefore, understanding the molecular mechanism that underlies the sexual differentiation of M. rosenbergii is of both commercial and scientific importance. Insulin-like androgenic gland hormone (IAG) plays a key role in the differentiation of sex in M. rosenbergii. Although IAG has been investigated, the regulatory relationship between IAG and its binding protein partner, the insulin-like androgenic gland hormone-binding protein (IAGBP), has not been studied in M. rosenbergii. Here, we cloned and characterized the IAGBP from M. rosenbergii (Mr-IAGBP) for the very first time. Transcriptomic analysis showed that Mr-IAGBP mRNA was detected in a wide array of tissues with the highest expression found in the androgenic gland. The importance of IAG in male development was further demonstrated by an increase in IAG transcripts during the development of the androgenic gland and Mr-IAG was only highly transcribed in the androgenic gland of M. rosenbergii. Interestingly, we found that the Mr-IAG gene expression started during the 20th-day larva after hatching stage (LH20), followed (20th-day post-larval stage, PL20) by a gradual elevation of Mr-IAGBP levels. The levels of both genes peaked at the adult stage. The relationship between Mr-IAGBP and Mr-IAG was further analyzed using RNA interference. The injection of Mr-IAGBP double-stranded RNA (dsRNA) significantly reduced the transcription of Mr-IAG, while the amount of Mr-IAGBP mRNA and the translation of IAGBP protein was significantly reduced by the injection of Mr-IAG dsRNA. These results revealed that IAGBP is involved in IAG signaling. Furthermore, our data supports the hypothesis that (IAG and IAGBP)-IAG receptor signaling schemes exist in M. rosenbergii. Our results will provide important information for the further study of determining the sex of M. rosenbergii.

Project description:Elucidating the molecular basis of adaptation to different environmental conditions is important because adaptive ability of a species can shape its distribution, influence speciation, and also drive a variety of evolutionary processes. For crustaceans, colonization of freshwater habitats has significantly impacted diversity, but the molecular basis of this process is poorly understood. In the current study, we examined three prawn species from the genus Macrobrachium (M. australiense, M. tolmerum, and M. novaehollandiae) to better understand the molecular basis of freshwater adaptation using a comparative transcriptomics approach. Each of these species naturally inhabit environments with different salinity levels; here, we exposed them to the same experimental salinity conditions (0‰ and 15‰), to compare expression patterns of candidate genes that previously have been shown to influence phenotypic traits associated with freshwater adaptation (e.g., genes associated with osmoregulation). Differential gene expression analysis revealed 876, 861, and 925 differentially expressed transcripts under the two salinities for M. australiense, M. tolmerum, and M. novaehollandiae, respectively. Of these, 16 were found to be unannotated novel transcripts and may be taxonomically restricted or orphan genes. Functional enrichment and molecular pathway mapping revealed 13 functionally enriched categories and 11 enriched molecular pathways that were common to the three Macrobrachium species. Pattern of selection analysis revealed 26 genes with signatures of positive selection among pairwise species comparisons. Overall, our results indicate that the same key genes and similar molecular pathways are likely to be involved with freshwater adaptation widely across this decapod group; with nonoverlapping sets of genes showing differential expression (mainly osmoregulatory genes) and signatures of positive selection (genes involved with different life history traits).

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In-depth tanscriptomic analysis on giant freshwater prawns.

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In-depth tanscriptomic analysis on giant freshwater prawns.

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