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Transcriptome changes in Eriocheir sinensis megalopae after desalination provide insights into osmoregulation and stress adaption in larvae.

Hui M, Liu Y, Song C, Li Y, Shi G, Cui Z - PLoS ONE (2014)

Bottom Line: The DEGs primarily belonged to the Gene Ontology groups "Energy metabolism," "Oxidoreductase activity," "Translation," "Transport," "Metabolism," and "Stress response." In total, 33 DEGs related to transport processes were found, including 12 proton pump genes, three ATP-binding cassettes (ABCs), 13 solute carrier (SLC) family members, two sweet sugar transporter (ST) family members and three other substance transporters.Additionally, 33 salinity and oxidative stress induced genes were found to be differentially expressed, such as the LEA2, HSPs, GST and coagulation factor genes.This study provides the first genome-wide transcriptome analysis of E. sinensis megalopae for studying its osmoregulation and stress adaption mechanisms.

View Article: PubMed Central - PubMed

Affiliation: EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.

ABSTRACT
Eriocheir sinensis, an extremely invasive alien crab species, has important economic value in China. It encounters different salinities during its life cycle, and at the megalopal stage it faces a turning point regarding the salinity in its environment. We applied RNA sequencing to E. sinensis megalopae before (MB) and after (MA) desalination, resulting in the discovery of 21,042 unigenes and 908 differentially expressed genes (DEGs, 4.32% of the unigenes). The DEGs primarily belonged to the Gene Ontology groups "Energy metabolism," "Oxidoreductase activity," "Translation," "Transport," "Metabolism," and "Stress response." In total, 33 DEGs related to transport processes were found, including 12 proton pump genes, three ATP-binding cassettes (ABCs), 13 solute carrier (SLC) family members, two sweet sugar transporter (ST) family members and three other substance transporters. Mitochondrial genes as well as genes involved in the tricarboxylic acid cycle, glycolytic pathway, or β-oxidation pathway, which can generate energy in the form of ATP, were typically up-regulated in MA. 11 unigenes related to amino acid metabolism and a large number of genes related to protein synthesis were differentially expressed in MB and MA, indicating that E. sinensis possibly adjusts its concentration of free amino acid osmolytes for hyper-osmoregulation. Additionally, 33 salinity and oxidative stress induced genes were found to be differentially expressed, such as the LEA2, HSPs, GST and coagulation factor genes. Notably, LEA2 is an extremely hydrophilic protein that responds to desiccation and reported for the first time in crabs. Therefore, we suppose that when the environment is hypo-osmotic, the megalopae might compensate for ion loss via hyper-osmoregulation by consuming more energy, accompanied by a series of stress induced adaptions. This study provides the first genome-wide transcriptome analysis of E. sinensis megalopae for studying its osmoregulation and stress adaption mechanisms.

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GO distributions of the differentially expressed genes (DEGs) from the transcriptomes of MB and MA in Eriocheir sinensis.(A) Different functional distribution of the DEGs involved with biological processes; (B) Different functional distribution of the DEGs involved with cellular components and molecular functions; (C) Differentially expressed functional processes. The horizontal line indicates the significance thresholds (p<0.05).
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pone-0114187-g002: GO distributions of the differentially expressed genes (DEGs) from the transcriptomes of MB and MA in Eriocheir sinensis.(A) Different functional distribution of the DEGs involved with biological processes; (B) Different functional distribution of the DEGs involved with cellular components and molecular functions; (C) Differentially expressed functional processes. The horizontal line indicates the significance thresholds (p<0.05).

Mentions: The functional distribution of the DEGs in various processes was analyzed by GO, KEGG and eggNOG enrichment. In the GO enrichment, 512 DEGs with GO terms were categorized into different functional groups. In the ‘Biological process’ group, the first 10 processes were ‘Biosynthetic process (11.02%)’, ‘Cellular nitrogen compound metabolic process (7.93%)’, ‘Catabolic process (7.52%)’, ‘Small molecule metabolic process (6.85%)’, ‘Oxidoreductase activity (6.59%)’, ‘Carbohydrate metabolic process (3.49%)’, ‘Translation (6.59%)’, ‘Transport (6.45%)’, ‘Signal transduction (3.22%)’, and ‘Response to stress (2.96%)’ (Figure 2A). In the ‘Cell component’ group, the main components were ‘Cell (25.81%)’ and ‘Intracellular (25.16%)’ (Figure 2B), while in the ‘Molecular function’ group, ‘Ion binding (45.41%)’ covered the largest number of DEGs followed by ‘Structural molecule activity (33.67%)’ (Figure 2B). Many of these GO terms are also common in the transcriptomic study for E. sinensis adult treated with high salinity [13]. After the overall comparison was completed, the top 20 significantly changed categories were obtained (p<0.05; Figure 2C), including ‘Hydrolase activity, acting on glycosyl bonds’ and ‘Ion binding’, which might be induced by changes in salinity.


Transcriptome changes in Eriocheir sinensis megalopae after desalination provide insights into osmoregulation and stress adaption in larvae.

Hui M, Liu Y, Song C, Li Y, Shi G, Cui Z - PLoS ONE (2014)

GO distributions of the differentially expressed genes (DEGs) from the transcriptomes of MB and MA in Eriocheir sinensis.(A) Different functional distribution of the DEGs involved with biological processes; (B) Different functional distribution of the DEGs involved with cellular components and molecular functions; (C) Differentially expressed functional processes. The horizontal line indicates the significance thresholds (p<0.05).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4254945&req=5

pone-0114187-g002: GO distributions of the differentially expressed genes (DEGs) from the transcriptomes of MB and MA in Eriocheir sinensis.(A) Different functional distribution of the DEGs involved with biological processes; (B) Different functional distribution of the DEGs involved with cellular components and molecular functions; (C) Differentially expressed functional processes. The horizontal line indicates the significance thresholds (p<0.05).
Mentions: The functional distribution of the DEGs in various processes was analyzed by GO, KEGG and eggNOG enrichment. In the GO enrichment, 512 DEGs with GO terms were categorized into different functional groups. In the ‘Biological process’ group, the first 10 processes were ‘Biosynthetic process (11.02%)’, ‘Cellular nitrogen compound metabolic process (7.93%)’, ‘Catabolic process (7.52%)’, ‘Small molecule metabolic process (6.85%)’, ‘Oxidoreductase activity (6.59%)’, ‘Carbohydrate metabolic process (3.49%)’, ‘Translation (6.59%)’, ‘Transport (6.45%)’, ‘Signal transduction (3.22%)’, and ‘Response to stress (2.96%)’ (Figure 2A). In the ‘Cell component’ group, the main components were ‘Cell (25.81%)’ and ‘Intracellular (25.16%)’ (Figure 2B), while in the ‘Molecular function’ group, ‘Ion binding (45.41%)’ covered the largest number of DEGs followed by ‘Structural molecule activity (33.67%)’ (Figure 2B). Many of these GO terms are also common in the transcriptomic study for E. sinensis adult treated with high salinity [13]. After the overall comparison was completed, the top 20 significantly changed categories were obtained (p<0.05; Figure 2C), including ‘Hydrolase activity, acting on glycosyl bonds’ and ‘Ion binding’, which might be induced by changes in salinity.

Bottom Line: The DEGs primarily belonged to the Gene Ontology groups "Energy metabolism," "Oxidoreductase activity," "Translation," "Transport," "Metabolism," and "Stress response." In total, 33 DEGs related to transport processes were found, including 12 proton pump genes, three ATP-binding cassettes (ABCs), 13 solute carrier (SLC) family members, two sweet sugar transporter (ST) family members and three other substance transporters.Additionally, 33 salinity and oxidative stress induced genes were found to be differentially expressed, such as the LEA2, HSPs, GST and coagulation factor genes.This study provides the first genome-wide transcriptome analysis of E. sinensis megalopae for studying its osmoregulation and stress adaption mechanisms.

View Article: PubMed Central - PubMed

Affiliation: EMBL, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.

ABSTRACT
Eriocheir sinensis, an extremely invasive alien crab species, has important economic value in China. It encounters different salinities during its life cycle, and at the megalopal stage it faces a turning point regarding the salinity in its environment. We applied RNA sequencing to E. sinensis megalopae before (MB) and after (MA) desalination, resulting in the discovery of 21,042 unigenes and 908 differentially expressed genes (DEGs, 4.32% of the unigenes). The DEGs primarily belonged to the Gene Ontology groups "Energy metabolism," "Oxidoreductase activity," "Translation," "Transport," "Metabolism," and "Stress response." In total, 33 DEGs related to transport processes were found, including 12 proton pump genes, three ATP-binding cassettes (ABCs), 13 solute carrier (SLC) family members, two sweet sugar transporter (ST) family members and three other substance transporters. Mitochondrial genes as well as genes involved in the tricarboxylic acid cycle, glycolytic pathway, or β-oxidation pathway, which can generate energy in the form of ATP, were typically up-regulated in MA. 11 unigenes related to amino acid metabolism and a large number of genes related to protein synthesis were differentially expressed in MB and MA, indicating that E. sinensis possibly adjusts its concentration of free amino acid osmolytes for hyper-osmoregulation. Additionally, 33 salinity and oxidative stress induced genes were found to be differentially expressed, such as the LEA2, HSPs, GST and coagulation factor genes. Notably, LEA2 is an extremely hydrophilic protein that responds to desiccation and reported for the first time in crabs. Therefore, we suppose that when the environment is hypo-osmotic, the megalopae might compensate for ion loss via hyper-osmoregulation by consuming more energy, accompanied by a series of stress induced adaptions. This study provides the first genome-wide transcriptome analysis of E. sinensis megalopae for studying its osmoregulation and stress adaption mechanisms.

Show MeSH
Related in: MedlinePlus