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Ping Chen - One of the best experts on this subject based on the ideXlab platform.
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transcriptome analysis of the Portunus trituberculatus de novo assembly growth related gene identification and marker discovery
PLOS ONE, 2014Co-Authors: Ping Liu, Yu Wang, Baoquan Gao, Zheng Wang, Ping ChenAbstract:Background The swimming crab, Portunus trituberculatus, is an important farmed species in China, has been attracting extensive studies, which require more and more genome background knowledge. To date, the sequencing of its whole genome is unavailable and transcriptomic information is also scarce for this species. In the present study, we performed de novo transcriptome sequencing to produce a comprehensive transcript dataset for major tissues of Portunus trituberculatus by the Illumina paired-end sequencing technology. Results Total RNA was isolated from eyestalk, gill, heart, hepatopancreas and muscle. Equal quantities of RNA from each tissue were pooled to construct a cDNA library. Using the Illumina paired-end sequencing technology, we generated a total of 120,137 transcripts with an average length of 1037 bp. Further assembly analysis showed that all contigs contributed to 87,100 unigenes, of these, 16,029 unigenes (18.40% of the total) can be matched in the GenBank non-redundant database. Potential genes and their functions were predicted by GO, KEGG pathway mapping and COG analysis. Based on our sequence analysis and published literature, many putative genes with fundamental roles in growth and muscle development, including actin, myosin, tropomyosin, troponin and other potentially important candidate genes were identified for the first time in this specie. Furthermore, 22,673 SSRs and 66,191 high-confidence SNPs were identified in this EST dataset. Conclusion The transcriptome provides an invaluable new data for a functional genomics resource and future biological research in Portunus trituberculatus. The data will also instruct future functional studies to manipulate or select for genes influencing growth that should find practical applications in aquaculture breeding programs. 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.
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transcriptome analysis of Portunus trituberculatus in response to salinity stress provides insights into the molecular basis of osmoregulation
PLOS ONE, 2013Co-Authors: Ping Liu, Yu Wang, Baoquan Gao, Ping ChenAbstract:Background The swimming crab, Portunus trituberculatus, which is naturally distributed in the coastal waters of Asia-Pacific countries, is an important farmed species in China. Salinity is one of the most important abiotic factors that influence not only the distribution and abundance of crustaceans, it is also an important factor for artificial propagation of the crab. To better understand the interaction between salinity stress and osmoregulation, we performed a transcriptome analysis in the gills of Portunus trituberculatus challenged with salinity stress, using the Illumina Deep Sequencing technology. Results We obtained 27,696,835, 28,268,353 and 33,901,271 qualified Illumina read pairs from low salinity challenged (LC), non-challenged (NC), and high salinity challenged (HC) Portunus trituberculatus cDNA libraries, respectively. The overall de novo assembly of cDNA sequence data generated 94,511 unigenes, with an average length of 644 bp. Comparative genomic analysis revealed that 1,705 genes differentially expressed in salinity stress compared to the controls, including 615 and 1,516 unigenes in NC vs LC and NC vs HC respectively. GO functional enrichment analysis results showed some differentially expressed genes were involved in crucial processes related to osmoregulation, such as ion transport processes, amino acid metabolism and synthesis processes, proteolysis process and chitin metabolic process. Conclusion This work represents the first report of the utilization of the next generation sequencing techniques for transcriptome analysis in Portunus trituberculatus and provides valuable information on salinity adaptation mechanism. Results reveal a substantial number of genes modified by salinity stress and a few important salinity acclimation pathways, which will serve as an invaluable resource for revealing the molecular basis of osmoregulation in Portunus trituberculatus. In addition, the most comprehensive sequences of transcripts reported in this study provide a rich source for identification of novel genes in the crab.
Yu Wang - One of the best experts on this subject based on the ideXlab platform.
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transcriptome analysis of the Portunus trituberculatus de novo assembly growth related gene identification and marker discovery
PLOS ONE, 2014Co-Authors: Ping Liu, Yu Wang, Baoquan Gao, Zheng Wang, Ping ChenAbstract:Background The swimming crab, Portunus trituberculatus, is an important farmed species in China, has been attracting extensive studies, which require more and more genome background knowledge. To date, the sequencing of its whole genome is unavailable and transcriptomic information is also scarce for this species. In the present study, we performed de novo transcriptome sequencing to produce a comprehensive transcript dataset for major tissues of Portunus trituberculatus by the Illumina paired-end sequencing technology. Results Total RNA was isolated from eyestalk, gill, heart, hepatopancreas and muscle. Equal quantities of RNA from each tissue were pooled to construct a cDNA library. Using the Illumina paired-end sequencing technology, we generated a total of 120,137 transcripts with an average length of 1037 bp. Further assembly analysis showed that all contigs contributed to 87,100 unigenes, of these, 16,029 unigenes (18.40% of the total) can be matched in the GenBank non-redundant database. Potential genes and their functions were predicted by GO, KEGG pathway mapping and COG analysis. Based on our sequence analysis and published literature, many putative genes with fundamental roles in growth and muscle development, including actin, myosin, tropomyosin, troponin and other potentially important candidate genes were identified for the first time in this specie. Furthermore, 22,673 SSRs and 66,191 high-confidence SNPs were identified in this EST dataset. Conclusion The transcriptome provides an invaluable new data for a functional genomics resource and future biological research in Portunus trituberculatus. The data will also instruct future functional studies to manipulate or select for genes influencing growth that should find practical applications in aquaculture breeding programs. 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.
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transcriptome analysis of Portunus trituberculatus in response to salinity stress provides insights into the molecular basis of osmoregulation
PLOS ONE, 2013Co-Authors: Ping Liu, Yu Wang, Baoquan Gao, Ping ChenAbstract:Background The swimming crab, Portunus trituberculatus, which is naturally distributed in the coastal waters of Asia-Pacific countries, is an important farmed species in China. Salinity is one of the most important abiotic factors that influence not only the distribution and abundance of crustaceans, it is also an important factor for artificial propagation of the crab. To better understand the interaction between salinity stress and osmoregulation, we performed a transcriptome analysis in the gills of Portunus trituberculatus challenged with salinity stress, using the Illumina Deep Sequencing technology. Results We obtained 27,696,835, 28,268,353 and 33,901,271 qualified Illumina read pairs from low salinity challenged (LC), non-challenged (NC), and high salinity challenged (HC) Portunus trituberculatus cDNA libraries, respectively. The overall de novo assembly of cDNA sequence data generated 94,511 unigenes, with an average length of 644 bp. Comparative genomic analysis revealed that 1,705 genes differentially expressed in salinity stress compared to the controls, including 615 and 1,516 unigenes in NC vs LC and NC vs HC respectively. GO functional enrichment analysis results showed some differentially expressed genes were involved in crucial processes related to osmoregulation, such as ion transport processes, amino acid metabolism and synthesis processes, proteolysis process and chitin metabolic process. Conclusion This work represents the first report of the utilization of the next generation sequencing techniques for transcriptome analysis in Portunus trituberculatus and provides valuable information on salinity adaptation mechanism. Results reveal a substantial number of genes modified by salinity stress and a few important salinity acclimation pathways, which will serve as an invaluable resource for revealing the molecular basis of osmoregulation in Portunus trituberculatus. In addition, the most comprehensive sequences of transcripts reported in this study provide a rich source for identification of novel genes in the crab.
Ping Liu - One of the best experts on this subject based on the ideXlab platform.
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transcriptome analysis of the Portunus trituberculatus de novo assembly growth related gene identification and marker discovery
PLOS ONE, 2014Co-Authors: Ping Liu, Yu Wang, Baoquan Gao, Zheng Wang, Ping ChenAbstract:Background The swimming crab, Portunus trituberculatus, is an important farmed species in China, has been attracting extensive studies, which require more and more genome background knowledge. To date, the sequencing of its whole genome is unavailable and transcriptomic information is also scarce for this species. In the present study, we performed de novo transcriptome sequencing to produce a comprehensive transcript dataset for major tissues of Portunus trituberculatus by the Illumina paired-end sequencing technology. Results Total RNA was isolated from eyestalk, gill, heart, hepatopancreas and muscle. Equal quantities of RNA from each tissue were pooled to construct a cDNA library. Using the Illumina paired-end sequencing technology, we generated a total of 120,137 transcripts with an average length of 1037 bp. Further assembly analysis showed that all contigs contributed to 87,100 unigenes, of these, 16,029 unigenes (18.40% of the total) can be matched in the GenBank non-redundant database. Potential genes and their functions were predicted by GO, KEGG pathway mapping and COG analysis. Based on our sequence analysis and published literature, many putative genes with fundamental roles in growth and muscle development, including actin, myosin, tropomyosin, troponin and other potentially important candidate genes were identified for the first time in this specie. Furthermore, 22,673 SSRs and 66,191 high-confidence SNPs were identified in this EST dataset. Conclusion The transcriptome provides an invaluable new data for a functional genomics resource and future biological research in Portunus trituberculatus. The data will also instruct future functional studies to manipulate or select for genes influencing growth that should find practical applications in aquaculture breeding programs. 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.
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transcriptome analysis of Portunus trituberculatus in response to salinity stress provides insights into the molecular basis of osmoregulation
PLOS ONE, 2013Co-Authors: Ping Liu, Yu Wang, Baoquan Gao, Ping ChenAbstract:Background The swimming crab, Portunus trituberculatus, which is naturally distributed in the coastal waters of Asia-Pacific countries, is an important farmed species in China. Salinity is one of the most important abiotic factors that influence not only the distribution and abundance of crustaceans, it is also an important factor for artificial propagation of the crab. To better understand the interaction between salinity stress and osmoregulation, we performed a transcriptome analysis in the gills of Portunus trituberculatus challenged with salinity stress, using the Illumina Deep Sequencing technology. Results We obtained 27,696,835, 28,268,353 and 33,901,271 qualified Illumina read pairs from low salinity challenged (LC), non-challenged (NC), and high salinity challenged (HC) Portunus trituberculatus cDNA libraries, respectively. The overall de novo assembly of cDNA sequence data generated 94,511 unigenes, with an average length of 644 bp. Comparative genomic analysis revealed that 1,705 genes differentially expressed in salinity stress compared to the controls, including 615 and 1,516 unigenes in NC vs LC and NC vs HC respectively. GO functional enrichment analysis results showed some differentially expressed genes were involved in crucial processes related to osmoregulation, such as ion transport processes, amino acid metabolism and synthesis processes, proteolysis process and chitin metabolic process. Conclusion This work represents the first report of the utilization of the next generation sequencing techniques for transcriptome analysis in Portunus trituberculatus and provides valuable information on salinity adaptation mechanism. Results reveal a substantial number of genes modified by salinity stress and a few important salinity acclimation pathways, which will serve as an invaluable resource for revealing the molecular basis of osmoregulation in Portunus trituberculatus. In addition, the most comprehensive sequences of transcripts reported in this study provide a rich source for identification of novel genes in the crab.
Kohji Shiota - One of the best experts on this subject based on the ideXlab platform.
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Recruitment strategy of swimming crab, Portunus trituberculatus, in Hiuchi-Nada, Japan
Fisheries Oceanography, 1995Co-Authors: Tetsuo Yanagi, Hideshi Tsukamoto, Shujo Igawa, Kohji ShiotaAbstract:The recruitment strategy of swimming crabs, Portunus trituberculatus, was investigated by field observations and numerical experiments in Hiuchi-Nada, Japan. Calculated dispersal patterns of zoeal and megalopal stages in a three-dimensional numerical model reproduce observed patterns accurately. The temporal change of vertical migration patterns between the 1st and 2nd zoeas and the 3rd and 4th zoeas plays an important role in the process of recruitment of P. trituberculatus from spawning ground to nursery ground.
Jose Josileen - One of the best experts on this subject based on the ideXlab platform.
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cmfri marine fisheries policy series no 15 fishery management plan for palk bay blue swimming crab
2019Co-Authors: Jose Josileen, G Maheswarudu, Shelton Padua, Geetha Sasikumar, Eldho Varghese, K S MohamedAbstract:Crabs are widely distributed in Indian seas and form minor fishery at various regions along the east and west coasts. Crabs contribute a share of 11.1 % in total crustacean landings, with an approximate production of 53476 tonnes in 2017. Three portunid crabs, Portunus pelagicus, Portunus sanguinolentus and Charybdis feriatus form the majority of the regular crab landings in India. The demand for Portunus pelagicus, commonly known as Blue Swimming Crab (BSC) is consistently increasing ever since its export started in the beginning of the century. The State of Tamil Nadu is leading in marine crab landings particularly for the blue swimming crab production in India. The major landing centres for BSC are located in the Palk Bay (PB) and Gulf of Mannar (GoM) areas of Ramanathapuram, Pudukkottai and Thanjavur districts of the state. BSC products form the most important internationally traded commodity from the region and contribute significantly to the livelihood of crab merchants and crab fishers of the area. The Central Marine Fisheries Research Institute has been monitoring the BSC fishery and studying the biology the species along with other marine resources. During the last decade of the 20th century more focused and in-depth studies have been conducted on Portunus pelagicus and established the fact that apart from its fisheries importance, BSC is also a suitable candidate species for farming. This document gives insights on BSC fishing zones, major fishing craft and gears, area wise and centre wise production details, trade, processing industry and export markets. Furthermore, it elucidates the complete life cycle of the species including its growth and reproductive biology as these form essential and integral inputs while formulating the management decisions. As BSC is a highly valuable commodity it necessitates urgent attention to its responsible exploitation and action plan for the judicious management of the resource to accomplish BSC as a sustained fishery. Conclusions have drawn based on the facts and evidences, acquired from exhaustive field and laboratory studies and guidance on a Fishery Management Plan for Palk Bay BSC fishery are presented.
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Taxonomic identification of Portunus pelagicus species complex in Indian waters using morphological and mitochondrial DNA Makers
2014Co-Authors: Jose Josileen, A. Gopalakrishnan, P. R. Divya, V. S. Basheer, G MaheswaruduAbstract:Taxonomic identification of Portunus pelagicus species complex in Indian waters using morphological and mitochondrial DNA Makers
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On the fishery, biology and the hatchery technology of the portunid crab Portunus pelagicus (TH 099)
2001Co-Authors: Jose JosileenAbstract:Crabs belonging to more than 4500 extant species of decapod crustaceans are included in the infraorder Brachyura. The brachyura show extreme versatility in distribution. They are found in all climates, and in terrestrial, semi terrestrial and from the shore to deep sea, in marine, brackish as well as freshwater environments. Although earlier surveys have recorded above 640 species of crabs from Indian waters, only eight species are commonly referred to as 'edible crabs' inhabiting the coastal waters and adjoining brackishwater environment and support localised and sustenance fishery to some extent. Crabs are members of Crustacea, a class of invertebrate phylum Arthropoda that includes the animals with jointed legs and a hardened outer covering or exoskeleton. Crab belong to the order Decapoda a name which refers to this fact that the members of this order have 5 pairs of legs. The true crabs are placed in the suborder Brachyura an appropriate name for this group, as their shortened flap-like abdomen or tail is folded under the body CRees, 1963). The presently studied crab Portunus (Portunus) pelagicus, is a marine species belongs to the family Portunidae and subfamily Portuninae. Although the latest nomenclature of the crab is Portllnus (Portunus) pelagicus (Linnaeus), for the sake of brevity, ' Portllnus pelagicus' is used throughout the text. In the Indian Ocean, the crab fauna of Portunidae family is included under sub families, PodoPhthaimidae (Borradaile), Catoptrinae (Sakai), Portuninae (Rafinesque), Caphyrinae (Alcock), Carcininae (Macleay) and Polybiinae (Ortmann). Most of the edible crabs caught from marine and brackishwater environments belong to the sub family Portuninae. In the seas around India, five genera of Portuninae have been reported by various authors. They are Scylla, Por/unlls, Charybdis, Lupocyc/us and Thalamita. Among them the first three genera contribute to the commercial crab fishery. The richness, variety and fishery of marine crabs of Indian seas have been investigated by many workers over the past 100 years. Among them the notable works are of Alcock (1895,1896,1898-1900), de Man (1908), Kemp (1915,1919a,b), Chopra ( 1931 , 1939), Prasad and Tampi (1951, 1953), Menon (1952), Jones and Sujansingani (1952), Chhapgar (1957,1962), Sankarankutty (196Ia, b,1965), George and Nayak (1961), Ramamurthy (1972), Prasad and Nair (1973), Rao el al. (1973), Dhawan el al. (1976) and Kurup el al. (1990).
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Crabs and Crab Fishery of the Mandapam Area
2000Co-Authors: Jose JosileenAbstract:In our country, crab fishery is mainly contributed by portunid crabs those which belong to three generae ie., Scylla. Portunus and Charybdis. They have the typical portunid shape with carapace having 4-9 anterolateral teeth. Chelepeds are longer than all legs and last pair typically paddle shaped.
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Blue swimming crab hatchery
1998Co-Authors: Jose Josileen, G Maheswarudu, M R ArputharajAbstract:The blue swimming crab Portunus pelagicus is one of the major marine crabs used for domestic consumption as well as for export.
