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Zhou C, Yang MJ, Hu Z, Shi P, Li YR, Guo YJ, Zhang T, Song H. Molecular evidence for the adaptive evolution in euryhaline bivalves. MARINE ENVIRONMENTAL RESEARCH 2023; 192:106240. [PMID: 37944349 DOI: 10.1016/j.marenvres.2023.106240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/26/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
Marine bivalves inhabiting intertidal and estuarine areas are frequently exposed to salinity stress due to persistent rainfall and drought. Through prolonged adaptive evolution, numerous bivalves have developed eurysalinity, which are capable of tolerating a wide range of salinity fluctuations through the sophisticated regulation of physiological metabolism. Current research has predominantly focused on investigating the physiological responses of bivalves to salinity stress, leaving a significant gap in our understanding of the adaptive evolutionary characteristics in euryhaline bivalves. Here, comparative genomics analyses were performed in two groups of bivalve species, including 7 euryhaline species and 5 stenohaline species. We identified 24 significantly expanded gene families and 659 positively selected genes in euryhaline bivalves. A significant co-expansion of solute carrier family 23 (SLC23) facilitates the transmembrane transport of ascorbic acids in euryhaline bivalves. Positive selection of antioxidant genes, such as GST and TXNRD, augments the capacity of active oxygen species (ROS) scavenging under salinity stress. Additionally, we found that the positively selected genes were significantly enriched in KEGG pathways associated with carbohydrates, lipids and amino acids metabolism (ALDH, ADH, and GLS), as well as GO terms related to transmembrane transport and inorganic anion transport (SLC22, CLCND, and VDCC). Positive selection of MCT might contribute to prevent excessive accumulation of intracellular lactic acids during anaerobic metabolism. Positive selection of PLA2 potentially promote the removal of damaged membranes lipids under salinity stress. Our findings suggest that adaptive evolution has occurred in osmoregulation, ROS scavenging, energy metabolism, and membrane lipids adjustments in euryhaline bivalves. This study enhances our understanding of the molecular mechanisms underlying the remarkable salinity adaption of euryhaline bivalves.
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Affiliation(s)
- Cong Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China
| | - Mei-Jie Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China
| | - Zhi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China
| | - Pu Shi
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China
| | - Yong-Ren Li
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China
| | - Yong-Jun Guo
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China
| | - Tao Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China.
| | - Hao Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China.
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Guo X, Puritz JB, Wang Z, Proestou D, Allen S, Small J, Verbyla K, Zhao H, Haggard J, Chriss N, Zeng D, Lundgren K, Allam B, Bushek D, Gomez-Chiarri M, Hare M, Hollenbeck C, La Peyre J, Liu M, Lotterhos KE, Plough L, Rawson P, Rikard S, Saillant E, Varney R, Wikfors G, Wilbur A. Development and Evaluation of High-Density SNP Arrays for the Eastern Oyster Crassostrea virginica. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:174-191. [PMID: 36622459 DOI: 10.1007/s10126-022-10191-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The eastern oyster Crassostrea virginica is a major aquaculture species for the USA. The sustainable development of eastern oyster aquaculture depends upon the continued improvement of cultured stocks through advanced breeding technologies. The Eastern Oyster Breeding Consortium (EOBC) was formed to advance the genetics and breeding of the eastern oyster. To facilitate efficient genotyping needed for genomic studies and selection, the consortium developed two single-nucleotide polymorphism (SNP) arrays for the eastern oyster: one screening array with 566K SNPs and one breeders' array with 66K SNPs. The 566K screening array was developed based on whole-genome resequencing data from 292 oysters from Atlantic and Gulf of Mexico populations; it contains 566,262 SNPs including 47K from protein-coding genes with a marker conversion rate of 48.34%. The 66K array was developed using best-performing SNPs from the screening array, which contained 65,893 oyster SNPs including 22,984 genic markers with a calling rate of 99.34%, a concordance rate of 99.81%, and a much-improved marker conversion rate of 92.04%. Null alleles attributable to large indels were found in 13.1% of the SNPs, suggesting that copy number variation is pervasive. Both arrays provided easy identification and separation of selected stocks from wild progenitor populations. The arrays contain 31 mitochondrial SNPs that allowed unambiguous identification of Gulf mitochondrial genotypes in some Atlantic populations. The arrays also contain 756 probes from 13 oyster and human pathogens for possible detection. Our results show that marker conversion rate is low in high polymorphism species and that the two-step process of array development can greatly improve array performance. The two arrays will advance genomic research and accelerate genetic improvement of the eastern oyster by delineating genetic architecture of production traits and enabling genomic selection. The arrays also may be used to monitor pedigree and inbreeding, identify selected stocks and their introgression into wild populations, and assess the success of oyster restoration.
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Affiliation(s)
- Ximing Guo
- Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA.
| | - Jonathan B Puritz
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Zhenwei Wang
- Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Dina Proestou
- USDA ARS NCWMAC Shellfish Genetics Lab, 120 Flagg Rd., Kingston, RI, 02881, USA
| | - Standish Allen
- Virginia Institute of Marine Science, 1375 Greate Rd., Gloucester Pt., VA, 23062, USA
| | - Jessica Small
- Virginia Institute of Marine Science, 1375 Greate Rd., Gloucester Pt., VA, 23062, USA
| | | | - Honggang Zhao
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, USA
| | - Jaime Haggard
- Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Noah Chriss
- Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Dan Zeng
- Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Kathryn Lundgren
- USDA ARS NCWMAC Shellfish Genetics Lab, 120 Flagg Rd., Kingston, RI, 02881, USA
| | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - David Bushek
- Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Marta Gomez-Chiarri
- Department of Fisheries, Animal and Veterinary Science, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Matthew Hare
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, USA
| | - Christopher Hollenbeck
- Texas A&M University - Corpus Christi, Texas A&M AgriLife Research, 6300 Ocean Drive Unit 5892, Corpus Christi, TX, 78412, USA
| | - Jerome La Peyre
- School of Animal Sciences, Louisiana State University Agricultural Center, 201 Animal and Food Sciences Laboratory Building, Forestry Lane, Baton Rouge, LA, 70803, USA
| | - Ming Liu
- Patuxent Environmental and Aquatic Research Laboratory, Morgan State University, 10545 Mackall Road, Saint Leonard, MD, 20685, USA
| | - Katie E Lotterhos
- Northeastern Marine Science Center, 430 Nahant Rd, Nahant, MA, 01908, USA
| | - Louis Plough
- Horn Point Lab, University of Maryland, 5745 Lovers Lane, Cambridge, MD, 21613, USA
| | - Paul Rawson
- School of Marine Sciences, University of Maine, 5751 Murray Hall, , Orono, ME, 04469, USA
| | - Scott Rikard
- School of Fisheries Aquaculture and Aquatic Sciences, Auburn University Shellfish Laboratory, Auburn University, 150 Agassiz St., Dauphin Island, AL, 36528, USA
| | - Eric Saillant
- School of Ocean Science and Engineering, The University of Southern Mississippi, 103 McIlwain Drive, Ocean Springs, MS, 39564, USA
| | - Robin Varney
- Shellfish Research Hatchery, University of North Carolina Wilmington, 5600 Marvin K. Moss Ln., Wilmington, NC, 28409, USA
| | - Gary Wikfors
- Milford CT Laboratory, NOAA Fisheries, 212 Rogers Avenue, Milford, CT, 06460, USA
| | - Ami Wilbur
- Shellfish Research Hatchery, University of North Carolina Wilmington, 5600 Marvin K. Moss Ln., Wilmington, NC, 28409, USA
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Gong J, Li Q, Yu H, Liu S, Kong L. Effects of low salinity on hemolymph osmolality and transcriptome of the Iwagaki oyster, Crassostrea nippona. FISH & SHELLFISH IMMUNOLOGY 2022; 126:211-216. [PMID: 35636697 DOI: 10.1016/j.fsi.2022.05.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/06/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Crassostrea nippona is a kind of oysters with great development value as it can be edible in summer for its late reproductive period. Salinity is one of the important limiting abiotic factors to the survival and distribution of this stenohaline species. To better understand the physiological and immunological response of C. nippona to varying environmental salinities, the effects of low salinity on the hemolymph osmolality and gill transcriptome were investigated in this study. The osmolality of hemolymph in vivo and surrounding water were assessed regularly over one week at five test salinities ranging from 5 psμ to 30 psμ. They reached osmotic equilibrium within hours above 15 psμ but remained hyperosmotic at 10 and 5 psμ for the whole sampling period. Through comparative transcriptome analysis, there were less differentially expressed genes (DEGs) in pairwise comparison of S1 (10 psμ) vs S3 (30 psμ) than in S2 (20 psμ) vs S3. KEGG enrichment analysis identified ubiquitin-mediated proteolysis and mitochondrial apoptosis pathway specifically enriched at 10 psμ. This study gained comprehensive insights on the low salinity response of C. nippona at the molecular level, which provide a theoretical basis for understanding the immune mechanism under low salinity stress.
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Affiliation(s)
- Jianwen Gong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 66003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 66003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 66003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 66003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 66003, China
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4
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López-Landavery EA, Amador-Cano G, Tripp-Valdez MA, Ramírez-Álvarez N, Cicala F, Gómez-Reyes RJE, Díaz F, Re-Araujo AD, Galindo-Sánchez CE. Hydrocarbon exposure effect on energetic metabolism and immune response in Crassostrea virginica. MARINE POLLUTION BULLETIN 2022; 180:113738. [PMID: 35635877 DOI: 10.1016/j.marpolbul.2022.113738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Crassostrea virginica was exposed to different light crude oil levels to assess the effect on transcriptomic response and metabolic rate. The exposure time was 21 days, and levels of 100 and 200 μg/L were used, including a control. The most significant difference among treatments was the overexpression of several genes associated with energy production, reactive oxygen species (ROS) regulation, immune system response, and inflammatory response. Also, a hydrocarbon concentration-related pattern was identified in ROS regulation, with a gene expression ratio near 1.8:1 between 200 and 100 μg/L treatments. Statistical analysis showed no interaction effect for metabolic rate; however, significant differences were found for oil concentration and time factors, with a higher oxygen consumption at 200 μg/L. Our findings provide novel information about the metabolic response of C. virginica during hydrocarbons exposure. In addition, our results point out which biological processes should be investigated as targets for searching bioindicators.
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Affiliation(s)
- E A López-Landavery
- Laboratorio de Genómica Funcional, Departamento de Biotecnología Marina, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, BC, Mexico; Laboratorio de Genética, Fisiología y Reproducción, Facultad de Ciencias, Universidad Nacional del Santa, Nuevo Chimbote, Ancash, Peru
| | - G Amador-Cano
- Universidad Tecnológica del Mar de Tamaulipas Bicentenario, La Pesca, Soto La Marina, Tamaulipas, Mexico
| | - M A Tripp-Valdez
- Departamento de Acuicultura, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, BC, Mexico
| | - N Ramírez-Álvarez
- Instituto de Investigaciones Oceanológicas (IIO), Universidad Autónoma de Baja California (UABC), Carretera Tijuana-Ensenada No. 3917, Ensenada, BC, Mexico
| | - F Cicala
- Laboratorio de Genómica Funcional, Departamento de Biotecnología Marina, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, BC, Mexico
| | - R J E Gómez-Reyes
- Laboratorio de Genómica Funcional, Departamento de Biotecnología Marina, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, BC, Mexico; Facultad de Ciencias Marinas, Universidad Autónoma de Baja California (UABC), Carretera Tijuana-Ensenada No. 3917, Ensenada, BC, Mexico
| | - F Díaz
- Laboratorio de Genómica Funcional, Departamento de Biotecnología Marina, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, BC, Mexico
| | - A D Re-Araujo
- Laboratorio de Genómica Funcional, Departamento de Biotecnología Marina, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, BC, Mexico
| | - C E Galindo-Sánchez
- Laboratorio de Genómica Funcional, Departamento de Biotecnología Marina, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, BC, Mexico.
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Sun J, Chen M, Fu Z, Yu G, Ma Z, Xing Y. Transcriptome analysis of the mantle tissue of Pinctada fucata with red and black shells under salinity stress. Gene 2022; 823:146367. [PMID: 35202732 DOI: 10.1016/j.gene.2022.146367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 11/16/2022]
Abstract
To understand the molecular responses of Pinctada fucata with different shell colors to salinity stress, we used transcriptome sequencing on the mantle of P. fucata with a black shell and red shell color under the salinity of 20, 35, and 50. The 414 and 2371 differentially expressed genes (DEGs) in P. fucata with a black shell under low- or high-salt stress, while there were 588 and 3009 DEGs in P. fucata with a red shell. KEGG pathway enrichment analysis showed that, under low salt stress, the DEGs of P. fucata with the black shell were significantly enriched in pathways MAPK signaling pathway, protein processing in endoplasmic reticulum, vitamin B6 metabolism, longevity regulating pathway-multiple species, estrogen signaling pathway and antigen processing and presentation, the DEGs of P. fucata with a red shell were significantly enriched in pathways vitamin B6 metabolism. Under high salt stress, the DEGs of P. fucata with a red shell were significantly enriched in pathways arginine biosynthesis. 11 DEGs were randomly selected for quantitative real-time PCR, and the results were consistent with the RNA-seq. In addition, under high salt stress, DEGs were enriched into some pathways related to osmotic regulation and immune defense of P. fucata with black shell and red shell, such as Glycolysis / Gluconeogenesis, AMPK signaling pathway, Beta-Alanine metabolism, Glycine, serine and threonine metabolism, MAPK signaling pathway and Phagosome. The study showed that high salt stress had a greater influence on P. fucata with two shell colors, and P. fucata with a black shell made a positive immune defense response. Our results will improve to further understand the salt tolerance mechanism of P. fucata with different shell colors.
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Affiliation(s)
- Jing Sun
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, PR China; Sanya Fisheries Research Institute, Sanya 572018, PR China; Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Guangzhou 510300, PR China; College of Fisheries, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Mingqiang Chen
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, PR China; Sanya Fisheries Research Institute, Sanya 572018, PR China; Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Guangzhou 510300, PR China
| | - Zhengyi Fu
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, PR China; Sanya Fisheries Research Institute, Sanya 572018, PR China; Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Guangzhou 510300, PR China
| | - Gang Yu
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, PR China; Sanya Fisheries Research Institute, Sanya 572018, PR China; Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Guangzhou 510300, PR China
| | - Zhenhua Ma
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, PR China; Sanya Fisheries Research Institute, Sanya 572018, PR China; Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Guangzhou 510300, PR China; College of Fisheries, Tianjin Agricultural University, Tianjin 300384, PR China.
| | - Yingchun Xing
- Resource and Environmental Research Center, Chinese Academy of Fishery Sciences, Beijing 100141, PR China.
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Population transcriptomics reveals the effect of gene flow on the evolution of range limits. Sci Rep 2022; 12:1318. [PMID: 35079049 PMCID: PMC8789792 DOI: 10.1038/s41598-022-05248-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 01/10/2022] [Indexed: 11/17/2022] Open
Abstract
One of the most important questions in evolutionary biology is how the spatial distribution of species is limited. Asymmetric gene flow from core populations is suggested to increase the number of poorly adapted immigrants in the populations at the range edge. Genetic load due to migration, i.e., migration load, should prevent adaptation to the local habitat, leading to decreases in distribution range via local extinction or the limiting range expansion. However, few experimental studies have examined the effects of immigration on fitness and natural selection within recipient populations. To investigate the influence of migration load on the evolution of distribution range, we performed field and laboratory observations as well as population transcriptomics for the common river snail, Semisulcospira reiniana. This species meets the conditions that migration from source populations can prevent local adaptation in a sink population because they inhabit the broader range of environments, including middle/upper reaches of a river and estuaries within a single river and they may be more vulnerable to being swept away by water currents due to lowered spontaneous (upward) locomotion activity. We found that river steepness was related to the lower distribution limit of S. reiniana, with a narrower distribution range in the steeper river. Population transcriptomic analysis showed that gene flow was heavily asymmetric from the upstream populations to downstream ones in the steep river, suggesting a greater migration load in the steep river. The number of genes putatively involved in adaptation to the local habitat was lower in the steep river than in the gentle river. Gene expression profiles suggested that individuals achieve better local adaptation in the gentle river. Laboratory experiments suggested that evolutionary differences in salinity tolerance among local populations were only found in the gentle river. Our results consistent with the hypothesis that migration load owing to asymmetric gene flow disturbs local adaptation and restricts the distribution range of river snails.
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McCarty AJ, Allen SK, Plough LV. Genome-wide analysis of acute low salinity tolerance in the eastern oyster Crassostrea virginica and potential of genomic selection for trait improvement. G3 (BETHESDA, MD.) 2022; 12:6409860. [PMID: 34849774 PMCID: PMC8727987 DOI: 10.1093/g3journal/jkab368] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/11/2021] [Indexed: 11/12/2022]
Abstract
As the global demand for seafood increases, research into the genetic basis of traits that can increase aquaculture production is critical. The eastern oyster (Crassostrea virginica) is an important aquaculture species along the Atlantic and Gulf Coasts of the United States, but increases in heavy rainfall events expose oysters to acute low salinity conditions, which negatively impact production. Low salinity survival is known to be a moderately heritable trait, but the genetic architecture underlying this trait is still poorly understood. In this study, we used ddRAD sequencing to generate genome-wide single-nucleotide polymorphism (SNP) data for four F2 families to investigate the genomic regions associated with survival in extreme low salinity (<3). SNP data were also used to assess the feasibility of genomic selection (GS) for improving this trait. Quantitative trait locus (QTL) mapping and combined linkage disequilibrium analysis revealed significant QTL on eastern oyster chromosomes 1 and 7 underlying both survival and day to death in a 36-day experimental challenge. Significant QTL were located in genes related to DNA/RNA function and repair, ion binding and membrane transport, and general response to stress. GS was investigated using Bayesian linear regression models and prediction accuracies ranged from 0.48 to 0.57. Genomic prediction accuracies were largest using the BayesB prior and prediction accuracies did not substantially decrease when SNPs located within the QTL region on Chr1 were removed, suggesting that this trait is controlled by many genes of small effect. Our results suggest that GS will likely be a viable option for improvement of survival in extreme low salinity.
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Affiliation(s)
- Alexandra J McCarty
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613, USA
| | - Standish K Allen
- Virginia Institute of Marine Science, Aquaculture Genetics and Breeding Technology Center, Gloucester Point, VA 23062, USA
| | - Louis V Plough
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613, USA
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Hornick KM, Plough LV. Genome-wide analysis of natural and restored eastern oyster populations reveals local adaptation and positive impacts of planting frequency and broodstock number. Evol Appl 2022; 15:40-59. [PMID: 35126647 PMCID: PMC8792482 DOI: 10.1111/eva.13322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/22/2021] [Accepted: 10/24/2021] [Indexed: 01/20/2023] Open
Abstract
The release of captive-bred plants and animals has increased worldwide to augment declining species. However, insufficient attention has been given to understanding how neutral and adaptive genetic variation are partitioned within and among proximal natural populations, and the patterns and drivers of gene flow over small spatial scales, which can be important for restoration success. A seascape genomics approach was used to investigate population structure, local adaptation, and the extent to which environmental gradients influence genetic variation among natural and restored populations of Chesapeake Bay eastern oysters Crassostrea virginica. We also investigated the impact of hatchery practices on neutral genetic diversity of restored reefs and quantified the broader genetic impacts of large-scale hatchery-based bivalve restoration. Restored reefs showed similar levels of diversity as natural reefs, and striking relationships were found between planting frequency and broodstock numbers and genetic diversity metrics (effective population size and relatedness), suggesting that hatchery practices can have a major impact on diversity. Despite long-term restoration activities, haphazard historical translocations, and high dispersal potential of larvae that could homogenize allele frequencies among populations, moderate neutral population genetic structure was uncovered. Moreover, environmental factors, namely salinity, pH, and temperature, play a major role in the distribution of neutral and adaptive genetic variation. For marine invertebrates in heterogeneous seascapes, collecting broodstock from large populations experiencing similar environments to candidate sites may provide the most appropriate sources for restoration and ensure population resilience in the face of rapid environmental change. This is one of a few studies to demonstrate empirically that hatchery practices have a major impact on the retention of genetic diversity. Overall, these results contribute to the growing body of evidence for fine-scale genetic structure and local adaptation in broadcast-spawning marine species and provide novel information for the management of an important fisheries resource.
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Affiliation(s)
- Katherine M. Hornick
- University of Maryland Center for Environmental ScienceHorn Point LaboratoryCambridgeMarylandUSA
| | - Louis V. Plough
- University of Maryland Center for Environmental ScienceHorn Point LaboratoryCambridgeMarylandUSA
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Furr D, Ketchum RN, Phippen BL, Reitzel AM, Ivanina AV. Physiological Variation in Response to Vibrio and Hypoxia by Aquacultured Eastern Oysters in the Southeastern United States. Integr Comp Biol 2021; 61:1715-1729. [PMID: 34351419 DOI: 10.1093/icb/icab176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/12/2021] [Indexed: 02/04/2023] Open
Abstract
Eastern oysters (Crassostrea virginica) have long been recognized as model organisms of extreme environmental tolerance, showing resilience to variation in temperature, salinity, hypoxia and microbial pathogens. These phenotypic responses, however, show variability between geographic locations or habitats (e.g., tidal). Physiological, morphological and genetic differences occur in populations throughout a species' geographical range, which may have been shaped by regional abiotic and biotic variations. Few studies of C. virginica have explored the combined factors of physiological mechanisms of divergent phenotypes between locations and the genetic relationships of individuals between these locations. To characterize genetic relationships of four locations with aquacultured oysters along the North Carolina and Virginia coast, we sequenced a portion of cytochrome oxidase subunit I (COI) that revealed significant variation in haplotype distribution between locations. We then measured mitochondrial physiology and expression of the innate immunity response of hemocytes to lab acclimation and combined stress conditions to compare basal expression and stress response in oysters between these locations. For stress sensing genes, toll-like receptors had the strongest location-specific response to hypoxia and Vibrio, whereas mannose receptor and a stress-receptor were specific to hypoxia and bacteria, respectively. The expression of stress response genes also showed location-specific and stressor-specific changes in expression, particularly for big defensin and the complement gene Cq3. Our results further suggested that genetic similarity of oysters from different locations was not clearly related to physiological and molecular responses. These results are informative for understanding the range of physiological plasticity for stress responses in this commercially important oyster species. They also have implications in the oyster farming industry as well as conservation efforts to restore endangered native oyster beds.
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Affiliation(s)
- Denise Furr
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Remi N Ketchum
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Britney L Phippen
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Anna V Ivanina
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA.,Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
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10
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Marshall DA, Casas SM, Walton WC, Rikard FS, Palmer TA, Breaux N, La Peyre MK, Beseres Pollack J, Kelly M, La Peyre JF. Divergence in salinity tolerance of northern Gulf of Mexico eastern oysters under field and laboratory exposure. CONSERVATION PHYSIOLOGY 2021; 9:coab065. [PMID: 34447578 PMCID: PMC8384081 DOI: 10.1093/conphys/coab065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/30/2021] [Accepted: 08/18/2021] [Indexed: 05/04/2023]
Abstract
The eastern oyster, Crassostrea virginica, is a foundation species within US Gulf of Mexico (GoM) estuaries that has experienced substantial population declines. As changes from management and climate are expected to continue to impact estuarine salinity, understanding how local oyster populations might respond and identifying populations with adaptations to more extreme changes in salinity could inform resource management, including restoration and aquaculture programs. Wild oysters were collected from four estuarine sites from Texas [Packery Channel (PC): 35.5, annual mean salinity, Aransas Bay (AB): 23.0] and Louisiana [Calcasieu Lake (CL): 16.2, Vermilion Bay (VB): 7.4] and spawned. The progeny were compared in field and laboratory studies under different salinity regimes. For the field study, F1 oysters were deployed at low (6.4) and intermediate (16.5) salinity sites in Alabama. Growth and mortality were measured monthly. Condition index and Perkinsus marinus infection intensity were measured quarterly. For the laboratory studies, mortality was recorded in F1 oysters that were exposed to salinities of 2.0, 4.0, 20.0/22.0, 38.0 and 44.0 with and without acclimation. The results of the field study and laboratory study with acclimation indicated that PC oysters are adapted to high-salinity conditions and do not tolerate very low salinities. The AB stock had the highest plasticity as it performed as well as the PC stock at high salinities and as well as Louisiana stocks at the lowest salinity. Louisiana stocks did not perform as well as the Texas stocks at high salinities. Results from the laboratory studies without salinity acclimation showed that all F1 stocks experiencing rapid mortality at low salinities when 3-month oysters collected at a salinity of 24 were used and at both low and high salinities when 7-month oysters collected at a salinity of 14.5 were used.
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Affiliation(s)
- Danielle A Marshall
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Sandra M Casas
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - William C Walton
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Dauphin Island, AL 36528, USA
| | - F Scott Rikard
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Dauphin Island, AL 36528, USA
| | - Terence A Palmer
- Harte Research Institute for Gulf of Mexico Studies, Texas A&M University-Corpus Christi, TX, 78412, USA
| | - Natasha Breaux
- Harte Research Institute for Gulf of Mexico Studies, Texas A&M University-Corpus Christi, TX, 78412, USA
| | - Megan K La Peyre
- US Geological Survey, Louisiana Fish and Wildlife Cooperative Research Unit, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Jennifer Beseres Pollack
- Harte Research Institute for Gulf of Mexico Studies, Texas A&M University-Corpus Christi, TX, 78412, USA
| | - Morgan Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jerome F La Peyre
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
- Corresponding author: School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA. Tel: (225) 578-5419.
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11
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Kosicka E, Lesicki A, Pieńkowska JR. Molluscan aquaporins: an overview, with some notes on their role in the entry into aestivation in gastropods. MOLLUSCAN RESEARCH 2020. [DOI: 10.1080/13235818.2020.1716442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Ewa Kosicka
- Department of Cell Biology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Andrzej Lesicki
- Department of Cell Biology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Joanna R. Pieńkowska
- Department of Cell Biology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
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12
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Sillanpää JK, Cardoso JCDR, Félix RC, Anjos L, Power DM, Sundell K. Dilution of Seawater Affects the Ca 2 + Transport in the Outer Mantle Epithelium of Crassostrea gigas. Front Physiol 2020; 11:1. [PMID: 32038307 PMCID: PMC6987452 DOI: 10.3389/fphys.2020.00001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/01/2020] [Indexed: 12/18/2022] Open
Abstract
Varying salinities of coastal waters are likely to affect the physiology and ion transport capabilities of calcifying marine organisms such as bivalves. To investigate the physiological effect of decreased environmental salinity in bivalves, adult oysters (Crassostrea gigas) were exposed for 14 days to 50% seawater (14) and the effects on mantle ion transport, electrophysiology and the expression of Ca2+ transporters and channels relative to animals maintained in full strength sea water (28) was evaluated. Exposure of oysters to a salinity of 14 decreased the active mantle transepithelial ion transport and specifically affected Ca2+ transfer. Gene expression of the Na+/K+-ATPase and the sarco(endo)plasmic reticulum Ca2+-ATPase was decreased whereas the expression of the T-type voltage-gated Ca channel and the Na+/Ca2+-exchanger increased compared to animals maintained in full SW. The results indicate that decreased environmental salinities will most likely affect not only osmoregulation but also bivalve biomineralization and shell formation.
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Affiliation(s)
- J Kirsikka Sillanpää
- Fish Endocrinology Laboratory, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Joao Carlos Dos Reis Cardoso
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - Rute Castelo Félix
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - Liliana Anjos
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - Deborah Mary Power
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - Kristina Sundell
- Fish Endocrinology Laboratory, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
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13
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Jones HR, Johnson KM, Kelly MW. Synergistic Effects of Temperature and Salinity on the Gene Expression and Physiology of Crassostrea virginica. Integr Comp Biol 2019; 59:306-319. [DOI: 10.1093/icb/icz035] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Abstract
The eastern oyster, Crassostrea virginica, forms reefs that provide critical services to the surrounding ecosystem. These reefs are at risk from climate change, in part because altered rainfall patterns may amplify local fluctuations in salinity, impacting oyster recruitment, survival, and growth. As in other marine organisms, warming water temperatures might interact with these changes in salinity to synergistically influence oyster physiology. In this study, we used comparative transcriptomics, measurements of physiology, and a field assessment to investigate what phenotypic changes C. virginica uses to cope with combined temperature and salinity stress in the Gulf of Mexico. Oysters from a historically low salinity site (Sister Lake, LA) were exposed to fully crossed temperature (20°C and 30°C) and salinity (25, 15, and 7 PSU) treatments. Using comparative transcriptomics on oyster gill tissue, we identified a greater number of genes that were differentially expressed (DE) in response to low salinity at warmer temperatures. Functional enrichment analysis showed low overlap between genes DE in response to thermal stress compared with hypoosmotic stress and identified enrichment for gene ontologies associated with cell adhesion, transmembrane transport, and microtubule-based process. Experiments also showed that oysters changed their physiology at elevated temperatures and lowered salinity, with significantly increased respiration rates between 20°C and 30°C. However, despite the higher energetic demands, oysters did not increase their feeding rate. To investigate transcriptional differences between populations in situ, we collected gill tissue from three locations and two time points across the Louisiana Gulf coast and used quantitative PCR to measure the expression levels of seven target genes. We found an upregulation of genes that function in osmolyte transport, oxidative stress mediation, apoptosis, and protein synthesis at our low salinity site and sampling time point. In summary, oysters altered their phenotype more in response to low salinity at higher temperatures as evidenced by a higher number of DE genes during laboratory exposure, increased respiration (higher energetic demands), and in situ differential expression by season and location. These synergistic effects of hypoosmotic stress and increased temperature suggest that climate change will exacerbate the negative effects of low salinity exposure on eastern oysters.
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Affiliation(s)
- H R Jones
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - K M Johnson
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - M W Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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14
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Ertl NG, O'Connor WA, Elizur A. Molecular effects of a variable environment on Sydney rock oysters, Saccostrea glomerata: Thermal and low salinity stress, and their synergistic effect. Mar Genomics 2019; 43:19-32. [DOI: 10.1016/j.margen.2018.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 10/07/2018] [Accepted: 10/18/2018] [Indexed: 12/26/2022]
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15
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iTRAQ-based proteome profiling of hyposaline responses in zygotes of the Pacific oyster Crassostrea gigas. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 30:14-24. [PMID: 30771561 DOI: 10.1016/j.cbd.2018.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 11/22/2022]
Abstract
Low salinity treatment is proven to be the practical polyploidy inducing method for shellfish with advantages of lower cost, higher operability and reliable food security. However, little is known about the possible molecular mechanism of hypotonic induction. In this study, isobaric tags for relative and absolute quantitation (iTRAQ) based proteomic profiling was pursued to investigate the responses of zygotes of the Pacific oyster Crassostrea gigas to low salinity. A total of 2235 proteins were identified and 87 proteins were considered differentially expressed, of which 14 were up-regulated and 69 were down-regulated. Numerous functional proteins including ADP ribosylation factor 2, DNA repair protein Rad50, splicing factor 3B, tubulin-specific Chaperone D were significantly changed in abundance, and were involved in various biology processes including energy generation, vesicle trafficking, DNA/RNA/protein metabolism and cytoskeleton modification, indicating the prominent modulation of cell division and embryonic development. Parallel reaction monitoring (PRM) analyses were carried out for validation of the expression levels of differentially expressed proteins (DEPs), which indicated high reliability of the proteomic results. Our study not only demonstrated the proteomic alterations in oyster zygotes under low salinity, but also provided, in part, clues to the relatively lower hatching rate and higher mortality of induced larvae. Above all, this study presents a valuable foundation for further studies on mechanisms of hypotonic induction.
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16
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Xiao S, Wong NK, Li J, Lin Y, Zhang Y, Ma H, Mo R, Zhang Y, Yu Z. Analysis of in situ Transcriptomes Reveals Divergent Adaptive Response to Hyper- and Hypo-Salinity in the Hong Kong Oyster, Crassostrea hongkongensis. Front Physiol 2018; 9:1491. [PMID: 30416453 PMCID: PMC6212563 DOI: 10.3389/fphys.2018.01491] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/02/2018] [Indexed: 02/05/2023] Open
Abstract
Crassostrea hongkongensis, a commercially valuable aquaculture species dwelling in estuaries along the coast of the South China Sea, is remarkable for its eurysalinity traits that enable its successful colonization of diverse osmotic niches ranging from near freshwater to seawater. In order to elucidate how this oyster copes with coastal waters with immense salinity differences, we performed in situ transcriptomic analysis (RNA-seq) to characterize the global expression patterns of oysters distributed across naturally formed salinity gradients in Zhenhai Bay along the northern coast of the South China Sea. Principal component analysis reveals distinct expression profiles of oysters living in the extreme conditions of hypo-salinity and hyper-salinity. Compared with the situation of optimal salinity for oyster growth, hypo-salinity mainly regulated expression of genes involved in FoxO and oxytocin signaling, tight junction and several immune pathways, while hyper-salinity altered gene expression implicated in amino acid metabolism, AMPK and PI3K-AKt signaling pathways, demonstrating the complexity and plasticity of transcriptomic expression underpinning oyster eurysalinity. Furthermore, the expression patterns of several genes correlated with salinity gradients reveals the fine-tuned coordination of molecular networks necessary for adaptive homeostasis in C. hongkongensis. In conclusion, a striking capacity and distinct patterns of transcriptomic expression contribute to eurysalinity adaptation in C. hongkongensis, which provides new mechanistic insights into the adaptive plasticity and resilience of marine mollusks.
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Affiliation(s)
- Shu Xiao
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Nai-Kei Wong
- State Key Discipline of Infection Diseases, Shenzhen Third People's Hospital, Shenzhen, China
| | - Jun Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Yue Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Yuehuan Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Haitao Ma
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Riguan Mo
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Yang Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Ziniu Yu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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17
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Maynard A, Bible JM, Pespeni MH, Sanford E, Evans TG. Transcriptomic responses to extreme low salinity among locally adapted populations of Olympia oyster (Ostrea lurida). Mol Ecol 2018; 27:4225-4240. [PMID: 30193406 DOI: 10.1111/mec.14863] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 08/23/2018] [Accepted: 08/27/2018] [Indexed: 12/26/2022]
Abstract
The Olympia oyster (Ostrea lurida) is a foundation species inhabiting estuaries along the North American west coast. In California estuaries, O. lurida is adapted to local salinity regimes and populations differ in low salinity tolerance. In this study, oysters from three California populations were reared for two generations in a laboratory common garden and subsequently exposed to low salinity seawater. Comparative transcriptomics was then used to understand species-level responses to hyposmotic stress and population-level mechanisms underlying divergent salinity tolerances. Gene expression patterns indicate Olympia oysters are sensitive to hyposmotic stress: All populations respond to low salinity by up-regulating transcripts indicative of protein unfolding, DNA damage and cell cycle arrest after sub-lethal exposure. Among O. lurida populations, transcriptomic profiles differed constitutively and in response to low salinity. Despite two generations in common-garden conditions, transcripts encoding apoptosis modulators were constitutively expressed at significantly different levels in the most tolerant population. Expression of cell death regulators may facilitate cell fate decisions when salinity declines. Following low salinity exposure, oysters from the more tolerant population expressed a small number of mRNAs at significantly higher levels than less tolerant populations. Proteins encoded by these transcripts regulate ciliary activity within the mantle cavity and may function to prolong valve closure and reduce mortality in low salinity seawater. Collectively, gene expression patterns suggest sub-lethal impacts of hyposmotic stress in Olympia oysters are considerable and that even oysters with greater low salinity tolerance may be vulnerable to future freshwater flooding events.
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Affiliation(s)
- Ashley Maynard
- Department of Biological Sciences, California State University East Bay, Hayward, California
| | - Jillian M Bible
- Department of Evolution and Ecology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, California.,Department of Environmental Science and Studies, Washington College, Chestertown, Maryland
| | | | - Eric Sanford
- Department of Evolution and Ecology and Bodega Marine Laboratory, University of California Davis, Bodega Bay, California
| | - Tyler G Evans
- Department of Biological Sciences, California State University East Bay, Hayward, California
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18
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Sivka U, Toplak N, Koren S, Jakše J. De novo transcriptome of the pallial gland of the date mussel ( Lithophaga lithophaga ). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 26:1-9. [DOI: 10.1016/j.cbd.2018.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 11/28/2022]
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19
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Tine M. Evidence of the Complexity of Gene Expression Analysis in Fish Wild Populations. Int J Genomics 2017; 2017:1258396. [PMID: 29201893 PMCID: PMC5672613 DOI: 10.1155/2017/1258396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/24/2017] [Accepted: 09/18/2017] [Indexed: 11/17/2022] Open
Abstract
The present work examines the induction of the band 3 anion transport protein, mitogen-activated protein kinase, and lactate dehydrogenase, respectively related to osmolyte transport, cell volume regulation, and energy production in the gills of two tilapia strains exposed to either freshwater or hypersaline water. Overall, genes showed similar expression patterns between strains. However, a wild population survey across a range of natural habitats and salinities did not reveal the expected patterns. Although significant, the correlations between gene expression and salinity were slightly ambiguous and did not show any link with phenotypic differences in life history traits previously reported between the same populations. The differential expression was also not associated with the population genetic structure inferred from neutral markers. The results suggest that the differential expression observed is not the result of evolutionary forces such as genetic drift or adaptation by natural selection. Instead, it can be speculated that genes responded to various abiotic and biotic stressors, including factors intrinsic to animals. This study provides clear evidence of the complexity of gene expression analysis in wild populations and shows that more attention needs to be paid when selecting candidates as potential biomarkers for monitoring adaptive responses to a specific environmental perturbation.
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Affiliation(s)
- Mbaye Tine
- UFR des Sciences Agronomiques, de l'Aquaculture et des Technologies Alimentaires (UFR S2ATA), Universite Gaston Berger (UGB), Route de Ngallele BP 234, Saint-Louis, Senegal
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20
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Ochsenkühn MA, Röthig T, D’Angelo C, Wiedenmann J, Voolstra CR. The role of floridoside in osmoadaptation of coral-associated algal endosymbionts to high-salinity conditions. SCIENCE ADVANCES 2017; 3:e1602047. [PMID: 28835914 PMCID: PMC5559212 DOI: 10.1126/sciadv.1602047] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 07/19/2017] [Indexed: 05/12/2023]
Abstract
The endosymbiosis between Symbiodinium dinoflagellates and stony corals provides the foundation of coral reef ecosystems. The survival of these ecosystems is under threat at a global scale, and better knowledge is needed to conceive strategies for mitigating future reef loss. Environmental disturbance imposing temperature, salinity, and nutrient stress can lead to the loss of the Symbiodinium partner, causing so-called coral bleaching. Some of the most thermotolerant coral-Symbiodinium associations occur in the Persian/Arabian Gulf and the Red Sea, which also represent the most saline coral habitats. We studied whether Symbiodinium alter their metabolite content in response to high-salinity environments. We found that Symbiodinium cells exposed to high salinity produced high levels of the osmolyte 2-O-glycerol-α-d-galactopyranoside (floridoside), both in vitro and in their coral host animals, thereby increasing their capacity and, putatively, the capacity of the holobiont to cope with the effects of osmotic stress in extreme environments. Given that floridoside has been previously shown to also act as an antioxidant, this osmolyte may serve a dual function: first, to serve as a compatible organic osmolyte accumulated by Symbiodinium in response to elevated salinities and, second, to counter reactive oxygen species produced as a consequence of potential salinity and heat stress.
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Affiliation(s)
- Michael A. Ochsenkühn
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Division of Science and Engineering, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Till Röthig
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Cecilia D’Angelo
- Coral Reef Laboratory/Institute for Life Sciences, Ocean and Earth Science, University of Southampton, Southampton, UK
| | - Jörg Wiedenmann
- Coral Reef Laboratory/Institute for Life Sciences, Ocean and Earth Science, University of Southampton, Southampton, UK
| | - Christian R. Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Corresponding author.
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High throughput sequencing of RNA transcriptomes in Ruditapes philippinarum identifies genes involved in osmotic stress response. Sci Rep 2017; 7:4953. [PMID: 28694531 PMCID: PMC5504028 DOI: 10.1038/s41598-017-05397-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 05/30/2017] [Indexed: 02/03/2023] Open
Abstract
Ruditapes philippinarum, is an economically important marine bivalve species. The ability to cope with low salinity stress is quite important for the survival of aquatic species under natural conditions. In this study, the transcriptional response of the Manila clam to low salinity stress was characterized using RNA sequencing. The transcriptomes of a low salinity-treatment group (FRp1, FRp2), which survived under low salinity stress, and control group (SRp1, SRp2), which was not subjected to low salinity stress, were sequenced with the Illumina HiSeq platform. A total of 196,578 unigenes were generated. GO and KEGG analyses revealed that signal transduction, immune response, cellular component organization or biogenesis, and energy production processes were the most highly enriched pathways among the genes that were differentially expressed under low salinity stress. All these pathways could be assigned to the following biological functions in the low salinity tolerant Manila clam: signal response to low salinity stress, antioxidant response, intracellular free amino acid transport and metabolism, energy production and conversion, cell signaling pathways, and regulation of ionic content and cell volume. In summary, this is the first study using high-throughput sequencing to identify gene targets that could explain osmotic regulation mechanisms under salinity stress in R. philippinarum.
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Abdelrahman H, ElHady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao L, Beck B, Blackburn H, Bosworth B, Buchanan J, Chappell J, Daniels W, Dong S, Dunham R, Durland E, Elaswad A, Gomez-Chiarri M, Gosh K, Guo X, Hackett P, Hanson T, Hedgecock D, Howard T, Holland L, Jackson M, Jin Y, Khalil K, Kocher T, Leeds T, Li N, Lindsey L, Liu S, Liu Z, Martin K, Novriadi R, Odin R, Palti Y, Peatman E, Proestou D, Qin G, Reading B, Rexroad C, Roberts S, Salem M, Severin A, Shi H, Shoemaker C, Stiles S, Tan S, Tang KFJ, Thongda W, Tiersch T, Tomasso J, Prabowo WT, Vallejo R, van der Steen H, Vo K, Waldbieser G, Wang H, Wang X, Xiang J, Yang Y, Yant R, Yuan Z, Zeng Q, Zhou T. Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics 2017; 18:191. [PMID: 28219347 PMCID: PMC5319170 DOI: 10.1186/s12864-017-3557-1] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/06/2017] [Indexed: 12/31/2022] Open
Abstract
Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.
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Affiliation(s)
- Hisham Abdelrahman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Mohamed ElHady
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | | | - Standish Allen
- Aquaculture Genetics & Breeding Technology Center, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA
| | - Rafet Al-Tobasei
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Lisui Bao
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ben Beck
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Harvey Blackburn
- USDA-ARS-NL Wheat & Corn Collections at a Glance GRP, National Animal Germplasm Program, 1111 S. Mason St., Fort Collins, CO, 80521-4500, USA
| | - Brian Bosworth
- USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA
| | - John Buchanan
- Center for Aquaculture Technologies, 8395 Camino Santa Fe, Suite E, San Diego, CA, 92121, USA
| | - Jesse Chappell
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - William Daniels
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Sheng Dong
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Rex Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Evan Durland
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Ahmed Elaswad
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Marta Gomez-Chiarri
- Department of Fisheries, Animal & Veterinary Science, 134 Woodward Hall, 9 East Alumni Avenue, Kingston, RI, 02881, USA
| | - Kamal Gosh
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Perry Hackett
- Department of Genetics, Cell Biology and Development, 5-108 MCB, 420 Washington Avenue SE, Minneapolis, MN, 55455, USA
| | - Terry Hanson
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dennis Hedgecock
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Tiffany Howard
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Leigh Holland
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Molly Jackson
- Taylor Shellfish Farms, 130 SE Lynch RD, Shelton, WA, 98584, USA
| | - Yulin Jin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Karim Khalil
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Thomas Kocher
- Department of Biology, University of Maryland, 2132 Biosciences Research Building, College Park, MD, 20742, USA
| | - Tim Leeds
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Ning Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Lauren Lindsey
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Shikai Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zhanjiang Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
| | - Kyle Martin
- Troutlodge, 27090 Us Highway 12, Naches, WA, 98937, USA
| | - Romi Novriadi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ramjie Odin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Eric Peatman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dina Proestou
- USDA ARS NEA NCWMAC Shellfish Genetics at the University Rhode Island, 469 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Guyu Qin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Benjamin Reading
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695-7617, USA
| | - Caird Rexroad
- USDA ARS Office of National Programs, George Washington Carver Center Room 4-2106, 5601 Sunnyside Avenue, Beltsville, MD, 20705, USA
| | - Steven Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98105, USA
| | - Mohamed Salem
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Andrew Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, 50011, USA
| | - Huitong Shi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Craig Shoemaker
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Sheila Stiles
- USDOC/NOAA, National Marine Fisheries Service, NEFSC, Milford Laboratory, Milford, Connectcut, 06460, USA
| | - Suxu Tan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Kathy F J Tang
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Wilawan Thongda
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Terrence Tiersch
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA, 70820, USA
| | - Joseph Tomasso
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Wendy Tri Prabowo
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Roger Vallejo
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | | | - Khoi Vo
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Geoff Waldbieser
- USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA
| | - Hanping Wang
- Aquaculture Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, OH, 45661, USA
| | - Xiaozhu Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yujia Yang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Roger Yant
- Hybrid Catfish Company, 1233 Montgomery Drive, Inverness, MS, 38753, USA
| | - Zihao Yuan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qifan Zeng
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tao Zhou
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
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Yan L, Su J, Wang Z, Yan X, Yu R, Ma P, Li Y, Du J. Transcriptomic analysis of Crassostrea sikamea × Crassostrea angulata hybrids in response to low salinity stress. PLoS One 2017; 12:e0171483. [PMID: 28182701 PMCID: PMC5300195 DOI: 10.1371/journal.pone.0171483] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/21/2017] [Indexed: 11/17/2022] Open
Abstract
Hybrid oysters often show heterosis in growth rate, weight, survival and adaptability to extremes of salinity. Oysters have also been used as model organisms to study the evolution of host-defense system. To gain comprehensive knowledge about various physiological processes in hybrid oysters under low salinity stress, we performed transcriptomic analysis of gill tissue of Crassostrea sikamea ♀ × Crassostrea angulata♂ hybrid using the deep-sequencing platform Illumina HiSeq. We exploited the high-throughput technique to delineate differentially expressed genes (DEGs) in oysters maintained in hypotonic conditions. A total of 199,391 high quality unigenes, with average length of 644 bp, were generated. Of these 35 and 31 genes showed up- and down-regulation, respectively. Functional categorization and pathway analysis of these DEGs revealed enrichment for immune mechanism, apoptosis, energy metabolism and osmoregulation under low salinity stress. The expression patterns of 41 DEGs in hybrids and their parental species were further analyzed by quantitative real-time PCR (qRT-PCR). This study will serve as a platform for subsequent gene expression analysis regarding environmental stress. Our findings will also provide valuable information about gene expression to better understand the immune mechanism, apoptosis, energy metabolism and osmoregulation in hybrid oysters under low salinity stress.
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Affiliation(s)
- Lulu Yan
- Fisheries College, Ocean University of China, Qingdao, Shandong, China
| | - Jiaqi Su
- The Key Lab of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Zhaoping Wang
- Fisheries College, Ocean University of China, Qingdao, Shandong, China
| | - Xiwu Yan
- Engineering Research Center of Shellfish Culture and Breeding of Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning, China
| | - Ruihai Yu
- Fisheries College, Ocean University of China, Qingdao, Shandong, China
| | - Peizhen Ma
- Fisheries College, Ocean University of China, Qingdao, Shandong, China
| | - Yangchun Li
- Fisheries College, Ocean University of China, Qingdao, Shandong, China
| | - Junpeng Du
- Fisheries College, Ocean University of China, Qingdao, Shandong, China
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24
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Jenny MJ, Walton WC, Payton SL, Powers JM, Findlay RH, O'Shields B, Diggins K, Pinkerton M, Porter D, Crane DM, Tapley J, Cunningham C. Transcriptomic evaluation of the American oyster, Crassostrea virginica, deployed during the Deepwater Horizon oil spill: Evidence of an active hydrocarbon response pathway. MARINE ENVIRONMENTAL RESEARCH 2016; 120:166-181. [PMID: 27564836 DOI: 10.1016/j.marenvres.2016.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 08/01/2016] [Accepted: 08/11/2016] [Indexed: 06/06/2023]
Abstract
Estuarine organisms were impacted by the Deepwater Horizon oil spill which released ∼5 million barrels of crude oil into the Gulf of Mexico in the spring and summer of 2010. Crassostrea virginica, the American oyster, is a keystone species in these coastal estuaries and is routinely used for environmental monitoring purposes. However, very little is known about their cellular and molecular responses to hydrocarbon exposure. In response to the spill, a monitoring program was initiated by deploying hatchery-reared oysters at three sites along the Alabama and Mississippi coast (Grand Bay, MS, Fort Morgan, AL, and Orange Beach, AL). Oysters were deployed for 2-month periods at five different time points from May 2010 to May 2011. Gill and digestive gland tissues were harvested for gene expression analysis and determination of aliphatic and polycyclic aromatic hydrocarbon (PAH) concentrations. To facilitate identification of stress response genes that may be involved in the hydrocarbon response, a nearly complete transcriptome was assembled using Roche 454 and Illumina high-throughput sequencing from RNA samples obtained from the gill and digestive gland tissues of deployed oysters. This effort resulted in the assembly and annotation of 27,227 transcripts comprised of a large assortment of stress response genes, including members of the aryl hydrocarbon receptor (AHR) pathway, Phase I and II biotransformation enzymes, antioxidant enzymes and xenobiotic transporters. From this assembly several potential biomarkers of hydrocarbon exposure were chosen for expression profiling, including the AHR, two cytochrome P450 1A genes (CYP1A-like 1 and CYP1A-like 2), Cu/Zn superoxide dismutase (CuZnSOD), glutathione S-transferase theta (GST theta) and multidrug resistance protein 3 (MRP3). Higher expression levels of GST theta and MRP3 were observed in gill tissues from all three sites during the summer to early fall 2010 deployments. Linear regression analysis indicated a statistically significant relationship between total PAH levels in digestive gland tissue samples with CYP1A-like 2, CuZnSOD, GST theta and MRP3 induction. These observations provide evidence of a potentially conserved AHR pathway in invertebrates and yield new insight into the development of novel biomarkers for use in environmental monitoring activities.
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Affiliation(s)
- Matthew J Jenny
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA.
| | - William C Walton
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Dauphin Island, AL 36528, USA
| | - Samantha L Payton
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - John M Powers
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Robert H Findlay
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Britton O'Shields
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Kirsten Diggins
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Mark Pinkerton
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Danielle Porter
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Daniel M Crane
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Jeffrey Tapley
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Charles Cunningham
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
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Dineshram R, Chandramouli K, Ko GWK, Zhang H, Qian PY, Ravasi T, Thiyagarajan V. Quantitative analysis of oyster larval proteome provides new insights into the effects of multiple climate change stressors. GLOBAL CHANGE BIOLOGY 2016; 22:2054-2068. [PMID: 26990129 DOI: 10.1111/gcb.13249] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 01/26/2016] [Accepted: 01/27/2016] [Indexed: 06/05/2023]
Abstract
The metamorphosis of planktonic larvae of the Pacific oyster (Crassostrea gigas) underpins their complex life-history strategy by switching on the molecular machinery required for sessile life and building calcite shells. Metamorphosis becomes a survival bottleneck, which will be pressured by different anthropogenically induced climate change-related variables. Therefore, it is important to understand how metamorphosing larvae interact with emerging climate change stressors. To predict how larvae might be affected in a future ocean, we examined changes in the proteome of metamorphosing larvae under multiple stressors: decreased pH (pH 7.4), increased temperature (30 °C), and reduced salinity (15 psu). Quantitative protein expression profiling using iTRAQ-LC-MS/MS identified more than 1300 proteins. Decreased pH had a negative effect on metamorphosis by down-regulating several proteins involved in energy production, metabolism, and protein synthesis. However, warming switched on these down-regulated pathways at pH 7.4. Under multiple stressors, cell signaling, energy production, growth, and developmental pathways were up-regulated, although metamorphosis was still reduced. Despite the lack of lethal effects, significant physiological responses to both individual and interacting climate change related stressors were observed at proteome level. The metamorphosing larvae of the C. gigas population in the Yellow Sea appear to have adequate phenotypic plasticity at the proteome level to survive in future coastal oceans, but with developmental and physiological costs.
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Affiliation(s)
- Ramadoss Dineshram
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong Island, Hong Kong SAR, China
| | - Kondethimmanahalli Chandramouli
- Division of Biological, Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences and KAUST Environmental Epigenetic Program (KEEP), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ginger Wai Kuen Ko
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong Island, Hong Kong SAR, China
| | - Huoming Zhang
- Division of Biological, Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences and KAUST Environmental Epigenetic Program (KEEP), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Timothy Ravasi
- Division of Biological, Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences and KAUST Environmental Epigenetic Program (KEEP), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong Island, Hong Kong SAR, China
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High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response. Sci Rep 2016; 6:22687. [PMID: 26940974 PMCID: PMC4778033 DOI: 10.1038/srep22687] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/17/2016] [Indexed: 11/21/2022] Open
Abstract
Increasing evidence suggests that microRNAs post-transcriptionally regulate gene expression and are involved in responses to biotic and abiotic stress. However, the role of miRNAs involved in osmotic plasticity remains largely unknown in marine bivalves. In the present study, we performed low salinity challenge with two Crassostrea species (C. gigas and C. hongkongensis), and conducted high-throughput sequencing of four small RNA libraries constructed from the gill tissues. A total of 202 and 87 miRNAs were identified from C. gigas and C. hongkongensis, respectively. Six miRNAs in C. gigas and two in C. hongkongensis were differentially expressed in response to osmotic stress. The expression profiles of these eight miRNAs were validated by qRT-PCR. Based on GO enrichment and KEGG pathway analysis, genes associated with microtubule-based process and cellular component movement were enriched in both species. In addition, five miRNA-mRNA interaction pairs that showed opposite expression patterns were identified in the C. hongkongensis, Differential expression analysis identified the miRNAs that play important regulatory roles in response to low salinity stress, providing insights into molecular mechanisms that are essential for salinity tolerance in marine bivalves.
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Jiang L, You W, Zhang X, Xu J, Jiang Y, Wang K, Zhao Z, Chen B, Zhao Y, Mahboob S, Al-Ghanim KA, Ke C, Xu P. Construction of the BAC Library of Small Abalone (Haliotis diversicolor) for Gene Screening and Genome Characterization. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:49-56. [PMID: 26438131 DOI: 10.1007/s10126-015-9666-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 09/10/2015] [Indexed: 05/28/2023]
Abstract
The small abalone (Haliotis diversicolor) is one of the most important aquaculture species in East Asia. To facilitate gene cloning and characterization, genome analysis, and genetic breeding of it, we constructed a large-insert bacterial artificial chromosome (BAC) library, which is an important genetic tool for advanced genetics and genomics research. The small abalone BAC library includes 92,610 clones with an average insert size of 120 Kb, equivalent to approximately 7.6× of the small abalone genome. We set up three-dimensional pools and super pools of 18,432 BAC clones for target gene screening using PCR method. To assess the approach, we screened 12 target genes in these 18,432 BAC clones and identified 16 positive BAC clones. Eight positive BAC clones were then sequenced and assembled with the next generation sequencing platform. The assembled contigs representing these 8 BAC clones spanned 928 Kb of the small abalone genome, providing the first batch of genome sequences for genome evaluation and characterization. The average GC content of small abalone genome was estimated as 40.33%. A total of 21 protein-coding genes, including 7 target genes, were annotated into the 8 BACs, which proved the feasibility of PCR screening approach with three-dimensional pools in small abalone BAC library. One hundred fifty microsatellite loci were also identified from the sequences for marker development in the future. The BAC library and clone pools provided valuable resources and tools for genetic breeding and conservation of H. diversicolor.
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Affiliation(s)
- Likun Jiang
- CAFS Key Laboratory of Aquatic Genomics & Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China
- College of Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, 361005, China
| | - Xiaojun Zhang
- Institute of Oceanology, Chinese Academy of Science, Qingdao, 266071, China
| | - Jian Xu
- CAFS Key Laboratory of Aquatic Genomics & Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Yanliang Jiang
- CAFS Key Laboratory of Aquatic Genomics & Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Kai Wang
- CAFS Key Laboratory of Aquatic Genomics & Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Zixia Zhao
- CAFS Key Laboratory of Aquatic Genomics & Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Baohua Chen
- CAFS Key Laboratory of Aquatic Genomics & Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China
- College of Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Yunfeng Zhao
- CAFS Key Laboratory of Aquatic Genomics & Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
- Department of Zoology, GC University, Faisalabad, Pakistan
| | - Khalid A Al-Ghanim
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, 361005, China.
| | - Peng Xu
- CAFS Key Laboratory of Aquatic Genomics & Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
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28
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Guo X, He Y, Zhang L, Lelong C, Jouaux A. Immune and stress responses in oysters with insights on adaptation. FISH & SHELLFISH IMMUNOLOGY 2015; 46:107-119. [PMID: 25989624 DOI: 10.1016/j.fsi.2015.05.018] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 05/08/2015] [Accepted: 05/09/2015] [Indexed: 06/04/2023]
Abstract
Oysters are representative bivalve molluscs that are widely distributed in world oceans. As successful colonizers of estuaries and intertidal zones, oysters are remarkably resilient against harsh environmental conditions including wide fluctuations in temperature and salinity as well as prolonged air exposure. Oysters have no adaptive immunity but can thrive in microbe-rich estuaries as filter-feeders. These unique adaptations make oysters interesting models to study the evolution of host-defense systems. Recent advances in genomic studies including sequencing of the oyster genome have provided insights into oyster's immune and stress responses underlying their amazing resilience. Studies show that the oyster genomes are highly polymorphic and complex, which may be key to their resilience. The oyster genome has a large gene repertoire that is enriched for immune and stress response genes. Thousands of genes are involved in oyster's immune and stress responses, through complex interactions, with many gene families expanded showing high sequence, structural and functional diversity. The high diversity of immune receptors and effectors may provide oysters with enhanced specificity in immune recognition and response to cope with diverse pathogens in the absence of adaptive immunity. Some members of expanded immune gene families have diverged to function at different temperatures and salinities or assumed new roles in abiotic stress response. Most canonical innate immunity pathways are conserved in oysters and supported by a large number of diverse and often novel genes. The great diversity in immune and stress response genes exhibited by expanded gene families as well as high sequence and structural polymorphisms may be central to oyster's adaptation to highly stressful and widely changing environments.
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Affiliation(s)
- Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ 08345, USA.
| | - Yan He
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong 266003, China
| | - Linlin Zhang
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Christophe Lelong
- UMR BOREA, "Biologie des Organismes et Ecosystèmes Aquatiques", MNHN, UPMC, UCBN, CNRS-7208, IRD, Université de Caen Basse-Normandie, Esplanade de la Paix, 14032 Caen, France; Centre de Référence sur l'Huître (CRH), Université de Caen Basse Normandie, Esplanade de la Paix, 14032 Caen, France
| | - Aude Jouaux
- UMR BOREA, "Biologie des Organismes et Ecosystèmes Aquatiques", MNHN, UPMC, UCBN, CNRS-7208, IRD, Université de Caen Basse-Normandie, Esplanade de la Paix, 14032 Caen, France; Centre de Référence sur l'Huître (CRH), Université de Caen Basse Normandie, Esplanade de la Paix, 14032 Caen, France
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Eierman LE, Hare MP. Reef-Specific Patterns of Gene Expression Plasticity in Eastern Oysters (Crassostrea virginica). J Hered 2015; 107:90-100. [DOI: 10.1093/jhered/esv057] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 06/10/2015] [Indexed: 12/30/2022] Open
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The use of -omic tools in the study of disease processes in marine bivalve mollusks. J Invertebr Pathol 2015; 131:137-54. [PMID: 26021714 DOI: 10.1016/j.jip.2015.05.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/09/2015] [Accepted: 05/05/2015] [Indexed: 01/01/2023]
Abstract
Our understanding of disease processes and host-pathogen interactions in model species has benefited greatly from the application of medium and high-throughput genomic, metagenomic, epigenomic, transcriptomic, and proteomic analyses. The rate at which new, low-cost, high-throughput -omic technologies are being developed has also led to an expansion in the number of studies aimed at gaining a better understanding of disease processes in bivalves. This review provides a catalogue of the genetic and -omic tools available for bivalve species and examples of how -omics has contributed to the advancement of marine bivalve disease research, with a special focus in the areas of immunity, bivalve-pathogen interactions, mechanisms of disease resistance and pathogen virulence, and disease diagnosis. The analysis of bivalve genomes and transcriptomes has revealed that many immune and stress-related gene families are expanded in the bivalve taxa examined thus far. In addition, the analysis of proteomes confirms that responses to infection are influenced by epigenetic, post-transcriptional, and post-translational modifications. The few studies performed in bivalves show that epigenetic modifications are non-random, suggesting a role for epigenetics in regulating the interactions between bivalves and their environments. Despite the progress -omic tools have enabled in the field of marine bivalve disease processes, there is much more work to be done. To date, only three bivalve genomes have been sequenced completely, with assembly status at different levels of completion. Transcriptome datasets are relatively easy and inexpensive to generate, but their interpretation will benefit greatly from high quality genome assemblies and improved data analysis pipelines. Finally, metagenomic, epigenomic, proteomic, and metabolomic studies focused on bivalve disease processes are currently limited but their expansion should be facilitated as more transcriptome datasets and complete genome sequences become available for marine bivalve species.
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Picone B, Rhode C, Roodt-Wilding R. Transcriptome profiles of wild and cultured South African abalone, Haliotis midae. Mar Genomics 2015; 20:3-6. [PMID: 25622884 DOI: 10.1016/j.margen.2015.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/13/2015] [Accepted: 01/14/2015] [Indexed: 11/30/2022]
Abstract
This report describes the use of pyrosequencing technologies to generate the first comparative analysis of de novo assembled transcriptome data from cultured and wild specimens of the South African abalone. The transcriptome data and database described here provide a significant genomic resource for abalone research. The data set annotated 11,240 genes, which matched genes with known functions in other species. A large number of transmembrane protein domains (4087) that may indicate a high portion of undiscovered gene receptors were identified. Further, we detected an interesting set of transcription factors (516) that are valuable candidates for participating in regulatory events in developmental (such as cell proliferation and differentiation) and reproductive processes.
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Affiliation(s)
- Barbara Picone
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa.
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Rouvay Roodt-Wilding
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
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Zhang Y, Sun J, Mu H, Li J, Zhang Y, Xu F, Xiang Z, Qian PY, Qiu JW, Yu Z. Proteomic basis of stress responses in the gills of the pacific oyster Crassostrea gigas. J Proteome Res 2014; 14:304-17. [PMID: 25389644 DOI: 10.1021/pr500940s] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The Pacific oyster Crassostrea gigas is one of the dominant sessile inhabitants of the estuarine intertidal zone, which is a physically harsh environment due to the presence of a number of stressors. Oysters have adapted to highly dynamic and stressful environments, but the molecular mechanisms underlying such stress adaptation are largely unknown. In the present study, we examined the proteomic responses in the gills of C. gigas exposed to three stressors (high temperature, low salinity, and aerial exposure) they often encounter in the field. We quantitatively compared the gill proteome profiles using iTRAQ-coupled 2-D LC-MS/MS. There were 3165 identified proteins among which 2379 proteins could be quantified. Heat shock, hyposalinity, and aerial exposure resulted in 50, 15, and 33 differentially expressed gill proteins, respectively. Venn diagram analysis revealed substantial different responses to the three stressors. Only xanthine dehydrogenase/oxidase showed a similar expression pattern across the three stress treatments, suggesting that reduction of ROS accumulation may be a conserved response to these stressors. Heat shock caused significant overexpression of molecular chaperones and production of S-adenosyl-l-methionine, indicating their crucial protective roles against protein denature. In addition, heat shock also activated immune responses, Ca(2+) binding protein expression. By contrast, hyposalinity and aerial exposure resulted in the up-regulation of 3-demethylubiquinone-9 3-methyltransferase, indicating that increase in ubiquinone synthesis may contribute to withstanding both the osmotic and desiccation stress. Strikingly, the majority of desiccation-responsive proteins, including those involved in metabolism, ion transportation, immune responses, DNA duplication, and protein synthesis, were down-regulated, indicating conservation of energy as an important strategy to cope with desiccation stress. There was a high consistency between the expression levels determined by iTRAQ and Western blotting, highlighting the high reproducibility of our proteomic approach and its great value in revealing molecular mechanisms of stress responses.
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Affiliation(s)
- Yang Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
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