1
|
Fu Q, Li Y, Zhang H, Cao M, Zhang L, Gao C, Cai X, Chen D, Yang Z, Li J, Yang N, Li C. Comparative Transcriptome Analysis of Spleen Reveals Potential Regulation of Genes and Immune Pathways Following Administration of Aeromonas salmonicida subsp. masoucida Vaccine in Atlantic Salmon (Salmo salar). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:97-115. [PMID: 35084599 PMCID: PMC8792528 DOI: 10.1007/s10126-021-10089-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Aeromonas salmonicida is a global fish pathogen. Aeromonas salmonicida subsp. masoucida (ASM) is classified as atypical A. salmonicida and caused huge losses to salmonid industry in China. Hence, it is of great significance to develop ASM vaccine and explore its protection mechanism in salmonids. In this regard, we conducted RNA-seq analysis with spleen tissue of Atlantic salmon after ASM vaccination to reveal genes, their expression patterns, and pathways involved in immune protections. In our results, a total of 441.63 million clean reads were obtained, and 389.37 million reads were mapped onto the Atlantic salmon reference genome. In addition, 1125, 2126, 1098, 820, and 1351 genes were significantly up-regulated, and 747, 2626, 818, 254, and 908 genes were significantly down-regulated post-ASM vaccination at 12 h, 24 h, 1 month, 2 months, and 3 months, respectively. Subsequent pathway analysis revealed that many differentially expressed genes (DEGs) following ASM vaccination were involved in cytokine-cytokine receptor interaction (TNFRSF11b, IL-17RA, CCR9, and CXCL11), HTLV-I infection (MR1 and HTLV-1), MAPK signaling pathway (MAPK, IL8, and TNF-α-1), PI3K-Akt signaling pathway (PIK3R3, THBS4, and COL2A1), and TNF signaling pathway (PTGS2, TNFRSF21-l, and CXCL10). Finally, the results of qRT-PCR showed a significant correlation with RNA-seq results, suggesting the reliability of RNA-seq for gene expression analysis. This study provided insights into regulation of gene expression and their involved pathways in Atlantic salmon spleen in responses to vaccine, and set the foundation for further study on the vaccine protective mechanism in Atlantic salmon as well as other teleost species.
Collapse
Affiliation(s)
- Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yuqing Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hao Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lu Zhang
- Shandong Sinder Technology Co., Ltd, Zhucheng, 262200, China
| | - Chengbin Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xin Cai
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Defeng Chen
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ziying Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jie Li
- Key Laboratory of Maricultural Organism Disease Control, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
| |
Collapse
|
2
|
Daane JM, William Detrich H. Adaptations and Diversity of Antarctic Fishes: A Genomic Perspective. Annu Rev Anim Biosci 2021; 10:39-62. [PMID: 34748709 DOI: 10.1146/annurev-animal-081221-064325] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Antarctic notothenioid fishes are the classic example of vertebrate adaptive radiation in a marine environment. Notothenioids diversified from a single common ancestor ∼25 Mya to more than 140 species today, and they represent ∼90% of fish biomass on the continental shelf of Antarctica. As they diversified in the cold Southern Ocean, notothenioids evolved numerous traits, including osteopenia, anemia, cardiomegaly, dyslipidemia, and aglomerular kidneys, that are beneficial or tolerated in their environment but are pathological in humans. Thus, notothenioids are models for understanding adaptive radiations, physiological and biochemical adaptations to extreme environments, and genetic mechanisms of human disease. Since 2014, 16 notothenioid genomes have been published, which enable a first-pass holistic analysis of the notothenioid radiation and the genetic underpinnings of novel notothenioid traits. Here, we review the notothenioid radiation from a genomic perspective and integrate our insights with recent observations from other fish radiations. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Jacob M Daane
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts, USA
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts, USA
| |
Collapse
|
3
|
Joyce W, Axelsson M. Regulation of splenic contraction persists as a vestigial trait in white-blooded Antarctic fishes. JOURNAL OF FISH BIOLOGY 2021; 98:287-291. [PMID: 33090461 DOI: 10.1111/jfb.14579] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/30/2020] [Accepted: 10/05/2020] [Indexed: 06/11/2023]
Abstract
In fishes, the spleen can function as an important reservoir for red blood cells (RBCs), which, following splenic contraction, may be released into the circulation to increase haematocrit during energy-demanding activities. This trait is particularly pronounced in red-blooded Antarctic fishes in which the spleen can sequester a large proportion of RBCs during rest, thereby reducing blood viscosity, which may serve as an adaptation to life in cold environments. In one species, Pagothenia borchgrevinki, it has previously been shown that splenic contraction primarily depends on cholinergic stimulation. The aim of the present study was to investigate the regulation of splenic contraction in five other Antarctic fish species, three red-blooded notothenioids (Dissostichus mawsoni Norman, 1937, Gobionotothen gibberifrons Lönnberg, 1905, Notothenia coriiceps Richardson 1844) and two white-blooded "icefish" (Chaenocephalus aceratus Lönnberg, 1906 and Champsocephalus gunnari Lönnberg, 1905), which lack haemoglobin and RBCs, but nevertheless possess a large spleen. In all species, splenic strips constricted in response to both cholinergic (carbachol) and adrenergic (adrenaline) agonists. Surprisingly, in the two species of icefish, the spleen responded with similar sensitivity to red-blooded species, despite contraction being of little obvious benefit for releasing RBCs into the circulation. Although the icefish lineage lost functional haemoglobin before diversifying over the past 7.8-4.8 millions of years, they retain the capacity to contract the spleen, likely as a vestige inherited from their red-blooded ancestors.
Collapse
Affiliation(s)
- William Joyce
- Department of Biology - Zoophysiology, Aarhus University, Aarhus, Denmark
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Axelsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
4
|
Chatzidimitriou E, Bisaccia P, Corrà F, Bonato M, Irato P, Manuto L, Toppo S, Bakiu R, Santovito G. Copper/Zinc Superoxide Dismutase from the Crocodile Icefish Chionodraco hamatus: Antioxidant Defense at Constant Sub-Zero Temperature. Antioxidants (Basel) 2020; 9:antiox9040325. [PMID: 32316382 PMCID: PMC7222407 DOI: 10.3390/antiox9040325] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 12/11/2022] Open
Abstract
In the present study, we describe the purification and molecular characterization of Cu,Zn superoxide dismutase (SOD) from Chionodraco hamatus, an Antarctic teleost widely distributed in many areas of the Ross Sea that plays a pivotal role in the Antarctic food chain. The primary sequence was obtained using biochemical and molecular biology approaches and compared with Cu,Zn SODs from other organisms. Multiple sequence alignment using the amino acid sequence revealed that Cu,Zn SOD showed considerable sequence similarity with its orthologues from various vertebrate species, but also some specific substitutions directly linked to cold adaptation. Phylogenetic analyses presented the monophyletic status of Antartic Teleostei among the Perciformes, confirming the erratic differentiation of these proteins and concurring with the theory of the "unclock-like" behavior of Cu,Zn SOD evolution. Expression of C. hamatus Cu,Zn SOD at both the mRNA and protein levels were analyzed in various tissues, highlighting the regulation of gene expression related to environmental stress conditions and also animal physiology. The data presented are the first on the antioxidant enzymes of a fish belonging to the Channichthyidae family and represent an important starting point in understanding the antioxidant systems of these organisms that are subject to constant risk of oxidative stress.
Collapse
Affiliation(s)
- Evangelia Chatzidimitriou
- Institute of Natural Resource Sciences, ZHAW Zurich University of Applied Sciences, 8820 Wädenswil, Switzerland;
| | - Paola Bisaccia
- Department of Biology, University of Padova, 35131 Padova, Italy; (P.B.); (F.C.); (M.B.); (P.I.)
| | - Francesca Corrà
- Department of Biology, University of Padova, 35131 Padova, Italy; (P.B.); (F.C.); (M.B.); (P.I.)
| | - Marco Bonato
- Department of Biology, University of Padova, 35131 Padova, Italy; (P.B.); (F.C.); (M.B.); (P.I.)
| | - Paola Irato
- Department of Biology, University of Padova, 35131 Padova, Italy; (P.B.); (F.C.); (M.B.); (P.I.)
| | - Laura Manuto
- Department of Molecular Medicine, University of Padova, 35131 Padova, Italy; (L.M.); (S.T.)
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, 35131 Padova, Italy; (L.M.); (S.T.)
- CRIBI Biotech Centre, University of Padova, 35131 Padova, Italy
| | - Rigers Bakiu
- Department of Aquaculture and Fisheries, Agricultural University of Tirana, 1000 Tiranë, Albania;
| | - Gianfranco Santovito
- Department of Biology, University of Padova, 35131 Padova, Italy; (P.B.); (F.C.); (M.B.); (P.I.)
- Correspondence:
| |
Collapse
|
5
|
Allais L, Zhao C, Fu M, Hu J, Qin JG, Qiu L, Ma Z. Nutrition and water temperature regulate the expression of heat-shock proteins in golden pompano larvae (Trachinotus ovata, Limmaeus 1758). FISH PHYSIOLOGY AND BIOCHEMISTRY 2019; 45:485-497. [PMID: 30397841 DOI: 10.1007/s10695-018-0578-x] [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: 04/07/2018] [Accepted: 10/03/2018] [Indexed: 06/08/2023]
Abstract
Understanding fish larval development is of a great interest for aquaculture production efficiency. Identifying possible indicators of fish larvae stress could improve the production and limit the mortality rate that larval stage is subjected to. Heat-shock proteins (HSPs) and heat-shock factors (HSFs) are well known as indicators of response to many kinds of stressor (e.g., environmental, morphological, or pathological changes). In this study, golden pompano larvae were raised at different temperatures (23 °C, 26 °C, and 29 °C), as well as three different diets (Artemia nauplii unenriched, Artemia nauplii enriched with Nannochloropsis sp., and Artemia nauplii enriched with Algamac 3080), and the expression of HSP60, HSP70, HSF1, HSP2, and GRP94 were monitored. While stress genes were widely expressed in the larval tissues, HSP60 and HSP70 were principally from the gills and heart; HSF1 principally from the muscle, brain, and heart; and GRP94 principally from the head kidney and spleen. Golden pompano larvae were found to be more sensitive to thermal changes at later larval stage, and 29 °C was showed to likely be the best condition for golden pompano larval development. Nannochloropsis sp.-enriched Artemia nauplii treatment was found to be the most appropriate feed type with moderate relative expressions of HSP60, HSP70, HSF1, HSF2, and GRP94.
Collapse
Affiliation(s)
- Laetitia Allais
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya, 572018, China
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia
| | - Chao Zhao
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya, 572018, China
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Guangzhou, 510300, People's Republic of China
| | - Mingjun Fu
- College of Life Science, Longyan University, Longyan, 364012, Fujian, China
| | - Jing Hu
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya, 572018, China
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Guangzhou, 510300, People's Republic of China
| | - Jian G Qin
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia
| | - Lihua Qiu
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya, 572018, China
| | - Zhenhua Ma
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya, 572018, China.
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia.
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Guangzhou, 510300, People's Republic of China.
| |
Collapse
|
6
|
Gu L, Xia C. Cluster expansion of apolipoprotein D (ApoD) genes in teleost fishes. BMC Evol Biol 2019; 19:9. [PMID: 30621595 PMCID: PMC6325677 DOI: 10.1186/s12862-018-1323-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/11/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene and genome duplication play important roles in the evolution of gene function. Compared to individual duplicated genes, gene clusters attract particular attention considering their frequent associations with innovation and adaptation. Here, we report for the first time the expansion of the apolipoprotein D (ApoD) ligand-transporter genes in a cluster manner specific to teleost fishes. RESULTS Based on comparative genomic and transcriptomic analyses, protein 3D structure comparison, positive selection detection and breakpoints detection, the single ApoD gene in the ancestor expanded into two clusters following a dynamic evolutionary pattern in teleost fishes. Orthologous genes show conserved expression patterns, whereas lineage-specific duplicated genes show tissue-specific expression patterns and even evolve new gene expression profiles. Positive selection occurred in branches before and after gene duplication, especially for lineage-specific duplicated genes. Cluster analyses based on protein 3D structure comparisons, especially comparisons of the four loops at the opening side, show gene duplication-segregating patterns. Duplicated ApoD genes are predicted to be associated with forkhead transcription factors and MAPK genes. ApoD clusters are located next to the breakpoints of genome rearrangements. CONCLUSIONS Here, we report the expansion of ApoD genes specific to teleost fishes in a cluster manner for the first time. Neofunctionalization and subfunctionalization were observed at both the protein and expression levels after duplication. Evidence from different aspects-i.e., abnormal expression-induced disease in humans, fish-specific expansion, predicted associations with forkhead transcription factors and MAPK genes, specific expression patterns in tissues related to sexual selection and adaptation, duplicated genes under positive selection and their location next to the breakpoints of genome rearrangements-suggests the potentially advantageous roles of ApoD genes in teleost fishes. The cluster expansion of ApoD genes specific to teleost fishes provides thus an ideal evo-devo model for studying gene duplication, cluster maintenance and new gene function emergence.
Collapse
Affiliation(s)
- Langyu Gu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Canwei Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| |
Collapse
|
7
|
Berthelot C, Clarke J, Desvignes T, William Detrich H, Flicek P, Peck LS, Peters M, Postlethwait JH, Clark MS. Adaptation of Proteins to the Cold in Antarctic Fish: A Role for Methionine? Genome Biol Evol 2019; 11:220-231. [PMID: 30496401 PMCID: PMC6336007 DOI: 10.1093/gbe/evy262] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2018] [Indexed: 12/25/2022] Open
Abstract
The evolution of antifreeze glycoproteins has enabled notothenioid fish to flourish in the freezing waters of the Southern Ocean. Whereas successful at the biodiversity level to life in the cold, paradoxically at the cellular level these stenothermal animals have problems producing, folding, and degrading proteins at their ambient temperatures of -1.86 °C. In this first multi-species transcriptome comparison of the amino acid composition of notothenioid proteins with temperate teleost proteins, we show that, unlike psychrophilic bacteria, Antarctic fish provide little evidence for the mass alteration of protein amino acid composition to enhance protein folding and reduce protein denaturation in the cold. The exception was the significant overrepresentation of positions where leucine in temperate fish proteins was replaced by methionine in the notothenioid orthologues. We hypothesize that these extra methionines have been preferentially assimilated into the genome to act as redox sensors in the highly oxygenated waters of the Southern Ocean. This redox hypothesis is supported by analyses of notothenioids showing enrichment of genes associated with responses to environmental stress, particularly reactive oxygen species. So overall, although notothenioid fish show cold-associated problems with protein homeostasis, they may have modified only a selected number of biochemical pathways to work efficiently below 0 °C. Even a slight warming of the Southern Ocean might disrupt the critical functions of this handful of key pathways with considerable impacts for the functioning of this ecosystem in the future.
Collapse
Affiliation(s)
- Camille Berthelot
- Laboratoire Dynamique et Organisation des Génomes (Dyogen), Institut de Biologie de l'Ecole Normale Supérieure – UMR 8197, INSERM U1024, Paris Cedex 05, France
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, United Kingdom
| | | | - H William Detrich
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Lloyd S Peck
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Michael Peters
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University
| | | | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| |
Collapse
|
8
|
Jacobson G, Muncaster S, Mensink K, Forlenza M, Elliot N, Broomfield G, Signal B, Bird S. Omics and cytokine discovery in fish: Presenting the Yellowtail kingfish (Seriola lalandi) as a case study. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:63-76. [PMID: 28416435 DOI: 10.1016/j.dci.2017.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/01/2017] [Accepted: 04/01/2017] [Indexed: 06/07/2023]
Abstract
A continued programme of research is essential to overcome production bottlenecks in any aquacultured fish species. Since the introduction of genetic and molecular techniques, the quality of immune research undertaken in fish has greatly improved. Thousands of species specific cytokine genes have been discovered, which can be used to conduct more sensitive studies to understand how fish physiology is affected by aquaculture environments or disease. Newly available transcriptomic technologies, make it increasingly easier to study the immunogenetics of farmed species for which little data exists. This paper reviews how the application of transcriptomic procedures such as RNA Sequencing (RNA-Seq) can advance fish research. As a case study, we present some preliminary findings using RNA-Seq to identify cytokine related genes in Seriola lalandi. These will allow in-depth investigations to understand the immune responses of these fish in response to environmental change or disease and help in the development of therapeutic approaches.
Collapse
Affiliation(s)
- Gregory Jacobson
- Molecular Genetics, Department of Biological Sciences, School of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Simon Muncaster
- School Applied Science, Bay of Plenty Polytechnic, 70 Windermere Dr, Poike, Tauranga 3112, New Zealand
| | - Koen Mensink
- Cell Biology and Immunology Group, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Maria Forlenza
- Cell Biology and Immunology Group, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Nick Elliot
- Molecular Genetics, Department of Biological Sciences, School of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Grant Broomfield
- Molecular Genetics, Department of Biological Sciences, School of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Beth Signal
- Molecular Genetics, Department of Biological Sciences, School of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Steve Bird
- Molecular Genetics, Department of Biological Sciences, School of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.
| |
Collapse
|
9
|
Papetti C, Lucassen M, Pörtner HO. Integrated studies of organismal plasticity through physiological and transcriptomic approaches: examples from marine polar regions. Brief Funct Genomics 2016; 15:365-72. [PMID: 27345433 DOI: 10.1093/bfgp/elw024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transcriptomic methods are now widely used in functional genomic research. The vast amount of information received from these studies comes along with the challenge of developing a precise picture of the functional consequences and the characteristic regulatory mechanisms. Here we assess recent studies in marine species and their adaptation to polar (and seasonal) cold and explore how they have been able to draw reliable conclusions from transcriptomic patterns on functional consequences in the organisms. Our analysis indicates that the interpretation of transcriptomic data suffers from insufficient understanding of the consequences for whole organism performance and fitness and comes with the risk of supporting only preliminary and superficial statements.We propose that the functional understanding of transcriptomic data may be improved by their tighter integration into overarching physiological concepts that support the more specific interpretation of the 'omics' data and, at the same time, can be developed further through embedding the transcriptomic phenomena observed. Such possibilities have not been fully exploited.In the context of thermal adaptation and limitation, we explore preliminary evidence that the concept of oxygen and capacity limited thermal tolerance (OCLTT) may provide sufficient complexity to guide the integration of such data and the development of associated functional hypotheses. At the same time, we identify a lack of methodological approaches linking genes and function to higher levels of integration, in terms of organism and ecosystem functioning, at temporal and geographical scales, to support more reliable conclusions and be predictive with respect to the effects of global changes.
Collapse
|
10
|
Papetti C, Harms L, Jürgens J, Sandersfeld T, Koschnick N, Windisch HS, Knust R, Pörtner HO, Lucassen M. Microsatellite markers for the notothenioid fish Lepidonotothen nudifrons and two congeneric species. BMC Res Notes 2016; 9:238. [PMID: 27112435 PMCID: PMC4845337 DOI: 10.1186/s13104-016-2039-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 04/14/2016] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND Loss of genetic variability due to environmental changes, limitation of gene flow between pools of individuals or putative selective pressure at specific markers, were previously documented for Antarctic notothenioid fish species. However, so far no studies were performed for the Gaudy notothen Lepidonotothen nudifrons. Starting from a species-specific spleen transcriptome library, we aimed at isolating polymorphic microsatellites (Type I; i.e. derived from coding sequences) suitable to quantify the genetic variability in this species, and additionally to assess the population genetic structure and demography in nototheniids. RESULTS We selected 43,269 transcripts resulting from a MiSeq sequencer run, out of which we developed 19 primer pairs for sequences containing microsatellite repeats. Sixteen loci were successfully amplified in L. nudifrons. Eleven microsatellites were polymorphic and allele numbers per locus ranged from 2 to 17. In addition, we amplified loci identified from L. nudifrons in two other congeneric species (L. squamifrons and L. larseni). Thirteen loci were highly transferable to the two congeneric species. Differences in polymorphism among species were detected. CONCLUSIONS Starting from a transcriptome of a non-model organism, we were able to identify promising polymorphic nuclear markers that are easily transferable to other closely related species. These markers can be a key instrument to monitor the genetic structure of the three Lepidonotothen species if genotyped in larger population samples. When compared with anonymous loci isolated in other notothenioids, i.e. Type II (isolated from genomic libraries), they offer the possibility to test how the effects of occurring environmental change influence the population genetic structure in each species and subsequently the composition of the entire ecosystem.
Collapse
Affiliation(s)
- Chiara Papetti
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, 27570, Germany.
| | - Lars Harms
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, 27570, Germany
| | - Jutta Jürgens
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, 27570, Germany
| | - Tina Sandersfeld
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, 27570, Germany.,University of Bremen, BreMarE-Bremen Marine Ecology, Leobener Str. NW2, 28359, Bremen, Germany
| | - Nils Koschnick
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, 27570, Germany
| | - Heidrun Sigrid Windisch
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, 27570, Germany.,Institute for Cell Biology and Zoology, Heinrich-Heine-University, Universitätsstrasse 1, Düsseldorf, 40225, Germany
| | - Rainer Knust
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, 27570, Germany
| | - Hans-Otto Pörtner
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, 27570, Germany
| | - Magnus Lucassen
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, 27570, Germany
| |
Collapse
|
11
|
Lee X, Yi Y, Weng S, Zeng J, Zhang H, He J, Dong C. Transcriptomic analysis of koi (Cyprinus carpio) spleen tissue upon cyprinid herpesvirus 3 (CyHV3) infection using next generation sequencing. FISH & SHELLFISH IMMUNOLOGY 2016; 49:213-24. [PMID: 26690666 DOI: 10.1016/j.fsi.2015.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/07/2015] [Accepted: 12/08/2015] [Indexed: 05/18/2023]
Abstract
Cyprinid Herpesvirus 3 (CyHV-3) can infect and specifically cause a huge economic loss in both common carp (Cyprinus carpio) and its ornamental koi variety. The molecular mechanisms underlying CyHV-3 infection are not well understood. In this study, koi spleen tissues of both mock and CyHV-3 infection groups were collected, and high-throughput sequencing technology was used to analyze the differentially expressed genes (DEGs) at the transcriptome level. A total of 105,356,188 clean reads from two libraries were obtained. After the de novo assembly of the transcripts, 129,314 unigenes were generated. Of these unigenes, 70,655 unigenes were matched to the known proteins in the database, while 2190 unigenes were predicted by ESTScan software. Comparing the infection group to the mock group, a total of 23,029 significantly differentially expressed unigenes were identified, including 10,493 up-regulated DEGs and 12,536 down-regulated DEGs. GO (Gene Ontology) annotation and functional enrichment analysis indicated that all of the DEGs were annotated into GO terms in three main GO categories: biological process, cellular component and molecular function. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis of the DEGs showed that a total of 12,002 DEG unigenes were annotated into 256 pathways classified into 6 main categories. Additionally, 20 differentially expressed genes were validated by quantitative real-time PCR. As the first report of a transcriptome analysis of koi carp with CyHV-3 infection, the data presented here provide knowledge of the innate immune response against CyHV-3 in koi carp and useful data for further research of the molecular mechanism of CyHV-3 infection.
Collapse
Affiliation(s)
- Xuezhu Lee
- State Key Laboratory for Bio-control / MOE Key Laboratory of Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Yang Yi
- State Key Laboratory for Bio-control / MOE Key Laboratory of Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Shaoping Weng
- State Key Laboratory for Bio-control / MOE Key Laboratory of Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jie Zeng
- State Key Laboratory for Bio-control / MOE Key Laboratory of Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Hetong Zhang
- State Key Laboratory for Bio-control / MOE Key Laboratory of Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jianguo He
- State Key Laboratory for Bio-control / MOE Key Laboratory of Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China.
| | - Chuanfu Dong
- State Key Laboratory for Bio-control / MOE Key Laboratory of Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou 510275, PR China.
| |
Collapse
|
12
|
Papetti C, Windisch HS, La Mesa M, Lucassen M, Marshall C, Lamare MD. Non-Antarctic notothenioids: Past phylogenetic history and contemporary phylogeographic implications in the face of environmental changes. Mar Genomics 2015; 25:1-9. [PMID: 26610933 DOI: 10.1016/j.margen.2015.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/12/2015] [Accepted: 11/12/2015] [Indexed: 12/31/2022]
Abstract
The non-Antarctic Notothenioidei families, Bovichtidae, Pseudaphritidae and Eleginopsidae, diverged early from the main notothenioid lineage. They are important in clarifying the early evolutionary processes that triggered notothenioid evolution in the Antarctic. The early-diverged group represents 8% of all notothenioid species and never established themselves on the Antarctic shelf. Most attention has been paid to the Antarctic notothenioids and their limited physiological tolerance to climate change and increased temperatures. In this review, we discuss key life history traits that are characteristic of the non-Antarctic early-diverged notothenioid taxa as well as the genetic resources and population differentiation information available for this group. We emphasise the population fitness and dynamics of these species and indicate how resource management and conservation of the group can be strengthened through an integrative approach. Both Antarctic waters and the non-Antarctic regions face rapid temperature rises combined with strong anthropogenic exploitation. While it is expected that early-diverged notothenioid species may have physiological advantages over high Antarctic species, it is difficult to predict how climate changes might alter the geographic range, behaviour, phenology and ultimately genetic variability of these species. It is possible, however, that their high degree of endemism and dependence on local environmental specificities to complete their life cycles might enhance their vulnerability.
Collapse
Affiliation(s)
- Chiara Papetti
- Section of Integrative Ecophysiology, Alfred-Wegener-Institute for Polar and Marine Research, Am Handelshafen 12, Bremerhaven 27570, Germany.
| | - Heidrun S Windisch
- Institute for Cell Biology and Zoology, Heinrich-Heine-University, Universitätsstrasse 1, Düsseldorf 40225, Germany.
| | - Mario La Mesa
- ISMAR-CNR, Istituto di Scienze Marine, Sede di Ancona, Largo Fiera della Pesca, 60125 Ancona, Italy.
| | - Magnus Lucassen
- Section of Integrative Ecophysiology, Alfred-Wegener-Institute for Polar and Marine Research, Am Handelshafen 12, Bremerhaven 27570, Germany.
| | - Craig Marshall
- Department of Biochemistry and Genetics, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - Miles D Lamare
- Department of Marine Sciences, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| |
Collapse
|