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Sultana M, Tayyab M, Parveen S, Hussain M, Shafique L. Genetic characterization, structural analysis, and detection of positive selection in small heat shock proteins of Cypriniformes and Clupeiformes. FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:843-864. [PMID: 38587724 DOI: 10.1007/s10695-024-01337-2] [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: 09/09/2023] [Accepted: 03/22/2024] [Indexed: 04/09/2024]
Abstract
In the current investigation, a total of 42 full-length, non-redundant small heat shock proteins (sHsp) were detected in Cyprinus carpio, Labeo rohita, Danio rerio, Salmo salar, Oncorhynchus mykiss, and Clupea harengus. The sHsp genes were classified into three groups based on phylogenetic analysis. All the sHsps were shown to have higher aliphatic index values, which is an indication that these proteins are more thermally stable. The hydrophilic nature of sHsps was deduced from the fact that all fish species had negative GRAVY scores. In all of the representative fish species, sHsp genes were assigned to distinct chromosomes in an inconsistent and unequal manner. Segmental duplications are the main events that have contributed to the expansion of the sHsp genes in all species. We were also able to determine the selective pressure that was placed on particular codons and discovered several significant coding sites within the coding region of sHsps. Eventually, diversifying positive selection was found to be connected with evolutionary changes in sHsp proteins, which showed that gene evolution controlled the fish adaption event in response to environmental conditions. Clarification of the links between sHsps and environmental stress in fish will be achieved through rigorous genomic comparison, which will also yield substantial new insights.
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Affiliation(s)
- Mehwish Sultana
- Department of Zoology, Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Muhammad Tayyab
- Department of Zoology, Wildlife & Fisheries, University of Agriculture, Faisalabad, 38000, Punjab, Pakistan
| | - Shakeela Parveen
- Department of Zoology, Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan.
- Department of Zoology, Wildlife & Fisheries, University of Agriculture, Faisalabad, 38000, Punjab, Pakistan.
| | - Muhammad Hussain
- Department of Veterinary Science, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Laiba Shafique
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi, 535011, People's Republic of China.
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Yan W, Liu X, Wang X. The heat shock protein 20 gene family in large yellow croaker (Larimichthys crocea): Identification, phylogenetic relationships, expression analyses. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 264:106700. [PMID: 37837866 DOI: 10.1016/j.aquatox.2023.106700] [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: 08/14/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 10/16/2023]
Abstract
Large yellow croaker (Larimichthys crocea) is an economically important fish in China, but its aquaculture industry has been threatened by both biotic and abiotic stressors such as hypoxia and pathogens. In the current study, hsp20 genes were identified and analyzed systematically for the first time from the genome of large yellow croaker, and their roles in hypoxia response and Aeromonas hydrophila, Pseudomonas plecoglossicida infection were investigated. Herein, 11 hsp20 genes were identified and annotated, phylogenetic analysis and selection pressure analysis showed that the hsp20 genes were evolutionarily-constrained and their function was conserved among fishes. Besides, we observed the expression patterns of the hsp20 genes under hypoxia and two pathogens' stress. In brief, seven, four, seven genes responded to hypoxia stress, A. hydrophila infection and P. plecoglossicida challenge, respectively, which indicated that they were involved in hypoxia and disease responses. Furthermore, pathogen- and time-specific pattern was observed after A. hydrophila and P. plecoglossicida infection whereas tissue-specific pattern was observed after hypoxia exposure, revealing that hsp20 genes showed differential functions in response to hypoxia and immune stress. Taken together, these results provided preliminary information for future analysis of the roles of hsp20 genes in both biotic and abiotic stress response in fish.
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Affiliation(s)
- Weijie Yan
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, China
| | - Xubo Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China; National Engineering Research Laboratory of marine biotechnology and Engineering, Ningbo University, China.
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Xie H, Hu J, Wang Y, Wang X. Identification of the matrix metalloproteinase (MMP) gene family in Japanese flounder (Paralichthys olivaceus): Involved in immune response regulation to temperature stress and Edwardsiella tarda infection. FISH & SHELLFISH IMMUNOLOGY 2023:108878. [PMID: 37271328 DOI: 10.1016/j.fsi.2023.108878] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
Abstract
The Matrix metalloproteinase (MMP) gene family is responsible for regulating the degradation of Extra Cellular Matrix (ECM) proteins, which are important for physiological processes such as wound healing, tissue remodeling, and stress response. Although MMPs have been studied in many species, their role in immune response in Japanese flounder (Paralichthys olivaceus) is still not fully understood. This study conducted a comprehensive analysis of MMPs in flounder, including gene structures, evolutionary relationships, conserved domains, molecular evolution, and expression patterns. Analysis revealed that MMP genes could be grouped into 17 subfamilies and were evolutionarily conserved and functionally-constrained. Meanwhile, MMP genes were found to express in different embryonic and larval stages and might play the role of sentinel in healthy tissues. Furthermore, expression profiling showed that MMPs had diverse functions in environmental stress, with 60% (9/15) and 73% (11/15) of MMPs showing differential expression patterns under temperature stress and Edwardsiella tarda (E. tarda) infection, respectively. These findings provide a useful resource for understanding the immune functions of MMP genes in Japanese flounder.
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Affiliation(s)
- Huihui Xie
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, China; Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Key Laboratory of Green Mariculture (Co-construction By Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, China
| | - Jiabao Hu
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, China; Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Key Laboratory of Green Mariculture (Co-construction By Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, China; School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China
| | - Yajun Wang
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, China; Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Key Laboratory of Green Mariculture (Co-construction By Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, China.
| | - Xubo Wang
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, China; Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Key Laboratory of Green Mariculture (Co-construction By Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, China.
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Popovic I, Riginos C. Comparative genomics reveals divergent thermal selection in warm‐ and cold‐tolerant marine mussels. Mol Ecol 2020; 29:519-535. [DOI: 10.1111/mec.15339] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Iva Popovic
- School of Biological Sciences University of Queensland St Lucia Qld Australia
| | - Cynthia Riginos
- School of Biological Sciences University of Queensland St Lucia Qld Australia
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Liu K, Hao X, Wang Q, Hou J, Lai X, Dong Z, Shao C. Genome-wide identification and characterization of heat shock protein family 70 provides insight into its divergent functions on immune response and development of Paralichthys olivaceus. PeerJ 2019; 7:e7781. [PMID: 31737440 PMCID: PMC6855204 DOI: 10.7717/peerj.7781] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 08/28/2019] [Indexed: 01/16/2023] Open
Abstract
Flatfish undergo extreme morphological development and settle to a benthic in the adult stage, and are likely to be more susceptible to environmental stress. Heat shock proteins 70 (hsp70) are involved in embryonic development and stress response in metazoan animals. However, the evolutionary history and functions of hsp70 in flatfish are poorly understood. Here, we identified 15 hsp70 genes in the genome of Japanese flounder (Paralichthys olivaceus), a flatfish endemic to northwestern Pacific Ocean. Gene structure and motifs of the Japanese flounder hsp70 were conserved, and there were few structure variants compared to other fish species. We constructed a maximum likelihood tree to understand the evolutionary relationship of the hsp70 genes among surveyed fish. Selection pressure analysis suggested that four genes, hspa4l, hspa9, hspa13, and hyou1, showed signs of positive selection. We then extracted transcriptome data on the Japanese flounder with Edwardsiella tarda to induce stress, and found that hspa9, hspa12b, hspa4l, hspa13, and hyou1 were highly expressed, likely to protect cells from stress. Interestingly, expression patterns of hsp70 genes were divergent in different developmental stages of the Japanese flounder. We found that at least one hsp70 gene was always highly expressed at various stages of embryonic development of the Japanese flounder, thereby indicating that hsp70 genes were constitutively expressed in the Japanese flounder. Our findings provide basic and useful resources to better understand hsp70 genes in flatfish.
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Affiliation(s)
- Kaiqiang Liu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resource, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, QingDao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, QingDao, China
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, China
| | - Xiancai Hao
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resource, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, QingDao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, QingDao, China
| | - Qian Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resource, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, QingDao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, QingDao, China
| | - Jilun Hou
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Beidaihe, China
| | - Xiaofang Lai
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, China
| | - Zhiguo Dong
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, China
| | - Changwei Shao
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resource, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, QingDao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, QingDao, China
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Bates SS, Hubbard KA, Lundholm N, Montresor M, Leaw CP. Pseudo-nitzschia, Nitzschia, and domoic acid: New research since 2011. HARMFUL ALGAE 2018; 79:3-43. [PMID: 30420013 DOI: 10.1016/j.hal.2018.06.001] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 05/11/2023]
Abstract
Some diatoms of the genera Pseudo-nitzschia and Nitzschia produce the neurotoxin domoic acid (DA), a compound that caused amnesic shellfish poisoning (ASP) in humans just over 30 years ago (December 1987) in eastern Canada. This review covers new information since two previous reviews in 2012. Nitzschia bizertensis was subsequently discovered to be toxigenic in Tunisian waters. The known distribution of N. navis-varingica has expanded from Vietnam to Malaysia, Indonesia, the Philippines and Australia. Furthermore, 15 new species (and one new variety) of Pseudo-nitzschia have been discovered, bringing the total to 52. Seven new species were found to produce DA, bringing the total of toxigenic species to 26. We list all Pseudo-nitzschia species, their ability to produce DA, and show their global distribution. A consequence of the extended distribution and increased number of toxigenic species worldwide is that DA is now found more pervasively in the food web, contaminating new marine organisms (especially marine mammals), affecting their physiology and disrupting ecosystems. Recent findings highlight how zooplankton grazers can induce DA production in Pseudo-nitzschia and how bacteria interact with Pseudo-nitzschia. Since 2012, new discoveries have been reported on physiological controls of Pseudo-nitzschia growth and DA production, its sexual reproduction, and infection by an oomycete parasitoid. Many advances are the result of applying molecular approaches to discovering new species, and to understanding the population genetic structure of Pseudo-nitzschia and mechanisms used to cope with iron limitation. The availability of genomes from three Pseudo-nitzschia species, coupled with a comparative transcriptomic approach, has allowed advances in our understanding of the sexual reproduction of Pseudo-nitzschia, its signaling pathways, its interactions with bacteria, and genes involved in iron and vitamin B12 and B7 metabolism. Although there have been no new confirmed cases of ASP since 1987 because of monitoring efforts, new blooms have occurred. A massive toxic Pseudo-nitzschia bloom affected the entire west coast of North America during 2015-2016, and was linked to a 'warm blob' of ocean water. Other smaller toxic blooms occurred in the Gulf of Mexico and east coast of North America. Knowledge gaps remain, including how and why DA and its isomers are produced, the world distribution of potentially toxigenic Nitzschia species, the prevalence of DA isomers, and molecular markers to discriminate between toxigenic and non-toxigenic species and to discover sexually reproducing populations in the field.
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Affiliation(s)
- Stephen S Bates
- Fisheries and Oceans Canada, Gulf Fisheries Centre, P.O. Box 5030, Moncton, New Brunswick, E1C 9B6, Canada.
| | - Katherine A Hubbard
- Fish and Wildlife Research Institute (FWRI), Florida Fish and Wildlife Conservation Commission (FWC), 100 Eighth Avenue SE, St. Petersburg, FL 33701 USA; Woods Hole Center for Oceans and Human Health, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA, 02543 USA
| | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83S, DK-1307 Copenhagen K, Denmark
| | - Marina Montresor
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Chui Pin Leaw
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
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Godhe A, Rynearson T. The role of intraspecific variation in the ecological and evolutionary success of diatoms in changing environments. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0399. [PMID: 28717025 DOI: 10.1098/rstb.2016.0399] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2017] [Indexed: 01/27/2023] Open
Abstract
Intraspecific variation in diatoms has been shown to play a key role in species' responses to several important environmental factors such as light, salinity, temperature and nutrients. Furthermore, modelling efforts indicate that this variation within species extends bloom periods, and likely provides sufficient variability in competitive interactions between species under hydrographically variable conditions. The intraspecific variation most likely corresponds to optimal fitness in temporary microhabitats and may help to explain the paradox of the plankton. Here, we examine the implications of intraspecific variation for the ecology and success of diatoms in general and emphasize the potential implications for our understanding of carbon metabolism in these important organisms. Additionally, data from palaeoecological studies have the potential for evaluating genetic variation through past climate changes, going thousands of years back in time. We suggest pathways for future research including the adoption of multiple strains of individual species into studies of diatom carbon metabolism, to refine our understanding of the variation within and between species, and the inclusion of experimental evolution as a tool for understanding potential evolutionary responses of diatom carbon metabolism to climate change.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.
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Affiliation(s)
- Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
| | - Tatiana Rynearson
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI 02882, USA
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Teng L, Han W, Fan X, Xu D, Zhang X, Dittami SM, Ye N. Evolution and Expansion of the Prokaryote-Like Lipoxygenase Family in the Brown Alga Saccharina japonica. FRONTIERS IN PLANT SCIENCE 2017; 8:2018. [PMID: 29234336 PMCID: PMC5712309 DOI: 10.3389/fpls.2017.02018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 11/13/2017] [Indexed: 05/07/2023]
Abstract
Lipoxygenase (LOX) plays important roles in fatty acid oxidation and lipid mediator biosynthesis. In this study, we give first insights into brown algal LOX evolution. Whole genome searches revealed four, three, and eleven LOXs in Ectocarpus siliculosus, Cladosiphon okamuranus, and Saccharina japonica, respectively. In phylogenetic analyses, LOXs from brown algae form a robust clade with those from prokaryotes, suggesting an ancestral origin and slow evolution. Brown algal LOXs were divided into two clades, C1 and C2 in a phylogenetic tree. Compared to the two species of Ectocarpales, LOX gene expansion occurred in the kelp S. japonica through tandem duplication and segmental duplication. Selection pressure analysis showed that LOX genes in brown algae have undergone strong purifying selection, while the selective constraint in the C2 clade was more relaxed than that in the C1 clade. Furthermore, within each clade, LOXs of S. japonica evolved under more relaxed selection constraints than E. siliculosus and C. okamuranus. Structural modeling showed that unlike LOXs of plants and animals, which contain a β barrel in the N-terminal part of the protein, LOXs in brown algae fold into a single domain. Analysis of previously published transcriptomic data showed that LOXs in E. siliculosus are responsive to hyposaline, hypersaline, oxidative, and copper stresses. Moreover, clear divergence of expression patterns was observed among different life stages, as well as between duplicate gene pairs. In E. siliculosus, all four LOXs are male-biased in immature gametophytes, and mature gametophytes showed significantly higher LOX mRNA levels than immature gametophytes and sporophytes. In S. japonica, however, our RNA-Seq data showed that most LOXs are highly expressed in sporophytes. Even the most recently duplicated gene pairs showed divergent expression patterns, suggesting that functional divergence has likely occurred since LOX genes duplicated, which potentially contributes to the production of various oxylipins in brown algae.
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Affiliation(s)
- Linhong Teng
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wentao Han
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Simon M. Dittami
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Brembu T, Chauton MS, Winge P, Bones AM, Vadstein O. Dynamic responses to silicon in Thalasiossira pseudonana - Identification, characterisation and classification of signature genes and their corresponding protein motifs. Sci Rep 2017; 7:4865. [PMID: 28687794 PMCID: PMC5501833 DOI: 10.1038/s41598-017-04921-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/22/2017] [Indexed: 11/10/2022] Open
Abstract
The diatom cell wall, or frustule, is a highly complex, three-dimensional structure consisting of nanopatterned silica as well as proteins and other organic components. While some key components have been identified, knowledge on frustule biosynthesis is still fragmented. The model diatom Thalassiosira pseudonana was subjected to silicon (Si) shift-up and shift-down situations. Cellular and molecular signatures, dynamic changes and co-regulated clusters representing the hallmarks of cellular and molecular responses to changing Si availabilities were characterised. Ten new proteins with silaffin-like motifs, two kinases and a novel family of putatively frustule-associated transmembrane proteins induced by Si shift-up with a possible role in frustule biosynthesis were identified. A separate cluster analysis performed on all significantly regulated silaffin-like proteins (SFLPs), as well as silaffin-like motifs, resulted in the classification of silaffins, cingulins and SFLPs into distinct clusters. A majority of the genes in the Si-responsive clusters are highly divergent, but positive selection does not seem to be the driver behind this variability. This study provides a high-resolution map over transcriptional responses to changes in Si availability in T. pseudonana. Hallmark Si-responsive genes are identified, characteristic motifs and domains are classified, and taxonomic and evolutionary implications outlined and discussed.
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Affiliation(s)
- Tore Brembu
- NTNU Norwegian University of Science and Technology, Departments of Biology, N-7491, Trondheim, Norway.
| | | | - Per Winge
- NTNU Norwegian University of Science and Technology, Departments of Biology, N-7491, Trondheim, Norway
| | - Atle M Bones
- NTNU Norwegian University of Science and Technology, Departments of Biology, N-7491, Trondheim, Norway
| | - Olav Vadstein
- Biotechnology and Food Science, N-7491, Trondheim, Norway
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Venuleo M, Raven JA, Giordano M. Intraspecific chemical communication in microalgae. THE NEW PHYTOLOGIST 2017; 215:516-530. [PMID: 28328079 DOI: 10.1111/nph.14524] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 02/05/2017] [Indexed: 06/06/2023]
Abstract
Contents 516 I. 516 II. 518 III. 518 IV. 521 V. 523 VI. 523 VII. 526 526 References 526 SUMMARY: The relevance of infochemicals in the relationships between organisms is emerging as a fundamental aspect of aquatic ecology. Exchanges of chemical cues are likely to occur not only between organisms of different species, but also between conspecific individuals. Especially intriguing is the investigation of chemical communication in microalgae, because of the relevance of these organisms for global primary production and their key role in trophic webs. Intraspecific communication between algae has been investigated mostly in relation to sexuality and mating. The literature also contains information on other types of intraspecific chemical communication that have not always been explicitly tagged as ways to communicate to conspecifics. However, the proposed role of certain compounds as intraspecific infochemicals appears questionable. In this article, we make use of this plethora of information to describe the various instances of intraspecific chemical communication between conspecific microalgae and to identify the common traits and ecological significance of intraspecific communication. We also discuss the evolutionary implications of intraspecific chemical communication and the mechanisms by which it can be inherited. A special focus is the genetic diversity among conspecific algae, including the possibility that genetic diversity is an absolute requirement for intraspecific chemical communication.
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Affiliation(s)
- Marianna Venuleo
- Laboratory of Algal and Plant Physiology, Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131, Ancona, Italy
| | - John A Raven
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Dundee, Invergowrie, DD2 5DA, UK
- Functional Plant Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Mario Giordano
- Laboratory of Algal and Plant Physiology, Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131, Ancona, Italy
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Algatech, 379 81, Trebon, Czech Republic
- National Research Council, Institute of Marine Science, 30122, Venice, Italy
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Teng L, Fan X, Xu D, Zhang X, Mock T, Ye N. Identification of Genes under Positive Selection Reveals Differences in Evolutionary Adaptation between Brown-Algal Species. FRONTIERS IN PLANT SCIENCE 2017; 8:1429. [PMID: 28861104 PMCID: PMC5559719 DOI: 10.3389/fpls.2017.01429] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/03/2017] [Indexed: 05/07/2023]
Abstract
Brown algae are an important taxonomic group in coastal ecosystems. The model brown algal species Ectocarpus siliculosus and Saccharina japonica are closely related lineages. Despite their close phylogenetic relationship, they vary greatly in morphology and physiology. To obtain further insights into the evolutionary forces driving divergence in brown algae, we analyzed 3,909 orthologs from both species to identify Genes Under Positive Selection (GUPS). About 12% of the orthologs in each species were considered to be under positive selection. Many GUPS are involved in membrane transport, regulation of homeostasis, and sexual reproduction in the small sporophyte of E. siliculosus, which is known to have a complex life cycle and to occupy a wide range of habitats. Genes involved in photosynthesis and cell division dominated the group of GUPS in the large kelp of S. japonica, which might explain why this alga has evolved the ability to grow very rapidly and to form some of the largest sporophytes. A significant number of molecular chaperones (e.g., heat-shock proteins) involved in stress responses were identified to be under positive selection in both species, potentially indicating their important roles for macroalgae to cope with the relatively variable environment of coastal ecosystems. Moreover, analysis of previously published microarray data of E. siliculosus showed that many GUPS in E. siliculosus were responsive to stress conditions, such as oxidative and hyposaline stress, whereas our RNA-seq data of S. japonica showed that GUPS in this species were most highly expressed in large sporophytes, which supports the suggestion that selection largely acts on different sets of genes in both marcoalgal species, potentially reflecting their adaptation to different ecological niches.
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Affiliation(s)
- Linhong Teng
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesQingdao, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesQingdao, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesQingdao, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesQingdao, China
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research ParkNorwich, United Kingdom
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesQingdao, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
- *Correspondence: Naihao Ye
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Jiang SY, Ramachandran S. Expansion Mechanisms and Evolutionary History on Genes Encoding DNA Glycosylases and Their Involvement in Stress and Hormone Signaling. Genome Biol Evol 2016; 8:1165-84. [PMID: 27026054 PMCID: PMC4860697 DOI: 10.1093/gbe/evw067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
DNA glycosylases catalyze the release of methylated bases. They play vital roles in the base excision repair pathway and might also function in DNA demethylation. At least three families of DNA glycosylases have been identified, which included 3′-methyladenine DNA glycosylase (MDG) I, MDG II, and HhH-GPD (Helix–hairpin–Helix and Glycine/Proline/aspartate (D)). However, little is known on their genome-wide identification, expansion, and evolutionary history as well as their expression profiling and biological functions. In this study, we have genome-widely identified and evolutionarily characterized these family members. Generally, a genome encodes only one MDG II gene in most of organisms. No MDG I or MDG II gene was detected in green algae. However, HhH-GPD genes were detectable in all available organisms. The ancestor species contain small size of MDG I and HhH-GPD families. These two families were mainly expanded through the whole-genome duplication and segmental duplication. They were evolutionarily conserved and were generally under purifying selection. However, we have detected recent positive selection among the Oryza genus, which might play roles in species divergence. Further investigation showed that expression divergence played important roles in gene survival after expansion. All of these family genes were expressed in most of developmental stages and tissues in rice plants. High ratios of family genes were downregulated by drought and fungus pathogen as well as abscisic acid (ABA) and jasmonic acid (JA) treatments, suggesting a negative regulation in response to drought stress and pathogen infection through ABA- and/or JA-dependent hormone signaling pathway.
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Affiliation(s)
- Shu-Ye Jiang
- Genome Structural Biology Group, Temasek Life Science Laboratory, The National University of Singapore, Singapore
| | - Srinivasan Ramachandran
- Genome Structural Biology Group, Temasek Life Science Laboratory, The National University of Singapore, Singapore
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Sucrose metabolism gene families and their biological functions. Sci Rep 2015; 5:17583. [PMID: 26616172 PMCID: PMC4663468 DOI: 10.1038/srep17583] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/02/2015] [Indexed: 01/30/2023] Open
Abstract
Sucrose, as the main product of photosynthesis, plays crucial roles in plant development. Although studies on general metabolism pathway were well documented, less information is available on the genome-wide identification of these genes, their expansion and evolutionary history as well as their biological functions. We focused on four sucrose metabolism related gene families including sucrose synthase, sucrose phosphate synthase, sucrose phosphate phosphatase and UDP-glucose pyrophosphorylase. These gene families exhibited different expansion and evolutionary history as their host genomes experienced differentiated rates of the whole genome duplication, tandem and segmental duplication, or mobile element mediated gene gain and loss. They were evolutionarily conserved under purifying selection among species and expression divergence played important roles for gene survival after expansion. However, we have detected recent positive selection during intra-species divergence. Overexpression of 15 sorghum genes in Arabidopsis revealed their roles in biomass accumulation, flowering time control, seed germination and response to high salinity and sugar stresses. Our studies uncovered the molecular mechanisms of gene expansion and evolution and also provided new insight into the role of positive selection in intra-species divergence. Overexpression data revealed novel biological functions of these genes in flowering time control and seed germination under normal and stress conditions.
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Hart MW. Models of selection, isolation, and gene flow in speciation. THE BIOLOGICAL BULLETIN 2014; 227:133-145. [PMID: 25411372 DOI: 10.1086/bblv227n2p133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Many marine ecologists aspire to use genetic data to understand how selection and demographic history shape the evolution of diverging populations as they become reproductively isolated species. I propose combining two types of genetic analysis focused on this key early stage of the speciation process to identify the selective agents directly responsible for population divergence. Isolation-with-migration (IM) models can be used to characterize reproductive isolation between populations (low gene flow), while codon models can be used to characterize selection for population differences at the molecular level (especially positive selection for high rates of amino acid substitution). Accessible transcriptome sequencing methods can generate the large quantities of data needed for both types of analysis. I highlight recent examples (including our work on fertilization genes in sea stars) in which this confluence of interest, models, and data has led to taxonomically broad advances in understanding marine speciation at the molecular level. I also highlight new models that incorporate both demography and selection: simulations based on these theoretical advances suggest that polymorphisms shared among individuals (a key source of information in IM models) may lead to false-positive evidence of selection (in codon models), especially during the early stages of population divergence and speciation that are most in need of study. The false-positive problem may be resolved through a combination of model improvements plus experiments that document the phenotypic and fitness effects of specific polymorphisms for which codon models and IM models indicate selection and reproductive isolation (such as genes that mediate sperm-egg compatibility at fertilization).
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Affiliation(s)
- Michael W Hart
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
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Collins S, Rost B, Rynearson TA. Evolutionary potential of marine phytoplankton under ocean acidification. Evol Appl 2013; 7:140-55. [PMID: 24454553 PMCID: PMC3894903 DOI: 10.1111/eva.12120] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 09/12/2013] [Indexed: 01/22/2023] Open
Abstract
Marine phytoplankton have many obvious characters, such as rapid cell division rates and large population sizes, that give them the capacity to evolve in response to global change on timescales of weeks, months or decades. However, few studies directly investigate if this adaptive potential is likely to be realized. Because of this, evidence of to whether and how marine phytoplankton may evolve in response to global change is sparse. Here, we review studies that help predict evolutionary responses to global change in marine phytoplankton. We find limited support from experimental evolution that some taxa of marine phytoplankton may adapt to ocean acidification, and strong indications from studies of variation and structure in natural populations that selection on standing genetic variation is likely. Furthermore, we highlight the large body of literature on plastic responses to ocean acidification available, and evolutionary theory that may be used to link plastic and evolutionary responses. Because of the taxonomic breadth spanned by marine phytoplankton, and the diversity of roles they fill in ocean ecosystems and biogeochemical cycles, we stress the necessity of treating taxa or functional groups individually.
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Affiliation(s)
- Sinéad Collins
- Ashworth Laboratories, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh Edinburgh, UK
| | - Björn Rost
- Alfred Wegener Institute for Polar and Marine Research Bremerhaven, Germany
| | - Tatiana A Rynearson
- Graduate School of Oceanography, University of Rhode Island Narragansett, RI, USA
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