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Jan K, Ahmed I, Dar NA, Farah MA, Khan FR, Shah BA, Fazio F. LC-MS/MS based characterisation and differential expression of proteins in Himalayan snow trout, Schizothorax labiatus using LFQ technique. Sci Rep 2023; 13:10134. [PMID: 37349327 PMCID: PMC10287682 DOI: 10.1038/s41598-023-35646-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/22/2023] [Indexed: 06/24/2023] Open
Abstract
Molecular characterization of fish muscle proteins are nowadays considered as a key component to understand the role of specific proteins involved in various physiological and metabolic processes including their up and down regulation in the organisms. Coldwater fish specimens including snow trouts hold different types of proteins which help them to survive in highly diversified temperatures fluctuating from 0 to 20 °C. So, in current study, the liquid chromatography mass spectrometry using label free quantification technique has been used to investigate the muscle proteome profile of Schizothorax labiatus. For proteomic study, two weight groups of S. labiatus were taken from river Sindh. The proteomic analysis of group 1 revealed that a total of 235 proteins in male and 238 in female fish were recorded. However, when male and female S. labiatus were compared with each other on the basis of spectral count and abundance of peptides by ProteinLynx Global Server software, a total of 14 down-regulated and 22 up-regulated proteins were noted in this group. The highly down-regulated ones included homeodomain protein HoxA2b, retinol-binding protein 4, MHC class II beta chain and proopiomelanocortin while as the highly expressed up-regulated proteins comprised of gonadotropin I beta subunit, NADH dehydrogenase subunit 4, manganese superoxide dismutase, recombinase-activating protein 2, glycosyltransferase, chymotrypsin and cytochrome b. On the other hand, the proteomic characterisation of group 2 of S. labiatus revealed that a total of 227 proteins in male and 194 in female fish were recorded. When male and female S. labiatus were compared with each other by label free quantification, a total of 20 down-regulated and 18 up-regulated proteins were recorded. The down-regulated protein expression of group 2 comprised hepatic lipase, allograft inflammatory factor-1, NADH dehydrogenase subunit 4 and myostatin 1 while the highly expressed up-regulated proteins included glycogen synthase kinase-3 beta variant 2, glycogen synthase kinase-3 beta variant 5, cholecystokinin, glycogen synthase kinase-3 beta variant 3 and cytochrome b. Significant (P < 0.05) difference in the expression of down-regulated and up-regulated proteins was also noted between the two sexes of S. labiatus in each group. According to MS analysis, the proteins primarily concerned with the growth, skeletal muscle development and metabolism were down-regulated in river Sindh, which indicates that growth of fish during the season of collection i.e., winter was slow owing to less food availability, gonad development and low metabolic activity. While, the proteins related to immune response of fish were also noted to be down-regulated thereby signifying that the ecosystem has less pollution loads, microbial, pathogenic and anthropogenic activities. It was also found that the proteins involved in glycogen metabolism, reproductive and metabolic processes, particularly lipid metabolism were up-regulated in S. labiatus. The significant expression of these proteins may be connected to pre-spawning, gonad development and use of stored food as source of energy. The information generated in this study can be applied to future research aimed at enhancing food traceability, food safety, risk management and authenticity analysis.
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Affiliation(s)
- Kousar Jan
- Fish Nutrition Research Laboratory, Department of Zoology, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir, 190 006, India
| | - Imtiaz Ahmed
- Fish Nutrition Research Laboratory, Department of Zoology, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir, 190 006, India.
| | - Nazir Ahmad Dar
- Department of Biochemistry, University of Kashmir, Hazratbal, Srinagar, 190006, India
| | - Mohammad Abul Farah
- Department of Zoology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Fatin Raza Khan
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
| | - Basit Amin Shah
- Department of Biotechnology, University of Kashmir, Hazratbal, Srinagar, 190006, India
| | - Francesco Fazio
- Department of Veterinary Sciences, Polo Universitario Annunziata, University of Messina, 98168, Messina, Italy
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Fitzpatrick SW, Mittan-Moreau C, Miller M, Judson JM. Genetic rescue remains underused for aiding recovery of federally listed vertebrates in the United States. J Hered 2023; 114:354-366. [PMID: 36975379 PMCID: PMC10287150 DOI: 10.1093/jhered/esad002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
Restoring gene flow among fragmented populations is discussed as a potentially powerful management strategy that could reduce inbreeding depression and cause genetic rescue. Yet, examples of assisted migration for genetic rescue remain sparse in conservation, prompting several outspoken calls for its increased use in genetic management of fragmented populations. We set out to evaluate the extent to which this strategy is underused and to determine how many imperiled species would realistically stand to benefit from genetic rescue, focusing on federally threatened or endangered vertebrate species in the United States. We developed a "genetic rescue suitability index (GR index)" based on concerns about small population problems relative to risks associated with outbreeding depression and surveyed the literature for 222 species. We found that two-thirds of these species were good candidates for consideration of assisted migration for the purpose of genetic rescue according to our suitability index. Good candidate species spanned all taxonomic groups and geographic regions, though species with more missing data tended to score lower on the suitability index. While we do not recommend a prescriptive interpretation of our GR index, we used it here to establish that assisted migration for genetic rescue is an underused strategy. For example, we found in total, "genetic rescue" was only mentioned in 11 recovery plans and has only been implemented in 3 of the species we surveyed. A potential way forward for implementation of this strategy is incorporating genetic rescue as a priority in USFWS recovery documentation. In general, our results suggest that although not appropriate for all imperiled species, many more species stand to benefit from a conservation strategy of assisted migration for genetic rescue than those for which it has previously been considered or implemented.
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Affiliation(s)
- Sarah W Fitzpatrick
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
- Department of Integrative Biology, Michigan State University, East Lansing, MI, United States
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, United States
| | - Cinnamon Mittan-Moreau
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, United States
| | - Madison Miller
- Savannah River Ecology Lab, University of Georgia, Aiken, SC, United States
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, United States
| | - Jessica M Judson
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, United States
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Mezzasalma M, Brunelli E, Odierna G, Guarino FM. Evolutionary and Genomic Diversity of True Polyploidy in Tetrapods. Animals (Basel) 2023; 13:ani13061033. [PMID: 36978574 PMCID: PMC10044425 DOI: 10.3390/ani13061033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/02/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
True polyploid organisms have more than two chromosome sets in their somatic and germline cells. Polyploidy is a major evolutionary force and has played a significant role in the early genomic evolution of plants, different invertebrate taxa, chordates, and teleosts. However, the contribution of polyploidy to the generation of new genomic, ecological, and species diversity in tetrapods has traditionally been underestimated. Indeed, polyploidy represents an important pathway of genomic evolution, occurring in most higher-taxa tetrapods and displaying a variety of different forms, genomic configurations, and biological implications. Herein, we report and discuss the available information on the different origins and evolutionary and ecological significance of true polyploidy in tetrapods. Among the main tetrapod lineages, modern amphibians have an unparalleled diversity of polyploids and, until recently, they were considered to be the only vertebrates with closely related diploid and polyploid bisexual species or populations. In reptiles, polyploidy was thought to be restricted to squamates and associated with parthenogenesis. In birds and mammals, true polyploidy has generally been considered absent (non-tolerated). These views are being changed due to an accumulation of new data, and the impact as well as the different evolutionary and ecological implications of polyploidy in tetrapods, deserve a broader evaluation.
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Affiliation(s)
- Marcello Mezzasalma
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
- Correspondence: (M.M.); (E.B.)
| | - Elvira Brunelli
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
- Correspondence: (M.M.); (E.B.)
| | - Gaetano Odierna
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy (F.M.G.)
| | - Fabio Maria Guarino
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy (F.M.G.)
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Song S, Du B, Chung-Davidson YW, Cui W, Li Y, Chen H, Huang R, Li W, Li F, Wang C, Ren J. Disruption of T-box transcription factor eomesa results in abnormal development of median fins in Oujiang color common carp Cyprinus carpio. PLoS One 2023; 18:e0281297. [PMID: 36862620 PMCID: PMC9980737 DOI: 10.1371/journal.pone.0281297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 01/19/2023] [Indexed: 03/03/2023] Open
Abstract
Median fins are thought to be ancestors of paired fins which in turn give rise to limbs in tetrapods. However, the developmental mechanisms of median fins remain largely unknown. Nonsense mutation of the T-box transcription factor eomesa in zebrafish results in a phenotype without dorsal fin. Compared to zebrafish, the common carp undergo an additional round of whole genome duplication, acquiring an extra copy of protein-coding genes. To verify the function of eomesa genes in common carp, we established a biallelic gene editing technology in this tetraploidy fish through simultaneous disruption of two homologous genes, eomesa1 and eomesa2. We targeted four sites located upstream or within the sequences encoding the T-box domain. Sanger sequencing data indicated the average knockout efficiency was around 40% at T1-T3 sites and 10% at T4 site in embryos at 24 hours post fertilization. The individual editing efficiency was high to about 80% at T1-T3 sites and low to 13.3% at T4 site in larvae at 7 days post fertilization. Among 145 mosaic F0 examined at four months old, three individuals (Mutant 1-3) showed varying degrees of maldevelopment in the dorsal fin and loss of anal fin. Genotyping showed the genomes of all three mutants were disrupted at T3 sites. The null mutation rates on the eomesa1 and eomesa2 loci were 0% and 60% in Mutant 1, 66.7% and 100% in Mutant 2, and 90% and 77.8% in Mutant 3, respectively. In conclusion, we demonstrated a role of eomesa in the formation and development of median fins in Oujiang color common carp and established an method that simultaneously disrupt two homologous genes with one gRNA, which would be useful in genome editing in other polyploidy fishes.
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Affiliation(s)
- Shiying Song
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Institute of Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Bobo Du
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Yu-Wen Chung-Davidson
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, United States of America
| | - Wenyao Cui
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Yaru Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Honglin Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Rong Huang
- Guangdong Aquarium Association, Guangzhou, China
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, United States of America
| | - Fei Li
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Chenghui Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Jianfeng Ren
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
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Penny FM, Bugg WS, Kieffer JD, Jeffries KM, Pavey SA. Atlantic sturgeon and shortnose sturgeon exhibit highly divergent transcriptomic responses to acute heat stress. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101058. [PMID: 36657229 DOI: 10.1016/j.cbd.2023.101058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023]
Abstract
In comparison to most modern teleost fishes, sturgeons generally display muted stress responses. While a muted stress response appears to be ubiquitous across sturgeon species, the mechanisms unpinning this muted response have not been fully described. The objective of this study was to determine the patterns of hematological and transcriptomic change in muscle tissue following an acute high temperature stress (critical thermal maxima; CTmax) in two locally co-occurring but evolutionarily distant sturgeon species (Atlantic and shortnose sturgeon). The most striking pattern found was that Atlantic sturgeon launched a vigorous transcriptomic response at CTmax, whereas shortnose sturgeon did not. In contrast, shortnose sturgeon have significantly higher cortisol than Atlantics at CTmax, reconfirming that shortnose have a less muted cortisol stress response. Atlantic sturgeon downregulated a number of processes, included RNA creation/processing, methylation and immune processes. Furthermore, a number of genes related to heat shock proteins were differentially expressed at CTmax in Atlantic sturgeon but none of these genes were significantly changed in shortnose sturgeon. We also note that the majority of differentially expressed genes of both species are undescribed and have no known orthologues. These results suggest that, while sturgeons as a whole may show muted stress responses, individual sturgeon species likely use different inducible strategies to cope with acute high temperature stress.
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Affiliation(s)
- F M Penny
- Department of Biological Sciences and Canadian Rivers Institute (CRI Genomics), University of New Brunswick, Saint John, New Brunswick E2L 4L5, Canada.
| | - W S Bugg
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - J D Kieffer
- Department of Biological Sciences (MADSAM Lab), University of New Brunswick, Saint John, New Brunswick E2L 4L5, Canada
| | - K M Jeffries
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - S A Pavey
- Department of Biological Sciences and Canadian Rivers Institute (CRI Genomics), University of New Brunswick, Saint John, New Brunswick E2L 4L5, Canada
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Palatnikov GM. A Comparative Analysis of Morphofunctional Characteristics of Cartilaginous Ganoid Fishes (Order Chondrostei). J EVOL BIOCHEM PHYS+ 2022. [DOI: 10.1134/s002209302202003x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Wang J, He W, Wang W, Luo Z, Han L, Xiang C, Chai M, Li T, Li J, Luo K, Zhao R, Liu S. A Novel Allotriploid Hybrid Derived From Female Goldfish × Male Bleeker's Yellow Tail. Front Genet 2022; 13:880591. [PMID: 35518352 PMCID: PMC9061998 DOI: 10.3389/fgene.2022.880591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/21/2022] [Indexed: 11/23/2022] Open
Abstract
Hybridization is a traditional and effective strategy to alter the genotypes and phenotypes of the offspring, and distant hybridization is a useful strategy to generate polyploids in fish. In this study, goldfish (Carassius auratus, GF, 2n = 100) and Bleeker’s yellow tail (Xenocypris davidi Bleeker, YT, 2n = 48), which belong to different subfamilies, were crossed with each other. The cross of female GF × male YT successfully obtained hybrid offspring (GFYT hybrids), while the cross of female YT × male GF was lethal, and all the fertilized eggs stopped developing before the neurula stage of embryogenesis. All GFYT hybrids possessed 124 chromosomes (3n = 124) with two sets from GF and one set from YT. The measurable and countable traits of GFYT hybrids were identified, and the genetic characteristics of 5S rDNA between GFYT hybrids and their parents were also revealed. There were, respectively, four and three different 5S rDNA types in GF (assigned as GF-Ⅰ∼Ⅳ) and YT (assigned as YT-Ⅰ∼Ⅲ), and GFYT hybrids specifically inherited YT-Ⅰ and YT-Ⅱ 5S rDNA types from YT and GF-Ⅲ and GF-Ⅳ from GF. In addition, there were only testis-like and fat-like gonads been found in GFYT hybrids. Interestingly, there were pyknotic and heteromorphous chromatin and invaginated cell membrane observed in the spermatids of testis-like gonads, but no mature sperm were found. Furthermore, TUNEL assays indicated that, compared with control, apparent apoptotic signals, which were mainly distributed around spermatid regions, were detected in the testis-like gonads, and the expression of apoptosis pathway-related genes including p53, bcl-2, bax, and caspase9 was significantly upregulated. Moreover, the expression of meiosis-related genes including spo11, dmc1, and rad51 showed an abnormally high expression, but mns1 and meig1, two key genes involved in the maturation of spermatid, were extremely downregulated. In brief, this is the first report of allotriploid via distant hybridization between GF and YT that possessing different chromosome numbers in vertebrates. The obtainment of GFYT hybrids not only harbors potential benefits and application in aquaculture but also further extends the understanding of the influence of hybridization and polyploidization on the genomic constitution of the hybrid offspring. Furthermore, they can be used as a model to test the origin and consequences of polyploidization and served as a proper resource to study the underlying mechanisms of spermatogenesis dysfunctions.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Weiguo He
- Clinical Anatomy and Reproductive Medicine Application Institute, Hengyang Medical School, University of South China, Hengyang, China
| | - Wen Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Ziye Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Linmei Han
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Caixia Xiang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Mingli Chai
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Tangluo Li
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy and Pharmacology, University of South China, Hengyang, China
| | - Jihong Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Kaikun Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
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Zhou Y, Zhu L, Sun Y, Zhang H, Wang J, Qin W, He W, Zhou L, Li Q, Zhao R, Luo K, Tang C, Zhang C, Liu S. Localization of RNA Pol II CTD (S5) and Transcriptome Analysis of Testis in Diploid and Tetraploid Hybrids of Red Crucian Carp (♀) × Common Carp (♂). Front Genet 2021; 12:717871. [PMID: 34567072 PMCID: PMC8458772 DOI: 10.3389/fgene.2021.717871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/03/2021] [Indexed: 11/15/2022] Open
Abstract
Polyploidy occurs naturally in fish; however, the appearance of these species is an occasional and gradual process, which makes it difficult to trace the changes in phenotypes, genotypes, and regulation of gene expression. The allotetraploid hybrids (4nAT) of red crucian carp (RCC; ♀) × common carp (CC; ♂) generated from interspecies crossing are a good model to investigate the initial changes after allopolyploidization. In the present study, we focused on the changes in the active sites of the testicular transcriptome of the allotetraploid by localization of RNA Pol II CTD YSPTSPS (phospho S5) using immunofluorescence and RNA-seq data via bioinformatic analysis. The results showed that there was no significant difference in signal counts of the RNA Pol II CTD (S5) between the different types of fish at the same stages, including RCC, CC, 2nF1, and 4nAT, which means that the number of transcriptionally active sites on germ cell chromosomes was not affected by the increase in chromosome number. Similarly, RNA-seq analysis indicated that in the levels of chromosomes and 10-kb regions in the genome, there were no significant changes in the highly active sites in RCC, 2nF1, and 4nAT. These findings suggest that at the beginning of tetraploid origin, the active transcriptome site of 4nAT in the testis was conserved in the regions of the genome compared to that in RCC and 2nF1. In conclusion, 4nAT shared a similar gene expression model in the regions of the genome with RCC and 2nF1 with significantly different expression levels.
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Affiliation(s)
- Yi Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - La Zhu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Yu Sun
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Hui Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Jiaojiao Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Weilin Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Wangchao He
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Luojing Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Qi Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Kaikun Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, China
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9
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Comparative Transcriptome Analysis Revealed Genes Involved in Sexual and Polyploid Growth Dimorphisms in Loach ( Misgurnus anguillicaudatus). BIOLOGY 2021; 10:biology10090935. [PMID: 34571812 PMCID: PMC8468957 DOI: 10.3390/biology10090935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/05/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Misgurnus anguillicaudatus not only exhibits sexual size dimorphism, but also shows polyploid size dimorphism. Here, we performed comparative transcriptome integration analysis of multiple tissues of diploid and tetraploid M. anguillicaudatus of both sexes. We found that differences in energy metabolism and steroid hormone synthesis levels may be the main causes of sexual and polyploidy growth dimorphisms of M. anguillicaudatus. Fast-growing M. anguillicaudatus (tetraploids, females) have higher levels of energy metabolism and lower steroid hormone synthesis and fatty acid degradation abilities than slow-growing M. anguillicaudatus (diploids, males). Abstract Sexual and polyploidy size dimorphisms are widespread phenomena in fish, but the molecular mechanisms remain unclear. Loach (Misgurnus anguillicaudatus) displays both sexual and polyploid growth dimorphism phenomena, and are therefore ideal models to study these two phenomena. In this study, RNA-seq was used for the first time to explore the differentially expressed genes (DEGs) between both sexes of diploid and tetraploid loaches in four tissues (brain, gonad, liver, and muscle). Results showed that 21,003, 17, and 1 DEGs were identified in gonad, liver, and muscle tissues, respectively, between females and males in both diploids and tetraploids. Regarding the ploidy levels, 4956, 1496, 2187, and 1726 DEGs were identified in the brain, gonad, liver, and muscle tissues, respectively, between tetraploids and diploids of the same sex. When both sexual and polyploid size dimorphisms were considered simultaneously in the four tissues, only 424 DEGs were found in the gonads, indicating that these gonadal DEGs may play an important regulatory role in regulating sexual and polyploid size dimorphisms. Regardless of the sex or ploidy comparison, the significant DEGs involved in glycolysis/gluconeogenesis and oxidative phosphorylation pathways were upregulated in faster-growing individuals, while steroid hormone biosynthesis-related genes and fatty acid degradation and elongation-related genes were downregulated. This suggests that fast-growing loaches (tetraploids, females) have higher energy metabolism levels and lower steroid hormone synthesis and fatty acid degradation abilities than slow-growing loaches (diploids, males). Our findings provide an archive for future systematic research on fish sexual and polyploid dimorphisms.
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Otero MA, Grenat PR, Bionda CL, Baraquet M, Pollo FE, Salas NE, Martino AL. Age and growth in an anuran hybrid zone: Fitness-related traits of the diploid/polyploid ground frog complex (genus Odontophrynus) from central Argentina. ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Chandra RK, Bhardwaj AK, Tripathi MK. Evaluation of triazophos induced immunotoxicity of spleen and head kidney in fresh water teleost, Channa punctata. Comp Biochem Physiol C Toxicol Pharmacol 2021; 245:109029. [PMID: 33722765 DOI: 10.1016/j.cbpc.2021.109029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/20/2021] [Accepted: 03/11/2021] [Indexed: 11/30/2022]
Abstract
The utilization of pesticides has increased for destroying pests and protecting crops in the agriculture field. Triazophos is a commonly used organophosphorous insecticide that causes alterations in haematological and histological parameters in fish. The present study was designed to evaluate the effect of triazophos induced innate and cell mediated immunotoxicity in freshwater teleost, Channa punctata. Fishes were exposed to triazophos at concentrations 5 and 10% of LC50 value for 10 and 20 days. Splenic and head kidney macrophage phagocytosis, nitric oxide production and superoxide production were assayed to evaluate the innate immunity. Cell-mediated immunity was measured through splenic and head kidney lymphocyte proliferation in presence of T and B cell mitogens. Results of the present study revealed that macrophage phagocytosis was significantly reduced after in vivo triazophos treatment. Differential suppressive effect of triazophos was also observed where mitogen induced splenic and head kidney lymphocyte proliferations were reduced after 10 and 20 days treatment. Concentration dependent effect of triazophos was observed in in vivo studies where the production of reactive oxygen and nitrogen intermediates were suppressed. This study describes the first investigation of the effect of triazophos on immune functions and will help to determine appropriate ecotoxicity and immunotoxicity in freshwater teleosts.
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Affiliation(s)
- Rakesh Kumar Chandra
- Department of Zoology, School of Life Sciences, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur, Chhattisgarh, India
| | - Ajay Kumar Bhardwaj
- Department of Zoology, School of Life Sciences, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur, Chhattisgarh, India
| | - Manish Kumar Tripathi
- Department of Zoology, School of Life Sciences, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur, Chhattisgarh, India.
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12
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Van de Peer Y, Ashman TL, Soltis PS, Soltis DE. Polyploidy: an evolutionary and ecological force in stressful times. THE PLANT CELL 2021; 33:11-26. [PMID: 33751096 PMCID: PMC8136868 DOI: 10.1093/plcell/koaa015] [Citation(s) in RCA: 252] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/07/2020] [Indexed: 05/10/2023]
Abstract
Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than nonpolyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus nonpolyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy.
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Affiliation(s)
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
- Department of Biology, University of Florida, Gainesville, Florida 32611
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13
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Faulkes CG, Faulkner SC. Steven Clive Le Comber (19 June 1966–14 September 2019). J Zool (1987) 2020. [DOI: 10.1111/jzo.12758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C. G. Faulkes
- School of Biological and Chemical Sciences Queen Mary University of London London UK
| | - S. C. Faulkner
- School of Biological and Chemical Sciences Queen Mary University of London London UK
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14
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Spoelhof JP, Keeffe R, McDaniel SF. Does reproductive assurance explain the incidence of polyploidy in plants and animals? THE NEW PHYTOLOGIST 2020; 227:14-21. [PMID: 31883115 DOI: 10.1111/nph.16396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/17/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Jonathan P Spoelhof
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Rachel Keeffe
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Stuart F McDaniel
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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15
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Ranallo-Benavidez TR, Jaron KS, Schatz MC. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat Commun 2020; 11:1432. [PMID: 32188846 PMCID: PMC7080791 DOI: 10.1038/s41467-020-14998-3] [Citation(s) in RCA: 534] [Impact Index Per Article: 133.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 02/10/2020] [Indexed: 11/09/2022] Open
Abstract
An important assessment prior to genome assembly and related analyses is genome profiling, where the k-mer frequencies within raw sequencing reads are analyzed to estimate major genome characteristics such as size, heterozygosity, and repetitiveness. Here we introduce GenomeScope 2.0 (https://github.com/tbenavi1/genomescope2.0), which applies combinatorial theory to establish a detailed mathematical model of how k-mer frequencies are distributed in heterozygous and polyploid genomes. We describe and evaluate a practical implementation of the polyploid-aware mixture model that quickly and accurately infers genome properties across thousands of simulated and several real datasets spanning a broad range of complexity. We also present a method called Smudgeplot (https://github.com/KamilSJaron/smudgeplot) to visualize and estimate the ploidy and genome structure of a genome by analyzing heterozygous k-mer pairs. We successfully apply the approach to systems of known variable ploidy levels in the Meloidogyne genus and the extreme case of octoploid Fragaria × ananassa.
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Affiliation(s)
| | - Kamil S Jaron
- University of Lausanne, Lausanne, CH, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, CH, Switzerland
| | - Michael C Schatz
- Johns Hopkins University, Baltimore, MD, USA.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
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16
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Shen Y, Yang N, Liu Z, Chen Q, Li Y. Phylogenetic perspective on the relationships and evolutionary history of the Acipenseriformes. Genomics 2020; 112:3511-3517. [PMID: 32105795 DOI: 10.1016/j.ygeno.2020.02.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/06/2020] [Accepted: 02/21/2020] [Indexed: 11/16/2022]
Abstract
The Acipenseriformes, as one of the earliest extant vertebrates, plays an important role in the evolution of fishes and even the whole vertebrates. Here we collected and analyzed all complete mitochondrial genomes of Acipenseriformes species. Phylogenetic analyses demonstrated that the polytomous branch included Acipenseridae and Polyodontidae formed five clades. The Polyodontidae clade and the Scaphirhynchus clade both were monophyletic group, whereas the Acipenser species and the Huso species both were polyphyletic group. The Bayesian divergence times showed that the origin time for Acipenseriformes was at 318.0 Mya, which was similar to the some previous results of 312.1 Mya, 346.9 Mya and 389.7 Mya. The result was in good consistent with the paleontological data available and the split time of the Pacific and Atlantic Oceans from the Jurassic to the Cretaceous (Laurasia splits in North America and Eurasia). The dN/dS ratios showed the evolutionary rates gradually slow down in five major Acipenseriformes clades from the Clade A (the Pacific sturgeons species) to Clade C (the genus Scaphirhynchus), which was related to the process of geographical formation.
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Affiliation(s)
- Yanjun Shen
- Chongqing Key Laboratory of Animal Biology, School of Life Sciences, Chongqing Normal University, Chongqing 401331, China.
| | - Na Yang
- Chongqing Key Laboratory of Animal Biology, School of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Zhihao Liu
- Chongqing Key Laboratory of Animal Biology, School of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Qiliang Chen
- Chongqing Key Laboratory of Animal Biology, School of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Yingwen Li
- Chongqing Key Laboratory of Animal Biology, School of Life Sciences, Chongqing Normal University, Chongqing 401331, China.
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17
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De novo European eel transcriptome provides insights into the evolutionary history of duplicated genes in teleost lineages. PLoS One 2019; 14:e0218085. [PMID: 31188893 PMCID: PMC6561569 DOI: 10.1371/journal.pone.0218085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 05/25/2019] [Indexed: 12/18/2022] Open
Abstract
Paralogues pairs are more frequently observed in eels (Anguilla sp.) than in other teleosts. The paralogues often show low phylogenetic distances; however, they have been assigned to the third round of whole genome duplication (WGD), shared by all teleosts (3R), due to their conserved synteny. The apparent contradiction of low phylogenetic difference and 3R conserved synteny led us to study the duplicated gene complement of the freshwater eels. With this aim, we assembled de novo transcriptomes of two highly relevant freshwater eel species: The European (Anguilla anguilla) and the Japanese eel (Anguilla japonica). The duplicated gene complement was analysed in these transcriptomes, and in the genomes and transcriptomes of other Actinopterygii species. The study included an assessment of neutral genetic divergence (4dTv), synteny, and the phylogenetic origins and relationships of the duplicated gene complements. The analyses indicated a high accumulation of duplications (1217 paralogue pairs) among freshwater eel genes, which may have originated in a WGD event after the Elopomorpha lineage diverged from the remaining teleosts, and thus not at the 3R. However, very similar results were observed in the basal Osteoglossomorpha and Clupeocephala branches, indicating that the specific genomic regions of these paralogues may still have been under tetrasomic inheritance at the split of the teleost lineages. Therefore, two potential hypotheses may explain the results: i) The freshwater eel lineage experienced an additional WGD to 3R, and ii) Some duplicated genomic regions experienced lineage specific rediploidization after 3R in the ancestor to freshwater eels. The supporting/opposing evidence for both hypotheses is discussed.
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18
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Abstract
Polyploid cells contain more than two homologous sets of chromosomes. The original observations of liver polyploidy date back to the 1940s, but functional roles for polyploid cells are still unclear. Liver polyploidy may influence regeneration, stress response, and cancer, although little evidence has established direct causal links between polyploidy and these biological phenotypes. In this review, we will introduce broad concepts about polyploidy including its distribution in nature and how polyploids form in normal and pathological situations. Then we will examine recent discoveries that have begun to clarify functionality and disease relevance of liver polyploidy. Finally, we will discuss implications and future directions of research about polyploidy in the liver.
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Affiliation(s)
- Shuyuan Zhang
- a Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine , University of Texas Southwestern Medical Center , Dallas , USA
| | - Yu-Hsuan Lin
- a Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine , University of Texas Southwestern Medical Center , Dallas , USA
| | - Branden Tarlow
- b Department of Internal Medicine , University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Hao Zhu
- a Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine , University of Texas Southwestern Medical Center , Dallas , USA
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19
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Pollo FE, Grenat PR, Otero MA, Babini S, Salas NE, Martino AL. Evaluation in situ of genotoxic and cytotoxic response in the diploid/polyploid complex Odontophrynus (Anura: Odontophrynidae) inhabiting agroecosystems. CHEMOSPHERE 2019; 216:306-312. [PMID: 30384299 DOI: 10.1016/j.chemosphere.2018.10.149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/18/2018] [Accepted: 10/21/2018] [Indexed: 06/08/2023]
Abstract
Polyploidization has been documented across a wide range of vertebrates. Gene duplication could promote better adaptation to environmental changes and to chronic injury or stress. We investigated if genotoxic and cytotoxic responses to agricultural impact are affected by ploidy. We evaluate syntopic populations of the cryptic diploid/polyploid complex Odontophrynus cordobae/O. americanus breeding in an agroecosystem from Central Argentina. The blood of 72 adult anurans was analysed. We used erythrometry to distinguish Odontophrynus individuals with different ploidy levels. We calculated micronucleus frequencies (Mn) and erythrocytic nuclear abnormalities (ENAs) as genotoxic effects and enucleated, mitotic, pyknotic and immature erythrocytes as cytotoxic endpoints (CYT). Mn, ENAs and CYT frequencies were significantly different between diploid and polyploid organisms. The higher frequencies of Mn and CYT were recorded in polyploid organisms, and the higher frequency of ENAs was recorded in diploids. These results indicate that stress response, as indicated by most genotoxic and cytotoxic endpoints, was higher in polyploids respect to diploids. Polyploidy could provide greater genetic flexibility increasing buffering against exogenous DNA-damaging agents and thus confer an advantage over diploids under certain environmental conditions.
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Affiliation(s)
- Favio E Pollo
- Ecología-Educación Ambiental, Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, National University of Río Cuarto, ruta 36km 601, Río Cuarto, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Pablo R Grenat
- Ecología-Educación Ambiental, Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, National University of Río Cuarto, ruta 36km 601, Río Cuarto, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
| | - Manuel A Otero
- Ecología-Educación Ambiental, Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, National University of Río Cuarto, ruta 36km 601, Río Cuarto, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Selene Babini
- Ecología-Educación Ambiental, Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, National University of Río Cuarto, ruta 36km 601, Río Cuarto, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Nancy E Salas
- Ecología-Educación Ambiental, Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, National University of Río Cuarto, ruta 36km 601, Río Cuarto, Córdoba, Argentina
| | - Adolfo L Martino
- Ecología-Educación Ambiental, Departamento de Ciencias Naturales, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, National University of Río Cuarto, ruta 36km 601, Río Cuarto, Córdoba, Argentina
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20
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Qin Y, Li X, Yang Y, Li Z, Liang Y, Zhang X, Jiang S. Toxic effects of copper sulfate on diploid and triploid fin cell lines in Misgurnus anguillicaudatus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 643:1419-1426. [PMID: 30189558 DOI: 10.1016/j.scitotenv.2018.06.315] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 06/08/2023]
Abstract
The effects of different concentrations of copper sulfate on diploid and triploid fin cell lines (named DIMF and TRMF, respectively) in Misgurnus anguillicaudatus were studied. The LC50 of copper sulfate estimated by an MTT assay was 268.39 in DIMF cells, and 311.54 μmol/L in TRMF cells, respectively. Activity of superoxide dismutase (SOD) in DIMF cells gradually increased as the concentration of copper sulfate increased (up to 200 μmol/L), and then gradually decreased. SOD activity in triploid loach fin cells, as well as glutathione peroxidase (GSH-Px) and glutathione-S-transferase (GST) activity in both diploid and triploid cells, decreased as the concentration of copper sulfate increased, which suggested that excessive copper exposure at the concentrations tested in this study was detrimental to anti-oxidative capability. In general, SOD, GST and GSH-Px activity was higher in triploid fin cells than in diploid cells. DNA breaks were observed by comet assays after 24 h exposure to 400 and 800 μM copper; DNA percent in the comet's tail was lower in TRMF than in DIMF. Ultrastructurally, there were no significant differences in the organelles of both cells, although a higher number of vesicles were observed in TRMF cells after copper exposure. Pathological changes induced by copper sulfate were similar in DIMF and TRMF cells, and were indicative of cell necrosis. Results above suggested that excessive copper sulfate exposure would lead to antioxidant enzymes activity reduction, along with antioxidant defenses disruption and superoxide radicals increasing, and then to DNA damage, ultrastructural changes and necrosis features in DIMF and TRMF M. anguillicaudatus fin cells. Triploid cell lines had higher resistance to copper than their diploid counterparts especially at higher concentrations of copper due to larger cells and higher intracellular content of detoxification enzymes to resist the toxicity of heavy metals.
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Affiliation(s)
- Yanjie Qin
- Key Laboratory of Marine Bio-resource Restoration and Habitat Reparation in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Xia Li
- Key Laboratory of Marine Bio-resource Restoration and Habitat Reparation in Liaoning Province, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, PRC, Dalian Ocean University, Dalian 116023, China.
| | - Yanjin Yang
- Key Laboratory of Marine Bio-resource Restoration and Habitat Reparation in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Zhuangzhuang Li
- Key Laboratory of Marine Bio-resource Restoration and Habitat Reparation in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Yan Liang
- Key Laboratory of Marine Bio-resource Restoration and Habitat Reparation in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Xiaoyu Zhang
- Key Laboratory of Marine Bio-resource Restoration and Habitat Reparation in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Shan Jiang
- Key Laboratory of Marine Bio-resource Restoration and Habitat Reparation in Liaoning Province, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, PRC, Dalian Ocean University, Dalian 116023, China
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21
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Jørgensen KM, Wennevik V, Eide Sørvik AG, Unneland L, Prusov S, Ayllon F, Glover KA. Investigating the frequency of triploid Atlantic salmon in wild Norwegian and Russian populations. BMC Genet 2018; 19:90. [PMID: 30285613 PMCID: PMC6171226 DOI: 10.1186/s12863-018-0676-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/19/2018] [Indexed: 12/18/2022] Open
Abstract
Background Fish may display variations in ploidy, including three sets of chromosomes, known as triploidy. A recent study revealed a frequency of ~ 2% spontaneous (i.e., non-intentional) triploidy in domesticated Atlantic salmon produced in Norwegian aquaculture in the period 2007–2014. In contrast, the frequency of triploidy in wild salmon populations has not been studied thus far, and in wild populations of other organisms, it has been very rarely studied. In population genetic data sets, individuals that potentially display chromosome abnormalities, such as triploids with three alleles, are typically excluded on the premise that they may reflect polluted or otherwise compromised samples. Here, we critically re-investigated the microsatellite genetic profile of ~ 6000 wild Atlantic salmon sampled from 80 rivers in Norway and Russia, to investigate the frequency of triploid individuals in wild salmon populations for the first time. Results We detected a single triploid salmon, and five individuals displaying three alleles at one of the loci, thus regarded as putatively trisomic. This gave an overall frequency of triploid and putatively trisomic individuals in the data set of 0.017 and 0.083% respectively. The triploid salmon was an adult female, and had spent 2 years in freshwater and 2 years in the sea. Conclusions We conclude that the frequency of naturally-occurring triploid Atlantic salmon in wild Norwegian and Russian populations is very low, and many-fold lower than the frequency of spontaneous triploids observed in aquaculture. Our results suggest that aquaculture rearing conditions substantially increase the probability of triploidy to develop, and/or permits greater survival of triploid individuals, in comparison to the wild. Electronic supplementary material The online version of this article (10.1186/s12863-018-0676-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Vidar Wennevik
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway
| | | | - Laila Unneland
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway
| | - Sergey Prusov
- The Knipovich Polar Research Institute of Marine Fisheries and Oceanography (PINRO), Murmansk, 183038, Russia
| | - Fernando Ayllon
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway
| | - Kevin A Glover
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway.,Sea lice Research Centre, Department of Biology, University of Bergen, N-5020, Bergen, Norway
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22
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Saenjundaeng P, de Bello Cioffi M, de Oliveira EA, Tanomtong A, Supiwong W, Phimphan S, Collares-Pereira MJ, Sember A, Bertollo LAC, Liehr T, Yano CF, Hatanaka T, Ráb P. Chromosomes of Asian cyprinid fishes: cytogenetic analysis of two representatives of small paleotetraploid tribe Probarbini. Mol Cytogenet 2018; 11:51. [PMID: 30202442 PMCID: PMC6123905 DOI: 10.1186/s13039-018-0399-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 08/23/2018] [Indexed: 12/01/2022] Open
Abstract
Background Polyploidy, although still poorly explored, represents an important evolutionary event in several cyprinid clades. Herein, Catlocarpio siamensis and Probarbus jullieni - representatives of the paleotetraploid tribe Probarbini, were characterized both by conventional and molecular cytogenetic methods. Results Alike most other paleotetraploid cyprinids (with 2n = 100), both species studied here shared 2n = 98 but differed in karyotypes: C. siamensis displayed 18m + 34sm + 46st/a; NF = 150, while P. jullieni exhibited 26m + 14sm + 58st/a; NF = 138. Fluorescence in situ hybridization (FISH) with rDNA probes revealed two (5S) and eight (18S) signals in C. siamensis, respectively, and six signals for both probes in P. jullieni. FISH with microsatellite motifs evidenced substantial genomic divergence between both species. The almost doubled size of the chromosome pairs #1 in C. siamensis and #14 in P. jullieni compared to the rest of corresponding karyotypes indicated chromosomal fusions. Conclusion Based on our findings, together with likely the same reduced 2n = 98 karyotypes in the remainder Probarbini species, we hypothesize that the karyotype 2n = 98 might represent a derived character, shared by all members of the Probarbini clade. Besides, we also witnessed considerable changes in the amount and distribution of certain repetitive DNA classes, suggesting complex post-polyploidization processes in this small paleotetraploid tribe.
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Affiliation(s)
- Pasakorn Saenjundaeng
- 1Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Muang District, Khon Kaen, Thailand
| | - Marcelo de Bello Cioffi
- 2Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Ezequiel Aguiar de Oliveira
- 2Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP Brazil.,Secretaria de Estado de Educação de Mato Grosso - SEDUC-MT, Cuiabá, MT Brazil
| | - Alongklod Tanomtong
- 1Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Muang District, Khon Kaen, Thailand
| | - Weerayuth Supiwong
- 4Faculty of Applied Science and Engineering, Khon Kaen University, Nong Kai Campus, Muang, Nong Kai Thailand
| | - Sumalee Phimphan
- 1Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Muang District, Khon Kaen, Thailand
| | - Maria João Collares-Pereira
- 5Faculdade de Ciencias, Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Campo Grande, PT-1749-016 Lisbon, Portugal
| | - Alexandr Sember
- 6Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | | | - Thomas Liehr
- 7Institute of Human Genetics, Jena University Hospital, Am Klinikum 1, D-07747 Jena, Germany
| | - Cassia Fernanda Yano
- 2Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Terumi Hatanaka
- 2Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Petr Ráb
- 6Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
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23
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Symonová R, Howell WM. Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics. Genes (Basel) 2018; 9:genes9020096. [PMID: 29443947 PMCID: PMC5852592 DOI: 10.3390/genes9020096] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 12/19/2022] Open
Abstract
To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species. Localization of repeats on chromosomes of hundreds of fish species and populations originating from diversified environments have revealed the biological importance of this genomic fraction. Ribosomal genes (rDNA) belong to the most informative repeats and in fish, they are subject to a more relaxed regulation than in higher vertebrates. This can result in formation of a literal 'rDNAome' consisting of more than 20,000 copies with their high proportion employed in extra-coding functions. Because rDNA has high rates of transcription and recombination, it contributes to genome diversification and can form reproductive barrier. Our overall knowledge of fish cytogenomics grows rapidly by a continuously increasing number of fish genomes sequenced and by use of novel sequencing methods improving genome assembly. The recently revealed exceptional compositional heterogeneity in an ancient fish lineage (gars) sheds new light on the compositional genome evolution in vertebrates generally. We highlight the power of synergy of cytogenetics and genomics in fish cytogenomics, its potential to understand the complexity of genome evolution in vertebrates, which is also linked to clinical applications and the chromosomal backgrounds of speciation. We also summarize the current knowledge on fish cytogenomics and outline its main future avenues.
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Affiliation(s)
- Radka Symonová
- Faculty of Science, Department of Biology, University of Hradec Králové, 500 03 Hradec Králové, Czech Republic.
| | - W Mike Howell
- Department of Biological and Environmental Sciences, Samford University, Birmingham, AL 35229, USA.
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Backström T, Winberg S. Serotonin Coordinates Responses to Social Stress-What We Can Learn from Fish. Front Neurosci 2017; 11:595. [PMID: 29163002 PMCID: PMC5669303 DOI: 10.3389/fnins.2017.00595] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/10/2017] [Indexed: 12/20/2022] Open
Abstract
Social interaction is stressful and subordinate individuals are often subjected to chronic stress, which greatly affects both their behavior and physiology. In teleost fish the social position of an individual may have long-term effects, such as effects on migration, age of sexual maturation or even sex. The brain serotonergic system plays a key role in coordinating autonomic, behavioral and neuroendocrine stress responses. Social subordination results in a chronic activation of the brain serotonergic system an effect, which seems to be central in the subordinate phenotype. However, behavioral effects of short-term acute activation of the serotonergic system are less obvious. As in other vertebrates, divergent stress coping styles, often referred to as proactive and reactive, has been described in teleosts. As demonstrated by selective breeding, stress coping styles appear to be partly heritable. However, teleost fish are characterized by plasticity, stress coping style being affected by social experience. Again, the brain serotonergic system appears to play an important role. Studies comparing brain gene expression of fish of different social rank and/or displaying divergent stress coping styles have identified several novel factors that seem important for controlling aggressive behavior and stress coping, e.g., histamine and hypocretin/orexin. These may also interact with brain monoaminergic systems, including serotonin.
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Affiliation(s)
- Tobias Backström
- Institute of Integrated Natural Sciences, University Koblenz-Landau, Koblenz, Germany
| | - Svante Winberg
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
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Are ploidy and age size-related? A comparative study on tetraploid Pleurodema kriegi and octoploid P. cordobae (Anura: Leptodactylidae) from Central Argentina. ZOOL ANZ 2017. [DOI: 10.1016/j.jcz.2016.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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26
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Pankova MV, Kukhlevsky AD, Brykov VA. Fish growth hormone genes: Divergence of coding sequences in salmonid fishes. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795416100082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Karami A, Teh SJ, Zakaria MP, Courtenay SC. Ploidy-, gender-, and dose-dependent alteration of selected biomarkers in Clarias gariepinus treated with benzo[a]pyrene. J Environ Sci (China) 2015; 38:95-102. [PMID: 26702972 DOI: 10.1016/j.jes.2015.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 02/10/2015] [Accepted: 05/04/2015] [Indexed: 06/05/2023]
Abstract
Naturally-occurring and artificially-induced polyploids have been documented in various fish species but to date no comparison has been reported of the impacts of ploidy on fish biomarker responses to organic pollutants. This study describes effects of ploidy, gender, and dose on biliary fluorescent aromatic compound (FAC) concentrations, hepatic ethoxyresorufin-O-deethylase (EROD) and glutathione S-transferase (GST) activities in one of the most commonly cultured warm-water species, the African catfish Clarias gariepinus. Recently matured male and female diploid and triploid fish were intraperitoneally (i.p.) injected with 0, 5 or 25mg/kg benzo[a]pyrene (BaP) and liver and gallbladder were sampled 48hr later. No significant differences were found between ploidies in bile concentrations of 7,8 dihydrodiolbenzo[a]pyrene (7,8D BaP), 1-hydroxybenzo[a]pyrene (1-OH BaP) or 3-hydroxybenzo[a]pyrene (3-OH BaP). However, concentrations of the biliary FACs did differ between males and females at different dose of injection with generally higher concentrations in females at the low dose of BaP and higher concentrations in males at the higher BaP concentration. Hepatic EROD activity did not exhibit gender-dependent difference, whereas it was significantly higher in triploids than diploids. GST activities were not significantly influenced by any of the tested factors. This work advanced our understanding of the role of ploidy, gender, and dose in biotransformation of pollutants in fish.
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Affiliation(s)
- Ali Karami
- Laboratory of Aquatic Toxicology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Selangor, Malaysia.
| | - Swee J Teh
- School of Veterinary Medicine, Department of Anatomy, Physiology, and Cell Biology, University of California, Davis, CA 95616, USA
| | - Mohamad Pauzi Zakaria
- Centre of Excellence for Environmental Forensics, Faculty of Environmental Studies, Universiti Putra Malaysia, 43400, UPM, Selangor, Malaysia
| | - Simon C Courtenay
- Department of Environment and Resource Studies, Canadian Water Network, Canadian Rivers Institute, University of Waterloo, Canada
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Abstract
This review summarizes the current status of the known extant genuine polyploid anuran and urodelan species, as well as spontaneously originated and/or experimentally produced amphibian polyploids. The mechanisms by which polyploids can originate, the meiotic pairing configurations, the diploidization processes operating in polyploid genomes, the phenomenon of hybridogenesis, and the relationship between polyploidization and sex chromosome evolution are discussed. The polyploid systems in some important amphibian taxa are described in more detail.
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Molina WF, Martinez PA, Bertollo LAC, Bidau CJ. Preferential accumulation of sex and Bs chromosomes in biarmed karyotypes by meiotic drive and rates of chromosomal changes in fishes. AN ACAD BRAS CIENC 2015; 86:1801-12. [PMID: 25590717 DOI: 10.1590/0001-3765201420130489] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 05/13/2014] [Indexed: 08/20/2023] Open
Abstract
Mechanisms of accumulation based on typical centromeric drive or of chromosomes carrying pericentric inversions are adjusted to the general karyotype differentiation in the principal Actinopterygii orders. Here, we show that meiotic drive in fish is also supported by preferential establishment of sex chromosome systems and B chromosomes in orders with predominantly bi-brachial chromosomes. The mosaic of trends acting at an infra-familiar level in fish could be explained as the interaction of the directional process of meiotic drive as background, modulated on a smaller scale by adaptive factors or specific karyotypic properties of each group, as proposed for the orthoselection model.
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Affiliation(s)
- Wagner F Molina
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, Brasil
| | - Pablo A Martinez
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, Brasil
| | - Luiz A C Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
| | - Claudio J Bidau
- Departamento de Ingeniería en Biotecnología, Universidad Nacional de Río Negro, Villa Regina, Argentina
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Modulation of immune response by organophosphorus pesticides: fishes as a potential model in immunotoxicology. J Immunol Res 2015; 2015:213836. [PMID: 25973431 PMCID: PMC4417994 DOI: 10.1155/2015/213836] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 01/07/2015] [Accepted: 01/12/2015] [Indexed: 02/06/2023] Open
Abstract
Immune response is modulated by different substances that are present in the environment. Nevertheless, some of these may cause an immunotoxic effect. In this paper, the effect of organophosphorus pesticides (frequent substances spilled in aquatic ecosystems) on the immune system of fishes and in immunotoxicology is reviewed. Furthermore, some cellular and molecular mechanisms that might be involved in immunoregulation mechanisms of organophosphorus pesticides are discussed.
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31
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Betto-Colliard C, Sermier R, Litvinchuk S, Perrin N, Stöck M. Origin and genome evolution of polyploid green toads in Central Asia: evidence from microsatellite markers. Heredity (Edinb) 2015; 114:300-8. [PMID: 25370211 PMCID: PMC4815583 DOI: 10.1038/hdy.2014.100] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 09/10/2014] [Accepted: 09/22/2014] [Indexed: 02/08/2023] Open
Abstract
Polyploidization, which is expected to trigger major genomic reorganizations, occurs much less commonly in animals than in plants, possibly because of constraints imposed by sex-determination systems. We investigated the origins and consequences of allopolyploidization in Palearctic green toads (Bufo viridis subgroup) from Central Asia, with three ploidy levels and different modes of genome transmission (sexual versus clonal), to (i) establish a topology for the reticulate phylogeny in a species-rich radiation involving several closely related lineages and (ii) explore processes of genomic reorganization that may follow polyploidization. Sibship analyses based on 30 cross-amplifying microsatellite markers substantiated the maternal origins and revealed the paternal origins and relationships of subgenomes in allopolyploids. Analyses of the synteny of linkage groups identified three markers affected by translocation events, which occurred only within the paternally inherited subgenomes of allopolyploid toads and exclusively affected the linkage group that determines sex in several diploid species of the green toad radiation. Recombination rates did not differ between diploid and polyploid toad species, and were overall much reduced in males, independent of linkage group and ploidy levels. Clonally transmitted subgenomes in allotriploid toads provided support for strong genetic drift, presumably resulting from recombination arrest. The Palearctic green toad radiation seems to offer unique opportunities to investigate the consequences of polyploidization and clonal transmission on the dynamics of genomes in vertebrates.
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Affiliation(s)
- C Betto-Colliard
- Department of Ecology and Evolution, Biophore Building University of Lausanne, Lausanne, Switzerland
| | - R Sermier
- Department of Ecology and Evolution, Biophore Building University of Lausanne, Lausanne, Switzerland
| | - S Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
| | - N Perrin
- Department of Ecology and Evolution, Biophore Building University of Lausanne, Lausanne, Switzerland
| | - M Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
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Discovery of triploidy in Palearctic green toads (Anura: Bufonidae) from Iran with indications for a reproductive system involving diploids and triploids. ZOOL ANZ 2015. [DOI: 10.1016/j.jcz.2015.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Hofberger JA, Nsibo DL, Govers F, Bouwmeester K, Schranz ME. A complex interplay of tandem- and whole-genome duplication drives expansion of the L-type lectin receptor kinase gene family in the brassicaceae. Genome Biol Evol 2015; 7:720-34. [PMID: 25635042 PMCID: PMC5322546 DOI: 10.1093/gbe/evv020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2015] [Indexed: 11/15/2022] Open
Abstract
The comparative analysis of plant gene families in a phylogenetic framework has greatly accelerated due to advances in next generation sequencing. In this study, we provide an evolutionary analysis of the L-type lectin receptor kinase and L-type lectin domain proteins (L-type LecRKs and LLPs) that are considered as components in plant immunity, in the plant family Brassicaceae and related outgroups. We combine several lines of evidence provided by sequence homology, HMM-driven protein domain annotation, phylogenetic analysis, and gene synteny for large-scale identification of L-type LecRK and LLP genes within nine core-eudicot genomes. We show that both polyploidy and local duplication events (tandem duplication and gene transposition duplication) have played a major role in L-type LecRK and LLP gene family expansion in the Brassicaceae. We also find significant differences in rates of molecular evolution based on the mode of duplication. Additionally, we show that LLPs share a common evolutionary origin with L-type LecRKs and provide a consistent gene family nomenclature. Finally, we demonstrate that the largest and most diverse L-type LecRK clades are lineage-specific. Our evolutionary analyses of these plant immune components provide a framework to support future plant resistance breeding.
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Affiliation(s)
- Johannes A Hofberger
- Biosystematics Group, Wageningen University, The Netherlands Chinese Academy of Sciences/Max Planck Partner Institute for Computational Biology, Shanghai, People's Republic of China
| | - David L Nsibo
- Biosystematics Group, Wageningen University, The Netherlands
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University, The Netherlands
| | - Klaas Bouwmeester
- Laboratory of Phytopathology, Wageningen University, The Netherlands Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, The Netherlands
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Qin Q, Wang Y, Wang J, Dai J, Liu Y, Liu S. Abnormal chromosome behavior during meiosis in the allotetraploid of Carassius auratus red var. (♀)×Megalobrama amblycephala (♂). BMC Genet 2014; 15:95. [PMID: 25178799 PMCID: PMC4236601 DOI: 10.1186/s12863-014-0095-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 08/21/2014] [Indexed: 11/21/2022] Open
Abstract
Background Allopolyploids generally undergo bivalent pairing at meiosis because only homologous chromosomes pair up. On the other hand, several studies have documented abnormal chromosome behavior during mitosis and meiosis in allopolyploids plants leading to the production of gametes with complete paternal or maternal chromosomes. Polyploidy is relatively rare in animals compared with plants; thus, chromosome behavior at meiosis in the allopolyploid animals is poorly understood. Results Tetraploid hybrids (abbreviated as 4nRB) (4n = 148, RRBB) of Carassius auratus red var. (abbreviated as RCC) (2n = 100, RR) (♀) × Megalobrama amblycephala (abbreviated as BSB) (2n = 48, BB) (♂) generated gametes of different size. To test the genetic composition of these gametes, the gynogenetic offspring and backcross progenies of 4nRB were produced, and their genetic composition were examined by chromosome analysis and FISH. Our results suggest that 4nRB can produce several types of gametes with different genetic compositions, including allotetraploid (RRBB), autotriploid (RRR), autodiploid (RR), and haploid (R) gametes. Conclusions This study provides direct evidence of abnormal chromosome behavior during meiosis in an allotetraploid fish.
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Affiliation(s)
| | | | | | | | | | - Shaojun Liu
- Key Laboratory of Protein Chemistry and Developmental Biology of the State Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha 410018, People's Republic of China.
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Spoz A, Boron A, Porycka K, Karolewska M, Ito D, Abe S, Kirtiklis L, Juchno D. Molecular cytogenetic analysis of the crucian carp, Carassius carassius (Linnaeus, 1758) (Teleostei, Cyprinidae), using chromosome staining and fluorescence in situ hybridisation with rDNA probes. COMPARATIVE CYTOGENETICS 2014; 8:233-48. [PMID: 25349674 PMCID: PMC4205492 DOI: 10.3897/compcytogen.v8i3.7718] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 07/28/2014] [Indexed: 05/13/2023]
Abstract
The crucian carp Carassius carassius (Linnaeus, 1758) is a species with restricted and decreasing distribution in Europe. Six males and six females of the species from the Baltic Sea basin in Poland were examined to show sequentially CMA3/AgNO3 staining pattern, DAPI staining, and, for the first time in literature, molecular cytogenetic analysis using double-colour fluorescence in situ hybridisation (FISH) with 28S and 5S rDNA probes. The karyotype consisted of 20 m, 36 sm and 44 sta chromosomes, NF=156. The AgNO3 stained NORs were most frequently located terminally in the short arms of two sm and two sta elements, and CMA3-positive sites were also observed suggesting abundant GC-rich repetitive DNA in the regions. Other CMA3-positive sites in the short arms of six to ten sm and sta chromosomes were detected. The results based on 28S rDNA FISH confirmed the location of rDNA sites. DAPI-negative staining of NORs suggested the scarcity of AT-rich DNA in the regions. FISH with 5S rDNA probe revealed 8-14 loci (ten and 12 in respectively 49 and 29% of metaphases). They were located in two sm and eight to ten sta chromosomes and six of them were larger than others. Simultaneously, mapping of the two rDNA families on the chromosomes of C. carassius revealed that both 28S and 5S rDNA probes were located in different chromosomes. Molecular cytogenetic data of C. carassius presented here for the first time give an important insight into the structure of chromosomes of this polyploid and declining species and may be useful in its systematics.
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Affiliation(s)
- Aneta Spoz
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowskiego Str. 5, 10-718 Olsztyn, Poland
| | - Alicja Boron
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowskiego Str. 5, 10-718 Olsztyn, Poland
| | - Katarzyna Porycka
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowskiego Str. 5, 10-718 Olsztyn, Poland
| | - Monika Karolewska
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowskiego Str. 5, 10-718 Olsztyn, Poland
| | - Daisuke Ito
- Instituto Gulbenkian de Ciência, Rua da Quinta Grade, 6, 2780-156, Oeiras, Portugal
| | - Syuiti Abe
- Sanriku Fisheries Research Center, Department of Revitalization for Sanriku-region, Iwate University, 3-75-1, Heita, Kamaishi 026-0001, Iwate, Japan
| | - Lech Kirtiklis
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowskiego Str. 5, 10-718 Olsztyn, Poland
| | - Dorota Juchno
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowskiego Str. 5, 10-718 Olsztyn, Poland
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Evidence for meiotic drive as an explanation for karyotype changes in fishes. Mar Genomics 2014; 15:29-34. [PMID: 24844732 DOI: 10.1016/j.margen.2014.05.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 05/05/2014] [Accepted: 05/05/2014] [Indexed: 11/21/2022]
Abstract
The process of preferential chromosome segregation during meiosis has been suggested to be responsible for the predominance of certain chromosome types in the karyotypes of mammals, birds and insects. We developed an extensive analysis of the fixation of mono- or bibrachial chromosomes in the karyotypes of the large Actinopterygii fish group, a key link in the evolution of terrestrial vertebrates, in order to investigate the generality of meiotic drive in determining karyotypic macrotrends. Unlike mammals, fishes have markedly undergone several types of preferential chromosomal rearrangements throughout evolution. Data from the analyzed orders indicate a prevalence of karyotypes with few (<33%) or many (>66%) acrocentric chromosomes and a low number of karyotypes with balanced numbers of mono- and bi-brachial elements. Parallel trends towards a higher number of karyotypes with prevalence of monobrachial chromosomes occurred in phylogenetically close orders (e.g. Perciformes and Tetraodontiformes, and in the order Mugiliformes) and in clades with prevalence of bibrachial elements (e.g. Characiformes, Gymnotiformes, Siluriformes, and Cypriniformes). Some orders where fewer species were available for study, such as Atheriniformes and Anguilliformes, showed karyotype assemblages where both trends were present. Our results strongly suggest a primary role of meiotic drive in karyotypic evolution as indicated by the accumulation of monobrachial chromosomes in Perciformes and Cypriniformes, or bibrachial chromosomes in Siluriformes and Characiformes. Further examinations of the interaction between life history traits, environmental characteristics, and the fixation of chromosomal rearrangements would be exceedingly valuable.
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Zhan SH, Glick L, Tsigenopoulos CS, Otto SP, Mayrose I. Comparative analysis reveals that polyploidy does not decelerate diversification in fish. J Evol Biol 2014; 27:391-403. [DOI: 10.1111/jeb.12308] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 11/18/2013] [Accepted: 11/24/2013] [Indexed: 11/30/2022]
Affiliation(s)
- S. H. Zhan
- University of British Columbia; Vancouver BC Canada
| | - L. Glick
- Department of Molecular Biology and Ecology of Plants; Tel Aviv University; Tel Aviv Israel
| | - C. S. Tsigenopoulos
- Institute of Marine Biology and Genetics; Hellenic Centre for Marine Research; Crete Greece
| | - S. P. Otto
- Department of Zoology; University of British Columbia; Vancouver BC Canada
| | - I. Mayrose
- Department of Molecular Biology and Ecology of Plants; Tel Aviv University; Tel Aviv Israel
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Tempo and mode of recurrent polyploidization in the Carassius auratus species complex (Cypriniformes, Cyprinidae). Heredity (Edinb) 2014; 112:415-27. [PMID: 24398883 DOI: 10.1038/hdy.2013.121] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 09/29/2013] [Accepted: 10/01/2013] [Indexed: 11/09/2022] Open
Abstract
Polyploidization is an evolutionarily rare but important mechanism in both plants and animals because it increases genetic diversity. Goldfish of the Carassius auratus species complex can be tetraploids, hexaploids and octaploids. Polyploidization events have occurred repeatedly in goldfish, yet the extent of this phenomenon and its phyletic history are poorly understood. We explore the origin, tempo and frequency of polyploidization in Chinese and Japanese goldfish using both mitochondrial (mtDNA) and nuclear DNA sequences from up to 1202 individuals including the outgroup taxon, Cyprinus carpio. Analyses of de novo nuclear gene data resolve two clusters of alleles and the pattern supports the prior hypothesis of an ancient allotetraploidization for Carassius. Alleles shared by tetraploid and hexaploid individuals indicate recent autoploidizations within the C. auratus complex. Sympatric tetraploids and hexaploids share mtDNA haplotypes and these frequently occur independently within six well-supported lineages and sublineages on a small spatial scale. Gene flow estimates (Fst values) indicate that hexaploids differ only slightly from sympatric tetraploids, if at all. In contrast, allopatric populations of tetraploids and hexaploids differ from one another to a far greater extent. Gene flow between sampled localities appears to be limited. Coalescence-based time estimations for hexaploids reveal that the oldest lineage within any sampled locality is around one million years old, which is very young. Sympatric, recurrent autoploidization occurs in all sampled populations of the C. auratus complex. Goldfish experience polyploidization events more frequently than any other vertebrate.
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He W, Xie L, Li T, Liu S, Xiao J, Hu J, Wang J, Qin Q, Liu Y. The formation of diploid and triploid hybrids of female grass carp × male blunt snout bream and their 5S rDNA analysis. BMC Genet 2013; 14:110. [PMID: 24267392 PMCID: PMC4222567 DOI: 10.1186/1471-2156-14-110] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 11/19/2013] [Indexed: 11/16/2022] Open
Abstract
Background Hybridization is a useful strategy to alter the genotypes and phenotypes of the offspring. It could transfer the genome of one species to another through combing the different genome of parents in the hybrid offspring. And the offspring may exhibit advantages in growth rate, disease resistance, survival rate and appearance, which resulting from the combination of the beneficial traits from both parents. Results Diploid and triploid hybrids of female grass carp (Ctenopharyngodon idellus, GC, Cyprininae, 2n = 48) × male blunt snout bream (Megalobrama amblycephala, BSB, Cultrinae, 2n = 48) were successfully obtained by distant hybridization. Diploid hybrids had 48 chromosomes, with one set from GC and one set from BSB. Triploid hybrids possessed 72 chromosomes, with two sets from GC and one set from BSB. The morphological traits, growth rates, and feeding ecology of the parents and hybrid offspring were compared and analyzed. The two kinds of hybrid offspring exhibited significantly phenotypic divergence from GC and BSB. 2nGB hybrids showed similar growth rate compared to that of GC, and 3nGB hybrids significantly higher results. Furthermore, the feeding ecology of hybrid progeny was omnivorous. The 5S rDNA of GC, BSB and their hybrid offspring were also cloned and sequenced. There was only one type of 5S rDNA (designated type I: 180 bp) in GC and one type of 5S rDNA (designated type II: 188 bp) in BSB. However, in the hybrid progeny, diploid and triploid hybrids both inherited type I and type II from their parents, respectively. In addition, a chimera of type I and type II was observed in the genome of diploid and triploid hybrids, excepting a 10 bp of polyA insertion in type II sequence of the chimera of the diploid hybrids. Conclusions This is the first report of diploid and triploid hybrids being produced by crossing GC and BSB, which have the same chromosome number. The obtainment of two new hybrid offspring has significance in fish genetic breeding. The results illustrate the effect of hybridization and polyploidization on the organization and variation of 5S rDNA in hybrid offspring.
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Affiliation(s)
- Weiguo He
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha 410081, P R, China.
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Molina W, Jacobina U. Protocolos Citogenéticos e Perspectivas Biotecnológicas Voltadas à Piscicultura Marinha e Conservação. BIOTA AMAZÔNIA 2013. [DOI: 10.18561/2179-5746/biotaamazonia.v3n2p155-168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Verburg-van Kemenade BML, Van der Aa LM, Chadzinska M. Neuroendocrine-immune interaction: regulation of inflammation via G-protein coupled receptors. Gen Comp Endocrinol 2013. [PMID: 23201149 DOI: 10.1016/j.ygcen.2012.11.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Neuroendocrine- and immune systems interact in a bi-directional fashion to communicate the status of pathogen recognition to the brain and the immune response is influenced by physiological changes. The network of ligands and their receptors involved includes cytokines and chemokines, corticosteroids, classical pituitary hormones, catecholamines and neuropeptides (e.g. opioids), as well as neural pathways. We studied the role of opioid, adrenergic and melatonin G-protein coupled receptors (GPCR) on carp (Cyprinus carpio) leucocytes. Ligand interaction by morphine and adrenaline both in vitro and in vivo resulted in considerable decrease of chemotaxis and expression of CXC chemokines and chemokine CXC receptors. These effects may have substantial influence on the process of inflammation, the efficacy of which is crucial for an effective immune response. Both opioid receptors and chemokine receptors are G-protein coupled receptors (GPCRs), and were classically assumed to function as monomers. This paradigm is now challenged by the emerging concept of homo- and hetero dimerization which may represent the native form of many receptors. G-protein coupling, downstream signaling and regulatory processes such as receptor internalization are largely influenced by the dimeric nature. The true functional importance of GPCR interactions remains enigmatic, but it certainly has implications with respect to the specificity of currently used medications. This review focuses on the important function of chemokine GPCRs during inflammation and the potential neuroendocrine modulation of this process through "neuroendocrine" GPCRs.
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Affiliation(s)
- B M L Verburg-van Kemenade
- Cell Biology and Immunology Group, Wageningen University, De Elst 1, P.O. Box 338, 6700 AH Wageningen, The Netherlands.
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Doering JA, Giesy JP, Wiseman S, Hecker M. Predicting the sensitivity of fishes to dioxin-like compounds: possible role of the aryl hydrocarbon receptor (AhR) ligand binding domain. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:1219-1224. [PMID: 23054770 DOI: 10.1007/s11356-012-1203-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 09/14/2012] [Indexed: 06/01/2023]
Abstract
Dioxin-like compounds are chronically toxic to most vertebrates. However, dramatic differences in sensitivity to these chemicals exist both within and among vertebrate classes. A recent study found that in birds, critical amino acid residues in the aryl hydrocarbon receptor (AhR) ligand binding domain are predictive of sensitivity to dioxin-like compounds in a range of species. It is currently unclear whether similar predictive relationships exist for fishes, a group of animals at risk of exposure to dioxin-like compounds. Effects of dioxin-like compounds are mediated through the AhR in fishes and birds. However, AhR dynamics are more complex among fishes. Fishes possess AhRs that can be grouped within at least three distinct clades (AhR1, AhR2, AhR3) with each clade possibly containing multiple isoforms. AhR2 has been shown to be the active form in most teleosts, with AhR1 not binding dioxin-like compounds. The role of AhR3 in dioxin-like toxicity has not been established to date and this clade is only known to be expressed in some cartilaginous fishes. Furthermore, multiple mechanisms of sensitivity to dioxin-like compounds that are not relevant in birds could exist among fishes. Although, at this time, deficiencies exist for the development of such a predictive relationship for application to fishes, successfully establishing such relationships would offer a substantial improvement in assessment of risks of dioxin-like compounds for this class of vertebrates. Elucidation of such relationships would provide a mechanistic foundation for extrapolation among species to allow the identification of the most sensitive fishes, with the ultimate goal of the prediction of risk posed to endangered species that are not easily studied.
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Affiliation(s)
- Jon A Doering
- Toxicology Centre, University of Saskatchewan, Toxicology Centre, 44 Campus Drive, Saskatoon, SK, Canada, S7N 5B3.
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Kakioka R, Kokita T, Kumada H, Watanabe K, Okuda N. A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae). BMC Genomics 2013; 14:32. [PMID: 23324215 PMCID: PMC3583795 DOI: 10.1186/1471-2164-14-32] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 01/14/2013] [Indexed: 11/10/2022] Open
Abstract
Background The construction of linkage maps is a first step in exploring the genetic basis for adaptive phenotypic divergence in closely related species by quantitative trait locus (QTL) analysis. Linkage maps are also useful for comparative genomics in non-model organisms. Advances in genomics technologies make it more feasible than ever to study the genetics of adaptation in natural populations. Restriction-site associated DNA (RAD) sequencing in next-generation sequencers facilitates the development of many genetic markers and genotyping. We aimed to construct a linkage map of the gudgeons of the genus Gnathopogon (Cyprinidae) for comparative genomics with the zebrafish Danio rerio (a member of the same family as gudgeons) and for the future QTL analysis of the genetic architecture underlying adaptive phenotypic evolution of Gnathopogon. Results We constructed the first genetic linkage map of Gnathopogon using a 198 F2 interspecific cross between two closely related species in Japan: river-dwelling Gnathopogon elongatus and lake-dwelling Gnathopogon caerulescens. Based on 1,622 RAD-tag markers, a linkage map spanning 1,390.9 cM with 25 linkage groups and an average marker interval of 0.87 cM was constructed. We also identified a region involving female-specific transmission ratio distortion (TRD). Synteny and collinearity were extensively conserved between Gnathopogon and zebrafish. Conclusions The dense SNP-based linkage map presented here provides a basis for future QTL analysis. It will also be useful for transferring genomic information from a “traditional” model fish species, zebrafish, to screen candidate genes underlying ecologically important traits of the gudgeons.
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Affiliation(s)
- Ryo Kakioka
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, 606-8502, Kyoto, Japan.
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Collares-Pereira M, Matos I, Morgado-Santos M, Coelho M. Natural Pathways towards Polyploidy in Animals: TheSqualius alburnoidesFish Complex as a Model System to Study Genome Size and Genome Reorganization in Polyploids. Cytogenet Genome Res 2013; 140:97-116. [DOI: 10.1159/000351729] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Mechanisms of Gene Duplication and Translocation and Progress towards Understanding Their Relative Contributions to Animal Genome Evolution. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:846421. [PMID: 22919542 PMCID: PMC3420103 DOI: 10.1155/2012/846421] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 05/30/2012] [Accepted: 06/27/2012] [Indexed: 01/10/2023]
Abstract
Duplication of genetic material is clearly a major route to genetic change, with consequences for both evolution and disease. A variety of forms and mechanisms of duplication are recognised, operating across the scales of a few base pairs upto entire genomes. With the ever-increasing amounts of gene and genome sequence data that are becoming available, our understanding of the extent of duplication is greatly improving, both in terms of the scales of duplication events as well as their rates of occurrence. An accurate understanding of these processes is vital if we are to properly understand important events in evolution as well as mechanisms operating at the level of genome organisation. Here we will focus on duplication in animal genomes and how the duplicated sequences are distributed, with the aim of maintaining a focus on principles of evolution and organisation that are most directly applicable to the shaping of our own genome.
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Murat F, de Peer YV, Salse J. Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes. Genome Biol Evol 2012; 4:917-28. [PMID: 22833223 PMCID: PMC3516226 DOI: 10.1093/gbe/evs066] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Continuing advances in genome sequencing technologies and computational methods for comparative genomics currently allow inferring the evolutionary history of entire plant and animal genomes. Based on the comparison of the plant and animal genome paleohistory, major differences are unveiled in 1) evolutionary mechanisms (i.e., polyploidization versus diploidization processes), 2) genome conservation (i.e., coding versus noncoding sequence maintenance), and 3) modern genome architecture (i.e., genome organization including repeats expansion versus contraction phenomena). This article discusses how extant animal and plant genomes are the result of inherently different rates and modes of genome evolution resulting in relatively stable animal and much more dynamic and plastic plant genomes.
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Affiliation(s)
- Florent Murat
- INRA/UBP UMR 1095 GDEC ‘Génétique, Diversité et Ecophysiologie des Céréales’, Clermont Ferrand, France
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Jérôme Salse
- INRA/UBP UMR 1095 GDEC ‘Génétique, Diversité et Ecophysiologie des Céréales’, Clermont Ferrand, France
- *Corresponding author: E-mail:
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He W, Qin Q, Liu S, Li T, Wang J, Xiao J, Xie L, Zhang C, Liu Y. Organization and variation analysis of 5S rDNA in different ploidy-level hybrids of red crucian carp × topmouth culter. PLoS One 2012; 7:e38976. [PMID: 22720007 PMCID: PMC3377697 DOI: 10.1371/journal.pone.0038976] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 05/14/2012] [Indexed: 11/18/2022] Open
Abstract
Through distant crossing, diploid, triploid and tetraploid hybrids of red crucian carp (Carassius auratus red var., RCC♀, Cyprininae, 2n = 100) × topmouth culter (Erythroculter ilishaeformis Bleeker, TC♂, Cultrinae, 2n = 48) were successfully produced. Diploid hybrids possessed 74 chromosomes with one set from RCC and one set from TC; triploid hybrids harbored 124 chromosomes with two sets from RCC and one set from TC; tetraploid hybrids had 148 chromosomes with two sets from RCC and two sets from TC. The 5S rDNA of the three different ploidy-level hybrids and their parents were sequenced and analyzed. There were three monomeric 5S rDNA classes (designated class I: 203 bp; class II: 340 bp; and class III: 477 bp) in RCC and two monomeric 5S rDNA classes (designated class IV: 188 bp, and class V: 286 bp) in TC. In the hybrid offspring, diploid hybrids inherited three 5S rDNA classes from their female parent (RCC) and only class IV from their male parent (TC). Triploid hybrids inherited class II and class III from their female parent (RCC) and class IV from their male parent (TC). Tetraploid hybrids gained class II and class III from their female parent (RCC), and generated a new 5S rDNA sequence (designated class I-N). The specific paternal 5S rDNA sequence of class V was not found in the hybrid offspring. Sequence analysis of 5S rDNA revealed the influence of hybridization and polyploidization on the organization and variation of 5S rDNA in fish. This is the first report on the coexistence in vertebrates of viable diploid, triploid and tetraploid hybrids produced by crossing parents with different chromosome numbers, and these new hybrids are novel specimens for studying the genomic variation in the first generation of interspecific hybrids, which has significance for evolution and fish genetics.
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Affiliation(s)
- Weiguo He
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
| | - Qinbo Qin
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
| | - Shaojun Liu
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
- * E-mail:
| | - Tangluo Li
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
| | - Jing Wang
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
| | - Jun Xiao
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
| | - Lihua Xie
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
| | - Chun Zhang
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
| | - Yun Liu
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
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Filipiak M, Tylko G, Kilarski W. Flow cytometric determination of genome size in European sunbleak Leucaspius delineatus (Heckel, 1843). FISH PHYSIOLOGY AND BIOCHEMISTRY 2012; 38:355-362. [PMID: 21614549 PMCID: PMC3309147 DOI: 10.1007/s10695-011-9512-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 05/13/2011] [Indexed: 05/30/2023]
Abstract
The aim of this study was to compare DNA content in hepatocyte and erythrocyte nuclei of the European sunbleak, Leucaspius delineatus, in relation to nuclear and cell size by means of flow cytometry and fluorescence microscopy. The DNA standards, chicken and rainbow trout erythrocytes, were prepared in parallel with both cell types, with initial separation of liver cells in pepsin solution followed by cell filtering. Standards and investigated cells were stained with a mixture of propidium iodide, citric acid, and Nonidet P40 in the presence of RNAse, and fluorescence of at least 50,000 nuclei was analyzed by flow cytometry. Average cell size was determined by flow cytometry, using fresh cell suspension in relation to latex beads of known diameter. The size of nuclei was examined on the basis of digital micrographs obtained by fluorescence microscopy after nuclei staining with DAPI. The sunbleak's erythrocyte nuclei contain 2.25 ± 0.06 pg of DNA, whereas the hepatocyte nuclei contain 2.46 ± 0.06 pg of DNA. This difference in DNA content was determined spectroscopically using isolated DNA from the two cell types. The modal diameters of the erythrocytes and hepatocytes were estimated to be 5.1 ± 0.2 and 22.3 ± 5.0 μm, respectively, and the corresponding modal dimensions of their nuclei (measured as surface area) were 15.2 and 21.4 μm(2), respectively. The nucleoplasmic index, as calculated from diameters estimated from surface area of nuclear profiles, was 2.51 for the erythrocytes compared with 0.08 for hepatocytes.
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Affiliation(s)
- Marta Filipiak
- Department of Cytology and Histology, Institute of Zoology, Jagiellonian University, 6 Ingardena, 30-060 Krakow, Poland
| | - Grzegorz Tylko
- Department of Cytology and Histology, Institute of Zoology, Jagiellonian University, 6 Ingardena, 30-060 Krakow, Poland
| | - Wincenty Kilarski
- Department of Cytology and Histology, Institute of Zoology, Jagiellonian University, 6 Ingardena, 30-060 Krakow, Poland
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Nikinmaa M, Rytkönen KT. From genomes to functions in aquatic biology. Mar Genomics 2012; 5:1-6. [DOI: 10.1016/j.margen.2011.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 08/17/2011] [Accepted: 08/17/2011] [Indexed: 11/25/2022]
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GUIGNARD MAÏTÉ, BÜCHI LUCIE, GÉTAZ MICHAEL, BETTO-COLLIARD CAROLINE, STÖCK MATTHIAS. Genome size rather than content might affect call properties in toads of three ploidy levels (Anura: Bufonidae: Bufo viridis subgroup). Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2011.01837.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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