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Toyota K. Crustacean endocrinology: Sexual differentiation and potential application for aquaculture. Gen Comp Endocrinol 2024; 356:114578. [PMID: 38971237 DOI: 10.1016/j.ygcen.2024.114578] [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: 04/26/2024] [Revised: 06/17/2024] [Accepted: 06/28/2024] [Indexed: 07/08/2024]
Abstract
Crustaceans, which represent a significant subset of arthropods, are classified into three major classes: Ostracoda, Malacostraca, and Branchiopoda. Among them, sex manipulation in decapod species from the Malacostraca class has been extensively researched for aquaculture purposes and to study reproductive physiology and sexual plasticity. Some decapods exhibit sexual dimorphism that influences their biological and economic value. Monosex culture, in which only one sex is cultivated, increases production yields while reducing the risk of invasiveness, as genetic leakage into natural waters is less likely to occur. Differences in yield are also observed when cultivating different sexes, with all-male cultures of Macrobrachium rosenbergii being more profitable than both mixed and all-female cultures. Research on decapod sexual differentiation has led to a better understanding of sex determination and sexual differentiation processes in arthropods. Similar to most mammals and other vertebrate classes, Malacostraca crustaceans, including decapods, exhibit a cell-non-autonomous mode of sexual development. Genetic factors (e.g., sex chromosomes) and endocrine factors (e.g., insulin-like androgenic gland factor and crustacean female sex hormone) play pivotal roles in the development of sexually dimorphic traits. This review synthesizes the existing understanding of sex determination mechanisms and the role of sex hormones in decapod species. Additionally, it provides an overview of the methyl farnesoate, which has been suggested to be involved in male sex differentiation in some crab species, as well as the phenomenon of male-to-female sex reversal in host decapods caused by parasitic crustaceans.
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Affiliation(s)
- Kenji Toyota
- Department of Bioresource Science, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima, Hiroshima 739-8528, Japan; Department of Biological Sciences, Faculty of Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan; Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
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2
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Yarbrough E, Chandler C. Patterns of molecular evolution in a parthenogenic terrestrial isopod ( Trichoniscus pusillus). PeerJ 2024; 12:e17780. [PMID: 39071119 PMCID: PMC11276757 DOI: 10.7717/peerj.17780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 06/30/2024] [Indexed: 07/30/2024] Open
Abstract
The "paradox of sex" refers to the question of why sexual reproduction is maintained in the wild, despite how costly it is compared to asexual reproduction. Because of these costs, one might expect nature to select for asexual reproduction, yet sex seems to be continually selected for. Multiple hypotheses have been proposed to explain this incongruence, including the niche differentiation hypothesis, the Red Queen hypothesis, and accumulation of harmful mutations in asexual species due to inefficient purifying selection. This study focuses on the accumulation of mutations in two terrestrial isopods, Trichoniscus pusillus, which has sexual diploid and parthenogenic triploid forms, and Hyloniscus riparius, an obligately sexual relative. We surveyed sex ratios of both species in an upstate New York population and obtained RNA-seq data from wild-caught individuals of both species to examine within- and between-species patterns of molecular evolution in protein-coding genes. The sex ratio and RNA-seq data together provide strong evidence that this T. pusillus population is entirely asexual and triploid, while the H. riparius population is sexual and diploid. Although all the wild T. pusillus individuals used for sequencing shared identical genotypes at nearly all SNPs, supporting a clonal origin, heterozygosity and SNP density were much higher in T. pusillus than in the sexually reproducing H. riparius. This observation suggests this parthenogenic lineage may have arisen via mating between two divergent diploid lineages. Between-species sequence comparisons showed no evidence of ineffective purifying selection in the asexual T. pusillus lineage, as measured by the ratio of nonsynonymous to synonymous substitutions (dN/dS ratios). Likewise, there was no difference between T. pusillus and H. riparius in the ratios of nonsynonymous to synonymous SNPs overall (pN/pS). However, pN/pS ratios in T. pusillus were significantly higher when considering only SNPs that may have arisen via recent mutation after the transition to parthenogenesis. Thus, these recent SNPs are consistent with the hypothesis that purifying selection is less effective against new mutations in asexual lineages, but only over long time scales. This system provides a useful model for future studies on the evolutionary tradeoffs between sexual and asexual reproduction in nature.
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Affiliation(s)
- Emily Yarbrough
- Department of Biological Sciences, State University of New York at Oswego, Oswego, NY, United States of America
- Department of Biological Sciences, State University of New York at Binghamton, Binghamton, NY, United States of America
| | - Christopher Chandler
- Department of Biological Sciences, State University of New York at Oswego, Oswego, NY, United States of America
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Luo L, Yang LS, Huang JH, Jiang SG, Zhou FL, Li YD, Jiang S, Yang QB. Effects of Different Salinity Stress on the Transcriptomic Responses of Freshwater Crayfish ( Procambarus clarkii, Girard, 1852). BIOLOGY 2024; 13:530. [PMID: 39056722 PMCID: PMC11273973 DOI: 10.3390/biology13070530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/03/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024]
Abstract
Salinization of freshwater ecosystems is a pressing global issue. Changes in salinity can exert severe pressure on aquatic animals and jeopardize their survival. Procambarus clarkii is a valuable freshwater aquaculture species that exhibits some degree of salinity tolerance, making it an excellent research model for freshwater aquaculture species facing salinity stress. In the present study, crayfish were exposed to acute low salt (6 ppt) and high salt (18 ppt) conditions. The organisms were continuously monitored at 6, 24, and 72 h using RNA-Seq to investigate the mechanisms of salt stress resistance. Transcriptome analysis revealed that the crayfish responded to salinity stress with numerous differentially expressed genes, and most of different expression genes was observed in high salinity group for 24h. GO and KEGG enrichment analyses indicated that metabolic pathways were the primary response pathways in crayfish under salinity stress. This suggests that crayfish may use metabolic pathways to compensate for energy loss caused by osmotic stress. Furthermore, gene expression analysis revealed the differential expression of immune and antioxidant-related pathway genes under salinity stress, implying that salinity stress induces immune disorders in crayfish. More genes related to cell proliferation, differentiation, and apoptosis, such as the Foxo, Wnt, Hippo, and Notch signaling pathways, responded to high-salinity stress. This suggests that regulating the cellular replication cycle and accelerating apoptosis may be necessary for crayfish to cope with high-salinity stress. Additionally, we identified 36 solute carrier family (SLC) genes related to ion transport, depicting possible ion exchange mechanisms in crayfish under salinity stress. These findings aimed to establish a foundation for understanding crustacean responses to salinity stress and their osmoregulatory mechanisms.
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Affiliation(s)
- Lei Luo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (L.L.); (J.-H.H.); (S.-G.J.); (F.-L.Z.); (Y.-D.L.); (S.J.)
- Shenzhen Base of South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen 518108, China
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Li-Shi Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (L.L.); (J.-H.H.); (S.-G.J.); (F.-L.Z.); (Y.-D.L.); (S.J.)
- Shenzhen Base of South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen 518108, China
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya 572018, China;
| | - Jian-Hua Huang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (L.L.); (J.-H.H.); (S.-G.J.); (F.-L.Z.); (Y.-D.L.); (S.J.)
- Shenzhen Base of South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen 518108, China
| | - Shi-Gui Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (L.L.); (J.-H.H.); (S.-G.J.); (F.-L.Z.); (Y.-D.L.); (S.J.)
- Shenzhen Base of South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen 518108, China
| | - Fa-Lin Zhou
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (L.L.); (J.-H.H.); (S.-G.J.); (F.-L.Z.); (Y.-D.L.); (S.J.)
- Shenzhen Base of South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen 518108, China
| | - Yun-Dong Li
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (L.L.); (J.-H.H.); (S.-G.J.); (F.-L.Z.); (Y.-D.L.); (S.J.)
- Shenzhen Base of South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen 518108, China
| | - Song Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (L.L.); (J.-H.H.); (S.-G.J.); (F.-L.Z.); (Y.-D.L.); (S.J.)
- Shenzhen Base of South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen 518108, China
| | - Qi-Bin Yang
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya 572018, China;
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Heinz J, Wenninger M. EVALUATION OF IMMERSION IN EMULSIFIED ISOFLURANE OR PROPOFOL AS PART OF A TWO-STEP EUTHANASIA PROTOCOL IN MARBLED CRAYFISH ( PROCAMBARUS VIRGINALIS). J Zoo Wildl Med 2024; 55:424-429. [PMID: 38875198 DOI: 10.1638/2023-0137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2024] [Indexed: 06/16/2024] Open
Abstract
The marbled crayfish (Procambarus virginalis) is a parthenogenetic invasive species across much of the world, and when found, euthanasia is often recommended to reduce spread to naïve ecosystems. Euthanasia recommendations in crustaceans includes a two-step method: first to produce nonresponsiveness and then to destroy central nervous tissue. Minimal data exist on adequate anesthetic or immobilization methods for crayfish. A population of 90 marbled crayfish was scheduled for euthanasia due to invasive species concerns. The population was divided into six treatment groups to evaluate whether immersion in emulsified isoflurane or propofol solutions could produce nonresponsiveness. Each group was exposed to one of six treatments for 1 h: isoflurane emulsified at 0.1%, 0.5%, 2%, 5%, and 15% or propofol at 10 mg/L and then increased to 100 mg/L. Crayfish from all treatment groups were moved to nonmedicated water after completion of 1 h and observed for an additional 4 h. All crayfish treated with isoflurane showed lack of a righting reflex at 5 min and loss of movement after 30 min. By 240 min (4 h), none of the crayfish from the isoflurane treatment groups regained movement. None of the crayfish in the propofol treatment achieved loss of reflexes or responsiveness, and all remained normal upon return to nonmedicated water. Isoflurane emulsified in water produces nonresponsiveness that is appropriate for the first step of euthanasia, while propofol was insufficient at these treatment doses.
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Affiliation(s)
- Jessica Heinz
- Cincinnati Zoo and Botanical Garden, Cincinnati OH 45220, USA,
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Wang Y, Duchen P, Chávez A, Sree KS, Appenroth KJ, Zhao H, Höfer M, Huber M, Xu S. Population genomics and epigenomics of Spirodela polyrhiza provide insights into the evolution of facultative asexuality. Commun Biol 2024; 7:581. [PMID: 38755313 PMCID: PMC11099151 DOI: 10.1038/s42003-024-06266-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
Many plants are facultatively asexual, balancing short-term benefits with long-term costs of asexuality. During range expansion, natural selection likely influences the genetic controls of asexuality in these organisms. However, evidence of natural selection driving asexuality is limited, and the evolutionary consequences of asexuality on the genomic and epigenomic diversity remain controversial. We analyzed population genomes and epigenomes of Spirodela polyrhiza, (L.) Schleid., a facultatively asexual plant that flowers rarely, revealing remarkably low genomic diversity and DNA methylation levels. Within species, demographic history and the frequency of asexual reproduction jointly determined intra-specific variations of genomic diversity and DNA methylation levels. Genome-wide scans revealed that genes associated with stress adaptations, flowering and embryogenesis were under positive selection. These data are consistent with the hypothesize that natural selection can shape the evolution of asexuality during habitat expansions, which alters genomic and epigenomic diversity levels.
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Affiliation(s)
- Yangzi Wang
- Institute of Organismic and Molecular Evolution, University of Mainz, 55128, Mainz, Germany
- Institute for Evolution and Biodiversity, University of Münster, 48161, Münster, Germany
| | - Pablo Duchen
- Institute of Organismic and Molecular Evolution, University of Mainz, 55128, Mainz, Germany
- Institute for Evolution and Biodiversity, University of Münster, 48161, Münster, Germany
| | - Alexandra Chávez
- Institute of Organismic and Molecular Evolution, University of Mainz, 55128, Mainz, Germany
- Institute for Evolution and Biodiversity, University of Münster, 48161, Münster, Germany
- Institute of Plant Biology and Biotechnology, University of Münster, 48161, Münster, Germany
| | - K Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periya, 671320, India
| | - Klaus J Appenroth
- Matthias Schleiden Institute - Plant Physiology, Friedrich Schiller University of Jena, 07743, Jena, Germany
| | - Hai Zhao
- Chengdu Institute of Biology, Chinese Academy of Sciences, 6100641, Chengdu, China
| | - Martin Höfer
- Institute of Organismic and Molecular Evolution, University of Mainz, 55128, Mainz, Germany
- Institute for Evolution and Biodiversity, University of Münster, 48161, Münster, Germany
| | - Meret Huber
- Institute of Organismic and Molecular Evolution, University of Mainz, 55128, Mainz, Germany
- Institute of Plant Biology and Biotechnology, University of Münster, 48161, Münster, Germany
| | - Shuqing Xu
- Institute of Organismic and Molecular Evolution, University of Mainz, 55128, Mainz, Germany.
- Institute for Evolution and Biodiversity, University of Münster, 48161, Münster, Germany.
- Institute for Quantitative and Computational Biosciences, University of Mainz, 55218, Mainz, Germany.
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Liu LK, Jian JT, Jing SS, Gao RL, Chi XD, Tian G, Liu HP. The crustacean DNA virus tegument protein VP26 binds to SNAP29 to inhibit SNARE complex assembly and autophagic degradation. J Virol 2024; 98:e0140823. [PMID: 38189252 PMCID: PMC10878264 DOI: 10.1128/jvi.01408-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
Autophagy generally functions as a cellular surveillance mechanism to combat invading viruses, but viruses have evolved various strategies to block autophagic degradation and even subvert it to promote viral propagation. White spot syndrome virus (WSSV) is the most highly pathogenic crustacean virus, but little is currently known about whether crustacean viruses such as WSSV can subvert autophagic degradation for escape. Here, we show that even though WSSV proliferation triggers the accumulation of autophagosomes, autophagic degradation is blocked in the crustacean species red claw crayfish. Interestingly, the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex including CqSNAP29, CqVAMP7, and the novel autophagosome SNARE protein CqSyx12 is required for autophagic flux to restrict WSSV replication, as revealed by gene silencing experiments. Simultaneously, the expressed WSSV tegument protein VP26, which likely localizes on autophagic membrane mediated by its transmembrane region, binds the Qb-SNARE domain of CqSNAP29 to competitively inhibit the binding of CqSyx12-Qa-SNARE with CqSNAP29-Qb-SNARE; this in turn disrupts the assembly of the CqSyx12-SNAP29-VAMP7 SNARE complex, which is indispensable for the proposed fusion of autophagosomes and lysosomes. Consequently, the autophagic degradation of WSSV is likely suppressed by the expressed VP26 protein in vivo in crayfish, thus probably protecting WSSV components from degradation via the autophagosome-lysosome pathway, resulting in evasion by WSSV. Collectively, these findings highlight how a DNA virus can subvert autophagic degradation by impairing the assembly of the SNARE complex to achieve evasion, paving the way for understanding host-DNA virus interactions from an evolutionary point of view, from crustaceans to mammals.IMPORTANCEWhite spot syndrome virus (WSSV) is one of the largest animal DNA viruses in terms of its genome size and has caused huge economic losses in the farming of crustaceans such as shrimp and crayfish. Detailed knowledge of WSSV-host interactions is still lacking, particularly regarding viral escape from host immune clearance. Intriguingly, we found that the presence of WSSV-VP26 might inhibit the autophagic degradation of WSSV in vivo in the crustacean species red claw crayfish. Importantly, this study is the first to show that viral protein VP26 functions as a core factor to benefit WSSV escape by disrupting the assembly of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex, which is necessary for the proposed fusion of autophagosomes with lysosomes for subsequent degradation. These findings highlight a novel mechanism of DNA virus evasion by blocking SNARE complex assembly and identify viral VP26 as a key candidate for anti-WSSV targeting.
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Affiliation(s)
- Ling-Ke Liu
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jiu-Ting Jian
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Shan-Shan Jing
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Rui-Lin Gao
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiao-Dong Chi
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Geng Tian
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Hai-Peng Liu
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, China
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Göpel T, Burggren WW. Temperature and hypoxia trigger developmental phenotypic plasticity of cardiorespiratory physiology and growth in the parthenogenetic marbled crayfish, Procambarus virginalis Lyko, 2017. Comp Biochem Physiol A Mol Integr Physiol 2024; 288:111562. [PMID: 38113959 DOI: 10.1016/j.cbpa.2023.111562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/06/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023]
Abstract
Attempting to differentiate phenotypic variation caused by environmentally-induced alterations in gene expression from that caused by actual allelic differences can be experimentally difficult. Environmental variables must be carefully controlled and then interindividual genetic differences ruled out as sources of phenotypic variation. We investigated phenotypic variability of cardiorespiratory physiology as well as biometric traits in the parthenogenetically-reproducing marbled crayfish Procambarus virginalis Lyko, 2017, all offspring being genetically identical clones. Populations of P. virginalis were reared from eggs tank-bred at four different temperatures (16, 19, 22 and 25 °C) or two different oxygen levels (9.5 and 20 kPa). Then, at Stage 3 and 4 juvenile stages, physiological (heart rate, oxygen consumption) and morphological (carapace length, body mass) variables were measured. Heart rate and oxygen consumption measured at 23 °C showed only small effects of rearing temperature in Stage 3 juveniles, with larger effects evident in older, Stage 4 juveniles. Additionally, coefficients of variation were calculated to compare our data to previously published data on P. virginalis as well as sexually-reproducing crayfish. Comparison revealed that carapace length, body mass and heart rate (but not oxygen consumption) indeed showed lower, yet notable coefficients of variation in clonal crayfish. Yet, despite being genetically identical, significant variation in their morphology and physiology in response to different rearing conditions nonetheless occurred in marbled crayfish. This suggests that epigenetically induced phenotypic variation might play a significant role in asexual but also sexually reproducing species.
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Affiliation(s)
- Torben Göpel
- Developmental Integrative Biology Research Group, Department of Biological Sciences, University of North Texas, Denton, TX, USA; Multiscale Biology, Georg-August-Universität Göttingen, Göttingen, Germany.
| | - Warren W Burggren
- Developmental Integrative Biology Research Group, Department of Biological Sciences, University of North Texas, Denton, TX, USA
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Neculae A, Barnett ZC, Miok K, Dalosto MM, Kuklina I, Kawai T, Santos S, Furse JM, Sîrbu OI, Stoeckel JA, Pârvulescu L. Living on the edge: Crayfish as drivers to anoxification of their own shelter microenvironment. PLoS One 2024; 19:e0287888. [PMID: 38165988 PMCID: PMC10760702 DOI: 10.1371/journal.pone.0287888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/14/2023] [Indexed: 01/04/2024] Open
Abstract
Burrowing is a common trait among crayfish thought to help species deal with adverse environmental challenges. However, little is known about the microhabitat ecology of crayfish taxa in relation to their burrows. To fill this knowledge gap, we assessed the availability of oxygen inside the crayfish shelter by series of in-vivo and in-silico modelling experiments. Under modeled condition, we found that, except for the entrance region of the 200 mm, a flooded burrow microenvironment became anoxic within 8 h, on average. Multiple 12-hour day-night cycles, with burrows occupied by crayfish for 12 h and empty for 12 h, were not sufficient for refreshing the burrow microenvironment. We then examined the degree to which crayfish species with different propensities for burrowing are tolerant of self-created anoxia. From these experiments, primary and secondary burrowers showed best and most consistent tolerance-exhibiting ≥ 64% survival to anoxia and 25-91% survival of ≥ 9 h at anoxia, respectively. Tertiary burrowers exhibited little to no tolerance of anoxia with 0-50% survival to anoxia and only one species exhibiting survival (2%) of ≥ 9 h at anoxia. Results suggest that moderate to strongly burrowing crayfish can quickly draw down the dissolved oxygen in burrow water but appear to have conserved a legacy of strong tolerance of anoxia from their monophyletic ancestors-the lobsters-whereas tertiary burrowers have lost (or never evolved) this ability.
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Affiliation(s)
- Adrian Neculae
- Faculty of Physics, West University of Timisoara, Timisoara, Romania
| | - Zanethia C. Barnett
- Center for Bottomland Hardwoods Research, Southern Research Station, USDA Forest Service, Oxford, MS, United States of Ameirca
| | - Kristian Miok
- Crayfish Research Centre, Institute for Advanced Environmental Research, West University of Timisoara, Timisoara, Romania
| | - Marcelo M. Dalosto
- Laboratório de Carcinologia, Programa de Pós-Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Iryna Kuklina
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Tadashi Kawai
- Central Fisheries Research Institute, Yoichi, Hokkaido, Japan
| | - Sandro Santos
- Laboratório de Carcinologia, Programa de Pós-Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - James M. Furse
- Coastal and Marine Research Centre, Griffith University, Gold Coast, Queensland, Australia
| | - Ovidiu I. Sîrbu
- Department of Biochemistry and Pharmacology, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy Timisoara, Timisoara, Romania
| | - James A. Stoeckel
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL, United States of America
| | - Lucian Pârvulescu
- Crayfish Research Centre, Institute for Advanced Environmental Research, West University of Timisoara, Timisoara, Romania
- Department of Biology-Chemistry, Faculty of Chemistry, Biology, Geography, West University of Timisoara, Timisoara, Romania
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Wahl M, Levy T, Ventura T, Sagi A. Monosex Populations of the Giant Freshwater Prawn Macrobrachium rosenbergii-From a Pre-Molecular Start to the Next Generation Era. Int J Mol Sci 2023; 24:17433. [PMID: 38139271 PMCID: PMC10743721 DOI: 10.3390/ijms242417433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 10/27/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Sexual manipulation in the giant freshwater prawn Macrobrachium rosenbergii has proven successful in generating monosex (both all-male and all-female) populations for aquaculture using a crustacean-specific endocrine gland, the androgenic gland (AG), which serves as a key masculinizing factor by producing and secreting an insulin-like AG hormone (IAG). Here, we provide a summary of the advancements from the discovery of the AG and IAG in decapods through to the development of monosex populations in M. rosenbergii. We discuss the broader sexual development pathway, which is highly divergent across decapods, and provide our future perspective on the utility of novel genetic and genomic tools in promoting refined approaches towards monosex biotechnology. Finally, the future potential benefits of deploying monosex prawn populations for environmental management are discussed.
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Affiliation(s)
- Melody Wahl
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel;
| | - Tom Levy
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA;
- Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
| | - Tomer Ventura
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia;
- School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
| | - Amir Sagi
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel;
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel
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10
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Legrand C, Andriantsoa R, Lichter P, Raddatz G, Lyko F. Time-resolved, integrated analysis of clonally evolving genomes. PLoS Genet 2023; 19:e1011085. [PMID: 38096267 PMCID: PMC10754456 DOI: 10.1371/journal.pgen.1011085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 12/28/2023] [Accepted: 11/27/2023] [Indexed: 12/29/2023] Open
Abstract
Clonal genome evolution is a key feature of asexually reproducing species and human cancer development. While many studies have described the landscapes of clonal genome evolution in cancer, few determine the underlying evolutionary parameters from molecular data, and even fewer integrate theory with data. We derived theoretical results linking mutation rate, time, expansion dynamics, and biological/clinical parameters. Subsequently, we inferred time-resolved estimates of evolutionary parameters from mutation accumulation, mutational signatures and selection. We then applied this framework to predict the time of speciation of the marbled crayfish, an enigmatic, globally invasive parthenogenetic freshwater crayfish. The results predict that speciation occurred between 1986 and 1990, which is consistent with biological records. We also used our framework to analyze whole-genome sequencing datasets from primary and relapsed glioblastoma, an aggressive brain tumor. The results identified evolutionary subgroups and showed that tumor cell survival could be inferred from genomic data that was generated during the resection of the primary tumor. In conclusion, our framework allowed a time-resolved, integrated analysis of key parameters in clonally evolving genomes, and provided novel insights into the evolutionary age of marbled crayfish and the progression of glioblastoma.
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Affiliation(s)
- Carine Legrand
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
- Université Paris Cité, Génomes, biologie cellulaire et thérapeutique U944, INSERM, CNRS, Paris, France
| | - Ranja Andriantsoa
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Precision Oncology, National Center for Tumor Diseases, Heidelberg, Germany
| | - Günter Raddatz
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
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11
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Sun R, Yi S, Shi L, Tan K, Shi R, Yang S, Li Y. Analysis of mRNA and MicroRNA Expression Profiles of Nervous Tissues and Reproductive Tissues in Male Procambarus clarkii After Silencing IAG. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:983-996. [PMID: 37831333 DOI: 10.1007/s10126-023-10254-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023]
Abstract
The insulin-like androgenic gland hormone gene (IAG), primarily expressed in the androgenic gland (AG), plays a crucial role in controlling male sex differentiation and maintaining male secondary sexual characteristics in decapods. In this study, we investigated the mRNA and microRNA expression profiles of male Procambarus clarkii to understand the transcriptomic regulatory mechanism of IAG after the injection of an efficient siRNA (GsiRNA) designed based on IAG. The results revealed that several differentially expressed genes were enriched in reproduction-related pathways, such as the wnt signaling pathway, MAPK signaling pathway, and GnRH signaling pathway. In the testis (Te), the injection of GsiRNA led to the up-regulation of many ovary-related genes and down-regulation of testis-related genes. Moreover, the brain (Br) and abdominal nerve cord (AN) appeared to be involved in the regulation of IAG, with numerous differentially expressed genes found in Br and AN. Notably, the expression of five neuropeptide genes, Crustacean hyperglycemic hormone, pigment-dispersing hormone, red pigment concentrating hormone precursor, corazonin, and gonadotropin-releasing hormone II receptor isoform X1 in Br/AN, was significantly changed. Additionally, three ovary-related miRNAs (miR-263a, miR-263b, miR-133) highly expressed in Te/AG showed significant up-regulation after GsiRNA injection. Furthermore, the long-term interference of GsiRNA was found to inhibit the development of male external sexual characteristics during the juvenile stage and delay it during the adult stage. This research provides valuable insights into the molecular regulatory mechanism and function of IAG in P. clarkii.
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Affiliation(s)
- Rong Sun
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Shaokui Yi
- School of Life Sciences, Huzhou University, Huzhou, 313000, Zhejiang, China
| | - Linlin Shi
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Kianann Tan
- College of Marine Sciences, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, 535011, Guangxi, China
| | - Ruixue Shi
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Siqi Yang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yanhe Li
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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12
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Rock SL, Oudendijk Z, Kürten FT, Veglia L, Tyukosova V, Bourtzi I, Verzé N, Sloggett JJ. The effect of stress on rates of asexual reproduction in an invasive planarian. ECOTOXICOLOGY (LONDON, ENGLAND) 2023; 32:1201-1208. [PMID: 37975975 PMCID: PMC10724090 DOI: 10.1007/s10646-023-02713-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Animal reproduction under stressful conditions is often reduced, with current survival and future reproduction being generally traded off against current reproductive activity. This study examines the impacts of physical and chemical stressors on the rates of asexual reproduction of the invasive planarian Girardia tigrina. 320 wild-caught planaria (mixed size class) were kept individually in Petri dishes such that their individual rates of fission through fragmentation could be easily monitored. Four treatment groups were compared, one chemical (5 mg/L ammonia) and one physical (decapitation), in comparison to a negative control (animals were starved of food) and a positive control where the animals were given an abundance of food. The two treatment groups immediately began reproducing asexually and accumulated the highest number of fissions over the course of the 12-day investigation period, while the positive control only began to fission after 7 days. We propose that the reproductive response observed here is an adaptive one to stressful conditions, whereby the likelihood of survival through numerical abundance is enhanced, although the size and vulnerability of resulting fragments may impose a balancing cost. The response may play a role in the invasiveness of G. tigrina by making it able to colonize environments where adverse conditions prevail.
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Affiliation(s)
- Sebastian L Rock
- Faculty of Health, Science and Technology, Department of Environmental and Life Sciences, Biology, Karlstad University, Karlstad, Sweden.
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands.
| | - Zowi Oudendijk
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Fabian T Kürten
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands
| | - Leonardo Veglia
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands
| | - Valentina Tyukosova
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands
| | - Ioanna Bourtzi
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands
| | - Nicholas Verzé
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands
| | - John J Sloggett
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands
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13
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Mengal K, Kor G, Siino V, Buřič M, Kozák P, Levander F, Niksirat H. Quantification of proteomic profile changes in the hemolymph of crayfish during in vitro coagulation. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 147:104760. [PMID: 37331675 DOI: 10.1016/j.dci.2023.104760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Abstract
Hemolymph is the circulatory fluid that fills the body cavity of crustaceans, analogous to blood in vertebrates. Hemolymph coagulation, similar to blood clotting in vertebrates, plays a crucial role in wound healing and innate immune responses. Despite extensive studies on the clotting process in crustaceans, no comparative quantitative analysis of the protein composition of non-clotted and clotted hemolymph in any decapod has been reported. In this study, we used label-free protein quantification with high-resolution mass spectrometry to identify the proteomic profile of hemolymph in crayfish and quantify significant changes in protein abundances between non-clotted and clotted hemolymph. Our analysis identified a total of two-hundred and nineteen proteins in both hemolymph groups. Furthermore, we discussed the potential functions of the top most high and low-abundant proteins in hemolymph proteomic profile. The quantity of most of the proteins was not significantly changed during coagulation between non-clotted and clotted hemolymph, which may indicate that clotting proteins are likely pre-synthesized, allowing for a swift coagulation response to injury. Four proteins still showed abundance differences (p < 0.05, fold change>2), including C-type lectin domain-containing proteins, Laminin A chain, Tropomyosin, and Reverse transcriptase domain-containing proteins. While the first three proteins were down-regulated, the last one was up-regulated. The down-regulation of structural and cytoskeletal proteins may affect the process of hemocyte degranulation needed for coagulation, while the up-regulation of an immune-related protein might be attributed to the phagocytosis ability of viable hemocytes during coagulation.
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Affiliation(s)
- Kifayatullah Mengal
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25, Vodňany, Czech Republic.
| | - Golara Kor
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25, Vodňany, Czech Republic
| | - Valentina Siino
- Lund University, Department of Immunotechnology, Medicon Village, House 406, 22387, Lund, Sweden
| | - Miloš Buřič
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25, Vodňany, Czech Republic
| | - Pavel Kozák
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25, Vodňany, Czech Republic
| | - Fredrik Levander
- Lund University, Department of Immunotechnology, Medicon Village, House 406, 22387, Lund, Sweden; National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Lund University, Lund, 223 87, Sweden
| | - Hamid Niksirat
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25, Vodňany, Czech Republic.
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14
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Faiad SM, Williams MA, Goodman M, Sokolow S, Olden JD, Mitchell K, Andriantsoa R, Gordon Jones JP, Andriamaro L, Ravoniarimbinina P, Rasamy J, Ravelomanana T, Ravelotafita S, Ravo R, Rabinowitz P, De Leo GA, Wood CL. Temperature affects predation of schistosome-competent snails by a novel invader, the marbled crayfish Procambarus virginalis. PLoS One 2023; 18:e0290615. [PMID: 37703262 PMCID: PMC10499222 DOI: 10.1371/journal.pone.0290615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 08/12/2023] [Indexed: 09/15/2023] Open
Abstract
The human burden of environmentally transmitted infectious diseases can depend strongly on ecological factors, including the presence or absence of natural enemies. The marbled crayfish (Procambarus virginalis) is a novel invasive species that can tolerate a wide range of ecological conditions and colonize diverse habitats. Marbled crayfish first appeared in Madagascar in 2005 and quickly spread across the country, overlapping with the distribution of freshwater snails that serve as the intermediate host of schistosomiasis-a parasitic disease of poverty with human prevalence ranging up to 94% in Madagascar. It has been hypothesized that the marbled crayfish may serve as a predator of schistosome-competent snails in areas where native predators cannot and yet no systematic study to date has been conducted to estimate its predation rate on snails. Here, we experimentally assessed marbled crayfish consumption of uninfected and infected schistosome-competent snails (Biomphalaria glabrata and Bulinus truncatus) across a range of temperatures, reflective of the habitat range of the marbled crayfish in Madagascar. We found that the relationship between crayfish consumption and temperature is unimodal with a peak at ~27.5°C. Per-capita consumption increased with body size and was not affected either by snail species or their infectious status. We detected a possible satiation effect, i.e., a small but significant reduction in per-capita consumption rate over the 72-hour duration of the predation experiment. Our results suggest that ecological parameters, such as temperature and crayfish weight, influence rates of consumption and, in turn, the potential impact of the marbled crayfish invasion on snail host populations.
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Affiliation(s)
- Sara M. Faiad
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States of America
| | - Maureen A. Williams
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States of America
- Department of Biology, McDaniel College, Westminster, MD, United States of America
| | - Maurice Goodman
- Hopkins Marine Station, Dept. of Oceans and of Earth System Science, Doerr School of Sustainability, Stanford University, Stanford, CA, United States of America
| | - Susanne Sokolow
- Hopkins Marine Station, Dept. of Oceans and of Earth System Science, Doerr School of Sustainability, Stanford University, Stanford, CA, United States of America
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | - Julian D. Olden
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States of America
| | - Kaitlyn Mitchell
- Hopkins Marine Station, Dept. of Oceans and of Earth System Science, Doerr School of Sustainability, Stanford University, Stanford, CA, United States of America
| | - Ranja Andriantsoa
- Réseau International Schistosomiase Environnement Aménagement et Lutte (RISEAL) Madagascar, Madagascar
| | | | - Luciano Andriamaro
- Réseau International Schistosomiase Environnement Aménagement et Lutte (RISEAL) Madagascar, Madagascar
| | | | - Jeanne Rasamy
- Réseau International Schistosomiase Environnement Aménagement et Lutte (RISEAL) Madagascar, Madagascar
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
| | - Tsilavina Ravelomanana
- Réseau International Schistosomiase Environnement Aménagement et Lutte (RISEAL) Madagascar, Madagascar
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
| | - Salohy Ravelotafita
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
| | - Ranaivosolo Ravo
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
| | - Peter Rabinowitz
- Department of Environmental/Occupational Health Sciences, Global Health, University of Washington, Seattle, WA, United States of America
- Center for One Health Research (COHR), University of Washington, Seattle, WA, United States of America
| | - Giulio A. De Leo
- Hopkins Marine Station, Dept. of Oceans and of Earth System Science, Doerr School of Sustainability, Stanford University, Stanford, CA, United States of America
- Woods Institute for the Environment, Stanford University, Stanford, CA, United States of America
| | - Chelsea L. Wood
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States of America
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15
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Sato DX, Matsuda Y, Usio N, Funayama R, Nakayama K, Makino T. Genomic adaptive potential to cold environments in the invasive red swamp crayfish. iScience 2023; 26:107267. [PMID: 37520695 PMCID: PMC10371857 DOI: 10.1016/j.isci.2023.107267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/31/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Biological invasion refers to the introduction, spread, and establishment of non-native species in a novel habitat. The ways in which invasive species successfully colonize new and different environments remain a fundamental topic of research in ecology and evolutionary biology. Here, we investigated the genomic and transcriptomic characteristics of the red swamp crayfish (Procambarus clarkii), a widespread invader in freshwater environments. Targeting a recently colonized population in Sapporo, Japan that appears to have acquired a high degree of cold tolerance, RNA-seq analysis revealed differentially expressed genes in response to cold exposure, and those involved in protease inhibitors and cuticle development were considered top candidates. We also found remarkable duplications for these gene families during evolution and their concerted expression patterns, suggesting functional amplification against low temperatures. Our study thus provides clues to the unique genetic characteristics of P. clarkii, possibly related to cold adaptation.
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Affiliation(s)
- Daiki X. Sato
- Institute for Advanced Academic Research, Chiba University, Chiba 263-8522, Japan
- Graduate School of Science, Chiba University, Chiba 263-8522, Japan
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Yuki Matsuda
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Nisikawa Usio
- Institute of Nature and Environmental Technology, Kanazawa University, Kanazawa 920-1192, Japan
| | - Ryo Funayama
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai 980-8575, Japan
| | - Keiko Nakayama
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai 980-8575, Japan
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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16
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Rutz C, Bonassin L, Kress A, Francesconi C, Boštjančić LL, Merlat D, Theissinger K, Lecompte O. Abundance and Diversification of Repetitive Elements in Decapoda Genomes. Genes (Basel) 2023; 14:1627. [PMID: 37628678 PMCID: PMC10454600 DOI: 10.3390/genes14081627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Repetitive elements are a major component of DNA sequences due to their ability to propagate through the genome. Characterization of Metazoan repetitive profiles is improving; however, current pipelines fail to identify a significant proportion of divergent repeats in non-model organisms. The Decapoda order, for which repeat content analyses are largely lacking, is characterized by extremely variable genome sizes that suggest an important presence of repetitive elements. Here, we developed a new standardized pipeline to annotate repetitive elements in non-model organisms, which we applied to twenty Decapoda and six other Crustacea genomes. Using this new tool, we identified 10% more repetitive elements than standard pipelines. Repetitive elements were more abundant in Decapoda species than in other Crustacea, with a very large number of highly repeated satellite DNA families. Moreover, we demonstrated a high correlation between assembly size and transposable elements and different repeat dynamics between Dendrobranchiata and Reptantia. The patterns of repetitive elements largely reflect the phylogenetic relationships of Decapoda and the distinct evolutionary trajectories within Crustacea. In summary, our results highlight the impact of repetitive elements on genome evolution in Decapoda and the value of our novel annotation pipeline, which will provide a baseline for future comparative analyses.
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Affiliation(s)
- Christelle Rutz
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Lena Bonassin
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Arnaud Kress
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Caterina Francesconi
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Ljudevit Luka Boštjančić
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Dorine Merlat
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
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17
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Vogt G. Phenotypic plasticity in the monoclonal marbled crayfish is associated with very low genetic diversity but pronounced epigenetic diversity. Curr Zool 2023; 69:426-441. [PMID: 37614917 PMCID: PMC10443617 DOI: 10.1093/cz/zoac094] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/19/2022] [Indexed: 08/25/2023] Open
Abstract
Clonal organisms are particularly useful to investigate the contribution of epigenetics to phenotypic plasticity, because confounding effects of genetic variation are negligible. In the last decade, the apomictic parthenogenetic marbled crayfish, Procambarus virginalis, has been developed as a model to investigate the relationships between phenotypic plasticity and genetic and epigenetic diversity in detail. This crayfish originated about 30 years ago by autotriploidy from a single slough crayfish Procambarus fallax. As the result of human releases and active spreading, marbled crayfish has established numerous populations in very diverse habitats in 22 countries from the tropics to cold temperate regions. Studies in the laboratory and field revealed considerable plasticity in coloration, spination, morphometric parameters, growth, food preference, population structure, trophic position, and niche width. Illumina and PacBio whole-genome sequencing of marbled crayfish from representatives of 19 populations in Europe and Madagascar demonstrated extremely low genetic diversity within and among populations, indicating that the observed phenotypic diversity and ability to live in strikingly different environments are not due to adaptation by selection on genetic variation. In contrast, considerable differences were found between populations in the DNA methylation patterns of hundreds of genes, suggesting that the environmentally induced phenotypic plasticity is mediated by epigenetic mechanisms and corresponding changes in gene expression. Specific DNA methylation fingerprints persisted in local populations over successive years indicating the existence of epigenetic ecotypes, but there is presently no information as to whether these epigenetic signatures are transgenerationally inherited or established anew in each generation and whether the recorded phenotypic plasticity is adaptive or nonadaptive.
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Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
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18
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Sperling AL, Glover DM. Parthenogenesis in dipterans: a genetic perspective. Proc Biol Sci 2023; 290:20230261. [PMID: 36946111 PMCID: PMC10031431 DOI: 10.1098/rspb.2023.0261] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/28/2023] [Indexed: 03/23/2023] Open
Abstract
Parthenogenesis has been documented in almost every phylum of animals, and yet this phenomenon is largely understudied. It has particular importance in dipterans since some parthenogenetic species are also disease vectors and agricultural pests. Here, we present a catalogue of parthenogenetic dipterans, although it is likely that many more remain to be identified, and we discuss how their developmental biology and interactions with diverse environments may be linked to different types of parthenogenetic reproduction. We discuss how the advances in genetics and genomics have identified chromosomal loci associated with parthenogenesis. In particular, a polygenic cause of facultative parthenogenesis has been uncovered in Drosophila mercatorum, allowing the corresponding genetic variants to be tested for their ability to promote parthenogenesis in another species, Drosophila melanogaster. This study probably identifies just one of many routes that could be followed in the evolution of parthenogenesis. We attempt to account for why the phenomenon has evolved so many times in the dipteran order and why facultative parthenogenesis appears particularly prevalent. We also discuss the significance of coarse genomic changes, including non-disjunction, aneuploidy, and polyploidy and how, together with changes to specific genes, these might relate to both facultative and obligate parthenogenesis in dipterans and other parthenogenetic animals.
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Affiliation(s)
- A. L. Sperling
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - D. M. Glover
- Department of Genetics, University of Cambridge, Cambridge, UK
- California Institute of Technology, Pasadena, CA, USA
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19
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Shao C, Sun S, Liu K, Wang J, Li S, Liu Q, Deagle BE, Seim I, Biscontin A, Wang Q, Liu X, Kawaguchi S, Liu Y, Jarman S, Wang Y, Wang HY, Huang G, Hu J, Feng B, De Pittà C, Liu S, Wang R, Ma K, Ying Y, Sales G, Sun T, Wang X, Zhang Y, Zhao Y, Pan S, Hao X, Wang Y, Xu J, Yue B, Sun Y, Zhang H, Xu M, Liu Y, Jia X, Zhu J, Liu S, Ruan J, Zhang G, Yang H, Xu X, Wang J, Zhao X, Meyer B, Fan G. The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights. Cell 2023; 186:1279-1294.e19. [PMID: 36868220 DOI: 10.1016/j.cell.2023.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 12/11/2022] [Accepted: 02/02/2023] [Indexed: 03/05/2023]
Abstract
Antarctic krill (Euphausia superba) is Earth's most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research.
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Affiliation(s)
- Changwei Shao
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China.
| | - Shuai Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaiqiang Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Jiahao Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Shuo Li
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Qun Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Bruce E Deagle
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian National Fish Collection, National Research Collections Australia, Hobart, TAS 7000, Australia; Australian Antarctic Division, Channel Highway, Kingston, TAS 7050, Australia
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | | | - Qian Wang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; BGI-Beijing, Beijing 102601, China; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA 6150, Australia
| | - So Kawaguchi
- Australian Antarctic Division, Channel Highway, Kingston, TAS 7050, Australia
| | - Yalin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Simon Jarman
- School of Molecular and Life Sciences, Curtin University, Perth, WA 6009, Australia
| | - Yue Wang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China
| | - Hong-Yan Wang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | | | - Jiang Hu
- Nextomics Biosciences Institute, Wuhan, Hubei 430073, China
| | - Bo Feng
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | | | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Rui Wang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Kailong Ma
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yiping Ying
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Gabrielle Sales
- Department of Biology, University of Padova, Padova 35121, Italy
| | - Tao Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Xinliang Wang
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yunxia Zhao
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Shanshan Pan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Xiancai Hao
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Yang Wang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Jiakun Xu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Bowen Yue
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Yanxu Sun
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - He Zhang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Mengyang Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yuyan Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Xiaodong Jia
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, Shandong 252000, China
| | - Jiancheng Zhu
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Shufang Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Jue Ruan
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Guojie Zhang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; James D. Watson Institute of Genome Science, Hangzhou 310058, China
| | - Xun Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Jun Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Xianyong Zhao
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Bettina Meyer
- Section Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany; Institute for Chemistry and Biology of the Marine Environment, Carlvon Ossietzky University of Oldenburg, 26111 Oldenburg, Germany; Helmholtz Institute for Functional Marine Biodiversity (HIFMB), University of Oldenburg, 26129 Oldenburg, Germany.
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China; Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen 518120, China.
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20
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Sun X, Wang G, Yang J, Yu W, Xu J, Tang B, Ding G, Zhang D. Whole genome evaluation analysis and preliminary Assembly of Oratosquilla oratoria (Stomatopoda: Squillidae). Mol Biol Rep 2023; 50:4165-4173. [PMID: 36894769 DOI: 10.1007/s11033-023-08356-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/23/2023] [Indexed: 03/11/2023]
Abstract
BACKGROUND As the dominant species of Stomatopoda, Oratosquilla oratoria has not been fully cultivated artificially, and the fishery production mainly depends on marine fishing. Due to the lack of stomatopod genome, the development of molecular breeding of mantis shrimps still lags behind. METHODS AND RESULTS A survey analysis was performed to obtain the genome size, GC content and heterozygosity ratio in order to provide a fundation for subsequent whole-genome sequencing. The results showed that the estimated genome size of the O. oratoria was about 2.56 G, and the heterozygosity ratio was 1.81%, indicating that it is a complex genome. Then the sequencing data was preliminarily assembled with k-mer = 51 by SOAPdenovo software to obtain a genome size of 3.01G and GC content of 40.37%. According to ReapeatMasker and RepeatModerler analysis, the percentage of repeats in O. oratoria was 45.23% in the total genome, similar to 44% in Survey analysis. The MISA tool was used to analyze the simple sequence repeat (SSR) characteristics of genome sequences including Oratosquilla oratoria, Macrobrachium nipponense, Fenneropenaeus chinensis, Eriocheir japonica sinensis, Scylla paramamosain and Paralithodes platypus. All crustacean genomes showed similar SSRs characteristics, with the highest proportion of di-nucleotide repeat sequences. And AC/GT and AGG/CCT repeats were the main types of di-nucleotide and tri-nucleotide repeats in O. oratoria. CONCLUSION This study provided a reference for the genome assembly and annotation of the O. oratoria, and also provided a theoretical basis for the development of molecular markers of O. oratoria.
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Affiliation(s)
- Xiaoli Sun
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Gang Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Jie Yang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Wei Yu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Jiayue Xu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Ge Ding
- Chemical and Biological Engineering College, Yancheng Institute of Technology, Yancheng, 224003, China
| | - Daizhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China.
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21
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Tseng SP, Darras H, Hsu PW, Yoshimura T, Lee CY, Wetterer JK, Keller L, Yang CCS. Genetic analysis reveals the putative native range and widespread double-clonal reproduction in the invasive longhorn crazy ant. Mol Ecol 2023; 32:1020-1033. [PMID: 36527320 DOI: 10.1111/mec.16827] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Clonal reproduction can provide an advantage for invasive species to establish as it can circumvent inbreeding depression which often plagues introduced populations. The world's most widespread invasive ant, Paratrechina longicornis, was previously found to display a double-clonal reproduction system, whereby both males and queens are produced clonally, resulting in separate male and queen lineages, while workers are produced sexually. Under this unusual reproduction mode, inbreeding is avoided in workers as they carry hybrid interlineage genomes. Despite the ubiquitous distribution of P. longicornis, the significance of this reproductive system for the ant's remarkable success remains unclear, as its prevalence is still unknown. Further investigation into the controversial native origin of P. longicornis is also required to reconstruct the evolutionary histories of double-clonal lineages. Here, we examine genetic variation and characterize the reproduction mode of P. longicornis populations sampled worldwide using microsatellites and mitochondrial DNA sequences to infer the ant's putative native range and the distribution of the double-clonal reproductive system. Analyses of global genetic variations indicate that the Indian subcontinent is a genetic diversity hotspot of this species, suggesting that P. longicornis probably originates from this geographical area. Our analyses revealed that both the inferred native and introduced populations exhibit double-clonal reproduction, with queens and males around the globe belonging to two separate, nonrecombining clonal lineages. By contrast, workers are highly heterozygous because they are first-generation interlineage hybrids. Overall, these data indicate a worldwide prevalence of double clonality in P. longicornis and support the prediction that the unusual genetic system may have pre-adapted this ant for global colonization by maintaining heterozygosity in the worker force and alleviating genetic bottlenecks.
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Affiliation(s)
- Shu-Ping Tseng
- Department of Entomology, National Taiwan University, Taipei, Taiwan.,Department of Entomology, University of California, Riverside, California, USA.,Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, Japan
| | - Hugo Darras
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Po-Wei Hsu
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Tsuyoshi Yoshimura
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, Japan
| | - Chow-Yang Lee
- Department of Entomology, University of California, Riverside, California, USA
| | - James K Wetterer
- Wilkes Honors College, Florida Atlantic University, Jupiter, Florida, USA
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Chin-Cheng Scotty Yang
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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22
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Göpel T, Richter S. Homologues and homology and their related terms in phylogenetic systematics. Cladistics 2023; 39:240-248. [PMID: 36738298 DOI: 10.1111/cla.12526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/28/2022] [Accepted: 12/22/2022] [Indexed: 02/05/2023] Open
Abstract
In the field of phylogenetic systematics, the terms homology and homologue and their relationship to cladistic terms such as character, character state, synapomorphy and symplesiomorphy, as well as their relationships to each other, have been and are still discussed frequently. A recent re-emergence of concepts of homology/homologue free of any reference to explanatory hypotheses prompted us to explore these concepts and their relationships to each other as well as to the concept of morpheme, as introduced recently. All concepts are examined with regard to their ontological status and their bearing in the epistemological process in morphology and phylogenetic systematics. To us, morphemes, homologues and in partem character states refer to things (concrete objects in the ontological sense). However, although morphemes are exclusively descriptive, the latter two represent objects of causal explanations. Homologue always refers to the things themselves, yet a character state also can be a property or the absence of a thing. In this context, a character as a transformation series of character states does not represent a thing but a natural kind. Character states of one character are connected by homology relationships, i.e. common descent. Synapomorphy and symplesiomorphy represent different states of a single transformation series. A nonexplanatory, purely descriptive, concept of homologues is contradictory to its original as well as the post-Darwinian, evolutionary, concept which refers to causal relationships between parts of organisms and their correspondences in the archetype or ancestor, respectively. Character states, homologues and synapomorphies/symplesiomorphies can only be approximated in the form of hypotheses. We argue that the high value of the concept of homology and its related concepts for evolutionary biology should be maintained by acknowledging their explanatory nature and that dilution with nonexplanatory (even idealistic) definitions should be avoided.
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Affiliation(s)
- Torben Göpel
- Developmental Integrative Biology Research Group, Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA.,Multiscale Biology, Johann-Friedrich-Blumenbach Institut für Zoologie und Anthropologie, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany
| | - Stefan Richter
- Allgemeine und Spezielle Zoologie, Institut für Biowissenschaften, Universität Rostock, Universitätsplatz 2, 18055, Rostock, Germany
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23
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Daly EZ, Chabrerie O, Massol F, Facon B, Hess MC, Tasiemski A, Grandjean F, Chauvat M, Viard F, Forey E, Folcher L, Buisson E, Boivin T, Baltora‐Rosset S, Ulmer R, Gibert P, Thiébaut G, Pantel JH, Heger T, Richardson DM, Renault D. A synthesis of biological invasion hypotheses associated with the introduction–naturalisation–invasion continuum. OIKOS 2023. [DOI: 10.1111/oik.09645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Ella Z. Daly
- Univ. of Rennes, CNRS, ECOBIO (Ecosystèmes, Biodiversité, Evolution), UMR 6553 Rennes France
| | - Olivier Chabrerie
- Univ. de Picardie Jules Verne, UMR 7058 CNRS EDYSAN Amiens Cedex 1 France
| | - Francois Massol
- Univ. Lille, CNRS, Inserm, CHU Lille, Inst. Pasteur de Lille, U1019 – UMR 9017 – CIIL – Center for Infection and Immunity of Lille Lille France
| | - Benoit Facon
- CBGP, INRAE, CIRAD, IRD, Montpellier Institut Agro, Univ. Montpellier Montpellier France
| | - Manon C.M. Hess
- Inst. Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale (IMBE), UMR: Aix Marseille Univ., Avignon Université, CNRS, IRD France
- Inst. de Recherche pour la Conservation des zones Humides Méditerranéennes Tour du Valat, Le Sambuc Arles France
| | - Aurélie Tasiemski
- Univ. Lille, CNRS, Inserm, CHU Lille, Inst. Pasteur de Lille, U1019 – UMR 9017 – CIIL – Center for Infection and Immunity of Lille Lille France
| | - Frédéric Grandjean
- Univ. de Poitiers, UMR CNRS 7267 EBI‐Ecologie et Biologie des Interactions, équipe EES Poitiers Cedex 09 France
| | | | | | - Estelle Forey
- Normandie Univ., UNIROUEN, INRAE, USC ECODIV Rouen France
| | - Laurent Folcher
- ANSES – Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Laboratoire de la Santé des Végétaux – Unité de Nématologie Le Rheu France
| | - Elise Buisson
- Inst. Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale (IMBE), UMR: Aix Marseille Univ., Avignon Université, CNRS, IRD France
| | - Thomas Boivin
- INRAE, UR629 Écologie des Forêts Méditerranéennes, Centre de Recherche Provence‐Alpes‐Côte d'Azur Avignon France
| | | | - Romain Ulmer
- Univ. de Picardie Jules Verne, UMR 7058 CNRS EDYSAN Amiens Cedex 1 France
| | - Patricia Gibert
- UMR 5558 CNRS – Univ. Claude Bernard Lyon 1, Biométrie et Biologie Evolutive, Bât. Gregor Mendel Villeurbanne Cedex France
| | - Gabrielle Thiébaut
- Univ. of Rennes, CNRS, ECOBIO (Ecosystèmes, Biodiversité, Evolution), UMR 6553 Rennes France
| | - Jelena H. Pantel
- Ecological Modelling, Faculty of Biology, Univ. of Duisburg‐Essen Essen Germany
| | - Tina Heger
- Leibniz Inst. of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Technical Univ. of Munich, Restoration Ecology Freising Germany
| | - David M. Richardson
- Centre for Invasion Biology, Dept. Botany & Zoology, Stellenbosch University Stellenbosch South Africa
- Inst. of Botany, Czech Academy of Sciences Průhonice Czech Republic
| | - David Renault
- Univ. of Rennes, CNRS, ECOBIO (Ecosystèmes, Biodiversité, Evolution), UMR 6553 Rennes France
- Inst. Universitaire de France Paris Cedex 05 France
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24
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Venkatesh G, Tönges S, Hanna K, Ng YL, Whelan R, Andriantsoa R, Lingenberg A, Roy S, Nagarajan S, Fong S, Raddatz G, Böhl F, Lyko F. Context-dependent DNA methylation signatures in animal livestock. ENVIRONMENTAL EPIGENETICS 2023; 9:dvad001. [PMID: 36936885 PMCID: PMC10019019 DOI: 10.1093/eep/dvad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 01/06/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
DNA methylation is an important epigenetic modification that is widely conserved across animal genomes. It is widely accepted that DNA methylation patterns can change in a context-dependent manner, including in response to changing environmental parameters. However, this phenomenon has not been analyzed in animal livestock yet, where it holds major potential for biomarker development. Building on the previous identification of population-specific DNA methylation in clonal marbled crayfish, we have now generated numerous base-resolution methylomes to analyze location-specific DNA methylation patterns. We also describe the time-dependent conversion of epigenetic signatures upon transfer from one environment to another. We further demonstrate production system-specific methylation signatures in shrimp, river-specific signatures in salmon and farm-specific signatures in chicken. Together, our findings provide a detailed resource for epigenetic variation in animal livestock and suggest the possibility for origin tracing of animal products by epigenetic fingerprinting.
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Affiliation(s)
- Geetha Venkatesh
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, Heidelberg 69120, Germany
| | - Sina Tönges
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, Heidelberg 69120, Germany
| | - Katharina Hanna
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, Heidelberg 69120, Germany
| | - Yi Long Ng
- School of Applied Science, Republic Polytechnic, 9 Woodlands Avenue 9, Singapore 738964, Singapore
| | - Rose Whelan
- Research, Development & Innovation, Evonik Operations GmbH, Rodenbacher Chaussee 4, Hanau-Wolfgang 63457, Germany
| | - Ranja Andriantsoa
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, Heidelberg 69120, Germany
| | - Annika Lingenberg
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, Heidelberg 69120, Germany
| | - Suki Roy
- Research, Development & Innovation, Evonik Operations GmbH, Rodenbacher Chaussee 4, Hanau-Wolfgang 63457, Germany
| | - Sanjanaa Nagarajan
- Research, Development & Innovation, Evonik Operations GmbH, Rodenbacher Chaussee 4, Hanau-Wolfgang 63457, Germany
| | - Steven Fong
- School of Applied Science, Republic Polytechnic, 9 Woodlands Avenue 9, Singapore 738964, Singapore
| | - Günter Raddatz
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, Heidelberg 69120, Germany
| | - Florian Böhl
- Research, Development & Innovation, Evonik Operations GmbH, Rodenbacher Chaussee 4, Hanau-Wolfgang 63457, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, Heidelberg 69120, Germany
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25
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Whelan R, Tönges S, Böhl F, Lyko F. Epigenetic biomarkers for animal welfare monitoring. Front Vet Sci 2023; 9:1107843. [PMID: 36713882 PMCID: PMC9874107 DOI: 10.3389/fvets.2022.1107843] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
Biomarkers for holistic animal welfare monitoring represent a considerable unmet need in veterinary medicine. Epigenetic modifications, like DNA methylation, provide important information about cellular states and environments, which makes them highly attractive for biomarker development. Up until now, much of the corresponding research has been focused on human cancers. However, the increasing availability of animal genomes and epigenomes has greatly improved our capacity for epigenetic biomarker development. In this review, we provide an overview about animal DNA methylation patterns and the technologies that enable the analysis of these patterns. We also describe the key frameworks for compound DNA methylation biomarkers, DNA methylation clocks and environment-specific DNA methylation signatures, that allow complex, context-dependent readouts about animal health and disease. Finally, we provide practical examples for how these biomarkers could be applied for health and environmental exposure monitoring, two key aspects of animal welfare assessments. Taken together, our article provides an overview about the molecular and biological foundations for the development of epigenetic biomarkers in veterinary science and their application potential in animal welfare monitoring.
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Affiliation(s)
- Rose Whelan
- Creavis, Evonik Operations GmbH, Hanau, Germany
| | - Sina Tönges
- Innovation Management, German Cancer Research Center, Heidelberg, Germany
| | | | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany,*Correspondence: Frank Lyko ✉
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26
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Vogt G. Environmental Adaptation of Genetically Uniform Organisms with the Help of Epigenetic Mechanisms-An Insightful Perspective on Ecoepigenetics. EPIGENOMES 2022; 7:1. [PMID: 36648862 PMCID: PMC9844400 DOI: 10.3390/epigenomes7010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022] Open
Abstract
Organisms adapt to different environments by selection of the most suitable phenotypes from the standing genetic variation or by phenotypic plasticity, the ability of single genotypes to produce different phenotypes in different environments. Because of near genetic identity, asexually reproducing populations are particularly suitable for the investigation of the potential and molecular underpinning of the latter alternative in depth. Recent analyses on the whole-genome scale of differently adapted clonal animals and plants demonstrated that epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs are among the molecular pathways supporting phenotypic plasticity and that epigenetic variation is used to stably adapt to different environments. Case studies revealed habitat-specific epigenetic fingerprints that were maintained over subsequent years pointing at the existence of epigenetic ecotypes. Environmentally induced epimutations and corresponding gene expression changes provide an ideal means for fast and directional adaptation to changing or new conditions, because they can synchronously alter phenotypes in many population members. Because microorganisms inclusive of human pathogens also exploit epigenetically mediated phenotypic variation for environmental adaptation, this phenomenon is considered a universal biological principle. The production of different phenotypes from the same DNA sequence in response to environmental cues by epigenetic mechanisms also provides a mechanistic explanation for the "general-purpose genotype hypothesis" and the "genetic paradox of invasions".
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Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
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27
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Herberholz J. The giant escape neurons of crayfish: Past discoveries and present opportunities. Front Physiol 2022; 13:1052354. [PMID: 36605900 PMCID: PMC9808059 DOI: 10.3389/fphys.2022.1052354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Crayfish are equipped with two prominent neural circuits that control rapid, stereotyped escape behaviors. Central to these circuits are bilateral pairs of giant neurons that transverse the nervous system and generate escape tail-flips in opposite directions away from threatening stimuli.
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28
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Lee CE, Charmantier G, Lorin-Nebel C. Mechanisms of Na + uptake from freshwater habitats in animals. Front Physiol 2022; 13:1006113. [PMID: 36388090 PMCID: PMC9644288 DOI: 10.3389/fphys.2022.1006113] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/28/2022] [Indexed: 07/20/2023] Open
Abstract
Life in fresh water is osmotically and energetically challenging for living organisms, requiring increases in ion uptake from dilute environments. However, mechanisms of ion uptake from freshwater environments are still poorly understood and controversial, especially in arthropods, for which several hypothetical models have been proposed based on incomplete data. One compelling model involves the proton pump V-type H+ ATPase (VHA), which energizes the apical membrane, enabling the uptake of Na+ (and other cations) via an unknown Na+ transporter (referred to as the "Wieczorek Exchanger" in insects). What evidence exists for this model of ion uptake and what is this mystery exchanger or channel that cooperates with VHA? We present results from studies that explore this question in crustaceans, insects, and teleost fish. We argue that the Na+/H+ antiporter (NHA) is a likely candidate for the Wieczorek Exchanger in many crustaceans and insects; although, there is no evidence that this is the case for fish. NHA was discovered relatively recently in animals and its functions have not been well characterized. Teleost fish exhibit redundancy of Na+ uptake pathways at the gill level, performed by different ion transporter paralogs in diverse cell types, apparently enabling tolerance of low environmental salinity and various pH levels. We argue that much more research is needed on overall mechanisms of ion uptake from freshwater habitats, especially on NHA and other potential Wieczorek Exchangers. Such insights gained would contribute greatly to our general understanding of ionic regulation in diverse species across habitats.
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Affiliation(s)
- Carol Eunmi Lee
- Department of Integrative Biology, University of Wisconsin, Madison, WI, United States
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Guy Charmantier
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
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29
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Lan T, Li H, Yang S, Shi M, Han L, Sahu SK, Lu Y, Wang J, Zhou M, Liu H, Huang J, Wang Q, Zhu Y, Wang L, Xu Y, Lin C, Liu H, Hou Z. The chromosome-scale genome of the raccoon dog: Insights into its evolutionary characteristics. iScience 2022; 25:105117. [PMID: 36185367 PMCID: PMC9523411 DOI: 10.1016/j.isci.2022.105117] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/07/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Tianming Lan
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shangchen Yang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Han
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yaxian Lu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Jiangang Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Mengchao Zhou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Hui Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), College of Forestry, Hainan University, Haikou 570228, China
| | - Junxuan Huang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yixin Zhu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yanchun Xu
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- Corresponding author
| | - Chuyu Lin
- Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen 518120, China
- Corresponding author
| | - Huan Liu
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- Corresponding author
| | - Zhijun Hou
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- Corresponding author
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Wang J, Chen X, Hou X, Wang J, Yue W, Huang S, Xu G, Yan J, Lu G, Hofreiter M, Li C, Wang C. "Omics" data unveil early molecular response underlying limb regeneration in the Chinese mitten crab, Eriocheir sinensis. SCIENCE ADVANCES 2022; 8:eabl4642. [PMID: 36112682 PMCID: PMC9481118 DOI: 10.1126/sciadv.abl4642] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/01/2022] [Indexed: 05/22/2023]
Abstract
Limb regeneration is a fascinating and medically interesting trait that has been well preserved in arthropod lineages, particularly in crustaceans. However, the molecular mechanisms underlying arthropod limb regeneration remain largely elusive. The Chinese mitten crab Eriocheir sinensis shows strong regenerative capacity, a trait that has likely allowed it to become a worldwide invasive species. Here, we report a chromosome-level genome of E. sinensis as well as large-scale transcriptome data during the limb regeneration process. Our results reveal that arthropod-specific genes involved in signal transduction, immune response, histone methylation, and cuticle development all play fundamental roles during the regeneration process. Particularly, Innexin2-mediated signal transduction likely facilitates the early stage of the regeneration process, while an effective crustacean-specific prophenoloxidase system (ProPo-AS) plays crucial roles in the initial immune response. Collectively, our findings uncover novel genetic pathways pertaining to arthropod limb regeneration and provide valuable resources for studies on regeneration from a comparative perspective.
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Affiliation(s)
- Jun Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaowen Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Xin Hou
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Jingan Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Wucheng Yue
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Shu Huang
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Gangchun Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization certified by the Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jizhou Yan
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Guoqing Lu
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Corresponding author. Email (M.H.); (C.L.); (C.W.)
| | - Chenhong Li
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
- Corresponding author. Email (M.H.); (C.L.); (C.W.)
| | - Chenghui Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
- Corresponding author. Email (M.H.); (C.L.); (C.W.)
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Yuan J, Zhang X, Li S, Liu C, Yu Y, Zhang X, Xiang J, Li F. Convergent evolution of barnacles and molluscs sheds lights in origin and diversification of calcareous shell and sessile lifestyle. Proc Biol Sci 2022; 289:20221535. [PMID: 36100022 PMCID: PMC9470267 DOI: 10.1098/rspb.2022.1535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 08/22/2022] [Indexed: 11/12/2022] Open
Abstract
The calcareous shell and sessile lifestyle are the representative phenotypes of many molluscs, which happen to be present in barnacles, a group of unique crustaceans. The origin of these phenotypes is unclear, but it may be embodied in the convergent genetics of such distant groups (interphylum). Herein, we perform comprehensive comparative genomics analysis in barnacles and molluscs, and reveal a genome-wide strong convergent molecular evolution between them, including coexpansion of biomineralization and organic matrix genes for shell formation, and origination of lineage-specific orphan genes for settlement. Notably, the expanded biomineralization gene encoding alkaline phosphatase evolves a novel, highly conserved motif that may trigger the origin of barnacle shell formation. Unlike molluscs, barnacles adopt novel organic matrices and cement proteins for shell formation and settlement, respectively, and their calcareous shells have potentially originated from the cuticle system of crustaceans. Therefore, our study corroborates the idea that selection pressures driving convergent evolution may strongly act in organisms inhabiting similar environments regardless of phylogenetic distance. The convergence signatures shed light on the origin of the shell and sessile lifestyle of barnacles and molluscs. In addition, notable non-convergence signatures are also present and may contribute to morphological and functional specificities.
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Affiliation(s)
- Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Shihao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Chengzhang Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Xiaoxi Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
| | - Jianhai Xiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
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32
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Boštjančić LL, Francesconi C, Rutz C, Hoffbeck L, Poidevin L, Kress A, Jussila J, Makkonen J, Feldmeyer B, Bálint M, Schwenk K, Lecompte O, Theissinger K. Host-pathogen coevolution drives innate immune response to Aphanomyces astaci infection in freshwater crayfish: transcriptomic evidence. BMC Genomics 2022; 23:600. [PMID: 35989333 PMCID: PMC9394032 DOI: 10.1186/s12864-022-08571-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/20/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND For over a century, scientists have studied host-pathogen interactions between the crayfish plague disease agent Aphanomyces astaci and freshwater crayfish. It has been hypothesised that North American crayfish hosts are disease-resistant due to the long-lasting coevolution with the pathogen. Similarly, the increasing number of latent infections reported in the historically sensitive European crayfish hosts seems to indicate that similar coevolutionary processes are occurring between European crayfish and A. astaci. Our current understanding of these host-pathogen interactions is largely focused on the innate immunity processes in the crayfish haemolymph and cuticle, but the molecular basis of the observed disease-resistance and susceptibility remain unclear. To understand how coevolution is shaping the host's molecular response to the pathogen, susceptible native European noble crayfish and invasive disease-resistant marbled crayfish were challenged with two A. astaci strains of different origin: a haplogroup A strain (introduced to Europe at least 50 years ago, low virulence) and a haplogroup B strain (signal crayfish in lake Tahoe, USA, high virulence). Here, we compare the gene expression profiles of the hepatopancreas, an integrated organ of crayfish immunity and metabolism. RESULTS We characterised several novel innate immune-related gene groups in both crayfish species. Across all challenge groups, we detected 412 differentially expressed genes (DEGs) in the noble crayfish, and 257 DEGs in the marbled crayfish. In the noble crayfish, a clear immune response was detected to the haplogroup B strain, but not to the haplogroup A strain. In contrast, in the marbled crayfish we detected an immune response to the haplogroup A strain, but not to the haplogroup B strain. CONCLUSIONS We highlight the hepatopancreas as an important hub for the synthesis of immune molecules in the response to A. astaci. A clear distinction between the innate immune response in the marbled crayfish and the noble crayfish is the capability of the marbled crayfish to mobilise a higher variety of innate immune response effectors. With this study we outline that the type and strength of the host immune response to the pathogen is strongly influenced by the coevolutionary history of the crayfish with specific A. astaci strains.
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Affiliation(s)
- Ljudevit Luka Boštjančić
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Caterina Francesconi
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany.
| | - Christelle Rutz
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Lucien Hoffbeck
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Laetitia Poidevin
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Arnaud Kress
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Japo Jussila
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, 70210, Kuopio, Finland
| | - Jenny Makkonen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, 70210, Kuopio, Finland
- Present address: BioSafe - Biological Safety Solutions, Microkatu 1, 70210, Kuopio, Finland
| | - Barbara Feldmeyer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Klaus Schwenk
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany
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33
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Stein W, DeMaegd ML, Benson AM, Roy RS, Vidal-Gadea AG. Combining Old and New Tricks: The Study of Genes, Neurons, and Behavior in Crayfish. Front Physiol 2022; 13:947598. [PMID: 35874546 PMCID: PMC9297122 DOI: 10.3389/fphys.2022.947598] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/13/2022] [Indexed: 12/04/2022] Open
Abstract
For over a century the nervous system of decapod crustaceans has been a workhorse for the neurobiology community. Many fundamental discoveries including the identification of electrical and inhibitory synapses, lateral and pre-synaptic inhibition, and the Na+/K+-pump were made using lobsters, crabs, or crayfish. Key among many advantages of crustaceans for neurobiological research is the unique access to large, accessible, and identifiable neurons, and the many distinct and complex behaviors that can be observed in lab settings. Despite these advantages, recent decades have seen work on crustaceans hindered by the lack of molecular and genetic tools required for unveiling the cellular processes contributing to neurophysiology and behavior. In this perspective paper, we argue that the recently sequenced marbled crayfish, Procambarus virginalis, is suited to become a genetic model system for crustacean neuroscience. P. virginalis are parthenogenetic and produce genetically identical offspring, suggesting that germline transformation creates transgenic animal strains that are easy to maintain across generations. Like other decapod crustaceans, marbled crayfish possess large neurons in well-studied circuits such as the giant tail flip neurons and central pattern generating neurons in the stomatogastric ganglion. We provide initial data demonstrating that marbled crayfish neurons are accessible through standard physiological and molecular techniques, including single-cell electrophysiology, gene expression measurements, and RNA-interference. We discuss progress in CRISPR-mediated manipulations of the germline to knock-out target genes using the ‘Receptor-mediated ovary transduction of cargo’ (ReMOT) method. Finally, we consider the impact these approaches will have for neurophysiology research in decapod crustaceans and more broadly across invertebrates.
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Affiliation(s)
- Wolfgang Stein
- School of Biological Sciences, Illinois State University, Normal, IL, United States
- Stiftung Alfried Krupp Kolleg Greifswald, Greifswald, Germany
- *Correspondence: Wolfgang Stein, ; Andrés G. Vidal-Gadea,
| | - Margaret L. DeMaegd
- School of Biological Sciences, Illinois State University, Normal, IL, United States
- Center for Neural Sciences, New York University, New York, NY, United States
| | - Abigail M. Benson
- School of Biological Sciences, Illinois State University, Normal, IL, United States
| | - Rajit S. Roy
- School of Biological Sciences, Illinois State University, Normal, IL, United States
| | - Andrés G. Vidal-Gadea
- School of Biological Sciences, Illinois State University, Normal, IL, United States
- *Correspondence: Wolfgang Stein, ; Andrés G. Vidal-Gadea,
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34
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Li XY, Mei J, Ge CT, Liu XL, Gui JF. Sex determination mechanisms and sex control approaches in aquaculture animals. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1091-1122. [PMID: 35583710 DOI: 10.1007/s11427-021-2075-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/14/2022] [Indexed: 01/21/2023]
Abstract
Aquaculture is one of the most efficient modes of animal protein production and plays an important role in global food security. Aquaculture animals exhibit extraordinarily diverse sexual phenotypes and underlying mechanisms, providing an ideal system to perform sex determination research, one of the important areas in life science. Moreover, sex is also one of the most valuable traits because sexual dimorphism in growth, size, and other economic characteristics commonly exist in aquaculture animals. Here, we synthesize current knowledge of sex determination mechanisms, sex chromosome evolution, reproduction strategies, and sexual dimorphism, and also review several approaches for sex control in aquaculture animals, including artificial gynogenesis, application of sex-specific or sex chromosome-linked markers, artificial sex reversal, as well as gene editing. We anticipate that better understanding of sex determination mechanisms and innovation of sex control approaches will facilitate sustainable development of aquaculture.
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Affiliation(s)
- Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jie Mei
- College of Fisheries, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chu-Tian Ge
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China
| | - Xiao-Li Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China.
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35
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Vogt G. Paradigm shifts in animal epigenetics: Research on non-model species leads to new insights into dependencies, functions and inheritance of DNA methylation. Bioessays 2022; 44:e2200040. [PMID: 35618444 DOI: 10.1002/bies.202200040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/06/2022]
Abstract
Recent investigations with non-model species and whole-genome approaches have challenged several paradigms in animal epigenetics. They revealed that epigenetic variation in populations is not the mere consequence of genetic variation, but is a semi-independent or independent source of phenotypic variation, depending on mode of reproduction. DNA methylation is not positively correlated with genome size and phylogenetic position as earlier believed, but has evolved differently between and within higher taxa. Epigenetic marks are usually not completely erased in the zygote and germ cells as generalized from mouse, but often persist and can be transgenerationally inherited, making them evolutionarily relevant. Gene body methylation and promoter methylation are similar in vertebrates and invertebrates with well methylated genomes but transposon silencing through methylation is variable. The new data also suggest that animals use epigenetic mechanisms to cope with rapid environmental changes and to adapt to new environments. The main benefiters are asexual populations, invaders, sessile taxa and long-lived species.
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Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
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36
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Yuan J, Zhang X, Kou Q, Sun Y, Liu C, Li S, Yu Y, Zhang C, Jin S, Xiang J, Li X, Li F. Genome of a giant isopod, Bathynomus jamesi, provides insights into body size evolution and adaptation to deep-sea environment. BMC Biol 2022; 20:113. [PMID: 35562825 PMCID: PMC9107163 DOI: 10.1186/s12915-022-01302-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/21/2022] [Indexed: 12/13/2022] Open
Abstract
Background The deep-sea may be regarded as a hostile living environment, due to low temperature, high hydrostatic pressure, and limited food and light. Isopods, a species-rich group of crustaceans, are widely distributed across different environments including the deep sea and as such are a useful model for studying adaptation, migration, and speciation. Similar to other deep-sea organisms, giant isopods have larger body size than their shallow water relatives and have large stomachs and fat bodies presumably to store organic reserves. In order to shed light on the genetic basis of these large crustaceans adapting to the oligotrophic environment of deep-sea, the high-quality genome of a deep-sea giant isopod Bathynomus jamesi was sequenced and assembled. Results B. jamesi has a large genome of 5.89 Gb, representing the largest sequenced crustacean genome to date. Its large genome size is mainly attributable to the remarkable proliferation of transposable elements (84%), which may enable high genome plasticity for adaptive evolution. Unlike its relatives with small body size, B. jamesi has expanded gene families related to pathways of thyroid and insulin hormone signaling that potentially contribute to its large body size. Transcriptomic analysis showed that some expanded gene families related to glycolysis and vesicular transport were specifically expressed in its digestive organs. In addition, comparative genomics and gene expression analyses in six tissues suggested that B. jamesi has inefficient lipid degradation, low basal metabolic rate, and bulk food storage, suggesting giant isopods adopt a more efficient mechanism of nutrient absorption, storage, and utilization to provide sustained energy supply for their large body size. Conclusions Taken together, the giant isopod genome may provide a valuable resource for understanding body size evolution and adaptation mechanisms of macrobenthic organisms to deep-sea environments. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01302-6.
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Affiliation(s)
- Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Qi Kou
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yamin Sun
- Research Center for Functional Genomics and Biochip, Tianjin, 300457, China
| | - Chengzhang Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Shihao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Chengsong Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Songjun Jin
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Jianhai Xiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Xinzheng Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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37
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Gao Y, Chen Y, Li S, Huang X, Hu J, Bock DG, MacIsaac HJ, Zhan A. Complementary genomic and epigenomic adaptation to environmental heterogeneity. Mol Ecol 2022; 31:3598-3612. [PMID: 35560847 DOI: 10.1111/mec.16500] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 04/18/2022] [Accepted: 05/05/2022] [Indexed: 12/01/2022]
Abstract
While adaptation is commonly thought to result from selection on DNA sequence-based variation, recent studies have highlighted an analogous epigenetic component as well. However, the relative roles of these mechanisms in facilitating population persistence under environmental heterogeneity remain unclear. To address the underlying genetic and epigenetic mechanisms and their relationship during environmental adaptation, we screened the genomes and epigenomes of nine global populations of a predominately sessile marine invasive tunicate, Botryllus schlosseri, using reduced-representation methods. We detected clear population differentiation at the genetic and epigenetic levels. Patterns of genetic and epigenetic structure were significantly influenced by local environmental variables. Among these variables, minimum annual sea surface temperature was identified as the top explanatory variable for both genetic and epigenetic variation. However, patterns of population structure driven by genetic and epigenetic variation were somewhat distinct, suggesting possible autonomy of epigenetic variation. We found both shared and specific genes and biological pathways among genetic and epigenetic loci associated with environmental factors, consistent with complementary and independent contributions of genetic and epigenetic variation to environmental adaptation in this system. Collectively, these mechanisms may facilitate population persistence under environmental change and sustain successful invasions across novel environments.
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Affiliation(s)
- Yangchun Gao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Juntao Hu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Dan G Bock
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Hugh J MacIsaac
- School of Ecology and Environmental Science, Yunnan University, Yunnan, 650091, China.,Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, N9B 3P4, Canada
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
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38
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Ren X, Lv J, Liu M, Wang Q, Shao H, Liu P, Li J. A chromosome-level genome of the kuruma shrimp (Marsupenaeus japonicus) provides insights into its evolution and cold-resistance mechanism. Genomics 2022; 114:110373. [PMID: 35460816 DOI: 10.1016/j.ygeno.2022.110373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/05/2022] [Accepted: 04/18/2022] [Indexed: 01/14/2023]
Abstract
Marsupenaeus japonicus is an important marine crustacean species. However, a lack of genomic resources hinders the use of whole genome sequencing to explore their genetic basis and molecular mechanisms for genome-assisted breeding. Consequently, we determined the chromosome-level genome of M. japonicus. Here we determine the chromosome-level genome assembly for M. japonicus with a total of 665.19 Gb genomic sequencing data, yielding an approximately1.54 Gb assembly with a contig N50 size of 229.97 kb and a scaffold N50 size of 38.27 Mb. With the high-throughput chromosome conformation capture (Hi-C) technology, we anchored 18,019 contigs onto 42 pseudo-chromosomes, accounting for 99.40% of the total genome assembly. Analysis of the present M. japonicus genome revealed 24,317 protein-coding genes and a high proportion of repetitive sequences (61.56%). The high-quality genome assembly enabled the identification of genes associated with cold-stress and cold tolerance in kuruma shrimp through the comparison of eyestalk transcriptomes between the low temperature-stressed shrimp (10 °C) and normal temperature shrimp (28 °C). The genome assembly presented here could be useful in future studies to reveal the molecular mechanisms of M. japonicus in response to low temperature stress and the molecular assisted breeding of M. japonicus in low temperature.
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Affiliation(s)
- Xianyun Ren
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Jianjian Lv
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Meng Liu
- Novogene Bioinformatics Institute, Beijing, PR China
| | - Qiong Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Huixin Shao
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, PR China
| | - Ping Liu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China.
| | - Jian Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China.
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Gutierrez A, Creehan KM, de Guglielmo G, Roberts AJ, Taffe MA. Behavioral effects of ethanol in the Red Swamp Crayfish (Procambarus clarkii). J Exp Anal Behav 2022; 117:472-492. [PMID: 35261037 DOI: 10.1002/jeab.746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/21/2021] [Accepted: 01/30/2022] [Indexed: 11/07/2022]
Abstract
Alcohol abuse remains one of the primary preventable sources of mortality in the United States. Model species can be used to evaluate behavioral and other biological changes associated with alcohol and to identify novel treatments. This report describes methods for evaluating the behavioral effects of ethanol (EtOH) in crayfish. Crayfish (Procambarus clarkii) were immersed in ethanol concentrations ranging from 0.1 to 1.0 molar, for 10-30 min. Studies evaluated hemolymph alcohol concentration, locomotion in an open field and anxiety-like behavior using a Light/Dark transfer approach. EtOH immersion produced dose-dependent increases in hemolymph EtOH (up to 249 mg/dL) and reductions in open field locomotion that depended on EtOH concentration or exposure duration. Untreated crayfish exhibit avoidance of the open parts of the locomotor arena and a preference for a covered portion. Acute EtOH immersion decreased time spent in the covered portion of the Light/Dark arena, consistent with a decrease in anxiety-like behavior. Daily EtOH immersion for 5 days did not alter locomotor responses, however, activity was increased 3 days after the repeated EtOH regimen. Overall, this study shows that this inexpensive, easily maintained species can be used for behavioral pharmacological experiments designed to assess the acute and repeated effects of EtOH.
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Affiliation(s)
| | - Kevin M Creehan
- Department of Psychiatry, University of California, San Diego
| | | | | | - Michael A Taffe
- Department of Psychiatry, University of California, San Diego
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40
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Vogt G. Studying phenotypic variation and DNA methylation across development, ecology and evolution in the clonal marbled crayfish: a paradigm for investigating epigenotype-phenotype relationships in macro-invertebrates. Naturwissenschaften 2022; 109:16. [PMID: 35099618 DOI: 10.1007/s00114-021-01782-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 12/17/2022]
Abstract
Animals can produce different phenotypes from the same genome during development, environmental adaptation and evolution, which is mediated by epigenetic mechanisms including DNA methylation. The obligatory parthenogenetic marbled crayfish, Procambarus virginalis, whose genome and methylome are fully established, proved very suitable to study this issue in detail. Comparison between developmental stages and DNA methylation revealed low expression of Dnmt methylation and Tet demethylation enzymes from the spawned oocyte to the 256 cell embryo and considerably increased expression thereafter. The global 5-methylcytosine level was 2.78% at mid-embryonic development and decreased slightly to 2.41% in 2-year-old adults. Genetically identical clutch-mates raised in the same uniform laboratory setting showed broad variation in morphological, behavioural and life history traits and differences in DNA methylation. The invasion of diverse habitats in tropical to cold-temperate biomes in the last 20 years by the marbled crayfish was associated with the expression of significantly different phenotypic traits and DNA methylation patterns, despite extremely low genetic variation on the whole genome scale, suggesting the establishment of epigenetic ecotypes. The evolution of marbled crayfish from its parent species Procambarus fallax by autotriploidy a few decades ago was accompanied by a significant increase in body size, fertility and life span, a 20% reduction of global DNA methylation and alteration of methylation in hundreds of genes, suggesting that epigenetic mechanisms were involved in speciation and fitness enhancement. The combined analysis of phenotypic traits and DNA methylation across multiple biological contexts in the laboratory and field in marbled crayfish may serve as a blueprint for uncovering the role of epigenetic mechanisms in shaping of phenotypes in macro-invertebrates.
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Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany.
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41
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Austin CM, Croft LJ, Grandjean F, Gan HM. The NGS Magic Pudding: A Nanopore-Led Long-Read Genome Assembly for the Commercial Australian Freshwater Crayfish, Cherax destructor. Front Genet 2022; 12:695763. [PMID: 35126445 PMCID: PMC8807398 DOI: 10.3389/fgene.2021.695763] [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: 04/15/2021] [Accepted: 12/23/2021] [Indexed: 11/26/2022] Open
Abstract
Cherax destructor, the yabby, is an iconic Australian freshwater crayfish species, which, similar to other major invertebrate groups, is grossly under-represented in genomic databases. The yabby is also the principal commercial freshwater crustacean species in Australia subject to explotation via inland fisheries and aquaculture. To address the genomics knowledge gap for this species and explore cost effective and efficient methods for genome assembly, we generated 106.8 gb of Nanopore reads and performed a long-read only assembly of the Cherax destructor genome. On a mini-server configured with an ultra-fast swap space, the de novo assembly took 131 h (∼5.5 days). Genome polishing with 126.3 gb of PCR-Free Illumina reads generated an assembled genome size of 3.3 gb (74.6% BUSCO completeness) with a contig N50 of 80,900 bp, making it the most contiguous for freshwater crayfish genome assemblies. We found an unusually large number of cellulase genes within the yabby genome which is relevant to understanding the nutritional biology, commercial feed development, and ecological role of this species and crayfish more generally. These resources will be useful for genomic research on freshwater crayfish and our methods for rapid and super-efficient genome assembly will have wide application.
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Affiliation(s)
- Christopher M. Austin
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Laurence J. Croft
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Frederic Grandjean
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Unité Mixte de Recherche 7267 Centre National de la Recherche Scientifique, Université de Poitiers, Poitiers, France
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Invasion genomics uncover contrasting scenarios of genetic diversity in a widespread marine invader. Proc Natl Acad Sci U S A 2021; 118:2116211118. [PMID: 34911766 PMCID: PMC8713979 DOI: 10.1073/pnas.2116211118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2021] [Indexed: 01/25/2023] Open
Abstract
Invasion rates have increased in the past 100 y irrespective of international conventions. What characterizes a successful invasion event? And how does genetic diversity translate into invasion success? Employing a whole-genome perspective using one of the most successful marine invasive species world-wide as a model, we resolve temporal invasion dynamics during independent invasion events in Eurasia. We reveal complex regionally independent invasion histories including cases of recurrent translocations, time-limited translocations, and stepping-stone range expansions with severe bottlenecks within the same species. Irrespective of these different invasion dynamics, which lead to contrasting patterns of genetic diversity, all nonindigenous populations are similarly successful. This illustrates that genetic diversity, per se, is not necessarily the driving force behind invasion success. Other factors such as propagule pressure and repeated introductions are an important contribution to facilitate successful invasions. This calls into question the dominant paradigm of the genetic paradox of invasions, i.e., the successful establishment of nonindigenous populations with low levels of genetic diversity.
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43
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Vogt G. Cytology, function and dynamics of stem and progenitor cells in decapod crustaceans. Biol Rev Camb Philos Soc 2021; 97:817-850. [PMID: 34914163 DOI: 10.1111/brv.12824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/26/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022]
Abstract
Stem cells play key roles in development, tissue homeostasis, regeneration, ageing and diseases. Comprehensive reviews on stem cells are available for the determinately growing mammals and insects and some lower invertebrates like hydra but are rare for larger, indeterminately growing invertebrates that can live for many decades. This paper reviews the cytology, function and dynamics of stem and progenitor cells in the decapod crustaceans, a species-rich and ecologically and economically important animal group that includes mainly indeterminate growers but also some determinate growers. Further advantages of decapods for stem cell research are almost 1000-fold differences in body size and longevity, the regeneration of damaged appendages and the virtual absence of age-related diseases and tumours in the indeterminately growing species. The available data demonstrate that the Decapoda possess a remarkable variety of structurally and functionally different stem cells in embryos and larvae, and in the epidermis, musculature, haematopoietic tissue, heart, brain, hepatopancreas, olfactory sense organs and gonads of adults. Some of these seem to be rather continuously active over a lifetime but others are cyclically activated and silenced in periods of days, weeks and years, depending on the specific organ and function. Stem cell proliferation is triggered by signals related to development, moulting, feeding, reproduction, injury, infection, environmental enrichment and social status. Some regulatory pathways have already been identified, including the evolutionarily conserved GATA-binding and runt-domain transcription factors, the widespread neurotransmitter serotonin, the arthropod-specific hormone 20-hydroxyecdysone and the novel astakine growth factors. Knowledge of stem cells in decapods primarily refines our picture on the development, growth and maintenance of tissues and organs in this animal group. Cultured decapod stem cells have good potential for toxicity testing and virus research with practical relevance for aquaculture. Knowledge of stem cells in decapods also broadens our understanding of the evolution of stem cells and regeneration in the animal kingdom. The stem cells of long-lived, indeterminately growing decapods may hold the key to understanding how stem and progenitor cells function into old age without adverse side effects, possibly evoking new ideas for the development of anti-ageing and anti-cancer treatments in humans.
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Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
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Tönges S, Venkatesh G, Andriantsoa R, Hanna K, Gatzmann F, Raddatz G, Carneiro VC, Lyko F. Location-Dependent DNA Methylation Signatures in a Clonal Invasive Crayfish. Front Cell Dev Biol 2021; 9:794506. [PMID: 34957121 PMCID: PMC8695926 DOI: 10.3389/fcell.2021.794506] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/22/2021] [Indexed: 01/16/2023] Open
Abstract
DNA methylation is an important epigenetic modification that has been repeatedly implied in organismal adaptation. However, many previous studies that have linked DNA methylation patterns to environmental parameters have been limited by confounding factors, such as cell-type heterogeneity and genetic variation. In this study, we analyzed DNA methylation variation in marbled crayfish, a clonal and invasive freshwater crayfish that is characterized by a largely tissue-invariant methylome and negligible genetic variation. Using a capture-based subgenome bisulfite sequencing approach that covers a small, variably methylated portion of the marbled crayfish genome, we identified specific and highly localized DNA methylation signatures for specimens from geographically and ecologically distinct wild populations. These results were replicated both biologically and technically by re-sampling at different time points and by using independent methodology. Finally, we show specific methylation signatures for laboratory animals and for laboratory animals that were reared at a lower temperature. Our results thus demonstrate the existence of context-dependent DNA methylation signatures in a clonal animal.
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Affiliation(s)
| | | | | | | | | | | | | | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Heidelberg, Germany
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45
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Sutherland WJ, Atkinson PW, Butchart SHM, Capaja M, Dicks LV, Fleishman E, Gaston KJ, Hails RS, Hughes AC, Le Anstey B, Le Roux X, Lickorish FA, Maggs L, Noor N, Oldfield TEE, Palardy JE, Peck LS, Pettorelli N, Pretty J, Spalding MD, Tonneijck FH, Truelove G, Watson JEM, Wentworth J, Wilson JD, Thornton A. A horizon scan of global biological conservation issues for 2022. Trends Ecol Evol 2021; 37:95-104. [PMID: 34809998 DOI: 10.1016/j.tree.2021.10.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 10/19/2022]
Abstract
We present the results of our 13th annual horizon scan of issues likely to impact on biodiversity conservation. Issues are either novel within the biological conservation sector or could cause a substantial step-change in impact, either globally or regionally. Our global panel of 26 scientists and practitioners identified 15 issues that we believe to represent the highest priorities for tracking and action. Many of the issues we identified, including the impact of satellite megaconstellations and the use of long-distance wireless energy transfer, have both elements of threats and emerging opportunities. A recent state-sponsored application to commence deep-sea mining represents a significant step-change in impact. We hope that this horizon scan will increase research and policy attention on the highlighted issues.
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Affiliation(s)
- William J Sutherland
- Conservation Science Group, Department of Zoology, Cambridge University, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK; Biosecurity Research Initiative at St Catharine's (BioRISC), St Catharine's College, University of Cambridge, Cambridge CB2 1RL, UK.
| | | | - Stuart H M Butchart
- Conservation Science Group, Department of Zoology, Cambridge University, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK; BirdLife International, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK
| | - Marcela Capaja
- Natural England, Eastbrook, Shaftesbury Rd, Cambridge CB2 8DR, UK
| | - Lynn V Dicks
- Conservation Science Group, Department of Zoology, Cambridge University, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK; School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Erica Fleishman
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Kevin J Gaston
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | | | - Alice C Hughes
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Xishuangbanna, Yunnan 666303, PR China
| | - Becky Le Anstey
- Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Xavier Le Roux
- Microbial Ecology Centre, UMR1418 INRAE, UMR5557 CNRS, University Lyon 1, University of Lyon, 69622 Villeurbanne, France; BiodivERsA, la Fondation pour la recherche sur la biodiversité, 195 rue Saint Jacques, 75005 Paris, France
| | - Fiona A Lickorish
- UK Research and Consultancy Services (RCS) Ltd, Valletts Cottage, Westhope, Hereford HR4 8BU, UK
| | - Luke Maggs
- Natural Resources Wales, Cambria House, 29 Newport Road, Cardiff CF24 0TP, UK
| | - Noor Noor
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), 219 Huntingdon Road, Cambridge CB3 0DL, UK
| | | | - James E Palardy
- The Pew Charitable Trusts, 901 E St NW, Washington, DC 20004, USA
| | - Lloyd S Peck
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge CB3 0ET, UK
| | - Nathalie Pettorelli
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - Jules Pretty
- Centre for Public and Policy Engagement and School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Mark D Spalding
- Conservation Science Group, Department of Zoology, Cambridge University, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK; The Nature Conservancy, Department of Physical, Earth and Environmental Sciences, University of Siena, Pian dei Mantellini, Siena 53100, Italy
| | | | - Gemma Truelove
- UK Research and Innovation, Natural Environment Research Council, Polaris House, North Star Avenue, Swindon SN2 1EU, UK
| | - James E M Watson
- School of Earth and Environmental Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Jonathan Wentworth
- Parliamentary Office of Science and Technology, 14 Tothill Street, Westminster, London SW1H 9NB, UK
| | - Jeremy D Wilson
- Royal Society for the Protection of Birds (RSPB) Centre for Conservation Science, 2 Lochside View, Edinburgh EH12 9DH, UK
| | - Ann Thornton
- Conservation Science Group, Department of Zoology, Cambridge University, The David Attenborough Building, Pembroke Street, Cambridge CB2 3QZ, UK
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Kawato S, Nishitsuji K, Arimoto A, Hisata K, Kawamitsu M, Nozaki R, Kondo H, Shinzato C, Ohira T, Satoh N, Shoguchi E, Hirono I. Genome and transcriptome assemblies of the kuruma shrimp, Marsupenaeus japonicus. G3 (BETHESDA, MD.) 2021; 11:jkab268. [PMID: 34515781 PMCID: PMC8527471 DOI: 10.1093/g3journal/jkab268] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/18/2021] [Indexed: 11/25/2022]
Abstract
The kuruma shrimp Marsupenaeus japonicus (order Decapoda, family Penaeidae) is an economically important crustacean that occurs in shallow, warm seas across the Indo-Pacific. Here, using a combination of Illumina and Oxford Nanopore Technologies platforms, we produced a draft genome assembly of M. japonicus (1.70 Gbp; 18,210 scaffolds; scaffold N50 = 234.9 kbp; 34.38% GC, 93.4% BUSCO completeness) and a complete mitochondrial genome sequence (15,969 bp). As with other penaeid shrimp genomes, the M. japonicus genome is extremely rich in simple repeats, which occupies 27.4% of the assembly. A total of 26,381 protein-coding gene models (94.7% BUSCO completeness) were predicted, of which 18,005 genes (68.2%) were assigned functional description by at least one method. We also produced an Illumina-based transcriptome shotgun assembly (40,991 entries; 93.0% BUSCO completeness) and a PacBio Iso-Seq transcriptome assembly (25,415 entries; 67.5% BUSCO completeness). We envision that the M. japonicus genome and transcriptome assemblies will serve as useful resources for the basic research, fisheries management, and breeding programs of M. japonicus.
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Affiliation(s)
- Satoshi Kawato
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Mayumi Kawamitsu
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Reiko Nozaki
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-0882, Japan
| | - Tsuyoshi Ohira
- Faculty of Science, Department of Biological Sciences, Kanagawa University, Kanagawa 221-8686, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
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Principe NG, Ash KT, Davis MA, Egly RM, Larson ER. A Molecular and Morphological Guide to the Pilose Crayfishes of Western North America. WEST N AM NATURALIST 2021. [DOI: 10.3398/064.081.0304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
| | - Kurt T. Ash
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996
| | - Mark A. Davis
- Illinois Natural History Survey, Champaign, IL 61820
| | - Rachel M. Egly
- Institute of Environmental Sustainability, Loyola University, Chicago, IL 60660
| | - Eric R. Larson
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801
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48
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Phylogeographic reconstruction of the marbled crayfish origin. Commun Biol 2021; 4:1096. [PMID: 34535758 PMCID: PMC8448756 DOI: 10.1038/s42003-021-02609-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/20/2021] [Indexed: 11/08/2022] Open
Abstract
The marbled crayfish (Procambarus virginalis) is a triploid and parthenogenetic freshwater crayfish species that has colonized diverse habitats around the world. Previous studies suggested that the clonal marbled crayfish population descended as recently as 25 years ago from a single specimen of P. fallax, the sexually reproducing parent species. However, the genetic, phylogeographic, and mechanistic origins of the species have remained enigmatic. We have now constructed a new genome assembly for P. virginalis to support a detailed phylogeographic analysis of the diploid parent species, Procambarus fallax. Our results strongly suggest that both parental haplotypes of P. virginalis were inherited from the Everglades subpopulation of P. fallax. Comprehensive whole-genome sequencing also detected triploid specimens in the same subpopulation, which either represent evolutionarily important intermediate genotypes or independent parthenogenetic lineages arising among the sexual parent population. Our findings thus clarify the geographic origin of the marbled crayfish and identify potential mechanisms of parthenogenetic speciation.
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49
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Bachvaroff TR, McDonald RC, Plough LV, Chung JS. Chromosome-level genome assembly of the blue crab, Callinectes sapidus. G3-GENES GENOMES GENETICS 2021; 11:6304867. [PMID: 34544121 PMCID: PMC8496215 DOI: 10.1093/g3journal/jkab212] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/15/2021] [Indexed: 11/14/2022]
Abstract
The blue crab, Callinectes sapidus (Rathbun, 1896) is an economically, culturally, and ecologically important species found across the temperate and tropical North and South American Atlantic coast. A reference genome will enable research for this high-value species. Initial assembly combined 200× coverage Illumina paired-end reads, a 60× 8 kb mate-paired library, and 50× PacBio data using the MaSuRCA assembler resulting in a 985 Mb assembly with a scaffold N50 of 153 kb. Dovetail Chicago and HiC sequencing with the 3d DNA assembler and Juicebox assembly tools were then used for chromosome scaffolding. The 50 largest scaffolds span 810 Mb are 1.5-37 Mb long and have a repeat content of 36%. The 190 Mb unplaced sequence is in 3921 sequences over 10 kb with a repeat content of 68%. The final assembly N50 is 18.9 Mb for scaffolds and 9317 bases for contigs. Of arthropod BUSCO, ∼88% (888/1013) were complete and single copies. Using 309 million RNAseq read pairs from 12 different tissues and developmental stages, 25,249 protein-coding genes were predicted. Between C. sapidus and Portunus trituberculatus genomes, 41 of 50 large scaffolds had high nucleotide identity and protein-coding synteny, but 9 scaffolds in both assemblies were not clear matches. The protein-coding genes included 9423 one-to-one putative orthologs, of which 7165 were syntenic between the two crab species. Overall, the two crab genome assemblies show strong similarities at the nucleotide, protein, and chromosome level and verify the blue crab genome as an excellent reference for this important seafood species.
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Affiliation(s)
- Tsvetan R Bachvaroff
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Ryan C McDonald
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Louis V Plough
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Horn Point, MD 21613, USA
| | - J Sook Chung
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
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50
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Tönges S, Masagounder K, Lenich F, Gutekunst J, Tönges M, Lohbeck J, Miller AK, Böhl F, Lyko F. Evaluating Invasive Marbled Crayfish as a Potential Livestock for Sustainable Aquaculture. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.651981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The marbled crayfish (Procambarus virginalis) is a recently discovered freshwater crayfish species, which reproduces by apomictic parthenogenesis, resulting in a monoclonal, and all-female population. The animals were widely distributed through the aquarium trade and have established numerous stable wild populations through anthropogenic releases. They are highly prevalent in Madagascar, where they have become a popular source of nutritional protein. As freshwater crayfish aquaculture in open systems is a thriving, but ecologically damaging global industry, alternatives are urgently needed. Although marbled crayfish are often branded by their invasive mode of reproduction, their overall invasiveness is not higher than for other cultured crayfish species. Furthermore, their resiliency and high adaptability provide a strong rationale for evaluating them for closed, and environmentally safe aquaculture approaches. Here we describe a novel population of marbled crayfish in a former German coal mining area that is characterized by acid and polluted water. Even under these adverse conditions, animals grew to sizes, and weights that are comparable to commercially farmed freshwater crayfish. Tailored feed development and laboratory testing demonstrated highly efficient feed conversion, suggesting a considerable capacity for sustainable production in closed systems. We further show that marbled crayfish meat can be readily introduced into European meals. Finally, chemical analysis of marbled crayfish exoskeletons revealed comparably high amounts of chitin, which is a valuable source for the synthesis of chitosan and bioplastics. Our results thus suggest that production of marbled crayfish in closed systems may represent a sustainable alternative for crayfish aquaculture.
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