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Rahi ML, Mather PB, de Bello Cioffi M, Ezaz T, Hurwood DA. Genomic Basis of Freshwater Adaptation in the Palaemonid Prawn Genus Macrobrachium: Convergent Evolution Following Multiple Independent Colonization Events. J Mol Evol 2023; 91:976-989. [PMID: 38010517 DOI: 10.1007/s00239-023-10149-6] [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: 10/14/2022] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Adaptation to different salinity environments can enhance morphological and genomic divergence between related aquatic taxa. Species of prawns in the genus Macrobrachium naturally inhabit different osmotic niches and possess distinctive lifecycle traits associated with salinity tolerance. This study was conducted to investigate the patterns of adaptive genomic divergence during freshwater colonization in 34 Macrobrachium species collected from four continents; Australia, Asia, North and South America. Genotyping-by-sequencing (GBS) technique identified 5018 loci containing 82,636 single nucleotide polymorphisms (SNPs) that were used to reconstruct a phylogenomic tree. An additional phylogeny was reconstructed based on 43 candidate genes, previously identified as being potentially associated with freshwater adaptation. Comparison of the two phylogenetic trees revealed contrasting topologies. The GBS tree indicated multiple independent continent-specific invasions into freshwater by Macrobrachium lineages following common marine ancestry, as species with abbreviated larval development (ALD), i.e., species having a full freshwater life history, appeared reciprocally monophyletic within each continent. In contrast, the candidate gene tree showed convergent evolution for all ALD species worldwide, forming a single, well-supported clade. This latter pattern is likely the result of common evolutionary pressures selecting key mutations favored in continental freshwater habitats Results suggest that following multiple independent invasions into continental freshwaters at different evolutionary timescales, Macrobrachium taxa experienced adaptive genomic divergence, and in particular, convergence in the same genomic regions with parallel shifts in specific conserved phenotypic traits, such as evolution of larger eggs with abbreviated larval developmental.
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Affiliation(s)
- Md Lifat Rahi
- Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna, Bangladesh.
| | - Peter B Mather
- Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD, 4001, Australia
| | - Marcelo de Bello Cioffi
- Department of Genetics and Evolution, Federal University of Sao Carlos, São Carlos, SP, Brazil
| | - Tariq Ezaz
- Institute for Applied Ecology (IAE), University of Canberra (UC), Canberra, ACT, 2617, Australia
| | - David A Hurwood
- Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD, 4001, Australia
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2
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Transcriptomic and Proteomic Analysis of Marine Nematode Litoditis marina Acclimated to Different Salinities. Genes (Basel) 2022; 13:genes13040651. [PMID: 35456458 PMCID: PMC9025465 DOI: 10.3390/genes13040651] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 02/05/2023] Open
Abstract
Salinity is a critical abiotic factor for all living organisms. The ability to adapt to different salinity environments determines an organism’s survival and ecological niches. Litoditis marina is a euryhaline marine nematode widely distributed in coastal ecosystems all over the world, although numerous genes involved in its salinity response have been reported, the adaptive mechanisms underlying its euryhalinity remain unexplored. Here, we utilized worms which have been acclimated to either low-salinity or high-salinity conditions and evaluated their basal gene expression at both transcriptomic and proteomic levels. We found that several conserved regulators, including osmolytes biosynthesis genes, transthyretin-like family genes, V-type H+-transporting ATPase and potassium channel genes, were involved in both short-term salinity stress response and long-term acclimation processes. In addition, we identified genes related to cell volume regulation, such as actin regulatory genes, Rho family small GTPases and diverse ion transporters, which might contribute to hyposaline acclimation, while the glycerol biosynthesis genes gpdh-1 and gpdh-2 accompanied hypersaline acclimation in L. marina. This study paves the way for further in-depth exploration of the adaptive mechanisms underlying euryhalinity and may also contribute to the study of healthy ecosystems in the context of global climate change.
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3
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Shamsi S, Sibraa L, Zhu X, Barton DP. Characterisation of Temnocephalidae flatworms in common Australian freshwater prawn, Macrobrachium australiense. Sci Rep 2022; 12:1396. [PMID: 35082314 PMCID: PMC8792052 DOI: 10.1038/s41598-022-05123-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 01/04/2022] [Indexed: 11/09/2022] Open
Abstract
Macrobrachium australiense, is one of Australia’s most widespread freshwater invertebrates. Although a significant amount of research has been conducted to understand the diversity of crustacean species in Australia, there has been considerably less effort focused on their Temnocephalidae symbionts. The present study aims to identify Temnocephalidae species found in M. australiense, along with determining their impacts on the fitness of their hosts. A total of 54 M. australiense (common Australian river prawn) were examined for evidence of infection with Temnocephalidae species, of which 96.3% showed at least one sign of infection with Temnocephalidae. Due to damage and immaturity of the worms collected from, they have been referred to as Temnocephalidae sp. based on the presence of tentacles on the anterior margin of the body, and pedunculate sucker located dorsally on the ventral surface. Possible mechanical damage to gill lamellae resulting from either egg deposition or autolysis is evident. In the phylogenetic tree built based on sequences of the 28S rRNA gene, specimens in the present study grouped separately from other Temnocephalidae species reported from Australia.
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4
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Rahi ML, Azad KN, Tabassum M, Irin HH, Hossain KS, Aziz D, Moshtaghi A, Hurwood DA. Effects of Salinity on Physiological, Biochemical and Gene Expression Parameters of Black Tiger Shrimp ( Penaeus monodon): Potential for Farming in Low-Salinity Environments. BIOLOGY 2021; 10:biology10121220. [PMID: 34943135 PMCID: PMC8698961 DOI: 10.3390/biology10121220] [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: 09/25/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 01/10/2023]
Abstract
Salinity is one of the most important abiotic factors affecting growth, metabolism, immunity and survival of aquatic species in farming environments. As a euryhaline species, the black tiger shrimp (Penaeus monodon) can tolerate a wide range of salinity levels and is farmed between brackish to marine water conditions. The current study tested the effects of six different salinity levels (0‱, 2.5‱, 5‱, 10‱, 20‱ and 30‱) on the selected physiological, biochemical and genetic markers (individual changes in the expression pattern of selected candidate genes) in the black tiger shrimp. Experimental salinity levels significantly affected growth and survival performance (p < 0.05); the highest levels of growth and survival performance were observed at the control (20‱) salinity. Salinity reductions significantly increased free fatty acid (FFA), but reduced free amino acid (FAA) levels. Lower salinity treatments (0-10‱) significantly reduced hemolymph osmolality levels while 30‱ significantly increased osmolality levels. The five different salinity treatments increased the expression of osmoregulatory and hemolymph regulatory genes by 1.2-8-fold. In contrast, 1.2-1.6-fold lower expression levels were observed at the five salinity treatments for growth (alpha amylase) and immunity (toll-like receptor) genes. O2 consumption, glucose and serotonin levels, and expression of osmoregulatory genes showed rapid increase initially with salinity change, followed by reducing trend and stable patterns from the 5th day to the end. Hemocyte counts, expression of growth and immunity related genes showed initial decreasing trends, followed by an increasing trend and finally stability from 20th day to the end. Results indicate the farming potential of P. monodon at low salinity environments (possibly at freshwater) by proper acclimation prior to stocking with minimal effects on production performance.
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Affiliation(s)
- Md. Lifat Rahi
- Fisheries and Marine Resource Technology Discipline, Life Science School, Khulna University, Khulna 9208, Bangladesh; (M.L.R.); (K.N.A.); (M.T.); (H.H.I.); (K.S.H.)
| | - Khairun Naher Azad
- Fisheries and Marine Resource Technology Discipline, Life Science School, Khulna University, Khulna 9208, Bangladesh; (M.L.R.); (K.N.A.); (M.T.); (H.H.I.); (K.S.H.)
| | - Maliha Tabassum
- Fisheries and Marine Resource Technology Discipline, Life Science School, Khulna University, Khulna 9208, Bangladesh; (M.L.R.); (K.N.A.); (M.T.); (H.H.I.); (K.S.H.)
| | - Hasna Hena Irin
- Fisheries and Marine Resource Technology Discipline, Life Science School, Khulna University, Khulna 9208, Bangladesh; (M.L.R.); (K.N.A.); (M.T.); (H.H.I.); (K.S.H.)
| | - Kazi Sabbir Hossain
- Fisheries and Marine Resource Technology Discipline, Life Science School, Khulna University, Khulna 9208, Bangladesh; (M.L.R.); (K.N.A.); (M.T.); (H.H.I.); (K.S.H.)
| | - Dania Aziz
- Department of Aquaculture, Faculty of Agriculture, University Putra Malaysia (UPM), Serdang 43400, Malaysia
- International Institute of Aquaculture and Aquatic Sciences (I-AQUAS), University Putra Malaysia (UPM), Port Dickson 70150, Malaysia; (A.M.); (D.A.H.)
- Correspondence:
| | - Azam Moshtaghi
- International Institute of Aquaculture and Aquatic Sciences (I-AQUAS), University Putra Malaysia (UPM), Port Dickson 70150, Malaysia; (A.M.); (D.A.H.)
| | - David A Hurwood
- International Institute of Aquaculture and Aquatic Sciences (I-AQUAS), University Putra Malaysia (UPM), Port Dickson 70150, Malaysia; (A.M.); (D.A.H.)
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5
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Van Nynatten A, Castiglione GM, de A Gutierrez E, Lovejoy NR, Chang BSW. Recreated Ancestral Opsin Associated with Marine to Freshwater Croaker Invasion Reveals Kinetic and Spectral Adaptation. Mol Biol Evol 2021; 38:2076-2087. [PMID: 33481002 PMCID: PMC8097279 DOI: 10.1093/molbev/msab008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Rhodopsin, the light-sensitive visual pigment expressed in rod photoreceptors, is specialized for vision in dim-light environments. Aquatic environments are particularly challenging for vision due to the spectrally dependent attenuation of light, which can differ greatly in marine and freshwater systems. Among fish lineages that have successfully colonized freshwater habitats from ancestrally marine environments, croakers are known as highly visual benthic predators. In this study, we isolate rhodopsins from a diversity of freshwater and marine croakers and find that strong positive selection in rhodopsin is associated with a marine to freshwater transition in South American croakers. In order to determine if this is accompanied by significant shifts in visual abilities, we resurrected ancestral rhodopsin sequences and tested the experimental properties of ancestral pigments bracketing this transition using in vitro spectroscopic assays. We found the ancestral freshwater croaker rhodopsin is redshifted relative to its marine ancestor, with mutations that recapitulate ancestral amino acid changes along this transitional branch resulting in faster kinetics that are likely to be associated with more rapid dark adaptation. This could be advantageous in freshwater due to the redshifted spectrum and relatively narrow interface and frequent transitions between bright and dim-light environments. This study is the first to experimentally demonstrate that positively selected substitutions in ancestral visual pigments alter protein function to freshwater visual environments following a transition from an ancestrally marine state and provides insight into the molecular mechanisms underlying some of the physiological changes associated with this major habitat transition.
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Affiliation(s)
- Alexander Van Nynatten
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Scarborough, ON, Canada
| | - Gianni M Castiglione
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Eduardo de A Gutierrez
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Nathan R Lovejoy
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Scarborough, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Belinda S W Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
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6
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Wang J, Sheng J, Zhu J, Hu Z, Diao Y. Comparative transcriptome analysis and identification of candidate adaptive evolution genes of Miscanthus lutarioriparius and Miscanthus sacchariflorus. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1499-1512. [PMID: 34366592 PMCID: PMC8295449 DOI: 10.1007/s12298-021-01030-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Miscanthus species are perennial C4 grasses that are considered promising energy crops because of their high biomass yields, excellent adaptability and low management costs. Miscanthus lutarioriparius and Miscanthus sacchariflorus are closely related subspecies that are distributed in different habitats. However, there are only a few reports on the mechanisms by which Miscanthus adapts to different environments. Here, comparative transcriptomic and morphological analyses were used to study the evolutionary adaptation of M. lutarioriparius and M. sacchariflorus to different habitats. In total, among 7586 identified orthologs, 2060 orthologs involved in phenylpropanoid biosynthesis and plant hormones were differentially expressed between the two species. Through an analysis of the Ka/Ks ratios of the orthologs, we estimated that the divergence time between the two species was approximately 4.37 Mya. In addition, 37 candidate positively selected orthologs (PSGs) that played important roles in the adaptation of these species to different habitats were identified. Then, the expression levels of 20 PSGs in response to flooding and drought stress were analyzed, and the analysis revealed significant changes in their expression levels. These results facilitate our understanding of the evolutionary adaptation to habitats and the speciation of M. lutarioriparius and M. sacchariflorus. We hypothesise that lignin synthesis genes are the main cause of the morphological differences between the two species. In summary, the plant nonspecific phospholipase C gene family and the receptor-like protein kinase gene family played important roles in the evolution of these two species. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01030-1.
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Affiliation(s)
- Jia Wang
- School of Medicine, Anhui University of Science and Technology, Huainan, 232001 People’s Republic of China
| | - Jiajing Sheng
- College of Life Sciences, Nantong University, Nantong, 226019 People’s Republic of China
| | - Jianyong Zhu
- College of Forestry and Life Sciences, Chongqing University of Arts and Sciences, Chongqing, 402160 People’s Republic of China
| | - Zhongli Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Hubei Lotus Engineering Center, Wuhan University, Wuhan, 430072 People’s Republic of China
| | - Ying Diao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023 People’s Republic of China
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7
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Maraschi AC, Faria SC, McNamara JC. Salt transport by the gill Na -K -2Cl symporter in palaemonid shrimps: exploring physiological, molecular and evolutionary landscapes. Comp Biochem Physiol A Mol Integr Physiol 2021; 257:110968. [DOI: 10.1016/j.cbpa.2021.110968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 12/22/2022]
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8
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Siriwut W, Jeratthitikul E, Panha S, Chanabun R, Ngor PB, Sutcharit C. Evidence of cryptic diversity in freshwater Macrobrachium prawns from Indochinese riverine systems revealed by DNA barcode, species delimitation and phylogenetic approaches. PLoS One 2021; 16:e0252546. [PMID: 34077477 PMCID: PMC8171930 DOI: 10.1371/journal.pone.0252546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/18/2021] [Indexed: 12/04/2022] Open
Abstract
The diversity of Indochinese prawns in genus Macrobrachium is enormous due to the habitat diversification and broad tributary networks of two river basins: the Chao Phraya and the Mekong. Despite long-standing interest in SE-Asian decapod diversity, the subregional Macrobrachium fauna is still not yet comprehensively clarified in terms of taxonomic identification or genetic diversification. In this study, integrative taxonomic approaches including morphological examination, DNA barcoding, and molecular species delimitation were used to emphasize the broad scale systematics of Macrobrachium prawns in Indochina. Twenty-seven nominal species were successfully re-verified by traditional and molecular taxonomy. Barcode gap analysis supported broad overlapping of species boundaries. Taxonomic ambiguity of several deposited samples in the public database is related to inter- and intraspecific genetic divergence as indicated by BOLD discordance. Diagnostic nucleotide positions were found in six Macrobrachium species. Eighteen additional putative lineages are herein assigned using the consensus of species delimitation methods. Genetic divergence indicates the possible existence of cryptic species in four morphologically complex and wide-ranging species: M. lanchesteri, M. niphanae, M. sintangense, and some members of the M. pilimanus group. The geographical distribution of some species supports the connections and barriers attributed to paleo-historical events of SE-Asian rivers and land masses. Results of this study show explicitly the importance of freshwater ecosystems in Indochinese subregions, especially for the Mekong River Basin due to its high genetic diversity and species composition found throughout its tributaries.
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Affiliation(s)
- Warut Siriwut
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Ekgachai Jeratthitikul
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Somsak Panha
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Academy of Science, The Royal Society of Thailand, Dusit, Bangkok, Thailand
| | - Ratmanee Chanabun
- Program in Animal Science, Faculty of Agricultural Technology, Sakon Nakhon Rajabhat University, Sakon Nakhon, Thailand
| | - Peng Bun Ngor
- Inland Fisheries Research and Development Institute (IFReDI), Fisheries Administration, Phnom Penh, Cambodia
- Wonders of the Mekong Project, Phnom Penh, Cambodia
| | - Chirasak Sutcharit
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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9
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Rahi ML, Mather PB, Hurwood DA. Do plasticity in gene expression and physiological responses in Palaemonid prawns facilitate adaptive response to different osmotic challenges? Comp Biochem Physiol A Mol Integr Physiol 2021; 251:110810. [DOI: 10.1016/j.cbpa.2020.110810] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 12/20/2022]
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10
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Niu J, Hu XL, Ip JCH, Ma KY, Tang Y, Wang Y, Qin J, Qiu JW, Chan TF, Chu KH. Multi-omic approach provides insights into osmoregulation and osmoconformation of the crab Scylla paramamosain. Sci Rep 2020; 10:21771. [PMID: 33303836 PMCID: PMC7728780 DOI: 10.1038/s41598-020-78351-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/23/2020] [Indexed: 12/18/2022] Open
Abstract
Osmoregulation and osmoconformation are two mechanisms through which aquatic animals adapt to salinity fluctuations. The euryhaline crab Scylla paramamosain, being both an osmoconformer and osmoregulator, is an excellent model organism to investigate salinity adaptation mechanisms in brachyurans. In the present study, we used transcriptomic and proteomic approaches to investigate the response of S. paramamosain to salinity stress. Crabs were transferred from a salinity of 25 ppt to salinities of 5 ppt or 33 ppt for 6 h and 10 days. Data from both approaches revealed that exposure to 5 ppt resulted in upregulation of ion transport and energy metabolism associated genes. Notably, acclimation to low salinity was associated with early changes in gene expression for signal transduction and stress response. In contrast, exposure to 33 ppt resulted in upregulation of genes related to amino acid metabolism, and amino acid transport genes were upregulated only at the early stage of acclimation to this salinity. Our study reveals contrasting mechanisms underlying osmoregulation and osmoconformation within the salinity range of 5–33 ppt in the mud crab, and provides novel candidate genes for osmotic signal transduction, thereby providing insights on understanding the salinity adaptation mechanisms of brachyuran crabs.
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Affiliation(s)
- Jiaojiao Niu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Xue Lei Hu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Jack C H Ip
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong, China
| | - Ka Yan Ma
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Yuanyuan Tang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Yaqin Wang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Jing Qin
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong, China
| | - Ting Fung Chan
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
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11
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Christie AE, Rivera CD, Call CM, Dickinson PS, Stemmler EA, Hull JJ. Multiple transcriptome mining coupled with tissue specific molecular cloning and mass spectrometry provide insights into agatoxin-like peptide conservation in decapod crustaceans. Gen Comp Endocrinol 2020; 299:113609. [PMID: 32916171 PMCID: PMC7747469 DOI: 10.1016/j.ygcen.2020.113609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/25/2020] [Accepted: 08/29/2020] [Indexed: 12/16/2022]
Abstract
Over the past decade, in silico genome and transcriptome mining has led to the identification of many new crustacean peptide families, including the agatoxin-like peptides (ALPs), a group named for their structural similarity to agatoxin, a spider venom component. Here, analysis of publicly accessible transcriptomes was used to expand our understanding of crustacean ALPs. Specifically, transcriptome mining was used to investigate the phylogenetic/structural conservation, tissue localization, and putative functions of ALPs in decapod species. Transcripts encoding putative ALP precursors were identified from one or more members of the Penaeoidea (penaeid shrimp), Sergestoidea (sergestid shrimps), Caridea (caridean shrimp), Astacidea (clawed lobsters and freshwater crayfish), Achelata (spiny/slipper lobsters), and Brachyura (true crabs), suggesting a broad, and perhaps ubiquitous, conservation of ALPs in decapods. Comparison of the predicted mature structures of decapod ALPs revealed high levels of amino acid conservation, including eight identically conserved cysteine residues that presumably allow for the formation of four identically positioned disulfide bridges. All decapod ALPs are predicted to have amidated carboxyl-terminals. Two isoforms of ALP appear to be present in most decapod species, one 44 amino acids long and the other 42 amino acids in length, both likely generated by alternative splicing of a single gene. In carideans, a gene or terminal exon duplication appears to have occurred, with alternative splicing producing four ALPs, two 44 and two 42 amino acid isoforms. The identification of ALP precursor-encoding transcripts in nervous system-specific transcriptomes (e.g., Homarus americanus brain, eyestalk ganglia, and cardiac ganglion assemblies, finding confirmed using RT-PCR) suggests that members of this peptide family may serve as locally-released and/or hormonally-delivered neuromodulators in decapods. Their detection in testis- and hepatopancreas-specific transcriptomes suggests that members of the ALP family may also play roles in male reproduction and innate immunity/detoxification.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
| | - Cindy D Rivera
- Department of Chemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011, USA
| | - Catherine M Call
- Department of Chemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011, USA
| | - Patsy S Dickinson
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME 04011, USA
| | - Elizabeth A Stemmler
- Department of Chemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011, USA
| | - J Joe Hull
- Pest Management and Biocontrol Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ 85138, USA.
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12
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Posavi M, Gulisija D, Munro JB, Silva JC, Lee CE. Rapid evolution of genome-wide gene expression and plasticity during saline to freshwater invasions by the copepod Eurytemora affinis species complex. Mol Ecol 2020; 29:4835-4856. [PMID: 33047351 DOI: 10.1111/mec.15681] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 09/18/2020] [Accepted: 10/01/2020] [Indexed: 01/01/2023]
Abstract
Saline migrants into freshwater habitats constitute among the most destructive invaders in aquatic ecosystems throughout the globe. However, the evolutionary and physiological mechanisms underlying such habitat transitions remain poorly understood. To explore the mechanisms of freshwater adaptation and distinguish between adaptive (evolutionary) and acclimatory (plastic) responses to salinity change, we examined genome-wide patterns of gene expression between ancestral saline and derived freshwater populations of the Eurytemora affinis species complex, reared under two different common-garden conditions (0 versus 15 PSU). We found that evolutionary shifts in gene expression (between saline and freshwater inbred lines) showed far greater changes and were more widespread than acclimatory responses to salinity (0 versus 15 PSU). Most notably, 30-40 genes showing evolutionary shifts in gene expression across the salinity boundary were associated with ion transport function, with inorganic cation transmembrane transport forming the largest Gene Ontology category. Of particular interest was the sodium transporter, the Na+ /H+ antiporter (NHA) gene family, which was discovered in animals relatively recently. Thirty key ion regulatory genes, such as NHA paralogue #7, demonstrated concordant evolutionary and plastic shifts in gene expression, suggesting the evolution of ion transporter function and plasticity during rapid invasions into novel salinities. Moreover, freshwater invasions were associated with the evolution of reduced plasticity in the freshwater population, again for the same key ion transporters, consistent with the predicted evolution of canalization following adaptation to stressful conditions. Our results have important implications for understanding evolutionary and physiological mechanisms of range expansions by some of the most widespread invaders in aquatic habitats.
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Affiliation(s)
- Marijan Posavi
- Department of Integrative Biology, University of Wisconsin, Madison, WI, USA
| | - Davorka Gulisija
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - James B Munro
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Carol Eunmi Lee
- Department of Integrative Biology, University of Wisconsin, Madison, WI, USA
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