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Lu H, Liu C, Yang C, He Z, Wang L, Song L. Genome-wide identification of the HSP70 genes in Pacific oyster Magallana gigas and their response to heat stress. Cell Stress Chaperones 2024; 29:589-602. [PMID: 38908469 DOI: 10.1016/j.cstres.2024.06.002] [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: 04/22/2024] [Revised: 06/11/2024] [Accepted: 06/11/2024] [Indexed: 06/24/2024] Open
Abstract
Heat shock protein 70 (HSP70), the most prominent and well-characterized stress protein in animals, plays an important role in assisting animals in responding to various adverse conditions. In the present study, a total of 113 HSP70 gene family members were identified in the updated genome of Magallana gigas (designated MgHSP70) (previously known as Crassostrea gigas). There were 75, 12, 11, and 8 HSP70s located in the cytoplasm, nucleus, mitochondria, and endoplasmic reticulum, respectively, and 7 HSP70s were located in both the nucleus and cytoplasm. Among 113 MgHSP70 genes, 107 were unevenly distributed in 8 chromosomes of M. gigas with the greatest number in chromosome 07 (61 genes, 57.01%). The MgHSP70 gene family members were mainly assigned into five clusters, among which the HSPa12 subfamily underwent lineage-specific expansion, consisting of 89 members. A total of 68 MgHSP70 genes (60.18%) were tandemly duplicated and formed 30 gene pairs, among which 14 gene pairs were under strong positive selection. In general, the expression of MgHSP70s was tissue-specific, with the highest expression in labial palp and gill and the lowest expression in adductor muscle and hemocytes. There were 35, 31, and 47 significantly upregulated genes at 6, 12, and 24 h after heat shock treatment (28 °C), respectively. The expression patterns of different tandemly duplicated genes exhibited distinct characteristics after shock treatment, indicating that these genes may have different functions. Nevertheless, genes within the same tandemly duplicated group exhibit similar expression patterns. Most of the tandemly duplicated HSP70 gene pairs showed the highest expression levels at 24 h. This study provides a comprehensive description of the MgHSP70 gene family in M. gigas and offers valuable insights into the functions of HSP70 in the mollusc adaptation of oysters to environmental stress.
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Affiliation(s)
- Hongbo Lu
- Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China
| | - Chang Liu
- Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China
| | - Chuanyan Yang
- Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian 116023, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China.
| | - Zhaoyu He
- Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China.
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian 116023, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China
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Bu L, Habib MR, Lu L, Mutuku MW, Loker ES, Zhang SM. Transcriptional profiling of Bulinus globosus provides insights into immune gene families in snails supporting the transmission of urogenital schistosomiasis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 154:105150. [PMID: 38367887 PMCID: PMC10932938 DOI: 10.1016/j.dci.2024.105150] [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] [Received: 12/11/2023] [Revised: 01/18/2024] [Accepted: 02/14/2024] [Indexed: 02/19/2024]
Abstract
Schistosomiasis, urogenital and intestinal, afflicts 251 million people worldwide with approximately two-thirds of the patients suffering from the urogenital form of the disease. Freshwater snails of the genus Bulinus (Gastropoda: Planorbidae) serve as obligate intermediate hosts for Schistosoma haematobium, the etiologic agent of human urogenital schistosomiasis. These snails also act as vectors for the transmission of schistosomiasis in livestock and wildlife. Despite their crucial role in human and veterinary medicine, our basic understanding at the molecular level of the entire Bulinus genus, which comprises 37 recognized species, is very limited. In this study, we employed Illumina-based RNA sequencing (RNAseq) to profile the genome-wide transcriptome of Bulinus globosus, one of the most important intermediate hosts for S. haematobium in Africa. A total of 179,221 transcripts (N50 = 1,235) were assembled and the benchmarking universal single-copy orthologs (BUSCO) was estimated to be 97.7%. The analysis revealed a substantial number of transcripts encoding evolutionarily conserved immune-related proteins, particularly C-type lectin (CLECT) domain-containing proteins (n = 316), Toll/Interleukin 1-receptor (TIR)-containing proteins (n = 75), and fibrinogen related domain-containing molecules (FReD) (n = 165). Notably, none of the FReDs are fibrinogen-related proteins (FREPs) (immunoglobulin superfamily (IgSF) + fibrinogen (FBG)). This RNAseq-based transcriptional profile provides new insights into immune capabilities of Bulinus snails, helps provide a framework to explain the complex patterns of compatibility between snails and schistosomes, and improves our overall understanding of comparative immunology.
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Affiliation(s)
- Lijing Bu
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Mohamed R Habib
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Lijun Lu
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Martin W Mutuku
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute (KEMRI), P.O Box 54840-00200, Nairobi, Kenya
| | - Eric S Loker
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA; Parasitology Division, Museum of Southwestern Biology, University of New Mexico, Albuquerque, 87131, USA
| | - Si-Ming Zhang
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA.
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3
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Hernández Elizárraga VH, Ballantyne S, O'Brien LG, Americo JA, Suhr ST, Senut MC, Minerich B, Merkes CM, Edwards TM, Klymus K, Richter CA, Waller DL, Passamaneck YJ, Rebelo MF, Gohl DM. Toward invasive mussel genetic biocontrol: Approaches, challenges, and perspectives. iScience 2023; 26:108027. [PMID: 37860763 PMCID: PMC10583111 DOI: 10.1016/j.isci.2023.108027] [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] [Indexed: 10/21/2023] Open
Abstract
Invasive freshwater mussels, such as the zebra (Dreissena polymorpha), quagga (Dreissena rostriformis bugensis), and golden (Limnoperna fortunei) mussel have spread outside their native ranges throughout many regions of the North American, South American, and European continents in recent decades, damaging infrastructure and the environment. This review describes ongoing efforts by multiple groups to develop genetic biocontrol methods for invasive mussels. First, we provide an overview of genetic biocontrol strategies that have been applied in other invasive or pest species. Next, we summarize physical and chemical methods that are currently in use for invasive mussel control. We then describe the multidisciplinary approaches our groups are employing to develop genetic biocontrol tools for invasive mussels. Finally, we discuss the challenges and limitations of applying genetic biocontrol tools to invasive mussels. Collectively, we aim to openly share information and combine expertise to develop practical tools to enable the management of invasive freshwater mussels.
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Affiliation(s)
| | - Scott Ballantyne
- Department of Biology, University of Wisconsin River Falls, River Falls, WI, USA
| | | | | | | | | | | | - Christopher M. Merkes
- U.S. Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, WI, USA
| | - Thea M. Edwards
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO, USA
| | - Katy Klymus
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO, USA
| | - Catherine A. Richter
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO, USA
| | - Diane L. Waller
- U.S. Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, WI, USA
| | - Yale J. Passamaneck
- Bureau of Reclamation, Technical Service Center, Hydraulic Investigations and Laboratory Services, Ecological Research Laboratory, Denver, CO, USA
| | - Mauro F. Rebelo
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Daryl M. Gohl
- University of Minnesota Genomics Center, Minneapolis, MN, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
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Moreira AMS, Freitas ETF, Reis MDP, Nogueira JM, Barbosa NPDU, Reis ALM, Pelli A, Camargo PRDS, Cardoso AV, de Paula RS, Jorge EC. Acute Exposure to Two Biocides Causes Morphological and Molecular Changes in the Gill Ciliary Epithelium of the Invasive Golden Mussel Limnoperna fortunei (Dunker, 1857). Animals (Basel) 2023; 13:3258. [PMID: 37893982 PMCID: PMC10603641 DOI: 10.3390/ani13203258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/29/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Limnoperna fortunei, the golden mussel, is a bivalve mollusk considered an invader in South America. This species is responsible for ecological and economic damages due to its voluminous fouling capability. Chemical biocides such as MXD-100™ and sodium dichloroisocyanurate (NaDCC) are often used to control L. fortunei infestations in hydraulic systems. Thus, we proposed to investigate the effects of different periods (24, 48 and 72 h) of exposure to MXD-100™ (0.56 mg L-1) and NaDCC (1.5 mg L-1) on the gills of L. fortunei through morphological and molecular analyses. NaDCC promoted progressive morphological changes during the analyzed periods and only an upregulation of SOD and HSP70 expression during the first 24 h of exposure. MXD-100™ led to severe morphological changes from the first period of exposure, in addition to an upregulation of SOD, CAT, HSP70 and CYP expression during the first 24 h. In contrast, MXD-100™ led to a downregulation of CAT transcription between 24 and 48 h. In static conditions, NaDCC causes lethal damage after 72 h of exposure, and that exposure needs to be continuous to achieve the control of the species. Meanwhile, the MXD-100™ treatment presented several effects during the first 24 h, showing acute toxicity in a shorter period of time.
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Affiliation(s)
- Amanda Maria Siqueira Moreira
- Laboratório de Biologia Oral e do Desenvolvimento, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil; (A.M.S.M.); (J.M.N.); (R.S.d.P.)
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Cidade Nova, Belo Horizonte 31035-536, MG, Brazil; (E.T.F.F.); (M.d.P.R.); (N.P.d.U.B.); (A.P.); (P.R.d.S.C.); (A.V.C.)
| | - Erico Tadeu Fraga Freitas
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Cidade Nova, Belo Horizonte 31035-536, MG, Brazil; (E.T.F.F.); (M.d.P.R.); (N.P.d.U.B.); (A.P.); (P.R.d.S.C.); (A.V.C.)
- Electron Optics Facility, Materials Science and Engineering, Michigan Technological University, Houghton, MI 49931, USA
| | - Mariana de Paula Reis
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Cidade Nova, Belo Horizonte 31035-536, MG, Brazil; (E.T.F.F.); (M.d.P.R.); (N.P.d.U.B.); (A.P.); (P.R.d.S.C.); (A.V.C.)
| | - Júlia Meireles Nogueira
- Laboratório de Biologia Oral e do Desenvolvimento, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil; (A.M.S.M.); (J.M.N.); (R.S.d.P.)
| | - Newton Pimentel de Ulhôa Barbosa
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Cidade Nova, Belo Horizonte 31035-536, MG, Brazil; (E.T.F.F.); (M.d.P.R.); (N.P.d.U.B.); (A.P.); (P.R.d.S.C.); (A.V.C.)
| | - André Luiz Martins Reis
- Center for Population Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia;
| | - Afonso Pelli
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Cidade Nova, Belo Horizonte 31035-536, MG, Brazil; (E.T.F.F.); (M.d.P.R.); (N.P.d.U.B.); (A.P.); (P.R.d.S.C.); (A.V.C.)
- Biotério Nico Nieser, Universidade Federal do Triângulo Mineiro, Uberaba 38025-100, MG, Brazil
| | - Paulo Ricardo da Silva Camargo
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Cidade Nova, Belo Horizonte 31035-536, MG, Brazil; (E.T.F.F.); (M.d.P.R.); (N.P.d.U.B.); (A.P.); (P.R.d.S.C.); (A.V.C.)
- Biotério Nico Nieser, Universidade Federal do Triângulo Mineiro, Uberaba 38025-100, MG, Brazil
| | - Antonio Valadão Cardoso
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Cidade Nova, Belo Horizonte 31035-536, MG, Brazil; (E.T.F.F.); (M.d.P.R.); (N.P.d.U.B.); (A.P.); (P.R.d.S.C.); (A.V.C.)
- Escola de Design, Universidade do Estado de Minas Gerais (UEMG), Belo Horizonte 30140-091, MG, Brazil
| | - Rayan Silva de Paula
- Laboratório de Biologia Oral e do Desenvolvimento, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil; (A.M.S.M.); (J.M.N.); (R.S.d.P.)
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Cidade Nova, Belo Horizonte 31035-536, MG, Brazil; (E.T.F.F.); (M.d.P.R.); (N.P.d.U.B.); (A.P.); (P.R.d.S.C.); (A.V.C.)
| | - Erika Cristina Jorge
- Laboratório de Biologia Oral e do Desenvolvimento, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil; (A.M.S.M.); (J.M.N.); (R.S.d.P.)
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5
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Collins M, Clark MS, Truebano M. The environmental cellular stress response: the intertidal as a multistressor model. Cell Stress Chaperones 2023; 28:467-475. [PMID: 37129699 PMCID: PMC10469114 DOI: 10.1007/s12192-023-01348-7] [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: 04/05/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023] Open
Abstract
The wild poses a multifaceted challenge to the maintenance of cellular function. Therefore, a multistressor approach is essential to predict the cellular mechanisms which promote homeostasis and underpin whole-organism tolerance. The intertidal zone is particularly dynamic, and thus, its inhabitants provide excellent models to assess mechanisms underpinning multistressor tolerance. Here, we critically review our current understanding of the regulation of the cellular stress response (CSR) under multiple abiotic stressors in intertidal organisms and consider to what extent a multistressor approach brings us closer to understanding responses in the wild. The function of the CSR has been well documented in laboratory and field exposures with a view to understanding single-stressor thermal effects. Multistressor studies still remain relatively limited in comparison but have applied three main approaches: (i) laboratory application of multiple stressors in isolation, (ii) multiple stressors applied in combination, and (iii) field-based correlation of multiple stressors against the CSR. The application of multiple stressors in isolation has allowed the identification of putative, shared stress pathways but overlooks non-additive stressor interactions on the CSR. Combined stressor studies are relatively limited in number but already highlight variable effects on the CSR dependent upon stressor type, timing, and magnitude. Field studies have allowed the identification of responsive components of the CSR to various stressors in situ but are correlative, not causative. A combined approach involving laboratory multistressor studies linking the CSR to whole-organism tolerance as well as field studies is required if we are to understand the role of the CSR in the natural environment.
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Affiliation(s)
- Michael Collins
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK.
| | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Manuela Truebano
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK
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Reis AC, Amaral D, Americo JA, Rebelo MF, Sousa SM. Cytogenetic characterization of the golden mussel (Limnoperna fortunei) reveals the absence of sex heteromorphic chromosomes. AN ACAD BRAS CIENC 2023; 95:e20201622. [PMID: 37341265 DOI: 10.1590/0001-3765202320201622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 05/12/2021] [Indexed: 06/22/2023] Open
Abstract
The golden mussel (Limnoperna fortunei) is an aggressive invasive species in South America, where it endangers native species and freshwater ecosystems, in addition to causing extensive economic losses, mainly to the hydroelectric sector. Currently, there's no efficient control method available and the invasion has progressed across the continent. Its high reproduction rate is one of the key factors of the golden mussel's high invasive potential and, recently, efforts have been done in order to understand the reproduction and the sexual features of this species. However, its cytogenetics characterization is incipient and the possible occurrence of sex-specific cytogenetic features was never investigated. In this study, we aimed to characterize the chromosomal morphometry, the distribution profile of heterochromatin, and to detect possible sex-related epigenetic marks in the golden mussel. Results revealed that the karyotypic structure is similar in both sexes and no chromosome heteromorphism was observed between males and females specimens. The data increment the cytogenetic characterization of Limnoperna fortunei and contribute for future studies that aim to further investigate its reproduction and underlying sex determination processes.
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Affiliation(s)
- Aryane C Reis
- Universidade Federal de Juiz de Fora, Departamento de Biologia, Laboratório de Genética e Biotecnologia, Rua José Lourenço Kelmer, s/n, 36036-900 Juiz de Fora, MG, Brazil
| | - Danielle Amaral
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Avenida Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro, RJ, Brazil
| | - Juliana A Americo
- Bio Bureau Biotecnologia, Rua Aloísio Teixeira, 278, Prédio 3, sala 310, 21941-850 Rio de Janeiro, RJ, Brazil
| | - Mauro F Rebelo
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Avenida Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro, RJ, Brazil
| | - Saulo M Sousa
- Universidade Federal de Juiz de Fora, Departamento de Biologia, Laboratório de Genética e Biotecnologia, Rua José Lourenço Kelmer, s/n, 36036-900 Juiz de Fora, MG, Brazil
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7
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Stanley TR, Guisbert KSK, Perez SM, Oneka M, Kernin I, Higgins NR, Lobo A, Subasi MM, Carroll DJ, Turingan RG, Guisbert E. Stress response gene family expansions correlate with invasive potential in teleost fish. J Exp Biol 2022; 225:274389. [PMID: 35258619 PMCID: PMC8987736 DOI: 10.1242/jeb.243263] [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: 08/02/2021] [Accepted: 01/24/2022] [Indexed: 11/20/2022]
Abstract
The bluegill sunfish Lepomis macrochirus and the closely related redear sunfish Lepomis microlophus have important ecological and recreational value and are widely used for research and aquaculture. While both species have been introduced outside of their native ranges, only the bluegill is considered invasive. Here, we report de novo transcriptome assemblies for these fish as a resource for sunfish biology. Comparative analyses of the transcriptomes revealed an unexpected, bluegill-specific expansion in the HSP70 and HSP90 molecular chaperone gene families. These expansions were not unique to the bluegill as expansions in HSP70s and HSP90s were identified in the genomes of other teleost fish using the NCBI RefSeq database. To determine whether gene family expansions are specific for thermal stress responses, GST and SOD gene families that are associated with oxidative stress responses were also analyzed. Species-specific expansions were also observed for these gene families in distinct fish species. Validating our approach, previously described expansions in the MHC gene family were also identified. Intriguingly, the number of HSP70 paralogs was positively correlated with thermotolerance range for each species, suggesting that these expansions can impact organismal physiology. Furthermore, fish that are considered invasive contained a higher average number of HSP70 paralogs than non-invasive fish. Invasive fish also had higher average numbers of HSP90, MHC and GST paralogs, but not SOD paralogs. Taken together, we propose that expansions in key cellular stress response gene families represent novel genetic signatures that correlate with invasive potential.
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Affiliation(s)
- Taylor R Stanley
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Karen S Kim Guisbert
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Sabrina M Perez
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Morgan Oneka
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Isabela Kernin
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Nicole R Higgins
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Alexandra Lobo
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Munevver M Subasi
- Department of Mathematical Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - David J Carroll
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Ralph G Turingan
- Department of Ocean Engineering and Marine Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Eric Guisbert
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
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8
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Freitas ETF, Moreira AMS, de Paula RS, Andrade GR, de Carvalho MD, Assis PS, Jorge EC, Cardoso AV. Ultrastructure of the gill ciliary epithelium of Limnoperna fortunei (Dunker 1857), the invasive golden mussel. BMC ZOOL 2022; 7:6. [PMID: 37170369 PMCID: PMC10127303 DOI: 10.1186/s40850-022-00107-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/31/2021] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Limnoperna fortunei is a freshwater bivalve mollusc originally from southern Asia that invaded South America in the 1990’s. Due to its highly efficient water pumping and filtering, and its capacity to form strong adhesions to a variety of substrates by byssus thread, this invasive species has been able to adapt to several environments across South America, causing significant ecological and economic damages. By gaining a deeper understanding of the biological and ecological aspects of L. fortunei we will be able to establish more effective strategies to manage its invasion. The gills of the mollusc are key structures responsible for several biological functions, including respiration and feeding. In this work, we characterized the ultrastructure of L. fortunei gills and its ciliary epithelium using light microscopy, transmission and scanning electron microscopies. This is the first report of the morphology of the epithelial cells and cilia of the gill of L. fortunei visualized in high resolution.
Results
The analysis showed highly organized and abundant ciliary structures (lateral cilia, laterofrontal cirri and frontal cilia) on the entire length of the branchial epithelium. Mitochondria, smooth endoplasmic reticulum and glycogen granules were abundantly found in the epithelial cells of the gills, demonstrating the energy-demanding function of these structures. Neutral mucopolysaccharides (low viscosity mucus) were observed on the frontal surface of the gill filaments and acid mucopolysaccharides (high viscosity mucus) were observed to be spread out, mainly on the lateral tract. Spherical vesicles, possibly containing mucus, could also be observed in these cells. These findings demonstrate the importance of the mucociliary processes in particle capture and selection.
Conclusions
Our data suggest that the mechanism used by this mollusc for particle capture and selection could contribute to a better understanding of key aspects of invasion and also in the establishment of more efficient and economically viable strategies of population control.
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Clark MS, Peck LS, Thyrring J. Resilience in Greenland intertidal Mytilus: The hidden stress defense. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:144366. [PMID: 33434840 DOI: 10.1016/j.scitotenv.2020.144366] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 05/20/2023]
Abstract
The Arctic is experiencing particularly rapid rates of warming, consequently invasive boreal species are now able to survive the less extreme Arctic winter temperatures. Whilst persistence of intertidal and terrestrial species in the Arctic is primarily determined by their ability to tolerate the freezing winters, air temperatures in the Arctic summer can reach 36 °C in the intertidal, which is beyond the upper thermal limits of many marine species. This is normally lethal for the conspicuous ecosystem engineer Mytilus edulis. Transcriptomic analyses were undertaken on both in situ collected and experimentally warmed animals to understand whether M. edulis is able to tolerate these very high summer temperatures. Surprisingly there was no significant enrichment for Gene Ontology terms (GO) when comparing the inner and outer fjord intertidal animals with outer fjord subtidal (control) animals, representing animals collected at 27 °C, 19 °C and 3 °C respectively. This lack of differentiation indicated a wide acclimation ability in this species. Conversely, significant enrichment for processes such as signal transduction, cytoskeleton and cellular protein modification was identified in the expression profiles of the 22 °C and 32 °C experimentally heated animals. This difference in gene expression between in situ collected and experimentally warmed animals was almost certainly due to the former being acclimated to a fluctuating, but predictable, temperature regime, which has increased their thermal tolerances. Interestingly, there was no evidence for enrichment of the classical cellular stress response in any of the animals sampled. Identification of a massive expansion of the HSPA12 heat shock protein 70 kDa gene family presented the possibility of these genes acting as intertidal regulators underpinning thermal resilience. This expansion has resulted in a modified cellular stress response, as an evolutionary adaptation to the rigour of the invasive intertidal life style. Thus, M. edulis appear to have considerable capacity to withstand the current rates of Arctic warming, and the very large attendant thermal variation.
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Affiliation(s)
- Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK.
| | - Lloyd S Peck
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Jakob Thyrring
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; Department of Zoology, University of British Columbia, 4200 - 6270 University Blvd., V6T 1Z4 Vancouver, British Columbia, Canada; Department of Bioscience - Marine Ecology, Aarhus University, Vejlsøvej 25, Silkeborg 8600, Denmark
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10
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Davey PA, Power AM, Santos R, Bertemes P, Ladurner P, Palmowski P, Clarke J, Flammang P, Lengerer B, Hennebert E, Rothbächer U, Pjeta R, Wunderer J, Zurovec M, Aldred N. Omics-based molecular analyses of adhesion by aquatic invertebrates. Biol Rev Camb Philos Soc 2021; 96:1051-1075. [PMID: 33594824 DOI: 10.1111/brv.12691] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 12/15/2022]
Abstract
Many aquatic invertebrates are associated with surfaces, using adhesives to attach to the substratum for locomotion, prey capture, reproduction, building or defence. Their intriguing and sophisticated biological glues have been the focus of study for decades. In all but a couple of specific taxa, however, the precise mechanisms by which the bioadhesives stick to surfaces underwater and (in many cases) harden have proved to be elusive. Since the bulk components are known to be based on proteins in most organisms, the opportunities provided by advancing 'omics technologies have revolutionised bioadhesion research. Time-consuming isolation and analysis of single molecules has been either replaced or augmented by the generation of massive data sets that describe the organism's translated genes and proteins. While these new approaches have provided resources and opportunities that have enabled physiological insights and taxonomic comparisons that were not previously possible, they do not provide the complete picture and continued multi-disciplinarity is essential. This review covers the various ways in which 'omics have contributed to our understanding of adhesion by aquatic invertebrates, with new data to illustrate key points. The associated challenges are highlighted and priorities are suggested for future research.
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Affiliation(s)
- Peter A Davey
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K
| | - Anne Marie Power
- Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Room 226, Galway, H91 TK33, Ireland
| | - Romana Santos
- Departamento de Biologia Animal, Faculdade de Ciências, Centro de Ciências do Mar e do Ambiente (MARE), Universidade de Lisboa, Lisbon, 1749-016, Portugal
| | - Philip Bertemes
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstrasse 25, Innsbruck, 6020, Austria
| | - Peter Ladurner
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstrasse 25, Innsbruck, 6020, Austria
| | - Pawel Palmowski
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K
| | - Jessica Clarke
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K
| | - Patrick Flammang
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons, Place du Parc 23, Mons, 7000, Belgium
| | - Birgit Lengerer
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstrasse 25, Innsbruck, 6020, Austria
| | - Elise Hennebert
- Laboratory of Cell Biology, Research Institute for Biosciences, University of Mons, Place du Parc 23, Mons, 7000, Belgium
| | - Ute Rothbächer
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstrasse 25, Innsbruck, 6020, Austria
| | - Robert Pjeta
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstrasse 25, Innsbruck, 6020, Austria
| | - Julia Wunderer
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstrasse 25, Innsbruck, 6020, Austria
| | - Michal Zurovec
- Biology Centre of the Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, 370 05, Czech Republic
| | - Nick Aldred
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, U.K
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11
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Hernando M, De Troch M, de la Rosa F, Giannuzzi L. Fatty acid response of the invasive bivalve Limnoperna fortunei fed with Microcystis aeruginosa exposed to high temperature. Comp Biochem Physiol C Toxicol Pharmacol 2021; 240:108925. [PMID: 33130072 DOI: 10.1016/j.cbpc.2020.108925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/07/2020] [Accepted: 10/22/2020] [Indexed: 10/23/2022]
Abstract
The success of Limnoperna fortunei as an invasive freshwater bivalve species is related to its physiological plasticity to endure changes in environmental conditions. The aim of this study was to investigate the physiological responses of L. fortunei after feeding on Microcystis aeruginosa grown at 26 °C (control) and 29 °C during 10 days. At the beginning, we measured biomass, fatty acids (FAs) composition on Cyanobacteria grown at both temperatures at different time intervals. Afterwards, mussels were fed with the thawed M. aeruginosa cells and their FA profile was measured after 15 days of feeding. M. aeruginosa exposed to 29 °C had the highest content of the FAs 18:2ω6 and cis-18:1ω9. The FA profile of the consumer L. fortunei fed with M. aeruginosa cultures grown at 29 °C was also significantly different to those fed with cultures grown at 26 °C, with a significant increased Eicosapentaenoic acid (EPA, 20:5ω3) and Arachidonic acid (ARA, 20:4ω6) concentrations. L. fortunei was already known to be physiologically adapted to live at 29 °C, but our results also shown a high biosynthesis of EPA and ARA (increase of 70 and 40% respectively, compared with 26 °C) and avoided the lipid peroxidation of both FAs. This increased EPA and ARA biosynthesis may be an important source of ω3 and ω6 polyunsaturated FAs (PUFAs) for higher trophic levels, such as the pelagic fishes or birds that mainly prey on these mussels. The transfer of the cyanobacterial response at higher temperature to higher trophic levels will influence the overall functioning of freshwater bodies.
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Affiliation(s)
- Marcelo Hernando
- Comisión Nacional de Energía Atómica (CNEA), Departamento de Radiobiología, Centro Atómico Constituyentes, Av. Gral. Paz 1499, 1650 San Martín, Buenos Aires, Argentina.
| | - Marleen De Troch
- Ghent University, Faculty of Sciences, Marine Biology, Krijgslaan 281-S8, Ghent, Belgium
| | - Florencia de la Rosa
- Instituto de Fisiología y Neurociencias (IFiNe), Universidad de Morón, Machado 914, 5to Piso, 1708 Morón, Buenos Aires, Argentina; CONICET, Godoy Cruz, 2290, Buenos Aires, Argentina
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12
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Sanson AL, Cosenza-Contreras M, DeMarco R, Neves LX, Mattei B, Silva GG, Magalhães PHV, de Andrade MHG, Castro-Borges W. The golden mussel proteome and its response to niclosamide: Uncovering rational targets for control or elimination. J Proteomics 2020; 217:103651. [PMID: 31972344 DOI: 10.1016/j.jprot.2020.103651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 12/12/2019] [Accepted: 01/16/2020] [Indexed: 11/19/2022]
Abstract
The Asian invasive species Limnoperna fortunei (Dunker, 1857), known as the golden mussel, causes great economic and environmental damage due to its fixative capacity and accelerated proliferation. Molecular studies for the control of larval and adult forms are of great economic, scientific and technological interest. Here, we first report on the compositional analysis of the L. fortunei proteome obtained through shotgun analysis using LC-MS/MS. Among those 2790 proteins identified, many of them related to secretory processes and membrane receptors. Our second approach consisted in exposing the mollusc to the molluscicide niclosamide to evaluate the induced proteomic alterations. Exposure to niclosamide at 0.25 mg/L for 24 h resulted in a pronounced differential abundance of proteins when compared to those obtained when exposure was reduced to 4 h at 2.3 mg/L. In total, 342 proteins were found differentially expressed in the responsive individuals as revealed by label-free quantitative proteomics. Regarding the affected cell processes were: cell division and differentiation, cytoskeletal organization and compartment acidification (upregulated), and energy metabolism (downregulated). Our findings constitute the first inventory of the expressed proteome of the golden mussel and have the potential to contribute with a more rational proposition of molecular targets for control and monitoring of this species. SIGNIFICANCE: With the recent availability of transcriptomic and genomic data applied to L. fortunei the timing is right to interrogate its putative gene repertoire using proteomic techniques. These have the potential to validate the existence of the predicted genes, infer their relative abundance and quantify their levels as a response to environmental stressors or various agents. Here we provided an inventory of the golden mussel proteome and evaluated its response to the molluscicide niclosamide. The obtained results open new avenues for intervention aimed at its control or elimination, particularly by targeting the various cellular processes that were uncovered.
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Affiliation(s)
- Ananda Lima Sanson
- Programa de Pós Graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Miguel Cosenza-Contreras
- Programa de Pós Graduação em Ciências Biológicas, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Ricardo DeMarco
- Departamento de Física e Ciência Interdisciplinar, Instituto de Física de São Carlos, Universidade de São Paulo, Brazil
| | - Leandro Xavier Neves
- Programa de Pós Graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Bruno Mattei
- Programa de Pós Graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil; Programa de Pós Graduação em Ciências Biológicas, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Gustavo Gonçalves Silva
- Programa de Pós Graduação em Ciências Biológicas, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | | | - Milton Hércules Guerra de Andrade
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - William Castro-Borges
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil.
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13
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Romero A, Aranguren R, Moreira R, Novoa B, Figueras A. Integrated transcriptomic and functional immunological approach for assessing the invasiveness of bivalve alien species. Sci Rep 2019; 9:19879. [PMID: 31882949 PMCID: PMC6934813 DOI: 10.1038/s41598-019-56421-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 11/24/2019] [Indexed: 11/17/2022] Open
Abstract
Biological invasions started when humans moved species beyond their normal geographic limits. Bivalves are the most notoriously invasive species in subtidal aquatic environments. Next-generation sequencing technologies are applied to understand the molecular mechanisms involved in the invasion. The ecological immunology focuses on the role of immunity in invasion, and its magnitude could help to predict the invasiveness of alien species. A remarkable case of invasion has been reported in the Ría de Vigo (Spain) by the black pygmy mussel Xenostrobus securis. In Galicia, the Mediterranean mussel Mytilus galloprovincialis is the predominant cultured bivalve species. Can we predict the invasiveness of alien bivalve species by analyzing their immune response? Can X. securis represent a risk for the autochthonous mussel? We evaluated the suitability of the immune-related hypotheses in our model by using an integrated transcriptomic and functional immunological approach. Our analysis suggests lower immune capabilities in X. securis compared to M. galloprovincialis, probably due to the relocation of energetic resources from the immune response to vital physiological processes to cope with salinity stress. This multidisciplinary approach will help us understand how the immune response can be influenced by the adaptive process and how this immune response can influence the invasion process.
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Affiliation(s)
- Alejandro Romero
- Instituto de Investigaciones Marinas (CSIC), Eduardo Cabello 6, 36208, Vigo, Spain
| | - Raquel Aranguren
- Instituto de Investigaciones Marinas (CSIC), Eduardo Cabello 6, 36208, Vigo, Spain
| | - Rebeca Moreira
- Instituto de Investigaciones Marinas (CSIC), Eduardo Cabello 6, 36208, Vigo, Spain
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas (CSIC), Eduardo Cabello 6, 36208, Vigo, Spain.
| | - Antonio Figueras
- Instituto de Investigaciones Marinas (CSIC), Eduardo Cabello 6, 36208, Vigo, Spain
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14
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Hu B, Li M, Yu X, Xun X, Lu W, Li X, Li Y, Lou J, Wang S, Zhang L, Cheng J, Hu X, Bao Z. Diverse expression regulation of Hsp70 genes in scallops after exposure to toxic Alexandrium dinoflagellates. CHEMOSPHERE 2019; 234:62-69. [PMID: 31203042 DOI: 10.1016/j.chemosphere.2019.06.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 05/26/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Heat shock proteins 70KD (Hsp70s) are highly conserved molecular chaperones with essential roles against biotic and abiotic stressors. Marine bivalves inhabit highly complex environments and could accumulate paralytic shellfish toxins (PSTs), the well-noted neurotoxins generated during harmful algal blooms. Here, we systematically analyzed Hsp70 genes (CfHsp70s) in Zhikong scallop (Chlamys farreri), an important aquaculture mollusk in China. Sixty-five CfHsp70s from eight sub-families were identified, and 47 of these genes showed expansion in the Hspa12 sub-family. After exposure to different PST-producing dinoflagellates, Alexandrium minutum and Alexandrium catenella, diverse CfHsp70s regulation presented in scallop hepatopancreas, mainly accumulating incoming PSTs, and kidneys, transforming PSTs into higher toxic analogs. All the up-regulated CfHsp70s were from CfHsp70B2, CfHspa12, and CfHspa5 sub-families. CfHsp70B2 sub-family was mainly induced in the hepatopancreas, and CfHspa12 sub-family was highly induced in the kidneys. CfHsp70s up-regulation under two dinoflagellates exposure was stronger in the kidneys (log2FC: 19.5 and 18.6) than that in hepatopancreas (log2FC: 4.3 and 6.1). Exposure to different Alexandrium species had varying effects, that in hepatopancreas, CfHsp70B2s were chronically induced only after A. catenella exposure, whereas in kidney, CfHspa12s were more acutely induced after exposure of A. minutum than A. caenella. Moreover, in Yesso scallops (Patinopecten yessoensis), only Hspa12s were up-regulated in hepatopancreas after A. catenella exposure, and all the Hsp70B2s were down-regulated. These organ-, toxin-, and species-dependent Hsp70 regulation suggested the functional diversity of duplicated Hsp70s in response to the stress by PST-producing algae. Our findings provide insights into the evolution and functional characteristics of Hsp70s in scallops.
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Affiliation(s)
- Boyang Hu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao, 266003, China
| | - Moli Li
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao, 266003, China
| | - Xiaohan Yu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao, 266003, China
| | - Xiaogang Xun
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Qingdao, 266237, China
| | - Wei Lu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao, 266003, China
| | - Xu Li
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao, 266003, China
| | - Yajuan Li
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao, 266003, China
| | - Jiarun Lou
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao, 266003, China
| | - Shi Wang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao, 266003, China; Marine Biology and Biotechnology Laboratory, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Qingdao, 266237, China
| | - Lingling Zhang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Qingdao, 266237, China
| | - Jie Cheng
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Qingdao, 266237, China.
| | - Xiaoli Hu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Qingdao, 266237, China.
| | - Zhenmin Bao
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Qingdao, 266237, China
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15
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Liu Y, Li L, Huang B, Wang W, Zhang G. RNAi based transcriptome suggests genes potentially regulated by HSF1 in the Pacific oyster Crassostrea gigas under thermal stress. BMC Genomics 2019; 20:639. [PMID: 31395030 PMCID: PMC6688261 DOI: 10.1186/s12864-019-6003-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 07/29/2019] [Indexed: 01/08/2023] Open
Abstract
Background The Pacific oyster Crassostrea gigas is an important fishery resource that is sensitive to temperature fluctuations. Thus, it has evolved a protection mechanism against heat stress by increasing the expression of the gene coding for heat shock protein (HSP) 70 under elevated temperatures. In other animals, heat shock response is a transcriptional response driven by the heat shock transcription factor 1 (HSF1) and thermal stress can trigger HSP70 expression to protect the organism via HSF1. However, the regulatory relationship between HSF1 and HSP remains unclear in Pacific oyster. Therefore, in the present study, we examined the transcriptomic response of several to thermal stress following HSF1 interference. Results We identified 150 genes responsive to heat shock including seven HSP genes, six of which belonging to the group of 17 HSP genes enriched in response to heat shock, according to weighted gene co-expression network analysis (WGCNA). The other gene was enriched in the module correlated with HSF1 interference. In addition, we found 48 and 47 genes that were upregulated and downregulated by HSF1 in response to heat shock, respectively. In the upregulated genes, we identified one HSP70 potentially regulated by HSF1 in response to heat shock. Furthermore, based on differentially expressed genes and WGCNA analyses, we found that the hypoxia signaling pathway was enriched under heat shock conditions. Five genes were then selected to detect dynamic changes through time. The results suggested that gene expression was correlated with HSF1 expression. The regulation of HSP70 by HSF1 was preliminarily confirmed by binding site predictions and by a dual luciferase assay. Conclusions Our results revealed that the expression of HSP70 and HSP20 was initially triggered after 2 h of heat shock, and one of the HSP70 genes was potentially regulated by HSF1. From these results, it is evident that not all heat-inducible genes were triggered simultaneously in response to heat shock stress. Overall, the results revealed a possible HSF1–HSP regulatory relationship in Pacific oyster, providing valuable information on the mechanisms of thermal tolerance in this commercially important oyster. Electronic supplementary material The online version of this article (10.1186/s12864-019-6003-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Youli Liu
- Key Laboratory of Experimental Marine Biology, 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, 266071, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Li Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China. .,National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China.
| | - Baoyu Huang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
| | - Wei Wang
- Key Laboratory of Experimental Marine Biology, 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, 266071, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
| | - Guofan Zhang
- Key Laboratory of Experimental Marine Biology, 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, 266071, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
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16
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do Amaral QDF, Da Rosa E, Wronski JG, Zuravski L, Querol MVM, Dos Anjos B, de Andrade CFF, Machado MM, de Oliveira LFS. Golden mussel (Limnoperna fortunei) as a bioindicator in aquatic environments contaminated with mercury: Cytotoxic and genotoxic aspects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 675:343-353. [PMID: 31030141 DOI: 10.1016/j.scitotenv.2019.04.108] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 04/01/2019] [Accepted: 04/08/2019] [Indexed: 06/09/2023]
Abstract
This study evaluated the Limnoperna fortunei (golden mussel) as a bioindicator of cytotoxicity and genotoxicity in aquatic environments contaminated by heavy metals. Five groups of 50 subjects each were exposed to different concentration of mercuric chloride (HgCl2) (0.001 mg/L, group I; 0.005 mg/L, group II; 0.01 mg/L, group II; 0.02 mg/L, group IV; and 0.1 mg/L, group V). The control group for both chronic and acute treatment did not receive HgCl2. For chronic exposure, the respective groups were placed in aquaria with water contaminated with the above concentrations of HgCl2. For acute exposure, the different concentrations of HgCl2 were injected into the posterior adductor muscle of the individuals belonging to the aforementioned groups. The biological matrix used in the tests was the whole body muscle. Tests (cell viability assay, alkaline comet test; enumeration of micronuclei and necrotic cells, quantification of Hg content in tissues and water, and histopathological analysis of tissues), were carried out on the 7th, 15th, and 30th treatment days or 2 h after injection. Our results demonstrated that L. fortunei showed cell damage in both chronic and acute exposure groups. Significant DNA damage was observed at both the 15th (0.1 mg/L) and 30th (0.01-0.1 mg/L) days of chronic exposure. However, in acute treatment all concentrations induced DNA breaks. The presence of necrosis increased at all concentrations tested for both acute and chronic exposure. Tissue mercury retention on the 15th day was higher than on the 30th day of exposure, while in the same period, there was a decrease in the mercury content of aquarium water. Taking the data together, it is concluded that L. fortunei as a possible bioindicator of the quality of aquatic environments.
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Affiliation(s)
| | - Emanoeli Da Rosa
- Graduate Program in Pharmaceutical Sciences, Universidade Federal do Pampa - UNIPAMPA, Uruguaiana, Brazil
| | - Júlia Gabriela Wronski
- Veterinary Pathology Laboratory, HUVET, Universidade Federal do Pampa - UNIPAMPA, Uruguaiana, Brazil
| | - Luísa Zuravski
- Graduate Program in Biochemistry, Universidade Federal do Pampa - UNIPAMPA, Uruguaiana, Brazil
| | | | - Bruno Dos Anjos
- Veterinary Pathology Laboratory, HUVET, Universidade Federal do Pampa - UNIPAMPA, Uruguaiana, Brazil
| | | | - Michel Mansur Machado
- Graduate Program in Pharmaceutical Sciences, Universidade Federal do Pampa - UNIPAMPA, Uruguaiana, Brazil
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Li S, Chen Y, Gao Y, Xia Z, Zhan A. Chemical oxidants affect byssus adhesion in the highly invasive fouling mussel Limnoperna fortunei. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 646:1367-1375. [PMID: 30235622 DOI: 10.1016/j.scitotenv.2018.07.434] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/20/2018] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
Biofouling by the invasive mussel species Limnoperna fortunei has caused severe negative consequences in various freshwater ecosystems, but there is still a lack of effective antifouling strategies for this species, particularly in drinking water treatment systems where many existing strategies cannot be used. Chemical oxidants have been proposed to potentially control fouling mussels by influencing 3,4‑dihydroxyphenylalanine oxidation involved in byssus adhesion. To test this potential control strategy, L. fortunei adults were exposed to four oxidants: sodium hypochlorite (NaClO), potassium permanganate (KMnO4), hydrogen peroxide (H2O2) and chloramine T (CAT) at concentrations of 0.5, 1.0, 3.0 and 5.0 mg L-1 for one week. The results showed that low concentrations of KMnO4 stimulated foot protein secretion, which was beneficial to byssus production (number and length). NaClO and H2O2, but not KMnO4 and CAT, significantly inhibited byssus production and reduced breaking force, causing an increased byssus shedding rate. However, only NaClO dissolved byssus and altered the failure location from the byssal thread to adhesive plaque, even when exposed at low concentrations, showing its great impacts on byssus adhesion. Further analysis of polyphenoloxidase activities and gene expression profiles of LfBP-1, LfFP-2 and LfBP-3 revealed that chemical oxidants affected byssus adhesion by altering Dopa oxidation and foot protein gene expressions. This study, therefore, suggests that a low concentration of NaClO can be used as an alternative and environmentally friendly chemical for controlling L. fortunei biofouling by weakening byssus adhesion.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - Zhiqiang Xia
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON 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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18
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Uliano-Silva M, Dondero F, Dan Otto T, Costa I, Lima NCB, Americo JA, Mazzoni CJ, Prosdocimi F, Rebelo MDF. A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel, Limnoperna fortunei. Gigascience 2018; 7:4750781. [PMID: 29267857 PMCID: PMC5836269 DOI: 10.1093/gigascience/gix128] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 12/11/2017] [Indexed: 11/13/2022] Open
Abstract
Background For more than 25 years, the golden mussel, Limnoperna fortunei, has aggressively invaded South American freshwaters, having travelled more than 5000 km upstream across 5 countries. Along the way, the golden mussel has outcompeted native species and economically harmed aquaculture, hydroelectric powers, and ship transit. We have sequenced the complete genome of the golden mussel to understand the molecular basis of its invasiveness and search for ways to control it. Findings We assembled the 1.6-Gb genome into 20 548 scaffolds with an N50 length of 312 Kb using a hybrid and hierarchical assembly strategy from short and long DNA reads and transcriptomes. A total of 60 717 coding genes were inferred from a customized transcriptome-trained AUGUSTUS run. We also compared predicted protein sets with those of complete molluscan genomes, revealing an exacerbation of protein-binding domains in L. fortunei. Conclusions We built one of the best bivalve genome assemblies available using a cost-effective approach using Illumina paired-end, mate-paired, and PacBio long reads. We expect that the continuous and careful annotation of L. fortunei's genome will contribute to the investigation of bivalve genetics, evolution, and invasiveness, as well as to the development of biotechnological tools for aquatic pest control.
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Affiliation(s)
- Marcela Uliano-Silva
- Carlos Chagas Filho Biophysics Institute (IBCCF), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Francesco Dondero
- Department of Science and Technological Innovation (DiSIT), Università del Piemonte Orientale Amedeo Avogadro, Vercelli-Novara-Alessandria, Italy
| | - Thomas Dan Otto
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.,Centre of Immunobiology, Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Igor Costa
- Leopoldo de Meis Biomedical Biochemistry Institute (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nicholas Costa Barroso Lima
- Leopoldo de Meis Biomedical Biochemistry Institute (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Bioinformatics Laboratory (LabInfo) of the National Laboratory for Scientific Computing, Petrópolis, Rio de Janeiro, Brazil
| | - Juliana Alves Americo
- Carlos Chagas Filho Biophysics Institute (IBCCF), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Camila Junqueira Mazzoni
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Francisco Prosdocimi
- Leopoldo de Meis Biomedical Biochemistry Institute (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mauro de Freitas Rebelo
- Carlos Chagas Filho Biophysics Institute (IBCCF), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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19
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Sivka U, Toplak N, Koren S, Jakše J. De novo transcriptome of the pallial gland of the date mussel ( Lithophaga lithophaga ). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 26:1-9. [DOI: 10.1016/j.cbd.2018.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 11/28/2022]
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20
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Li S, Xia Z, Chen Y, Gao Y, Zhan A. Byssus Structure and Protein Composition in the Highly Invasive Fouling Mussel Limnoperna fortunei. Front Physiol 2018; 9:418. [PMID: 29713291 PMCID: PMC5911496 DOI: 10.3389/fphys.2018.00418] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 04/04/2018] [Indexed: 12/28/2022] Open
Abstract
Biofouling mediated by byssus adhesion in invasive bivalves has become a global environmental problem in aquatic ecosystems, resulting in negative ecological and economic consequences. Previous studies suggested that mechanisms responsible for byssus adhesion largely vary among bivalves, but it is poorly understood in freshwater species. Understanding of byssus structure and protein composition is the prerequisite for revealing these mechanisms. Here, we used multiple methods, including scanning electron microscope, liquid chromatography–tandem mass spectrometry, transcriptome sequencing, real-time quantitative PCR, inductively coupled plasma mass spectrometry, to investigate structure, and protein composition of byssus in the highly invasive freshwater mussel Limnoperna fortunei. The results indicated that the structure characteristics of adhesive plaque, proximal and distal threads were conducive to byssus adhesion, contributing to the high biofouling capacity of this species. The 3,4-dihydroxyphenyl-α-alanine (Dopa) is a major post-transnationally modification in L. fortunei byssus. We identified 16 representative foot proteins with typical repetitive motifs and conserved domains by integrating transcriptomic and proteomic approaches. In these proteins, Lfbp-1, Lffp-2, and Lfbp-3 were specially located in foot tissue and highly expressed in the rapid byssus formation period, suggesting the involvement of these foot proteins in byssus production and adhesion. Multiple metal irons, including Ca2+, Mg2+, Zn2+, Al3+, and Fe3+, were abundant in both foot tissue and byssal thread. The heavy metals in these irons may be directly accumulated by L. fortunei from surrounding environments. Nevertheless, some metal ions (e.g., Ca2+) corresponded well with amino acid preferences of L. fortunei foot proteins, suggesting functional roles of these metal ions by interacting with foot proteins in byssus adhesion. Overall, this study provides structural and molecular bases of adhesive mechanisms of byssus in L. fortunei, and findings here are expected to develop strategies against biofouling by freshwater organisms.
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Affiliation(s)
- Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhiqiang Xia
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Department of Biological Sciences, Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yangchun Gao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
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21
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Cao S, Zhu L, Nie H, Yin M, Liu G, Yan X. De novo assembly, gene annotation, and marker development using Illumina paired-end transcriptome sequencing in the Crassadoma gigantea. Gene 2018. [PMID: 29524581 DOI: 10.1016/j.gene.2018.03.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Crassadoma gigantea is an important commercial marine bivalve species in Baja California and Mexico. In this study, we have applied RNA-Seq technology to profile the transcriptome of the C. gigantea for the first time. A total of 80,832,518 raw reads were produced from a Illumina HiSeq4000 platform, and 77,306,198 (95.64%) clean reads were generated after trimming the adaptor sequences. The transcriptome assembled into 158,855 transcripts with an N50 size of 1995 bp and an average size of 1008 bp. A number of DNA repair related genes, such as MSH3, EGF, TGF, IGF, FGF, encoding different groups of growth factors were found in the transcriptome data of C. gigantean. In addition, immune related genes Toll-like receptor (TLR) including TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, and TLR9 was also observed in C. gigantean. A set of 12 polymorphic microsatellite loci were firstly developed and characterized in C. gigantea. The results show that the number of alleles and expected heterozygosity ranged from 3 to 9 and from 0.254 to 0.820, respectively. The average polymorphic information content was 0.790. These microsatellite loci will facilitate future studies of population structure and conservation genetics in this species.
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Affiliation(s)
- Shanmao Cao
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Lijie Zhu
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian 116023, China.
| | - Minghao Yin
- Dalian City Oceanic and Fishery Administration, 100000 Dalian, China
| | - Gang Liu
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Xiwu Yan
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian 116023, China
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22
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Ponesakki V, Paul S, Mani DKS, Rajendiran V, Kanniah P, Sivasubramaniam S. Annotation of nerve cord transcriptome in earthworm Eisenia fetida. GENOMICS DATA 2017; 14:91-105. [PMID: 29204349 PMCID: PMC5688751 DOI: 10.1016/j.gdata.2017.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/02/2017] [Accepted: 10/07/2017] [Indexed: 11/26/2022]
Abstract
In annelid worms, the nerve cord serves as a crucial organ to control the sensory and behavioral physiology. The inadequate genome resource of earthworms has prioritized the comprehensive analysis of their transcriptome dataset to monitor the genes express in the nerve cord and predict their role in the neurotransmission and sensory perception of the species. The present study focuses on identifying the potential transcripts and predicting their functional features by annotating the transcriptome dataset of nerve cord tissues prepared by Gong et al., 2010 from the earthworm Eisenia fetida. Totally 9762 transcripts were successfully annotated against the NCBI nr database using the BLASTX algorithm and among them 7680 transcripts were assigned to a total of 44,354 GO terms. The conserve domain analysis indicated the over representation of P-loop NTPase domain and calcium binding EF-hand domain. The COG functional annotation classified 5860 transcript sequences into 25 functional categories. Further, 4502 contig sequences were found to map with 124 KEGG pathways. The annotated contig dataset exhibited 22 crucial neuropeptides having considerable matches to the marine annelid Platynereis dumerilii, suggesting their possible role in neurotransmission and neuromodulation. In addition, 108 human stem cell marker homologs were identified including the crucial epigenetic regulators, transcriptional repressors and cell cycle regulators, which may contribute to the neuronal and segmental regeneration. The complete functional annotation of this nerve cord transcriptome can be further utilized to interpret genetic and molecular mechanisms associated with neuronal development, nervous system regeneration and nerve cord function.
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Affiliation(s)
| | | | | | | | | | - Sudhakar Sivasubramaniam
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu 627012, India
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23
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Kang SW, Patnaik BB, Park SY, Hwang HJ, Chung JM, Sang MK, Min HR, Park JE, Seong J, Jo YH, Noh MY, Lee JD, Jung KY, Park HS, Han YS, Lee JS, Lee YS. Transcriptome analysis of the threatened snail Ellobium chinense reveals candidate genes for adaptation and identifies SSRs for conservation genetics. Genes Genomics 2017; 40:333-347. [PMID: 29892840 DOI: 10.1007/s13258-017-0620-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/26/2017] [Indexed: 11/29/2022]
Abstract
Ellobium chinense (Pfeiffer, 1854) is a brackish pulmonate species that inhabits the bases of mangrove trees and is most commonly found in salt grass meadows. Threats to mangrove ecosystems due to habitat degradation and overexploitation have threatened the species with extinction. In South Korea, E. chinense has been assessed as vulnerable, but there are limited data on its population structure and distribution. The nucleotide and protein sequences for this species are not available in databases, which limits the understanding of adaptation-related traits. We sequenced an E. chinense cDNA library using the Illumina platform, and the subsequent bioinformatics analysis yielded 227,032 unigenes. Of these unigenes, 69,088 were annotated to matched protein and nucleotide sequences in databases, for an annotation rate of 30.42%. Among the predominant gene ontology terms, cellular and metabolic processes (under the biological process category), membrane and cell (under the cellular component category), and binding and catalytic activity (under the molecular function category) were noteworthy. In addition, 4850 unigenes were distributed to 15 Kyoto Encyclopaedia of Genes and Genomes based enrichment categories. Among the candidate genes related to adaptation, angiotensin I converting enzyme, adenylate cyclase activating polypeptide, and AMP-activated protein kinase were the most prominent. A total of 15,952 simple sequence repeats (SSRs) were identified in sequences of > 1 kb in length. The di- and trinucleotide repeat motifs were the most common. Among the repeat motif types, AG/CT, AC/GT, and AAC/GTT dominated. Our study provides the first comprehensive genomics dataset for E. chinense, which favors conservation programs for the restoration of the species and provides sufficient evidence for genetic variability among the wild populations.
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Affiliation(s)
- Se Won Kang
- Biological Resources Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181, Ipsin-gil, Jungeup-si, Jeollabuk-do, 56212, South Korea
| | - Bharat Bhusan Patnaik
- Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Chandaka Industrial Estate, Chandrasekharpur, Bhubaneswar, Odisha, 751024, India
| | - So Young Park
- Nakdonggang National Institute of Biological Resources, Biodiversity Conservation and Climate Change Division, 137, Donam-2-gil, Sangju-si, Gyeongsangbuk-do, 37242, South Korea
| | - Hee-Ju Hwang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Jong Min Chung
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Min Kyu Sang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Hye Rin Min
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Jie Eun Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Jiyeon Seong
- Genomic Informatics Center, Hankyong National University, 327 Chungang-ro, Anseong-si, Kyonggi-do, 17579, South Korea
| | - Yong Hun Jo
- Division of Plant Biotechnology, Institute of Environmentally-Friendly (IEFA), College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, South Korea
| | - Mi Young Noh
- Division of Plant Biotechnology, Institute of Environmentally-Friendly (IEFA), College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, South Korea
| | - Jong Dae Lee
- Department of Environmental Health Science, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Ki Yoon Jung
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 34069, South Korea
| | - Yeon Soo Han
- Division of Plant Biotechnology, Institute of Environmentally-Friendly (IEFA), College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, South Korea
| | - Jun Sang Lee
- Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 243341, South Korea
| | - Yong Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do, 31538, South Korea.
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24
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Zhao M, Wang T, Stewart MJ, Bose U, Suwansa-ard S, Storey KB, Cummins SF. eSnail: A transcriptome-based molecular resource of the central nervous system for terrestrial gastropods. Mol Ecol Resour 2017; 18:147-158. [DOI: 10.1111/1755-0998.12722] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 09/01/2017] [Accepted: 09/07/2017] [Indexed: 01/04/2023]
Affiliation(s)
- Min Zhao
- School of Engineering; Faculty of Science, Health, Education and Engineering; University of the Sunshine Coast; Maroochydore DC Qld Australia
| | - Tianfang Wang
- School of Engineering; Faculty of Science, Health, Education and Engineering; University of the Sunshine Coast; Maroochydore DC Qld Australia
| | - Michael J. Stewart
- School of Engineering; Faculty of Science, Health, Education and Engineering; University of the Sunshine Coast; Maroochydore DC Qld Australia
| | - Utpal Bose
- School of Engineering; Faculty of Science, Health, Education and Engineering; University of the Sunshine Coast; Maroochydore DC Qld Australia
| | - Saowaros Suwansa-ard
- School of Engineering; Faculty of Science, Health, Education and Engineering; University of the Sunshine Coast; Maroochydore DC Qld Australia
| | - Kenneth B. Storey
- Department of Biology; Institute of Biochemistry; Carleton University; Ottawa ON Canada
| | - Scott F. Cummins
- School of Engineering; Faculty of Science, Health, Education and Engineering; University of the Sunshine Coast; Maroochydore DC Qld Australia
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25
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Gerdol M, Fujii Y, Hasan I, Koike T, Shimojo S, Spazzali F, Yamamoto K, Ozeki Y, Pallavicini A, Fujita H. The purplish bifurcate mussel Mytilisepta virgata gene expression atlas reveals a remarkable tissue functional specialization. BMC Genomics 2017; 18:590. [PMID: 28789640 PMCID: PMC5549309 DOI: 10.1186/s12864-017-4012-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/02/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Mytilisepta virgata is a marine mussel commonly found along the coasts of Japan. Although this species has been the subject of occasional studies concerning its ecological role, growth and reproduction, it has been so far almost completely neglected from a genetic and molecular point of view. In the present study we present a high quality de novo assembled transcriptome of the Japanese purplish mussel, which represents the first publicly available collection of expressed sequences for this species. RESULTS The assembled transcriptome comprises almost 50,000 contigs, with a N50 statistics of ~1 kilobase and a high estimated completeness based on the rate of BUSCOs identified, standing as one of the most exhaustive sequence resources available for mytiloid bivalves to date. Overall this data, accompanied by gene expression profiles from gills, digestive gland, mantle rim, foot and posterior adductor muscle, presents an accurate snapshot of the great functional specialization of these five tissues in adult mussels. CONCLUSIONS We highlight that one of the most striking features of the M. virgata transcriptome is the high abundance and diversification of lectin-like transcripts, which pertain to different gene families and appear to be expressed in particular in the digestive gland and in the gills. Therefore, these two tissues might be selected as preferential targets for the isolation of molecules with interesting carbohydrate-binding properties. In addition, by molecular phylogenomics, we provide solid evidence in support of the classification of M. virgata within the Brachidontinae subfamily. This result is in agreement with the previously proposed hypothesis that the morphological features traditionally used to group Mytilisepta spp. and Septifer spp. within the same clade are inappropriate due to homoplasy.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34126 Trieste, Italy
| | - Yuki Fujii
- Department of Pharmacy, Faculty of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298 Japan
| | - Imtiaj Hasan
- Department of Life and Environmental System Science, Graduate School of NanoBio Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, 236-0027 Japan
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Toru Koike
- Department of Pharmacy, Faculty of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298 Japan
| | - Shunsuke Shimojo
- Department of Pharmacy, Faculty of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298 Japan
| | - Francesca Spazzali
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34126 Trieste, Italy
| | - Kaname Yamamoto
- Department of Pharmacy, Faculty of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298 Japan
| | - Yasuhiro Ozeki
- Department of Life and Environmental System Science, Graduate School of NanoBio Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, 236-0027 Japan
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34126 Trieste, Italy
| | - Hideaki Fujita
- Department of Pharmacy, Faculty of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298 Japan
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26
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Duan X, Wang K, Su S, Tian R, Li Y, Chen M. De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae). PLoS One 2017; 12:e0172513. [PMID: 28212394 PMCID: PMC5315398 DOI: 10.1371/journal.pone.0172513] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/05/2017] [Indexed: 11/21/2022] Open
Abstract
The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not been investigated. In this study, we used transcriptome information obtained by RNA-Seq to develop polymorphic microsatellites for investigating population genetics in this species. The transcriptome of R. padi was sequenced on an Illumina HiSeq 2000 platform. A total of 114.4 million raw reads with a GC content of 40.03% was generated. The raw reads were cleaned and assembled into 29,467 unigenes with an N50 length of 1,580 bp. Using several public databases, 82.47% of these unigenes were annotated. Of the annotated unigenes, 8,022 were assigned to COG pathways, 9,895 were assigned to GO pathways, and 14,586 were mapped to 257 KEGG pathways. A total of 7,936 potential microsatellites were identified in 5,564 unigenes, 60 of which were selected randomly and amplified using specific primer pairs. Fourteen loci were found to be polymorphic in the four R. padi populations. The transcriptomic data presented herein will facilitate gene discovery, gene analyses, and development of molecular markers for future studies of R. padi and other closely related aphid species.
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Affiliation(s)
- Xinle Duan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China.,College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Sha Su
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Ruizheng Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Yuting Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Maohua Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
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Cheng J, Xun X, Kong Y, Wang S, Yang Z, Li Y, Kong D, Wang S, Zhang L, Hu X, Bao Z. Hsp70 gene expansions in the scallop Patinopecten yessoensis and their expression regulation after exposure to the toxic dinoflagellate Alexandrium catenella. FISH & SHELLFISH IMMUNOLOGY 2016; 58:266-273. [PMID: 27633676 DOI: 10.1016/j.fsi.2016.09.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 09/06/2016] [Accepted: 09/10/2016] [Indexed: 05/20/2023]
Abstract
Heat shock protein 70 (Hsp70s) family members are present in virtually all living organisms and perform a fundamental role against different types of environmental stressors and pathogenic organisms. Marine bivalves live in highly dynamic environments and may accumulate paralytic shellfish toxins (PSTs), a class of well-known neurotoxins closely associated with harmful algal blooms (HABs). Here, we provide a systematic analysis of Hsp70 genes (PyHsp70s) in the genome of Yesso scallop (Patinopecten yessoensis), an important aquaculture species in China, through in silico analysis using transcriptome and genome databases. Phylogenetic analyses indicated extensive expansion of Hsp70 genes from the Hspa12 sub-family in the Yesso scallop and also the bivalve lineages, with gene duplication events before or after the split between the Yesso scallop and the Pacific oyster. In addition, we determined the expression patterns of PyHsp70s after exposure to Alexandrium catenella, the dinoflagellate producing PSTs. Our results confirmed the inducible expression patterns of PyHsp70s under PSTs stress, and the responses to the toxic stress may have arisen through the adaptive recruitment of tandem duplication of Hsp70 genes. These findings provide a thorough overview of the evolution and modification of the Hsp70 family, which will gain insights into the functional characteristics of scallop Hsp70 genes in response to different stresses.
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Affiliation(s)
- Jie Cheng
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Xiaogang Xun
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Yifan Kong
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Shuyue Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Zhihui Yang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Yajuan Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Dexu Kong
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Shi Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266000, China.
| | - Lingling Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Xiaoli Hu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266000, China.
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266000, China.
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Kang SW, Patnaik BB, Hwang HJ, Park SY, Chung JM, Song DK, Patnaik HH, Lee JB, Kim C, Kim S, Park HS, Park SH, Park YS, Han YS, Lee JS, Lee YS. Sequencing and de novo assembly of visceral mass transcriptome of the critically endangered land snail Satsuma myomphala: Annotation and SSR discovery. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 21:77-89. [PMID: 28107688 DOI: 10.1016/j.cbd.2016.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 10/24/2016] [Accepted: 10/26/2016] [Indexed: 12/12/2022]
Abstract
Satsuma myomphala is critically endangered through loss of natural habitats, predation by natural enemies, and indiscriminate collection. It is a protected species in Korea but lacks genomic resources for an understanding of varied functional processes attributable to evolutionary success under natural habitats. For assessing the genetic information of S. myomphala, we performed for the first time, de novo transcriptome sequencing and functional annotation of expressed sequences using Illumina Next-Generation Sequencing (NGS) platform and bioinformatics analysis. We identified 103,774 unigenes of which 37,959, 12,890, and 17,699 were annotated in the PANM (Protostome DB), Unigene, and COG (Clusters of Orthologous Groups) databases, respectively. In addition, 14,451 unigenes were predicted under Gene Ontology functional categories, with 4581 assigned to a single category. Furthermore, 3369 sequences with 646 having Enzyme Commission (EC) numbers were mapped to 122 pathways in the Kyoto Encyclopedia of Genes and Genomes Pathway database. The prominent protein domains included the Zinc finger (C2H2-like), Reverse Transcriptase, Thioredoxin-like fold, and RNA recognition motif domain. Many unigenes with homology to immunity, defense, and reproduction-related genes were screened in the transcriptome. We also detected 3120 putative simple sequence repeats (SSRs) encompassing dinucleotide to hexanucleotide repeat motifs from >1kb unigene sequences. A list of PCR primers of SSR loci have been identified to study the genetic polymorphisms. The transcriptome data represents a valuable resource for further investigations on the species genome structure and biology. The unigenes information and microsatellites would provide an indispensable tool for conservation of the species in natural and adaptive environments.
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Affiliation(s)
- Se Won Kang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Republic of Korea
| | - Bharat Bhusan Patnaik
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Republic of Korea; Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Bhubaneswar, Odisha, 751024, India
| | - Hee-Ju Hwang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Republic of Korea
| | - So Young Park
- Biodiversity Conservation & Change Research Division, Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do, 37242, Republic of Korea
| | - Jong Min Chung
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Republic of Korea
| | - Dae Kwon Song
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Republic of Korea
| | - Hongray Howrelia Patnaik
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Republic of Korea
| | - Jae Bong Lee
- Korea Zoonosis Research Institute (KOZRI), Chonbuk National University, 820-120 Hana-ro, Iksan, Jeollabuk-do 54528, Republic of Korea
| | - Changmu Kim
- National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon 22689, Republic of Korea
| | - Soonok Kim
- National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon 22689, Republic of Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., Ltd., 621-6 Banseok-dong, Yuseong-gu, Daejeon 34069, Republic of Korea
| | - Seung-Hwan Park
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil (Shinjeong0dong), Jungeup-si, Jeollabuk-do,56212, Republic of Korea
| | - Young-Su Park
- Department of Nursing, College of Medicine, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Republic of Korea
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
| | - Jun Sang Lee
- Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon, Gangwon-do-si 243341, Republic of Korea
| | - Yong Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Republic of Korea.
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Cordeiro NIS, Andrade JTM, Montresor LC, Luz DMR, Araújo JM, Martinez CB, Pinheiro J, Vidigal THDA. Physiological response of invasive mussel Limnoperna fortunei (Dunker, 1857) (Bivalvia: Mytilidae) submitted to transport and experimental conditions. BRAZ J BIOL 2016; 77:191-198. [PMID: 27509217 DOI: 10.1590/1519-6984.15315] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/23/2015] [Indexed: 11/21/2022] Open
Abstract
Successful animal rearing under laboratory conditions for commercial processes or laboratory experiments is a complex chain that includes several stressors (e.g., sampling and transport) and incurs, as a consequence, the reduction of natural animal conditions, economic losses and inconsistent and unreliable biological results. Since the invasion of the bivalve Limnoperna fortunei (Dunker, 1857) in South America, several studies have been performed to help control and manage this fouling pest in industrial plants that use raw water. Relatively little attention has been given to the laboratory rearing procedure of L. fortunei, its condition when exposed to a stressor or its acclimation into laboratory conditions. Considering this issue, the aims of this study are to (i) investigate L. fortunei physiological responses when submitted to the depuration process and subsequent air transport (without water/dry condition) at two temperatures, based on glycogen concentrations, and (ii) monitor the glycogen concentrations in different groups when maintained for 28 days under laboratory conditions. Based on the obtained results, depuration did not affect either of the groups when they were submitted to approximately eight hours of transport. The variation in glycogen concentration among the specimens that were obtained from the field under depurated and non-depurated conditions was significant only in the first week of laboratory growth for the non-depurated group and in the second week for the depurated group. In addition, the tested temperature did not affect either of the groups that were submitted to transport. The glycogen concentrations were similar to those of the specimens that were obtained from the field in third week, which suggests that the specimens acclimated to laboratory conditions during this period of time. Thus, the results indicate that the air transport and acclimation time can be successfully incorporated into experimental studies of L. fortunei. Finally, the tolerance of L. fortunei specimens to the stressor tested herein can help us understand the invasive capacity of this mussel during the establishment process.
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Affiliation(s)
- N I S Cordeiro
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - J T M Andrade
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - L C Montresor
- Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - D M R Luz
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - J M Araújo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - C B Martinez
- Centro de Pesquisas Hidráulicas e Recursos Hídricos, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - J Pinheiro
- Instituto de Biologia, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brasil
| | - T H D A Vidigal
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
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Patnaik BB, Wang TH, Kang SW, Hwang HJ, Park SY, Park EB, Chung JM, Song DK, Kim C, Kim S, Lee JS, Han YS, Park HS, Lee YS. Sequencing, De Novo Assembly, and Annotation of the Transcriptome of the Endangered Freshwater Pearl Bivalve, Cristaria plicata, Provides Novel Insights into Functional Genes and Marker Discovery. PLoS One 2016; 11:e0148622. [PMID: 26872384 PMCID: PMC4752248 DOI: 10.1371/journal.pone.0148622] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/20/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The freshwater mussel Cristaria plicata (Bivalvia: Eulamellibranchia: Unionidae), is an economically important species in molluscan aquaculture due to its use in pearl farming. The species have been listed as endangered in South Korea due to the loss of natural habitats caused by anthropogenic activities. The decreasing population and a lack of genomic information on the species is concerning for environmentalists and conservationists. In this study, we conducted a de novo transcriptome sequencing and annotation analysis of C. plicata using Illumina HiSeq 2500 next-generation sequencing (NGS) technology, the Trinity assembler, and bioinformatics databases to prepare a sustainable resource for the identification of candidate genes involved in immunity, defense, and reproduction. RESULTS The C. plicata transcriptome analysis included a total of 286,152,584 raw reads and 281,322,837 clean reads. The de novo assembly identified a total of 453,931 contigs and 374,794 non-redundant unigenes with average lengths of 731.2 and 737.1 bp, respectively. Furthermore, 100% coverage of C. plicata mitochondrial genes within two unigenes supported the quality of the assembler. In total, 84,274 unigenes showed homology to entries in at least one database, and 23,246 unigenes were allocated to one or more Gene Ontology (GO) terms. The most prominent GO biological process, cellular component, and molecular function categories (level 2) were cellular process, membrane, and binding, respectively. A total of 4,776 unigenes were mapped to 123 biological pathways in the KEGG database. Based on the GO terms and KEGG annotation, the unigenes were suggested to be involved in immunity, stress responses, sex-determination, and reproduction. A total of 17,251 cDNA simple sequence repeats (cSSRs) were identified from 61,141 unigenes (size of >1 kb) with the most abundant being dinucleotide repeats. CONCLUSIONS This dataset represents the first transcriptome analysis of the endangered mollusc, C. plicata. The transcriptome provides a comprehensive sequence resource for the conservation of genetic information in this species and enrichment of the genetic database. The development of molecular markers will assist in the genetic improvement of C. plicata.
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Affiliation(s)
- Bharat Bhusan Patnaik
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
- Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Bhubaneswar- 751024, Odisha, India
| | - Tae Hun Wang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Se Won Kang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Hee-Ju Hwang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - So Young Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Eun Bi Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Jong Min Chung
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Dae Kwon Song
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Changmu Kim
- National Institute of Biological Resources, Incheon, 404-170, Republic of Korea
| | - Soonok Kim
- National Institute of Biological Resources, Incheon, 404-170, Republic of Korea
| | - Jun Sang Lee
- Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 200-701, Republic of Korea
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 300 Yongbong-Dong, Buk-gu, Gwangju, 500-757, Republic of Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 305-150, Republic of Korea
| | - Yong Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
- * E-mail:
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Cardoso JCR, Félix RC, Bjärnmark N, Power DM. Allatostatin-type A, kisspeptin and galanin GPCRs and putative ligands as candidate regulatory factors of mantle function. Mar Genomics 2015; 27:25-35. [PMID: 26751715 DOI: 10.1016/j.margen.2015.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/02/2015] [Accepted: 12/12/2015] [Indexed: 12/21/2022]
Abstract
Allatostatin-type A (AST-A), kisspeptin (KISS) and galanin (GAL) G-protein coupled receptor (GPCR) systems share a common ancestral origin in arthropods and the vertebrates where they regulate metabolism and reproduction. The molluscs are the second most diverse phylum in the animal kingdom, they occupy an important phylogenetic position, and their genome is more similar to deuterostomes than the arthropods and nematodes and thus they are good models for studies of gene family evolution and function. This mini-review intends to extend the current knowledge about AST-A, KISS and GAL GPCR system evolution and their putative function in the mollusc mantle. Comparative evolutionary analysis of the target GPCR systems was established by identifying homologues in genomes and tissue transcriptome datasets available for molluscs and comparing them to those of other metazoan systems. Studies in arthropods have revealed the existence of the AST-A system but the loss of homologues of the KISS and GAL systems. Homologues of the insect AST-AR and vertebrate KISSR genes were found in molluscs but putative GALR genes were absent. Receptor gene number suggested that members of this family have suffered lineage specific evolution during the molluscan radiation. In molluscs, orthologues of the insect AST-A peptides were not identified but buccalin peptides that are structurally related were identified and are putative receptor agonists. The identification of AST-AR and KISSR genes in molluscs strengthens the hypotheses that in metazoans members of the AST-AR subfamily share evolutionary proximity with KISSRs. The variable number of receptors and large repertoire of buccalin peptides may be indicative of the functional diversity of the AST-AR/KISSR systems in molluscs. The identification of AST-A and KISS receptors and ligands in the mantle transcriptome indicates that in molluscs they may have acquired a novel function and may play a role in shell development or sensory detection in the mantle.
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Affiliation(s)
- João C R Cardoso
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
| | - Rute C Félix
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Nadège Bjärnmark
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Deborah M Power
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
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The complete mitochondrial genome of the golden mussel Limnoperna fortunei and comparative mitogenomics of Mytilidae. Gene 2015; 577:202-8. [PMID: 26639990 DOI: 10.1016/j.gene.2015.11.043] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 01/08/2023]
Abstract
Here we describe the mitochondrial genome of the golden mussel Limnoperna fortunei, an Asian bivalve which has become one of the most aggressive invasive species in Japan and South America. The mitochondrial genome of L. fortunei does not present conserved gene arrangement when compared to the other Mytilidae species suggesting a high degree of gene recombination in the mitochondria of this clade. In addition, the golden mussel mitogenome encodes two copies of tRNA(Lys) and presents a putative pseudogene for the atp8 gene sequence that encodes a 27 amino acid peptide containing an in-frame stop codon. The presence of this pseudogene raises the question as to whether atp8 is encoded in some bivalve mitochondrial genomes or not. The phylogenetic analysis of all complete mitochondrial genomes available from Mytilidae mussels confirmed the close evolutionary relationships among bivalves from the genus Mytilys and placed L. fortunei coming from a more ancestral branch on the family. The supermatrix phylogeny described used the concatenation of all 12 genes from the mitochondria and disputed the monophyly of the genus Perna, as Perna perna was shown to be more closely related to Brachidontes exustus than to Perna viridis. The comparative analysis of mitogenome synteny also confirmed the polyphyly of the genus Perna. The complete and annotated mitogenome has been published in GenBank under the accession number KP756905.
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Chen X, Li J, Xiao S, Liu X. De novo assembly and characterization of foot transcriptome and microsatellite marker development for Paphia textile. Gene 2015; 576:537-43. [PMID: 26546834 DOI: 10.1016/j.gene.2015.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/18/2015] [Accepted: 11/01/2015] [Indexed: 11/27/2022]
Abstract
Paphia textile is an important, aquaculture bivalve clam species distributed mainly in China, Philippines, and Malaysia. Recent studies of P. textile have focused mainly on artificial breeding and nutrition analysis, and the transcriptome and genome of P. textile have rarely been reported. In this work, the transcriptome of P. textile foot tissue was sequenced on an Illumina HiSeq™ 2000 platform. A total of 20,219,795 reads were generated, resulting in 4.08 Gb of raw data. The raw reads were cleaned and assembled into 54,852 unigenes with an N50 length of 829 bp. Of these unigenes, 38.92% were successfully annotated based on their matches to sequences in seven public databases. Among the annotated unigenes, 14,571 were assigned Gene Ontology terms, 5448 were classified to Clusters of Orthologous Groups categories, and 6738 were mapped to 228 pathways in the Kyoto Encyclopedia of Genes and Genomes database. For functional marker development, 5605 candidate simple sequence repeats were identified in the transcriptome and 80 primer pairs were selected randomly and amplified in a wild population of P. textile. A total of 36 loci that exhibited obvious repeat length polymorphisms were detected. The transcriptomic data and microsatellite markers will provide valuable resources for future functional gene analyses, genetic map construction, and quantitative trait loci mapping in P. textile.
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Affiliation(s)
- Xiaoming Chen
- Key Laboratory of Mariculture in the East China Sea, Ministry of Agriculture of China, Fisheries College, Jimei University, Xiamen 361021, China
| | - Jiakai Li
- Key Laboratory of Mariculture in the East China Sea, Ministry of Agriculture of China, Fisheries College, Jimei University, Xiamen 361021, China
| | - Shijun Xiao
- Key Laboratory of Mariculture in the East China Sea, Ministry of Agriculture of China, Fisheries College, Jimei University, Xiamen 361021, China
| | - Xiande Liu
- Key Laboratory of Mariculture in the East China Sea, Ministry of Agriculture of China, Fisheries College, Jimei University, Xiamen 361021, China.
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Stewart MJ, Stewart P, Rivera-Posada J. De novo assembly of the transcriptome ofAcanthaster plancitestes. Mol Ecol Resour 2014; 15:953-66. [DOI: 10.1111/1755-0998.12360] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 12/04/2014] [Accepted: 12/08/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Michael James Stewart
- Genecology Research Centre; Faculty of Science, Health, Education and Engineering; University of the Sunshine Coast; Maroochydore DC Queensland 4558 Australia
| | - Praphaporn Stewart
- Genecology Research Centre; Faculty of Science, Health, Education and Engineering; University of the Sunshine Coast; Maroochydore DC Queensland 4558 Australia
| | - Jairo Rivera-Posada
- ARC Centre of Excellence for Coral Reefs Studies; James Cook University; Townsville Queensland 4812 Australia
- Australian Institute of Marine Science; PMB No. 3 Townsville Queensland 4810 Australia
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