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Ghildiyal K, Nayak SS, Rajawat D, Sharma A, Chhotaray S, Bhushan B, Dutt T, Panigrahi M. Genomic insights into the conservation of wild and domestic animal diversity: A review. Gene 2023; 886:147719. [PMID: 37597708 DOI: 10.1016/j.gene.2023.147719] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/20/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Due to environmental change and anthropogenic activities, global biodiversity has suffered an unprecedented loss, and the world is now heading toward the sixth mass extinction event. This urges the need to step up our efforts to promote the sustainable use of animal genetic resources and plan effective strategies for their conservation. Although habitat preservation and restoration are the primary means of conserving biodiversity, genomic technologies offer a variety of novel tools for identifying biodiversity hotspots and thus, support conservation efforts. Conservation genomics is a broad area of science that encompasses the application of genomic data from thousands or tens of thousands of genome-wide markers to address important conservation biology concerns. Genomic approaches have revolutionized the way we understand and manage animal populations, providing tools to identify and preserve unique genetic variants and alleles responsible for adaptive genetic variation, reducing the deleterious consequences of inbreeding, and increasing the adaptive potential of threatened species. The advancement of genomic technologies, particularly comparative genomic approaches, and the increased accessibility of genomic resources in the form of genome-enabled taxa for non-model organisms, provides a distinct advantage in defining conservation units over traditional genetics approaches. The objective of this review is to provide an exhaustive overview of the concept of conservation genomics, discuss the rationale behind the transition from conservation genetics to genomic approaches, and emphasize the potential applications of genomic techniques for conservation purposes. We also highlight interesting case studies in both livestock and wildlife species where genomic techniques have been used to accomplish conservation goals. Finally, we address some challenges and future perspectives in this field.
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Affiliation(s)
- Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Supriya Chhotaray
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
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Shan B, Liu Y, Yang C, Wang L, Li Y, Sun D. De novo assembly and annotation of the whole transcriptome of Muraenesox cinereus. Mar Genomics 2021; 61:100910. [PMID: 34673307 DOI: 10.1016/j.margen.2021.100910] [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] [Revised: 09/26/2021] [Accepted: 09/26/2021] [Indexed: 10/20/2022]
Abstract
In this study, we generated the transcriptome of Muraenesox cinereus from four combined tissues (muscle, sexual, liver and heart) using high-seq sequencing technology. De novo assembly was performed using Trinity software and a total of 62,125,296 high-quality clean reads were assembled and clustered into 75,862 unigene with an N50 of 2034 nt. After annotation, 43,157 unigenes had significant hit in Nr database. And then, 24,510 unigenes were annotated into three GO categories: biological processes, cellular components, and molecular functions. Moreover, 33,032 unigenes were mapped 25 different clusters of eukaryotic proteins. Furthermore, we predicted the structure of all unigenes using HMMER and MISA software, respectively. The result showed that a total of 33,183 nucleotide sequences of coding regions (direction of the sequences is 5'- > 3') were confirmed to the protein database and a total of 29,487 simple sequence repeats (SSR) were identified. The whole transcriptome is an important foundation for future genomic research on the M. cinereus, it could provide comprehensively understanding and further characterizations of transcriptomes of non-model organisms.
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Affiliation(s)
- Binbin Shan
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture Rural Affairs, Guangzhou 510300, China; Key Laboratory of Fishery Ecology and Environment, Guangdong Province, Guangzhou 510300, China; South China Sea Fishers Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; Scientific Observation and Research Field Station of Pearl River Estuary Ecosystem, Guangdong Province, Guangzhou, 510300, China
| | - Yan Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture Rural Affairs, Guangzhou 510300, China; Key Laboratory of Fishery Ecology and Environment, Guangdong Province, Guangzhou 510300, China; South China Sea Fishers Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; Scientific Observation and Research Field Station of Pearl River Estuary Ecosystem, Guangdong Province, Guangzhou, 510300, China
| | - Changping Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture Rural Affairs, Guangzhou 510300, China; Key Laboratory of Fishery Ecology and Environment, Guangdong Province, Guangzhou 510300, China; South China Sea Fishers Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; Scientific Observation and Research Field Station of Pearl River Estuary Ecosystem, Guangdong Province, Guangzhou, 510300, China
| | - Liangming Wang
- South China Sea Fishers Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China
| | - Yuan Li
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Dianrong Sun
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture Rural Affairs, Guangzhou 510300, China; Key Laboratory of Fishery Ecology and Environment, Guangdong Province, Guangzhou 510300, China; South China Sea Fishers Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; Scientific Observation and Research Field Station of Pearl River Estuary Ecosystem, Guangdong Province, Guangzhou, 510300, China.
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Lou F, Gao T, Han Z. Transcriptome analyses reveal alterations in muscle metabolism, immune responses and reproductive behavior of Japanese mantis shrimp (Oratosquilla oratoria) at different cold temperature. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 32:100615. [PMID: 31419604 DOI: 10.1016/j.cbd.2019.100615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/28/2019] [Accepted: 07/31/2019] [Indexed: 12/16/2022]
Abstract
Low temperature reduction is thought to cause widespread effects on the physical and behavioral traits of marine organisms, which include metabolic processes, immune responses, and reproductive behavior. Crustaceans are generally considered sensitive to temperature reduction due to the lack of efficient regulators. To better understand the molecular regulatory mechanisms of crustacean exposure to cold stress, Japanese mantis shrimp (Oratosquilla oratoria) was chosen as a representative crustacean. Transcriptomic responses in O. oratoria from five temperatures (25 °C, 22 °C, 19 °C, 16 °C, and 13 °C) were studied using RNA-seq. A total of 64.91 Gb of clean transcriptomic data were generated in 10 libraries and then spliced into 52,107 unigenes with an average length of 1089 bp and an N50 length of 1872 bp. A total of 14,841 unigenes was annotated in at least one database using Blastx alignment. Compared with the control temperature (25 °C), 7, 21, 58, and 236 unigenes were significantly differentially expressed at 22 °C, 19 °C, 16 °C, and 13 °C, respectively. GO analysis showed that 6, 20, 27, and 35 terms were significantly enriched at 22 °C, 19 °C, 16 °C, and 13 °C, respectively. In addition, 2, 5, 2, and 10 significant pathways were presented at 22 °C, 19 °C, 16 °C, and 13 °C, respectively. Combining NR, GO, and KEGG annotation information, many genes significantly differentially expressed at low temperatures may be associated with metabolic processes, immune response, and reproductive behavior. Additionally, we reconstructed the phylogenetic relationship based on 366 orthologous genes and the predicted differentiation time of O. oratoria and P. vannamei range from 212.82 to 365.30 Mya. Furthermore, 16 orthologous genes were identified as PSGs and 30 orthologous genes were identified as FEGs and these adaptive genes were associated with energy metabolism, stress response and immunity, and multiple cellular processing. These results provide fundamental information about molecular mechanisms regulating cold stress response of O. oratoria.
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Affiliation(s)
- Fangrui Lou
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China; Fishery College, Ocean University of China, Qingdao, Shandong 266003, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Zhiqiang Han
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China.
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Diaz de Cerio O, Bilbao E, Ruiz P, Pardo BG, Martínez P, Cajaraville MP, Cancio I. Hepatic gene transcription profiles in turbot (Scophthalmus maximus) experimentally exposed to heavy fuel oil nº 6 and to styrene. MARINE ENVIRONMENTAL RESEARCH 2017; 123:14-24. [PMID: 27846414 DOI: 10.1016/j.marenvres.2016.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/04/2016] [Accepted: 11/08/2016] [Indexed: 06/06/2023]
Abstract
Oil and chemical spills in the marine environment, although sporadic, are highly dangerous to biota inhabiting coastal and estuarine areas. Effects of spilled compounds in exposed organisms occur at different biological organization levels: from molecular, cellular or tissue levels to the physiological one. The present study aims to determine the specific hepatic gene transcription profiles observed in turbot juveniles under exposure to fuel oil n °6 and styrene vs controls using an immune enriched turbot (Scophthalmus maximus) oligo-microarray containing 2716 specific gene probes. After 3 days of exposure, fuel oil specifically induced aryl hydrocarbon receptor mediated transcriptional response through up-regulation of genes, such as ahrr and cyp1a1. More gene transcripts were regulated after 14 days of exposure involved in ribosomal biosynthesis, immune modulation, and oxidative response among the most significantly regulated functional pathways. On the contrary, gene transcription alterations caused by styrene did not highlight any significantly regulated molecular or metabolic pathway. This was also previously reported at cell and tissue level where no apparent responses were distinguishable. For the fuel oil experiment, obtained specific gene profiles could be related to changes in cell-tissue organization in the same individuals, such as increased hepatocyte vacuolization, decrease in melano-macrophage centers and the regulation of leukocyte numbers. In conclusion, the mode of action reflected by gene transcription profiles analyzed hereby in turbot livers could be linked with the responses previously reported at higher biological organization levels. Molecular alterations described hereby could be preceding observed alterations at cell and tissue levels.
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Affiliation(s)
- Oihane Diaz de Cerio
- CBET Research Group, Dept. of Zoology and Animal Cell Biology, Fac. Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), E-48080 Bilbao, PO Box 644, Basque Country, Spain
| | - Eider Bilbao
- CBET Research Group, Dept. of Zoology and Animal Cell Biology, Fac. Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), E-48080 Bilbao, PO Box 644, Basque Country, Spain
| | - Pamela Ruiz
- CBET Research Group, Dept. of Zoology and Animal Cell Biology, Fac. Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), E-48080 Bilbao, PO Box 644, Basque Country, Spain
| | - Belén G Pardo
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, 27002, Spain
| | - Paulino Martínez
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, 27002, Spain
| | - Miren P Cajaraville
- CBET Research Group, Dept. of Zoology and Animal Cell Biology, Fac. Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), E-48080 Bilbao, PO Box 644, Basque Country, Spain
| | - Ibon Cancio
- CBET Research Group, Dept. of Zoology and Animal Cell Biology, Fac. Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), E-48080 Bilbao, PO Box 644, Basque Country, Spain.
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Kwarteng A, Ahuno ST. The Potentials and Pitfalls of Microarrays in Neglected Tropical Diseases: A Focus on Human Filarial Infections. MICROARRAYS 2016; 5:microarrays5030020. [PMID: 27600086 PMCID: PMC5040967 DOI: 10.3390/microarrays5030020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 06/01/2016] [Accepted: 06/28/2016] [Indexed: 12/01/2022]
Abstract
Data obtained from expression microarrays enables deeper understanding of the molecular signatures of infectious diseases. It provides rapid and accurate information on how infections affect the clustering of gene expression profiles, pathways and networks that are transcriptionally active during various infection states compared to conventional diagnostic methods, which primarily focus on single genes or proteins. Thus, microarray technologies offer advantages in understanding host-parasite interactions associated with filarial infections. More importantly, the use of these technologies can aid diagnostics and helps translate current genomic research into effective treatment and interventions for filarial infections. Studying immune responses via microarray following infection can yield insight into genetic pathways and networks that can have a profound influence on the development of anti-parasitic vaccines.
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Affiliation(s)
- Alexander Kwarteng
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Private Mail Bag, Kwame Nkrumah University Science & Technology, KNUST, Kumasi 233, Ghana.
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University Science & Technology, KNUST, Kumasi 233, Ghana.
| | - Samuel Terkper Ahuno
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University Science & Technology, KNUST, Kumasi 233, Ghana.
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Schulze S, Schleicher J, Guthke R, Linde J. How to Predict Molecular Interactions between Species? Front Microbiol 2016; 7:442. [PMID: 27065992 PMCID: PMC4814556 DOI: 10.3389/fmicb.2016.00442] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/18/2016] [Indexed: 12/21/2022] Open
Abstract
Organisms constantly interact with other species through physical contact which leads to changes on the molecular level, for example the transcriptome. These changes can be monitored for all genes, with the help of high-throughput experiments such as RNA-seq or microarrays. The adaptation of the gene expression to environmental changes within cells is mediated through complex gene regulatory networks. Often, our knowledge of these networks is incomplete. Network inference predicts gene regulatory interactions based on transcriptome data. An emerging application of high-throughput transcriptome studies are dual transcriptomics experiments. Here, the transcriptome of two or more interacting species is measured simultaneously. Based on a dual RNA-seq data set of murine dendritic cells infected with the fungal pathogen Candida albicans, the software tool NetGenerator was applied to predict an inter-species gene regulatory network. To promote further investigations of molecular inter-species interactions, we recently discussed dual RNA-seq experiments for host-pathogen interactions and extended the applied tool NetGenerator (Schulze et al., 2015). The updated version of NetGenerator makes use of measurement variances in the algorithmic procedure and accepts gene expression time series data with missing values. Additionally, we tested multiple modeling scenarios regarding the stimuli functions of the gene regulatory network. Here, we summarize the work by Schulze et al. (2015) and put it into a broader context. We review various studies making use of the dual transcriptomics approach to investigate the molecular basis of interacting species. Besides the application to host-pathogen interactions, dual transcriptomics data are also utilized to study mutualistic and commensalistic interactions. Furthermore, we give a short introduction into additional approaches for the prediction of gene regulatory networks and discuss their application to dual transcriptomics data. We conclude that the application of network inference on dual-transcriptomics data is a promising approach to predict molecular inter-species interactions.
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Affiliation(s)
- Sylvie Schulze
- Research Group Systems Biology and Bioinformatics, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
| | - Jana Schleicher
- Research Group Systems Biology and Bioinformatics, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
| | - Reinhard Guthke
- Research Group Systems Biology and Bioinformatics, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
| | - Jörg Linde
- Research Group Systems Biology and Bioinformatics, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
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7
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Alvarez M, Schrey AW, Richards CL. Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution? Mol Ecol 2015; 24:710-25. [PMID: 25604587 DOI: 10.1111/mec.13055] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 12/16/2014] [Accepted: 12/18/2014] [Indexed: 12/13/2022]
Abstract
Molecular ecology has moved beyond the use of a relatively small number of markers, often noncoding, and it is now possible to use whole-genome measures of gene expression with microarrays and RNAseq (i.e. transcriptomics) to capture molecular response to environmental challenges. While transcriptome studies are shedding light on the mechanistic basis of traits as complex as personality or physiological response to catastrophic events, these approaches are still challenging because of the required technical expertise, difficulties with analysis and cost. Still, we found that in the last 10 years, 575 studies used microarrays or RNAseq in ecology. These studies broadly address three questions that reflect the progression of the field: (i) How much variation in gene expression is there and how is it structured? (ii) How do environmental stimuli affect gene expression? (iii) How does gene expression affect phenotype? We discuss technical aspects of RNAseq and microarray technology, and a framework that leverages the advantages of both. Further, we highlight future directions of research, particularly related to moving beyond correlation and the development of additional annotation resources. Measuring gene expression across an array of taxa in ecological settings promises to enrich our understanding of ecology and genome function.
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Affiliation(s)
- Mariano Alvarez
- Department of Integrative Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL, 33620, USA
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8
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Fassbinder-Orth CA. Methods for quantifying gene expression in ecoimmunology: from qPCR to RNA-Seq. Integr Comp Biol 2014; 54:396-406. [PMID: 24812328 DOI: 10.1093/icb/icu023] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Historically, the use of cutting-edge molecular techniques to study immunological gene expression and related cellular pathways has been largely limited to model organisms. Few studies have been performed that quantify the molecular immunological responses of non-model species, especially in response to environmental factors, life-history events, or exposure to parasites. This dearth of information has largely occurred due to the lack of available non-model species-specific gene sequences and immunological reagents and also due to prohibitively expensive technology. However, with the rapid development of various sequencing and transcriptomic technologies, profiling the gene expression of non-model organisms has become possible. Technologies and concepts explored here include an overview of current technologies for quantifying gene expression, including: qPCR, multiplex branched DNA assays, microarrays, and profiling gene expression (RNA sequencing [RNA-Seq]) based on next-generation sequencing. Examples of the advancement of these technologies in non-model systems are discussed. Additionally, applications, limitations, and feasibility of the use of these methodologies in non-model systems to address questions in ecological immunology and disease-ecology are specifically addressed.
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Jeffries KM, Hinch SG, Sierocinski T, Pavlidis P, Miller KM. Transcriptomic responses to high water temperature in two species of Pacific salmon. Evol Appl 2013; 7:286-300. [PMID: 24567748 PMCID: PMC3927889 DOI: 10.1111/eva.12119] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 09/18/2013] [Indexed: 11/29/2022] Open
Abstract
Characterizing the cellular stress response (CSR) of species at ecologically relevant temperatures is useful for determining whether populations and species can successfully respond to current climatic extremes and future warming. In this study, populations of wild-caught adult pink (Oncorhynchus gorbuscha) and sockeye (Oncorhynchus nerka) salmon from the Fraser River, British Columbia, Canada, were experimentally treated to ecologically relevant 'cool' or 'warm' water temperatures to uncover common transcriptomic responses to elevated water temperature in non-lethally sampled gill tissue. We detected the differential expression of 49 microarray features (29 unique annotated genes and one gene with unknown function) associated with protein folding, protein synthesis, metabolism, oxidative stress and ion transport that were common between populations and species of Pacific salmon held at 19°C compared with fish held at a cooler temperature (13 or 14°C). There was higher mortality in fish held at 19°C, which suggests a possible relationship between a temperature-induced CSR and mortality in these species. Our results suggest that frequently encountered water temperatures ≥19°C, which are capable of inducing a common CSR across species and populations, may increase risk of upstream spawning migration failure for pink and sockeye salmon.
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Affiliation(s)
- Ken M Jeffries
- Centre for Applied Conservation Research Department of Forest and Conservation Sciences, University of British Columbia Vancouver, BC, Canada
| | - Scott G Hinch
- Centre for Applied Conservation Research Department of Forest and Conservation Sciences, University of British Columbia Vancouver, BC, Canada
| | - Thomas Sierocinski
- Centre for High-Throughput Biology Department of Psychiatry, University of British Columbia Vancouver, BC, Canada
| | - Paul Pavlidis
- Centre for High-Throughput Biology Department of Psychiatry, University of British Columbia Vancouver, BC, Canada
| | - Kristi M Miller
- Fisheries and Oceans Canada, Molecular Genetics Section Nanaimo, BC, Canada
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Ruiz-Mirazo K, Briones C, de la Escosura A. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chem Rev 2013; 114:285-366. [DOI: 10.1021/cr2004844] [Citation(s) in RCA: 563] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kepa Ruiz-Mirazo
- Biophysics
Unit (CSIC-UPV/EHU), Leioa, and Department of Logic and Philosophy
of Science, University of the Basque Country, Avenida de Tolosa 70, 20080 Donostia−San Sebastián, Spain
| | - Carlos Briones
- Department
of Molecular Evolution, Centro de Astrobiología (CSIC−INTA, associated to the NASA Astrobiology Institute), Carretera de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Andrés de la Escosura
- Organic
Chemistry Department, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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11
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Cano LM, Raffaele S, Haugen RH, Saunders DGO, Leonelli L, MacLean D, Hogenhout SA, Kamoun S. Major transcriptome reprogramming underlies floral mimicry induced by the rust fungus Puccinia monoica in Boechera stricta. PLoS One 2013; 8:e75293. [PMID: 24069397 PMCID: PMC3775748 DOI: 10.1371/journal.pone.0075293] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 08/12/2013] [Indexed: 01/08/2023] Open
Abstract
Pucciniamonoica is a spectacular plant parasitic rust fungus that triggers the formation of flower-like structures (pseudoflowers) in its Brassicaceae host plant Boecherastricta. Pseudoflowers mimic in shape, color, nectar and scent co-occurring and unrelated flowers such as buttercups. They act to attract insects thereby aiding spore dispersal and sexual reproduction of the rust fungus. Although much ecological research has been performed on P. monoica-induced pseudoflowers, this system has yet to be investigated at the molecular or genomic level. To date, the molecular alterations underlying the development of pseudoflowers and the genes involved have not been described. To address this, we performed gene expression profiling to reveal 256 plant biological processes that are significantly altered in pseudoflowers. Among these biological processes, plant genes involved in cell fate specification, regulation of transcription, reproduction, floral organ development, anthocyanin (major floral pigments) and terpenoid biosynthesis (major floral volatile compounds) were down-regulated in pseudoflowers. In contrast, plant genes involved in shoot, cotyledon and leaf development, carbohydrate transport, wax biosynthesis, cutin transport and L-phenylalanine metabolism (pathway that results in phenylethanol and phenylacetaldehyde volatile production) were up-regulated. These findings point to an extensive reprogramming of host genes by the rust pathogen to induce floral mimicry. We also highlight 31 differentially regulated plant genes that are enriched in the biological processes mentioned above, and are potentially involved in the formation of pseudoflowers. This work illustrates the complex perturbations induced by rust pathogens in their host plants, and provides a starting point for understanding the molecular mechanisms of pathogen-induced floral mimicry.
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Affiliation(s)
| | - Sylvain Raffaele
- The Sainsbury Laboratory, Norwich, United Kingdom
- Laboratoire des Interactions Plantes Micro-organismes, UMR441 INRA - UMR2594 CNRS, Castanet Tolosan, France
| | - Riston H. Haugen
- Black Hills State University, Integrative Genomics Program, Spearfish, South Dakota, United States of America
| | | | - Lauriebeth Leonelli
- The Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Dan MacLean
- The Sainsbury Laboratory, Norwich, United Kingdom
| | - Saskia A. Hogenhout
- Cell and Developmental Biology, The John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich, United Kingdom
- * E-mail:
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12
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Magnanou E, Malenke JR, Dearing MD. Hepatic gene expression in herbivores on diets with natural and novel plant secondary compounds. Physiol Genomics 2013; 45:774-85. [DOI: 10.1152/physiolgenomics.00033.2013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Herbivores are predicted to evolve appropriate mechanisms to process the plant secondary compounds (PSCs) in their diet, and these mechanisms are likely specific to particular suites of PSCs. Changes in diet composition over evolutionary time should select for appropriate alterations in metabolism of the more recent dietary components. We investigated differences in gene expression profiles in the liver with respect to prior ecological and evolutionary experience with PSCs in the desert woodrat, Neotoma lepida. This woodrat species has populations in the Mojave Desert that have switched from feeding on juniper to feeding on creosote at the end of the Holocene as well as populations in the Great Basin Desert that still feed on the ancestral diet of juniper and are naïve to creosote. Juniper and creosote have notable differences in secondary chemistry. Woodrats from the Mojave and Great Basin Deserts were subjected to a fully crossed feeding trial on diets of juniper and creosote after which their livers were analyzed for gene expression. Hybridization of hepatic mRNAs to laboratory rat microarrays resulted in a total of 20,031 genes that met quality control standards. We analyzed differences in large-scale patterns of liver gene expression with respect to GO term enrichment. Diet had a larger effect on gene expression than population membership. However, woodrats with no prior evolutionary experience to the diet upregulated a greater proportion of genes indicative of physiological stress compared with those on their natural diet. This pattern may be the result of a naïve animal's attempting to mitigate physiological damage caused by novel PSCs.
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Affiliation(s)
- Elodie Magnanou
- Université Pierre et Marie Curie-Paris 6, Laboratoire ARAGO, Banyuls-sur-Mer, France
- CNRS, UMR7232, Biologie Intégrative des Organismes Marins, Banyuls-sur-Mer, France; and
- Department of Biology, University of Utah, Salt Lake City, Utah
| | - Jael R. Malenke
- Department of Biology, University of Utah, Salt Lake City, Utah
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Jansen M, Vergauwen L, Vandenbrouck T, Knapen D, Dom N, Spanier KI, Cielen A, De Meester L. Gene expression profiling of three different stressors in the water flea Daphnia magna. ECOTOXICOLOGY (LONDON, ENGLAND) 2013; 22:900-914. [PMID: 23564370 DOI: 10.1007/s10646-013-1072-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/29/2013] [Indexed: 06/02/2023]
Abstract
Microarrays are an ideal tool to screen for differences in gene expression of thousands of genes simultaneously. However, often commercial arrays are not available. In this study, we performed microarray analyses to evaluate patterns of gene transcription following exposure to two natural and one anthropogenic stressor. cDNA microarrays compiled of three life stage specific and three stressor-specific EST libraries, yielding 1734 different EST sequences, were used. We exposed juveniles of the water flea Daphnia magna for 48, 96 and 144 h to three stressors known to exert strong selection in natural populations of this species i.e. a sublethal concentration of the pesticide carbaryl, infective spores of the endoparasite Pasteuria ramosa, and fish predation risk mimicked by exposure to fish kairomones. A total of 148 gene fragments were differentially expressed compared to the control. Based on a PCA, the exposure treatments were separated into two main groups based on the extent of the transcriptional response: a low and a high (144 h of fish or carbaryl exposure and 96 h of parasite exposure) stress group. Firstly, we observed a general stress-related transcriptional expression profile independent of the treatment characterized by repression of transcripts involved in transcription, translation, signal transduction and energy metabolism. Secondly, we observed treatment-specific responses including signs of migration to deeper water layers in response to fish predation, structural challenge of the cuticle in response to carbaryl exposure, and disturbance of the ATP production in parasite exposure. A third important conclusion is that transcription expression patterns exhibit stress-specific changes over time. Parasite exposure shows the most differentially expressed gene fragments after 96 h. The peak of differentially expressed transcripts came only after 144 h of fish exposure, while carbaryl exposure induced a more stable number of differently expressed gene fragments over time.
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Affiliation(s)
- Mieke Jansen
- Laboratory of Aquatic Ecology, Evolution and Conservation, Catholic University of Leuven, Charles Deberiotstraat 32, 3000 Leuven, Belgium.
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14
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Studying Ecologically Important Traits: Ecogenomics, QTL Analysis, and Reverse Genetics. Mol Ecol 2012. [DOI: 10.1002/9780470979365.ch5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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References. Mol Ecol 2012. [DOI: 10.1002/9780470979365.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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16
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Settles ML, Coram T, Soule T, Robison BD. An improved algorithm for the detection of genomic variation using short oligonucleotide expression microarrays. Mol Ecol Resour 2012; 12:1079-89. [PMID: 22966828 DOI: 10.1111/1755-0998.12006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/30/2012] [Accepted: 08/01/2012] [Indexed: 11/30/2022]
Abstract
High-throughput microarray experiments often generate far more biological information than is required to test the experimental hypotheses. Many microarray analyses are considered finished after differential expression and additional analyses are typically not performed, leaving untapped biological information left undiscovered. This is especially true if the microarray experiment is from an ecological study of multiple populations. Comparisons across populations may also contain important genomic polymorphisms, and a subset of these polymorphisms may be identified with microarrays using techniques for the detection of single feature polymorphisms (SFP). SFPs are differences in microarray probe level intensities caused by genetic polymorphisms such as single-nucleotide polymorphisms and small insertions/deletions and not expression differences. In this study, we provide a new algorithm for the detection of SFPs, evaluate the algorithm using existing data from two publicly available Affymetrix Barley (Hordeum vulgare) microarray data sets and compare them to two previously published SFP detection algorithms. Results show that our algorithm provides more consistent and sensitive calling of SFPs with a lower false discovery rate. Simultaneous analysis of SFPs and differential expression is a low-cost method for the enhanced analysis of microarray data, enabling additional biological inferences to be made.
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Affiliation(s)
- Matthew L Settles
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844-3051, USA.
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17
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Renaut S, Maillet N, Normandeau E, Sauvage C, Derome N, Rogers SM, Bernatchez L. Genome-wide patterns of divergence during speciation: the lake whitefish case study. Philos Trans R Soc Lond B Biol Sci 2012; 367:354-63. [PMID: 22201165 DOI: 10.1098/rstb.2011.0197] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The nature, size and distribution of the genomic regions underlying divergence and promoting reproductive isolation remain largely unknown. Here, we summarize ongoing efforts using young (12 000 yr BP) species pairs of lake whitefish (Coregonus clupeaformis) to expand our understanding of the initial genomic patterns of divergence observed during speciation. Our results confirmed the predictions that: (i) on average, phenotypic quantitative trait loci (pQTL) show higher F(ST) values and are more likely to be outliers (and therefore candidates for being targets of divergent selection) than non-pQTL markers; (ii) large islands of divergence rather than small independent regions under selection characterize the early stages of adaptive divergence of lake whitefish; and (iii) there is a general trend towards an increase in terms of numbers and size of genomic regions of divergence from the least (East L.) to the most differentiated species pair (Cliff L.). This is consistent with previous estimates of reproductive isolation between these species pairs being driven by the same selective forces responsible for environment specialization. Altogether, dwarf and normal whitefish species pairs represent a continuum of both morphological and genomic differentiation contributing to ecological speciation. Admittedly, much progress is still required to more finely map and circumscribe genomic islands of speciation. This will be achieved through the use of next generation sequencing data but also through a better quantification of phenotypic traits moulded by selection as organisms adapt to new environmental conditions.
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Affiliation(s)
- S Renaut
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada.
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18
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Richards CL, Rosas U, Banta J, Bhambhra N, Purugganan MD. Genome-wide patterns of Arabidopsis gene expression in nature. PLoS Genet 2012; 8:e1002662. [PMID: 22532807 PMCID: PMC3330097 DOI: 10.1371/journal.pgen.1002662] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Accepted: 03/05/2012] [Indexed: 02/01/2023] Open
Abstract
Organisms in the wild are subject to multiple, fluctuating environmental factors, and it is in complex natural environments that genetic regulatory networks actually function and evolve. We assessed genome-wide gene expression patterns in the wild in two natural accessions of the model plant Arabidopsis thaliana and examined the nature of transcriptional variation throughout its life cycle and gene expression correlations with natural environmental fluctuations. We grew plants in a natural field environment and measured genome-wide time-series gene expression from the plant shoot every three days, spanning the seedling to reproductive stages. We find that 15,352 genes were expressed in the A. thaliana shoot in the field, and accession and flowering status (vegetative versus flowering) were strong components of transcriptional variation in this plant. We identified between ∼110 and 190 time-varying gene expression clusters in the field, many of which were significantly overrepresented by genes regulated by abiotic and biotic environmental stresses. The two main principal components of vegetative shoot gene expression (PC(veg)) correlate to temperature and precipitation occurrence in the field. The largest PC(veg) axes included thermoregulatory genes while the second major PC(veg) was associated with precipitation and contained drought-responsive genes. By exposing A. thaliana to natural environments in an open field, we provide a framework for further understanding the genetic networks that are deployed in natural environments, and we connect plant molecular genetics in the laboratory to plant organismal ecology in the wild.
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Affiliation(s)
- Christina L. Richards
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
- Department of Integrative Biology, University of South Florida, Tampa, Florida, United States of America
| | - Ulises Rosas
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Joshua Banta
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
- Department of Biology, University of Texas at Tyler, Tyler, Texas, United States of America
| | - Naeha Bhambhra
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Michael D. Purugganan
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
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Manzano AI, van Loon JJWA, Christianen PCM, Gonzalez-Rubio JM, Medina FJ, Herranz R. Gravitational and magnetic field variations synergize to cause subtle variations in the global transcriptional state of Arabidopsis in vitro callus cultures. BMC Genomics 2012; 13:105. [PMID: 22435851 PMCID: PMC3368779 DOI: 10.1186/1471-2164-13-105] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 03/21/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biological systems respond to changes in both the Earth's magnetic and gravitational fields, but as experiments in space are expensive and infrequent, Earth-based simulation techniques are required. A high gradient magnetic field can be used to levitate biological material, thereby simulating microgravity and can also create environments with a reduced or an enhanced level of gravity (g), although special attention should be paid to the possible effects of the magnetic field (B) itself. RESULTS Using diamagnetic levitation, we exposed Arabidopsis thaliana in vitro callus cultures to five environments with different levels of effective gravity and magnetic field strengths. The environments included levitation, i.e. simulated μg* (close to 0 g* at B = 10.1 T), intermediate g* (0.1 g* at B = 14.7 T) and enhanced gravity levels (1.9 g* at B = 14.7 T and 2 g* at B = 10.1 T) plus an internal 1 g* control (B = 16.5 T). The asterisk denotes the presence of the background magnetic field, as opposed to the effective gravity environments in the absence of an applied magnetic field, created using a Random Position Machine (simulated μg) and a Large Diameter Centrifuge (2 g).Microarray analysis indicates that changes in the overall gene expression of cultured cells exposed to these unusual environments barely reach significance using an FDR algorithm. However, it was found that gravitational and magnetic fields produce synergistic variations in the steady state of the transcriptional profile of plants. Transcriptomic results confirm that high gradient magnetic fields (i.e. to create μg* and 2 g* conditions) have a significant effect, mainly on structural, abiotic stress genes and secondary metabolism genes, but these subtle gravitational effects are only observable using clustering methodologies. CONCLUSIONS A detailed microarray dataset analysis, based on clustering of similarly expressed genes (GEDI software), can detect underlying global-scale responses, which cannot be detected by means of individual gene expression techniques using raw or corrected p values (FDR). A subtle, but consistent, genome-scale response to hypogravity environments was found, which was opposite to the response in a hypergravity environment.
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Affiliation(s)
- Ana I Manzano
- Centro de Investigaciones Biológicas (CSIC), C/Ramiro de Maeztu 9, E-28040 Madrid, Spain
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Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2011; 7:110-23. [PMID: 22277925 DOI: 10.1016/j.cbd.2011.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 12/13/2011] [Accepted: 12/20/2011] [Indexed: 11/20/2022]
Abstract
The copepod, Calanus finmarchicus is a keystone species for the North Atlantic. Because of recent changes in the geographic distribution of this species, there are questions as to how this organism responds physiologically to environmental cues. Molecular techniques allow for examination and new understanding of these physiological changes. Here, we describe the development of a microarray for high-throughput studies of the physiological ecology of C. finmarchicus. An EST database was generated for this species using a normalized cDNA library derived from adult and sub-adult individuals. Sequence data were clustered into contigs and annotated using Blastx. Target transcripts were selected, and unique, 50 base-pair, oligomer probes were generated for 995 genes. Blast2GO processing provided detailed information on gene function. The selected targets included broad representation of biological processes, cellular components, and molecular functions. The microarray was tested in two sets of comparisons: adult females maintained at different food concentrations and field-caught sub-adults showing differences in lipid storage. Up-regulated and down-regulated transcripts were identified for both comparisons. Only a small subset of the genes up-regulated in low food individuals were also up-regulated in lipid-poor animals; no overlap was seen between the genes down-regulated in the two comparisons.
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21
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Pavey SA, Sutherland BJG, Leong J, Robb A, von Schalburg K, Hamon TR, Koop BF, Nielsen JL. Ecological transcriptomics of lake-type and riverine sockeye salmon (Oncorhynchus nerka). BMC Ecol 2011; 11:31. [PMID: 22136247 PMCID: PMC3295673 DOI: 10.1186/1472-6785-11-31] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 12/02/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There are a growing number of genomes sequenced with tentative functions assigned to a large proportion of the individual genes. Model organisms in laboratory settings form the basis for the assignment of gene function, and the ecological context of gene function is lacking. This work addresses this shortcoming by investigating expressed genes of sockeye salmon (Oncorhynchus nerka) muscle tissue. We compared morphology and gene expression in natural juvenile sockeye populations related to river and lake habitats. Based on previously documented divergent morphology, feeding strategy, and predation in association with these distinct environments, we expect that burst swimming is favored in riverine population and continuous swimming is favored in lake-type population. In turn we predict that morphology and expressed genes promote burst swimming in riverine sockeye and continuous swimming in lake-type sockeye. RESULTS We found the riverine sockeye population had deep, robust bodies and lake-type had shallow, streamlined bodies. Gene expression patterns were measured using a 16 k microarray, discovering 141 genes with significant differential expression. Overall, the identity and function of these genes was consistent with our hypothesis. In addition, Gene Ontology (GO) enrichment analyses with a larger set of differentially expressed genes found the "biosynthesis" category enriched for the riverine population and the "metabolism" category enriched for the lake-type population. CONCLUSIONS This study provides a framework for understanding sockeye life history from a transcriptomic perspective and a starting point for more extensive, targeted studies determining the ecological context of genes.
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Affiliation(s)
- Scott A Pavey
- National Park Service, Katmai National Park; PO Box 7, King Salmon, AK 99613, USA.
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22
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Angeloni F, Wagemaker N, Vergeer P, Ouborg J. Genomic toolboxes for conservation biologists. Evol Appl 2011; 5:130-43. [PMID: 25568036 PMCID: PMC3353346 DOI: 10.1111/j.1752-4571.2011.00217.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 10/18/2011] [Indexed: 12/01/2022] Open
Abstract
Conservation genetics is expanding its research horizon with a genomic approach, by incorporating the modern techniques of next-generation sequencing (NGS). Application of NGS overcomes many limitations of conservation genetics. First, NGS allows for genome-wide screening of markers, which may lead to a more representative estimation of genetic variation within and between populations. Second, NGS allows for distinction between neutral and non-neutral markers. By screening populations on thousands of single nucleotide polymorphism markers, signals of selection can be found for some markers. Variation in these markers will give insight into functional rather than neutral genetic variation. Third, NGS facilitates the study of gene expression. Conservation genomics will increase our insight in how the environment and genes interact to affect phenotype and fitness. In addition, the NGS approach opens a way to study processes such as inbreeding depression and local adaptation mechanistically. Conservation genetics programs are directed to a fundamental understanding of the processes involved in conservation genetics and should preferably be started in species for which large databases on ecology, demography and genetics are available. Here, we describe and illustrate the connection between the application of NGS technologies and the research questions in conservation. The perspectives of conservation genomics programs are also discussed.
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Affiliation(s)
- Francesco Angeloni
- Institute for Water and Wetland Research (IWWR), Department of Molecular Ecology, Radboud University Nijmegen AJ Nijmegen, The Netherlands
| | - Niels Wagemaker
- Institute for Water and Wetland Research (IWWR), Department of Molecular Ecology, Radboud University Nijmegen AJ Nijmegen, The Netherlands
| | - Philippine Vergeer
- Institute for Water and Wetland Research (IWWR), Department of Molecular Ecology, Radboud University Nijmegen AJ Nijmegen, The Netherlands
| | - Joop Ouborg
- Institute for Water and Wetland Research (IWWR), Department of Molecular Ecology, Radboud University Nijmegen AJ Nijmegen, The Netherlands
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23
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Ekblom R, Galindo J. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity (Edinb) 2011; 107:1-15. [PMID: 21139633 PMCID: PMC3186121 DOI: 10.1038/hdy.2010.152] [Citation(s) in RCA: 633] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 09/10/2010] [Accepted: 11/02/2010] [Indexed: 11/09/2022] Open
Abstract
As most biologists are probably aware, technological advances in molecular biology during the last few years have opened up possibilities to rapidly generate large-scale sequencing data from non-model organisms at a reasonable cost. In an era when virtually any study organism can 'go genomic', it is worthwhile to review how this may impact molecular ecology. The first studies to put the next generation sequencing (NGS) to the test in ecologically well-characterized species without previous genome information were published in 2007 and the beginning of 2008. Since then several studies have followed in their footsteps, and a large number are undoubtedly under way. This review focuses on how NGS has been, and can be, applied to ecological, population genetic and conservation genetic studies of non-model species, in which there is no (or very limited) genomic resources. Our aim is to draw attention to the various possibilities that are opening up using the new technologies, but we also highlight some of the pitfalls and drawbacks with these methods. We will try to provide a snapshot of the current state of the art for this rapidly advancing and expanding field of research and give some likely directions for future developments.
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Affiliation(s)
- R Ekblom
- Department of Animal and Plant Sciences, University of Sheffield, UK.
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24
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Gotelli NJ, Smith AM, Ellison AM, Ballif BA. Proteomic characterization of the major arthropod associates of the carnivorous pitcher plant Sarracenia purpurea. Proteomics 2011; 11:2354-8. [PMID: 21538880 DOI: 10.1002/pmic.201000256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 01/10/2011] [Accepted: 02/28/2011] [Indexed: 11/06/2022]
Abstract
The array of biomolecules generated by a functioning ecosystem represents both a potential resource for sustainable harvest and a potential indicator of ecosystem health and function. The cupped leaves of the carnivorous pitcher plant, Sarracenia purpurea, harbor a dynamic food web of aquatic invertebrates in a fully functional miniature ecosystem. The energetic base of this food web consists of insect prey, which is shredded by aquatic invertebrates and decomposed by microbes. Biomolecules and metabolites produced by this food web are actively exchanged with the photosynthesizing plant. In this report, we provide the first proteomic characterization of the sacrophagid fly (Fletcherimyia fletcheri), the pitcher plant mosquito (Wyeomyia smithii), and the pitcher-plant midge (Metriocnemus knabi). These three arthropods act as predators, filter feeders, and shredders at distinct trophic levels within the S. purpurea food web. More than 50 proteins from each species were identified, ten of which were predominantly or uniquely found in one species. Furthermore, 19 peptides unique to one of the three species were identified using an assembled database of 100 metazoan myosin heavy chain orthologs. These molecular signatures may be useful in species monitoring within heterogeneous ecosystem biomass and may also serve as indicators of ecosystem state.
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25
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De Boer TE, Birlutiu A, Bochdanovits Z, Timmermans MJTN, Dijkstra TMH, Van Straalen NM, Ylstra B, Roelofs D. Transcriptional plasticity of a soil arthropod across different ecological conditions. Mol Ecol 2011; 20:1144-54. [PMID: 21255171 DOI: 10.1111/j.1365-294x.2010.04985.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ecological functional genomics, dealing with the responses of organisms to their natural environment is confronted with a complex pattern of variation and a large number of confounding environmental factors. For gene expression studies to provide meaningful information on conditions deviating from normal, a baseline or normal operating range (NOR) response needs to be established which indicates how an organism's transcriptome reacts to naturally varying ecological factors. Here we determine the transcriptional plasticity of a soil arthropod, Folsomia candida, exposed to various natural environments, as part of a first attempt in establishing such a NOR. Animals were exposed to 26 different field soils after which gene expression levels were measured. The main factor found to regulate gene expression was soil-type (sand or clay). Cell homeostasis and DNA replication were affected in collembolans exposed to sandy soil, indicating general stress. Multivariate analysis identified soil fertility as the main factor influencing gene expression. Regarding land-use, only forest soils showed an expression pattern deviating from the others. No significant effect of land-use, agricultural practice or soil type on fitness was observed, but arsenic concentration was negatively correlated with reproductive output. In conclusion, transcriptional responses remained within a limited range across the different land-uses but were significantly affected by soil-type. This may be caused by the contrasting soil physicochemical properties to which F. candida strongly responds. The broad range of conditions over which this soil-living detritivore is able to survive and reproduce, indicates a strategy of high plasticity, which comes with extensive gene expression regulation.
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Affiliation(s)
- Tjalf E De Boer
- Department of Ecological Science, VU University, Amsterdam, the Netherlands.
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26
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Affiliation(s)
- Raoul K. Boughton
- Avian Ecology, Archbold Biological Station, 123 Main Drive, Venus, Florida, USA
| | - Gerrit Joop
- Institute of Integrative Biology,
Experimental Ecology, ETH Zürich, CH‐8092 Zürich, Switzerland
| | - Sophie A.O. Armitage
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, D‐48149 Münster, Germany
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Larsen PF, Schulte PM, Nielsen EE. Gene expression analysis for the identification of selection and local adaptation in fishes. JOURNAL OF FISH BIOLOGY 2011; 78:1-22. [PMID: 21235543 DOI: 10.1111/j.1095-8649.2010.02834.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In recent years, variation in gene expression has been recognized as an important component of environmental adaptation in multiple model species, including a few fish species. There is, however, still little known about the genetic basis of adaptation in gene expression resulting from variation in the aquatic environment (e.g. temperature, salinity and oxygen) and the physiological effect and costs of such differences in gene expression. This review presents and discusses progress and pitfalls of applying gene expression analyses to fishes and suggests simple frameworks to get started with gene expression analysis. It is emphasized that well-planned gene expression studies can serve as an important tool for the identification of selection in local populations of fishes, even for non-traditional model species where limited genomic information is available. Recent studies focusing on gene expression variation among natural fish populations are reviewed, highlighting the latest applications that combine genetic evidence from neutral markers and gene expression data.
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Affiliation(s)
- P F Larsen
- Department of Biological Sciences, Aarhus Universit, Ny Munkegade, DK-8000 Aarhus C, Denmark.
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Abstract
Ecological speciation is the process by which barriers to gene flow between populations evolve due to adaptive divergence via natural selection. A relatively unexplored area in ecological speciation is the role of gene expression. Gene expression may be associated with ecologically important phenotypes not evident from morphology and play a role during colonization of new environments. Here we review two potential roles of gene expression in ecological speciation: (1) its indirect role in facilitating population persistence and (2) its direct role in contributing to genetically based reproductive isolation. We find indirect evidence that gene expression facilitates population persistence, but direct tests are lacking. We also find clear examples of gene expression having effects on phenotypic traits and adaptive genetic divergence, but links to the evolution of reproductive isolation itself remain indirect. Gene expression during adaptive divergence seems to often involve complex genetic architectures controlled by gene networks, regulatory regions, and “eQTL hotspots.” Nonetheless, we review how approaches for isolating the functional mutations contributing to adaptive divergence are proving to be successful. The study of gene expression has promise for increasing our understanding ecological speciation, particularly when integrative approaches are applied.
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Affiliation(s)
- Scott A Pavey
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
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29
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Anderson JT, Mitchell-Olds T. Ecological genetics and genomics of plant defenses: Evidence and approaches. Funct Ecol 2010; 25:312-324. [PMID: 21532968 DOI: 10.1111/j.1365-2435.2010.01785.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Herbivores exert significant selection on plants, and plants have evolved a variety of constitutive and inducible defenses to resist and tolerate herbivory. Assessing the genetic mechanisms that influence defenses against herbivores will deepen our understanding of the evolution of essential phenotypic traits.Ecogenomics is a powerful interdisciplinary approach that can address fundamental questions about the ecology and evolutionary biology of species, such as: which evolutionary forces maintain variation within a population? and What is the genetic architecture of adaptation? This field seeks to identify gene regions that influence ecologically-important traits, assess the fitness consequences under natural conditions of alleles at key quantitative trait loci (QTLs), and test how the abiotic and biotic environment affects gene expression.Here, we review ecogenomics techniques and emphasize how this framework can address long-standing and emerging questions relating to anti-herbivore defenses in plants. For example, ecogenomics tools can be used to investigate: inducible vs. constitutive defenses; tradeoffs between resistance and tolerance; adaptation to the local herbivore community; selection on alleles that confer resistance and tolerance in natural populations; and whether different genes are activated in response to specialist vs. generalist herbivores and to different types of damage.Ecogenomic studies can be conducted with model species, such as Arabidopsis, or their relatives, in which case myriad molecular tools are already available. Burgeoning sequence data will also facilitate ecogenomic studies of non-model species. Throughout this paper, we highlight approaches that are particularly suitable for ecological studies of non-model organisms, discuss the benefits and disadvantages of specific techniques, and review bioinformatic tools for analyzing data.We focus on established and promising techniques, such as QTL mapping with pedigreed populations, genome wide association studies, transcription profiling strategies, population genomics, and transgenic methodologies. Many of these techniques are complementary and can be used jointly to investigate the genetic architecture of defense traits and selection on alleles in nature.
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Affiliation(s)
- Jill T Anderson
- Institute for Genome Sciences and Policy, Department of Biology, Duke University, P.O. Box 90338, Durham, North Carolina 27708, USA
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30
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Li X, Wu HX, Southerton SG. Seasonal reorganization of the xylem transcriptome at different tree ages reveals novel insights into wood formation in Pinus radiata. THE NEW PHYTOLOGIST 2010; 187:764-76. [PMID: 20561208 DOI: 10.1111/j.1469-8137.2010.03333.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
*Seasonal wood development produces earlywood (EW) and latewood (LW) with distinct properties. The molecular mechanisms controlling EW and LW formation at different tree ages are poorly understood. *Seasonal reorganization of the xylem transcriptome was investigated in Pinus radiata at four tree ages using cDNA microarrays. Transcriptome profiles were compared with seasonal wood variation measured by SilviScan (CSIRO, Clayton, Australia). *The xylem transcriptome was considerably reorganized during seasonal change, and this reorganization showed a maturation-related pattern. The greater reorganization occurred at the transition (30%) and juvenile (21%) stages, but it declined with tree maturity (11-13%). However, this pattern does not correlate well with maturation-related patterns of seasonal wood variation. In total, 319 seasonal-responsive xylem candidate genes were identified. Many transcripts involved in primary and secondary wall biosynthesis were preferentially accumulated in EW and LW, respectively. A large proportion (45-81%) of the candidate genes are preferentially regulated at a single age and their transcript abundance may influence maturation-related patterns of seasonal wood variation. *Seasonal reorganization of the xylem transcriptome is significantly affected by tree age. Physiological changes at the transition stage may contribute to its greater seasonal transcriptome reorganization. Identified stage-preferential xylem transcripts could influence seasonal wood variation at different tree ages.
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Affiliation(s)
- Xinguo Li
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia.
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Chelaifa H, Mahé F, Ainouche M. Transcriptome divergence between the hexaploid salt-marsh sister species Spartina maritima and Spartina alterniflora (Poaceae). Mol Ecol 2010; 19:2050-63. [PMID: 20550634 DOI: 10.1111/j.1365-294x.2010.04637.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Invasive species are ideal model systems to investigate the evolutionary processes associated with their ecological success by comparison with closely related species. In this article, we explore transcriptome evolution following divergence between two closely related salt-marsh species, the invasive Spartina alterniflora (native to the East-American Atlantic coast, introduced in several continents) and the declining Spartina maritima (native to the Euro-African Atlantic coast). We have explored the utility of cross-species hybridization microarrays using rice (Oryza sativa) oligo-microarrays to compare leaf expression patterns between these species. Coding sequence comparisons from 10 nuclear genes (2256 bp) revealed that nucleotide divergence between Spartina and Oryza range from 8% to 14%. More than 70% of the 60-mer oligonucleotide sequences spotted on the rice microarray exhibited stable and repeatable patterns when hybridized against Spartina RNA. In total, 9353 (44.5%) genes on the array hybridized with both species S. maritima and S. alterniflora. Among these genes, 1247 genes were found to be differentially expressed between the two Spartina species, most of them (957) being up-regulated in S. alterniflora. In particular, developmental and cellular growth genes (gene ontology, biological process) were highly up-regulated in S. alterniflora and down-regulated in S. maritima, whereas genes involved in stress response were up-regulated in S. maritima. Our findings indicate the suitability of cross-species microarray hybridization between Spartina and O. sativa and reveal the extent of leaf transcriptome evolution that took place during the divergence between S. alterniflora and S. maritima. Expression patterns are consistent with the morphological differentiation and differential expansion of the two species.
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Affiliation(s)
- H Chelaifa
- UMR CNRS 6553 University of Rennes 1, Bât. 14A Campus de Beaulieu, 35 042 Rennes Cedex, France
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Polato NR, Voolstra CR, Schnetzer J, DeSalvo MK, Randall CJ, Szmant AM, Medina M, Baums IB. Location-specific responses to thermal stress in larvae of the reef-building coral Montastraea faveolata. PLoS One 2010; 5:e11221. [PMID: 20585643 PMCID: PMC2890407 DOI: 10.1371/journal.pone.0011221] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 05/16/2010] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The potential to adapt to a changing climate depends in part upon the standing genetic variation present in wild populations. In corals, the dispersive larval phase is particularly vulnerable to the effects of environmental stress. Larval survival and response to stress during dispersal and settlement will play a key role in the persistence of coral populations. METHODOLOGY/PRINCIPAL FINDINGS To test the hypothesis that larval transcription profiles reflect location-specific responses to thermal stress, symbiont-free gametes from three to four colonies of the scleractinian coral Montastraea faveolata were collected from Florida and Mexico, fertilized, and raised under mean and elevated (up 1 to 2 degrees C above summer mean) temperatures. These locations have been shown to exchange larvae frequently enough to prevent significant differentiation of neutral loci. Differences among 1,310 unigenes were simultaneously characterized using custom cDNA microarrays, allowing investigation of gene expression patterns among larvae generated from wild populations under stress. Results show both conserved and location-specific variation in key processes including apoptosis, cell structuring, adhesion and development, energy and protein metabolism, and response to stress, in embryos of a reef-building coral. CONCLUSIONS/SIGNIFICANCE These results provide first insights into location-specific variation in gene expression in the face of gene flow, and support the hypothesis that coral host genomes may house adaptive potential needed to deal with changing environmental conditions.
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Affiliation(s)
- Nicholas R. Polato
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Christian R. Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Julia Schnetzer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Michael K. DeSalvo
- School of Natural Sciences, University of California Merced, Merced, California, United States of America
| | - Carly J. Randall
- Center for Marine Sciences, University of North Carolina Wilmington, Wilmington, North Carolina, United States of America
| | - Alina M. Szmant
- Center for Marine Sciences, University of North Carolina Wilmington, Wilmington, North Carolina, United States of America
| | - Mónica Medina
- School of Natural Sciences, University of California Merced, Merced, California, United States of America
| | - Iliana B. Baums
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
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Fedorenkova A, Vonk JA, Lenders HJR, Ouborg NJ, Breure AM, Hendriks AJ. Ecotoxicogenomics: bridging the gap between genes and populations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:4328-4333. [PMID: 20459122 DOI: 10.1021/es9037287] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Ecotoxicogenomics might help solving open questions that cannot be answered by standard ecotoxicity tests currently used in environmental risk assessment. Changes in gene expression are claimed to serve potentially as early warning indicators for environmental effects and as sensitive and specific ecotoxicological end points. Ecotoxicogenomics focus on the lowest rather than the highest levels of biological organization. Our aim was to explore the links between gene expression responses and population level responses, both mechanistically (conceptual framework) and correlatively (Species Sensitivity Distribution). The effects of cadmium on aquatic species were compared for gene level responses (Lowest Observed Effect Concentrations) and individual level responses (median Lethal Concentrations, LC(50), and No Observed Effect Concentrations, NOEC). Responses in gene expression were on average four times above the NOEC and eleven times below the LC(50) values. Currently, use of gene expression changes as early warning indicators of environmental effects is not underpinned due to a lack of data. To confirm the sensitivity claimed by ecotoxicogenomics more testing at low concentrations is needed. From the conceptual framework, we conclude that for a mechanistic gene population link in risk management, research is required that includes at least one meaningful end point at each level of organization.
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Affiliation(s)
- Anastasia Fedorenkova
- Department of Environmental Science, Radboud University, Heyendaalseweg, AJ Nijmegen, The Netherlands.
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de Boer TE, Holmstrup M, van Straalen NM, Roelofs D. The effect of soil pH and temperature on Folsomia candida transcriptional regulation. JOURNAL OF INSECT PHYSIOLOGY 2010; 56:350-355. [PMID: 19931278 DOI: 10.1016/j.jinsphys.2009.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 11/05/2009] [Accepted: 11/10/2009] [Indexed: 05/28/2023]
Abstract
Differences in abiotic factors like temperature and soil pH can have a significant physiological impact on soil dwelling invertebrates and may confound results in ecotoxicological testing. In this study we exposed Folsomia candida to a range of two abiotic stress treatments (pH and temperature) for 3 days and measured gene expression of a panel of nine stress response genes with real-time Q-PCR. The exposure to different pH values had a minimal effect on the expression of the nine selected genes: only V-ATPase expression was significantly increased due to decreasing pH. ATPase expression was up-regulated, possibly due to increased proton trafficking across the cell membrane, at a lower pH. HSP70 was up-regulated in collembolans exposed to 30 degrees C, and along with HSP40 at 0 degrees C. We speculate that the minor pH effect on gene expression, compared to the temperature treatment, can be explained by the spatial restricted exposure to the external pH in the gut. Our data showed that only 1 or 2 stress response genes were transcriptionally affected by pH and temperature thus exerting minimal effects. The physiological effects of these treatments on F. candida might indicate interesting novel molecular mechanisms.
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Affiliation(s)
- Tjalf E de Boer
- Department of Ecological Sciences, VU University, de Boelelaan 1085, 1081 HV, Amsterdam, the Netherlands.
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Ouborg NJ, Pertoldi C, Loeschcke V, Bijlsma RK, Hedrick PW. Conservation genetics in transition to conservation genomics. Trends Genet 2010; 26:177-87. [PMID: 20227782 DOI: 10.1016/j.tig.2010.01.001] [Citation(s) in RCA: 216] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Revised: 01/03/2010] [Accepted: 01/04/2010] [Indexed: 11/16/2022]
Affiliation(s)
- N Joop Ouborg
- Molecular Ecology and Ecological Genomics Group, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands.
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Gotelli NJ, Ulrich W. The empirical Bayes approach as a tool to identify non-random species associations. Oecologia 2009; 162:463-77. [PMID: 19826839 DOI: 10.1007/s00442-009-1474-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Accepted: 09/18/2009] [Indexed: 11/25/2022]
Abstract
A statistical challenge in community ecology is to identify segregated and aggregated pairs of species from a binary presence-absence matrix, which often contains hundreds or thousands of such potential pairs. A similar challenge is found in genomics and proteomics, where the expression of thousands of genes in microarrays must be statistically analyzed. Here we adapt the empirical Bayes method to identify statistically significant species pairs in a binary presence-absence matrix. We evaluated the performance of a simple confidence interval, a sequential Bonferroni test, and two tests based on the mean and the confidence interval of an empirical Bayes method. Observed patterns were compared to patterns generated from null model randomizations that preserved matrix row and column totals. We evaluated these four methods with random matrices and also with random matrices that had been seeded with an additional segregated or aggregated species pair. The Bayes methods and Bonferroni corrections reduced the frequency of false-positive tests (type I error) in random matrices, but did not always correctly identify the non-random pair in a seeded matrix (type II error). All of the methods were vulnerable to identifying spurious secondary associations in the seeded matrices. When applied to a set of 272 published presence-absence matrices, even the most conservative tests indicated a fourfold increase in the frequency of perfectly segregated "checkerboard" species pairs compared to the null expectation, and a greater predominance of segregated versus aggregated species pairs. The tests did not reveal a large number of significant species pairs in the Vanuatu bird matrix, but in the much smaller Galapagos bird matrix they correctly identified a concentration of segregated species pairs in the genus Geospiza. The Bayesian methods provide for increased selectivity in identifying non-random species pairs, but the analyses will be most powerful if investigators can use a priori biological criteria to identify potential sets of interacting species.
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Affiliation(s)
- Nicholas J Gotelli
- Department of Biology, University of Vermont, Burlington, VT 05405, USA.
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STILLMAN JONATHONH, TAGMOUNT ABDERRAHMANE. Seasonal and latitudinal acclimatization of cardiac transcriptome responses to thermal stress in porcelain crabs, Petrolisthes cinctipes. Mol Ecol 2009; 18:4206-26. [DOI: 10.1111/j.1365-294x.2009.04354.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Bay LK, Nielsen HB, Jarmer H, Seneca F, van Oppen MJH. Transcriptomic variation in a coral reveals pathways of clonal organisation. Mar Genomics 2009; 2:119-25. [PMID: 21798180 DOI: 10.1016/j.margen.2009.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 07/21/2009] [Indexed: 11/18/2022]
Abstract
A microarray study was undertaken to examine the potential for clonal gene expression variation in a branching reef building coral, Acropora millepora. The role of small-scale gradients in light and water flow was examined by comparing gene expression levels between branch elevation (tip and base) and position (centre and edge) of replicate coral colonies (n=3). Analyses of variance revealed that almost 60% of variation in gene expression was present between colonies and 34 genes were considered differentially expressed between colonies (minimum P=6.5×10(-4)). These genes are associated with energy metabolism, protein biosynthesis and cell-cell recognition representing either genotypic variation in gene expression or the effects of specific environmental conditions that affect patterns of energy acquisition, growth and pathogen encounters. Less variation was present between central and peripheral branches (7%) and only a single gene was deemed differentially expressed (P=1.493×10(-3)). The function of this gene, a phosphatidylserine decarboxylase, suggests different growth patterns between branch positions within colonies and is consistent with the usual higher growth rates on the perimeter of corymbose-like branching coral colonies such as A. millepora. Four genes were differentially expressed between the tip and base of branches (P=3.239×10(-4)) and were associated with lysosome lipase activity and fluorescence, suggesting that branch tips may encounter higher pathogen loads or levels of mechanical stress and require greater levels of photo-protection associated with higher water flow and light levels. This study therefore confirms transcriptomic variation in response to small-scale environmental gradients consistent with differential resource allocation in clonal coral colonies.
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Affiliation(s)
- Line K Bay
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia; Australian Institute of Marine Science, PMB #3, Townsville MC, QLD 4810, Australia
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Bay LK, Ulstrup KE, Nielsen HB, Jarmer H, Goffard N, Willis BL, Miller DJ, Van Oppen MJH. Microarray analysis reveals transcriptional plasticity in the reef building coral Acropora millepora. Mol Ecol 2009; 18:3062-75. [PMID: 19538339 DOI: 10.1111/j.1365-294x.2009.04257.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We investigated variation in transcript abundance in the scleractinian coral, Acropora millepora, within and between populations characteristically exposed to different turbidity regimes and hence different levels of light and suspended particulate matter. We examined phenotypic plasticity by comparing levels of gene expression between source populations and following 10 days of acclimatization to a laboratory environment. Analyses of variance revealed that 0.05% of genes were differentially expressed between source populations, 1.32% following translocation into a common laboratory and 0.07% in the interaction (source population-dependent responses to translocation). Functional analyses identified an over-representation of differentially expressed genes associated with metabolism and fluorescence categories (primarily downregulated), and environmental information processing (primarily upregulated) following translocation to a lower light and turbidity environment. Such metabolic downregulation may indicate nonoxidative stress, hibernation or caloric restriction associated with the changed environmental conditions. Green fluorescent protein-related genes were the most differentially expressed and were exclusively downregulated; however, green fluorescent protein levels remained unchanged following translocation. Photophysiological responses of corals from both locations were characterized by a decline when introduced to the common laboratory environment but remained healthy (F(v)/F(m) > 0.6). Declines in total lipid content following translocation were the greatest for inshore corals, suggesting that turbid water corals have a strong reliance on heterotrophic feeding.
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Affiliation(s)
- Line K Bay
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld 4811, Australia
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Nevo E. Darwinian Evolution: Evolution in Action Across Life at "Evolution Canyon", Israel. Isr J Ecol Evol 2009. [DOI: 10.1560/ijee.55.3.215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Eviatar Nevo
- Institute of Evolution and the International Graduate School of Evolution, University of Haifa
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CLARKE AG. The Frozen Ark Project: the role of zoos and aquariums in preserving the genetic material of threatened animals. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1748-1090.2008.00074.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Systems toxicology: using the systems biology approach to assess chemical pollutants in the environment. COMPARATIVE TOXICOGENOMICS 2008. [DOI: 10.1016/s1872-2423(08)00007-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Affiliation(s)
- Oliver Bossdorf
- Department of Community Ecology, Helmholtz Centre for Environmental Research-UFZ, Theodor-Lieser-Str. 4, D-06120 Halle, Germany.
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Host–parasitoid interaction as affected by interkingdom competition. Oecologia 2007; 155:161-8. [DOI: 10.1007/s00442-007-0900-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Accepted: 10/15/2007] [Indexed: 10/22/2022]
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Kant MR, Baldwin IT. The ecogenetics and ecogenomics of plant-herbivore interactions: rapid progress on a slippery road. Curr Opin Genet Dev 2007; 17:519-24. [PMID: 17951047 DOI: 10.1016/j.gde.2007.09.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Revised: 08/24/2007] [Accepted: 09/03/2007] [Indexed: 10/22/2022]
Abstract
The -omics era has brought together two traditionally quite distinct disciplines in the study of plant-herbivore interactions: ecology and molecular biology. Microarrays, in particular, appeared to be the matchmakers between these, but proteomics and metabolomics also found roles to play. We show how they have dramatically enriched our appreciation of the massive metabolic reconfigurations that take place when herbivores eat plants and explain where they fall short in revealing how plants optimize the allocation of fitness-limiting resources among growth, defense, and tolerance responses while competing with other plants in nature. While the first offspring from this partnership between ecology and molecular biology searched for the 'master plan' of plant-herbivore interactions, the next generation now celebrates the diversity of outcomes that result from the co-evolutionary process.
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Affiliation(s)
- Merijn R Kant
- Department of Molecular Ecology, Max-Planck-Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll-Str 8, D-07745, Jena, Germany
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Paun O, Fay MF, Soltis DE, Chase MW. Genetic and epigenetic alterations after hybridization and genome doubling. TAXON 2007; 56:649-656. [PMID: 21082042 DOI: 10.2307/25065849] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Hybridization and polyploidization are now recognized as major phenomena in the evolution of plants, promoting genetic diversity, adaptive radiation and speciation. Modern molecular techniques have recently provided evidence that allopolyploidy can induce several types of genetic and epigenetic events that are of critical importance for the evolutionary success of hybrids: (1) chromosomal rearrangements within one or both parental genomes contribute toward proper meiotic pairing and isolation of the hybrid from its progenitors; (2) demethylation and activation of dormant transposable elements may trigger insertional mutagenesis and changes in local patterns of gene expression, facilitating rapid genomic reorganisation; (3) rapid and reproducible loss of low copy DNA sequence appears to result in further differentiation of homoeologous chromosomes; and (4) organ-specific up- or down-regulation of one of the duplicated genes, resulting in unequal expression or silencing one copy. All these alterations also have the potential, while stabilizing allopolyploid genomes, to produce novel expression patterns and new phenotypes, which together with increased heterozygosity and gene redundancy might confer on hybrids an elevated evolutionary potential, with effects at scales ranging from molecular to ecological. Although important advances have been made in understanding genomic responses to allopolyploidization, further insights are still expected to be gained in the near future, such as the direction and nature of the diploidization process, functional relevance of gene expression alterations, molecular mechanisms that result in adaptation to different ecologies/habitats, and ecological and evolutionary implications of recurrent polyploidization.
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Affiliation(s)
- Ovidiu Paun
- Molecular Systematics Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
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