51
|
Domestication and Temperature Modulate Gene Expression Signatures and Growth in the Australasian Snapper Chrysophrys auratus. G3-GENES GENOMES GENETICS 2019; 9:105-116. [PMID: 30591433 PMCID: PMC6325909 DOI: 10.1534/g3.118.200647] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Identifying genes and pathways involved in domestication is critical to understand how species change in response to human-induced selection pressures, such as increased temperatures. Given the profound influence of temperature on fish metabolism and organismal performance, a comparison of how temperature affects wild and domestic strains of snapper is an important question to address. We experimentally manipulated temperature conditions for F1-hatchery and wild Australasian snapper (Chrysophrys auratus) for 18 days to mimic seasonal extremes and measured differences in growth, white muscle RNA transcription and hematological parameters. Over 2.2 Gb paired-end reads were assembled de novo for a total set of 33,017 transcripts (N50 = 2,804). We found pronounced growth and gene expression differences between wild and domesticated individuals related to global developmental and immune pathways. Temperature-modulated growth responses were linked to major pathways affecting metabolism, cell regulation and signaling. This study is the first step toward gaining an understanding of the changes occurring in the early stages of domestication, and the mechanisms underlying thermal adaptation and associated growth in poikilothermic vertebrates. Our study further provides the first transcriptome resources for studying biological questions in this non-model fish species.
Collapse
|
52
|
Abstract
Genomics drives the current progress in molecular biology, generating unprecedented volumes of data. The scientific value of these sequences depends on the ability to evaluate their completeness using a biologically meaningful approach. Here, we describe the use of the BUSCO tool suite to assess the completeness of genomes, gene sets, and transcriptomes, using their gene content as a complementary method to common technical metrics. The chapter introduces the concept of universal single-copy genes, which underlies the BUSCO methodology, covers the basic requirements to set up the tool, and provides guidelines to properly design the analyses, run the assessments, and interpret and utilize the results.
Collapse
Affiliation(s)
- Mathieu Seppey
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Geneva, Switzerland
| | - Mosè Manni
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Geneva, Switzerland
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Geneva, Switzerland.
| |
Collapse
|
53
|
Richards DJ, Renaud L, Agarwal N, Starr Hazard E, Hyde J, Hardiman G. De Novo Hepatic Transcriptome Assembly and Systems Level Analysis of Three Species of Dietary Fish, Sardinops sagax, Scomber japonicus, and Pleuronichthys verticalis. Genes (Basel) 2018; 9:genes9110521. [PMID: 30366465 PMCID: PMC6266404 DOI: 10.3390/genes9110521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 10/17/2018] [Indexed: 12/31/2022] Open
Abstract
The monitoring of marine species as sentinels for ecosystem health has long been a valuable tool worldwide, providing insight into how both anthropogenic pollution and naturally occurring phenomena (i.e., harmful algal blooms) may lead to human and animal dietary concerns. The marine environments contain many contaminants of anthropogenic origin that have sufficient similarities to steroid and thyroid hormones, to potentially disrupt normal endocrine physiology in humans, fish, and other animals. An appropriate understanding of the effects of these endocrine disrupting chemicals (EDCs) on forage fish (e.g., sardine, anchovy, mackerel) can lead to significant insight into how these contaminants may affect local ecosystems in addition to their potential impacts on human health. With advancements in molecular tools (e.g., high-throughput sequencing, HTS), a genomics approach offers a robust toolkit to discover putative genetic biomarkers in fish exposed to these chemicals. However, the lack of available sequence information for non-model species has limited the development of these genomic toolkits. Using HTS and de novo assembly technology, the present study aimed to establish, for the first time for Sardinops sagax (Pacific sardine), Scomber japonicas (Pacific chub mackerel) and Pleuronichthys verticalis (hornyhead turbot), a de novo global transcriptome database of the liver, the primary organ involved in detoxification. The assembled transcriptomes provide a foundation for further downstream validation, comparative genomic analysis and biomarker development for future applications in ecotoxicogenomic studies, as well as environmental evaluation (e.g., climate change) and public health safety (e.g., dietary screening).
Collapse
Affiliation(s)
- Dylan J Richards
- Bioengineering Department, Clemson University, Charleston, SC 29425, USA.
| | - Ludivine Renaud
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA.
- Center for Genomic Medicine, Bioinformatics, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Nisha Agarwal
- Biomedical Informatics Research Center, San Diego State University, San Diego, CA 92182, USA.
| | - E Starr Hazard
- Center for Genomic Medicine, Bioinformatics, Medical University of South Carolina, Charleston, SC 29425, USA.
- Academic Affairs Faculty & Computational Biology Resource Center, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - John Hyde
- NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, CA 92037, USA.
| | - Gary Hardiman
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA.
- Center for Genomic Medicine, Bioinformatics, Medical University of South Carolina, Charleston, SC 29425, USA.
- Biomedical Informatics Research Center, San Diego State University, San Diego, CA 92182, USA.
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
- Laboratory for Marine Systems Biology, Hollings Marine Laboratory, Charleston, SC 29412, USA.
- School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Stranmillis Road, Belfast BT9 5AG, UK.
| |
Collapse
|
54
|
Carruthers M, Yurchenko AA, Augley JJ, Adams CE, Herzyk P, Elmer KR. Correction to: De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species. BMC Genomics 2018; 19:448. [PMID: 29890942 PMCID: PMC5994836 DOI: 10.1186/s12864-018-4840-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 05/30/2018] [Indexed: 11/18/2022] Open
Affiliation(s)
- Madeleine Carruthers
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, Glasgow, UK
| | - Andrey A Yurchenko
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, Glasgow, UK
| | - Julian J Augley
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, G61 1QH, Glasgow, UK.,Present Address: Fios Genomics Ltd., Nine Edinburgh Bioquarter, 9 Little France Road, Edinburgh, EH16 4UX, UK
| | - Colin E Adams
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, Glasgow, UK.,Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, G63 0AW, UK
| | - Pawel Herzyk
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, G61 1QH, Glasgow, UK.,Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, Glasgow, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, Glasgow, UK.
| |
Collapse
|