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Ding K, Xu Q, Zhao L, Li Y, Li Z, Shi W, Zeng Q, Wang X, Zhang X. Chromosome-level genome provides insights into environmental adaptability and innate immunity in the common dolphin (delphinus delphis). BMC Genomics 2024; 25:373. [PMID: 38627659 PMCID: PMC11022445 DOI: 10.1186/s12864-024-10268-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/28/2024] [Indexed: 04/19/2024] Open
Abstract
The common dolphin (Delphinus delphis) is widely distributed worldwide and well adapted to various habitats. Animal genomes store clues about their pasts, and can reveal the genes underlying their evolutionary success. Here, we report the first high-quality chromosome-level genome of D. delphis. The assembled genome size was 2.56 Gb with a contig N50 of 63.85 Mb. Phylogenetically, D. delphis was close to Tursiops truncatus and T. aduncus. The genome of D. delphis exhibited 428 expanded and 1,885 contracted gene families, and 120 genes were identified as positively selected. The expansion of the HSP70 gene family suggested that D. delphis has a powerful system for buffering stress, which might be associated with its broad adaptability, longevity, and detoxification capacity. The expanded IFN-α and IFN-ω gene families, as well as the positively selected genes encoding tripartite motif-containing protein 25, peptidyl-prolyl cis-trans isomerase NIMA-interacting 1, and p38 MAP kinase, were all involved in pathways for antiviral, anti-inflammatory, and antineoplastic mechanisms. The genome data also revealed dramatic fluctuations in the effective population size during the Pleistocene. Overall, the high-quality genome assembly and annotation represent significant molecular resources for ecological and evolutionary studies of Delphinus and help support their sustainable treatment and conservation.
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Affiliation(s)
- Kui Ding
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Qinzeng Xu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Liyuan Zhao
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Yixuan Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Zhong Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Wenge Shi
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Qianhui Zeng
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xianyan Wang
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
| | - Xuelei Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China.
- National Engineering Laboratory for Integrated Aero-Space-Ground-Ocean Big Data Application Technology, Xi'an, China.
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2
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Transcriptome profiling of blood from common bottlenose dolphins (Tursiops truncatus) in the northern Gulf of Mexico to enhance health assessment capabilities. PLoS One 2022; 17:e0272345. [PMID: 36001538 PMCID: PMC9401185 DOI: 10.1371/journal.pone.0272345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 07/18/2022] [Indexed: 12/01/2022] Open
Abstract
Following the 2010 Deepwater Horizon disaster and subsequent unusual mortality event, adverse health impacts have been reported in bottlenose dolphins in Barataria Bay, LA including impaired stress response and reproductive, pulmonary, cardiac, and immune function. These conditions were primarily diagnosed through hands-on veterinary examinations and analysis of standard diagnostic panels. In human and veterinary medicine, gene expression profiling has been used to identify molecular mechanisms underlying toxic responses and disease states. Identification of molecular markers of exposure or disease may enable earlier detection of health effects or allow for health evaluation when the use of specialized methodologies is not feasible. To date this powerful tool has not been applied to augment the veterinary data collected concurrently during dolphin health assessments. This study examined transcriptomic profiles of blood from 76 dolphins sampled in health assessments during 2013–2018 in the waters near Barataria Bay, LA and Sarasota Bay, FL. Gene expression was analyzed in conjunction with the substantial suite of health data collected using principal component analysis, differential expression testing, over-representation analysis, and weighted gene co-expression network analysis. Broadly, transcript profiles of Barataria Bay dolphins indicated a shift in immune response, cytoskeletal alterations, and mitochondrial dysfunction, most pronounced in dolphins likely exposed to Deepwater Horizon oiling. While gene expression profiles in Barataria Bay dolphins were altered compared to Sarasota Bay for all years, profiles from 2013 exhibited the greatest alteration in gene expression. Differentially expressed transcripts included genes involved in immunity, inflammation, reproductive failure, and lung or cardiac dysfunction, all of which have been documented in dolphins from Barataria Bay following the Deepwater Horizon oil spill. The genes and pathways identified in this study may, with additional research and validation, prove useful as molecular markers of exposure or disease to assist wildlife veterinarians in evaluating the health of dolphins and other cetaceans.
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3
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Sundaray JK, Dixit S, Rather A, Rasal KD, Sahoo L. Aquaculture omics: An update on the current status of research and data analysis. Mar Genomics 2022; 64:100967. [PMID: 35779450 DOI: 10.1016/j.margen.2022.100967] [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: 06/17/2021] [Revised: 05/26/2022] [Accepted: 06/15/2022] [Indexed: 11/28/2022]
Abstract
Aquaculture is the fast-growing agricultural sector and has the ability to meet the growing demand for protein nutritional security for future population. In future aquaculture is going to be the major source of fish proteins as capture fisheries reached at its maximum. However, several challenges need to overcome such as lack of genetically improved strains/varieties, lack of species-specific feed/functional feed, round the year availability of quality fish seed, pollution of ecosystems and increased frequencies of disease occurrence etc. In recent years, the continuous development of high throughput sequencing technology has revolutionized the biological sciences and provided necessary tools. Application of 'omics' in aquaculture research have been successfully used to resolve several productive and reproductive issues and thus ensure its sustainability and profitability. To date, high quality draft genomes of over fifty fish species have been generated and successfully used to develop large number of single nucleotide polymorphism markers (SNPs), marker panels and other genomic resources etc in several aquaculture species. Similarly, transcriptome profiling and miRNAs analysis have been used in aquaculture research to identify key transcripts and expression analysis of candidate genes/miRNAs involved in reproduction, immunity, growth, development, stress toxicology and disease. Metagenome analysis emerged as a promising scientific tool to analyze the complex genomes contained within microbial communities. Metagenomics has been successfully used in the aquaculture sector to identify novel and potential pathogens, antibiotic resistance genes, microbial roles in microcosms, microbial communities forming biofloc, probiotics etc. In the current review, we discussed application of high-throughput technologies (NGS) in the aquaculture sector.
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Affiliation(s)
- Jitendra Kumar Sundaray
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India
| | - Sangita Dixit
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan University (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Ashraf Rather
- Division of Fish Genetics and Biotechnology, College of Fisheries, Sher-e- Kashmir University of Agricultural Science and Technology, Rangil-Ganderbal 190006, Jammu and Kashmir, India
| | - Kiran D Rasal
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai 400 061, Maharastra, India
| | - Lakshman Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India.
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The Landscape of Genome-Wide and Gender-Specific Microsatellites in Indo-Pacific Humpback Dolphin and Potential Applications in Cetacean Resource Investigation. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10060834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microsatellites are one of the important genome characterizations that can be a valuable resource for variety identification, genetic diversity, phylogenetic analysis, as well as comparative and conservation genomics research. Here, we developed comprehensive microsatellites through genome-wide mining for the threatened cetacean Indo-Pacific humpback dolphin (Sousa chinensis). We found 87,757 microsatellites with 2–6 bp nucleotide motifs, showing that about 32.5 microsatellites per megabase comprises microsatellites sequences. Approximately 97.8% of the markers developed in this study were consistent with the published identified markers. About 75.3% microsatellites were with dinucleotide motifs, followed by tetranucleotide motifs (17.4%), sharing the same composition pattern as other cetaceans. The microsatellites were not evenly distributed in the S. chinensis genome, mainly in non-coding regions, with only about 0.5% of the markers located in coding regions. The microsatellite-containing genes were mainly functionally enriched in the methylation process, probably demonstrating the potential impacts of microsatellites on biological functions. Polymorphic microsatellites were developed between different genders of S. chinensis, which was expected to lay the foundation for genetic diversity investigation in cetaceans. The specific markers for a male Indo-Pacific humpback dolphin will provide comprehensive and representative male candidate markers for sex identification, providing a potential biomolecular tool for further analysis of population structure and social behavior of wild populations, population trend evaluation, and species conservation management.
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Dai Y, Sakornwimon W, Chantra R, Zhao L, Wu F, Aierken R, Kittiwattanawong K, Wang X. High genetic differentiation of Indo‐Pacific humpback dolphins (
Sousa chinensis
) along the Asian Coast of the Pacific Ocean. Ecol Evol 2022; 12:e8901. [PMID: 35571759 PMCID: PMC9077734 DOI: 10.1002/ece3.8901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Yufei Dai
- Laboratory of Marine Biology and Ecology Third Institute of Oceanography Ministry of Natural Resources Xiamen China
- Key Laboratory of Marine Ecological Conservation and Restoration Ministry of Natural Resources Xiamen China
- Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration Xiamen China
| | - Watchara Sakornwimon
- Marine and Coastal Resources Research Center The Central Gulf of Thailand Chumphon Thailand
| | - Rachawadee Chantra
- Marine and Coastal Resources Research Center The Upper Gulf of Thailand Samut Sakhon Thailand
| | - Liyuan Zhao
- Laboratory of Marine Biology and Ecology Third Institute of Oceanography Ministry of Natural Resources Xiamen China
- Key Laboratory of Marine Ecological Conservation and Restoration Ministry of Natural Resources Xiamen China
- Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration Xiamen China
| | - Fuxing Wu
- Laboratory of Marine Biology and Ecology Third Institute of Oceanography Ministry of Natural Resources Xiamen China
- Key Laboratory of Marine Ecological Conservation and Restoration Ministry of Natural Resources Xiamen China
- Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration Xiamen China
| | - Reyilamu Aierken
- Laboratory of Marine Biology and Ecology Third Institute of Oceanography Ministry of Natural Resources Xiamen China
| | | | - Xianyan Wang
- Laboratory of Marine Biology and Ecology Third Institute of Oceanography Ministry of Natural Resources Xiamen China
- Key Laboratory of Marine Ecological Conservation and Restoration Ministry of Natural Resources Xiamen China
- Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration Xiamen China
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Aciole Barbosa D, Araújo BC, Branco GS, Simeone AS, Hilsdorf AWS, Jabes DL, Nunes LR, Moreira RG, Menegidio FB. Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:255-262. [PMID: 34855031 DOI: 10.1007/s10126-021-10081-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
Cobia (Rachycentron canadum) is a marine teleost species with great productive potential worldwide. However, the genomic information currently available for this species in public databases is limited. Such lack of information hinders gene expression assessments that might bring forward novel insights into the physiology, ecology, evolution, and genetics of this potential aquaculture species. In this study, we report the first de novo transcriptome assembly of R. canadum liver, improving the availability of novel gene sequences for this species. Illumina sequencing of liver transcripts generated 1,761,965,794 raw reads, which were filtered into 1,652,319,304 high-quality reads. De novo assembly resulted in 101,789 unigenes and 163,096 isoforms, with an average length of 950.61 and 1,617.34 nt, respectively. Moreover, we found that 126,013 of these transcripts bear potentially coding sequences, and 125,993 of these elements (77.3%) correspond to functionally annotated genes found in six different databases. We also identified 701 putative ncRNA and 35,414 putative lncRNA. Interestingly, homologues for 410 of these putative lncRNAs have already been observed in previous analyses with Danio rerio, Lates calcarifer, Seriola lalandi dorsalis, Seriola dumerili, or Echeneis naucrates. Finally, we identified 7894 microsatellites related to cobia's putative lncRNAs. Thus, the information derived from the transcriptome assembly described herein will likely assist future nutrigenomics and breeding programs involving this important fish farming species.
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Affiliation(s)
- David Aciole Barbosa
- Center of Biotechnology, University of Mogi das Cruzes, Av. Dr. Cândido X. de Almeida e Souza, 200 - Centro Cívico, Mogi das Cruzes, SP, 08780-911, Brazil
| | | | - Giovana Souza Branco
- Department of Physiology, Bioscience Institute, University of São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Alexandre S Simeone
- Center of Biotechnology, University of Mogi das Cruzes, Av. Dr. Cândido X. de Almeida e Souza, 200 - Centro Cívico, Mogi das Cruzes, SP, 08780-911, Brazil
| | - Alexandre W S Hilsdorf
- Center of Biotechnology, University of Mogi das Cruzes, Av. Dr. Cândido X. de Almeida e Souza, 200 - Centro Cívico, Mogi das Cruzes, SP, 08780-911, Brazil
| | - Daniela L Jabes
- Center of Biotechnology, University of Mogi das Cruzes, Av. Dr. Cândido X. de Almeida e Souza, 200 - Centro Cívico, Mogi das Cruzes, SP, 08780-911, Brazil
| | - Luiz R Nunes
- Center for Natural and Human Sciences, Federal University of ABC, Santo André, SP, 09210-580, Brazil
| | - Renata G Moreira
- Department of Physiology, Bioscience Institute, University of São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Fabiano B Menegidio
- Center of Biotechnology, University of Mogi das Cruzes, Av. Dr. Cândido X. de Almeida e Souza, 200 - Centro Cívico, Mogi das Cruzes, SP, 08780-911, Brazil.
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7
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Batley KC, Sandoval-Castillo J, Kemper CM, Zanardo N, Tomo I, Beheregaray LB, Möller LM. Whole genomes reveal multiple candidate genes and pathways involved in the immune response of dolphins to a highly infectious virus. Mol Ecol 2021; 30:6434-6448. [PMID: 33675577 DOI: 10.1111/mec.15873] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/11/2021] [Accepted: 02/22/2021] [Indexed: 01/02/2023]
Abstract
Wildlife species are challenged by various infectious diseases that act as important demographic drivers of populations and have become a great conservation concern particularly under growing environmental changes. The new era of whole genome sequencing provides new opportunities and avenues to explore the role of genetic variants in the plasticity of immune responses, particularly in non-model systems. Cetacean morbillivirus (CeMV) has emerged as a major viral threat to cetacean populations worldwide, contributing to the death of thousands of individuals of multiple dolphin and whale species. To understand the genomic basis of immune responses to CeMV, we generated and analysed whole genomes of 53 Indo-Pacific bottlenose dolphins (Tursiops aduncus) exposed to Australia's largest known CeMV-related mortality event that killed at least 50 dolphins from three different species. The genomic data set consisted of 10,168,981 SNPs anchored onto 23 chromosome-length scaffolds and 77 short scaffolds. Whole genome analysis indicated that levels of inbreeding in the dolphin population did not influence the outcome of an individual. Allele frequency estimates between survivors and nonsurvivors of the outbreak revealed 15,769 candidate SNPs, of which 689 were annotated to 295 protein coding genes. These included 50 genes with functions related to innate and adaptive immune responses, and cytokine signalling pathways and genes thought to be involved in immune responses to other morbilliviruses. Our study characterised genomic regions and pathways that may contribute to CeMV immune responses in dolphins. This represents a stride towards clarifying the complex interactions of the cetacean immune system and emphasises the value of whole genome data sets in understanding genetic elements that are essential for species conservation, including disease susceptibility and adaptation.
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Affiliation(s)
- Kimberley C Batley
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.,Cetacean Ecology, Behaviour, and Evolution Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | | | - Nikki Zanardo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.,Cetacean Ecology, Behaviour, and Evolution Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Ikuko Tomo
- South Australian Museum, Adelaide, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Luciana M Möller
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.,Cetacean Ecology, Behaviour, and Evolution Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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8
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Integrated Full-Length Transcriptome and RNA-Seq to Identify Immune System Genes from the Skin of Sperm Whale ( Physeter macrocephalus). Genes (Basel) 2021; 12:genes12020233. [PMID: 33562637 PMCID: PMC7914425 DOI: 10.3390/genes12020233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/22/2022] Open
Abstract
Cetaceans are a group of secondary aquatic mammals whose ancestors returned to the ocean from land, and during evolution, their immune systems adapted to the aquatic environment. Their skin, as the primary barrier to environmental pathogens, supposedly evolved to adapt to a new living environment. However, the immune system in the skin of cetaceans and the associated molecular mechanisms are still largely unknown. To better understand the immune system, we extracted RNA from the sperm whale's (Physeter macrocephalus) skin and performed PacBio full-length sequencing and RNA-seq sequencing. We obtained a total of 96,350 full-length transcripts with an average length of 1705 bp and detected 5150 genes that were associated with 21 immune-related pathways by gene annotation enrichment analysis. Moreover, we found 89 encoding genes corresponding to 33 proteins were annotated in the NOD-like receptor (NLR)-signaling pathway, including NOD1, NOD2, RIP2, and NF-kB genes, which were discussed in detail and predicted to play essential roles in the immune system of the sperm whale. Furthermore, NOD1 was highly conservative during evolution by the sequence comparison and phylogenetic tree. These results provide new information about the immune system in the skin of cetaceans, as well as the evolution of immune-related genes.
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McGowen MR, Tsagkogeorga G, Álvarez-Carretero S, Dos Reis M, Struebig M, Deaville R, Jepson PD, Jarman S, Polanowski A, Morin PA, Rossiter SJ. Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture. Syst Biol 2020; 69:479-501. [PMID: 31633766 PMCID: PMC7164366 DOI: 10.1093/sysbio/syz068] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 10/02/2019] [Accepted: 10/06/2019] [Indexed: 12/20/2022] Open
Abstract
The evolution of cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, although the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for \documentclass[12pt]{minimal}
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}{}$\sim $\end{document}3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from \documentclass[12pt]{minimal}
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}{}$>$\end{document}38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic data set for cetaceans, spanning 6,527,596 aligned base pairs (bp) and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among oceanic dolphins, especially the problematic subfamily Delphinidae. We carried out Bayesian estimation of species divergence times using MCMCTree and compared our complete data set to a subset of clocklike genes. Analyses using the complete data set consistently showed less variance in divergence times than the reduced data set. In addition, integration of new fossils (e.g., Mystacodon selenensis) indicates that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene. [Cetaceans; phylogenomics; Delphinidae; Ziphiidae; dolphins; whales.]
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Affiliation(s)
- Michael R McGowen
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.,Department of Vertebrate Zoology, Smithsonian Museum of Natural History, 10th & Constitution Ave. NW, Washington DC 20560, USA
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Sandra Álvarez-Carretero
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Monika Struebig
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Robert Deaville
- Institute of Zoology, Zoological Society of London, Outer Circle, London NW1 4RY, UK
| | - Paul D Jepson
- Institute of Zoology, Zoological Society of London, Outer Circle, London NW1 4RY, UK
| | - Simon Jarman
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Perth WA 6009, Australia
| | - Andrea Polanowski
- Australian Antarctic Division, 203 Channel Highway, Kingston TAS 7050, Australia
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla CA 92037 USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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10
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Kang M, Ahn B, Yum J, Cho H, Choi M, Hong K, Choi Y, Kim J, Park C. Influence of habitat change from land to sea on the evolution of antimicrobial peptide gene families, including
β‐defensin
gene clusters, in mammals. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mingue Kang
- Department of Stem Cell and Regenerative Biotechnology Konkuk University Seoul South Korea
| | - Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology Konkuk University Seoul South Korea
| | - Joori Yum
- Department of Stem Cell and Regenerative Biotechnology Konkuk University Seoul South Korea
| | - Hye‐sun Cho
- Department of Stem Cell and Regenerative Biotechnology Konkuk University Seoul South Korea
| | - Munjeong Choi
- Department of Stem Cell and Regenerative Biotechnology Konkuk University Seoul South Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology Konkuk University Seoul South Korea
| | - Youngsok Choi
- Department of Stem Cell and Regenerative Biotechnology Konkuk University Seoul South Korea
| | - Jin‐Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology Konkuk University Seoul South Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology Konkuk University Seoul South Korea
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11
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Tian R, Seim I, Zhang Z, Yang Y, Ren W, Xu S, Yang G. Distinct evolution of toll-like receptor signaling pathway genes in cetaceans. Genes Genomics 2019; 41:1417-1430. [PMID: 31535317 DOI: 10.1007/s13258-019-00861-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/19/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND The relatively rapid spread and diversity of marine pathogens posed an initial and ongoing challenge for cetaceans (whales, dolphins, and porpoises), descendants of terrestrial mammals that transitioned from land to sea approximately 56 million years ago. Toll-like receptors (TLRs) play important roles in regulating immunity against pathogen infections by detecting specific molecular patterns and activating a wide range of downstream signaling pathways. The ever-increasing catalogue of mammalian genomes offers unprecedented opportunities to reveal genetic changes associated with evolutionary and ecological processes. OBJECTIVE This study aimed to explore the molecular evolution of TLR signaling pathway genes in cetaceans. METHODS Genes involved in the TLR signaling pathway were retrieved by BLAST searches using human coding sequences as queries. We tested each gene for positive selection along the cetacean branches using PAML and Hyphy. Physicochemical property changes of amino acids at all positively selected residues were assessed by TreeSAAP and visualized with WebLogo. Bovine and dolphin TLR4 was assessed using human embryonic kidney cell line HEK293, which lacks TLR4 and its co-receptor MD-2. RESULTS We demonstrate that eight TLR signaling pathway genes are under positive selection in cetaceans. These include key genes in the response to Gram-negative bacteria: TLR4, CD14, and LY96 (MD-2). Moreover, 41 out of 65 positively selected sites were inferred to harbor substitution that dramatically changes the physicochemical properties of amino acids, with most of them situated in or adjacent to functional regions. We also found strong evidence that positive selection occurred in the lineage of the Yangtze finless porpoise, likely reflecting relatively recent adaptions to a freshwater milieu. Species-specific differences in TLR4 response were observed between cetacean and terrestrial species. Cetacean TLR4 was significantly less responsive to lipopolysaccharides from a terrestrial E. coli strain, possibly a reflection of the arms race of host-pathogen co-evolution faced by cetaceans in an aquatic environment. CONCLUSION This study provides further impetus for studies on the evolution and function of the cetacean immune system.
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Affiliation(s)
- Ran Tian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.,Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.,Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Zepeng Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Ying Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Wenhua Ren
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.
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12
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Whole Genome Sequencing of Chinese White Dolphin ( Sousa chinensis) for High-Throughput Screening of Antihypertensive Peptides. Mar Drugs 2019; 17:md17090504. [PMID: 31466310 PMCID: PMC6780146 DOI: 10.3390/md17090504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/16/2019] [Accepted: 08/26/2019] [Indexed: 01/17/2023] Open
Abstract
Chinese white dolphin (Sousa chinensis), also known as the Indo-Pacific humpback dolphin, has been classified as “Vulnerable” on the IUCN Red List of Threatened Species. It is a special cetacean species that lives in tropical and subtropical nearshore waters, with significant differences from other cetaceans. Here, we sequenced and assembled a draft genome of the Chinese white dolphin with a total length of 2.3 Gb and annotation of 18,387 protein-coding genes. Genes from certain expanded families are potentially involved in DNA replication and repairing, suggesting that they may be related to adaptation of this marine mammal to nearshore environments. We also discovered that its historical population had undergone a remarkable bottleneck incident before the Mindel glaciation. In addition, a comparative genomic survey on antihypertensive peptides (AHTPs) among five representative mammals with various residential habitats (such as remarkable differences in exogenous ion concentrations and sea depth) revealed that these small bioactive peptides were highly conserved among these examined mammals, and they had the most abundant hits in collagen subunit proteins, especially for two putative AHTP peptides Gly-Leu-Pro (GLP) and Leu-Gly-Pro (LGP). Our genome assembly will be a valuable resource for further genetic researches on adaptive ecology and conservation biology of cetaceans, and for in-depth investigations into bioactive peptides in aquatic and terrestrial mammals for development of peptide-based drugs to treat various human cardiovascular diseases.
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Ming Y, Jian J, Yu X, Wang J, Liu W. The genome resources for conservation of Indo-Pacific humpback dolphin, Sousa chinensis. Sci Data 2019; 6:68. [PMID: 31118413 PMCID: PMC6531461 DOI: 10.1038/s41597-019-0078-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/16/2019] [Indexed: 11/24/2022] Open
Abstract
The Indo-Pacific humpback dolphin (Sousa chinensis), is a threatened marine mammal and belongs to the First Order of the National Key Protected Wild Aquatic Animals List in China. However, limited genomic information is available for studies of its population genetics and biological conservation. Here, we have assembled a genomic sequence of this species using a whole genome shotgun (WGS) sequencing strategy after a pilot low coverage genome survey. The total assembled genome size was 2.34 Gb: with a contig N50 of 67 kb and a scaffold N50 of 9 Mb (107.6-fold sequencing coverage). The S. chinensis genome contained 24,640 predicted protein-coding genes and had approximately 37% repeated sequences. The completeness of the genome assembly was evaluated by benchmarking universal single copy orthologous genes (BUSCOs): 94.3% of a total 4,104 expected mammalian genes were identified as complete, and 2.3% were identified as fragmented. This newly produced high-quality assembly and annotation of the genome will greatly promote the future studies of the genetic diversity, conservation and evolution.
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Affiliation(s)
- Yao Ming
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Jianbo Jian
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Xueying Yu
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, Guangxi, 535011, P.R. China
| | - Jingzhen Wang
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, Guangxi, 535011, P.R. China.
| | - Wenhua Liu
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China.
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14
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Xiang Y, Jia P, Liu W, Yi M, Jia K. Comparative transcriptome analysis reveals the role of p53 signalling pathway during red-spotted grouper nervous necrosis virus infection in Lateolabrax japonicus brain cells. JOURNAL OF FISH DISEASES 2019; 42:585-595. [PMID: 30659619 PMCID: PMC7166548 DOI: 10.1111/jfd.12960] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/22/2018] [Accepted: 12/23/2018] [Indexed: 05/10/2023]
Abstract
Nervous necrosis virus (NNV) is one of the fish pathogens that have caused mass mortalities of many marine and freshwater fishes in the world. To better comprehend the molecular immune mechanism of sea perch (Lateolabrax japonicus) against NNV infection, the comparative transcriptome analysis of red-spotted grouper nervous necrosis virus (RGNNV)-infected or mock-infected L. japonicus brain (LJB) cells was performed via RNA sequencing technology. Here, 1,969 up-regulated genes and 9,858 down-regulated genes, which were widely implicated in immune response pathways, were identified. Furthermore, we confirmed that p53 signalling pathway was repressed at 48 hr post-RGNNV infection, as indicated by up-regulation of Mdm2 and down-regulation of p53 and its downstream target genes, including Bax, Casp8 and CytC. Overexpression of L. japonicus p53 (Ljp53) significantly inhibited RGNNV replication and up-regulated the expression of apoptosis-related genes, whereas the down-regulation caused by pifithrin-α led to the opposite effect, suggesting Ljp53 might promote cell apoptosis to repress virus replication. Luciferase assay indicated that Ljp53 could enhance the promoter activities of zebrafish interferon (IFN)1, indicating that Ljp53 could exert its anti-RGNNV activities by enforcing the type I IFN response. This study revealed the potential antiviral role of p53 during NNV infection.
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Affiliation(s)
- Yangxi Xiang
- School of Marine SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
- Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai)ZhuhaiGuangdongChina
- Zhuhai Key Laboratory of Marine Bioresources and EnvironmentSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Peng Jia
- School of Marine SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
- Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai)ZhuhaiGuangdongChina
- Zhuhai Key Laboratory of Marine Bioresources and EnvironmentSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Wei Liu
- School of Marine SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
- Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai)ZhuhaiGuangdongChina
- Zhuhai Key Laboratory of Marine Bioresources and EnvironmentSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Meisheng Yi
- School of Marine SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
- Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai)ZhuhaiGuangdongChina
- Zhuhai Key Laboratory of Marine Bioresources and EnvironmentSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Kuntong Jia
- School of Marine SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
- Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai)ZhuhaiGuangdongChina
- Zhuhai Key Laboratory of Marine Bioresources and EnvironmentSun Yat‐sen UniversityGuangzhouGuangdongChina
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15
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Autenrieth M, Hartmann S, Lah L, Roos A, Dennis AB, Tiedemann R. High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena). Mol Ecol Resour 2018; 18:1469-1481. [PMID: 30035363 DOI: 10.1111/1755-0998.12932] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 11/27/2022]
Abstract
The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation.
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Affiliation(s)
- Marijke Autenrieth
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
| | - Ljerka Lah
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Anna Roos
- Swedish Museum of Natural History, Stockholm, Sweden
| | - Alice B Dennis
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
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16
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Sanganyado E, Rajput IR, Liu W. Bioaccumulation of organic pollutants in Indo-Pacific humpback dolphin: A review on current knowledge and future prospects. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 237:111-125. [PMID: 29477865 DOI: 10.1016/j.envpol.2018.01.055] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/21/2017] [Accepted: 01/17/2018] [Indexed: 06/08/2023]
Abstract
Indo-Pacific humpback dolphin (Sousa chinensis) are chronically exposed to organic pollutants since they inhabit shallow coastal waters that are often impacted by anthropogenic activities. The aim of this review was to evaluate existing knowledge on the occurrence of organic pollutants in Indo-Pacific humpback dolphins, identify knowledge gaps, and offer recommendations for future research directions. We discussed the trends in the bioaccumulation of organic pollutants in Indo-Pacific humpback dolphins focusing on sources, physicochemical properties, and usage patterns. Furthermore, we examined factors that influence bioaccumulation such as gender, age, dietary intake and tissue-specific distribution. Studies on bioaccumulation in Indo-Pacific humpback dolphin remain scarce, despite high concentrations above 13,000 ng/g lw we previously detected for PFOS, ∑PBDE and chlorinated paraffins. The maximum concentration of organochlorines detected was 157,000 ng/g wt. Furthermore, variations in bioaccumulation were shown to be caused by factors such as usage patterns and physicochemical properties of the pollutant. However, restrictions in sampling inhibit investigations on exposure pathway and toxicity of organic pollutants in Indo-Pacific humpback dolphin. We proposed the use of biopsy sampling, predictive bioaccumulation and toxicity modeling, and monitoring other emerging contaminants such as microplastics and pharmaceuticals for future health risk assessment on this critically endangered marine mammal species.
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Affiliation(s)
- Edmond Sanganyado
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China
| | - Imran Rashid Rajput
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China
| | - Wenhua Liu
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China.
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17
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Abstract
Omics technologies have been developed in recent decades and applied to different subjects, although the greatest advancements have been achieved in human biology and disease. Genome sequencing and the exploration of its coding and noncoding regions are rapidly yielding meaningful answers to diverse questions, relating genome information to protein activity to environmental changes. In the past, marine mammal genetic and transcriptional studies have been restricted due to the lack of reference genomes. But the advance of high-throughput sequencing is revolutionizing the life sciences technologies. As long-lived organisms, at the top of the food chain, marine mammals play an important role in marine ecosystems and while their protected status is in favor of conservation of the species, it also complicates the researcher's approach to traditional measurements of health. Omics data generated by high-throughput technologies will represent an important key for improving the scientific basis for understanding both marine mammal and environment health.
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18
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Morey JS, Burek Huntington KA, Campbell M, Clauss TM, Goertz CE, Hobbs RC, Lunardi D, Moors AJ, Neely MG, Schwacke LH, Van Dolah FM. De novo transcriptome assembly and RNA-Seq expression analysis in blood from beluga whales of Bristol Bay, AK. Mar Genomics 2017; 35:77-92. [PMID: 28802692 DOI: 10.1016/j.margen.2017.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/01/2017] [Accepted: 08/02/2017] [Indexed: 11/18/2022]
Abstract
Assessing the health of marine mammal sentinel species is crucial to understanding the impacts of environmental perturbations on marine ecosystems and human health. In Arctic regions, beluga whales, Delphinapterus leucas, are upper level predators that may serve as a sentinel species, potentially forecasting impacts on human health. While gene expression profiling from blood transcriptomes has widely been used to assess health status and environmental exposures in human and veterinary medicine, its use in wildlife has been limited due to the lack of available genomes and baseline data. To this end we constructed the first beluga whale blood transcriptome de novo from samples collected during annual health assessments of the healthy Bristol Bay, AK stock during 2012-2014 to establish baseline information on the content and variation of the beluga whale blood transcriptome. The Trinity transcriptome assembly from beluga was comprised of 91,325 transcripts that represented a wide array of cellular functions and processes and was extremely similar in content to the blood transcriptome of another cetacean, the bottlenose dolphin. Expression of hemoglobin transcripts was much lower in beluga (25.6% of TPM, transcripts per million) than has been observed in many other mammals. A T12A amino acid substitution in the HBB sequence of beluga whales, but not bottlenose dolphins, was identified and may play a role in low temperature adaptation. The beluga blood transcriptome was extremely stable between sex and year, with no apparent clustering of samples by principle components analysis and <4% of genes differentially expressed (EBseq, FDR<0.05). While the impacts of season, sexual maturity, disease, and geography on the beluga blood transcriptome must be established, the presence of transcripts involved in stress, detoxification, and immune functions indicate that blood gene expression analyses may provide information on health status and exposure. This study provides a wealth of transcriptomic data on beluga whales and provides a sizeable pool of preliminary data for comparison with other studies in beluga whale.
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Affiliation(s)
- Jeanine S Morey
- Hollings Marine Laboratory, National Centers for Coastal Ocean Science, National Ocean Service, NOAA, 331 Fort Johnson Road, Charleston, SC 29412, USA; Jardon and Howard Technologies Incorporated, 2710 Discovery Drive, Orlando, FL 32826, USA.
| | | | | | - Tonya M Clauss
- Georgia Aquarium, 225 Baker Street, Atlanta, GA 30313, USA
| | | | - Roderick C Hobbs
- National Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, 7600 Sand Point Way N.E., Seattle, WA 95115, USA
| | - Denise Lunardi
- Department of Life Sciences and Biotechnology, University of Ferrara, via L. Borsari 46, 44121 Ferrara, Italy
| | - Amanda J Moors
- Hollings Marine Laboratory, National Institute of Standards and Technology, 331 Fort Johnson Road, Charleston, SC 29412, USA
| | - Marion G Neely
- Hollings Marine Laboratory, National Centers for Coastal Ocean Science, National Ocean Service, NOAA, 331 Fort Johnson Road, Charleston, SC 29412, USA; Jardon and Howard Technologies Incorporated, 2710 Discovery Drive, Orlando, FL 32826, USA
| | - Lori H Schwacke
- Hollings Marine Laboratory, National Centers for Coastal Ocean Science, National Ocean Service, NOAA, 331 Fort Johnson Road, Charleston, SC 29412, USA
| | - Frances M Van Dolah
- Hollings Marine Laboratory, National Centers for Coastal Ocean Science, National Ocean Service, NOAA, 331 Fort Johnson Road, Charleston, SC 29412, USA
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19
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Status and future perspectives of single nucleotide polymorphisms (SNPs) markers in farmed fishes: Way ahead using next generation sequencing. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2016.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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20
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De novo sequencing, assembly and analysis of eight different transcriptomes from the Malayan pangolin. Sci Rep 2016; 6:28199. [PMID: 27618997 PMCID: PMC5020319 DOI: 10.1038/srep28199] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 06/01/2016] [Indexed: 01/06/2023] Open
Abstract
Pangolins are scale-covered mammals, containing eight endangered species. Maintaining pangolins in captivity is a significant challenge, in part because little is known about their genetics. Here we provide the first large-scale sequencing of the critically endangered Manis javanica transcriptomes from eight different organs using Illumina HiSeq technology, yielding ~75 Giga bases and 89,754 unigenes. We found some unigenes involved in the insect hormone biosynthesis pathway and also 747 lipids metabolism-related unigenes that may be insightful to understand the lipid metabolism system in pangolins. Comparative analysis between M. javanica and other mammals revealed many pangolin-specific genes significantly over-represented in stress-related processes, cell proliferation and external stimulus, probably reflecting the traits and adaptations of the analyzed pregnant female M. javanica. Our study provides an invaluable resource for future functional works that may be highly relevant for the conservation of pangolins.
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21
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Cammen KM, Andrews KR, Carroll EL, Foote AD, Humble E, Khudyakov JI, Louis M, McGowen MR, Olsen MT, Van Cise AM. Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals. J Hered 2016; 107:481-95. [PMID: 27511190 DOI: 10.1093/jhered/esw044] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/12/2016] [Indexed: 12/18/2022] Open
Abstract
The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs.
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Affiliation(s)
- Kristina M Cammen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise).
| | - Kimberly R Andrews
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Emma L Carroll
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Andrew D Foote
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Emily Humble
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Jane I Khudyakov
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Marie Louis
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Michael R McGowen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Morten Tange Olsen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Amy M Van Cise
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
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22
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Yang H, Xu XL, Ma HM, Jiang J. Integrative analysis of transcriptomics and proteomics of skeletal muscles of the Chinese indigenous Shaziling pig compared with the Yorkshire breed. BMC Genet 2016; 17:80. [PMID: 27296698 PMCID: PMC4906580 DOI: 10.1186/s12863-016-0389-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 06/02/2016] [Indexed: 11/08/2022] Open
Abstract
Background The Shaziling pig (Sus scrofa) is a well-known indigenous breed in China. One of its main advantages over European breeds is its high meat quality. However, little genetic information is available for the Shaziling pig. To screen for differentially expressed genes and proteins that might be responsible for the meat quality, the longissimus dorsi muscles from Shaziling and Yorkshire pig breeds were investigated using an integrative analysis of transcriptomics and proteomics, involving high-throughput sequencing, the two-dimensional gel electrophoresis, and mass spectrometry. Results Sequencing produced 79,320 unigenes by de novo assembly, and 488 differentially expressed genes in the longissimus dorsi muscle of Shaziling pig compared with the Yorkshire breed were identified. Gene Ontology term enrichment of biological functions and Kyoto Encyclopedia of Genes and Genomes analysis showed that the gene products were mainly involved in metabolism, protein binding, and regulation of skeletal muscle development. At the protein level, 23 differentially expressed proteins were identified, which were potentially associated with fatty acid metabolism, the glycolytic pathway, and skeletal muscle growth. Eight differentially expressed genes were confirmed by real-time PCR. These results give an insight into the mechanisms underlying the formation of skeletal muscle in the Shaziling pig. Conclusions Certain differentially expressed genes and proteins are involved in fatty acid metabolism, intramuscular fat deposition, and skeletal muscle growth in the Shaziling pig. These results provide candidate genes for improving meat quality and will promote further transcriptomic research in Shaziling pigs. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0389-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hu Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, People's Republic of China.,College of Life Science and Resource Environment, Yichun University, Yichun, 336000, People's Republic of China
| | - Xing-Li Xu
- College of Life Science and Resource Environment, Yichun University, Yichun, 336000, People's Republic of China
| | - Hai-Ming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, People's Republic of China.
| | - Jun Jiang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, People's Republic of China
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23
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Chen QL, Luo Z, Huang C, Pan YX, Wu K. De novo characterization of the liver transcriptome of javelin goby Synechogobius hasta and analysis of its transcriptomic profile following waterborne copper exposure. FISH PHYSIOLOGY AND BIOCHEMISTRY 2016; 42:979-994. [PMID: 26719065 DOI: 10.1007/s10695-015-0190-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 12/25/2015] [Indexed: 06/05/2023]
Abstract
Previous studies have investigated the physiological responses to chronic copper (Cu) exposure in the liver of Synechogobius hasta; however, little information is available on the underlying molecular mechanisms. In an effort to better understand the mechanisms of Cu toxicity and to illuminate global gene expression patterns modulated by Cu exposure, we obtained the liver transcriptome information of S. hasta by RNA sequencing (RNA-seq) technology and also investigated the differential expression of genes following waterborne Cu exposure. Using the Illumina sequencing platform, as many as 60,217 unigenes were generated, with 815 bp of average length and 1298 bp of unigene N50 after filtering and assembly. For functional annotation analysis, 34,860, 31,526, 31,576, 25,808, 11,542, and 21,721 unigenes were annotated to the NR, NT, Swiss-Prot, KEGG, COG, and GO databases, respectively, and total annotation unigenes were 37,764. After 30 days of exposure to 55 μg Cu/l, a total of 292 and 1076 genes were significantly up- and down-regulated, respectively. By KEGG analysis, 660 had a specific pathway annotation. Subsequent bioinformatics analysis revealed that the differentially expressed genes were mainly related to lipid metabolism, immune system, apoptosis, and signal transduction, suggesting that these signaling pathways may be regulated by Cu exposure. The present study provides comprehensive sequence information for subsequent gene expression studies regarding S. hasta, and the transcriptome profiling after Cu exposure is also expected to improve our understanding of the molecular toxicology of Cu.
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Affiliation(s)
- Qi-Liang Chen
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture of China, Fishery College, Huazhong Agricultural University, Wuhan, 430070, China
- Freshwater Aquaculture Collaborative Innovative Centre of Hubei Province, Wuhan, 430070, China
| | - Zhi Luo
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture of China, Fishery College, Huazhong Agricultural University, Wuhan, 430070, China.
- Freshwater Aquaculture Collaborative Innovative Centre of Hubei Province, Wuhan, 430070, China.
- Department of Animal Sciences, Cornell University, Morrison Hall, Ithaca, NY, 14850, USA.
| | - Chao Huang
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture of China, Fishery College, Huazhong Agricultural University, Wuhan, 430070, China
- Freshwater Aquaculture Collaborative Innovative Centre of Hubei Province, Wuhan, 430070, China
| | - Ya-Xiong Pan
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture of China, Fishery College, Huazhong Agricultural University, Wuhan, 430070, China
- Freshwater Aquaculture Collaborative Innovative Centre of Hubei Province, Wuhan, 430070, China
| | - Kun Wu
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture of China, Fishery College, Huazhong Agricultural University, Wuhan, 430070, China
- Freshwater Aquaculture Collaborative Innovative Centre of Hubei Province, Wuhan, 430070, China
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24
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Teeling EC, Jones G, Rossiter SJ. Phylogeny, Genes, and Hearing: Implications for the Evolution of Echolocation in Bats. BAT BIOACOUSTICS 2016. [DOI: 10.1007/978-1-4939-3527-7_2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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25
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Tsagkogeorga G, McGowen MR, Davies KTJ, Jarman S, Polanowski A, Bertelsen MF, Rossiter SJ. A phylogenomic analysis of the role and timing of molecular adaptation in the aquatic transition of cetartiodactyl mammals. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150156. [PMID: 26473040 PMCID: PMC4593674 DOI: 10.1098/rsos.150156] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 09/02/2015] [Indexed: 05/30/2023]
Abstract
Recent studies have reported multiple cases of molecular adaptation in cetaceans related to their aquatic abilities. However, none of these has included the hippopotamus, precluding an understanding of whether molecular adaptations in cetaceans occurred before or after they split from their semi-aquatic sister taxa. Here, we obtained new transcriptomes from the hippopotamus and humpback whale, and analysed these together with available data from eight other cetaceans. We identified more than 11 000 orthologous genes and compiled a genome-wide dataset of 6845 coding DNA sequences among 23 mammals, to our knowledge the largest phylogenomic dataset to date for cetaceans. We found positive selection in nine genes on the branch leading to the common ancestor of hippopotamus and whales, and 461 genes in cetaceans compared to 64 in hippopotamus. Functional annotation revealed adaptations in diverse processes, including lipid metabolism, hypoxia, muscle and brain function. By combining these findings with data on protein-protein interactions, we found evidence suggesting clustering among gene products relating to nervous and muscular systems in cetaceans. We found little support for shared ancestral adaptations in the two taxa; most molecular adaptations in extant cetaceans occurred after their split with hippopotamids.
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Affiliation(s)
- Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Michael R. McGowen
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Kalina T. J. Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Simon Jarman
- Australian Antarctic Division, Channel Highway, Kingston, Tasmania 7050, Australia
| | - Andrea Polanowski
- Australian Antarctic Division, Channel Highway, Kingston, Tasmania 7050, Australia
| | - Mads F. Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, Frederiksberg 2000, Denmark
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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26
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Huang L, Li G, Mo Z, Xiao P, Li J, Huang J. De Novo assembly of the Japanese flounder (Paralichthys olivaceus) spleen transcriptome to identify putative genes involved in immunity. PLoS One 2015; 10:e0117642. [PMID: 25723398 PMCID: PMC4344349 DOI: 10.1371/journal.pone.0117642] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 12/30/2014] [Indexed: 12/23/2022] Open
Abstract
Background Japanese flounder (Paralichthys olivaceus) is an economically important marine fish in Asia and has suffered from disease outbreaks caused by various pathogens, which requires more information for immune relevant genes on genome background. However, genomic and transcriptomic data for Japanese flounder remain scarce, which limits studies on the immune system of this species. In this study, we characterized the Japanese flounder spleen transcriptome using an Illumina paired-end sequencing platform to identify putative genes involved in immunity. Methodology/Principal Findings A cDNA library from the spleen of P. olivaceus was constructed and randomly sequenced using an Illumina technique. The removal of low quality reads generated 12,196,968 trimmed reads, which assembled into 96,627 unigenes. A total of 21,391 unigenes (22.14%) were annotated in the NCBI Nr database, and only 1.1% of the BLASTx top-hits matched P. olivaceus protein sequences. Approximately 12,503 (58.45%) unigenes were categorized into three Gene Ontology groups, 19,547 (91.38%) were classified into 26 Cluster of Orthologous Groups, and 10,649 (49.78%) were assigned to six Kyoto Encyclopedia of Genes and Genomes pathways. Furthermore, 40,928 putative simple sequence repeats and 47, 362 putative single nucleotide polymorphisms were identified. Importantly, we identified 1,563 putative immune-associated unigenes that mapped to 15 immune signaling pathways. Conclusions/Significance The P. olivaceus transciptome data provides a rich source to discover and identify new genes, and the immune-relevant sequences identified here will facilitate our understanding of the mechanisms involved in the immune response. Furthermore, the plentiful potential SSRs and SNPs found in this study are important resources with respect to future development of a linkage map or marker assisted breeding programs for the flounder.
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Affiliation(s)
- Lin Huang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- College of Life Science, Qingdao University, Qingdao, China
| | - Guiyang Li
- Key Laboratory of Sustainable Development of Marine Fisheries, The Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhaolan Mo
- Key Laboratory of Sustainable Development of Marine Fisheries, The Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- National Laboratory for Marine Science and Technology, Qingdao, China
- * E-mail:
| | - Peng Xiao
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jie Li
- Key Laboratory of Sustainable Development of Marine Fisheries, The Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jie Huang
- Key Laboratory of Sustainable Development of Marine Fisheries, The Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- National Laboratory for Marine Science and Technology, Qingdao, China
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27
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Mikami Y, Fukushima A, Kuwada-Kusunose T, Sakurai T, Kitano T, Komiyama Y, Iwase T, Komiyama K. Whole transcriptome analysis using next-generation sequencing of sterile-cultured Eisenia andrei for immune system research. PLoS One 2015; 10:e0118587. [PMID: 25706644 PMCID: PMC4338202 DOI: 10.1371/journal.pone.0118587] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 01/21/2015] [Indexed: 11/18/2022] Open
Abstract
Recently, earthworms have become a useful model for research into the immune system, and it is expected that results obtained using this model will shed light on the sophisticated vertebrate immune system and the evolution of the immune response, and additionally help identify new biomolecules with therapeutic applications. However, for earthworms to be used as a genetic model of the invertebrate immune system, basic molecular and genetic resources, such as an expressed sequence tag (EST) database, must be developed for this organism. Next-generation sequencing technologies have generated EST libraries by RNA-seq in many model species. In this study, we used Illumina RNA-sequence technology to perform a comprehensive transcriptome analysis using an RNA sample pooled from sterile-cultured Eisenia andrei. All clean reads were assembled de novo into 41,423 unigenes using the Trinity program. Using this transcriptome data, we performed BLAST analysis against the GenBank non-redundant (NR) database and obtained a total of 12,285 significant BLAST hits. Furthermore, gene ontology (GO) analysis assigned 78 unigenes to 24 immune class GO terms. In addition, we detected a unigene with high similarity to beta-1,3-glucuronyltransferase 1 (GlcAT-P), which mediates a glucuronyl transfer reaction during the biosynthesis of the carbohydrate epitope HNK-1 (human natural killer-1, also known as CD57), a marker of NK cells. The identified transcripts will be used to facilitate future research into the immune system using E. andrei.
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Affiliation(s)
- Yoshikazu Mikami
- Department of Pathology, Nihon University School of Dentistry, 1-8-13, Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
| | - Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Takao Kuwada-Kusunose
- Department of Liberal Arts (Chemistry), Nihon University School of Dentistry at Matsudo, 2-870-1, Sakaecho-Nishi, Matsudo, Chiba 271-8587, Japan
| | - Tetsuya Sakurai
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Taiichi Kitano
- Department of Pathology, Nihon University School of Dentistry, 1-8-13, Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
| | - Yusuke Komiyama
- Intensive Care Unit, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takashi Iwase
- Department of Pathology, Nihon University School of Dentistry, 1-8-13, Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
| | - Kazuo Komiyama
- Department of Pathology, Nihon University School of Dentistry, 1-8-13, Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
- * E-mail:
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28
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Ruan R, Guo AH, Hao YJ, Zheng JS, Wang D. De novo assembly and characterization of narrow-ridged finless porpoise renal transcriptome and identification of candidate genes involved in osmoregulation. Int J Mol Sci 2015; 16:2220-38. [PMID: 25608655 PMCID: PMC4307359 DOI: 10.3390/ijms16012220] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/08/2014] [Accepted: 01/13/2015] [Indexed: 02/04/2023] Open
Abstract
During the evolutionary transition from land to water, cetaceans have undergone numerous critical challenges, with osmoregulation being the major one. Two subspecies of the narrow-ridged finless porpoise (Neophocaena asiaeorientalis), the freshwater Yangtze finless porpoise (N. a. asiaeorientalis, NAA) and the marine East Asian finless porpoise (N. a. sunameri, NAS), provide excellent subjects to understand the genetic basis of osmoregulatory divergence between freshwater and marine mammals. The kidney plays an important and well-established role in osmoregulation in marine mammals and thus, herein, we utilized RNA-seq to characterize the renal transcriptome and preliminarily analyze the divergence between the NAA and the NAS. Approximately 48.98 million clean reads from NAS and 49.40 million clean reads from NAA were obtained by RNA-Seq. And 73,449 (NAS) and 68,073 (NAA) unigenes were assembled. Among these annotations, 22,231 (NAS) and 21,849 (NAA) unigenes were annotated against the NCBI nr protein database. The ion channel complex GO term and four pathways were detected as relevant to osmoregulation by GO and KEGG pathway classification of these annotated unigenes. Although the endangered status of the study species prevented analysis of biological replicates, we identified nine differentially expressed genes (DEGs) that may be vital in the osmoregulation of the narrow-ridged finless porpoise and worthwhile for future studies. Of these DEGs, the differential expression and distribution of the aquaporin-2 (AQP2) in the collecting duct were verified using immunohistochemical experiments. Together, this work is the first report of renal transcriptome sequencing in cetaceans, and it will provide a valuable resource for future molecular genetics studies on cetacean osmoregulation.
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Affiliation(s)
- Rui Ruan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan 430072, China.
| | - Ai-Huan Guo
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan 430072, China.
| | - Yu-Jiang Hao
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan 430072, China.
| | - Jin-Song Zheng
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan 430072, China.
| | - Ding Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan 430072, China.
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