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Bukhari SA, Saul MC, Seward CH, Zhang H, Bensky M, James N, Zhao SD, Chandrasekaran S, Stubbs L, Bell AM. Temporal dynamics of neurogenomic plasticity in response to social interactions in male threespined sticklebacks. PLoS Genet 2017; 13:e1006840. [PMID: 28704398 PMCID: PMC5509087 DOI: 10.1371/journal.pgen.1006840] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/27/2017] [Indexed: 11/18/2022] Open
Abstract
Animals exhibit dramatic immediate behavioral plasticity in response to social interactions, and brief social interactions can shape the future social landscape. However, the molecular mechanisms contributing to behavioral plasticity are unclear. Here, we show that the genome dynamically responds to social interactions with multiple waves of transcription associated with distinct molecular functions in the brain of male threespined sticklebacks, a species famous for its behavioral repertoire and evolution. Some biological functions (e.g., hormone activity) peaked soon after a brief territorial challenge and then declined, while others (e.g., immune response) peaked hours afterwards. We identify transcription factors that are predicted to coordinate waves of transcription associated with different components of behavioral plasticity. Next, using H3K27Ac as a marker of chromatin accessibility, we show that a brief territorial intrusion was sufficient to cause rapid and dramatic changes in the epigenome. Finally, we integrate the time course brain gene expression data with a transcriptional regulatory network, and link gene expression to changes in chromatin accessibility. This study reveals rapid and dramatic epigenomic plasticity in response to a brief, highly consequential social interaction. Social interactions provoke changes in the brain and behavior but their underlying molecular mechanisms remain obscure. Male sticklebacks are small fish whose fitness depends on their ability to defend a territory. Here, by measuring the time course of gene expression in response to a territorial challenge in two brain regions, we show that a single brief territorial intrusion provoked waves of gene expression that persisted for hours afterwards, with waves of transcription associated with distinct biological processes. Moreover, a single territorial challenge caused dramatic changes to the epigenome. Changes in chromatin accessibility corresponded to changes in gene expression, and to the activity of transcription factors operating within gene regulatory networks. This study reveals rapid and dramatic epigenomic plasticity in response to a brief, highly consequential social interaction. These results suggest that meaningful social interactions (even brief ones) can provoke waves of transcription and changes to the epigenome which lead to changes in neural functioning, and those changes are a mechanism by which animals update their assessment of their social world.
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Affiliation(s)
- Syed Abbas Bukhari
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, IL, United States of America
- Illinois Informatics Institute, University of Illinois, Urbana Champaign, Urbana, IL, United States of America
| | - Michael C. Saul
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, IL, United States of America
| | - Christopher H. Seward
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, IL, United States of America
| | - Huimin Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, IL, United States of America
| | - Miles Bensky
- Program in Ecology, Evolution and Conservation Biology, University of Illinois, Urbana Champaign, Urbana, IL, United States of America
| | - Noelle James
- Neuroscience Program, University of Illinois, Urbana Champaign, Urbana, IL, United States of America
| | - Sihai Dave Zhao
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, IL, United States of America
- Department of Statistics, University of Illinois, Urbana Champaign, Urbana, IL United States of America
| | - Sriram Chandrasekaran
- Harvard Society of Fellows, Harvard University, Cambridge, MA, United States of America
- Faculty of Arts and Sciences, Harvard University, Cambridge, MA, United States of America
- Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Lisa Stubbs
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, IL, United States of America
- Department of Cell and Developmental Biology, University of Illinois, Urbana Champaign, Urbana, IL, United States of America
| | - Alison M. Bell
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, IL, United States of America
- Program in Ecology, Evolution and Conservation Biology, University of Illinois, Urbana Champaign, Urbana, IL, United States of America
- Neuroscience Program, University of Illinois, Urbana Champaign, Urbana, IL, United States of America
- * E-mail:
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Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SRS, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, Mwangi S, Lau D, Ngoh SY, Liew WC, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin CS, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Kumar Katneni V, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O'Brien SJ, Schatz MC, Dalmay T, Turner SW, Lok S, Christoffels A, Orbán L. Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet 2016; 12:e1005954. [PMID: 27082250 PMCID: PMC4833346 DOI: 10.1371/journal.pgen.1005954] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 03/03/2016] [Indexed: 11/18/2022] Open
Abstract
We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics.
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Affiliation(s)
- Shubha Vij
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Inna S. Kuznetsova
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
- Laboratory of Chromosome Structure and Function, Department of Cytology and Histology, Biological Faculty, Saint Petersburg State University, St. Petersburg, Russia
| | - Aleksey Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Andrey A. Yurchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Peter Van Heusden
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Siddharth Singh
- Pacific Biosciences, Menlo Park, California, United States of America
| | | | | | | | - Jolly M. Saju
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Junhui Jiang
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Stanley Kimbung Mbandi
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Mario Jonas
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Amy Hin Yan Tong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Sarah Mwangi
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Doreen Lau
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Si Yan Ngoh
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Woei Chang Liew
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Xueyan Shen
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Lawrence S. Hon
- Pacific Biosciences, Menlo Park, California, United States of America
| | - James P. Drake
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Matthew Boitano
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Richard Hall
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Chen-Shan Chin
- Pacific Biosciences, Menlo Park, California, United States of America
| | | | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Vladimir Trifonov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Marsel Kabilov
- Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey Tupikin
- Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Darrell Green
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Simon Moxon
- The Genome Analysis Centre, Norwich, United Kingdom
| | - Tyler Garvin
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America
| | - Fritz J. Sedlazeck
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Gregory W. Vurture
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America
| | - Gopikrishna Gopalapillai
- Nutrition, Genetics & Biotechnology Division, ICAR-Central Institute of Brackishwater Aquaculture, Tamil Nadu, India
| | - Vinaya Kumar Katneni
- Nutrition, Genetics & Biotechnology Division, ICAR-Central Institute of Brackishwater Aquaculture, Tamil Nadu, India
| | - Tansyn H. Noble
- College of Marine and Environmental Sciences and Center for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Dean R. Jerry
- College of Marine and Environmental Sciences and Center for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
| | - Stephen J. O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
- Oceanographic Center, Nova Southeastern University Ft. Lauderdale, Ft. Lauderdale, Florida, United States of America
| | - Michael C. Schatz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tamás Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Stephen W. Turner
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Si Lok
- The Centre for Applied Genomics, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Alan Christoffels
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - László Orbán
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
- Department of Animal Sciences and Animal Husbandry, Georgikon Faculty, University of Pannonia, Keszthely, Hungary
- Centre for Comparative Genomics, Murdoch University, Murdoch, Australia
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Sato Y, Hashiguchi Y, Nishida M. Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication. BMC Evol Biol 2009; 9:127. [PMID: 19500364 PMCID: PMC2702319 DOI: 10.1186/1471-2148-9-127] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Accepted: 06/05/2009] [Indexed: 11/10/2022] Open
Abstract
Background Recent genomic studies have revealed a teleost-specific third-round whole genome duplication (3R-WGD) event occurred in a common ancestor of teleost fishes. However, it is unclear how the genes duplicated in this event were lost or persisted during the diversification of teleosts, and therefore, how many of the duplicated genes contribute to the genetic differences among teleosts. This subject is also important for understanding the process of vertebrate evolution through WGD events. We applied a comparative evolutionary approach to this question by focusing on the genes involved in long-term potentiation, taste and olfactory transduction, and the tricarboxylic acid cycle, based on the whole genome sequences of four teleosts; zebrafish, medaka, stickleback, and green spotted puffer fish. Results We applied a state-of-the-art method of maximum-likelihood phylogenetic inference and conserved synteny analyses to each of 130 genes involved in the above biological systems of human. These analyses identified 116 orthologous gene groups between teleosts and tetrapods, and 45 pairs of 3R-WGD-derived duplicate genes among them. This suggests that more than half [(45×2)/(116+45)] = 56.5%) of the loci, probably more than ten thousand genes, present in a common ancestor of the four teleosts were still duplicated after the 3R-WGD. The estimated temporal pattern of gene loss suggested that, after the 3R-WGD, many (71/116) of the duplicated genes were rapidly lost during the initial 75 million years (MY), whereas on average more than half (27.3/45) of the duplicated genes remaining in the ancestor of the four teleosts (45/116) have persisted for about 275 MY. The 3R-WGD-derived duplicates that have persisted for a long evolutionary periods of time had significantly larger number of interacting partners and longer length of protein coding sequence, implying that they tend to be more multifunctional than the singletons after the 3R-WGD. Conclusion We have shown firstly the temporal pattern of gene loss process after 3R-WGD on the basis of teleost phylogeny and divergence time frameworks. The 3R-WGD-derived duplicates have not undergone constant exponential decay, suggesting that selection favoured the long-term persistence of a subset of duplicates that tend to be multi-functional. On the basis of these results obtained from the analysis of 116 orthologous gene groups, we propose that more than ten thousand of 3R-WGD-derived duplicates have experienced lineage-specific evolution, that is, the differential sub-/neo-functionalization or secondary loss between lineages, and contributed to teleost diversity.
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Affiliation(s)
- Yukuto Sato
- Division of Molecular Marine Biology, Ocean Research Institute, The University of Tokyo, 1-15-1 Minamidai, Nakano-ku, Tokyo 164-8639, Japan.
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