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Gao Y, Chen Y, Li S, Huang X, Hu J, Bock DG, MacIsaac HJ, Zhan A. Complementary genomic and epigenomic adaptation to environmental heterogeneity. Mol Ecol 2022; 31:3598-3612. [PMID: 35560847 DOI: 10.1111/mec.16500] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 04/18/2022] [Accepted: 05/05/2022] [Indexed: 12/01/2022]
Abstract
While adaptation is commonly thought to result from selection on DNA sequence-based variation, recent studies have highlighted an analogous epigenetic component as well. However, the relative roles of these mechanisms in facilitating population persistence under environmental heterogeneity remain unclear. To address the underlying genetic and epigenetic mechanisms and their relationship during environmental adaptation, we screened the genomes and epigenomes of nine global populations of a predominately sessile marine invasive tunicate, Botryllus schlosseri, using reduced-representation methods. We detected clear population differentiation at the genetic and epigenetic levels. Patterns of genetic and epigenetic structure were significantly influenced by local environmental variables. Among these variables, minimum annual sea surface temperature was identified as the top explanatory variable for both genetic and epigenetic variation. However, patterns of population structure driven by genetic and epigenetic variation were somewhat distinct, suggesting possible autonomy of epigenetic variation. We found both shared and specific genes and biological pathways among genetic and epigenetic loci associated with environmental factors, consistent with complementary and independent contributions of genetic and epigenetic variation to environmental adaptation in this system. Collectively, these mechanisms may facilitate population persistence under environmental change and sustain successful invasions across novel environments.
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Affiliation(s)
- Yangchun Gao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Juntao Hu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Dan G Bock
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Hugh J MacIsaac
- School of Ecology and Environmental Science, Yunnan University, Yunnan, 650091, China.,Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, N9B 3P4, Canada
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
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Chen Y, Gao Y, Huang X, Li S, Zhan A. Local environment-driven adaptive evolution in a marine invasive ascidian ( Molgula manhattensis). Ecol Evol 2021; 11:4252-4266. [PMID: 33976808 PMCID: PMC8093682 DOI: 10.1002/ece3.7322] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 12/04/2022] Open
Abstract
Elucidating molecular mechanisms of environment-driven adaptive evolution in marine invaders is crucial for understanding invasion success and further predicting their future invasions. Although increasing evidence suggests that adaptive evolution could contribute to organisms' adaptation to varied environments, there remain knowledge gaps regarding how environments influence genomic variation in invaded habitats and genetic bases underlying local adaptation for most marine invaders. Here, we performed restriction-site-associated DNA sequencing (RADseq) to assess population genetic diversity and further investigate genomic signatures of local adaptation in the marine invasive ascidian, Molgula manhattensis. We revealed that most invasive populations exhibited significant genetic differentiation, low recent gene flow, and no signal of significant population bottleneck. Based on three genome scan approaches, we identified 109 candidate loci potentially under environmental selection. Redundancy analysis and variance partitioning analysis suggest that local environmental factors, particularly the salinity-related variables, represent crucial evolutionary forces in driving adaptive divergence. Using the newly developed transcriptome as a reference, 14 functional genes were finally obtained with potential roles in salinity adaptation, including SLC5A1 and SLC9C1 genes from the solute carrier gene (SLC) superfamily. Our findings confirm that differed local environments could rapidly drive adaptive divergence among invasive populations and leave detectable genomic signatures in marine invaders.
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Affiliation(s)
- Yiyong Chen
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesShijingshan DistrictBeijingChina
| | - Yangchun Gao
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesShijingshan DistrictBeijingChina
- Guangdong Key Laboratory of Animal Conservation and Resource UtilizationInstitute of ZoologyGuangdong Academy of SciencesHaizhu DistrictGuangzhouChina
| | - Xuena Huang
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
| | - Shiguo Li
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesShijingshan DistrictBeijingChina
| | - Aibin Zhan
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesShijingshan DistrictBeijingChina
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Assessing the Ecotoxicity of Copper and Polycyclic Aromatic Hydrocarbons: Comparison of Effects on Paracentrotus lividus and Botryllus schlosseri, as Alternative Bioassay Methods. WATER 2021. [DOI: 10.3390/w13050711] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Adult sea urchins and their embryos are ideal targets to investigate the medium- and long-term effects of various toxic agents, such as organic and inorganic pollutants, to forecast and mitigate their environmental effects. Similarly, small colonial tunicates such as Botryllid ascidians may reveal acute toxicity processes and permit quick responses for the management of contaminants impacting coastal waters, to preserve the functional integrity of marine ecosystems. This investigation compares the functional responses of two model invertebrates, the sea urchin Paracentrotus lividus and the sea squirt Botryllus schlosseri, to chronic and acute exposures to organic and inorganic toxic agents. Such heavy metals as copper produce both acute and chronic effects on marine biota, while polycyclic aromatic hydrocarbons (PAHs) mainly produce chronic effects at the concentrations ordinarily measured in marine coastal waters. Both models were tested over a range of concentrations of copper and PAHs. Copper triggered a clear effect in both species, producing a delay in the embryo development of P. lividus and a rapid death of sea squirts. B. schlosseri was less sensitive to PAHs than P. lividus. The results on both species may synergistically contribute to assess the toxicity of organic and inorganic compounds at various concentrations and different physiologic levels.
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Cong Z, Li Q, Yang Y, Guo X, Cui L, You T. The SNP of rs6854845 suppresses transcription via the DNA looping structure alteration of super-enhancer in colon cells. Biochem Biophys Res Commun 2019; 514:734-741. [PMID: 31078271 DOI: 10.1016/j.bbrc.2019.04.190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 04/28/2019] [Indexed: 12/01/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) identified by Genome-Wide Association Studies (GWASs) have been determined to closely connect with multiple diseases. Previous studies revealed one underlying mechanism that SNPs located within the regulatory elements could affect the encoding gene expression through long-range regulation. SNP rs6854845 was suggested to be a risk of colon cancer in human population. Nevertheless, the underlying molecular mechanism for colon carcinogenesis remains largely unknown. In present study, rs6854845 with G > T mutation in situ in FHC, HCT-116 and SW-480 cells were generated by Crispr/Cas9. The nearby chromatin organization was investigated by chromatin conformation capture (3C). And the expression of coding gene regulated by super-enhancer (SE) was detected by real-time PCR. We observed a significantly different pattern of the genome organization upon rs6854845 generation in colon epithelial cells but not in colon cancer cells. Moreover, we observed the shifted enrichment of H3K4me1 and H3K27ac at the SE (chr4:75.7M-76.0 M) where rs6854845 located. Furthermore, we observed that the transcription of the gene clusters regulated by SE were affected by rs6854845 in colon cells. Overall, our results demonstrated that SNP rs6854845 located in SE could destroy the long-range chromosomal interaction between SE and target gene clusters thereby affecting the transcription of these genes.
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Affiliation(s)
- Zhuangzhi Cong
- Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, Shanghai 200438, PR China
| | - Qinghua Li
- Department of Hepatobiliary Surgery, Shanghai East Hospital, Tongji University School of Medicine, 150 Ji-Mo Road, Shanghai, 200120, PR China
| | - Yongkang Yang
- Department of Hepatobiliary Surgery, Shanghai East Hospital, Tongji University School of Medicine, 150 Ji-Mo Road, Shanghai, 200120, PR China
| | - Xinlai Guo
- Department of Hepatobiliary Surgery, Shanghai East Hospital, Tongji University School of Medicine, 150 Ji-Mo Road, Shanghai, 200120, PR China
| | - Longjiu Cui
- Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, Shanghai 200438, PR China
| | - Tiangeng You
- Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, Shanghai 200438, PR China.
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