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Xu M, Liu P, Huang Q, Xu S, Dumont HJ, Han BP. High-quality genome of Diaphanosoma dubium provides insights into molecular basis of its broad ecological adaptation. iScience 2023; 26:106006. [PMID: 36798432 PMCID: PMC9926121 DOI: 10.1016/j.isci.2023.106006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/20/2022] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Diaphanosoma dubium Manuilova, 1964, is a widespread planktonic water flea in Asian freshwater. Although sharing similar ecological roles with species of Daphnia, studies on D. dubium and its congeners are still few and lacking a genome for the further studies. Here, we assembled a high quality and chromosome level genome of D. dubium by combining long reads sequencing and Hi-C technologies. The total length of assembled genome was 101.8 Mb, with 98.92 Mb (97.2%) anchored into 22 chromosomes. Through comparative genomic analysis, we found the genes, involved in anti-ROS, detoxification, protein digestion, germ cells regulation and protection, underwent expansion in D. dubium. These genes and their expansion helpfully explain its widespread geographical distribution and dominance in eutrophic waters. This study provides insight into the adaptive evolution of D. dubium at genomic perspectives, and the present high quality genomic resource will be a footstone for future omics studies of the species and its congeners.
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Affiliation(s)
- Meng Xu
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China
| | - Ping Liu
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China,College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China
| | - Qi Huang
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China
| | - Shaolin Xu
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China
| | - Henri J. Dumont
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China,Ghent University, Department of Biology, Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Bo-Ping Han
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China,Corresponding author
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2
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Ebert D. Daphnia as a versatile model system in ecology and evolution. EvoDevo 2022; 13:16. [PMID: 35941607 PMCID: PMC9360664 DOI: 10.1186/s13227-022-00199-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 06/20/2022] [Indexed: 11/10/2022] Open
Abstract
Water fleas of the genus Daphnia have been a model system for hundreds of years and is among the best studied ecological model organisms to date. Daphnia are planktonic crustaceans with a cyclic parthenogenetic life-cycle. They have a nearly worldwide distribution, inhabiting standing fresh- and brackish water bodies, from small temporary pools to large lakes. Their predominantly asexual reproduction allows for the study of phenotypes excluding genetic variation, enabling us to separate genetic from non-genetic effects. Daphnia are often used in studies related to ecotoxicology, predator-induced defence, host–parasite interactions, phenotypic plasticity and, increasingly, in evolutionary genomics. The most commonly studied species are Daphnia magna and D. pulex, for which a rapidly increasing number of genetic and genomic tools are available. Here, I review current research topics, where the Daphnia model system plays a critical role.
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Affiliation(s)
- Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland.
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3
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O'Grady CJ, Dhandapani V, Colbourne JK, Frisch D. Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs. Mol Ecol Resour 2021; 22:946-961. [PMID: 34672105 DOI: 10.1111/1755-0998.13524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 12/14/2022]
Abstract
Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia, a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimized workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10 and 300 years old. Resulting genome coverage breadth in most samples was ~70%, including those from >100-year-old isolates. Sequence read distribution was highly correlated among samples amplified with the same kit, but less correlated between kits. Despite this, a high percentage of genomic positions with single nucleotide polymorphisms in one or more samples (maximum of 74% between kits, and 97% within kits) were recovered at a depth required for genotyping. As a by-product of sequencing we obtained 100% coverage of the mitochondrial genomes even from the oldest isolates (~300 years). The mitochondrial DNA provides an additional source for evolutionary studies of these populations. We provide an optimized workflow for WGA followed by whole genome sequencing including steps to minimize exogenous DNA.
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Affiliation(s)
- Christopher James O'Grady
- School of Life Sciences, University of Warwick, Coventry, UK.,Cell and Gene Therapy Catapult, London, UK.,School of Biosciences, University of Birmingham, Birmingham, UK
| | | | | | - Dagmar Frisch
- School of Biosciences, University of Birmingham, Birmingham, UK.,Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
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Clark AD, Howell BK, Wilson AE, Schwartz TS. Draft genomes for one Microcystis-resistant and one Microcystis-sensitive strain of the water flea, Daphnia pulicaria. G3 (BETHESDA, MD.) 2021; 11:jkab266. [PMID: 34849790 PMCID: PMC8527513 DOI: 10.1093/g3journal/jkab266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/23/2021] [Indexed: 11/17/2022]
Abstract
Daphnia species are well-suited for studying local adaptation and evolutionary responses to stress(ors) including those caused by algal blooms. Algal blooms, characterized by an overgrowth (bloom) of cyanobacteria, are detrimental to the health of aquatic and terrestrial members of freshwater ecosystems. Some strains of Daphnia pulicaria have demonstrated resistance to toxic algae and the ability to mitigate toxic algal blooms. Understanding the genetic mechanism associated with this toxin resistance requires adequate genomic resources. Using whole-genome sequence data mapped to the Daphnia pulex reference genome (PA42), we present reference-guided draft assemblies from one tolerant and one sensitive strain of D. pulicaria, Wintergreen-6 (WI-6), and Bassett-411 (BA-411), respectively. Assessment of the draft assemblies reveal low contamination levels, and high levels (95%) of genic content. Reference scaffolds had coverage breadths of 98.9-99.4%, and average depths of 33X and 29X for BA-411 and WI-6, respectively. Within, we discuss caveats and suggestions for improving these draft assemblies. These genomic resources are presented with a goal of contributing to the resources necessary to understand the genetic mechanisms and associations of toxic prey resistance observed in this species.
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Affiliation(s)
- Amanda D Clark
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Bailey K Howell
- Bioinformatics REU Program, Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Alan E Wilson
- Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Tonia S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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Cordellier M, Wojewodzic MW, Wessels M, Kuster C, von Elert E. Next-generation sequencing of DNA from resting eggs: signatures of eutrophication in a lake's sediment. ZOOLOGY 2021; 145:125895. [PMID: 33561655 DOI: 10.1016/j.zool.2021.125895] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 01/25/2023]
Abstract
Hatching resting stages of ecologically important organisms such as Daphnia from lake sediments, referred to as resurrection ecology, is a powerful approach to assess changes in alleles and traits over time. However, the utility of the approach is constrained by a few obstacles, including low and/or biased hatching among genotypes. Here, we eliminated such bottlenecks by investigating DNA sequences isolated directly (i.e. without hatching) from resting eggs found in the sediments of Lake Constance spanning pre-, peri-, and post-eutrophication. While we expected genome-wide changes, we specifically expected changes in alleles related to pathways involved in mitigating effects of cyanobacterial toxins. We used pairwise FST-analyses to identify transcripts that showed strongest divergence among the four different populations and a clustering analysis to identify correlations between allele frequency shifts and changes in abiotic and biotic lake parameters. In a cluster that correlated with the increased abundance of cyanobacteria in Lake Constance we find genes that have been reported earlier to be differentially expressed in response to the cyanobacterial toxin microcystin and to microcystin-free cyanobacteria. We further reveal the enrichment of gene ontology terms that have been shown to be involved in microcystin-related responses in other organisms but not yet in Daphnia and as such are candidate loci for adaptation of natural Daphnia populations to increased cyanobacterial abundances. In conclusion this approach of investigating DNA extracted from Daphnia resting stages allowed to determine frequency changes of loci in a natural population over time.
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Affiliation(s)
- Mathilde Cordellier
- Universität Hamburg, Biozentrum Grindel, Martin-Luther-King Platz 3, 20146, Hamburg, Germany.
| | - Marcin W Wojewodzic
- Cancer Registry of Norway (Kreftregisteret), Institute of Population-Based Cancer Research, Etiology Group, NO-0304, Oslo, Norway; School of Biosciences, University of Birmingham, B15 2TT, United Kingdom.
| | - Martin Wessels
- Institute for Lake Research at the Agency for Environment Baden-Württemberg, 88085, Langenargen, Germany.
| | - Christian Kuster
- Aquatic Chemical Ecology, Institute of Zoology, University of Koeln, Biocenter, Zuelpicher Strasse 47 B, 50858, Koeln, Germany.
| | - Eric von Elert
- Aquatic Chemical Ecology, Institute of Zoology, University of Koeln, Biocenter, Zuelpicher Strasse 47 B, 50858, Koeln, Germany.
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Wu W, Wu D, Yan W, Wang Y, You J, Wan X, Xi D, Luo X, Han M, Ning Q. Interferon-Induced Macrophage-Derived Exosomes Mediate Antiviral Activity Against Hepatitis B Virus Through miR-574-5p. J Infect Dis 2020; 223:686-698. [PMID: 32663850 DOI: 10.1093/infdis/jiaa399] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/13/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Interferon alfa (IFN-α) has been proved effective in treating chronic hepatitis B (CHB), owing to its ability to suppress hepatitis B surface antigen and hepatitis B virus (HBV) covalently closed circular DNA. However, the underlying mechanisms are unclear. METHODS We investigated the antiviral activities of exosomes from responders and nonresponders to pegylated IFN-α (PegIFN-α) as well as the supernatants of IFN-α-treated macrophages derived from THP-1 (the human leukemia monocyte cell line). Then the expression profiles of exosomal microRNAs (miRNAs) were analyzed using miRNA sequencing. The luciferase reporter assay was used to locate the binding position of HBV genomic sequence targeted by the identified miRNA. RESULTS Exosomes from PegIFN-α-treated patients, particularly responders, as well as the supernatants of IFN-α-treated macrophages exhibited anti-HBV activities, as manifested by the suppression of hepatitis B surface antigen, hepatitis B e antigen, HBV DNA, and covalently closed circular DNA levels in HBV-related cell lines. PegIFN-α treatment up-regulated exosomal hsa-miR-193a-5p, hsa-miR-25-5p, and hsa-miR-574-5p, which could partially inhibit HBV replication and transcription, and hsa-miR-574-5p reduced pregenomic RNA and polymerase messenger RNA levels by binding to the 2750-2757 position of the HBV genomic sequence. CONCLUSIONS Exosomes can transfer IFN-α-related miRNAs from macrophages to HBV-infected hepatocytes, and they exhibit antiviral activities against HBV replication and expression.
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Affiliation(s)
- Wenyu Wu
- Department and Institute of Infectious Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Di Wu
- Department and Institute of Infectious Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weiming Yan
- Department and Institute of Infectious Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yongli Wang
- Department and Institute of Infectious Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jie You
- Department and Institute of Infectious Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyang Wan
- Department and Institute of Infectious Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dong Xi
- Department and Institute of Infectious Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoping Luo
- Department of Pediatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meifang Han
- Department and Institute of Infectious Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qin Ning
- Department and Institute of Infectious Disease, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Dead or alive: sediment DNA archives as tools for tracking aquatic evolution and adaptation. Commun Biol 2020; 3:169. [PMID: 32265485 PMCID: PMC7138834 DOI: 10.1038/s42003-020-0899-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/10/2020] [Indexed: 12/18/2022] Open
Abstract
DNA can be preserved in marine and freshwater sediments both in bulk sediment and in intact, viable resting stages. Here, we assess the potential for combined use of ancient, environmental, DNA and timeseries of resurrected long-term dormant organisms, to reconstruct trophic interactions and evolutionary adaptation to changing environments. These new methods, coupled with independent evidence of biotic and abiotic forcing factors, can provide a holistic view of past ecosystems beyond that offered by standard palaeoecology, help us assess implications of ecological and molecular change for contemporary ecosystem functioning and services, and improve our ability to predict adaptation to environmental stress. Ellegaard et al. discuss the potential for using ancient environmental DNA (eDNA), combined with resurrection ecology, to analyse trophic interactions and evolutionary adaptation to changing environments. Their Review suggests that these techniques will improve our ability to predict genetic and phenotypic adaptation to environmental stress.
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Ma X, Hu W, Smilauer P, Yin M, Wolinska J. Daphnia galeata
and D. dentifera
are geographically and ecologically separated whereas their hybrids occur in intermediate habitats: A survey of 44 Chinese lakes. Mol Ecol 2019; 28:785-802. [DOI: 10.1111/mec.14991] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 11/21/2018] [Accepted: 12/14/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Xiaolin Ma
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science; Fudan University; Shanghai China
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science; Fudan University; Shanghai China
| | - Petr Smilauer
- Department of Ecosystem Biology, Faculty of Science; University of South Bohemia; Ceske Budejovice Czech Republic
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science; Fudan University; Shanghai China
| | - Justyna Wolinska
- Department of Ecosystem Research; Leibniz-Institute of Freshwater Ecology and Inland Fisheries; Berlin Germany
- Department of Biology, Chemistry, Institute of Biology; Freie Universität Berlin; Berlin Germany
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