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Pitt WJ, Cooper WR, Pouchnik D, Headrick H, Nachappa P. High-throughput molecular gut content analysis of aphids identifies plants relevant for potato virus Y epidemiology. Insect Sci 2024. [PMID: 38319817 DOI: 10.1111/1744-7917.13327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/24/2023] [Accepted: 12/07/2023] [Indexed: 02/08/2024]
Abstract
Aphids are phloem-feeding insects that reduce crop productivity due to feeding and transmission of plant viruses. When aphids disperse across the landscape to colonize new host plants, they will often probe on a wide variety of nonhost plants before settling on a host suitable for feeding and reproduction. There is limited understanding of the diversity of plants that aphids probe on within a landscape, and characterizing this diversity can help us better understand host use patterns of aphids. Here, we used gut content analysis (GCA) to identify plant genera that were probed by aphid vectors of potato virus Y (PVY). Aphids were trapped weekly near potato fields during the growing seasons of 2020 and 2021 in San Luis Valley in Colorado. High-throughput sequencing of plant barcoding genes, trnF and ITS2, from 200 individual alate (i.e., winged) aphids representing nine vector species of PVY was performed using the PacBio sequencing platform, and sequences were identified to genus using NCBI BLASTn. We found that 34.7% of aphids probed upon presumed PVY host plants and that two of the most frequently detected plant genera, Solanum and Brassica, represent important crops and weeds within the study region. We found that 75% of aphids frequently probed upon PVY nonhosts including many species that are outside of their reported host ranges. Additionally, 19% of aphids probed upon more than one plant species. This study provides the first evidence from high-throughput molecular GCA of aphids and reveals host use patterns that are relevant for PVY epidemiology.
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Affiliation(s)
- William Jacob Pitt
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | | | - Derek Pouchnik
- Laboratory for Biotechnology and Bioanalysis, Washington State University, Pullman, Washington, USA
| | - Heather Headrick
- USDA-ARS Temperate Tree Fruit and Vegetable Research Unit, Wapato, Washington, USA
| | - Punya Nachappa
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
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2
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Zhao Z, Attanasio C, Pedano MS, Cadenas de Llano-Pérula M. Comparison of human dental tissue RNA extraction methods for RNA sequencing. Arch Oral Biol 2023; 148:105646. [PMID: 36812743 DOI: 10.1016/j.archoralbio.2023.105646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/13/2023]
Abstract
OBJECTIVE The purpose of this study was to identify an efficient RNA extraction method for periodontal ligament (PDL) and dental pulp (DP) tissues to be used in RNA sequencing studies, given the increased use of these techniques in dental research and the lack of standard protocols. DESIGN PDL and DP were harvested from extracted third molars. Total RNA was extracted with four RNA extraction kits. RNA concentration, purity and integrity were assessed by means of NanoDrop and Bioanalyzer and statistically compared. RESULTS RNA from PDL was more likely to be degraded than that of DP. The TRIzol method yielded the highest RNA concentration from both tissues. All methods harvested RNA with A260/A280 close to 2.0 and with A260/A230 above 1.5, except for the A260/A230 from PDL obtained with the RNeasy Mini kit. For RNA integrity, the RNeasy Fibrous Tissue Mini kit yielded the highest RIN values and 28 S/18 S from PDL, while the RNeasy Mini kit obtained relatively high RIN values with an appropriate 28 S/18 S for DP. CONCLUSION Significantly different results were obtained for PDL and DP when using the RNeasy Mini kit. The RNeasy Mini kit provided the highest RNA yields and quality for DP, while the RNeasy Fibrous Tissue Mini kit obtained the highest quality RNA from PDL.
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Affiliation(s)
- Zuodong Zhao
- Department of Oral Health Sciences-Orthodontics, KU Leuven and Dentistry, University Hospitals Leuven, Kapucijnenvoer 7, 3000 Leuven, Belgium.
| | - Catia Attanasio
- Laboratory of Gene Regulation and Disease, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Mariano Simón Pedano
- Department of Oral Health Sciences-Endodontics and BIOMAT - Biomaterials Research group, KU Leuven and Dentistry, University Hospitals Leuven, Kapucijnenvoer 7, 3000 Leuven, Belgium
| | - Maria Cadenas de Llano-Pérula
- Department of Oral Health Sciences-Orthodontics, KU Leuven and Dentistry, University Hospitals Leuven, Kapucijnenvoer 7, 3000 Leuven, Belgium
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Chiari Y, Howard L, Moreno N, Relyea S, Dunnigan J, Boyer MC, Kardos M, Glaberman S, Luikart G. Influence of RNA-Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation. Mol Ecol Resour 2023; 23:803-817. [PMID: 36704853 DOI: 10.1111/1755-0998.13757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 12/14/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023]
Abstract
RNA sequencing (RNA-Seq) is popular for measuring gene expression in non-model organisms, including wild populations. While RNA-Seq can detect gene expression variation among wild-caught individuals and yield important insights into biological function, sampling methods can also affect gene expression estimates. We examined the influence of multiple technical variables on estimated gene expression in a non-model fish, the westslope cutthroat trout (Oncorhynchus clarkii lewisi), using two RNA-Seq library types: 3' RNA-Seq (QuantSeq) and whole mRNA-Seq (NEB). We evaluated effects of dip netting versus electrofishing, and of harvesting tissue immediately versus 5 min after euthanasia on estimated gene expression in blood, gill, and muscle. We found no significant differences in gene expression between sampling methods or tissue collection times with either library type. When library types were compared using the same blood samples, 58% of genes detected by both NEB and QuantSeq showed significantly different expression between library types, and NEB detected 31% more genes than QuantSeq. Although the two library types recovered different numbers of genes and expression levels, results with NEB and QuantSeq were consistent in that neither library type showed differences in gene expression between sampling methods and tissue harvesting times. Our study suggests that researchers can safely rely on different fish sampling strategies in the field. In addition, while QuantSeq is more cost effective, NEB detects more expressed genes. Therefore, when it is crucial to detect as many genes as possible (especially low expressed genes), when alternative splicing is of interest, or when working with an organism lacking good genomic resources, whole mRNA-Seq is more powerful.
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Affiliation(s)
- Ylenia Chiari
- Department of Biology, George Mason University, Fairfax, Virginia, USA
| | - Leif Howard
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Science, University of Montana, Missoula, Montana, USA.,Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, USA
| | - Nickolas Moreno
- Department of Biology, George Mason University, Fairfax, Virginia, USA
| | - Scott Relyea
- Sekokini Springs Hatchery, Montana Fish Wildlife and Parks, Bozeman, Montana, USA
| | - James Dunnigan
- Sekokini Springs Hatchery, Montana Fish Wildlife and Parks, Bozeman, Montana, USA
| | | | - Marty Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Scott Glaberman
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - Gordon Luikart
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Science, University of Montana, Missoula, Montana, USA.,Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, USA
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Sommer KM, Lee Y, Donovan SM, Dilger RN. Purification methods to reduce interference by dextran sodium sulfate with quantification of gene expression in intestinal tissue samples from a piglet model of colitis. J Anim Sci 2023; 101:skad202. [PMID: 37330677 PMCID: PMC10317179 DOI: 10.1093/jas/skad202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023] Open
Abstract
Dextran sodium sulfate (DSS) is commonly used to induce intestinal (i.e., colonic) inflammation in a variety of animal models. However, DSS is known to cause interference when using quantitative-real time polymerase chain reaction (qRT-PCR) methods, thereby invalidating accurate and precise measurement of tissue gene expression. Therefore, the goal of this study was to determine whether different mRNA purification methods would reduce DSS-interference. Colonic tissue samples were collected at postnatal days (PND) 27 or 28 from pigs that had not been administered DSS (Control), and two independent groups of pigs that received 1.25 g of DSS/kg of BW/d (DSS-1 and DSS-2) from PND 14 to 18. Tissue samples collected were subsequently stratified into three purification methods (i.e., 9 total treatment × method combinations), including: 1) no purification, 2) purification with lithium chloride (LiCl), or 3) purification using spin column filtration. All data were analyzed using a one-way ANOVA in the Mixed procedure of SAS. The average RNA concentrations across all treatments were between 1,300 and 1,800 μg/μL for all three in vivo groups. Although there were statistical differences among purification methods, the 260/280 and 260/230 ratios fell between acceptable limits of 2.0 to 2.1 and 2.0 to 2.2, respectively, for all treatment groups. This confirms the RNA quality was adequate and not influenced by purification method in addition to suggesting the absence of phenol, salts, and carbohydrate contamination. For pigs in the Control group that did not receive DSS, qRT-PCR Ct values of four cytokines were achieved, though these values were not altered by purification method. For pigs that had undergone DSS dosing, those tissues subjected to either no purification or purification using LiCl did not generate applicable Ct values. However, when tissues derive from DSS-treated pigs underwent spin column purification, half of the samples from DSS-1 and DSS-2 groups generated appropriate Ct estimates. Therefore, spin column purification appeared to be more effective than LiCl purification, but no method was 100% effective, so caution should be exercised when interpreting gene expression results from studies where animals are exposed to DSS-induced colitis.
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Affiliation(s)
- Kaitlyn M Sommer
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, USA
| | - Youngsoo Lee
- Department of Food Science and Human Nutrition, University of Illinois, Urbana, Illinois, USA
| | - Sharon M Donovan
- Department of Food Science and Human Nutrition, University of Illinois, Urbana, Illinois, USA
| | - Ryan N Dilger
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, USA
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Hao RH, Guo Y, Wang C, Chen F, Di CX, Dong SS, Cao QL, Guo J, Rong Y, Yao S, Zhu DL, Chen YX, Chen H, Yang TL. Lineage-specific rearrangement of chromatin loops and epigenomic features during adipocytes and osteoblasts commitment. Cell Death Differ 2022; 29:2503-2518. [PMID: 35906483 PMCID: PMC9751090 DOI: 10.1038/s41418-022-01035-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 01/31/2023] Open
Abstract
Human mesenchymal stem cells (hMSCs) can be differentiated into adipocytes and osteoblasts. The processes are driven by the rewiring of chromatin architectures and transcriptomic/epigenomic changes. Here, we induced hMSCs to adipogenic and osteogenic differentiation, and performed 2 kb resolution Hi-C experiments for chromatin loops detection. We also generated matched RNA-seq, ChIP-seq and ATAC-seq data for integrative analysis. After comprehensively comparing adipogenesis and osteogenesis, we quantitatively identified lineage-specific loops and screened out lineage-specific enhancers and open chromatin. We reveal that lineage-specific loops can activate gene expression and facilitate cell commitment through combining enhancers and accessible chromatin in a lineage-specific manner. We finally proposed loop-mediated regulatory networks and identified the controlling factors for adipocytes and osteoblasts determination. Functional experiments validated the lineage-specific regulation networks towards IRS2 and RUNX2 that are associated with adipogenesis and osteogenesis, respectively. These results are expected to help better understand the chromatin conformation determinants of hMSCs fate commitment.
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Affiliation(s)
- Ruo-Han Hao
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Yan Guo
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Chen Wang
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Fei Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Chen-Xi Di
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Shan-Shan Dong
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Qi-Long Cao
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
- Research and Development Department, Qingdao Haier Biotech Co. Ltd, Qingdao, Shandong, 266109, P. R. China
| | - Jing Guo
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Yu Rong
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Shi Yao
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, P. R. China
| | - Dong-Li Zhu
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Yi-Xiao Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, P. R. China
| | - Hao Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Tie-Lin Yang
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China.
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, P. R. China.
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Gu X, Ye T, Zhang XR, Nie L, Wang H, Li W, Lu R, Fu C, Du LL, Zhou JQ. Single-chromosome fission yeast models reveal the configuration robustness of a functional genome. Cell Rep 2022; 40:111237. [PMID: 36001961 DOI: 10.1016/j.celrep.2022.111237] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/02/2022] [Accepted: 07/28/2022] [Indexed: 11/03/2022] Open
Abstract
In eukaryotic organisms, genetic information is usually carried on multiple chromosomes. Whether and how the number and configuration of chromosomes affect organismal fitness and speciation remain unclear. Here, we have successfully established several single-chromosome fission yeast Schizosaccharomyces pombe strains, in which the three natural chromosomes have been fused into one giant chromosome in different orders. Chromosome fusions accompanied by the deletions of telomeres and centromeres result in the loss of chromosomal interactions and a drastic change of global chromosome organization, but alter gene expression marginally. The single-chromosome strains display little defects in cell morphology, mitosis, genotoxin sensitivity, and meiosis. Crosses between a wild-type strain and a single-chromosome strain or between two single-chromosome strains with different fusion orders suffer defective meiosis and poor spore viability. We conclude that eukaryotic genomes are robust against dramatic chromosomal reconfiguration, and stochastic changes in chromosome number and genome organization during evolution underlie reproductive isolation and speciation.
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Affiliation(s)
- Xin Gu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tiantian Ye
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Ran Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lingyun Nie
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, CAS Center for Excellence in Molecular Cell Sciences, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Huan Wang
- Frasergen Bioinformatics, Wuhan, China
| | - Wei Li
- Frasergen Bioinformatics, Wuhan, China
| | - Rui Lu
- Frasergen Bioinformatics, Wuhan, China
| | - Chuanhai Fu
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, CAS Center for Excellence in Molecular Cell Sciences, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing 102206, China.
| | - Jin-Qiu Zhou
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou 310024, China.
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Chevignon G, Dotto-Maurel A, Serpin D, Chollet B, Arzul I. De Novo Transcriptome Assembly and Analysis of the Flat Oyster Pathogenic Protozoa Bonamia Ostreae. Front Cell Infect Microbiol 2022; 12:921136. [PMID: 35909967 PMCID: PMC9329632 DOI: 10.3389/fcimb.2022.921136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/22/2022] [Indexed: 12/05/2022] Open
Abstract
The flat oyster Ostrea edulis is an oyster species native to Europe. It has declined to functional extinction in many areas of the NE Atlantic for several decades. Factors explaining this decline include over-exploitation of natural populations and diseases like bonamiosis, regulated across both the EU and the wider world and caused by the intracellular protozoan parasite Bonamia ostreae. To date, very limited sequence data are available for this Haplosporidian species. We present here the first transcriptome of B. ostreae. As this protozoan is not yet culturable, it remains extremely challenging to obtain high-quality -omic data. Thanks to a specific parasite isolation protocol and a dedicated bioinformatic pipeline, we were able to obtain a high-quality transcriptome for an intracellular marine micro-eukaryote, which will be very helpful to better understand its biology and to consider the development of new relevant diagnostic tools.
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Razak MR, Aris AZ, Md Yusoff F, Yusof ZNB, Kim SD, Kim KW. Assessment of RNA extraction protocols from cladocerans. PLoS One 2022; 17:e0264989. [PMID: 35472091 PMCID: PMC9041806 DOI: 10.1371/journal.pone.0264989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/18/2022] [Indexed: 11/18/2022] Open
Abstract
The usage of cladocerans as non-model organisms in ecotoxicological and risk assessment studies has intensified in recent years due to their ecological importance in aquatic ecosystems. The molecular assessment such as gene expression analysis has been introduced in ecotoxicological and risk assessment to link the expression of specific genes to a biological process in the cladocerans. The validity and accuracy of gene expression analysis depends on the quantity, quality and integrity of extracted ribonucleic acid (RNA) of the sample. However, the standard methods of RNA extraction from the cladocerans are still lacking. This study evaluates the extraction of RNA from tropical freshwater cladocerans Moina micrura using two methods: the phenol-chloroform extraction method (QIAzol) and a column-based kit (Qiagen Micro Kit). Glycogen was introduced in both approaches to enhance the recovery of extracted RNA and the extracted RNA was characterised using spectrophotometric analysis (NanoDrop), capillary electrophoresis (Bioanalyzer). Then, the extracted RNA was analysed with reverse transcription polymerase chain reaction (RT-PCR) to validate the RNA extraction method towards downstream gene expression analysis. The results indicate that the column-based kit is most suitable for the extraction of RNA from M. micrura, with the quantity (RNA concentration = 26.90 ± 6.89 ng/μl), quality (A260:230 = 1.95 ± 0.15, A280:230 = 1.85 ± 0.09) and integrity (RNA integrity number, RIN = 7.20 ± 0.16). The RT-PCR analysis shows that the method successfully amplified both alpha tubulin and actin gene at 33-35 cycles (i.e. Ct = 32.64 to 33.48). The results demonstrate that the addition of glycogen is only suitable for the phenol-chloroform extraction method. RNA extraction with high and comprehensive quality control assessment will increase the accuracy and reliability of downstream gene expression, thus providing more ecotoxicological data at the molecular biological level on other freshwater zooplankton species.
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Affiliation(s)
- Muhammad Raznisyafiq Razak
- Faculty of Forestry and Environment, Department of Environment, Universiti Putra Malaysia, Selangor, Malaysia
| | - Ahmad Zaharin Aris
- Faculty of Forestry and Environment, Department of Environment, Universiti Putra Malaysia, Selangor, Malaysia
- International Institute of Aquaculture and Aquatic Sciences, Universiti Putra Malaysia, Negeri Sembilan, Malaysia
| | - Fatimah Md Yusoff
- International Institute of Aquaculture and Aquatic Sciences, Universiti Putra Malaysia, Negeri Sembilan, Malaysia
- Faculty of Agriculture, Department of Aquaculture, Universiti Putra Malaysia, Selangor, Malaysia
| | - Zetty Norhana Balia Yusof
- Faculty of Biotechnology and Biomolecular Science, Department of Biochemistry, Universiti Putra Malaysia, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, Selangor, Malaysia
| | - Sang Don Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Buk-gu, Gwangju, Republic of Korea
| | - Kyoung Woong Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Buk-gu, Gwangju, Republic of Korea
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Fernández-González LE, Sánchez-Marín P, Gestal C, Beiras R, Diz AP. Vitellogenin gene expression in marine mussels exposed to ethinylestradiol: No induction at the transcriptional level. Mar Environ Res 2021; 168:105315. [PMID: 33853012 DOI: 10.1016/j.marenvres.2021.105315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Vitellogenin (Vtg), a large multidomain protein precursor of egg-yolk proteins, is used as an endocrine disruption biomarker in fish, and in the last decades, its use has been extended to invertebrates like mollusks. However, it remains unclear whether invertebrate endocrine system produces Vtg in response to estrogens, like it occurs in oviparous vertebrates. In a previous study, no evidence of induction of Vtg expression at protein level was found in gonads of the marine mussel Mytilus galloprovincialis after exposure to the estrogenic chemical 17α-ethinylestradiol (EE2). In the present follow-up study, it was investigated whether there is any effect of EE2 on Vtg abundance at transcriptional level in M. galloprovincialis gonads. To this aim, RT-qPCR analysis targeting three different domains of Vtg transcript was performed on gonads of mussels that were exposed either 4 or 24 days to 100 ng/L EE2. In addition, several reference genes were analysed and a selection of these for potential use in further RT-qPCR analyses on mussel male and female gonads is provided. Results showed higher expression in females than in males for the three analysed Vtg domains, and no evidence of Vtg mRNA induction due to EE2 either in females or males. The present results, together with those obtained from previous analysis at protein level, support that Vtg is not an adequate biomarker for xenoestrogenicity in marine mussels. Additionally, nucleotide sequences of Vtg transcripts of three closely-related species from Mytilus edulis complex (M. galloprovincialis, M. edulis and M. trossulus) are provided and compared with Vtg sequences from other mollusk species to assess the level of conservation and evolutionary relationships among species.
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Affiliation(s)
- Laura Emilia Fernández-González
- Department of Ecology and Animal Biology, University of Vigo, 36310, Vigo, Spain; Marine Research Centre, University of Vigo (CIM-UVIGO), Isla de Toralla, Vigo, Spain; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | - Paula Sánchez-Marín
- Department of Ecology and Animal Biology, University of Vigo, 36310, Vigo, Spain; Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, 36390, Vigo, Spain
| | - Camino Gestal
- Marine Molecular Pathobiology Group, Institute of Marine Research (IIM-CSIC), Vigo, Spain
| | - Ricardo Beiras
- Department of Ecology and Animal Biology, University of Vigo, 36310, Vigo, Spain; Marine Research Centre, University of Vigo (CIM-UVIGO), Isla de Toralla, Vigo, Spain
| | - Angel P Diz
- Marine Research Centre, University of Vigo (CIM-UVIGO), Isla de Toralla, Vigo, Spain; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain.
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Shi H, Zhou Y, Jia E, Pan M, Bai Y, Ge Q. Bias in RNA-seq Library Preparation: Current Challenges and Solutions. Biomed Res Int 2021; 2021:6647597. [PMID: 33987443 DOI: 10.1155/2021/6647597] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 04/09/2021] [Indexed: 12/26/2022]
Abstract
Although RNA sequencing (RNA-seq) has become the most advanced technology for transcriptome analysis, it also confronts various challenges. As we all know, the workflow of RNA-seq is extremely complicated and it is easy to produce bias. This may damage the quality of RNA-seq dataset and lead to an incorrect interpretation for sequencing result. Thus, our detailed understanding of the source and nature of these biases is essential for the interpretation of RNA-seq data, finding methods to improve the quality of RNA-seq experimental, or development bioinformatics tools to compensate for these biases. Here, we discuss the sources of experimental bias in RNA-seq. And for each type of bias, we discussed the method for improvement, in order to provide some useful suggestions for researcher in RNA-seq experimental.
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Hasegawa N, Techer M, Mikheyev AS. A toolkit for studying Varroa genomics and transcriptomics: preservation, extraction, and sequencing library preparation. BMC Genomics 2021; 22:54. [PMID: 33446105 PMCID: PMC7809802 DOI: 10.1186/s12864-020-07363-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/30/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The honey bee parasite, Varroa destructor, is a leading cause of honey bee population declines. In addition to being an obligate ectoparasitic mite, Varroa carries several viruses that infect honey bees and act as the proximal cause of colony collapses. Nevertheless, until recently, studies of Varroa have been limited by the paucity of genomic tools. Lab- and field-based methods exploiting such methods are still nascent. This study developed a set of methods for preserving Varroa DNA and RNA from the field to the lab and processing them into sequencing libraries. We performed preservation experiments in which Varroa mites were immersed in TRIzol, RNAlater, and absolute ethanol for preservation periods up to 21 days post-treatment to assess DNA and RNA integrity. RESULTS For both DNA and RNA, mites preserved in TRIzol and RNAlater at room temperature degraded within 10 days post-treatment. Mites preserved in ethanol at room temperature and 4 °C remained intact through 21 days. Varroa mite DNA and RNA libraries were created and sequenced for ethanol preserved samples, 15 and 21 days post-treatment. All DNA sequences mapped to the V. destructor genome at above 95% on average, while RNA sequences mapped to V. destructor, but also sometimes to high levels of the deformed-wing virus and to various organisms. CONCLUSIONS Ethanolic preservation of field-collected mites is inexpensive and simple, and allows them to be shipped and processed successfully in the lab for a wide variety of sequencing applications. It appears to preserve RNA from both Varroa and at least some of the viruses it vectors.
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Affiliation(s)
- Nonno Hasegawa
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, 904-0495, Okinawa, Japan.
| | - Maeva Techer
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, 904-0495, Okinawa, Japan
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, 904-0495, Okinawa, Japan.
- Australian National University, 2600, Canberra, ACT, Australia.
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Gaafar ARZ, Al-Qurainy F, Alshameri A, Khan S, Nadeem M, Tarroum M, Alansi S, Shaikhaldein HO, Salih AM, Arrak Alenezi N. High RNA quality extracted from the tolerant crop Cyamopsis tetragonoloba (L.) despite possession of low RNA integrity number. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1910567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
| | - Fahad Al-Qurainy
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Aref Alshameri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Salim Khan
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Nadeem
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed Tarroum
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh Alansi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hassan O. Shaikhaldein
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdalrhaman M. Salih
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Norah Arrak Alenezi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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Knutson VL, Brenzinger B, Schrödl M, Wilson NG, Giribet G. Most Cephalaspidea have a shell, but transcriptomes can provide them with a backbone (Gastropoda: Heterobranchia). Mol Phylogenet Evol 2020; 153:106943. [DOI: 10.1016/j.ympev.2020.106943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/21/2020] [Indexed: 01/14/2023]
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15
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Townsend K, Ness J, Hoguet J, Stacy NI, Komoroske LM, Lynch JM. Testing the Stability of Plasma Protein and Whole Blood RNA in Archived Blood of Loggerhead Sea Turtles, Caretta caretta. Biopreserv Biobank 2020; 18:358-366. [PMID: 32589445 DOI: 10.1089/bio.2020.0026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Sample storage conditions can affect accuracy and reproducibility of biological measurements. Storing samples rapidly at the lowest available temperatures is considered ideal but is not always feasible when sampling in remote and logistically challenging field conditions, as is often the case with sea turtles. The objective of this study was to examine the stability of plasma proteins and quality of whole blood RNA from loggerhead sea turtle samples collected as part of an eighteen-year-long curated specimen collection. These biological variables are often used to assess sea turtle health; therefore, it is necessary to maintain the integrity of these components during storage. Protein electrophoresis was conducted on heparinized plasma from individual turtles collected in 2018 (n = 3), 2008 (n = 3), and 2001 (n = 3). Plasma was also pooled from four turtles sampled in 2018 and subjected to various storage temperatures. Whole blood was collected in blood collection tubes containing sodium heparin or PAXgene tubes with an RNA preservative. These were subjected to different storage treatments that can possibly occur during logistically difficult field sampling. Following various treatments, plasma proteins showed minor differences across collection years and no differences among storage treatments were observed, even when exposed to 38°C for three hours. RNA quality was assessed from whole blood using an RNA integrity number (RIN). RINs were poor from sodium heparin tubes that were frozen and from PAXgene tubes after an extended thaw. High-quality RNA was obtained from sodium heparin tubes that were never frozen and from PAXgene tubes with freezing delayed by up to 11 days. Overall, these results indicate that plasma proteins remain stable over time and when exposed to undesirable storage conditions, and RNA degrades rapidly in sea turtle blood after freezing and when not properly preserved. These aspects are important to consider when planning sampling protocols and logistics for optimal long-term sample preservation.
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Affiliation(s)
- Kelly Townsend
- Grice Marine Laboratory, College of Charleston, Charleston, South Carolina, USA.,Elmhurst College, Elmhurst, Illinois, USA
| | - Jennifer Ness
- Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, South Carolina, USA
| | - Jennifer Hoguet
- Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, South Carolina, USA
| | - Nicole I Stacy
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Lisa M Komoroske
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Jennifer M Lynch
- Chemical Sciences Division, National Institute of Standards and Technology, Waimanalo, Hawaii, USA.,Center for Marine Debris Research, Hawaii Pacific University, Waimanalo, Hawaii, USA
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16
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Dang Z, Huang L, Jia Y, Lockhart PJ, Fong Y, Tian Y. Identification of Genic SSRs Provide a Perspective for Studying Environmental Adaptation in the Endemic Shrub Tetraena mongolica. Genes (Basel) 2020; 11:E322. [PMID: 32197402 PMCID: PMC7140860 DOI: 10.3390/genes11030322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/10/2020] [Accepted: 03/16/2020] [Indexed: 02/03/2023] Open
Abstract
Tetraena mongolica is a xerophytic shrub endemic to desert regions in Inner Mongolia. This species has evolved distinct survival strategies that allow it to adapt to hyper-drought and heterogeneous habitats. Simple sequence repeats (SSRs) may provide a molecular basis in plants for fast adaptation to environmental change. Thus, identifying SSRs and their possible effects on gene behavior has the potential to provide valuable information for studies of adaptation. In this study, we sequenced six individual transcriptomes of T. mongolica from heterogeneous habitats, focused on SSRs located in genes, and identified 811 polymorphic SSRs. Of the identified SSRs, 172, 470, and 76 were located in 5' UTRs, CDSs, and 3' UTRs in 591 transcripts; and AG/CT, AAC/GTT, and AT/AT were the most abundant repeats in each gene region. Functional annotation showed that many of the identified polymorphic SSRs were in genes that were enriched in several GO terms and KEGG pathways, suggesting the functional significance of these genes in the environmental adaptation process. The identification of polymorphic genic SSRs in our study lays a foundation for future studies investigating the contribution of SSRs to regulation of genes in natural populations of T. mongolica and their importance for adaptive evolution of this species.
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Affiliation(s)
- Zhenhua Dang
- Inner Mongolia Key Laboratory of Grassland Ecology & Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Z.D.); (L.H.); (Y.J.)
| | - Lei Huang
- Inner Mongolia Key Laboratory of Grassland Ecology & Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Z.D.); (L.H.); (Y.J.)
| | - Yuanyuan Jia
- Inner Mongolia Key Laboratory of Grassland Ecology & Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Z.D.); (L.H.); (Y.J.)
| | - Peter J. Lockhart
- School of Fundamental Sciences, College of Sciences, Massey University, Palmerston North 4442, New Zealand; (P.J.L.); (Y.F.)
| | - Yang Fong
- School of Fundamental Sciences, College of Sciences, Massey University, Palmerston North 4442, New Zealand; (P.J.L.); (Y.F.)
| | - Yunyun Tian
- Ministry of Education Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China
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Taguchi K, Chen L, Usawachintachit M, Hamamoto S, Kang M, Sugino T, Unno R, Tzou DT, Sherer BA, Okada A, Yasui T, Ho SP, Stoller ML, Chi T. Fatty acid-binding protein 4 downregulation drives calcification in the development of kidney stone disease. Kidney Int 2020; 97:1042-1056. [PMID: 32247632 DOI: 10.1016/j.kint.2020.01.042] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 12/30/2022]
Abstract
Nephrolithiasis is a significant source of morbidity, and its incidence has increased significantly over the last decades. This rise has been attributed to concurrent increasing rates of obesity, associated with a 3-time risk of developing NL. To date, the mechanism by which obesity is linked to stone formation has not been elucidated. We aimed to utilize a transcriptomics approach to discover the missing link between these two epidemic diseases. We investigated gene expression profiling of nephrolithiasis patients by two RNA-sequencing approaches: comparison between renal papilla tissue with and without the presence of calcified Randall's plaques (RP), and comparison between the papilla, medulla, and cortex regions from within a single recurrent stone forming kidney. Results were overlaid between differently expressed genes found in the patient cohort and in the severely lithogenic kidney to identify common genes. Overlay of these two RNA-sequencing datasets demonstrated there is impairment of lipid metabolism in renal papilla tissue containing RP linked to downregulation of fatty acid binding protein (FABP) 4. Immunohistochemistry of human kidney specimens and microarray analysis of renal tissue from a nephrolithiasis mouse model confirmed that FABP4 downregulation is associated with renal stone formation. In a FABP4 knockout mouse model, FABP4 deficiency resulted in development of both renal and urinary crystals. Our study revealed that FABP4 plays an important, previously unrecognized role in kidney stone formation, providing a feasible mechanism to explain the link between nephrolithiasis and metabolic syndrome.
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Affiliation(s)
- Kazumi Taguchi
- Department of Urology, University of California, San Francisco, California, USA; Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Ling Chen
- Division of Biomaterials and Bioengineering, Department of Preventive and Restorative Dental Sciences, University of California San Francisco, San Francisco, California, USA
| | - Manint Usawachintachit
- Department of Urology, University of California, San Francisco, California, USA; Division of Urology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Shuzo Hamamoto
- Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Misun Kang
- Division of Biomaterials and Bioengineering, Department of Preventive and Restorative Dental Sciences, University of California San Francisco, San Francisco, California, USA
| | - Teruaki Sugino
- Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Rei Unno
- Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - David T Tzou
- Department of Urology, University of California, San Francisco, California, USA
| | - Benjamin A Sherer
- Department of Urology, University of California, San Francisco, California, USA
| | - Atsushi Okada
- Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Takahiro Yasui
- Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Sunita P Ho
- Division of Biomaterials and Bioengineering, Department of Preventive and Restorative Dental Sciences, University of California San Francisco, San Francisco, California, USA
| | - Marshall L Stoller
- Department of Urology, University of California, San Francisco, California, USA
| | - Thomas Chi
- Department of Urology, University of California, San Francisco, California, USA.
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18
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Rodríguez A, Duyvejonck H, Van Belleghem JD, Gryp T, Van Simaey L, Vermeulen S, Van Mechelen E, Vaneechoutte M. Comparison of procedures for RNA-extraction from peripheral blood mononuclear cells. PLoS One 2020; 15:e0229423. [PMID: 32084228 PMCID: PMC7034890 DOI: 10.1371/journal.pone.0229423] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/05/2020] [Indexed: 02/06/2023] Open
Abstract
RNA quality and quantity are important factors for ensuring the accuracy of gene expression analysis and other RNA-based downstream applications. Thus far, only a limited number of methodological studies have compared sample storage and RNA extraction procedures for human cells. We compared three commercially available RNA extraction kits, i.e., (NucliSENS) easyMAG, RNeasy (Mini Kit) and RiboPure (RNA Purification Kit–blood). In addition, additional conditions, such as storage medium and storage temperature of human peripheral blood mononuclear cells were evaluated, i.e., 4 °C for RNAlater or -80 °C for QIAzol and for the respective cognate lysis buffers; easyMAG, RNeasy or RiboPure. RNA was extracted from aliquots that had been stored for one day (Run 1) or 83 days (Run 2). After DNase treatment, quantity and quality of RNA were assessed by means of a NanoDrop spectrophotometer, 2100 Bioanalyzer and RT-qPCR for the ACTB reference gene. We observed that high-quality RNA can be obtained using RNeasy and RiboPure, regardless of the storage medium, whereas samples stored in RNAlater resulted in the least amount of RNA extracted. In addition, RiboPure combined with storage of samples in its cognate lysis buffer yielded twice as much RNA as all other procedures. These results were supported by RT-qPCR and by the reproducibility observed for two independent extraction runs.
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Affiliation(s)
- Antonio Rodríguez
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- * E-mail:
| | - Hans Duyvejonck
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Ghent, Belgium
| | - Jonas D. Van Belleghem
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Tessa Gryp
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Leen Van Simaey
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Stefan Vermeulen
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Ghent, Belgium
| | - Els Van Mechelen
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Ghent, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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19
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Dillon ME, Lozier JD. Adaptation to the abiotic environment in insects: the influence of variability on ecophysiology and evolutionary genomics. Curr Opin Insect Sci 2019; 36:131-139. [PMID: 31698151 DOI: 10.1016/j.cois.2019.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/10/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
Advances in tools to gather environmental, phenotypic, and molecular data have accelerated our ability to detect abiotic drivers of variation across the genome-to-phenome spectrum in model and non-model insects. However, differences in the spatial and temporal resolution of these data sets may create gaps in our understanding of linkages between environment, genotype, and phenotype that yield missed or misleading results about adaptive variation. In this review we highlight sources of variability that might impact studies of phenotypic and 'omic environmental adaptation, challenges to collecting data at relevant scales, and possible solutions that link intensive fine-scale reductionist studies of mechanisms to large-scale biogeographic patterns.
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Affiliation(s)
- Michael E Dillon
- Department of Zoology & Physiology and Program in Ecology, The University of Wyoming, Laramie, Wyoming 82071, USA.
| | - Jeffrey D Lozier
- Department of Biological Sciences, The University of Alabama, Box 870344, Tuscaloosa, Alabama 35487, USA
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20
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Waits DS, Simpson DY, Sparkman AM, Bronikowski AM, Schwartz TS. The utility of reptile blood transcriptomes in molecular ecology. Mol Ecol Resour 2019; 20:308-317. [PMID: 31660689 DOI: 10.1111/1755-0998.13110] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 08/25/2019] [Accepted: 10/15/2019] [Indexed: 02/02/2023]
Abstract
Reptiles and other nonmammalian vertebrates have transcriptionally active nucleated red blood cells. If blood transcriptomes can provide quantitative data to address questions relevant to molecular ecology, this could circumvent the need to euthanize animals to assay tissues. This would allow longitudinal sampling of animals' responses to treatments, as well as sampling of protected taxa. We developed and annotated blood transcriptomes from six reptile species and found on average 25,000 proteins are being transcribed in the blood, and there is a CORE group of 9,282 orthogroups that are found in at least four of six species. In comparison to liver transcriptomes from the same taxa, approximately two-thirds of the orthogroups were found in both blood and liver; and a similar percentage of ecologically relevant gene groups (insulin and insulin-like signalling, electron transport chain, oxidative stress, glucocorticoid receptors) were found transcribed in both blood and liver. As a resource, we provide a user-friendly database of gene ids identified in each blood transcriptome. Although on average 37% of reads mapped to haemoglobin, importantly, the majority of nonhaemoglobin transcripts had sufficient depth (e.g., 97% at ≥10 reads) to be included in differential gene expression analysis. Thus, we demonstrate that RNAseq blood transcriptomes from a very small blood sample (<10 μl) is a minimally invasive option in nonmammalian vertebrates for quantifying expression of a large number of ecologically relevant genes that would allow longitudinal sampling and sampling of protected populations.
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Affiliation(s)
- Damien S Waits
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Dasia Y Simpson
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | | | - Anne M Bronikowski
- Ecology, Evolution and Organismal Biology Department, Iowa State University, Ames, IA, USA
| | - Tonia S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
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21
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Hiki K, Nakajima F, Tobino T, Watanabe H, Yamamoto H. Whole transcriptome analysis of an estuarine amphipod exposed to highway road dust. Sci Total Environ 2019; 675:141-150. [PMID: 31026638 DOI: 10.1016/j.scitotenv.2019.04.201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
Urban road dust can potentially have adverse effects on aquatic and benthic ecosystems if discharged into receiving waters; however, little is known about the mode of action of road dust toxicity within aquatic organisms. With an aim to reveal the biological effects of road dust on benthic crustacean species, we performed a de novo transcriptome analysis of the estuarine amphipod Grandidierella japonica exposed to road dust collected from highways around Tokyo. A transcriptome analysis by Illumina HiSeq 2500 identified differentially expressed genes related to the gamma-aminobutyric acid (GABA) signaling pathway, oxidative damage, and cuticle metabolism. Among these, a GABAB receptor subunit showed down-regulation in the road dust treatment, but a constant expression in the treatment of road dust with a carbonaceous resin XAD-4, which can reduce the acute toxicity of road dust to G. japonica. These results and the time course expressions of the related genes were partially confirmed by quantitative PCR (qPCR) experiments. Although the linkage between acute lethal toxicity and the molecular initiating events induced by road dust was still unclear, our findings provide lines of evidence to identify the causative toxicants in urban road dust.
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Affiliation(s)
- Kyoshiro Hiki
- Center for Environmental Risk Research, National Institute for Environmental Studies, Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan; Department of Urban Engineering, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Fumiyuki Nakajima
- Environmental Science Center, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomohiro Tobino
- Department of Urban Engineering, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Haruna Watanabe
- Center for Environmental Risk Research, National Institute for Environmental Studies, Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan
| | - Hiroshi Yamamoto
- Center for Environmental Risk Research, National Institute for Environmental Studies, Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan
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22
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Kimball RT, Oliveros CH, Wang N, White ND, Barker FK, Field DJ, Ksepka DT, Chesser RT, Moyle RG, Braun MJ, Brumfield RT, Faircloth BC, Smith BT, Braun EL. A Phylogenomic Supertree of Birds. Diversity 2019; 11:109. [DOI: 10.3390/d11070109] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.
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Hilgers L, Hartmann S, Hofreiter M, von Rintelen T. Novel Genes, Ancient Genes, and Gene Co-Option Contributed to the Genetic Basis of the Radula, a Molluscan Innovation. Mol Biol Evol 2019; 35:1638-1652. [PMID: 29672732 PMCID: PMC5995198 DOI: 10.1093/molbev/msy052] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The radula is the central foraging organ and apomorphy of the Mollusca. However, in contrast to other innovations, including the mollusk shell, genetic underpinnings of radula formation remain virtually unknown. Here, we present the first radula formative tissue transcriptome using the viviparous freshwater snail Tylomelania sarasinorum and compare it to foot tissue and the shell-building mantle of the same species. We combine differential expression, functional enrichment, and phylostratigraphic analyses to identify both specific and shared genetic underpinnings of the three tissues as well as their dominant functions and evolutionary origins. Gene expression of radula formative tissue is very distinct, but nevertheless more similar to mantle than to foot. Generally, the genetic bases of both radula and shell formation were shaped by novel orchestration of preexisting genes and continuous evolution of novel genes. A significantly increased proportion of radula-specific genes originated since the origin of stem-mollusks, indicating that novel genes were especially important for radula evolution. Genes with radula-specific expression in our study are frequently also expressed during the formation of other lophotrochozoan hard structures, like chaetae (hes1, arx), spicules (gbx), and shells of mollusks (gbx, heph) and brachiopods (heph), suggesting gene co-option for hard structure formation. Finally, a Lophotrochozoa-specific chitin synthase with a myosin motor domain (CS-MD), which is expressed during mollusk and brachiopod shell formation, had radula-specific expression in our study. CS-MD potentially facilitated the construction of complex chitinous structures and points at the potential of molecular novelties to promote the evolution of different morphological innovations.
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Affiliation(s)
- Leon Hilgers
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- Adaptive Evolutionary Genomics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Corresponding author: E-mail:
| | - Stefanie Hartmann
- Adaptive Evolutionary Genomics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michael Hofreiter
- Adaptive Evolutionary Genomics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Thomas von Rintelen
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
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24
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Xie P, Yi SK, Yao H, Chi W, Guo Y, Ma XF, Wang HP. Comparative transcriptome analysis reveals potential evolutionary differences in adaptation of temperature and body shape among four Percidae species. PLoS One 2019; 14:e0215933. [PMID: 31063465 DOI: 10.1371/journal.pone.0215933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 04/10/2019] [Indexed: 12/18/2022] Open
Abstract
Considering the divergent temperature habitats and morphological traits of four Percidae species: yellow perch (Perca flavescens), Eurasian perch (Perca fluviatilis), pike perch (Sander lucioperca), and ruffe (Gymnocephalus cernua), we stepped into the transcriptome level to discover genes and mechanisms that drive adaptation to different temperature environments and evolution in body shape. Based on 93,566 to 181,246 annotated unigenes of the four species, we identified 1,117 one-to-one orthologous genes and subsequently constructed the phylogenetic trees that are consistent with previous studies. Together with the tree, the ratios of nonsynonymous to synonymous substitutions presented decreased evolutionary rates from the D. rerio branch to the sub-branch clustered by P. flavescens and P. fluviatilis. The specific 93 fast-evolving genes and 57 positively selected genes in P. flavescens, compared with 22 shared fast-evolving genes among P. fluviatilis, G. cernua, and S. lucioperca, showed an intrinsic foundation that ensure its adaptation to the warmer Great Lakes and farther south, especially in functional terms like “Cul4-RING E3 ubiquitin ligase complex.” Meanwhile, the specific 78 fast-evolving genes and 41 positively selected genes in S. lucioperca drew a clear picture of how it evolved to a large and elongated body with camera-type eyes and muscle strength so that it could occupy the highest position in the food web. Overall, our results uncover genetic basis that support evolutionary adaptation of temperature and body shape in four Percid species, and could furthermore assist studies on environmental adaptation in fishes.
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25
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Diz AP, Romero MR, Pérez-Figueroa A, Swanson WJ, Skibinski DOF. RNA-seq data from mature male gonads of marine mussels Mytilus edulis and M. galloprovincialis. Data Brief 2018; 21:167-175. [PMID: 30364736 PMCID: PMC6197779 DOI: 10.1016/j.dib.2018.09.086] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/21/2018] [Accepted: 09/30/2018] [Indexed: 02/01/2023] Open
Abstract
The mussels Mytilus edulis and Mytilus galloprovincialis are marine organisms with external fertilization able to hybridize where their distributions overlap allowing the study of reproductive isolation mechanisms in nature. We provide raw data of a transcriptomic analysis of mature male gonads from these two Mytilus spp. using NGS (Illumina) technology and a preliminary list of transcript that were functionally annotated showing species-specific differential expression. A shortlist including some of these genes and their corresponding proteins have been thoroughly analysed and discussed in Romero et al. (2018, Submitted for publication).
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Affiliation(s)
- Angel P Diz
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, Spain.,Marine Research Centre, University of Vigo (CIM-UVIGO), Isla de Toralla, Vigo, Spain
| | - Mónica R Romero
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, Spain.,Marine Research Centre, University of Vigo (CIM-UVIGO), Isla de Toralla, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, Spain
| | - Willie J Swanson
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, USA
| | - David O F Skibinski
- Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, UK
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26
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Zhou C, Carotenuto Y, Vitiello V, Wu C, Zhang J, Buttino I. De novo transcriptome assembly and differential gene expression analysis of the calanoid copepod Acartia tonsa exposed to nickel nanoparticles. Chemosphere 2018; 209:163-172. [PMID: 29929122 DOI: 10.1016/j.chemosphere.2018.06.096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/04/2018] [Accepted: 06/12/2018] [Indexed: 06/08/2023]
Abstract
The calanoid copepod Acartia tonsa is a reference species in standardized ecotoxicology bioassay. Despite this interest, there is a lack of knowledge on molecular responses of A. tonsa to contaminants. We generated a de novo assembled transcriptome of A. tonsa exposed 4 days to 8.5 and 17 mg/L nickel nanoparticles (NiNPs), which have been shown to reduce egg hatching success and larval survival but had no effects on the adults. Aims of our study were to 1) improve the knowledge on the molecular responses of A. tonsa copepod and 2) increase the genomic resources of this copepod for further identification of potential biomarkers of NP exposure. The de novo assembled transcriptome of A. tonsa consisted of 53,619 unigenes, which were further annotated to nr, GO, KOG and KEGG databases. In particular, most unigenes were assigned to Metabolic and Cellular processes (34-45%) GO terms, and to Human disease (28%) and Organismal systems (23%) KEGG categories. Comparison among treatments showed that 373 unigenes were differentially expressed in A. tonsa exposed to NiNPs at 8.5 and 17 mg/L, with respect to control. Most of these genes were downregulated and took part in ribosome biogenesis, translation and protein turnover, thus suggesting that NiNPs could affect the copepod ribosome synthesis machinery and functioning. Overall, our study highlights the potential of toxicogenomic approach in gaining more mechanistic and functional information about the mode of action of emerging compounds on marine organisms, for biomarker discovering in crustaceans.
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Affiliation(s)
- Chao Zhou
- National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science and Technology, Zhejiang Ocean University, No.1 Haida South Road, Lincheng Changzhi Island, Zhoushan, Zhejiang 316022, PR China
| | - Ylenia Carotenuto
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale, Napoli, Italy
| | - Valentina Vitiello
- Istituto Superiore per La Protezione e Ricerca Ambientale ISPRA, Via del cedro 38, 57122, Livorno, Italy
| | - Changwen Wu
- National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science and Technology, Zhejiang Ocean University, No.1 Haida South Road, Lincheng Changzhi Island, Zhoushan, Zhejiang 316022, PR China
| | - Jianshe Zhang
- National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science and Technology, Zhejiang Ocean University, No.1 Haida South Road, Lincheng Changzhi Island, Zhoushan, Zhejiang 316022, PR China
| | - Isabella Buttino
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale, Napoli, Italy; Istituto Superiore per La Protezione e Ricerca Ambientale ISPRA, Via del cedro 38, 57122, Livorno, Italy.
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27
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Gervais O, Renault T, Arzul I. Molecular and cellular characterization of apoptosis in flat oyster a key mechanisms at the heart of host-parasite interactions. Sci Rep 2018; 8:12494. [PMID: 30131502 DOI: 10.1038/s41598-018-29776-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/14/2018] [Indexed: 01/09/2023] Open
Abstract
Bonamia ostreae has been associated with the decline of flat oyster Ostrea edulis populations in some European countries. This obligatory intracellular parasite persists and multiplies into hemocytes. Previous in vitro experiments showed that apoptosis is activated in hemocytes between 1 h and 4 h of contact with the parasite. The flat oyster uses the apoptosis pathway to defend against B. ostreae. However, the parasite might be also able to modulate this response in order to survive in its host. In order to investigate this hypothesis the apoptotic response of the host was evaluated using flow cytometry, transmission electron microscopy and by measuring the response of genes involved in the apoptotic pathway after 4 h. In parallel, the parasite response was investigated by measuring the expression of B. ostreae genes involved in different biological functions including cell cycle and cell death. Obtained results allow describing molecular apoptotic pathways in O. edulis and confirm that apoptosis is early activated in hemocytes after a contact with B. ostreae. Interestingly, at cellular and molecular levels this process appeared downregulated after 44 h of contact. Concurrently, parasite gene expression appeared reduced suggesting that the parasite could inhibit its own metabolism to escape the immune response.
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28
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Shao Y, Lu N, Wu Z, Cai C, Wang S, Zhang LL, Zhou F, Xiao S, Liu L, Zeng X, Zheng H, Yang C, Zhao Z, Zhao G, Zhou JQ, Xue X, Qin Z. Creating a functional single-chromosome yeast. Nature 2018; 560:331-335. [PMID: 30069045 DOI: 10.1038/s41586-018-0382-x] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 06/22/2018] [Indexed: 02/02/2023]
Abstract
Eukaryotic genomes are generally organized in multiple chromosomes. Here we have created a functional single-chromosome yeast from a Saccharomyces cerevisiae haploid cell containing sixteen linear chromosomes, by successive end-to-end chromosome fusions and centromere deletions. The fusion of sixteen native linear chromosomes into a single chromosome results in marked changes to the global three-dimensional structure of the chromosome due to the loss of all centromere-associated inter-chromosomal interactions, most telomere-associated inter-chromosomal interactions and 67.4% of intra-chromosomal interactions. However, the single-chromosome and wild-type yeast cells have nearly identical transcriptome and similar phenome profiles. The giant single chromosome can support cell life, although this strain shows reduced growth across environments, competitiveness, gamete production and viability. This synthetic biology study demonstrates an approach to exploration of eukaryote evolution with respect to chromosome structure and function.
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Affiliation(s)
- Yangyang Shao
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ning Lu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhenfang Wu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Chen Cai
- University of Chinese Academy of Sciences, Beijing, China.,The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Shanshan Wang
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Ling-Li Zhang
- University of Chinese Academy of Sciences, Beijing, China.,The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Fan Zhou
- Frasergen Bioinformatics Co., Ltd, Wuhan, China
| | - Shijun Xiao
- Frasergen Bioinformatics Co., Ltd, Wuhan, China
| | - Lin Liu
- Frasergen Bioinformatics Co., Ltd, Wuhan, China
| | | | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Chen Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, Beijing, China
| | - Guoping Zhao
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China. .,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China. .,Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China. .,State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Jin-Qiu Zhou
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.
| | - Xiaoli Xue
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| | - Zhongjun Qin
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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29
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Romiguier J, Rolland J, Morandin C, Keller L. Phylogenomics of palearctic Formica species suggests a single origin of temporary parasitism and gives insights to the evolutionary pathway toward slave-making behaviour. BMC Evol Biol 2018; 18:40. [PMID: 29592795 PMCID: PMC5872393 DOI: 10.1186/s12862-018-1159-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 03/19/2018] [Indexed: 11/20/2022] Open
Abstract
Background The ants of the Formica genus are classical model species in evolutionary biology. In particular, Darwin used Formica as model species to better understand the evolution of slave-making, a parasitic behaviour where workers of another species are stolen to exploit their workforce. In his book “On the Origin of Species” (1859), Darwin first hypothesized that slave-making behaviour in Formica evolved in incremental steps from a free-living ancestor. Methods The absence of a well-resolved phylogenetic tree of the genus prevent an assessment of whether relationships among Formica subgenera are compatible with this scenario. In this study, we resolve the relationships among the 4 palearctic Formica subgenera (Formica str. s., Coptoformica, Raptiformica and Serviformica) using a phylogenomic dataset of 945 genes for 16 species. Results We provide a reference tree resolving the relationships among the main Formica subgenera with high bootstrap supports. Discussion The branching order of our tree suggests that the free-living lifestyle is ancestral in the Formica genus and that parasitic colony founding could have evolved a single time, probably acting as a pre-adaptation to slave-making behaviour. Conclusion This phylogenetic tree provides a solid backbone for future evolutionary studies in the Formica genus and slave-making behaviour. Electronic supplementary material The online version of this article (10.1186/s12862-018-1159-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jonathan Romiguier
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland. .,CNRS UMR-5554, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, 34095, Montpellier, France.
| | - Jonathan Rolland
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland.,Department of Zoology, University of British Columbia, #4200-6270 University Blvd, Vancouver, B.C., Canada.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland
| | - Claire Morandin
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Laurent Keller
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
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30
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Schnytzer Y, Simon-Blecher N, Li J, Waldman Ben-Asher H, Salmon-Divon M, Achituv Y, Hughes ME, Levy O. Tidal and diel orchestration of behaviour and gene expression in an intertidal mollusc. Sci Rep 2018; 8:4917. [PMID: 29559663 PMCID: PMC5861051 DOI: 10.1038/s41598-018-23167-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 03/07/2018] [Indexed: 12/17/2022] Open
Abstract
Intertidal inhabitants are exposed to the 24-hour solar day, and the 12.4 hour rising and falling of the tides. One or both of these cycles govern intertidal organisms' behaviour and physiology, yet little is known about the molecular clockworks of tidal rhythmicity. Here, we show that the limpet Cellana rota exhibits robust tidally rhythmic behaviour and gene expression. We assembled a de-novo transcriptome, identifying novel tidal, along with known circadian clock genes. Surprisingly, most of the putative circadian clock genes, lack a typical rhythmicity. We identified numerous tidally rhythmic genes and pathways commonly associated with the circadian clock. We show that not only is the behaviour of an intertidal organism in tune with the tides, but so too are many of its genes and pathways. These findings highlight the plasticity of biological timekeeping in nature, strengthening the growing notion that the role of 'canonical' circadian clock genes may be more fluid than previously thought, as exhibited in an organism which has evolved in an environment where tidal oscillations are the dominant driving force.
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Affiliation(s)
- Y Schnytzer
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, USA.
| | - N Simon-Blecher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - J Li
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - H Waldman Ben-Asher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - M Salmon-Divon
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Y Achituv
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - M E Hughes
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - O Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
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31
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Bigot D, Atyame CM, Weill M, Justy F, Herniou EA, Gayral P. Discovery of Culex pipiens associated tunisia virus: a new ssRNA(+) virus representing a new insect associated virus family. Virus Evol 2018; 4:vex040. [PMID: 29340209 PMCID: PMC5763275 DOI: 10.1093/ve/vex040] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In the global context of arboviral emergence, deep sequencing unlocks the discovery of new mosquito-borne viruses. Mosquitoes of the species Culex pipiens, C. torrentium, and C. hortensis were sampled from 22 locations worldwide for transcriptomic analyses. A virus discovery pipeline was used to analyze the dataset of 0.7 billion reads comprising 22 individual transcriptomes. Two closely related 6.8 kb viral genomes were identified in C. pipiens and named as Culex pipiens associated tunisia virus (CpATV) strains Ayed and Jedaida. The CpATV genome contained four ORFs. ORF1 possessed helicase and RNA-dependent RNA polymerase (RdRp) domains related to new viral sequences recently found mainly in dipterans. ORF2 and 4 contained a capsid protein domain showing strong homology with Virgaviridae plant viruses. ORF3 displayed similarities with eukaryotic Rhoptry domain and a merozoite surface protein (MSP7) domain only found in mosquito-transmitted Plasmodium, suggesting possible interactions between CpATV and vertebrate cells. Estimation of a strong purifying selection exerted on each ORFs and the presence of a polymorphism maintained in the coding region of ORF3 suggested that both CpATV sequences are genuine functional viruses. CpATV is part of an entirely new and highly diversified group of viruses recently found in insects, and that bears the genomic hallmarks of a new viral family.
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Affiliation(s)
- Diane Bigot
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université François-Rabelais, 37200 Tours, France
| | - Célestine M Atyame
- Institut des Sciences de l'Evolution, UMR 5554, Université Montpellier–CNRS–IRD–EPHE, Montpellier, France
| | - Mylène Weill
- Institut des Sciences de l'Evolution, UMR 5554, Université Montpellier–CNRS–IRD–EPHE, Montpellier, France
| | - Fabienne Justy
- Institut des Sciences de l'Evolution, UMR 5554, Université Montpellier–CNRS–IRD–EPHE, Montpellier, France
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université François-Rabelais, 37200 Tours, France
| | - Philippe Gayral
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université François-Rabelais, 37200 Tours, France
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32
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Bigot D, Dalmon A, Roy B, Hou C, Germain M, Romary M, Deng S, Diao Q, Weinert LA, Cook JM, Herniou EA, Gayral P. The discovery of Halictivirus resolves the Sinaivirus phylogeny. J Gen Virol 2017; 98:2864-2875. [DOI: 10.1099/jgv.0.000957] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Diane Bigot
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Anne Dalmon
- INRA UR 406 Abeilles et environnement, Centre de recherche Provence-Alpes-Côte d'Azur, Site Agroparc, Domaine St Paul 228, Route de l'aérodrome CS40509 84914 Avignon, France
| | - Bronwen Roy
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Chunsheng Hou
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, PR China
| | - Michèle Germain
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Manon Romary
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Shuai Deng
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, PR China
| | - Qingyun Diao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, PR China
| | - Lucy A. Weinert
- Institut des Sciences de l'Evolution UMR5554, Université Montpellier–CNRS–IRD–EPHE, Montpellier, France
- Present address: Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - James M. Cook
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Elisabeth A. Herniou
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Philippe Gayral
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
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Taguchi K, Usawachintachit M, Hamamoto S, Unno R, Tzou DT, Sherer BA, Wang Y, Okada A, Stoller ML, Yasui T, Chi T. Optimizing RNA Extraction of Renal Papilla Biopsy Tissue in Kidney Stone Formers: A New Methodology for Genomic Study. J Endourol 2017; 31:922-929. [PMID: 28719978 DOI: 10.1089/end.2017.0320] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION Endoscopic tools have provided versatile examination and treatment for kidney stone procedures. Despite endourologists researching urinary stone disease using endoscopes to collect tissue, this tissue collection method is limited. Endoscopically removed tissues are small in size, restricting the types of genome-based examination possible. We investigated a new method of renal papilla biopsy and RNA extraction to establish a genomic research methodology for kidney stone disease. PATIENTS AND METHODS We conducted a prospective multi-institutional study and collected renal papilla specimens from consecutive percutaneous nephrolithotomy and ureteroscopy (URS) cases performed for removal of upper urinary tract stones. Renal papilla tissue was extracted using ureteroscopic biopsy forceps after stone removal. RNA was extracted using two different extraction kits, and their quantity and quality were examined. Additionally, the impact of biopsy on surgical complications was compared between cases performed with and without biopsy by matched case-control analysis adjusted for age, gender, body mass index, bilaterality, and stone burden. RESULTS A total of 90 biopsies from 49 patients were performed, and the median duration between specimen collection and RNA extraction was 61 days. Both univariate and multivariate analyses showed BIGopsy® forceps usage significantly increased the total yield (p = 0.004) and quality (p = 0.001 for A260/280, p = 0.004 for A260/A230) of extracted RNA. Extraction using the RNeasy Micro Kit® also improved A260/A230, whereas reduced RNA integrity number of extracted RNA by univariate and multivariate analyses (p = 0.002 and p < 0.001, respectively). Moreover, matched case-control study demonstrated that endoscopic renal papilla biopsy caused no significant surgical complications, including bleeding, decreased stone clearance and hematocrit, and renal dysfunction. Biopsies during URS imparted an average of 20 minutes of procedure time over nonbiopsy cases. CONCLUSIONS We demonstrate a safe methodology for optimal RNA extraction of renal papilla tissue. This technique will accelerate advanced genomic studies for kidney stone formers by facilitating larger tissue yields.
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Affiliation(s)
- Kazumi Taguchi
- 1 Department of Urology, University of California , San Francisco, San Francisco, California.,2 Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences , Nagoya, Japan
| | - Manint Usawachintachit
- 1 Department of Urology, University of California , San Francisco, San Francisco, California.,3 Division of Urology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital , The Thai Red Cross Society, Bangkok, Thailand
| | - Shuzo Hamamoto
- 2 Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences , Nagoya, Japan
| | - Rei Unno
- 2 Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences , Nagoya, Japan
| | - David T Tzou
- 1 Department of Urology, University of California , San Francisco, San Francisco, California
| | - Benjamin A Sherer
- 1 Department of Urology, University of California , San Francisco, San Francisco, California
| | - Yongmei Wang
- 4 Endocrine Research Unit, Veterans Affairs Medical Center, San Francisco and University of California , San Francisco, California
| | - Atsushi Okada
- 2 Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences , Nagoya, Japan
| | - Marshall L Stoller
- 1 Department of Urology, University of California , San Francisco, San Francisco, California
| | - Takahiro Yasui
- 2 Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences , Nagoya, Japan
| | - Thomas Chi
- 1 Department of Urology, University of California , San Francisco, San Francisco, California
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Hiki K, Nakajima F, Tobino T. Application of cDNA-AFLP to biomarker exploration in a non-model species Grandidierella japonica. Ecotoxicol Environ Saf 2017; 140:206-213. [PMID: 28260686 DOI: 10.1016/j.ecoenv.2017.02.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/23/2017] [Accepted: 02/24/2017] [Indexed: 06/06/2023]
Abstract
Biomarkers of exposure can be used to identify specific contaminants that are adversely affecting aquatic organisms. However, it remains prohibitively costly to investigate multiple novel biomarkers of exposure in a non-model species, despite the development of next-generation sequencing technology. In this study, we focused on the use of cDNA-amplified fragment length polymorphism (AFLP) as a cost-effective biomarker discovery tool to test whether it could identify biomarkers of exposure in the non-model amphipod species Grandidierella japonica. Loci were identified that were differentially expressed in amphipods exposed to reference chemicals (Cu, Zn, and nicotine) and to an environmental sample (road dust) at sublethal concentrations. Eight loci were shown to respond consistently to nicotine at different concentrations, but not to Cu or Zn. Some of the loci also responded to an environmental road dust sample containing nicotine. These findings suggest that loci identified using cDNA-AFLP could be used as biomarkers of nicotine exposure in environmental samples with complex matrices. Further studies with other organisms and toxicants are needed, but we have demonstrated that the use of cDNA-AFLP to identify biomarkers for ecotoxicological studies of non-model species is at least feasible.
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Affiliation(s)
- Kyoshiro Hiki
- Department of Urban Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Fumiyuki Nakajima
- Department of Urban Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tomohiro Tobino
- Environmental Science Center, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
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Rix MG, Cooper SJ, Meusemann K, Klopfstein S, Harrison SE, Harvey MS, Austin AD. Post-Eocene climate change across continental Australia and the diversification of Australasian spiny trapdoor spiders (Idiopidae: Arbanitinae). Mol Phylogenet Evol 2017; 109:302-320. [DOI: 10.1016/j.ympev.2017.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/16/2016] [Accepted: 01/16/2017] [Indexed: 01/08/2023]
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Ballenghien M, Faivre N, Galtier N. Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions. BMC Biol 2017; 15:25. [PMID: 28356154 DOI: 10.1186/s12915-017-0366-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/13/2017] [Indexed: 01/06/2023] Open
Abstract
Background Contamination is a well-known but often neglected problem in molecular biology. Here, we investigated the prevalence of cross-contamination among 446 samples from 116 distinct species of animals, which were processed in the same laboratory and subjected to subcontracted transcriptome sequencing. Results Using cytochrome oxidase 1 as a barcode, we identified a minimum of 782 events of between-species contamination, with approximately 80% of our samples being affected. An analysis of laboratory metadata revealed a strong effect of the sequencing center: nearly all the detected events of between-species contamination involved species that were sent the same day to the same company. We introduce new methods to address the amount of within-species, between-individual contamination, and to correct for this problem when calling genotypes from base read counts. Conclusions We report evidence for pervasive within-species contamination in this data set, and show that classical population genomic statistics, such as synonymous diversity, the ratio of non-synonymous to synonymous diversity, inbreeding coefficient FIT, and Tajima’s D, are sensitive to this problem to various extents. Control analyses suggest that our published results are probably robust to the problem of contamination. Recommendations on how to prevent or avoid contamination in large-scale population genomics/molecular ecology are provided based on this analysis. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0366-6) contains supplementary material, which is available to authorized users.
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Ruocco N, Costantini S, Zupo V, Romano G, Ianora A, Fontana A, Costantini M. High-quality RNA extraction from the sea urchin Paracentrotus lividus embryos. PLoS One 2017; 12:e0172171. [PMID: 28199408 PMCID: PMC5310894 DOI: 10.1371/journal.pone.0172171] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/31/2017] [Indexed: 01/03/2023] Open
Abstract
The sea urchin Paracentrotus lividus (Lamarck, 1816) is a keystone herbivore in the Mediterranean Sea due to its ability to transform macroalgal-dominated communities into barren areas characterized by increased cover of bare substrates and encrusting coralline algae, reduced biodiversity and altered ecosystem functions. P. lividus is also an excellent animal model for toxicology, physiology and biology investigations having been used for more than a century as a model for embryological studies with synchronously developing embryos which are easy to manipulate and analyze for morphological aberrations. Despite its importance for the scientific community, the complete genome is still not fully annotated. To date, only a few molecular tools are available and a few Next Generation Sequencing (NGS) studies have been performed. Here we aimed at setting-up an RNA extraction method to obtain high quality and sufficient quantity of RNA for NGS from P. lividus embryos at the pluteus stage. We compared five different RNA extraction protocols from four different pools of plutei (500, 1000, 2500 and 5000 embryos): TRIzol®, and four widely-used Silica Membrane kits, GenElute™ Mammalian Total RNA Miniprep Kit, RNAqueous® Micro Kit, RNeasy® Micro Kit and Aurum™ Total RNA Mini Kit. The quantity of RNA isolated was evaluated using NanoDrop. The quality, considering the purity, was measured as A260/A280 and A260/230 ratios. The integrity was measured by RNA Integrity Number (RIN). Our results demonstrated that the most efficient procedures were GenElute, RNeasy and Aurum, producing a sufficient quantity of RNA for NGS. The Bioanalyzer profiles and RIN values revealed that the most efficient methods guaranteeing for RNA integrity were RNeasy and Aurum combined with an initial preservation in RNAlater. This research represents the first attempt to standardize a method for high-quality RNA extraction from sea urchin embryos at the pluteus stage, providing a new resource for this established model marine organism.
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Affiliation(s)
- Nadia Ruocco
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cinthia, Napoli, Italy
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, Pozzuoli, Naples, Italy
| | - Susan Costantini
- CROM, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS, Napoli, Italy
| | - Valerio Zupo
- Center of Villa Dohrn Ischia-Benthic Ecology, Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, P.ta S. Pietro, Ischia, Naples, Italy
| | - Giovanna Romano
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
| | - Adrianna Ianora
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
| | - Angelo Fontana
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, Pozzuoli, Naples, Italy
- * E-mail: (MC); (AF)
| | - Maria Costantini
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
- * E-mail: (MC); (AF)
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Weber AAT, Abi-Rached L, Galtier N, Bernard A, Montoya-Burgos JI, Chenuil A. Positive selection on sperm ion channels in a brooding brittle star: consequence of life-history traits evolution. Mol Ecol 2017; 26:3744-3759. [PMID: 28099777 DOI: 10.1111/mec.14024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/04/2017] [Accepted: 01/09/2017] [Indexed: 01/12/2023]
Abstract
Closely related species are key models to investigate mechanisms leading to reproductive isolation and early stages of diversification, also at the genomic level. The brittle star cryptic species complex Ophioderma longicauda encompasses the sympatric broadcast-spawning species C3 and the internal brooding species C5. Here, we used de novo transcriptome sequencing and assembly in two closely related species displaying contrasting reproductive modes to compare their genetic diversity and to investigate the role of natural selection in reproductive isolation. We reconstructed 20 146 and 22 123 genes for C3 and C5, respectively, and characterized a set of 12 229 orthologs. Genetic diversity was 1.5-2 times higher in C3 compared to C5, confirming that species with low parental investment display higher levels of genetic diversity. Forty-eight genes were the targets of positive diversifying selection during the evolution of the two species. Notably, two genes (NHE and TetraKCNG) are sperm-specific ion channels involved in sperm motility. Ancestral sequence reconstructions show that natural selection targeted the two genes in the brooding species. This may result from an adaptation to the novel environmental conditions surrounding sperm in the brooding species, either directly affecting sperm or via an increase in male/female conflict. This phenomenon could have promoted prezygotic reproductive isolation between C3 and C5. Finally, the sperm receptors to egg chemoattractants differed between C3 and C5 in the ligand-binding region. We propose that mechanisms of species-specific gamete recognition in brittle stars occur during sperm chemotaxis (sperm attraction towards the eggs), contrary to other marine invertebrates where prezygotic barriers to interspecific hybridization typically occur before sperm-egg fusion.
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Affiliation(s)
- A A-T Weber
- Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE) - CNRS - IRD - UAPV, Aix-Marseille Université, Station Marine d'Endoume, Chemin de la Batterie des Lions, 13007, Marseille, France.,Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - L Abi-Rached
- Equipe ATIP, URMITE UM 63 CNRS 7278 IRD 198 Inserm U1095, IHU Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - N Galtier
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, IRD, EPHE, Université de Montpellier, Place E. Bataillon, 34095, Montpellier, France
| | - A Bernard
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, IRD, EPHE, Université de Montpellier, Place E. Bataillon, 34095, Montpellier, France
| | - J I Montoya-Burgos
- Department of Genetics and Evolution, University of Geneva, 4, Bvd d'Yvoy, 1205, Geneva, Switzerland
| | - A Chenuil
- Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE) - CNRS - IRD - UAPV, Aix-Marseille Université, Station Marine d'Endoume, Chemin de la Batterie des Lions, 13007, Marseille, France
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Romiguier J, Fournier A, Yek SH, Keller L. Convergent evolution of social hybridogenesis in Messor harvester ants. Mol Ecol 2016; 26:1108-1117. [PMID: 27813203 DOI: 10.1111/mec.13899] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/26/2016] [Accepted: 10/12/2016] [Indexed: 12/14/2022]
Abstract
Sexual reproduction generally requires no more than two partners. Here, we show convergent evolution of social hybridogenesis, a reproductive system requiring three reproductive partners in harvester ants. In this unorthodox reproductive system, two distinct genetic lineages live in sympatry and queens have to mate with males of their own lineage to produce queens along with males of the alternative lineage to produce workers. Using a large transcriptomic data set of nine species, we show that social hybridogenesis evolved at least three times independently in the genus Messor. Moreover, a study of 13 populations of Messor barbarus revealed that this mode of reproduction is fixed in the whole range of this ecologically dominant species. Finally, we show that workers can produce males carrying genes of the two genetic lineages, raising the possibility of rare gene flow between lineages contributing to the long-term maintenance of pairs of interdependent lineages. These results emphasize the evolutionary importance of social hybridogenesis, a major transition possibly linked to the peculiar ecology of harvester ants.
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Affiliation(s)
- Jonathan Romiguier
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Axel Fournier
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Sze Huei Yek
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
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Rousselle M, Faivre N, Ballenghien M, Galtier N, Nabholz B. Hemizygosity Enhances Purifying Selection: Lack of Fast-Z Evolution in Two Satyrine Butterflies. Genome Biol Evol 2016; 8:3108-3119. [PMID: 27590089 PMCID: PMC5174731 DOI: 10.1093/gbe/evw214] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The fixation probability of a recessive beneficial mutation is increased on the X or Z chromosome, relative to autosomes, because recessive alleles carried by X or Z are exposed to selection in the heterogametic sex. This leads to an increased dN/dS ratio on sex chromosomes relative to autosomes, a pattern called the “fast-X” or “fast-Z” effect. Besides positive selection, the strength of genetic drift and the efficacy of purifying selection, which affect the rate of molecular evolution, might differ between sex chromosomes and autosomes. Disentangling the complex effects of these distinct forces requires the genome-wide analysis of polymorphism, divergence and gene expression data in a variety of taxa. Here we study the influence of hemizygosity of the Z chromosome in Maniola jurtina and Pyronia tithonus, two species of butterflies (Lepidoptera, Nymphalidae, Satyrinae). Using transcriptome data, we compare the strength of positive and negative selection between Z and autosomes accounting for sex-specific gene expression. We show that M. jurtina and P. tithonus do not experience a faster, but rather a slightly slower evolutionary rate on the Z than on autosomes. Our analysis failed to detect a significant difference in adaptive evolutionary rate between Z and autosomes, but comparison of male-biased, unbiased and female-biased Z-linked genes revealed an increased efficacy of purifying selection against recessive deleterious mutations in female-biased Z-linked genes. This probably contributes to the lack of fast-Z evolution of satyrines. We suggest that the effect of hemizygosity on the fate of recessive deleterious mutations should be taken into account when interpreting patterns of molecular evolution in sex chromosomes vs. autosomes.
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Affiliation(s)
- Marjolaine Rousselle
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Nicolas Faivre
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Marion Ballenghien
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Nicolas Galtier
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Benoit Nabholz
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
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François S, Filloux D, Roumagnac P, Bigot D, Gayral P, Martin DP, Froissart R, Ogliastro M. Discovery of parvovirus-related sequences in an unexpected broad range of animals. Sci Rep 2016; 6:30880. [PMID: 27600734 PMCID: PMC5013282 DOI: 10.1038/srep30880] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/11/2016] [Indexed: 02/06/2023] Open
Abstract
Our knowledge of the genetic diversity and host ranges of viruses is fragmentary. This is particularly true for the Parvoviridae family. Genetic diversity studies of single stranded DNA viruses within this family have been largely focused on arthropod- and vertebrate-infecting species that cause diseases of humans and our domesticated animals: a focus that has biased our perception of parvovirus diversity. While metagenomics approaches could help rectify this bias, so too could transcriptomics studies. Large amounts of transcriptomic data are available for a diverse array of animal species and whenever this data has inadvertently been gathered from virus-infected individuals, it could contain detectable viral transcripts. We therefore performed a systematic search for parvovirus-related sequences (PRSs) within publicly available transcript, genome and protein databases and eleven new transcriptome datasets. This revealed 463 PRSs in the transcript databases of 118 animals. At least 41 of these PRSs are likely integrated within animal genomes in that they were also found within genomic sequence databases. Besides illuminating the ubiquity of parvoviruses, the number of parvoviral sequences discovered within public databases revealed numerous previously unknown parvovirus-host combinations; particularly in invertebrates. Our findings suggest that the host-ranges of extant parvoviruses might span the entire animal kingdom.
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Affiliation(s)
- S. François
- INRA, UMR DGIMI, F-34095, Montpellier, France
| | - D. Filloux
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France
| | - P. Roumagnac
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France
| | - D. Bigot
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS–Université François Rabelais, 37200 Tours, France
| | - P. Gayral
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS–Université François Rabelais, 37200 Tours, France
- UMR5554–Institut des Sciences de l’Evolution UMR5554, Université Montpellier–CNRS–IRD–EPHE, 34000 Montpellier, France
| | - D. P. Martin
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - R. Froissart
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France
- CNRS-IRD-UM, UMR 5290, MIVEGEC, 911 avenue Agropolis, 34394, Montpellier, France
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Ament-Velásquez SL, Figuet E, Ballenghien M, Zattara EE, Norenburg JL, Fernández-Álvarez FA, Bierne J, Bierne N, Galtier N. Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea): hybridization, polyploidy and the Meselson effect. Mol Ecol 2016; 25:3356-69. [DOI: 10.1111/mec.13717] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 04/18/2016] [Accepted: 05/02/2016] [Indexed: 12/28/2022]
Affiliation(s)
- S. L. Ament-Velásquez
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
- Department of Organismal Biology; Systematic Biology; Uppsala University; PO Box 256 SE-751 05 Uppsala Sweden
| | - E. Figuet
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
| | - M. Ballenghien
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
| | - E. E. Zattara
- Department of Biology; Indiana University; 107 S Indiana Ave Bloomington IN 47405 USA
- Department of Invertebrate Zoology; National Museum of Natural History; Smithsonian Institution; 10th St. & Constitution Ave. NW Washington DC 20560 USA
| | - J. L. Norenburg
- Department of Invertebrate Zoology; National Museum of Natural History; Smithsonian Institution; 10th St. & Constitution Ave. NW Washington DC 20560 USA
| | | | - J. Bierne
- Laboratoire de Biologie Cellulaire et Moléculaire; Université de Reims Champagne-Ardenne; 9 Boulevard de la Paix 51100 Reims France
| | - N. Bierne
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
| | - N. Galtier
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
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Bataillon T, Galtier N, Bernard A, Cryer N, Faivre N, Santoni S, Severac D, Mikkelsen TN, Larsen KS, Beier C, Sørensen JG, Holmstrup M, Ehlers BK. A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate. Glob Chang Biol 2016; 22:2370-2379. [PMID: 27109012 PMCID: PMC5021122 DOI: 10.1111/gcb.13293] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 01/15/2016] [Accepted: 02/17/2016] [Indexed: 06/05/2023]
Abstract
Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out in natural field conditions. We examined the evolutionary response to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that about 12% of the genetic polymorphisms exhibit differences in allele frequencies associated to changes in soil temperature and soil moisture. This shows an evolutionary response to realistic climate change happening over short-time scale, and calls for incorporating evolution into models predicting future response of species to climate change. It also shows that designed climate change experiments coupled with genome sequencing offer great potential to test for the occurrence (or lack) of an evolutionary response.
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Affiliation(s)
- Thomas Bataillon
- Bioinformatics Research Center (BiRC)Aarhus UniversityC.F. Møllers Allé 8, Building 11108000Aarhus CDenmark
| | - Nicolas Galtier
- CNRS UMR 5554Institut des Sciences de l'Evolution de MontpellierUniversité Montpellier 234095 Montpellier Cedex 05France
| | - Aurelien Bernard
- CNRS UMR 5554Institut des Sciences de l'Evolution de MontpellierUniversité Montpellier 234095 Montpellier Cedex 05France
| | - Nicolai Cryer
- Bioinformatics Research Center (BiRC)Aarhus UniversityC.F. Møllers Allé 8, Building 11108000Aarhus CDenmark
| | - Nicolas Faivre
- CNRS UMR 5554Institut des Sciences de l'Evolution de MontpellierUniversité Montpellier 234095 Montpellier Cedex 05France
| | | | - Dany Severac
- c/o Institut de Génomique FonctionnelleMGX‐Montpellier GenomiX34094 Montpellier Cedex 05France
| | - Teis N. Mikkelsen
- Department of Chemical and Biochemical EngineeringEcosystems CentreTechnical University of Denmark2800Kgs. LyngbyDenmark
| | - Klaus S. Larsen
- Department for Geosciences and Natural Resource ManagementUniversity of CopenhagenRolighedsvej 23DK‐1958FrederiksbergDenmark
| | - Claus Beier
- Department for Geosciences and Natural Resource ManagementUniversity of CopenhagenRolighedsvej 23DK‐1958FrederiksbergDenmark
- Centre for Catchments and Urban Water ResearchNorwegian Institute for Water Research (NIVA)Gaustadalléen 210349OsloNorway
| | - Jesper G. Sørensen
- Department of BioscienceAarhus UniversityNy Munkegade 1168000Aarhus CDenmark
| | - Martin Holmstrup
- Department of BioscienceAarhus UniversityVejlsøvej 258600SilkeborgDenmark
| | - Bodil K. Ehlers
- Department of BioscienceAarhus UniversityVejlsøvej 258600SilkeborgDenmark
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Humble E, Martinez-Barrio A, Forcada J, Trathan PN, Thorne MAS, Hoffmann M, Wolf JBW, Hoffman JI. A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them. Mol Ecol Resour 2016; 16:909-21. [DOI: 10.1111/1755-0998.12502] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 12/01/2015] [Accepted: 12/15/2015] [Indexed: 01/19/2023]
Affiliation(s)
- E. Humble
- Department of Animal Behaviour; University of Bielefeld; Postfach 100131 33501 Bielefeld Germany
- British Antarctic Survey; High Cross, Madingley Road Cambridge CB3 OET UK
| | - A. Martinez-Barrio
- Science of Life Laboratories and Department of Cell and Molecular Biology; Uppsala University; Husargatan 3 75124 Uppsala Sweden
| | - J. Forcada
- British Antarctic Survey; High Cross, Madingley Road Cambridge CB3 OET UK
| | - P. N. Trathan
- British Antarctic Survey; High Cross, Madingley Road Cambridge CB3 OET UK
| | - M. A. S. Thorne
- British Antarctic Survey; High Cross, Madingley Road Cambridge CB3 OET UK
| | - M. Hoffmann
- Max Planck Institute for Developmental Biology; Spemannstrasse 35 72076 Tübingen Germany
| | - J. B. W. Wolf
- Science of Life Laboratories and Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D 75236 Uppsala Sweden
| | - J. I. Hoffman
- Department of Animal Behaviour; University of Bielefeld; Postfach 100131 33501 Bielefeld Germany
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Abstract
The rate at which genomes adapt to environmental changes and the prevalence of adaptive processes in molecular evolution are two controversial issues in current evolutionary genetics. Previous attempts to quantify the genome-wide rate of adaptation through amino-acid substitution have revealed a surprising diversity of patterns, with some species (e.g. Drosophila) experiencing a very high adaptive rate, while other (e.g. humans) are dominated by nearly-neutral processes. It has been suggested that this discrepancy reflects between-species differences in effective population size. Published studies, however, were mainly focused on model organisms, and relied on disparate data sets and methodologies, so that an overview of the prevalence of adaptive protein evolution in nature is currently lacking. Here we extend existing estimators of the amino-acid adaptive rate by explicitly modelling the effect of favourable mutations on non-synonymous polymorphism patterns, and we apply these methods to a newly-built, homogeneous data set of 44 non-model animal species pairs. Data analysis uncovers a major contribution of adaptive evolution to the amino-acid substitution process across all major metazoan phyla—with the notable exception of humans and primates. The proportion of adaptive amino-acid substitution is found to be positively correlated to species effective population size. This relationship, however, appears to be primarily driven by a decreased rate of nearly-neutral amino-acid substitution because of more efficient purifying selection in large populations. Our results reveal that adaptive processes dominate the evolution of proteins in most animal species, but do not corroborate the hypothesis that adaptive substitutions accumulate at a faster rate in large populations. Implications regarding the factors influencing the rate of adaptive evolution and positive selection detection in humans vs. other organisms are discussed. The rate at which species adapt to environmental changes is a controversial topic. The theory predicts that adaptation is easier in large than in small populations, and the genomic studies of model organisms have revealed a much higher adaptive rate in large population-sized flies than in small population-sized humans and apes. Here we build and analyse a large data set of protein-coding sequences made of thousands of genes in 44 pairs of species from various groups of animals including insects, molluscs, annelids, echinoderms, reptiles, birds, and mammals. Extending and improving existing data analysis methods, we show that adaptation is a major process in protein evolution across all phyla of animals: the proportion of amino-acid substitutions that occurred adaptively is above 50% in a majority of species, and reaches up to 90%. Our analysis does not confirm that population size, here approached through species genetic diversity and ecological traits, does influence the rate of adaptive molecular evolution, but points to human and apes as a special case, compared to other animals, in terms of adaptive genomic processes.
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Affiliation(s)
- Nicolas Galtier
- Institut des Sciences de l'Evolution UMR5554, Université Montpellier–CNRS–IRD–EPHE, Montpellier, France
- * E-mail:
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47
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Jarman SN, Polanowski AM, Faux CE, Robbins J, De Paoli-Iseppi R, Bravington M, Deagle BE. Molecular biomarkers for chronological age in animal ecology. Mol Ecol 2016; 24:4826-47. [PMID: 26308242 DOI: 10.1111/mec.13357] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/08/2015] [Accepted: 08/21/2015] [Indexed: 01/07/2023]
Abstract
The chronological age of an individual animal predicts many of its biological characteristics, and these in turn influence population-level ecological processes. Animal age information can therefore be valuable in ecological research, but many species have no external features that allow age to be reliably determined. Molecular age biomarkers provide a potential solution to this problem. Research in this area of molecular ecology has so far focused on a limited range of age biomarkers. The most commonly tested molecular age biomarker is change in average telomere length, which predicts age well in a small number of species and tissues, but performs poorly in many other situations. Epigenetic regulation of gene expression has recently been shown to cause age-related modifications to DNA and to cause changes in abundance of several RNA types throughout animal lifespans. Age biomarkers based on these epigenetic changes, and other new DNA-based assays, have already been applied to model organisms, humans and a limited number of wild animals. There is clear potential to apply these marker types more widely in ecological studies. For many species, these new approaches will produce age estimates where this was previously impractical. They will also enable age information to be gathered in cross-sectional studies and expand the range of demographic characteristics that can be quantified with molecular methods. We describe the range of molecular age biomarkers that have been investigated to date and suggest approaches for developing the newer marker types as age assays in nonmodel animal species.
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Affiliation(s)
- Simon N Jarman
- Australian Antarctic Division, 203 Channel Highway, Kingston, Tas., 7050, Australia
| | - Andrea M Polanowski
- Australian Antarctic Division, 203 Channel Highway, Kingston, Tas., 7050, Australia
| | - Cassandra E Faux
- Australian Antarctic Division, 203 Channel Highway, Kingston, Tas., 7050, Australia
| | - Jooke Robbins
- Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA, 02657, USA
| | - Ricardo De Paoli-Iseppi
- Australian Antarctic Division, 203 Channel Highway, Kingston, Tas., 7050, Australia.,Institute of Marine and Antarctic Studies, University of Tasmania, Castray Esplanade, Hobart, Tas., 7000, Australia
| | - Mark Bravington
- Marine Laboratory, Commonwealth Scientific and Industrial Research Organisation, Castray Esplanade, Hobart, Tas., 7000, Australia
| | - Bruce E Deagle
- Australian Antarctic Division, 203 Channel Highway, Kingston, Tas., 7050, Australia
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Brinke A, Buchinger S. Toxicogenomics in Environmental Science. In vitro Environmental Toxicology - Concepts, Application and Assessment 2016; 157:159-186. [DOI: 10.1007/10_2016_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Dedeine F, Weinert LA, Bigot D, Josse T, Ballenghien M, Cahais V, Galtier N, Gayral P. Comparative Analysis of Transcriptomes from Secondary Reproductives of Three Reticulitermes Termite Species. PLoS One 2015; 10:e0145596. [PMID: 26698123 PMCID: PMC4689415 DOI: 10.1371/journal.pone.0145596] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 12/07/2015] [Indexed: 01/24/2023] Open
Abstract
Termites are eusocial insects related to cockroaches that feed on lignocellulose. These insects are key species in ecosystems since they recycle a large amount of nutrients but also are pests, exerting major economic impacts. Knowledge on the molecular pathways underlying reproduction, caste differentiation or lignocellulose digestion would largely benefit from additional transcriptomic data. This study focused on transcriptomes of secondary reproductive females (nymphoid neotenics). Thirteen transcriptomes were used: 10 of Reticulitermes flavipes and R. grassei sequenced from a previous study, and two transcriptomes of R. lucifugus sequenced for the present study. After transcriptome assembly and read mapping, we examined interspecific variations of genes expressed by termites or gut microorganisms. A total of 18,323 orthologous gene clusters were detected. Functional annotation and taxonomic assignment were performed on a total of 41,287 predicted contigs in the three termite species. Between the termite species studied, functional categories of genes were comparable. Gene ontology (GO) terms analysis allowed the discovery of 9 cellulases and a total of 79 contigs potentially involved in 11 enzymatic activities used in wood metabolism. Altogether, results of this study illustrate the strong potential for the use of comparative interspecific transcriptomes, representing a complete resource for future studies including differentially expressed genes between castes or SNP analysis for population genetics.
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Affiliation(s)
- Franck Dedeine
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS—Université François Rabelais, 37200, Tours, France
| | - Lucy A. Weinert
- Institut des Sciences de l’Evolution, UMR 5554, Université de Montpellier—CNRS—IRD—EPHE, Montpellier, France
| | - Diane Bigot
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS—Université François Rabelais, 37200, Tours, France
| | - Thibaut Josse
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS—Université François Rabelais, 37200, Tours, France
| | - Marion Ballenghien
- Institut des Sciences de l’Evolution, UMR 5554, Université de Montpellier—CNRS—IRD—EPHE, Montpellier, France
| | - Vincent Cahais
- Institut des Sciences de l’Evolution, UMR 5554, Université de Montpellier—CNRS—IRD—EPHE, Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l’Evolution, UMR 5554, Université de Montpellier—CNRS—IRD—EPHE, Montpellier, France
| | - Philippe Gayral
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS—Université François Rabelais, 37200, Tours, France
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Kono N, Nakamura H, Ito Y, Tomita M, Arakawa K. Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly. Mol Ecol Resour 2015; 16:662-72. [PMID: 26561354 DOI: 10.1111/1755-0998.12485] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 10/26/2015] [Accepted: 10/29/2015] [Indexed: 11/30/2022]
Abstract
With advances in high-throughput sequencing technologies, de novo transcriptome sequencing and assembly has become a cost-effective method to obtain comprehensive genetic information of a species of interest, especially in nonmodel species with large genomes such as spiders. However, high-quality RNA is essential for successful sequencing, and sample preservation conditions require careful consideration for the effective storage of field-collected samples. To this end, we report a streamlined feasibility study of various storage conditions and their effects on de novo transcriptome assembly results. The storage parameters considered include temperatures ranging from room temperature to -80°C; preservatives, including ethanol, RNAlater, TRIzol and RNAlater-ICE; and sample submersion states. As a result, intact RNA was extracted and assembly was successful when samples were preserved at low temperatures regardless of the type of preservative used. The assemblies as well as the gene expression profiles were shown to be robust to RNA degradation, when 30 million 150-bp paired-end reads are obtained. The parameters for sample storage, RNA extraction, library preparation, sequencing and in silico assembly considered in this work provide a guideline for the study of field-collected samples of spiders.
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Affiliation(s)
- Nobuaki Kono
- Institute for Advanced Biosciences, Keio University, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Hiroyuki Nakamura
- Spiber Inc., Mizukami 234-1, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Yusuke Ito
- Spiber Inc., Mizukami 234-1, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
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