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Liao Z, Zhang Q, Yang L, Li H, Mo W, Song Z, Huang X, Wen S, Cheng X, He M. Increased hsa-miR-100-5p Expression Improves Hepatocellular Carcinoma Prognosis in the Asian Population with PLK1 Variant rs27770A>G. Cancers (Basel) 2023; 16:129. [PMID: 38201556 PMCID: PMC10778516 DOI: 10.3390/cancers16010129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Hepatocellular carcinoma (HCC) has the highest incidence and mortality in the Asian population, and race is an independent risk factor affecting survival time in liver cancer. Micro RNAs (miRNAs) are remarkably dysregulated in HCC and closely associated with HCC prognosis. Recent studies show that genetic variability between ethnic groups may result in differences in the specificity of HCC miRNA biomarkers. Here, we reveal a high expression level of hsa-miR-100-5p, an HCC prognosis-related miRNA, which improves HCC prognosis in the Asian Population with Polo-like kinase 1 (PLK1) variant rs27770A>G. In this study, we discovered that hsa-miR-100-5p was downregulated in various HCC cell lines. While mimics transient transfection and mouse liver cancer model confirmed the interaction between hsa-miR-100-5p and PLK1, a stratified analysis based on the Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) data suggest both low hsa-miR-100-5p expression level and high PLK1 expression level associated with poor HCC prognosis, especially in the Asian population. According to the 1000 Genomes Project database, the SNP rs27770 located in 3'UTR of PLK1 had a significantly higher G allele frequency in the East Asian population. Bioinformatics analysis suggested that rs27770 A>G affects PLK1 mRNA secondary structure and alters the hsa-miR-100-5p/PLK1 interaction by forming an additional seedless binding site. This racial variation caused PLK1 to be more vulnerable to hsa-miR-100-5p inhibition, resulting in hsa-miR-100-5p being more favorable for HCC prognosis in the Asian population.
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Affiliation(s)
- Zhouxiang Liao
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
| | - Qi Zhang
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
| | - Lichao Yang
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
| | - Hui Li
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
| | - Wanling Mo
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
| | - Zhenyu Song
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
| | - Xuejing Huang
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
| | - Sha Wen
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
| | - Xiaojing Cheng
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
- Life Sciences Institute, Guangxi Medical University, Nanning 530021, China
| | - Min He
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
- Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning 530021, China
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2
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Choquet M, Lenner F, Cocco A, Toullec G, Corre E, Toullec JY, Wallberg A. Comparative Population Transcriptomics Provide New Insight into the Evolutionary History and Adaptive Potential of World Ocean Krill. Mol Biol Evol 2023; 40:msad225. [PMID: 37816123 PMCID: PMC10642690 DOI: 10.1093/molbev/msad225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/31/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Genetic variation is instrumental for adaptation to changing environments but it is unclear how it is structured and contributes to adaptation in pelagic species lacking clear barriers to gene flow. Here, we applied comparative genomics to extensive transcriptome datasets from 20 krill species collected across the Atlantic, Indian, Pacific, and Southern Oceans. We compared genetic variation both within and between species to elucidate their evolutionary history and genomic bases of adaptation. We resolved phylogenetic interrelationships and uncovered genomic evidence to elevate the cryptic Euphausia similis var. armata into species. Levels of genetic variation and rates of adaptive protein evolution vary widely. Species endemic to the cold Southern Ocean, such as the Antarctic krill Euphausia superba, showed less genetic variation and lower evolutionary rates than other species. This could suggest a low adaptive potential to rapid climate change. We uncovered hundreds of candidate genes with signatures of adaptive evolution among Antarctic Euphausia but did not observe strong evidence of adaptive convergence with the predominantly Arctic Thysanoessa. We instead identified candidates for cold-adaptation that have also been detected in Antarctic fish, including genes that govern thermal reception such as TrpA1. Our results suggest parallel genetic responses to similar selection pressures across Antarctic taxa and provide new insights into the adaptive potential of important zooplankton already affected by climate change.
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Affiliation(s)
- Marvin Choquet
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Felix Lenner
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Arianna Cocco
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Gaëlle Toullec
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Erwan Corre
- CNRS, Sorbonne Université, FR 2424, ABiMS Platform, Station Biologique de Roscoff, Roscoff, France
| | - Jean-Yves Toullec
- CNRS, UMR 7144, AD2M, Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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3
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Martínez M, Harms L, Abele D, Held C. Mitochondrial Heteroplasmy and PCR Amplification Bias Lead to Wrong Species Delimitation with High Confidence in the South American and Antarctic Marine Bivalve Aequiyoldia eightsii Species Complex. Genes (Basel) 2023; 14:genes14040935. [PMID: 37107693 PMCID: PMC10138075 DOI: 10.3390/genes14040935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
The species delimitation of the marine bivalve species complex Aequiyoldia eightsii in South America and Antarctica is complicated by mitochondrial heteroplasmy and amplification bias in molecular barcoding. In this study, we compare different data sources (mitochondrial cytochrome c oxidase subunit I (COI) sequences; nuclear and mitochondrial SNPs). Whilst all the data suggest that populations on either side of the Drake Passage belong to different species, the picture is less clear within Antarctic populations, which harbor three distinct mitochondrial lineages (p-dist ≈ 6%) that coexist in populations and in a subset of individuals with heteroplasmy. Standard barcoding procedures lead to amplification bias favoring either haplotype unpredictably and thus overestimate the species richness with high confidence. However, nuclear SNPs show no differentiation akin to the trans-Drake comparison, suggesting that the Antarctic populations represent a single species. Their distinct haplotypes likely evolved during periods of temporary allopatry, whereas recombination eroded similar differentiation patterns in the nuclear genome after secondary contact. Our study highlights the importance of using multiple data sources and careful quality control measures to avoid bias and increase the accuracy of molecular species delimitation. We recommend an active search for mitochondrial heteroplasmy and haplotype-specific primers for amplification in DNA-barcoding studies.
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Affiliation(s)
- Mariano Martínez
- Functional Ecology, Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Oceanografía y Ecología Marina, Instituto de Ecología y Ciencias Ambientales, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Lars Harms
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Herrstrasse 231, 26129 Oldenburg, Germany
| | - Doris Abele
- Functional Ecology, Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Christoph Held
- Functional Ecology, Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, 27570 Bremerhaven, Germany
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4
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Priscilla L, Malathi E, Moses Inbaraj R. Sex steroid profile during oocyte development and maturation in the intertidal worm Marphysa madrasi (Polychaeta: Eunicidae) from the east coast of India. Gen Comp Endocrinol 2023; 331:114118. [PMID: 36037874 DOI: 10.1016/j.ygcen.2022.114118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 08/04/2022] [Accepted: 08/18/2022] [Indexed: 02/07/2023]
Abstract
Marphysa madrasi is a commercially valuable maturation diet in crustacean aquaculture. This study presents the first detailed investigation of oogenesis in the intertidal polychaete worm M. madrasi and reports the steroid profile during oocyte growth and development. Oogenesis is extraovarian type I, originating from coelomic epithelial cells, with four stages of development - primary growth, early vitellogenic, late vitellogenic, and maturation. The primary growth phase contains oogonial cells and previtellogenic oocyte clusters in the early, mid, and late stages of development form a dispersed ovary attached to blood vessels. The late previtellogenic oocytes detach from the ovary at the onset of vitellogenesis. The detached oocytes complete vitellogenesis and final maturation in the coelomic fluid as solitary free-floating cells without any connection with follicle cells. The worms display asynchronous reproduction with a heterogeneous population of developing oocytes. Steroid extracts from the polychaete homogenates in different stages of oogenesis were identified by HPLC and confirmed by LC-MS/MS. In M. madrasi, two vertebrate-type steroids, pregnenolone (P5) and 17α-hydroxyprogesterone (17-OHP) were detected and quantified. The P5 levels were low in immature worms but increased significantly by ∼ 8.3-fold in the previtellogenic stage and peaked during oocyte maturation. 17-OHP levels were low in immature worms but gradually increase as the oogenesis progress to the primary growth and early vitellogenic phase, with a significant increase (p < 0.001) during the late vitellogenic phase. Although an increase in the concentration of P5 and 17-OHP during vitellogenesis and maturation of oocytes points to a possible role in reproduction, the absence of other vertebrate-type steroids in the investigated polychaete signifies a plausible uptake of P5 and 17-OHP from the environment.
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Affiliation(s)
- Lyndsay Priscilla
- Department of Zoology, Queen Mary's College (Autonomous), Affiliated to the University of Madras, Chennai 600004, Tamil Nadu, India; Endocrinology Unit, Department of Zoology, Madras Christian College, Affiliated to the University of Madras, Chennai, India
| | - E Malathi
- Department of Zoology, Queen Mary's College (Autonomous), Affiliated to the University of Madras, Chennai 600004, Tamil Nadu, India
| | - R Moses Inbaraj
- Endocrinology Unit, Department of Zoology, Madras Christian College, Affiliated to the University of Madras, Chennai, India.
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5
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Genomic data is missing for many highly invasive species, restricting our preparedness for escalating incursion rates. Sci Rep 2022; 12:13987. [PMID: 35977991 PMCID: PMC9385848 DOI: 10.1038/s41598-022-17937-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/03/2022] [Indexed: 11/14/2022] Open
Abstract
Biological invasions drive environmental change, potentially threatening native biodiversity, human health, and global economies. Population genomics is an increasingly popular tool in invasion biology, improving accuracy and providing new insights into the genetic factors that underpin invasion success compared to research based on a small number of genetic loci. We examine the extent to which population genomic resources, including reference genomes, have been used or are available for invasive species research. We find that 82% of species on the International Union for Conservation of Nature “100 Worst Invasive Alien Species” list have been studied using some form of population genetic data, but just 32% of these species have been studied using population genomic data. Further, 55% of the list’s species lack a reference genome. With incursion rates escalating globally, understanding how genome-driven processes facilitate invasion is critical, but despite a promising trend of increasing uptake, “invasion genomics” is still in its infancy. We discuss how population genomic data can enhance our understanding of biological invasion and inform proactive detection and management of invasive species, and we call for more research that specifically targets this area.
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6
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McElroy KE, Bankers L, Soper D, Hehman G, Boore JL, Logsdon JM, Neiman M. Patterns of gene expression in ovaries of sexual vs. asexual lineages of a freshwater snail. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.845640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Why sexual reproduction is so common when asexual reproduction should be much more efficient and less costly remains an open question in evolutionary biology. Comparisons between otherwise similar sexual and asexual taxa allow us to characterize the genetic architecture underlying asexuality, which can, in turn, illuminate how this reproductive mode transition occurred and the mechanisms by which it is maintained or disrupted. Here, we used transcriptome sequencing to compare patterns of ovarian gene expression between actively reproducing obligately sexual and obligately asexual females from multiple lineages of Potamopyrgus antipodarum, a freshwater New Zealand snail characterized by frequent separate transitions to asexuality and coexistence of otherwise similar sexual and asexual lineages. We also used these sequence data to evaluate whether population history accounts for variation in patterns of gene expression. We found that source population was a major source of gene expression variation, and likely more influential than reproductive mode. This outcome for these common garden-raised snails is strikingly similar to earlier results from field-collected snails. While we did not identify a likely set of candidate genes from expression profiles that could plausibly explain how transitions to asexuality occurred, we identified around 1,000 genes with evidence of differential expression between sexual and asexual reproductive modes, and 21 genes that appear to exhibit consistent expression differences between sexuals and asexuals across genetic backgrounds. This second smaller set of genes provides a good starting point for further exploration regarding a potential role in the transition to asexual reproduction. These results mark the first effort to characterize the causes of asexuality in P. antipodarum, demonstrate the apparently high heritability of gene expression patterns in this species, and hint that for P. antipodarum, transitions to asexuality might not necessarily be strongly associated with broad changes in gene expression.
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7
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Yan H, Haak DC, Li S, Huang L, Bombarely A. Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice. PLANT COMMUNICATIONS 2022; 3:100270. [PMID: 35576152 PMCID: PMC9251385 DOI: 10.1016/j.xplc.2021.100270] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 10/29/2021] [Accepted: 12/16/2021] [Indexed: 06/10/2023]
Abstract
Transposable elements (TEs) are a major force in the production of new alleles during domestication; nevertheless, their use in association studies has been limited because of their complexity. We have developed a TE genotyping pipeline (TEmarker) and applied it to whole-genome genome-wide association study (GWAS) data from 176 Oryza sativa subsp. japonica accessions to identify genetic elements associated with specific agronomic traits. TE markers recovered a large proportion (69%) of single-nucleotide polymorphism (SNP)-based GWAS peaks, and these TE peaks retained ca. 25% of the SNPs. The use of TEs in GWASs may reduce false positives associated with linkage disequilibrium (LD) among SNP markers. A genome scan revealed positive selection on TEs associated with agronomic traits. We found several cases of insertion and deletion variants that potentially resulted from the direct action of TEs, including an allele of LOC_Os11g08410 associated with plant height and panicle length traits. Together, these findings reveal the utility of TE markers for connecting genotype to phenotype and suggest a potential role for TEs in influencing phenotypic variations in rice that impact agronomic traits.
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Affiliation(s)
- Haidong Yan
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - David C Haak
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; Graduate Program in Genetics, Bioinformatics and Computational Biology (GBCB), Virginia Tech, Blacksburg, VA 24061, USA
| | - Song Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; Graduate Program in Genetics, Bioinformatics and Computational Biology (GBCB), Virginia Tech, Blacksburg, VA 24061, USA
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China
| | - Aureliano Bombarely
- Department of Bioscience, Universita degli Studi di Milano (UNIMI), 20133 Milano, Italy; Instituto de Biologıa Molecular y Celular de Plantas (IBMCP), UPV-CSIC, 46022 Valencia, Spain.
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8
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SNP Development in Penaeus vannamei via Next-Generation Sequencing and DNA Pool Sequencing. FISHES 2021. [DOI: 10.3390/fishes6030036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Next-generation sequencing and pool sequencing have been widely used in SNP (single-nucleotide polymorphism) detection and population genetics research; however, there are few reports on SNPs related to the growth of Penaeus vannamei. The purpose of this study was to call SNPs from rapid-growing (RG) and slow-growing (SG) individuals’ transcriptomes and use DNA pool sequencing to assess the reliability of SNPs. Two parameters were applied to detect SNPs. One parameter was the p-values generated using Fisher’s exact test, which were used to calculate the significance of allele frequency differences between RG and SG. The other one was the AFI (minor allele frequency imbalance), which was defined to highlight the fold changes in MAF (minor allele frequency) values between RG and SG. There were 216,015 hypothetical SNPs, which were obtained based on the transcriptome data. Finally, 104 high-quality SNPs and 96,819 low-quality SNPs were predicted. Then, 18 high-quality SNPs and 17 low-quality SNPs were selected to assess the reliability of the detection process. Here, 72.22% (13/18) accuracy was achieved for high-quality SNPs, while only 52.94% (9/17) accuracy was achieved for low-quality SNPs. These SNPs enrich the data for population genetics studies of P. vannamei and may play a role in the development of SNP markers for future breeding studies.
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Christiansen H, Heindler FM, Hellemans B, Jossart Q, Pasotti F, Robert H, Verheye M, Danis B, Kochzius M, Leliaert F, Moreau C, Patel T, Van de Putte AP, Vanreusel A, Volckaert FAM, Schön I. Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. BMC Genomics 2021; 22:625. [PMID: 34418978 PMCID: PMC8380342 DOI: 10.1186/s12864-021-07917-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/26/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. RESULTS In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. CONCLUSIONS Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.
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Affiliation(s)
- Henrik Christiansen
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.
| | - Franz M Heindler
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Quentin Jossart
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Henri Robert
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Marie Verheye
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Bruno Danis
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Marc Kochzius
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Frederik Leliaert
- Marine Biology Research Group, Ghent University, Ghent, Belgium.,Meise Botanic Garden, Meise, Belgium
| | - Camille Moreau
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Université de Bourgogne Franche-Comté (UBFC) UMR CNRS 6282 Biogéosciences, Dijon, France
| | - Tasnim Patel
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Anton P Van de Putte
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.,OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ann Vanreusel
- Marine Biology Research Group, Ghent University, Ghent, Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Isa Schön
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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10
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Current and Future Pathotyping Platforms for Plasmodiophora brassicae in Canada. PLANTS 2021; 10:plants10071446. [PMID: 34371649 PMCID: PMC8309272 DOI: 10.3390/plants10071446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 11/17/2022]
Abstract
Clubroot, caused by Plasmodiophora brassicae, is one of the most detrimental threats to crucifers worldwide and has emerged as an important disease of canola (Brassica napus) in Canada. At present, pathotypes are distinguished phenotypically by their virulence patterns on host differential sets, including the systems of Williams, Somé et al., the European Clubroot Differential set, and most recently the Canadian Clubroot Differential set and the Sinitic Clubroot Differential set. Although these are frequently used because of their simplicity of application, they are time-consuming, labor-intensive, and can lack sensitivity. Early, preventative pathotype detection is imperative to maximize productivity and promote sustainable crop production. The decreased turnaround time and increased sensitivity and specificity of genotypic pathotyping will be valuable for the development of integrated clubroot management plans, and interest in molecular techniques to complement phenotypic methods is increasing. This review provides a synopsis of current and future molecular pathotyping platforms for P. brassicae and aims to provide information on techniques that may be most suitable for the development of rapid, reliable, and cost-effective pathotyping assays.
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11
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Genomic Approaches for Conservation Management in Australia under Climate Change. Life (Basel) 2021; 11:life11070653. [PMID: 34357024 PMCID: PMC8304512 DOI: 10.3390/life11070653] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 12/28/2022] Open
Abstract
Conservation genetics has informed threatened species management for several decades. With the advent of advanced DNA sequencing technologies in recent years, it is now possible to monitor and manage threatened populations with even greater precision. Climate change presents a number of threats and challenges, but new genomics data and analytical approaches provide opportunities to identify critical evolutionary processes of relevance to genetic management under climate change. Here, we discuss the applications of such approaches for threatened species management in Australia in the context of climate change, identifying methods of facilitating viability and resilience in the face of extreme environmental stress. Using genomic approaches, conservation management practices such as translocation, targeted gene flow, and gene-editing can now be performed with the express intention of facilitating adaptation to current and projected climate change scenarios in vulnerable species, thus reducing extinction risk and ensuring the protection of our unique biodiversity for future generations. We discuss the current barriers to implementing conservation genomic projects and the efforts being made to overcome them, including communication between researchers and managers to improve the relevance and applicability of genomic studies. We present novel approaches for facilitating adaptive capacity and accelerating natural selection in species to encourage resilience in the face of climate change.
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12
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Michalek K, Vendrami DLJ, Bekaert M, Green DH, Last KS, Telesca L, Wilding TA, Hoffman JI. Mytilus trossulus introgression and consequences for shell traits in longline cultivated mussels. Evol Appl 2021; 14:1830-1843. [PMID: 34295367 PMCID: PMC8288009 DOI: 10.1111/eva.13245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/30/2021] [Accepted: 04/14/2021] [Indexed: 01/13/2023] Open
Abstract
Mussels belonging to the Mytilus species complex (M. edulis, ME; M. galloprovincialis, MG; and M. trossulus, MT) often occur in sympatry, facilitating introgressive hybridization. This may be further promoted by mussel aquaculture practices, with MT introgression often resulting in commercially unfavourable traits such as low meat yield and weak shells. To investigate the relationship between genotype and shell phenotype, genetic and morphological variability was quantified across depth (1 m to 7 m) along a cultivation rope at a mussel farm on the West coast of Scotland. A single nuclear marker (Me15/16) and a novel panel of 33 MT-diagnostic single nucleotide polymorphisms were used to evaluate stock structure and the extent of MT introgression across depth. Variation in shell strength, determined as the maximum compression force for shell puncture, and shell shape using geometric morphometric analysis were evaluated in relation to cultivation depth and the genetic profiles of the mussels. Overall, ME was the dominant genotype across depth, followed by ME × MG hybrids and smaller quantities of ME × MT hybrids and pure MT individuals. In parallel, we identified multiple individuals that were either predominantly homozygous or heterozygous for MT-diagnostic alleles, likely representing pure MT and first-generation ME × MT hybrids, respectively. Both the proportion of individuals carrying MT alleles and MT allele frequency declined with depth. Furthermore, MT-introgressed individuals had significantly weaker and more elongate shells than nonintrogressed individuals. This study provides detailed insights into stock structure along a cultivation rope and suggests that practical methods to assess shell strength and shape of cultivated mussels may facilitate the rapid identification of MT, limiting the impact of this commercially damaging species.
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Affiliation(s)
| | | | - Michaël Bekaert
- Institute of AquacultureFaculty of Natural SciencesUniversity of StirlingStirlingUK
| | | | - Kim S. Last
- The Scottish Association for Marine ScienceObanUK
| | - Luca Telesca
- Department of Earth SciencesUniversity of CambridgeCambridgeUK
- British Antarctic SurveyCambridgeUK
- Present address:
Lamont‐Doherty Earth Observatory of Columbia UniversityPalisadesNYUSA
| | | | - Joseph I. Hoffman
- Department of Animal BehaviourUniversity of BielefeldBielefeldGermany
- British Antarctic SurveyCambridgeUK
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13
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Xu M, Xing S, Zhao Y, Zhao C. Peptide nucleic acid-assisted colorimetric detection of single-nucleotide polymorphisms based on the intrinsic peroxidase-like activity of hemin-carbon nanotube nanocomposites. Talanta 2021; 232:122420. [PMID: 34074407 DOI: 10.1016/j.talanta.2021.122420] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
Here, taking the advantage of single-stranded (ss) DNA specific nuclease (S1) and peptide nucleic acid (PNA), we demonstrated a novel, rapid, and label-free colorimetric nanosensor for the sensitive and accurate detection of SNPs based on the intrinsic peroxidase-like activity of hemin-functionalized single-walled carbon nanotubes (hemin-SWCNTs). PNA, a man-made mimic of DNA with extraordinary stability toward enzymatic degradation, can effectively protect DNA in the fully matched DNA/PNA duplexes from nuclease digestion. While the DNA in DNA/PNA duplexes containing a mismatch can be cleaved into small fragments. This difference can be visually monitored from the specific color change of TMB/H2O2 system by employing the peroxidase activity of hemin-SWCNTs because of its different aggregation states responding to ssPNA or DNA/PNA duplex. Under optimized conditions, the SNPs in the human tumor suppressor gene TP53 have been successfully genotyped in a linear range of 50-1000 nM with a detection limit of 0.11 nM. Moreover, this platform can effectively discriminate a series of single-base mismatches. This assay avoids the assistance of sophisticated instruments and complicated modifications of probes or nanomaterials, and function well for both cell lysate samples and PCR amplicons from standard cell lines, implying its potential practical applications for bioanalysis and biosensors.
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Affiliation(s)
- Mengjia Xu
- Affiliated Cixi Hospital, Wenzhou Medical University, Cixi, 315300, Zhejiang, PR China
| | - Shu Xing
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, PR China
| | - Yang Zhao
- College of Science and Technology, Ningbo University, Ningbo, 315300, PR China
| | - Chao Zhao
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China.
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14
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Pespeni MH, Moczek AP. Signals of selection beyond bottlenecks between exotic populations of the bull-headed dung beetle, Onthophagus taurus. Evol Dev 2021; 23:86-99. [PMID: 33522675 DOI: 10.1111/ede.12367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/02/2020] [Accepted: 12/15/2020] [Indexed: 11/27/2022]
Abstract
Colonization of new environments can lead to population bottlenecks and rapid phenotypic evolution that could be due to neutral and selective processes. Exotic populations of the bull-headed dung beetle (Onthophagus taurus) have differentiated in opposite directions from native beetles in male horn-to-body size allometry and female fecundity. Here we test for genetic and transcriptional differences among two exotic and one native O. taurus populations after three generations in common garden conditions. We sequenced RNA from 24 individuals for each of the three populations including both sexes, and spanning four developmental stages for the two exotic, differentiated populations. Identifying 270,400 high-quality single nucleotide polymorphisms, we revealed a strong signal of genetic differentiation between the three populations, and evidence of recent bottlenecks within and an excess of outlier loci between exotic populations. Differences in gene expression between populations were greatest in prepupae and early adult life stages, stages during which differences in male horn development and female fecundity manifest. Finally, genes differentially expressed between exotic populations also had greater genetic differentiation and performed functions related to chitin biosynthesis and nutrient sensing, possibly underlying allometry and fecundity trait divergences. Our results suggest that beyond bottlenecks, recent introductions have led to genetic and transcriptional differences in genes correlated with observed phenotypic differences.
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Affiliation(s)
- Melissa H Pespeni
- Department of Biology, University of Vermont, Burlington, Vermont, USA.,Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Armin P Moczek
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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15
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Chen L, Lang K, Mei Y, Shi Z, He K, Li F, Xiao H, Ye G, Han Z. FastD: Fast detection of insecticide target-site mutations and overexpressed detoxification genes in insect populations from RNA-Seq data. Ecol Evol 2020; 10:14346-14358. [PMID: 33391720 PMCID: PMC7771117 DOI: 10.1002/ece3.7037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 08/26/2020] [Accepted: 09/21/2020] [Indexed: 11/24/2022] Open
Abstract
Target-site mutations and detoxification gene overexpression are two major mechanisms conferring insecticide resistance. Molecular assays applied to detect these resistance genetic markers are time-consuming and with high false-positive rates. RNA-Seq data contains information on the variations within expressed genomic regions and expression of detoxification genes. However, there is no corresponding method to detect resistance markers at present. Here, we collected 66 reported resistance mutations of four insecticide targets (AChE, VGSC, RyR, and nAChR) from 82 insect species. Next, we obtained 403 sequences of the four target genes and 12,665 sequences of three kinds of detoxification genes including P450s, GSTs, and CCEs. Then, we developed a Perl program, FastD, to detect target-site mutations and overexpressed detoxification genes from RNA-Seq data and constructed a web server for FastD (http://www.insect-genome.com/fastd). The estimation of FastD on simulated RNA-Seq data showed high sensitivity and specificity. We applied FastD to detect resistant markers in 15 populations of six insects, Plutella xylostella, Aphis gossypii, Anopheles arabiensis, Musca domestica, Leptinotarsa decemlineata and Apis mellifera. Results showed that 11 RyR mutations in P. xylostella, one nAChR mutation in A. gossypii, one VGSC mutation in A. arabiensis and five VGSC mutations in M. domestica were found to be with frequency difference >40% between resistant and susceptible populations including previously confirmed mutations G4946E in RyR, R81T in nAChR and L1014F in VGSC. And 49 detoxification genes were found to be overexpressed in resistant populations compared with susceptible populations including previously confirmed detoxification genes CYP6BG1, CYP6CY22, CYP6CY13, CYP6P3, CYP6M2, CYP6P4 and CYP4G16. The candidate target-site mutations and detoxification genes were worth further validation. Resistance estimates according to confirmed markers were consistent with population phenotypes, confirming the reliability of this program in predicting population resistance at omics-level.
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Affiliation(s)
- Longfei Chen
- Institute of Insect SciencesCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- Department of EntomologyNanjing Agricultural UniversityNanjingChina
| | - Kun Lang
- Institute of Insect SciencesCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- Department of EntomologyNanjing Agricultural UniversityNanjingChina
| | - Yang Mei
- Institute of Insect SciencesCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Zhenmin Shi
- Institute of Insect SciencesCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Kang He
- Institute of Insect SciencesCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Fei Li
- Institute of Insect SciencesCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Huamei Xiao
- Institute of Insect SciencesCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- Key Laboratory of Crop Growth and Development Regulation of Jiangxi ProvinceCollege of Life Sciences and Resource EnvironmentYichun UniversityYichunChina
| | - Gongyin Ye
- Institute of Insect SciencesCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Zhaojun Han
- Department of EntomologyNanjing Agricultural UniversityNanjingChina
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16
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Xu Z, Asakawa S. Physiological RNA dynamics in RNA-Seq analysis. Brief Bioinform 2020; 20:1725-1733. [PMID: 30010714 DOI: 10.1093/bib/bby045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/24/2018] [Indexed: 02/06/2023] Open
Abstract
Physiological RNA dynamics cause problems in transcriptome analysis. Physiological RNA accumulation affects the analysis of RNA quantification, and physiological RNA degradation affects the analysis of the RNA sequence length, feature site and quantification. In the present article, we review the effects of physiological degradation and accumulation of RNA on analysing RNA sequencing data. Physiological RNA accumulation and degradation probably led to such phenomena as incorrect estimations of transcription quantification, differential expressions, co-expressions, RNA decay rates, alternative splicing, boundaries of transcription, novel genes, new single-nucleotide polymorphisms, small RNAs and gene fusion. Thus, the transcriptomic data obtained up to date warrant further scrutiny. New and improved techniques and bioinformatics software are needed to produce accurate data in transcriptome research.
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Affiliation(s)
- Zhongneng Xu
- Department of Ecology, Jinan University, Guangzhou 510632, China
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
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17
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Wang Y, Nie F, Shahid MQ, Baloch FS. Molecular footprints of selection effects and whole genome duplication (WGD) events in three blueberry species: detected by transcriptome dataset. BMC PLANT BIOLOGY 2020; 20:250. [PMID: 32493212 PMCID: PMC7268529 DOI: 10.1186/s12870-020-02461-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 05/24/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Both selection effects and whole genome duplication played very important roles in plant speciation and evolution, and to decipher the corresponding molecular footprint has always been a central task of geneticists. Vaccinium is species rich genus that comprised of about 450 species, and blueberry is one of the most important species of Vaccinium genus, which is gaining popularity because of high healthful value. In this article, we aimed to decipher the molecular footprints of natural selection on the single copy genes and WGD events occur in the evolutionary history of blueberry species. RESULTS We identified 30,143, 29,922 and 28,891 putative protein coding sequences from 45,535, 42,914 and 43,630 unigenes assembled from the leaves' transcriptome assembly of 19 rabbiteye (T1), 13 southern highbush (T2) and 22 northern highbush (T3) blueberry cultivars. A total of 17, 21 and 27 single copy orthologs were found to undergone positive selection in T1 versus T2, T1 versus T3, and T2 versus T3, respectively, and these orthologs were enriched in metabolic pathways including "Terpenoid backbone biosynthesis", "Valine, leucine and isoleucine biosynthesis", "Butanoate metabolism", "C5-Branched dibasic acid metabolism" "Pantothenate and CoA biosynthesis". We also detected significant molecular footprints of a recent (about 9.04 MYA), medium (about 43.44 MYA) and an ancient (about 116.39 MYA) WGD events that occurred in the evolutionary history of three blueberry species. CONCLUSION Some important functional genes revealed positive selection effect in blueberry. At least three rounds of WGD events were detected in the evolutionary history of blueberry species. Our work provides insights about the genetic mechanism of adaptive evolution in blueberry and species radiation of Vaccinium in short geological scale time.
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Affiliation(s)
- Yunsheng Wang
- College of Health and Life Science, Kaili University, Kaili City, 556011 Guizhou Province China
| | - Fei Nie
- Biological institute of Guizhou Province, Guiyang City, 556000 Guizhou Province China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong Province China
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
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18
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Lang PLM, Weiß CL, Kersten S, Latorre SM, Nagel S, Nickel B, Meyer M, Burbano HA. Hybridization ddRAD-sequencing for population genomics of nonmodel plants using highly degraded historical specimen DNA. Mol Ecol Resour 2020; 20:1228-1247. [PMID: 32306514 DOI: 10.1111/1755-0998.13168] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/06/2020] [Accepted: 03/30/2020] [Indexed: 12/29/2022]
Abstract
Species' responses at the genetic level are key to understanding the long-term consequences of anthropogenic global change. Herbaria document such responses, and, with contemporary sampling, provide high-resolution time-series of plant evolutionary change. Characterizing genetic diversity is straightforward for model species with small genomes and a reference sequence. For nonmodel species-with small or large genomes-diversity is traditionally assessed using restriction-enzyme-based sequencing. However, age-related DNA damage and fragmentation preclude the use of this approach for ancient herbarium DNA. Here, we combine reduced-representation sequencing and hybridization-capture to overcome this challenge and efficiently compare contemporary and historical specimens. Specifically, we describe how homemade DNA baits can be produced from reduced-representation libraries of fresh samples, and used to efficiently enrich historical libraries for the same fraction of the genome to produce compatible sets of sequence data from both types of material. Applying this approach to both Arabidopsis thaliana and the nonmodel plant Cardamine bulbifera, we discovered polymorphisms de novo in an unbiased, reference-free manner. We show that the recovered genetic variation recapitulates known genetic diversity in A. thaliana, and recovers geographical origin in both species and over time, independent of bait diversity. Hence, our method enables fast, cost-efficient, large-scale integration of contemporary and historical specimens for assessment of genome-wide genetic trends over time, independent of genome size and presence of a reference genome.
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Affiliation(s)
- Patricia L M Lang
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Clemens L Weiß
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Department of Genetics, Stanford University, Stanford, CA, USA
| | - Sonja Kersten
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sergio M Latorre
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hernán A Burbano
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, London, UK
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19
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Choo LQ, Bal TMP, Choquet M, Smolina I, Ramos-Silva P, Marlétaz F, Kopp M, Hoarau G, Peijnenburg KTCA. Novel genomic resources for shelled pteropods: a draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance. BMC Genomics 2020; 21:11. [PMID: 31900119 PMCID: PMC6942316 DOI: 10.1186/s12864-019-6372-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/05/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Pteropods are planktonic gastropods that are considered as bio-indicators to monitor impacts of ocean acidification on marine ecosystems. In order to gain insight into their adaptive potential to future environmental changes, it is critical to use adequate molecular tools to delimit species and population boundaries and to assess their genetic connectivity. We developed a set of target capture probes to investigate genetic variation across their large-sized genome using a population genomics approach. Target capture is less limited by DNA amount and quality than other genome-reduced representation protocols, and has the potential for application on closely related species based on probes designed from one species. RESULTS We generated the first draft genome of a pteropod, Limacina bulimoides, resulting in a fragmented assembly of 2.9 Gbp. Using this assembly and a transcriptome as a reference, we designed a set of 2899 genome-wide target capture probes for L. bulimoides. The set of probes includes 2812 single copy nuclear targets, the 28S rDNA sequence, ten mitochondrial genes, 35 candidate biomineralisation genes, and 41 non-coding regions. The capture reaction performed with these probes was highly efficient with 97% of the targets recovered on the focal species. A total of 137,938 single nucleotide polymorphism markers were obtained from the captured sequences across a test panel of nine individuals. The probes set was also tested on four related species: L. trochiformis, L. lesueurii, L. helicina, and Heliconoides inflatus, showing an exponential decrease in capture efficiency with increased genetic distance from the focal species. Sixty-two targets were sufficiently conserved to be recovered consistently across all five species. CONCLUSION The target capture protocol used in this study was effective in capturing genome-wide variation in the focal species L. bulimoides, suitable for population genomic analyses, while providing insights into conserved genomic regions in related species. The present study provides new genomic resources for pteropods and supports the use of target capture-based protocols to efficiently characterise genomic variation in small non-model organisms with large genomes.
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Affiliation(s)
- Le Qin Choo
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands.
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
| | - Thijs M P Bal
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Marvin Choquet
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Irina Smolina
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Paula Ramos-Silva
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Ferdinand Marlétaz
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Onna-son, Japan
| | - Martina Kopp
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Katja T C A Peijnenburg
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands.
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
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20
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Gardiner LJ, Brabbs T, Akhunov A, Jordan K, Budak H, Richmond T, Singh S, Catchpole L, Akhunov E, Hall A. Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat. Gigascience 2019; 8:5304888. [PMID: 30715311 PMCID: PMC6461119 DOI: 10.1093/gigascience/giz018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/21/2018] [Accepted: 01/27/2019] [Indexed: 11/17/2022] Open
Abstract
Background Whole-genome shotgun resequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome, making it difficult to unambiguously assign variation. Resequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented complementary DNA/exon or gene-based probe sets in which the promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences. Results We present and validate 2 gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high-confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low-confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for single-nucleotide polymorphism calling while significantly reducing cost per sample for gene and putative promoter capture. Conclusions We show that a capture design employing an “island strategy” can enable analysis of the large gene/putative promoter space of wheat with only 2 × 160 Mbp probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.
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Affiliation(s)
- Laura-Jayne Gardiner
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.,IBM Research, The Hartree Centre STFC Laboratory, Sci-Tech Daresbury, Warrington, WA4 4AD, UK
| | - Thomas Brabbs
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Alina Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Katherine Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Todd Richmond
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA
| | - Sukhwinder Singh
- CIMMYT, Calle Dr Norman E Borlaug, Ciudad Obregon, 85208, Mexico
| | - Leah Catchpole
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
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21
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García G, Ríos N, Gutiérrez V, Serra S, Loureiro M. Transcriptome-Based SNP Discovery and Validation in the Hybrid Zone of the Neotropical Annual Fish Genus Austrolebias. Genes (Basel) 2019; 10:genes10100789. [PMID: 31614537 PMCID: PMC6826752 DOI: 10.3390/genes10100789] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/13/2019] [Accepted: 09/15/2019] [Indexed: 02/04/2023] Open
Abstract
The genus Austrolebias (Cyprinodontiformes: Rivulidae) represents a specious group of taxa following annual life cycles in the neotropical ichthyofauna. They live in temporary ponds and each generation must be completed in a few months, depending on environmental stochasticity. Annual fish survive the dry season through diapausing eggs buried in the substrate of these ponds. A hypothesized bimodal hybrid zone between two taxa of the genus, A. charrua and A. reicherti from Dos Patos Merin lagoon system, was recently proposed based on genetics and morphological analyses. However, hundreds of additional nuclear molecular markers should be used to strongly support this hypothesized bimodal pattern. In the present paper, we conducted RNA-seq-based sequencing of the transcriptomes from pools of individuals of A. charrua, A. reicherti and their putative natural hybrids from the previously characterized hybrid zone. As a result, we identified a set of 111,725 SNP (single nucleotide polymorphism) markers, representing presumably fixed allelic differences among the two species. The present study provided the first panel of 106 SNP markers as a single diagnostic multiplex assay and validated their capacity to reconstruct the patterns of the hybrid zone between both taxa. These nuclear markers combined with Cytb gene and morphological analyses detected a population structure in which some groups among the hybrid swarms showed different level of introgression towards one or the other parental species according to their geographic distribution. High-quality transcriptomes and a large set of gene-linked SNPs should greatly facilitate functional and population genomics studies in the hybrid zone of these endangered species.
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Affiliation(s)
- Graciela García
- Sección Genética Evolutiva, Facultad de Ciencias, UdelaR, Iguá 4225, Montevideo 11400, Uruguay.
| | - Néstor Ríos
- Sección Genética Evolutiva, Facultad de Ciencias, UdelaR, Iguá 4225, Montevideo 11400, Uruguay.
| | - Verónica Gutiérrez
- Sección Genética Evolutiva, Facultad de Ciencias, UdelaR, Iguá 4225, Montevideo 11400, Uruguay.
| | - Sebastián Serra
- Sección Genética Evolutiva, Facultad de Ciencias, UdelaR, Iguá 4225, Montevideo 11400, Uruguay.
- Departamento de Ecología y Evolución, Facultad de Ciencias, UdelaR, Iguá 4225, Montevideo 11400, Uruguay.
- Sección Ictiología, Museo Nacional de Historia Natural, Montevideo 11400, Uruguay.
| | - Marcelo Loureiro
- Departamento de Ecología y Evolución, Facultad de Ciencias, UdelaR, Iguá 4225, Montevideo 11400, Uruguay.
- Sección Ictiología, Museo Nacional de Historia Natural, Montevideo 11400, Uruguay.
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22
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Bhardwaj A, Bag SK. PLANET-SNP pipeline: PLants based ANnotation and Establishment of True SNP pipeline. Genomics 2019; 111:1066-1077. [PMID: 31533899 DOI: 10.1016/j.ygeno.2018.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 06/10/2018] [Accepted: 07/02/2018] [Indexed: 12/30/2022]
Abstract
Acute prediction of SNPs (Single Nucleotide Polymorphisms) from high throughput sequencing data is a challenging problem, having potential to explore possible variation within plants species. For the extraction of profitable information from bulk of data, machine learning (ML) could lead to development of accurate model based on the learning of prior information. We performed state of art, in-depth learning on six different plant species. Comparative evaluation of five different algorithms showed that Random Forest substantially outperformed in selection of potential SNPs, with markedly improved prediction accuracy via 10-fold cross validation technique and integrated in system known as PLANET-SNP. We present the accurate method to extract the potential SNPs with user specific customizable parameters. It will facilitate the identification of efficient and functional SNPs in most easy and intuitive way. PLANET-SNP pipeline is very flexible in terms of data input and output formats. PLANET-SNP Pipeline is available at http://www.ncgd.nbri.res.in/PLANET-SNP-Pipeline.aspx.
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Affiliation(s)
- Archana Bhardwaj
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India; Computational Biology Lab, Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh 226001, India
| | - Sumit K Bag
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India; Computational Biology Lab, Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh 226001, India.
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23
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Wang H, Ding J, Ding S, Chang Y. Transcriptome analysis to characterize the genes related to gonad growth and fatty acid metabolism in the sea urchin Strongylocentrotus intermedius. Genes Genomics 2019; 41:1397-1415. [PMID: 31485990 DOI: 10.1007/s13258-019-00864-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/27/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND Sea urchin gonads of both sexes, commonly termed "roe", are highly valued seafood delicacies, and Strongylocentrotus intermedius is considered one of the tastiest sea urchins. In order to produce high-quality gonads for consumption and clarify the mechanism of gonad growth and development of the sea urchin, more genetic information, especially at the transcriptome level, is needed. OBJECTIVE A more thorough understanding of sea urchin gonad growth and development in both sexes could enable regulation of these processes at several stages with the aim of suppressing gametogenesis in order to produce high-quality gonads for consumption. METHODS The adult sea urchins S. intermedius were cultured for 3 months, and were sampled for the gonadal transcriptome analysis which has been performed on the RNAs of three male and female adults of S. intermedius in each gonad development stage. RESULTS Illumina sequencing raw sequence data was deposited in the NCBI Sequence Read Archive (SRA) database (PRJNA532998). It generated 560,196,356 raw reads and 548,956,944 clean reads were acquired, which were assembled into 107,850 transcripts with 44,124 genes. Comparative analysis showed the differentially expressed genes (DEGs) from 114 to 2566. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to determine the functional significance of these DEGs. We have selected 9 genes related to growth and 12 genes related to fatty acid biosynthesis and metabolism in sea urchin gonads. CONCLUSION These data for sea urchins were intended to provide markers for gonad growth and development that can be accumulated for use in aquaculture applications.
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Affiliation(s)
- Heng Wang
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Jun Ding
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China.
| | - Siyu Ding
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Yaqing Chang
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China.
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Wang Y, Shahid MQ, Ghouri F, Ercişli S, Baloch FS. Development of EST-based SSR and SNP markers in Gastrodia elata (herbal medicine) by sequencing, de novo assembly and annotation of the transcriptome. 3 Biotech 2019; 9:292. [PMID: 31321198 DOI: 10.1007/s13205-019-1823-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 06/23/2019] [Indexed: 01/28/2023] Open
Abstract
Tianma (Gastrodia elata Blume) has unique biological characteristics and high medicinal value. The wild resource of G. elata is being overutilized and should be conserved as it is already included in the list of endangered species in China. The population size of cultivated G. elata is small because of domestication bottleneck. Therefore, it is of utmost importance to evolve high-quality varieties and conserve wild resources of G. elata. In this study, we sequenced tuber transcriptomes of three major cultivated sub-species of Gastrodia elata, namely G. elata BI. f. elata, G. elata Bl. f. glauca S. Chow, and G. elata Bl. f. Viridis, and obtained about 7.8G clean data. The assembled high-quality reads of three sub-species were clustered into 56,884 unigenes. Of these, 31,224 (54.89%), 25,733 (45.24%), 22,629 (39.78%), and 11,856 (20.84%) unigenes were annotated by Nr, Swiss-Port, Eukaryotic Ortholog Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. Here, a total of 3766 EST-SSRs and 128,921 SNPs were identified from the unigenes. The results not only offer huge number of genes that were responsible for the growth, development, and metabolism of bioactive components, but also a large number of molecular markers were detected for future studies on the conservation genetics and molecular breeding of G. elata.
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Rougeux C, Gagnaire PA, Bernatchez L. Model-based demographic inference of introgression history in European whitefish species pairs'. J Evol Biol 2019; 32:806-817. [PMID: 31038776 DOI: 10.1111/jeb.13482] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/27/2019] [Accepted: 04/22/2019] [Indexed: 12/25/2022]
Abstract
Parallel phenotypic differentiation is generally attributed to parallel adaptive divergence as an evolutionary response to similar environmental contrasts. Such parallelism may actually originate from several evolutionary scenarios ranging from repeated parallel divergence caused by divergent selection to a unique divergence event followed by gene flow. Reconstructing the evolutionary history underlying parallel phenotypic differentiation is thus fundamental to understand the relative contribution of demography and selection on genomic divergence during speciation. In this study, we investigate the divergence history of replicate European whitefish (Coregonus lavaretus), limnetic and benthic species pairs from two lakes in Norway and two lakes in Switzerland. Demographic models accounting for semi-permeability and linked selection were fitted to the unfolded joint allele frequency spectrum built from genome-wide SNPs and compared to each other in each species pair. We found strong support for a model of asymmetrical post-glacial secondary contact between glacial lineages in all four lakes. Moreover, our results suggest that heterogeneous genomic differentiation has been shaped by the joint action of linked selection accelerating lineage sorting during allopatry, and heterogeneous migration eroding divergence at different rates along the genome following secondary contact. Our analyses reveal how the interplay between demography, selection and historical contingency has influenced the levels of diversity observed in previous whitefish phylogeographic studies. This study thus provides new insights into the historical demographic and selective processes that shaped the divergence associated with ecological speciation in European whitefish.
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Affiliation(s)
- Clément Rougeux
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Québec, Canada
| | | | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Québec, Canada
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26
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Gardiner LJ, Brabbs T, Akhunov A, Jordan K, Budak H, Richmond T, Singh S, Catchpole L, Akhunov E, Hall A. Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat. Gigascience 2019. [PMID: 30715311 DOI: 10.1101/363663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Whole-genome shotgun resequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome, making it difficult to unambiguously assign variation. Resequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented complementary DNA/exon or gene-based probe sets in which the promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences. RESULTS We present and validate 2 gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high-confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low-confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for single-nucleotide polymorphism calling while significantly reducing cost per sample for gene and putative promoter capture. CONCLUSIONS We show that a capture design employing an "island strategy" can enable analysis of the large gene/putative promoter space of wheat with only 2 × 160 Mbp probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.
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Affiliation(s)
- Laura-Jayne Gardiner
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
- IBM Research, The Hartree Centre STFC Laboratory, Sci-Tech Daresbury, Warrington, WA4 4AD, UK
| | - Thomas Brabbs
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Alina Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Katherine Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Todd Richmond
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA
| | - Sukhwinder Singh
- CIMMYT, Calle Dr Norman E Borlaug, Ciudad Obregon, 85208, Mexico
| | - Leah Catchpole
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
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27
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Gkagkavouzis K, Karaiskou N, Katopodi T, Leonardos I, Abatzopoulos TJ, Triantafyllidis A. The genetic population structure and temporal genetic stability of gilthead sea bream Sparus aurata populations in the Aegean and Ionian Seas, using microsatellite DNA markers. JOURNAL OF FISH BIOLOGY 2019; 94:606-613. [PMID: 30746701 DOI: 10.1111/jfb.13932] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 02/11/2019] [Indexed: 06/09/2023]
Abstract
We examined 662 gilthead sea bream Sparus aurata from wild samples of the species in the Aegean and Ionian Seas, using 20 EST-linked microsatellite markers, in three multiplex panels, as well as seven anonymous loci. Most of the markers were revealed to be highly polymorphic. We found low genetic differentiation between the sampling stations/areas with total FST 0.002 (P < 0.05). Based on comparison of five temporal samples, our results indicate genetic data consistency over time for all tested samples, pointing to stable populations, despite reported repeated escape events. Our results confirm the genetic population structure previously observed in these specific areas, using by far more markers than in previous studies in both coding and non-coding DNA loci. The limited genetic structure and the temporal genetic stability indicate neither major genetic differentiation of local populations by geographic isolation nor influence from anthropogenic factors. These results provide a baseline for future reference in any management programme of both wild and farmed population of S. aurata as well as of other aquaculture species with a potential introgression among farmed and wild populations.
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Affiliation(s)
- Konstantinos Gkagkavouzis
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikoleta Karaiskou
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Theodora Katopodi
- Department of Biological Sciences and Preventive Medicine, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis Leonardos
- Department of Biological Applications and Technologies, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Theodore J Abatzopoulos
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Alexander Triantafyllidis
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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28
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Zhu X, Wang J, Lv J, Liu P, Zhang L, Jiao W, Ma C, Bao Z, Wang S. Sequencing-Based Transcriptome-Wide Targeted Genotyping for Evolutionary and Ecological Studies. Evol Bioinform Online 2019; 15:1176934319836074. [PMID: 30886517 PMCID: PMC6413421 DOI: 10.1177/1176934319836074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/13/2019] [Indexed: 11/16/2022] Open
Abstract
Transcriptome-wide targeted genotyping is highly attractive for
evolutionary and ecological studies but, until recently, accomplishing
this goal presented a major technical barrier for the study of
non-model organisms. Our group has recently developed a
high-throughput targeted genotyping approach (called HD-Marker) based
on the high specificity and accuracy of oligo extension-ligation
assays that facilitates the design of assays tailored to meet specific
genotyping needs. HD-Marker allows for targeted genotyping of over 10
000 genes in a single tube, with strikingly high capture rate
(98%-99%) and genotyping accuracy (97%-99%). With the remarkable
advantages of cost-effectiveness and flexibility, we envision that
HD-Marker has broad application potential in evolutionary and
ecological studies.
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Affiliation(s)
- Xuan Zhu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jing Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jia Lv
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Pingping Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wenqian Jiao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Cen Ma
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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29
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Komoroske LM, Miller MR, O'Rourke SM, Stewart KR, Jensen MP, Dutton PH. A versatile Rapture (RAD‐Capture) platform for genotyping marine turtles. Mol Ecol Resour 2019; 19:497-511. [DOI: 10.1111/1755-0998.12980] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/21/2018] [Accepted: 11/27/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Lisa M. Komoroske
- Department of Environmental Conservation University of Massachusetts Amherst Amherst Massachusetts
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
| | - Michael R. Miller
- Department of Animal Science University of California, Davis Davis California
| | - Sean M. O'Rourke
- Department of Animal Science University of California, Davis Davis California
| | - Kelly R. Stewart
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
- The Ocean Foundation Washington District of Columbia
| | - Michael P. Jensen
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
| | - Peter H. Dutton
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
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30
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Azaiez A, Pavy N, Gérardi S, Laroche J, Boyle B, Gagnon F, Mottet MJ, Beaulieu J, Bousquet J. A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies). BMC Genomics 2018; 19:942. [PMID: 30558528 PMCID: PMC6296092 DOI: 10.1186/s12864-018-5247-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Norway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. Our main goal was to develop a large catalog of annotated high confidence gene SNPs that should sustain the development of genomic tools for the conservation of natural and domesticated genetic diversity resources, and hasten tree breeding efforts in this species. RESULTS Targeted sequencing was achieved by capturing P. abies exome with probes previously designed from the sequenced transcriptome of white spruce (Picea glauca (Moench) Voss). Capture efficiency was high (74.5%) given a high level of exome conservation between the two species. Using stringent criteria, we delimited a set of 61,771 high-confidence SNPs across 13,543 genes. To validate SNPs, a high-throughput genotyping array was developed for a subset of 5571 predicted SNPs representing as many different gene loci, and was used to genotype over 1000 trees. The estimated true positive rate of the resource was 84.2%, which was comparable with the genotyping success rate obtained for P. abies control SNPs recycled from previous genotyping efforts. We also analyzed SNP abundance across various gene functional categories. Several GO terms and gene families involved in stress response were found over-represented in highly polymorphic genes. CONCLUSION The annotated high-confidence SNP catalog developed herein represents a valuable genomic resource, being representative of over 13 K genes distributed across the P. abies genome. This resource should serve a variety of population genomics and breeding applications in Norway spruce.
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Affiliation(s)
- Aïda Azaiez
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Jérôme Laroche
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Brian Boyle
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - France Gagnon
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Marie-Josée Mottet
- Direction de la recherche forestière, Ministère des Forêts, de la Faune et des Parcs du Québec, 2700 Einstein, Québec, Québec G1P 3W8 Canada
| | - Jean Beaulieu
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
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31
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Rogier O, Chateigner A, Amanzougarene S, Lesage-Descauses MC, Balzergue S, Brunaud V, Caius J, Soubigou-Taconnat L, Jorge V, Segura V. Accuracy of RNAseq based SNP discovery and genotyping in Populusnigra. BMC Genomics 2018; 19:909. [PMID: 30541448 PMCID: PMC6291945 DOI: 10.1186/s12864-018-5239-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/09/2018] [Indexed: 12/30/2022] Open
Abstract
Backgroud Populus nigra is a major tree species of ecological and economic importance for which several initiatives have been set up to create genomic resources. In order to access the large number of Single Nucleotide Polymorphisms (SNPs) typically needed to carry out a genome scan, the present study aimed at evaluating RNA sequencing as a tool to discover and type SNPs in genes within natural populations of P. nigra. Results We have devised a bioinformatics pipeline to call and type SNPs from RNAseq reads and applied it to P. nigra transcriptomic data. The accuracy of the resulting RNAseq-based SNP calling and typing has been evaluated by (i) comparing their position and alleles to those previously reported in candidate genes, (ii) assessing their genotyping accuracy with respect to a previously available SNP chip and (iii) evaluating their inter-annual repeatability. We found that a combination of several callers yields a good compromise between the number of variants type and the accuracy of genotyping. We further used the resulting genotypic data to carry out basic genetic analyses whose results confirm the quality of the RNAseq-based SNP dataset. Conclusions We demonstrated the potential and accuracy of RNAseq as an efficient way to genotype SNPs in P. nigra. These results open prospects towards the use of this technology for quantitative and population genomics studies. Electronic supplementary material The online version of this article (10.1186/s12864-018-5239-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Sandrine Balzergue
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Paris-Saclay, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, 91405, France.,IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 QUASAV, Beaucouzé, 49071, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Paris-Saclay, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, 91405, France
| | - José Caius
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Paris-Saclay, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, 91405, France
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Paris-Saclay, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, 91405, France
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32
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De Wit P, Yamada K, Panova M, André C, Johannesson K. Diet-dependent gene expression highlights the importance of Cytochrome P450 in detoxification of algal secondary metabolites in a marine isopod. Sci Rep 2018; 8:16824. [PMID: 30429500 PMCID: PMC6235865 DOI: 10.1038/s41598-018-34937-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 10/15/2018] [Indexed: 11/22/2022] Open
Abstract
Isopods of the genus Idotea have an unusual ability to feed on algae containing high amounts of chemical defense molecules, such as species of the genera Fucus and Ulva. In this study, we compared gene expression patterns of Idotea balthica individuals fed with Fucus vesiculosus to individuals fed with Ulva lactuca. We generated the first-ever transcriptome assembly for this species, and found 3,233 differentially expressed genes across feeding regimes. However, only a handful of biological functions were enriched with regard to differentially expressed genes, the most notable being "alkaloid metabolic process". Within this category, we found eight differentially expressed cytochrome P450 (CYP) unigenes, all of which had a higher expression in the U. lactuca diet treatment. A phylogenetic analysis showed that the differentially expressed CYP genes are closely related to a CYP gene described from the hepatopancreas of the spiny lobster Panulirus argus, and we hypothesize that these transcripts are involved in metabolite detoxification. This is a first step in the understanding of this algae-grazer interaction, and will form a basis for future work to characterize cytochrome P450 functioning in marine crustaceans.
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Affiliation(s)
- Pierre De Wit
- University of Gothenburg, Department of Marine Sciences, Tjärnö, Sweden.
| | - Keith Yamada
- University of Turku, Department of Biochemistry, Turku, Finland
| | - Marina Panova
- University of Gothenburg, Department of Marine Sciences, Tjärnö, Sweden
| | - Carl André
- University of Gothenburg, Department of Marine Sciences, Tjärnö, Sweden
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Lv J, Jiao W, Guo H, Liu P, Wang R, Zhang L, Zeng Q, Hu X, Bao Z, Wang S. HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay. Genome Res 2018; 28:1919-1930. [PMID: 30409770 PMCID: PMC6280760 DOI: 10.1101/gr.235820.118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 10/25/2018] [Indexed: 01/03/2023]
Abstract
Targeted genotyping of transcriptome-scale genetic markers is highly attractive for genetic, ecological, and evolutionary studies, but achieving this goal in a cost-effective manner remains a major challenge, especially for laboratories working on nonmodel organisms. Here, we develop a high-throughput, sequencing-based GoldenGate approach (called HD-Marker), which addresses the array-related issues of original GoldenGate methodology and allows for highly multiplexed and flexible targeted genotyping of more than 12,000 loci in a single-tube assay (in contrast to fewer than 3100 in the original GoldenGate assay). We perform extensive analyses to demonstrate the power and performance of HD-Marker on various multiplex levels (296, 795, 1293, and 12,472 genic SNPs) across two sequencing platforms in two nonmodel species (the scallops Chlamys farreri and Patinopecten yessoensis), with extremely high capture rate (98%-99%) and genotyping accuracy (97%-99%). We also demonstrate the potential of HD-Marker for high-throughput targeted genotyping of alternative marker types (e.g., microsatellites and indels). With its remarkable cost-effectiveness (as low as $0.002 per genotype) and high flexibility in choice of multiplex levels and marker types, HD-Marker provides a highly attractive tool over array-based platforms for fulfilling genome/transcriptome-wide targeted genotyping applications, especially in nonmodel organisms.
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Affiliation(s)
- Jia Lv
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Wenqian Jiao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Haobing Guo
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Pingping Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Ruijia Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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Telfer E, Graham N, Macdonald L, Sturrock S, Wilcox P, Stanbra L. Approaches to variant discovery for conifer transcriptome sequencing. PLoS One 2018; 13:e0205835. [PMID: 30395612 PMCID: PMC6218030 DOI: 10.1371/journal.pone.0205835] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 10/02/2018] [Indexed: 12/30/2022] Open
Abstract
There is a wide diversity of bioinformatic tools available for the assembly of next generation sequence and subsequence variant calling to identify genetic markers at scale. Integration of genomics tools such as genomic selection, association studies, pedigree analysis and analysis of genetic diversity, into operational breeding is a goal for New Zealand’s most widely planted exotic tree species, Pinus radiata. In the absence of full reference genomes for large megagenomes such as in conifers, RNA sequencing in a range of genotypes and tissue types, offers a rich source of genetic markers for downstream application. We compared nine different assembler and variant calling software combinations in a single transcriptomic library and found that Single Nucleotide Polymorphism (SNPs) discovery could vary by as much as an order of magnitude (8,061 SNPs up to 86,815 SNPs). The assembler with the best realignment of the packages trialled, Trinity, in combination with several variant callers was then applied to a much larger multi-genotype, multi-tissue transcriptome and identified 683,135 in silico SNPs across a predicted 449,951 exons when mapped to the Pinus taeda ver 1.01e reference.
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Affiliation(s)
- Emily Telfer
- New Zealand Forest Research Institute LTD. trading as Scion, Rotorua, New Zealand
- * E-mail:
| | - Natalie Graham
- New Zealand Forest Research Institute LTD. trading as Scion, Rotorua, New Zealand
| | - Lucy Macdonald
- New Zealand Forest Research Institute LTD. trading as Scion, Rotorua, New Zealand
| | - Shane Sturrock
- New Zealand Forest Research Institute LTD. trading as Scion, Rotorua, New Zealand
- Real Time Genomics, Hamilton, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand
| | - Lisa Stanbra
- New Zealand Forest Research Institute LTD. trading as Scion, Rotorua, New Zealand
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35
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Andrews KR, Adams JR, Cassirer EF, Plowright RK, Gardner C, Dwire M, Hohenlohe PA, Waits LP. A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data. Mol Ecol Resour 2018; 18:1263-1281. [PMID: 29870119 PMCID: PMC6207459 DOI: 10.1111/1755-0998.12910] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 05/18/2018] [Accepted: 05/24/2018] [Indexed: 11/30/2022]
Abstract
The development of high-throughput sequencing technologies is dramatically increasing the use of single nucleotide polymorphisms (SNPs) across the field of genetics, but most parentage studies of wild populations still rely on microsatellites. We developed a bioinformatic pipeline for identifying SNP panels that are informative for parentage analysis from restriction site-associated DNA sequencing (RADseq) data. This pipeline includes options for analysis with or without a reference genome, and provides methods to maximize genotyping accuracy and select sets of unlinked loci that have high statistical power. We test this pipeline on small populations of Mexican gray wolf and bighorn sheep, for which parentage analyses are expected to be challenging due to low genetic diversity and the presence of many closely related individuals. We compare the results of parentage analysis across SNP panels generated with or without the use of a reference genome, and between SNPs and microsatellites. For Mexican gray wolf, we conducted parentage analyses for 30 pups from a single cohort where samples were available from 64% of possible mothers and 53% of possible fathers, and the accuracy of parentage assignments could be estimated because true identities of parents were known a priori based on field data. For bighorn sheep, we conducted maternity analyses for 39 lambs from five cohorts where 77% of possible mothers were sampled, but true identities of parents were unknown. Analyses with and without a reference genome produced SNP panels with ≥95% parentage assignment accuracy for Mexican gray wolf, outperforming microsatellites at 78% accuracy. Maternity assignments were completely consistent across all SNP panels for the bighorn sheep, and were 74.4% consistent with assignments from microsatellites. Accuracy and consistency of parentage analysis were not reduced when using as few as 284 SNPs for Mexican gray wolf and 142 SNPs for bighorn sheep, indicating our pipeline can be used to develop SNP genotyping assays for parentage analysis with relatively small numbers of loci.
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Affiliation(s)
- Kimberly R. Andrews
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844, USA
- Current address: Genetics and Genomics Group, University of Washington JISAO and NOAA Pacific Marine Environmental Lab, Seattle, WA 98115, USA
| | - Jennifer R. Adams
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844, USA
| | - E. Frances Cassirer
- Idaho Department of Fish and Game, 3316 16th Street, Lewiston, ID 83501, USA
| | - Raina K. Plowright
- Department of Microbiology and Immunology, Montana State University, 109 Lewis Hall, Bozeman, MT 59717, USA
| | - Colby Gardner
- U.S. Fish and Wildlife Service, 2105 Osuna Road NE, Albuquerque, NM 87113, USA
| | - Maggie Dwire
- U.S. Fish and Wildlife Service, 2105 Osuna Road NE, Albuquerque, NM 87113, USA
| | - Paul A. Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844, USA
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36
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Abolins-Abols M, Kornobis E, Ribeca P, Wakamatsu K, Peterson MP, Ketterson ED, Milá B. Differential gene regulation underlies variation in melanic plumage coloration in the dark-eyed junco (Junco hyemalis
). Mol Ecol 2018; 27:4501-4515. [DOI: 10.1111/mec.14878] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 08/22/2018] [Accepted: 09/07/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Mikus Abolins-Abols
- Department of Animal Biology; University of Illinois; Urbana Illinois
- Department of Biology; Indiana University; Bloomington Indiana
| | - Etienne Kornobis
- National Museum of Natural Sciences; Spanish National Research Council (CSIC); Madrid Spain
| | | | - Kazumasa Wakamatsu
- Department of Chemistry; Fujita Health University School of Health Sciences; Toyoake Aichi Japan
| | | | | | - Borja Milá
- National Museum of Natural Sciences; Spanish National Research Council (CSIC); Madrid Spain
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37
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Charrier NP, Couton M, Voordouw MJ, Rais O, Durand-Hermouet A, Hervet C, Plantard O, Rispe C. Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus. Parasit Vectors 2018; 11:364. [PMID: 29941016 PMCID: PMC6019515 DOI: 10.1186/s13071-018-2932-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/04/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Ixodes ricinus is the most important vector of tick-borne diseases in Europe. A better knowledge of its genome and transcriptome is important for developing control strategies. Previous transcriptomic studies of I. ricinus have focused on gene expression during the blood meal in specific tissues. To obtain a broader picture of changes in gene expression during the blood meal, our study analysed the transcriptome at the level of the whole body for both nymphal and adult ticks. Ixodes ricinus ticks from a highly inbred colony at the University of Neuchâtel were used. We also analysed previously published RNAseq studies to compare the genetic variation between three wild strains and three laboratory strains, including the strain from Neuchâtel. RESULTS RNA was extracted from whole tick bodies and the cDNA was sequenced, producing 162,872,698 paired-end reads. Our reference transcriptome contained 179,316 contigs, of which 31% were annotated using Trinotate. Gene expression was compared between ticks that differed by feeding status (unfed vs partially fed). We found that blood-feeding in nymphs and female adult ticks increased the expression of cuticle-associated genes. Using a set of 3866 single nucleotide polymorphisms to calculate the heterozygosity, we found that the wild tick populations of I. ricinus had much higher levels of heterozygosity than the three laboratory populations. CONCLUSION Using high throughput strand-oriented sequencing for whole ticks in different stages and feeding conditions, we obtained a de novo assembly that significantly increased the genomic resources available for I. ricinus. Our study illustrates the importance of analysing the transcriptome at the level of the whole body to gain additional insights into how gene expression changes over the life-cycle of an organism. Our comparison of several RNAseq datasets shows the power of transcriptomic data to accurately characterize genetic polymorphism and for comparing different populations or sources of sequencing material.
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Affiliation(s)
| | - Marjorie Couton
- BIOEPAR, INRA, Oniris, Université Bretagne Loire, 44307 Nantes, France
| | - Maarten J. Voordouw
- Laboratoire d’Ecologie et Evolution des parasites, Institut de Biologie, Université de Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Olivier Rais
- Laboratoire d’Ecologie et Evolution des parasites, Institut de Biologie, Université de Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | | | - Caroline Hervet
- BIOEPAR, INRA, Oniris, Université Bretagne Loire, 44307 Nantes, France
| | - Olivier Plantard
- BIOEPAR, INRA, Oniris, Université Bretagne Loire, 44307 Nantes, France
| | - Claude Rispe
- BIOEPAR, INRA, Oniris, Université Bretagne Loire, 44307 Nantes, France
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38
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Puritz JB, Lotterhos KE. Expressed exome capture sequencing: A method for cost‐effective exome sequencing for all organisms. Mol Ecol Resour 2018; 18:1209-1222. [DOI: 10.1111/1755-0998.12905] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 03/30/2018] [Accepted: 05/08/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Jonathan B. Puritz
- Department of Marine and Environmental Sciences Northeastern Marine Science Center Nahant Massachusetts
| | - Katie E. Lotterhos
- Department of Marine and Environmental Sciences Northeastern Marine Science Center Nahant Massachusetts
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39
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Mat AM, Klopp C, Payton L, Jeziorski C, Chalopin M, Amzil Z, Tran D, Wikfors GH, Hégaret H, Soudant P, Huvet A, Fabioux C. Oyster transcriptome response to Alexandrium exposure is related to saxitoxin load and characterized by disrupted digestion, energy balance, and calcium and sodium signaling. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 199:127-137. [PMID: 29621672 DOI: 10.1016/j.aquatox.2018.03.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/22/2018] [Accepted: 03/25/2018] [Indexed: 06/08/2023]
Abstract
Harmful Algal Blooms are worldwide occurrences that can cause poisoning in human seafood consumers as well as mortality and sublethal effets in wildlife, propagating economic losses. One of the most widespread toxigenic microalgal taxa is the dinoflagellate Genus Alexandrium, that includes species producing neurotoxins referred to as PST (Paralytic Shellfish Toxins). Blooms cause shellfish harvest restrictions to protect human consumers from accumulated toxins. Large inter-individual variability in toxin load within an exposed bivalve population complicates monitoring of shellfish toxicity for ecology and human health regulation. To decipher the physiological pathways involved in the bivalve response to PST, we explored the whole transcriptome of the digestive gland of the Pacific oyster Crassostrea gigas fed experimentally with a toxic Alexandrium minutum culture. The largest differences in transcript abundance were between oysters with contrasting toxin loads (1098 transcripts), rather than between exposed and non-exposed oysters (16 transcripts), emphasizing the importance of toxin load in oyster response to toxic dinoflagellates. Additionally, penalized regressions, innovative in this field, modeled accurately toxin load based upon only 70 transcripts. Transcriptomic differences between oysters with contrasting PST burdens revealed a limited suite of metabolic pathways affected, including ion channels, neuromuscular communication, and digestion, all of which are interconnected and linked to sodium and calcium exchanges. Carbohydrate metabolism, unconsidered previously in studies of harmful algal effects on shellfish, was also highlighted, suggesting energy challenge in oysters with high toxin loads. Associations between toxin load, genotype, and mRNA levels were revealed that open new doors for genetic studies identifying genetically-based low toxin accumulation.
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Affiliation(s)
- Audrey M Mat
- Ifremer, LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, CS 10070, 29280 Plouzané, France
| | | | - Laura Payton
- UMR 5805 EPOC, CNRS - Université de Bordeaux, F-33120 Arcachon, France
| | | | - Morgane Chalopin
- Ifremer, LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, CS 10070, 29280 Plouzané, France
| | - Zouher Amzil
- Ifremer, Laboratoire Phycotoxines, rue de l'Ile d'Yeu, BP 21105, F-44311 Nantes, France
| | - Damien Tran
- UMR 5805 EPOC, CNRS - Université de Bordeaux, F-33120 Arcachon, France
| | - Gary H Wikfors
- Northeast Fisheries Science Center, NOAA National Marine Fisheries Service, 212 Rogers Avenue, Milford, CT 06460, USA
| | - Hélène Hégaret
- LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, IUEM, rue Dumont d'Urville, 29280 Plouzané, France
| | - Philippe Soudant
- LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, IUEM, rue Dumont d'Urville, 29280 Plouzané, France
| | - Arnaud Huvet
- Ifremer, LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, CS 10070, 29280 Plouzané, France
| | - Caroline Fabioux
- LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, IUEM, rue Dumont d'Urville, 29280 Plouzané, France.
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40
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Olohan L, Gardiner LJ, Lucaci A, Steuernagel B, Wulff B, Kenny J, Hall N, Hall A. A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample. BMC Genomics 2018; 19:250. [PMID: 29653520 PMCID: PMC5899405 DOI: 10.1186/s12864-018-4640-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 04/03/2018] [Indexed: 01/01/2023] Open
Abstract
Background Bread wheat has a large complex genome that makes whole genome resequencing costly. Therefore, genome complexity reduction techniques such as sequence capture make re-sequencing cost effective. With a high-quality draft wheat genome now available it is possible to design capture probe sets and to use them to accurately genotype and anchor SNPs to the genome. Furthermore, in addition to genetic variation, epigenetic variation provides a source of natural variation contributing to changes in gene expression and phenotype that can be profiled at the base pair level using sequence capture coupled with bisulphite treatment. Here, we present a new 12 Mbp wheat capture probe set, that allows both the profiling of genotype and methylation from the same DNA sample. Furthermore, we present a method, based on Agilent SureSelect Methyl-Seq, that will use a single capture assay as a starting point to allow both DNA sequencing and methyl-seq. Results Our method uses a single capture assay that is sequentially split and used for both DNA sequencing and methyl-seq. The resultant genotype and epi-type data is highly comparable in terms of coverage and SNP/methylation site identification to that generated from separate captures for DNA sequencing and methyl-seq. Furthermore, by defining SNP frequencies in a diverse landrace from the Watkins collection we highlight the importance of having genotype data to prevent false positive methylation calls. Finally, we present the design of a new 12 Mbp wheat capture and demonstrate its successful application to re-sequence wheat. Conclusions We present a cost-effective method for performing both DNA sequencing and methyl-seq from a single capture reaction thus reducing reagent costs, sample preparation time and DNA requirements for these complementary analyses. Electronic supplementary material The online version of this article (10.1186/s12864-018-4640-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lisa Olohan
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | | | - Anita Lucaci
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | | | - Brande Wulff
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - John Kenny
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | - Neil Hall
- Earlham Institute, Norwich research Park, Norwich, UK.,University of East Anglia, Norwich, UK
| | - Anthony Hall
- Earlham Institute, Norwich research Park, Norwich, UK. .,University of East Anglia, Norwich, UK.
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41
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Wellband KW, Pettitt-Wade H, Fisk AT, Heath DD. Standing genetic diversity and selection at functional gene loci are associated with differential invasion success in two non-native fish species. Mol Ecol 2018; 27:1572-1585. [PMID: 29573310 DOI: 10.1111/mec.14557] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 02/25/2018] [Accepted: 03/07/2018] [Indexed: 12/30/2022]
Abstract
Invasive species are expected to experience a unique combination of high genetic drift due to demographic factors while also experiencing strong selective pressures. The paradigm that reduced genetic diversity should limit the evolutionary potential of invasive species, and thus, their potential for range expansion has received little empirical support, possibly due to the choice of genetic markers. Our goal was to test for effects of genetic drift and selection at functional genetic markers as they relate to the invasion success of two paired invasive goby species, one widespread (successful) and one with limited range expansion (less successful). We genotyped fish using two marker types: single nucleotide polymorphisms (SNPs) in known-function, protein-coding genes and microsatellites to contrast the effects of neutral genetic processes. We identified reduced allelic variation in the invaded range for the less successful tubenose goby. SNPs putatively under selection were responsible for the observed differences in population structure between marker types for round goby (successful) but not tubenose goby (less successful). A higher proportion of functional loci experienced divergent selection for round goby, suggesting increased evolutionary potential in invaded ranges may be associated with round goby's greater invasion success. Genes involved in thermal tolerance were divergent for round goby populations but not tubenose goby, consistent with the hypothesis that invasion success for fish in temperate regions is influenced by capacity for thermal tolerance. Our results highlight the need to incorporate functional genetic markers in studies to better assess evolutionary potential for the improved conservation and management of species.
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Affiliation(s)
- Kyle W Wellband
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Harri Pettitt-Wade
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Aaron T Fisk
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada.,Department of Biological Sciences, University of Windsor, Windsor, ON, Canada
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42
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Connon RE, Jeffries KM, Komoroske LM, Todgham AE, Fangue NA. The utility of transcriptomics in fish conservation. ACTA ACUST UNITED AC 2018; 221:221/2/jeb148833. [PMID: 29378879 DOI: 10.1242/jeb.148833] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is growing recognition of the need to understand the mechanisms underlying organismal resilience (i.e. tolerance, acclimatization) to environmental change to support the conservation management of sensitive and economically important species. Here, we discuss how functional genomics can be used in conservation biology to provide a cellular-level understanding of organismal responses to environmental conditions. In particular, the integration of transcriptomics with physiological and ecological research is increasingly playing an important role in identifying functional physiological thresholds predictive of compensatory responses and detrimental outcomes, transforming the way we can study issues in conservation biology. Notably, with technological advances in RNA sequencing, transcriptome-wide approaches can now be applied to species where no prior genomic sequence information is available to develop species-specific tools and investigate sublethal impacts that can contribute to population declines over generations and undermine prospects for long-term conservation success. Here, we examine the use of transcriptomics as a means of determining organismal responses to environmental stressors and use key study examples of conservation concern in fishes to highlight the added value of transcriptome-wide data to the identification of functional response pathways. Finally, we discuss the gaps between the core science and policy frameworks and how thresholds identified through transcriptomic evaluations provide evidence that can be more readily used by resource managers.
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Affiliation(s)
- Richard E Connon
- Department of Anatomy, Physiology & Cell Biology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Ken M Jeffries
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba, Canada R3T 2N2
| | - Lisa M Komoroske
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA 92037, USA.,Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Anne E Todgham
- Department of Animal Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Nann A Fangue
- Wildlife, Fish & Conservation Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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43
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Mäkinen H, Sävilammi T, Papakostas S, Leder E, Vøllestad LA, Primmer CR. Modularity Facilitates Flexible Tuning of Plastic and Evolutionary Gene Expression Responses during Early Divergence. Genome Biol Evol 2018; 10:77-93. [PMID: 29293993 PMCID: PMC5758911 DOI: 10.1093/gbe/evx278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2017] [Indexed: 12/14/2022] Open
Abstract
Gene expression changes have been recognized as important drivers of adaptation to changing environmental conditions. Little is known about the relative roles of plastic and evolutionary responses in complex gene expression networks during the early stages of divergence. Large gene expression data sets coupled with in silico methods for identifying coexpressed modules now enable systems genetics approaches also in nonmodel species for better understanding of gene expression responses during early divergence. Here, we combined gene coexpression analyses with population genetics to separate plastic and population (evolutionary) effects in expression networks using small salmonid populations as a model system. We show that plastic and population effects were highly variable among the six identified modules and that the plastic effects explained larger proportion of the total eigengene expression than population effects. A more detailed analysis of the population effects using a QST - FST comparison across 16,622 annotated transcripts revealed that gene expression followed neutral expectations within modules and at the global level. Furthermore, two modules showed enrichment for genes coding for early developmental traits that have been previously identified as important phenotypic traits in thermal responses in the same model system indicating that coexpression analysis can capture expression patterns underlying ecologically important traits. We suggest that module-specific responses may facilitate the flexible tuning of expression levels to local thermal conditions. Overall, our study indicates that plasticity and neutral evolution are the main drivers of gene expression variance in the early stages of thermal adaptation in this system.
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Affiliation(s)
| | | | | | - Erica Leder
- Department of Biology, University of Turku, Finland
- Natural History Museum, University of Oslo, Norway
| | - Leif A Vøllestad
- Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Craig R Primmer
- Department of Biosciences, University of Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Finland
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44
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45
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Fantastic Beasts and How To Sequence Them: Ecological Genomics for Obscure Model Organisms. Trends Genet 2017; 34:121-132. [PMID: 29198378 DOI: 10.1016/j.tig.2017.11.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/30/2017] [Accepted: 11/07/2017] [Indexed: 01/05/2023]
Abstract
The application of genomic approaches to 'obscure model organisms' (OMOs), meaning species with no prior genomic resources, enables increasingly sophisticated studies of the genomic basis of evolution, acclimatization, and adaptation in real ecological contexts. I consider here ecological questions that can be addressed using OMOs, and indicate optimal sequencing and data-handling solutions for each case. With this I hope to promote the diversity of OMO-based projects that would capitalize on the peculiarities of the natural history of OMOs and could feasibly be completed within the scope of a single PhD thesis.
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46
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Montero-Mendieta S, Grabherr M, Lantz H, De la Riva I, Leonard JA, Webster MT, Vilà C. A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog. PeerJ 2017; 5:e3702. [PMID: 28879061 PMCID: PMC5582611 DOI: 10.7717/peerj.3702] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/27/2017] [Indexed: 01/01/2023] Open
Abstract
Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembled de-novo. We used RNA-seq to obtain the transcriptomic profile for Oreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome of O. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to build de-novo transcriptome assemblies using readily available software and is freely available at: https://github.com/biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki.
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Affiliation(s)
- Santiago Montero-Mendieta
- Conservation and Evolutionary Genetics Group, Department of Integrative Ecology, Doñana Biological Station (EBD-CSIC), Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Manfred Grabherr
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden (BILS), Uppsala Universitet, Uppsala, Sweden
| | - Henrik Lantz
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden (BILS), Uppsala Universitet, Uppsala, Sweden
| | - Ignacio De la Riva
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Department of Integrative Ecology, Doñana Biological Station (EBD-CSIC), Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Department of Integrative Ecology, Doñana Biological Station (EBD-CSIC), Consejo Superior de Investigaciones Científicas, Seville, Spain
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47
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Balao F, Trucchi E, Wolfe TM, Hao B, Lorenzo MT, Baar J, Sedman L, Kosiol C, Amman F, Chase MW, Hedrén M, Paun O. Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima. Mol Ecol 2017; 26:3649-3662. [PMID: 28370647 PMCID: PMC5518283 DOI: 10.1111/mec.14123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 02/24/2017] [Accepted: 03/15/2017] [Indexed: 12/23/2022]
Abstract
The orchid family is the largest in the angiosperms, but little is known about the molecular basis of the significant variation they exhibit. We investigate here the transcriptomic divergence between two European terrestrial orchids, Dactylorhiza incarnata and Dactylorhiza fuchsii, and integrate these results in the context of their distinct ecologies that we also document. Clear signals of lineage-specific adaptive evolution of protein-coding sequences are identified, notably targeting elements of biotic defence, including both physical and chemical adaptations in the context of divergent pools of pathogens and herbivores. In turn, a substantial regulatory divergence between the two species appears linked to adaptation/acclimation to abiotic conditions. Several of the pathways affected by differential expression are also targeted by deviating post-transcriptional regulation via sRNAs. Finally, D. incarnata appears to suffer from insufficient sRNA control over the activity of RNA-dependent DNA polymerase, resulting in increased activity of class I transposable elements and, over time, in larger genome size than that of D. fuchsii. The extensive molecular divergence between the two species suggests significant genomic and transcriptomic shock in their hybrids and offers insights into the difficulty of coexistence at the homoploid level. Altogether, biological response to selection, accumulated during the history of these orchids, appears governed by their microenvironmental context, in which biotic and abiotic pressures act synergistically to shape transcriptome structure, expression and regulation.
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Affiliation(s)
- Francisco Balao
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Departamento de Biología Vegetal y EcologíaUniversity of SevilleSevillaSpain
| | - Emiliano Trucchi
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Department of Life Sciences and BiotechnologiesUniversity of FerraraFerraraItaly
| | - Thomas M. Wolfe
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | - Bao‐Hai Hao
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Maria Teresa Lorenzo
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Departamento de Biología Vegetal y EcologíaUniversity of SevilleSevillaSpain
| | - Juliane Baar
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Laura Sedman
- Gregor Mendel Institute for Plant Molecular BiologyViennaAustria
| | - Carolin Kosiol
- Institut für PopulationsgenetikVetmeduni ViennaViennaAustria
- Centre of Biological DiversitySchool of BiologyUniversity of St AndrewsSt AndrewsUK
| | - Fabian Amman
- Department of Chromosome BiologyUniversity of ViennaViennaAustria
| | - Mark W. Chase
- Royal Botanic Gardens KewRichmondUK
- School of Plant BiologyUniversity of Western AustraliaCrawley, PerthWAAustralia
| | | | - Ovidiu Paun
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
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48
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Pespeni MH, Ladner JT, Moczek AP. Signals of selection in conditionally expressed genes in the diversification of three horned beetle species. J Evol Biol 2017; 30:1644-1657. [PMID: 28379613 DOI: 10.1111/jeb.13079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 03/05/2017] [Indexed: 01/20/2023]
Abstract
Species radiations may be facilitated by phenotypic differences already present within populations, such as those arising through sex-specific development or developmental processes biased towards particular reproductive or trophic morphs. We sought to test this hypothesis by utilizing a comparative transcriptomic approach to contrast among- and within-species differentiation using three horned beetle species in the genus Onthophagus. These three species exhibit differences along three phenotypic axes reflective of much of the interspecific diversity present within the genus: horn location, polarity of sexual dimorphism and degree of nutritional sensitivity. Our approach combined de novo transcript assembly, assessment of amino acid substitutions (dN/dS) across orthologous gene pairs and integration of gene function and conditional gene expression data. We identified 17 genes across the three species pairs related to axis patterning, development and metabolism with dN/dS > 1 and detected elevated dN/dS in genes related to metabolism and biosynthesis in the most closely related species pair, which is characterized by a loss of nutritional polyphenism and a reversal of sexual dimorphism. Further, we found that genes that are conditionally expressed (i.e. as a function of sex, nutrition or body region) within one of our focal species also showed significantly stronger signals of positive or relaxed purifying selection between species divergent along the same morphological axis (i.e. polarity of sexual dimorphism, degree of nutritional sensitivity or location of horns). Our findings thus reveal a positive relationship between intraspecific differentiation due to condition-specific development and genetic divergences among species.
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Affiliation(s)
- M H Pespeni
- Department of Biology, Indiana University, Bloomington, IN, USA.,Department of Biology, University of Vermont, Burlington, VT, USA
| | - J T Ladner
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | - A P Moczek
- Department of Biology, Indiana University, Bloomington, IN, USA
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49
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Bankers L, Fields P, McElroy KE, Boore JL, Logsdon JM, Neiman M. Genomic evidence for population-specific responses to co-evolving parasites in a New Zealand freshwater snail. Mol Ecol 2017; 26:3663-3675. [PMID: 28429458 DOI: 10.1111/mec.14146] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 03/27/2017] [Accepted: 03/29/2017] [Indexed: 01/13/2023]
Abstract
Reciprocal co-evolving interactions between hosts and parasites are a primary source of strong selection that can promote rapid and often population- or genotype-specific evolutionary change. These host-parasite interactions are also a major source of disease. Despite their importance, very little is known about the genomic basis of co-evolving host-parasite interactions in natural populations, especially in animals. Here, we use gene expression and sequence evolution approaches to take critical steps towards characterizing the genomic basis of interactions between the freshwater snail Potamopyrgus antipodarum and its co-evolving sterilizing trematode parasite, Microphallus sp., a textbook example of natural coevolution. We found that Microphallus-infected P. antipodarum exhibit systematic downregulation of genes relative to uninfected P. antipodarum. The specific genes involved in parasite response differ markedly across lakes, consistent with a scenario where population-level co-evolution is leading to population-specific host-parasite interactions and evolutionary trajectories. We also used an FST -based approach to identify a set of loci that represent promising candidates for targets of parasite-mediated selection across lakes as well as within each lake population. These results constitute the first genomic evidence for population-specific responses to co-evolving infection in the P. antipodarum-Microphallus interaction and provide new insights into the genomic basis of co-evolutionary interactions in nature.
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Affiliation(s)
- Laura Bankers
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Peter Fields
- Zoologisches Institut, Universität Basel, Basel, Switzerland
| | - Kyle E McElroy
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Jeffrey L Boore
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA, USA
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50
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Moshtaghi A, Rahi ML, Mather PB, Hurwood DA. Understanding the Genomic Basis of Adaptive Response to Variable Osmotic Niches in Freshwater Prawns: A Comparative Intraspecific RNA-Seq Analysis of Macrobrachium australiense. J Hered 2017; 108:544-552. [DOI: 10.1093/jhered/esx045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 05/03/2017] [Indexed: 12/30/2022] Open
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