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Suchan T, Kusliy MA, Khan N, Chauvey L, Tonasso-Calvière L, Schiavinato S, Southon J, Keller M, Kitagawa K, Krause J, Bessudnov AN, Bessudnov AA, Graphodatsky AS, Valenzuela-Lamas S, Wilczyński J, Pospuła S, Tunia K, Nowak M, Moskal-delHoyo M, Tishkin AA, Pryor AJE, Outram AK, Orlando L. Performance and automation of ancient DNA capture with RNA hyRAD probes. Mol Ecol Resour 2021; 22:891-907. [PMID: 34582623 PMCID: PMC9291508 DOI: 10.1111/1755-0998.13518] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 01/23/2023]
Abstract
DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analysing ancient DNA (aDNA) extracts, which are often dominated by exogenous environmental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and design-free alternative to commercial capture protocols to obtain authentic aDNA data from osseous remains. HyRAD relies on double enzymatic restriction of fresh DNA extracts to produce RNA probes that cover only a fraction of the genome and can serve as baits for capturing homologous fragments from aDNA libraries. We found that this approach could retrieve sequence data from horse remains coming from a range of preservation environments, including beyond radiocarbon range, yielding up to 146.5-fold on-target enrichment for aDNA extracts showing extremely low endogenous content (<1%). Performance was, however, more limited for those samples already characterized by good DNA preservation (>20%-30%), while the fraction of endogenous reads mapping on- and off-target was relatively insensitive to the original endogenous DNA content. Procedures based on two instead of a single round of capture increased on-target coverage up to 3.6-fold. Additionally, we used methylation-sensitive restriction enzymes to produce probes targeting hypomethylated regions, which improved data quality by reducing post-mortem DNA damage and mapping within multicopy regions. Finally, we developed a fully automated hyRAD protocol utilizing inexpensive robotic platforms to facilitate capture processing. Overall, our work establishes hyRAD as a cost-effective strategy to recover a set of shared orthologous variants across multiple ancient samples.
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Affiliation(s)
- Tomasz Suchan
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Mariya A Kusliy
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.,Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Naveed Khan
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.,Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Loreleï Chauvey
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Laure Tonasso-Calvière
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Stéphanie Schiavinato
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - John Southon
- Earth System Science Department, University of California, Irvine, Irvine, California, USA
| | - Marcel Keller
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Keiko Kitagawa
- SFB 1070 ResourceCultures, University of Tübingen, Tübingen, Germany.,Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Alexander A Bessudnov
- Institute for the History of Material Culture, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Alexander S Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Silvia Valenzuela-Lamas
- Institución Milà i Fontanals de Humanidades, Consejo Superior de Investigaciones Científicas (IMF-CSIC), Barcelona, Spain
| | - Jarosław Wilczyński
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Sylwia Pospuła
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Krzysztof Tunia
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland
| | - Marek Nowak
- Institute of Archaeology, Jagiellonian University, Kraków, Poland
| | | | - Alexey A Tishkin
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | | | - Alan K Outram
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
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2
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Kirschner P, Arthofer W, Pfeifenberger S, Záveská E, Schönswetter P, Steiner FM, Schlick-Steiner BC. Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework. Sci Rep 2021; 11:3978. [PMID: 33597550 PMCID: PMC7889850 DOI: 10.1038/s41598-020-79778-x] [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: 01/28/2020] [Accepted: 12/09/2020] [Indexed: 01/31/2023] Open
Abstract
Multi-locus genetic data are pivotal in phylogenetics. Today, high-throughput sequencing (HTS) allows scientists to generate an unprecedented amount of such data from any organism. However, HTS is resource intense and may not be accessible to wide parts of the scientific community. In phylogeography, the use of HTS has concentrated on a few taxonomic groups, and the amount of data used to resolve a phylogeographic pattern often seems arbitrary. We explore the performance of two genetic marker sampling strategies and the effect of marker quantity in a comparative phylogeographic framework focusing on six species (arthropods and plants). The same analyses were applied to data inferred from amplified fragment length polymorphism fingerprinting (AFLP), a cheap, non-HTS based technique that is able to straightforwardly produce several hundred markers, and from restriction site associated DNA sequencing (RADseq), a more expensive, HTS-based technique that produces thousands of single nucleotide polymorphisms. We show that in four of six study species, AFLP leads to results comparable with those of RADseq. While we do not aim to contest the advantages of HTS techniques, we also show that AFLP is a robust technique to delimit evolutionary entities in both plants and animals. The demonstrated similarity of results from the two techniques also strengthens biological conclusions that were based on AFLP data in the past, an important finding given the wide utilization of AFLP over the last decades. We emphasize that whenever the delimitation of evolutionary entities is the central goal, as it is in many fields of biodiversity research, AFLP is still an adequate technique.
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Affiliation(s)
- Philipp Kirschner
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria ,grid.5771.40000 0001 2151 8122Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Wolfgang Arthofer
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Stefanie Pfeifenberger
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Eliška Záveská
- grid.5771.40000 0001 2151 8122Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Peter Schönswetter
- grid.5771.40000 0001 2151 8122Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | | | - Florian M. Steiner
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Birgit C. Schlick-Steiner
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
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3
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Gargiulo R, Kull T, Fay MF. Effective double-digest RAD sequencing and genotyping despite large genome size. Mol Ecol Resour 2021; 21:1037-1055. [PMID: 33351289 DOI: 10.1111/1755-0998.13314] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 12/03/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022]
Abstract
Obtaining informative data is the ambition of any genomic project, but in nonmodel species with very large genomes, pursuing such a goal requires surmounting a series of analytical challenges. Double-digest RAD sequencing is routinely used in nonmodel organisms and offers some control over the volume of data obtained. However, the volume of data recovered is not always an indication of the reliability of data sets, and quality checks are necessary to ensure that true and artefactual information is set apart. In the present study, we aim to fill the gap existing between the known applicability of RAD sequencing methods in plants with large genomes and the use of the retrieved loci for population genetic inference. By analysing two populations of Cypripedium calceolus, a nonmodel orchid species with a large genome size (1C ~ 31.6 Gbp), we provide a complete workflow from library preparation to bioinformatic filtering and inference of genetic diversity and differentiation. We show how filtering strategies to dismiss potentially misleading data need to be explored and adapted to data set-specific features. Moreover, we suggest that the occurrence of organellar sequences in libraries should not be neglected when planning the experiment and analysing the results. Finally, we explain how, in the absence of prior information about the genome of the species, seeking high standards of quality during library preparation and sequencing can provide an insurance against unpredicted technical or biological constraints.
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Affiliation(s)
| | - Tiiu Kull
- Estonian University of Life Sciences, Tartu, Estonia
| | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK.,School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
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4
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van Deventer R, Rhode C, Marx M, Roodt-Wilding R. The development of genome-wide single nucleotide polymorphisms in blue wildebeest using the DArTseq platform. Genomics 2020; 112:3455-3464. [PMID: 32574831 DOI: 10.1016/j.ygeno.2020.04.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/24/2020] [Accepted: 04/17/2020] [Indexed: 12/30/2022]
Abstract
Blue wildebeest (Connochaetes taurinus taurinus) are economically important antelope that are widely utilised in the South African wildlife industry. However, very few genomic resources are available for blue wildebeest that can assist in breeding management and facilitate research. This study aimed to develop a set of genome-wide single nucleotide polymorphism (SNP) markers for blue wildebeest. The DArTseq genotyping platform, commonly used in polyploid plant species, was selected for SNP discovery. A limited number of published articles have described the use of the DArTseq platform in animals and, therefore, this study also provided a unique opportunity to assess the performance of the DArTseq platform in an animal species. A total of 20,563 SNPs, each located within a 69 bp sequence, were generated. The developed SNP markers had a high average scoring reproducibility (>99%) and a low percentage missing data (~9.21%) compared to other reduced representation sequencing approaches that have been used in animal studies. Furthermore, the number of candidate SNPs per nucleotide position decreased towards the 3' end of sequence reads, and the ratio of transitions (Ts) to transversions (Tv) remained similar for each read position. These observations indicate that there was no read position bias, such as the identification of false SNPs due to low sequencing quality, towards the tail-end of sequencing reads. The DArTseq platform was also successful in identifying a large number of informative SNPs with desirable polymorphism parameters such as a high minor allele frequency (MAF). The Bos taurus genome was used for the in silico mapping of the marker sequences and a total of 6020 (29.28%) sequences were successfully mapped against the bovine genome. The marker sequences mapped to all of the bovine chromosomes establishing the genome-wide distribution of the SNPs. Moreover, the high observed Ts:Tv ratio (2.84:1) indicate that the DArTseq platform targeted gene-rich regions of the blue wildebeest genome. Finally, functional annotation of the marker sequences revealed a wide range of different putative functions indicating that these SNP markers can be useful in functional gene studies. The DArTseq platform, therefore, represents a high-throughput, robust and cost-effective genotyping platform, which may find adoption in several other African antelope and animal species.
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Affiliation(s)
- Riana van Deventer
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa; Unistel Medical Laboratories (Pty) Ltd, Parow North 7500, South Africa.
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa.
| | - Munro Marx
- Unistel Medical Laboratories (Pty) Ltd, Parow North 7500, South Africa.
| | - Rouvay Roodt-Wilding
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa.
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5
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Köbölkuti ZA, Tóth EG, Jahn D, Heinze B, Höhn M. SNP marker development in Pinus sylvestris L. in stress-responsive genes characterized from Pinus cembra L. transcriptomes. Mol Biol Rep 2020; 47:4841-4847. [PMID: 32430847 PMCID: PMC7295734 DOI: 10.1007/s11033-020-05527-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 05/14/2020] [Indexed: 11/27/2022]
Abstract
Massively parallel sequencing of cDNA is an efficient route for generating sequence collections that represent expressed genes under different environmental control. The analysis of their sequence helps in developing molecular markers, such as SNPs, which represent a useful tool in detecting adaptive signals in populations. In this study novel PCR markers, based on stress responsive genes, were designed from the transcriptome of the haploxylon Swiss stone pine (Pinus cembra L.) and tested for SNPs in the diploxylon Scots pine (Pinus sylvestris L.). 84 primers were tested on P. sylvestris DNA samples originating from three different types of habitat. After sequencing and BLAST search of the amplified products, parts of 19 different candidate genes were analysed by considering the polymorphic sites, insertions/deletions as well as synonymous and non-synonymous SNPs. In a total of 3735 sites no indels, eight synonymous and 11 non-synonymous SNPs were found. By providing de novo molecular markers developed in P. cembra and tested for transferability in Scots pine, our results give support for the use of de novo markers targeting conserved regions across different pines. The SNPs detected may have important applications in further studies of adaptive genetic variation, providing tools to study relevant genes important in the long-term adaptation of pine species.
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Affiliation(s)
- Zoltán A Köbölkuti
- Department of Botany, Faculty of Horticulture, Szent István University, Ménesi út 44, Budapest, 1118, Hungary.
- Department of Breeding, National Agricultural Research and Innovation Centre, Forest Research Institute, Várkerület 30/A, Sárvár, 9600, Hungary.
| | - Endre Gy Tóth
- Department of Breeding, National Agricultural Research and Innovation Centre, Forest Research Institute, Várkerület 30/A, Sárvár, 9600, Hungary
- Forest Research Institute (IRF), University of Quebec in Abitibi-Témiscamingue UQAT, 445 Boul. de l'Université, Rouyn-Noranda, QC, J9X 5E4, Canada
| | - Daniela Jahn
- Federal Research and Training Centre for Forests, Natural Hazards and Landscape (BFW), Seckendorff-Gudent-Weg 8, 1130, Vienna, Austria
| | - Berthold Heinze
- Federal Research and Training Centre for Forests, Natural Hazards and Landscape (BFW), Seckendorff-Gudent-Weg 8, 1130, Vienna, Austria
| | - Mária Höhn
- Department of Botany, Faculty of Horticulture, Szent István University, Ménesi út 44, Budapest, 1118, Hungary
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Daemi-Saeidabad M, Shojaeiyan A, Vivian-Smith A, Stenøien HK, Falahati-Anbaran M. The taxonomic significance of ddRADseq based microsatellite markers in the closely related species of Heracleum (Apiaceae). PLoS One 2020; 15:e0232471. [PMID: 32379780 PMCID: PMC7205262 DOI: 10.1371/journal.pone.0232471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 04/15/2020] [Indexed: 11/28/2022] Open
Abstract
Many studies on Heracleum have shown poor correspondence between observed molecular clusters and established taxonomic classification amongst closely related species. This might reflect both unresolved taxonomy but perhaps also a lack of good genetic markers. This lack of appropriate and cost effective species-specific genetic markers hinders a resolved relationship for the species complex, and this in turn causes profound management challenges for a genus that contains both endemic species, with important ecological roles, and species with an invasive potential. Microsatellites are traditionally considered markers of choice for comprehensive, yet inexpensive, analyses of genetic variation, including examination of population structure, species identity, linkage map construction and cryptic speciation. In this study, we have used double digest restriction site associated DNA sequencing (ddRADseq) to develop microsatellite markers in Heracleum rechingeri. Genomic DNA from three individuals were digested with Sbf1 and Nde1 and size selected for library construction. The size-selected fragments were sequenced on an Ion Torrent sequencer and a total of 54 microsatellite sequences were bioinformatically confirmed. Twenty five loci were then tested for amplification, resulting in 19 of these being successfully amplified across eight species, comprising both the so-called thick-stemmed species (H. persicum, H. rechingeri, H. gorganicum and H. lasiopetalum), and thin-stemmed species (H. anisactis, H. pastinasifolium and H. transcaucasicum). Both Bayesian and distance-based clustering, and principal coordinate analyses clearly separated these into two groups. Surprisingly, three H. pastinacifolium populations were not separated from populations of the morphologically similar endemic species, H. anisactis, suggesting lack of genetic differentiation. Likewise, high genetic similarity was found between H. persicum and H. rechingeri populations, questioning taxonomic separation at the species level between these taxa. Further analyses are needed to re-evaluate the taxonomic significance of observed morphological variability currently applied to distinguish these sister taxa. Nevertheless, our results represent progress in the effort to develop cost-efficient molecular tools for species discrimination in this genus.
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Affiliation(s)
- Mehdi Daemi-Saeidabad
- Department of Plant Sciences, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Abdolali Shojaeiyan
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Adam Vivian-Smith
- Department of Forest Genetics and Biodiversity, Norwegian Institute for Bioeconomy Research, Ås, Norway
| | - Hans K. Stenøien
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Mohsen Falahati-Anbaran
- Department of Plant Sciences, School of Biology, College of Science, University of Tehran, Tehran, Iran
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Clugston JAR, Kenicer GJ, Milne R, Overcast I, Wilson TC, Nagalingum NS. RADseq as a valuable tool for plants with large genomes—A case study in cycads. Mol Ecol Resour 2019; 19:1610-1622. [DOI: 10.1111/1755-0998.13085] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 11/26/2022]
Affiliation(s)
- James A. R. Clugston
- School of Biological Sciences The University of Edinburgh Edinburgh UK
- Royal Botanic Garden Edinburgh Edinburgh UK
| | | | - Richard Milne
- School of Biological Sciences The University of Edinburgh Edinburgh UK
| | - Isaac Overcast
- The Graduate Center of the City University of New York New York NY USA
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8
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Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs. FORESTS 2019. [DOI: 10.3390/f10080681] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Knowledge on population diversity and structure is of fundamental importance for conifer breeding programs. In this study, we concentrated on the development and application of high-density single nucleotide polymorphism (SNP) markers through a high-throughput sequencing technique termed as specific-locus amplified fragment sequencing (SLAF-seq) for the economically important conifer tree species, Chinese fir (Cunninghamia lanceolata). Based on the SLAF-seq, we successfully established a high-density SNP panel consisting of 108,753 genomic SNPs from Chinese fir. This SNP panel facilitated us in gaining insight into the genetic base of the Chinese fir advance breeding population with 221 genotypes for its genetic variation, relationship and diversity, and population structure status. Overall, the present population appears to have considerable genetic variability. Most (94.15%) of the variability was attributed to the genetic differentiation of genotypes, very limited (5.85%) variation occurred on the population (sub-origin set) level. Correspondingly, low FST (0.0285–0.0990) values were seen for the sub-origin sets. When viewing the genetic structure of the population regardless of its sub-origin set feature, the present SNP data opened a new population picture where the advanced Chinese fir breeding population could be divided into four genetic sets, as evidenced by phylogenetic tree and population structure analysis results, albeit some difference in membership of the corresponding set (cluster vs. group). It also suggested that all the genetic sets were admixed clades revealing a complex relationship of the genotypes of this population. With a step wise pruning procedure, we captured a core collection (core 0.650) harboring 143 genotypes that maintains all the allele, diversity, and specific genetic structure of the whole population. This generalist core is valuable for the Chinese fir advanced breeding program and further genetic/genomic studies.
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A Multi-Level Strategy Based on Metabolic and Molecular Genetic Approaches for the Characterization of Different Coptis Medicines Using HPLC-UV and RAD-seq Techniques. Molecules 2018; 23:molecules23123090. [PMID: 30486378 PMCID: PMC6321400 DOI: 10.3390/molecules23123090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/23/2018] [Accepted: 11/24/2018] [Indexed: 12/19/2022] Open
Abstract
Coptis plants (Ranunculaceae) to have played an important role in the prevention and treatment human diseases in Chinese history. In this study, a multi-level strategy based on metabolic and molecular genetic methods was performed for the characterization of four Coptis herbs (C. chinensis, C. deltoidea, C. omeiensis and C. teeta) using high performance liquid chromatography-ultraviolet (HPLC-UV) and restriction site-associated DNA sequencing (RAD-seq) techniques. Protoberberine alkaloids including berberine, palmatine, coptisine, epiberberine, columbamine, jatrorrhizine, magnoflorine and groenlandicine in rhizomes were identified and determined based on the HPLC-UV method. Among them, berberine was demonstrated as the most abundant compound in these plants. RAD-seq was applied to discover single nucleotide polymorphisms (SNPs) data. A total of 44,747,016 reads were generated and 2,443,407 SNPs were identified in regarding to four plants. Additionally, with respect to complicated metabolic and SNP data, multivariable statistical methods of principal component analysis (PCA) and hierarchical cluster analysis (HCA) were successively applied to interpret the structure characteristics. The metabolic variation and genetic relationship among different Coptis plants were successfully illustrated based on data visualization. Summarily, this comprehensive strategy has been proven as a reliable and effective approach to characterize Coptis plants, which can provide additional information for their quality assessment.
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Moran E, Lauder J, Musser C, Stathos A, Shu M. The genetics of drought tolerance in conifers. THE NEW PHYTOLOGIST 2017; 216:1034-1048. [PMID: 28895167 DOI: 10.1111/nph.14774] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/27/2017] [Indexed: 05/20/2023]
Abstract
Contents 1034 I. 1034 II. 1035 III. 1037 IV. 1038 V. 1042 VI. 1043 VII. 1045 References 1045 SUMMARY: As temperatures warm and precipitation patterns shift as a result of climate change, interest in the identification of tree genotypes that will thrive under more arid conditions has grown. In this review, we discuss the multiple definitions of 'drought tolerance' and the biological processes involved in drought responses. We describe the three major approaches taken in the study of genetic variation in drought responses, the advantages and shortcomings of each, and what each of these approaches has revealed about the genetic basis of adaptation to drought in conifers. Finally, we discuss how a greater knowledge of the genetics of drought tolerance may aid forest management, and provide recommendations for how future studies may overcome the limitations of past approaches. In particular, we urge a more direct focus on survival, growth and the traits that directly predict them (rather than on proxies, such as water use efficiency), combining research approaches with complementary strengths and weaknesses, and the inclusion of a wider range of taxa and life stages.
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Affiliation(s)
- Emily Moran
- UC Merced, 5200 N Lake Rd, Merced, CA, 95343, USA
| | | | - Cameron Musser
- Yale School of Forestry & Environmental Studies, 195 Prospect Street, New Haven, CT, 06511, USA
| | | | - Mengjun Shu
- UC Merced, 5200 N Lake Rd, Merced, CA, 95343, USA
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11
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Konar A, Choudhury O, Bullis R, Fiedler L, Kruser JM, Stephens MT, Gailing O, Schlarbaum S, Coggeshall MV, Staton ME, Carlson JE, Emrich S, Romero-Severson J. High-quality genetic mapping with ddRADseq in the non-model tree Quercus rubra. BMC Genomics 2017; 18:417. [PMID: 28558688 PMCID: PMC5450186 DOI: 10.1186/s12864-017-3765-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 05/04/2017] [Indexed: 11/10/2022] Open
Abstract
Background Restriction site associated DNA sequencing (RADseq) has the potential to be a broadly applicable, low-cost approach for high-quality genetic linkage mapping in forest trees lacking a reference genome. The statistical inference of linear order must be as accurate as possible for the correct ordering of sequence scaffolds and contigs to chromosomal locations. Accurate maps also facilitate the discovery of chromosome segments containing allelic variants conferring resistance to the biotic and abiotic stresses that threaten forest trees worldwide. We used ddRADseq for genetic mapping in the tree Quercus rubra, with an approach optimized to produce a high-quality map. Our study design also enabled us to model the results we would have obtained with less depth of coverage. Results Our sequencing design produced a high sequencing depth in the parents (248×) and a moderate sequencing depth (15×) in the progeny. The digital normalization method of generating a de novo reference and the SAMtools SNP variant caller yielded the most SNP calls (78,725). The major drivers of map inflation were multiple SNPs located within the same sequence (77% of SNPs called). The highest quality map was generated with a low level of missing data (5%) and a genome-wide threshold of 0.025 for deviation from Mendelian expectation. The final map included 849 SNP markers (1.8% of the 78,725 SNPs called). Downsampling the individual FASTQ files to model lower depth of coverage revealed that sequencing the progeny using 96 samples per lane would have yielded too few SNP markers to generate a map, even if we had sequenced the parents at depth 248×. Conclusions The ddRADseq technology produced enough high-quality SNP markers to make a moderately dense, high-quality map. The success of this project was due to high depth of coverage of the parents, moderate depth of coverage of the progeny, a good framework map, an optimized bioinformatics pipeline, and rigorous premapping filters. The ddRADseq approach is useful for the construction of high-quality genetic maps in organisms lacking a reference genome if the parents and progeny are sequenced at sufficient depth. Technical improvements in reduced representation sequencing (RRS) approaches are needed to reduce the amount of missing data. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3765-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arpita Konar
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Olivia Choudhury
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Rebecca Bullis
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Lauren Fiedler
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | | | - Melissa T Stephens
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Oliver Gailing
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Scott Schlarbaum
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, 37996, USA
| | - Mark V Coggeshall
- School of Natural Resources, University of Missouri-Columbia, Columbia, MO, 65211, USA.,Hardwood Tree Improvement and Regeneration Center, USDA Forest Service Northern Research Station, West Lafayette, IN, 47907, USA
| | - Margaret E Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA
| | - John E Carlson
- Department of Ecosystem Science and Management, Penn State, University Park, State College, PA, 16802, USA
| | - Scott Emrich
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Jeanne Romero-Severson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
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12
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Verdu CF, Guichoux E, Quevauvillers S, De Thier O, Laizet Y, Delcamp A, Gévaudant F, Monty A, Porté AJ, Lejeune P, Lassois L, Mariette S. Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L. Ecol Evol 2016; 6:7323-7333. [PMID: 28725400 PMCID: PMC5513258 DOI: 10.1002/ece3.2466] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/18/2016] [Accepted: 08/19/2016] [Indexed: 12/20/2022] Open
Abstract
The RADseq technology allows researchers to efficiently develop thousands of polymorphic loci across multiple individuals with little or no prior information on the genome. However, many questions remain about the biases inherent to this technology. Notably, sequence misalignments arising from paralogy may affect the development of single nucleotide polymorphism (SNP) markers and the estimation of genetic diversity. We evaluated the impact of putative paralog loci on genetic diversity estimation during the development of SNPs from a RADseq dataset for the nonmodel tree species Robinia pseudoacacia L. We sequenced nine genotypes and analyzed the frequency of putative paralogous RAD loci as a function of both the depth of coverage and the mismatch threshold allowed between loci. Putative paralogy was detected in a very variable number of loci, from 1% to more than 20%, with the depth of coverage having a major influence on the result. Putative paralogy artificially increased the observed degree of polymorphism and resulting estimates of diversity. The choice of the depth of coverage also affected diversity estimation and SNP validation: A low threshold decreased the chances of detecting minor alleles while a high threshold increased allelic dropout. SNP validation was better for the low threshold (4×) than for the high threshold (18×) we tested. Using the strategy developed here, we were able to validate more than 80% of the SNPs tested by means of individual genotyping, resulting in a readily usable set of 330 SNPs, suitable for use in population genetics applications.
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Affiliation(s)
- Cindy F Verdu
- Forest Management Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
| | | | - Samuel Quevauvillers
- Forest Management Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
| | - Olivier De Thier
- Forest Management Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
| | | | | | | | - Arnaud Monty
- Biodiversity and Landscape Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
| | | | - Philippe Lejeune
- Forest Management Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
| | - Ludivine Lassois
- Forest Management Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium.,Biodiversity and Landscape Unit Gembloux Agro-Bio Tech University of Liège Gembloux Belgium
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13
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Torres-Martínez L, Emery NC. Genome-wide SNP discovery in the annual herb, Lasthenia fremontii (Asteraceae): genetic resources for the conservation and restoration of a California vernal pool endemic. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0524-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Syring JV, Tennessen JA, Jennings TN, Wegrzyn J, Scelfo-Dalbey C, Cronn R. Targeted Capture Sequencing in Whitebark Pine Reveals Range-Wide Demographic and Adaptive Patterns Despite Challenges of a Large, Repetitive Genome. FRONTIERS IN PLANT SCIENCE 2016; 7:484. [PMID: 27148310 PMCID: PMC4838605 DOI: 10.3389/fpls.2016.00484] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/25/2016] [Indexed: 05/20/2023]
Abstract
Whitebark pine (Pinus albicaulis) inhabits an expansive range in western North America, and it is a keystone species of subalpine environments. Whitebark is susceptible to multiple threats - climate change, white pine blister rust, mountain pine beetle, and fire exclusion - and it is suffering significant mortality range-wide, prompting the tree to be listed as 'globally endangered' by the International Union for Conservation of Nature and 'endangered' by the Canadian government. Conservation collections (in situ and ex situ) are being initiated to preserve the genetic legacy of the species. Reliable, transferrable, and highly variable genetic markers are essential for quantifying the genetic profiles of seed collections relative to natural stands, and ensuring the completeness of conservation collections. We evaluated the use of hybridization-based target capture to enrich specific genomic regions from the 27 GB genome of whitebark pine, and to evaluate genetic variation across loci, trees, and geography. Probes were designed to capture 7,849 distinct genes, and screening was performed on 48 trees. Despite the inclusion of repetitive elements in the probe pool, the resulting dataset provided information on 4,452 genes and 32% of targeted positions (528,873 bp), and we were able to identify 12,390 segregating sites from 47 trees. Variations reveal strong geographic trends in heterozygosity and allelic richness, with trees from the southern Cascade and Sierra Range showing the greatest distinctiveness and differentiation. Our results show that even under non-optimal conditions (low enrichment efficiency; inclusion of repetitive elements in baits), targeted enrichment produces high quality, codominant genotypes from large genomes. The resulting data can be readily integrated into management and gene conservation activities for whitebark pine, and have the potential to be applied to other members of 5-needle pine group (Pinus subsect. Quinquefolia) due to their limited genetic divergence.
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Affiliation(s)
- John V. Syring
- Department of Biology, Linfield College, McMinnvilleOR, USA
- *Correspondence: John V. Syring,
| | - Jacob A. Tennessen
- Department of Integrative Biology, Oregon State University, CorvallisOR, USA
| | - Tara N. Jennings
- Department of Botany and Plant Pathology, Oregon State University, CorvallisOR, USA
| | - Jill Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, StorrsCT, USA
| | - Camille Scelfo-Dalbey
- Jack Baskin School of Engineering, University of California, Santa Cruz, Santa CruzCA, USA
| | - Richard Cronn
- Pacific Northwest Research Station, United States Department of Agriculture, Forest Service, CorvallisOR, USA
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