101
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Schön I, Martens K. Ostracod (Ostracoda, Crustacea) genomics - Promises and challenges. Mar Genomics 2016; 29:19-25. [PMID: 27020380 DOI: 10.1016/j.margen.2016.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/11/2016] [Accepted: 03/15/2016] [Indexed: 01/18/2023]
Abstract
Ostracods are well-suited model organisms for evolutionary research. Classic genetic techniques have mostly been used for phylogenetic studies on Ostracoda and were somewhat affected by the lack of large numbers of suitable markers. Genomic methods with their huge potential have so far rarely been applied to this group of crustaceans. We provide relevant examples of genomic studies on other organisms to propose future avenues of genomic ostracod research. At the same time, we suggest solutions to the potential problems in ostracods that the application of genomic techniques might present.
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Affiliation(s)
- Isa Schön
- Royal Belgian Institute of Natural Sciences, OD Nature, ATECO, Freshwater Biology, Vautierstraat 29, B-1000 Brussels, Belgium; University of Hasselt, Research Group Zoology, Agoralaan Building D, B-3590 Diepenbeek, Belgium.
| | - Koen Martens
- Royal Belgian Institute of Natural Sciences, OD Nature, ATECO, Freshwater Biology, Vautierstraat 29, B-1000 Brussels, Belgium; University of Ghent, Department of Biology, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
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102
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Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing. PLoS One 2015; 10:e0143929. [PMID: 26716693 PMCID: PMC4696846 DOI: 10.1371/journal.pone.0143929] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/12/2015] [Indexed: 01/30/2023] Open
Abstract
In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles being more successfully sequenced.
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103
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Hou Y, Nowak MD, Mirré V, Bjorå CS, Brochmann C, Popp M. RAD-seq data point to a northern origin of the arctic-alpine genus Cassiope (Ericaceae). Mol Phylogenet Evol 2015; 95:152-60. [PMID: 26691641 DOI: 10.1016/j.ympev.2015.11.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 11/13/2015] [Accepted: 11/14/2015] [Indexed: 12/31/2022]
Abstract
Many arctic-alpine plants display a highly disjunct distribution between the Arctic/Boreal regions and the southern Asian mountains. Two main hypotheses have been proposed to explain the origin of this biogeographic pattern: (1) south-to-north migration in the late Pliocene/early Pleistocene, and (2) north-to-south migration during the Miocene. The genus Cassiope is disjunctly distributed between the Arctic/Boreal regions and the Himalayan-Hengduan Mountains (HHM) and was selected to test these hypotheses. We constructed a fossil-calibrated phylogeny of Ericaceae using two plastid regions to estimate the crown group age of Cassiope, and used sequence data from thousands of loci produced by restriction site associated DNA sequencing (RAD-seq) to reconstruct the phylogeny of Cassiope. We also performed Bayesian divergence time analysis and biogeographic analysis. The Cassiope crown group was estimated to have originated in the Miocene, which predates the onset of Northern hemisphere glaciation. All HHM species formed a clade together with one eastern Siberian species, and this clade was sister to all other Arctic/Boreal species. This topology implies a northern origin of Cassiope, which is confirmed by our biogeographic analysis. Our results thus suggest that the ancient north-to-south migration hypothesis is most consistent with the origin of Cassiope.
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Affiliation(s)
- Yan Hou
- Natural History Museum, University of Oslo, NO-0318 Oslo, Norway.
| | - Michael D Nowak
- Natural History Museum, University of Oslo, NO-0318 Oslo, Norway; Science for Life Laboratory, Stockholm University, Tomtebodavägen 23, S-17165 Solna, Sweden
| | - Virginia Mirré
- Natural History Museum, University of Oslo, NO-0318 Oslo, Norway
| | | | | | - Magnus Popp
- Natural History Museum, University of Oslo, NO-0318 Oslo, Norway
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104
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McCormack JE, Tsai WLE, Faircloth BC. Sequence capture of ultraconserved elements from bird museum specimens. Mol Ecol Resour 2015; 16:1189-203. [PMID: 26391430 DOI: 10.1111/1755-0998.12466] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/19/2015] [Accepted: 09/03/2015] [Indexed: 01/22/2023]
Abstract
New DNA sequencing technologies are allowing researchers to explore the genomes of the millions of natural history specimens collected prior to the molecular era. Yet, we know little about how well specific next-generation sequencing (NGS) techniques work with the degraded DNA typically extracted from museum specimens. Here, we use one type of NGS approach, sequence capture of ultraconserved elements (UCEs), to collect data from bird museum specimens as old as 120 years. We targeted 5060 UCE loci in 27 western scrub-jays (Aphelocoma californica) representing three evolutionary lineages that could be species, and we collected an average of 3749 UCE loci containing 4460 single nucleotide polymorphisms (SNPs). Despite older specimens producing fewer and shorter loci in general, we collected thousands of markers from even the oldest specimens. More sequencing reads per individual helped to boost the number of UCE loci we recovered from older specimens, but more sequencing was not as successful at increasing the length of loci. We detected contamination in some samples and determined that contamination was more prevalent in older samples that were subject to less sequencing. For the phylogeny generated from concatenated UCE loci, contamination led to incorrect placement of some individuals. In contrast, a species tree constructed from SNPs called within UCE loci correctly placed individuals into three monophyletic groups, perhaps because of the stricter analytical procedures used for SNP calling. This study and other recent studies on the genomics of museum specimens have profound implications for natural history collections, where millions of older specimens should now be considered genomic resources.
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Affiliation(s)
- John E McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, 90041, USA
| | - Whitney L E Tsai
- Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, 90041, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA
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105
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Nicholls JA, Pennington RT, Koenen EJM, Hughes CE, Hearn J, Bunnefeld L, Dexter KG, Stone GN, Kidner CA. Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae). FRONTIERS IN PLANT SCIENCE 2015; 6:710. [PMID: 26442024 PMCID: PMC4584976 DOI: 10.3389/fpls.2015.00710] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/25/2015] [Indexed: 05/20/2023]
Abstract
Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown age of 2-10 MY, yet over 6 kb of plastid and nuclear DNA sequence data gives only poor phylogenetic resolution among species. Here we explore the use of larger-scale nuclear gene data obtained though targeted enrichment to increase phylogenetic resolution within Inga. Transcriptome data from three Inga species were used to select 264 nuclear loci for targeted enrichment and sequencing. Following quality control to remove probable paralogs from these sequence data, the final dataset comprised 259,313 bases from 194 loci for 24 accessions representing 22 Inga species and an outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci concatenated or a gene-tree/species-tree approach yielded highly resolved phylogenies. We used coalescent approaches to show that the same targeted enrichment data also have significant power to discriminate among alternative within-species population histories within the widespread species I. umbellifera. In either application, targeted enrichment simplifies the informatics challenge of identifying orthologous loci associated with de novo genome sequencing. We conclude that targeted enrichment provides the large volumes of phylogenetically-informative sequence data required to resolve relationships within recent plant species radiations, both at the species level and for within-species phylogeographic studies.
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Affiliation(s)
- James A. Nicholls
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of EdinburghEdinburgh, UK
- Royal Botanic Garden EdinburghEdinburgh, UK
| | | | - Erik J. M. Koenen
- Institute of Systematic Botany, University of ZurichZürich, Switzerland
| | - Colin E. Hughes
- Institute of Systematic Botany, University of ZurichZürich, Switzerland
| | - Jack Hearn
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of EdinburghEdinburgh, UK
| | - Lynsey Bunnefeld
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of EdinburghEdinburgh, UK
| | - Kyle G. Dexter
- School of Geosciences, University of EdinburghEdinburgh, UK
| | - Graham N. Stone
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of EdinburghEdinburgh, UK
| | - Catherine A. Kidner
- Royal Botanic Garden EdinburghEdinburgh, UK
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of EdinburghEdinburgh, UK
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106
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Dodsworth S. Genome skimming for next-generation biodiversity analysis. TRENDS IN PLANT SCIENCE 2015; 20:525-527. [PMID: 26205170 DOI: 10.1016/j.tplants.2015.06.012] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 06/26/2015] [Accepted: 06/30/2015] [Indexed: 05/18/2023]
Affiliation(s)
- Steven Dodsworth
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK.
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107
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Parks M, Subramanian S, Baroni C, Salvatore MC, Zhang G, Millar CD, Lambert DM. Ancient population genomics and the study of evolution. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130381. [PMID: 25487332 DOI: 10.1098/rstb.2013.0381] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recently, the study of ancient DNA (aDNA) has been greatly enhanced by the development of second-generation DNA sequencing technologies and targeted enrichment strategies. These developments have allowed the recovery of several complete ancient genomes, a result that would have been considered virtually impossible only a decade ago. Prior to these developments, aDNA research was largely focused on the recovery of short DNA sequences and their use in the study of phylogenetic relationships, molecular rates, species identification and population structure. However, it is now possible to sequence a large number of modern and ancient complete genomes from a single species and thereby study the genomic patterns of evolutionary change over time. Such a study would herald the beginnings of ancient population genomics and its use in the study of evolution. Species that are amenable to such large-scale studies warrant increased research effort. We report here progress on a population genomic study of the Adélie penguin (Pygoscelis adeliae). This species is ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica. This species will enable us to directly address many of the fundamental questions in ecology and evolution.
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Affiliation(s)
- M Parks
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - S Subramanian
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - C Baroni
- Dipartimento di Scienze della Terra, Universita di Pisa, Pisa, Italy
| | - M C Salvatore
- Dipartimento di Scienze della Terra, Universita di Pisa, Pisa, Italy
| | - G Zhang
- China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, Republic of China Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - C D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - D M Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
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108
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Bakker FT, Lei D, Yu J, Mohammadin S, Wei Z, van de Kerke S, Gravendeel B, Nieuwenhuis M, Staats M, Alquezar-Planas DE, Holmer R. Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12642] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Freek T. Bakker
- Biosystematics Group; Wageningen University; Wageningen the Netherlands
| | - Di Lei
- Biosystematics Group; Wageningen University; Wageningen the Netherlands
| | - Jiaying Yu
- Biosystematics Group; Wageningen University; Wageningen the Netherlands
| | | | - Zhen Wei
- Biosystematics Group; Wageningen University; Wageningen the Netherlands
| | - Sara van de Kerke
- Biosystematics Group; Wageningen University; Wageningen the Netherlands
| | - Barbara Gravendeel
- Naturalis Biodiversity Center; Leiden University; Leiden the Netherlands
- University of Applied Sciences Leiden; Leiden the Netherlands
- Plant Ecology and Phytochemistry Group; Institute Biology Leiden; Leiden University; Leiden the Netherlands
| | | | - Martijn Staats
- Biosystematics Group; Wageningen University; Wageningen the Netherlands
| | - David E. Alquezar-Planas
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Copenhagen Denmark
| | - Rens Holmer
- Biosystematics Group; Wageningen University; Wageningen the Netherlands
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109
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Bailey SE, Mao X, Struebig M, Tsagkogeorga G, Csorba G, Heaney LR, Sedlock J, Stanley W, Rouillard JM, Rossiter SJ. The use of museum samples for large-scale sequence capture: a study of congeneric horseshoe bats (family Rhinolophidae). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12620] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sebastian E. Bailey
- School of Biological and Chemical Sciences; Queen Mary University of London; London E1 4NS UK
| | - Xiuguang Mao
- School of Biological and Chemical Sciences; Queen Mary University of London; London E1 4NS UK
- SKLEC; Institute of Molecular Ecology and Evolution; East China Normal University; Shanghai 200062 China
| | - Monika Struebig
- School of Biological and Chemical Sciences; Queen Mary University of London; London E1 4NS UK
- The Genome Centre; John Vane Science Centre; Queen Mary University of London; Charterhouse Square London EC1M 6BQ UK
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences; Queen Mary University of London; London E1 4NS UK
| | - Gabor Csorba
- Hungarian Natural History Museum; Baross 13 1088 Budapest Hungary
| | - Lawrence R. Heaney
- The Field Museum of Natural History; 1400 S. Lake Shore Drive Chicago IL 60605-2496 USA
| | - Jodi Sedlock
- The Field Museum of Natural History; 1400 S. Lake Shore Drive Chicago IL 60605-2496 USA
| | - William Stanley
- The Field Museum of Natural History; 1400 S. Lake Shore Drive Chicago IL 60605-2496 USA
| | | | - Stephen J. Rossiter
- School of Biological and Chemical Sciences; Queen Mary University of London; London E1 4NS UK
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110
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Lam VKY, Soto Gomez M, Graham SW. The Highly Reduced Plastome of Mycoheterotrophic Sciaphila (Triuridaceae) Is Colinear with Its Green Relatives and Is under Strong Purifying Selection. Genome Biol Evol 2015; 105:480-494. [PMID: 26170229 DOI: 10.1002/ajb2.1070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/02/2018] [Indexed: 05/03/2023] Open
Abstract
The enigmatic monocot family Triuridaceae provides a potentially useful model system for studying the effects of an ancient loss of photosynthesis on the plant plastid genome, as all of its members are mycoheterotrophic and achlorophyllous. However, few studies have placed the family in a comparative context, and its phylogenetic placement is only partly resolved. It was also unclear whether any taxa in this family have retained a plastid genome. Here, we used genome survey sequencing to retrieve plastid genome data for Sciaphila densiflora (Triuridaceae) and ten autotrophic relatives in the orders Dioscoreales and Pandanales. We recovered a highly reduced plastome for Sciaphila that is nearly colinear with Carludovica palmata, a photosynthetic relative that belongs to its sister group in Pandanales, Cyclanthaceae-Pandanaceae. This phylogenetic placement is well supported and robust to a broad range of analytical assumptions in maximum-likelihood inference, and is congruent with recent findings based on nuclear and mitochondrial evidence. The 28 genes retained in the S. densiflora plastid genome are involved in translation and other nonphotosynthetic functions, and we demonstrate that nearly all of the 18 protein-coding genes are under strong purifying selection. Our study confirms the utility of whole plastid genome data in phylogenetic studies of highly modified heterotrophic plants, even when they have substantially elevated rates of substitution.
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Affiliation(s)
- Vivienne K Y Lam
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
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111
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Beck JB, Semple JC. Next-generation sampling: Pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae). APPLICATIONS IN PLANT SCIENCES 2015. [PMID: 26082877 DOI: 10.5061/dryad.16pj5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
PREMISE OF THE STUDY The ability to conduct species delimitation and phylogeny reconstruction with genomic data sets obtained exclusively from herbarium specimens would rapidly enhance our knowledge of large, taxonomically contentious plant genera. In this study, the utility of genotyping by sequencing is assessed in the notoriously difficult genus Solidago (Asteraceae) by attempting to obtain an informative single-nucleotide polymorphism data set from a set of specimens collected between 1970 and 2010. METHODS Reduced representation libraries were prepared and Illumina-sequenced from 95 Solidago herbarium specimen DNAs, and resulting reads were processed with the nonreference Universal Network-Enabled Analysis Kit (UNEAK) pipeline. Multidimensional clustering was used to assess the correspondence between genetic groups and morphologically defined species. RESULTS Library construction and sequencing were successful in 93 of 95 samples. The UNEAK pipeline identified 8470 single-nucleotide polymorphisms, and a filtered data set was analyzed for each of three Solidago subsections. Although results varied, clustering identified genomic groups that often corresponded to currently recognized species or groups of closely related species. DISCUSSION These results suggest that genotyping by sequencing is broadly applicable to DNAs obtained from herbarium specimens. The data obtained and their biological signal suggest that pairing genomics with large-scale herbarium sampling is a promising strategy in species-rich plant groups.
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Affiliation(s)
- James B Beck
- Department of Biological Sciences, Wichita State University, 537 Hubbard Hall, Wichita, Kansas 67260 USA ; Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, Texas 76107 USA
| | - John C Semple
- Department of Biology, University of Waterloo, Waterloo, Ontario NL2 3G1 Canada
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112
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Beck JB, Semple JC. Next-generation sampling: Pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae). APPLICATIONS IN PLANT SCIENCES 2015; 3:apps1500014. [PMID: 26082877 PMCID: PMC4467758 DOI: 10.3732/apps.1500014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/28/2015] [Indexed: 05/11/2023]
Abstract
PREMISE OF THE STUDY The ability to conduct species delimitation and phylogeny reconstruction with genomic data sets obtained exclusively from herbarium specimens would rapidly enhance our knowledge of large, taxonomically contentious plant genera. In this study, the utility of genotyping by sequencing is assessed in the notoriously difficult genus Solidago (Asteraceae) by attempting to obtain an informative single-nucleotide polymorphism data set from a set of specimens collected between 1970 and 2010. METHODS Reduced representation libraries were prepared and Illumina-sequenced from 95 Solidago herbarium specimen DNAs, and resulting reads were processed with the nonreference Universal Network-Enabled Analysis Kit (UNEAK) pipeline. Multidimensional clustering was used to assess the correspondence between genetic groups and morphologically defined species. RESULTS Library construction and sequencing were successful in 93 of 95 samples. The UNEAK pipeline identified 8470 single-nucleotide polymorphisms, and a filtered data set was analyzed for each of three Solidago subsections. Although results varied, clustering identified genomic groups that often corresponded to currently recognized species or groups of closely related species. DISCUSSION These results suggest that genotyping by sequencing is broadly applicable to DNAs obtained from herbarium specimens. The data obtained and their biological signal suggest that pairing genomics with large-scale herbarium sampling is a promising strategy in species-rich plant groups.
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Affiliation(s)
- James B. Beck
- Department of Biological Sciences, Wichita State University, 537 Hubbard Hall, Wichita, Kansas 67260 USA
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, Texas 76107 USA
- Author for correspondence:
| | - John C. Semple
- Department of Biology, University of Waterloo, Waterloo, Ontario NL2 3G1 Canada
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113
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Choudhary JS, Naaz N, Prabhakar CS, Rao MS, Das B. The mitochondrial genome of the peach fruit fly, Bactrocera zonata (Saunders) (Diptera: Tephritidae): Complete DNA sequence, genome organization, and phylogenetic analysis with other tephritids using next generation DNA sequencing. Gene 2015; 569:191-202. [PMID: 26031235 DOI: 10.1016/j.gene.2015.05.066] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/13/2015] [Accepted: 05/27/2015] [Indexed: 02/01/2023]
Abstract
Mitochondrial genome can provide information for genomic structure as well as for phylogenetic analysis and evolutionary biology. The complete 15,935 bp mitochondrial genome of Bactrocera zonata (Diptera: Tephritidae), is assembled from Illumina MiSeq read data. The mitogenome information for B. zonata was compared to the homologous sequences of other tephritids. Annotation indicated that the structure and orientation of 13 protein coding genes (PCGs), 22 tRNA and 2 rRNA sequences were typical of, and similar to, the ten closely related tephritid species. The nucleotide composition shows heavily biased toward As and Ts accounting 73.34% and exhibits a slightly positive AT skew, which is similar to other known tephritid species. All PCGs are initiated by ATN codons, except for cox1 with TCG and atp8 with GTG. Nine PCGs use a common stop codon of TAA or TAG, whereas the remaining four use an incomplete termination codon T or TA likely to be completed by adenylation. All tRNAs have the typical clover-leaf structure, with an exception for trnS((AGN)). Four short intergenic spacers showed high degree of conservation among B. zonata and other ten tephritids. A poly(T) stretch at the 5' end followed by [TA(A)]n-like stretch and a tandem repeats of 39 bp has been observed in CR. The analysis of gene evolutionary rate revealed that the cox1 and atp6 exhibits lowest and highest gene substitution rates, respectively than other genes. The phylogenetic relationships based on Maximum Likelihood method using all protein-coding genes and two ribosomal RNA genes confirmed that B. zonata is closely related to Bactrocera correcta, Bactrocera carambolae, Bactrocera papayae, and Bactrocera philippinensis and Bactrocera dorsalis belonging to B. dorsalis species complex forms a monophyletic clade, which is in accordance with the traditional morphological classification and recent molecular works.
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Affiliation(s)
- Jaipal S Choudhary
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi 834 010, Jharkhand, India.
| | - Naiyar Naaz
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi 834 010, Jharkhand, India.
| | - Chandra S Prabhakar
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi 834 010, Jharkhand, India; Department of Entomology, Bihar Agricultural University, Sabour, Bhagalpur 813 210, Bihar, India.
| | - Mathukumalli Srinivasa Rao
- Central Research Institute for Dryland Agriculture (CRIDA), Santoshnagar, Saidabad PO, Hyderabad 500 059, India.
| | - Bikash Das
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi 834 010, Jharkhand, India.
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114
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Dentinger BTM, Gaya E, O'Brien H, Suz LM, Lachlan R, Díaz-Valderrama JR, Koch RA, Aime MC. Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12553] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Bryn T. M. Dentinger
- Jodrell Laboratory; Royal Botanic Gardens; Kew TW9 3DS UK
- Institute of Biological, Environmental and Rural Sciences; Aberystwyth University; Cledwyn Building Penglais Aberystwyth SY23 3DD UK
| | - Ester Gaya
- Jodrell Laboratory; Royal Botanic Gardens; Kew TW9 3DS UK
| | - Heath O'Brien
- School of Biological Sciences; University of Bristol; Life Sciences Building 24 Tyndall Avenue Bristol BS8 1TQ UK
| | - Laura M. Suz
- Jodrell Laboratory; Royal Botanic Gardens; Kew TW9 3DS UK
| | - Robert Lachlan
- Department of Psychology; Queen Mary University of London; Mile End Road London E1 4NS UK
| | - Jorge R. Díaz-Valderrama
- Department of Botany and Plant Pathology; Purdue University; 915 W. State St. West Lafayette IN 47907 USA
| | - Rachel A. Koch
- Department of Botany and Plant Pathology; Purdue University; 915 W. State St. West Lafayette IN 47907 USA
| | - M. Catherine Aime
- Department of Botany and Plant Pathology; Purdue University; 915 W. State St. West Lafayette IN 47907 USA
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115
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Timmermans MJTN, Viberg C, Martin G, Hopkins K, Vogler AP. Rapid assembly of taxonomically validated mitochondrial genomes from historical insect collections. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12552] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martijn J. T. N. Timmermans
- Department of Life Sciences; Natural History Museum; London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
- Department of Natural Sciences; Middlesex University; Hendon Campus London NW4 4BT UK
| | - Carl Viberg
- Department of Life Sciences; Natural History Museum; London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
| | - Geoff Martin
- Department of Life Sciences; Natural History Museum; London SW7 5BD UK
| | - Kevin Hopkins
- Department of Life Sciences; Natural History Museum; London SW7 5BD UK
| | - Alfried P. Vogler
- Department of Life Sciences; Natural History Museum; London SW7 5BD UK
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot SL5 7PY UK
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116
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Xu C, Dong W, Shi S, Cheng T, Li C, Liu Y, Wu P, Wu H, Gao P, Zhou S. Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques. Mol Ecol Resour 2015; 15:1366-74. [DOI: 10.1111/1755-0998.12413] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 03/21/2015] [Accepted: 04/04/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Shuo Shi
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
- College of Life Science; Hebei Normal University; Shijiazhuang 050024 China
| | - Tao Cheng
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Changhao Li
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Yanlei Liu
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Ping Wu
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Hongkun Wu
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Peng Gao
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
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117
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Zedane L, Hong-Wa C, Murienne J, Jeziorski C, Baldwin BG, Besnard G. Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12509] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Loubab Zedane
- CNRS-UPS-ENFA; UMR5174; EDB (Laboratoire Evolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Cynthia Hong-Wa
- Missouri Botanical Garden; PO Box 299 St. Louis MO 63166-0299 USA
| | - Jérôme Murienne
- CNRS-UPS-ENFA; UMR5174; EDB (Laboratoire Evolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Céline Jeziorski
- INRA; UAR1209; département de Génétique Animale; INRA Auzeville 31326; Castanet-Tolosan France
- GeT-PlaGe; Genotoul; INRA Auzeville 31326; Castanet-Tolosan France
| | - Bruce G. Baldwin
- Jepson Herbarium and Department of Integrative Biology; University of California; Berkeley CA 94720-2465 USA
| | - Guillaume Besnard
- CNRS-UPS-ENFA; UMR5174; EDB (Laboratoire Evolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
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118
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Besnard G, Bertrand JAM, Delahaie B, Bourgeois YXC, Lhuillier E, Thébaud C. Valuing museum specimens: high-throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12494] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Joris A. M. Bertrand
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
- Institute of Oceanography; National Taiwan University; n°1, sec. 4, Roosevelt Road, Daan District Taipei 10617 Taiwan
| | - Boris Delahaie
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Yann X. C. Bourgeois
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
- Zoological Institute; Department of Evolutionary Biology; University of Basel; Vesalgasse 1 4051 Basel Switzerland
| | - Emeline Lhuillier
- INRA; GeT-PlaGe; UAR 1209 Département de Génétique Animale; INRA Auzeville; 31326 Castanet-Tolosan France
| | - Christophe Thébaud
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
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119
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Burrell AS, Disotell TR, Bergey CM. The use of museum specimens with high-throughput DNA sequencers. J Hum Evol 2015; 79:35-44. [PMID: 25532801 PMCID: PMC4312722 DOI: 10.1016/j.jhevol.2014.10.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/08/2014] [Accepted: 10/31/2014] [Indexed: 12/30/2022]
Abstract
Natural history collections have long been used by morphologists, anatomists, and taxonomists to probe the evolutionary process and describe biological diversity. These biological archives also offer great opportunities for genetic research in taxonomy, conservation, systematics, and population biology. They allow assays of past populations, including those of extinct species, giving context to present patterns of genetic variation and direct measures of evolutionary processes. Despite this potential, museum specimens are difficult to work with because natural postmortem processes and preservation methods fragment and damage DNA. These problems have restricted geneticists' ability to use natural history collections primarily by limiting how much of the genome can be surveyed. Recent advances in DNA sequencing technology, however, have radically changed this, making truly genomic studies from museum specimens possible. We review the opportunities and drawbacks of the use of museum specimens, and suggest how to best execute projects when incorporating such samples. Several high-throughput (HT) sequencing methodologies, including whole genome shotgun sequencing, sequence capture, and restriction digests (demonstrated here), can be used with archived biomaterials.
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Affiliation(s)
- Andrew S Burrell
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA.
| | - Todd R Disotell
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA; New York Consortium in Evolutionary Primatology, USA
| | - Christina M Bergey
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA; New York Consortium in Evolutionary Primatology, USA
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120
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Yoshida K, Sasaki E, Kamoun S. Computational analyses of ancient pathogen DNA from herbarium samples: challenges and prospects. FRONTIERS IN PLANT SCIENCE 2015; 6:771. [PMID: 26442080 PMCID: PMC4585160 DOI: 10.3389/fpls.2015.00771] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/07/2015] [Indexed: 05/20/2023]
Abstract
The application of DNA sequencing technology to the study of ancient DNA has enabled the reconstruction of past epidemics from genomes of historically important plant-associated microbes. Recently, the genome sequences of the potato late blight pathogen Phytophthora infestans were analyzed from 19th century herbarium specimens. These herbarium samples originated from infected potatoes collected during and after the Irish potato famine. Herbaria have therefore great potential to help elucidate past epidemics of crops, date the emergence of pathogens, and inform about past pathogen population dynamics. DNA preservation in herbarium samples was unexpectedly good, raising the possibility of a whole new research area in plant and microbial genomics. However, the recovered DNA can be extremely fragmented resulting in specific challenges in reconstructing genome sequences. Here we review some of the challenges in computational analyses of ancient DNA from herbarium samples. We also applied the recently developed linkage method to haplotype reconstruction of diploid or polyploid genomes from fragmented ancient DNA.
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Affiliation(s)
- Kentaro Yoshida
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe UniversityKobe, Japan
- The Sainsbury Laboratory, Norwich Research ParkNorwich, UK
- *Correspondence: Kentaro Yoshida, Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-Ku, Kobe, Japan,
| | - Eriko Sasaki
- Gregor Mendel Institute, Austrian Academy of Sciences, ViennaAustria
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research ParkNorwich, UK
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121
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Nicholls JA, Pennington RT, Koenen EJM, Hughes CE, Hearn J, Bunnefeld L, Dexter KG, Stone GN, Kidner CA. Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae). FRONTIERS IN PLANT SCIENCE 2015. [PMID: 26442024 DOI: 10.5061/dryad.r9c12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown age of 2-10 MY, yet over 6 kb of plastid and nuclear DNA sequence data gives only poor phylogenetic resolution among species. Here we explore the use of larger-scale nuclear gene data obtained though targeted enrichment to increase phylogenetic resolution within Inga. Transcriptome data from three Inga species were used to select 264 nuclear loci for targeted enrichment and sequencing. Following quality control to remove probable paralogs from these sequence data, the final dataset comprised 259,313 bases from 194 loci for 24 accessions representing 22 Inga species and an outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci concatenated or a gene-tree/species-tree approach yielded highly resolved phylogenies. We used coalescent approaches to show that the same targeted enrichment data also have significant power to discriminate among alternative within-species population histories within the widespread species I. umbellifera. In either application, targeted enrichment simplifies the informatics challenge of identifying orthologous loci associated with de novo genome sequencing. We conclude that targeted enrichment provides the large volumes of phylogenetically-informative sequence data required to resolve relationships within recent plant species radiations, both at the species level and for within-species phylogeographic studies.
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Affiliation(s)
- James A Nicholls
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh Edinburgh, UK ; Royal Botanic Garden Edinburgh Edinburgh, UK
| | | | - Erik J M Koenen
- Institute of Systematic Botany, University of Zurich Zürich, Switzerland
| | - Colin E Hughes
- Institute of Systematic Botany, University of Zurich Zürich, Switzerland
| | - Jack Hearn
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh Edinburgh, UK
| | - Lynsey Bunnefeld
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh Edinburgh, UK
| | - Kyle G Dexter
- School of Geosciences, University of Edinburgh Edinburgh, UK
| | - Graham N Stone
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh Edinburgh, UK
| | - Catherine A Kidner
- Royal Botanic Garden Edinburgh Edinburgh, UK ; Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh Edinburgh, UK
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122
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Besnard G, Christin PA, Malé PJG, Lhuillier E, Lauzeral C, Coissac E, Vorontsova MS. From museums to genomics: old herbarium specimens shed light on a C3 to C4 transition. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6711-21. [PMID: 25258360 DOI: 10.1093/jxb/eru395] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Collections of specimens held by natural history museums are invaluable material for biodiversity inventory and evolutionary studies, with specimens accumulated over 300 years readily available for sampling. Unfortunately, most museum specimens yield low-quality DNA. Recent advances in sequencing technologies, so called next-generation sequencing, are revolutionizing phylogenetic investigations at a deep level. Here, the Illumina technology (HiSeq) was used on herbarium specimens of Sartidia (subfamily Aristidoideae, Poaceae), a small African-Malagasy grass lineage (six species) characteristic of wooded savannas, which is the C3 sister group of Stipagrostis, an important C4 genus from Africa and SW Asia. Complete chloroplast and nuclear ribosomal sequences were assembled for two Sartidia species, one of which (S. perrieri) is only known from a single specimen collected in Madagascar 100 years ago. Partial sequences of a few single-copy genes encoding phosphoenolpyruvate carboxylases (ppc) and malic enzymes (nadpme) were also assembled. Based on these data, the phylogenetic position of Malagasy Sartidia in the subfamily Aristidoideae was investigated and the biogeographical history of this genus was analysed with full species sampling. The evolutionary history of two genes for C4 photosynthesis (ppc-aL1b and nadpme-IV) in the group was also investigated. The gene encoding the C4 phosphoenolpyruvate caroxylase of Stipagrostis is absent from S. dewinteri suggesting that it is not essential in C3 members of the group, which might have favoured its recruitment into a new metabolic pathway. Altogether, the inclusion of historical museum specimens in phylogenomic analyses of biodiversity opens new avenues for evolutionary studies.
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Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Evolution et Diversité Biologique), 118 route de Narbonne, F-31062 Toulouse, France
| | | | - Pierre-Jean G Malé
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Evolution et Diversité Biologique), 118 route de Narbonne, F-31062 Toulouse, France Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Emeline Lhuillier
- GeT-PlaGe, Campus INRA-Auzeville, F-31326 Castanet-Tolosan, France; INRA, UAR 1209 Département de Génétique Animale, INRA Auzeville, F-31326 Castanet-Tolosan, France
| | - Christine Lauzeral
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Evolution et Diversité Biologique), 118 route de Narbonne, F-31062 Toulouse, France
| | - Eric Coissac
- Laboratoire d'écologie Alpine (LECA), UMR5553, CNRS/Université Joseph Fourier-Grenoble I, Université de Savoie, F-38041 Grenoble, France
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123
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Maddison DR, Cooper KW. Species delimitation in the ground beetle subgenusLiocosmius(Coleoptera: Carabidae:Bembidion), including standard and next-generation sequencing of museum specimens. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12188] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- David R. Maddison
- Department of Integrative Biology; Oregon State University; 3029 Cordley Hall Corvallis OR 97331 USA
| | - Kenneth W. Cooper
- Department of Biology; University of California; Riverside CA 92521 USA
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124
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de Sousa F, Bertrand YJK, Nylinder S, Oxelman B, Eriksson JS, Pfeil BE. Phylogenetic properties of 50 nuclear loci in Medicago (Leguminosae) generated using multiplexed sequence capture and next-generation sequencing. PLoS One 2014; 9:e109704. [PMID: 25329401 PMCID: PMC4201463 DOI: 10.1371/journal.pone.0109704] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 09/10/2014] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing technology has increased the capacity to generate molecular data for plant biological research, including phylogenetics, and can potentially contribute to resolving complex phylogenetic problems. The evolutionary history of Medicago L. (Leguminosae: Trifoliae) remains unresolved due to incongruence between published phylogenies. Identification of the processes causing this genealogical incongruence is essential for the inference of a correct species phylogeny of the genus and requires that more molecular data, preferably from low-copy nuclear genes, are obtained across different species. Here we report the development of 50 novel LCN markers in Medicago and assess the phylogenetic properties of each marker. We used the genomic resources available for Medicago truncatula Gaertn., hybridisation-based gene enrichment (sequence capture) techniques and Next-Generation Sequencing to generate sequences. This alternative proves to be a cost-effective approach to amplicon sequencing in phylogenetic studies at the genus or tribe level and allows for an increase in number and size of targeted loci. Substitution rate estimates for each of the 50 loci are provided, and an overview of the variation in substitution rates among a large number of low-copy nuclear genes in plants is presented for the first time. Aligned sequences of major species lineages of Medicago and its sister genus are made available and can be used in further probe development for sequence-capture of the same markers.
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Affiliation(s)
- Filipe de Sousa
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
| | - Yann J. K. Bertrand
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Stephan Nylinder
- Department of Botany, Swedish Museum of Natural History, Stockholm, Sweden
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Jonna S. Eriksson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Bernard E. Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
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125
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Hemmer-Hansen J, Therkildsen NO, Pujolar JM. Population genomics of marine fishes: next-generation prospects and challenges. THE BIOLOGICAL BULLETIN 2014; 227:117-132. [PMID: 25411371 DOI: 10.1086/bblv227n2p117] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Over the past few years, technological advances have facilitated giant leaps forward in our ability to generate genome-wide molecular data, offering exciting opportunities for gaining new insights into the ecology and evolution of species where genomic information is still limited. Marine fishes are valuable organisms for advancing our understanding of evolution on historical and contemporary time scales, and here we highlight areas in which research on these species is likely to be particularly important in the near future. These include possibilities for gaining insights into processes on ecological time scales, identifying genomic signatures associated with population divergence under gene flow, and determining the genetic basis of phenotypic traits. We also consider future challenges pertaining to the implementation of genome-wide coverage through next-generation sequencing and genotyping methods in marine fishes. Complications associated with fast decay of linkage disequilibrium, as expected for species with large effective population sizes, and the possibility that adaptation is associated with both soft selective sweeps and polygenic selection, leaving complex genomic signatures in natural populations, are likely to challenge future studies. However, the combination of high genome coverage and new statistical developments offers promising solutions. Thus, the next generation of studies is likely to truly facilitate the transition from population genetics to population genomics in marine fishes. This transition will advance our understanding of basic evolutionary processes and will offer new possibilities for conservation and management of valuable marine resources.
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Affiliation(s)
- Jakob Hemmer-Hansen
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, DK-8600 Silkeborg, Denmark;
| | | | - José Martin Pujolar
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark
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126
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Mandáková T, Kovařík A, Zozomová-Lihová J, Shimizu-Inatsugi R, Shimizu KK, Mummenhoff K, Marhold K, Lysak MA. The more the merrier: recent hybridization and polyploidy in cardamine. THE PLANT CELL 2013; 25:3280-95. [PMID: 24082009 PMCID: PMC3809532 DOI: 10.1105/tpc.113.114405] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 08/26/2013] [Accepted: 09/12/2013] [Indexed: 05/19/2023]
Abstract
This article describes the use of cytogenomic and molecular approaches to explore the origin and evolution of Cardamine schulzii, a textbook example of a recent allopolyploid, in its ~110-year history of human-induced hybridization and allopolyploidy in the Swiss Alps. Triploids are typically viewed as bridges between diploids and tetraploids but rarely as parental genomes of high-level hybrids and polyploids. The genome of the triploid semifertile hybrid Cardamine × insueta (2n = 24, RRA) was shown to combine the parental genomes of two diploid (2n = 2x = 16) species, Cardamine amara (AA) and Cardamine rivularis (RR). These parental genomes have remained structurally stable within the triploid genome over the >100 years since its origin. Furthermore, we provide compelling evidence that the alleged recent polyploid C. schulzii is not an autohexaploid derivative of C. × insueta. Instead, at least two hybridization events involving C. × insueta and the hypotetraploid Cardamine pratensis (PPPP, 2n = 4x-2 = 30) have resulted in the origin of the trigenomic hypopentaploid (2n = 5x-2 = 38, PPRRA) and hypohexaploid (2n = 6x-2 = 46, PPPPRA). These data show that the semifertile triploid hybrid can promote a merger of three different genomes and demonstrate how important it is to reexamine the routinely repeated textbook examples using modern techniques.
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Affiliation(s)
- Terezie Mandáková
- Research Group Plant Cytogenomics, Central European Institute of Technology (CEITEC), Masaryk University, CZ-62500 Brno, Czech Republic
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, CZ-61265 Brno, Czech Republic
| | | | - Rie Shimizu-Inatsugi
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Kentaro K. Shimizu
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | | | - Karol Marhold
- Institute of Botany, Slovak Academy of Sciences, SK-84523 Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, CZ-12801 Prague, Czech Republic
| | - Martin A. Lysak
- Research Group Plant Cytogenomics, Central European Institute of Technology (CEITEC), Masaryk University, CZ-62500 Brno, Czech Republic
- Address correspondence to
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