51
|
Jones KE, Fér T, Schmickl RE, Dikow RB, Funk VA, Herrando‐Moraira S, Johnston PR, Kilian N, Siniscalchi CM, Susanna A, Slovák M, Thapa R, Watson LE, Mandel JR. An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae. APPLICATIONS IN PLANT SCIENCES 2019; 7:e11295. [PMID: 31667023 PMCID: PMC6814182 DOI: 10.1002/aps3.11295] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/05/2019] [Indexed: 05/23/2023]
Abstract
PREMISE Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here. METHODS Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae. RESULTS Alignments of the Asteraceae family-wide Hyb-Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches. DISCUSSION The approach used to build a Hyb-Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb-Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage-specific.
Collapse
Affiliation(s)
- Katy E. Jones
- Botanischer Garten und Botanisches Museum BerlinFreie Universität BerlinKönigin‐Luise‐Str. 6–814195BerlinGermany
| | - Tomáš Fér
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2CZ 12800PragueCzech Republic
| | - Roswitha E. Schmickl
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2CZ 12800PragueCzech Republic
- Institute of BotanyThe Czech Academy of SciencesZámek 1CZ 25243PrůhoniceCzech Republic
| | - Rebecca B. Dikow
- Data Science LabOffice of the Chief Information OfficerSmithsonian InstitutionWashingtonD.C.20013‐7012USA
| | - Vicki A. Funk
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionWashingtonD.C.20013‐7012USA
| | | | - Paul R. Johnston
- Freie Universität BerlinEvolutionary BiologyBerlinGermany
- Berlin Center for Genomics in Biodiversity ResearchBerlinGermany
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB)BerlinGermany
| | - Norbert Kilian
- Botanischer Garten und Botanisches Museum BerlinFreie Universität BerlinKönigin‐Luise‐Str. 6–814195BerlinGermany
| | - Carolina M. Siniscalchi
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB‐CSIC‐ICUB)Pg. del Migdia s.n.ES 08038BarcelonaSpain
| | - Marek Slovák
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2CZ 12800PragueCzech Republic
- Plant Science and Biodiversity CentreSlovak Academy of SciencesSK‐84523BratislavaSlovakia
| | - Ramhari Thapa
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
| | - Linda E. Watson
- Department of Plant Biology, Ecology, and EvolutionOklahoma State UniversityStillwaterOklahoma74078USA
| | - Jennifer R. Mandel
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
| |
Collapse
|
52
|
Hinsinger DD, Strijk JS. Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming. PHYTOKEYS 2019; 132:75-89. [PMID: 31607787 PMCID: PMC6783484 DOI: 10.3897/phytokeys.132.36365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/28/2019] [Indexed: 06/01/2023]
Abstract
The genus Quercus L. contains several of the most economically important species for timber production in the Northern Hemisphere. It was one of the first genera described, but genetic diversity at a global scale within and amongst oak species remains unclear, despite numerous regional or species-specific assessments. To evaluate global plastid diversity in oaks, we sequenced the complete chloroplast of Quercus xanthoclada and compared its sequence with those available from other main taxonomic groups in Quercus. We quantify genomic divergence amongst oaks and performed a sliding window analysis to detect the most variable regions amongst members of the various clades, as well as divergent regions occurring in specific pairs of species. We identified private and shared SNPs amongst oaks species and sections and stress the need for a large global assessment of genetic diversity in this economically and ecologically important genus.
Collapse
Affiliation(s)
- Damien Daniel Hinsinger
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Daxuedonglu 100, Nanning, Guangxi, 530005, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry, Guangxi University, Nanning, Guangxi 530005, China
| | - Joeri Sergej Strijk
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Daxuedonglu 100, Nanning, Guangxi, 530005, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry, Guangxi University, Nanning, Guangxi 530005, China
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000 Luang Prabang, Lao PDR
| |
Collapse
|
53
|
Tsai WLE, Schedl ME, Maley JM, McCormack JE. More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens. Mol Ecol Resour 2019; 20:1220-1227. [PMID: 31478338 DOI: 10.1111/1755-0998.13077] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/11/2019] [Accepted: 07/23/2019] [Indexed: 11/28/2022]
Abstract
Next-generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As the field of museum genomics grows, so does the need for extraction methods that maximize DNA yields. For avian museum specimens, the established method of extracting DNA from toe pads works well for most specimens. However, for some specimens, especially those of birds that are very small or very large, toe pads can be a poor source of DNA. In this study, we apply two DNA extraction methods (phenol-chloroform and silica column) to three different sources of DNA (toe pad, skin punch and bone) from 10 historical avian museum specimens. We show that a modified phenol-chloroform protocol yielded significantly more DNA than a silica column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across all tissue types. However, extractions using the silica column protocol contained longer fragments on average than those using the phenol-chloroform protocol, probably as a result of loss of small fragments through the silica column. While toe pads yielded more DNA than skin punches and bone fragments, skin punches proved to be a reliable alternative source of DNA and might be especially appealing when toe pad extractions are impractical. Overall, we found that historical bird museum specimens contain substantial amounts of DNA for genomic studies under most extraction scenarios, but that a phenol-chloroform protocol consistently provides the high quantities of DNA required for most current genomic protocols.
Collapse
Affiliation(s)
- Whitney L E Tsai
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California
| | - Margaret E Schedl
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California
| | - James M Maley
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California
| | - John E McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California.,Biology Department, Occidental College, Los Angeles, California
| |
Collapse
|
54
|
Derkarabetian S, Benavides LR, Giribet G. Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault. Mol Ecol Resour 2019; 19:1531-1544. [DOI: 10.1111/1755-0998.13072] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/22/2019] [Accepted: 07/31/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Shahan Derkarabetian
- Museum of Comparative Zoology Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| | - Ligia R. Benavides
- Museum of Comparative Zoology Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| |
Collapse
|
55
|
Brewer GE, Clarkson JJ, Maurin O, Zuntini AR, Barber V, Bellot S, Biggs N, Cowan RS, Davies NMJ, Dodsworth S, Edwards SL, Eiserhardt WL, Epitawalage N, Frisby S, Grall A, Kersey PJ, Pokorny L, Leitch IJ, Forest F, Baker WJ. Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms. FRONTIERS IN PLANT SCIENCE 2019; 10:1102. [PMID: 31620145 PMCID: PMC6759688 DOI: 10.3389/fpls.2019.01102] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/12/2019] [Indexed: 05/03/2023]
Abstract
The world's herbaria collectively house millions of diverse plant specimens, including endangered or extinct species and type specimens. Unlocking genetic data from the typically highly degraded DNA obtained from herbarium specimens was difficult until the arrival of high-throughput sequencing approaches, which can be applied to low quantities of severely fragmented DNA. Target enrichment involves using short molecular probes that hybridise and capture genomic regions of interest for high-throughput sequencing. In this study on herbariomics, we used this targeted sequencing approach and the Angiosperms353 universal probe set to recover up to 351 nuclear genes from 435 herbarium specimens that are up to 204 years old and span the breadth of angiosperm diversity. We show that on average 207 genes were successfully retrieved from herbarium specimens, although the mean number of genes retrieved and target enrichment efficiency is significantly higher for silica gel-dried specimens. Forty-seven target nuclear genes were recovered from a herbarium specimen of the critically endangered St Helena boxwood, Mellissia begoniifolia, collected in 1815. Herbarium specimens yield significantly less high-molecular-weight DNA than silica gel-dried specimens, and genomic DNA quality declines with sample age, which is negatively correlated with target enrichment efficiency. Climate, taxon-specific traits, and collection strategies additionally impact target sequence recovery. We also detected taxonomic bias in targeted sequencing outcomes for the 10 most numerous angiosperm families that were investigated in depth. We recommend that (1) for species distributed in wet tropical climates, silica gel-dried specimens should be used preferentially; (2) for species distributed in seasonally dry tropical climates, herbarium and silica gel-dried specimens yield similar results, and either collection can be used; (3) taxon-specific traits should be explored and established for effective optimisation of taxon-specific studies using herbarium specimens; (4) all herbarium sheets should, in future, be annotated with details of the preservation method used; (5) long-term storage of herbarium specimens should be in stable, low-humidity, and low-temperature environments; and (6) targeted sequencing with universal probes, such as Angiosperms353, should be investigated closely as a new approach for DNA barcoding that will ensure better exploitation of herbarium specimens than traditional Sanger sequencing approaches.
Collapse
Affiliation(s)
- Grace E. Brewer
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - James J. Clarkson
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Olivier Maurin
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Vanessa Barber
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Sidonie Bellot
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Nicola Biggs
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Robyn S. Cowan
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Nina M. J. Davies
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, Luton, BedfordshireUnited Kingdom
| | - Sara L. Edwards
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Wolf L. Eiserhardt
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Bioscience, Aarhus University, Ny Munkegade Aarhus C, Denmark
| | | | - Sue Frisby
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Aurélie Grall
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Paul J. Kersey
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Lisa Pokorny
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Centre for Plant Biotechnology and Genomics (CBGP, UPM-INIA), Pozuelo de Alarcón, Madrid, Spain
| | - Ilia J. Leitch
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Félix Forest
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - William J. Baker
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| |
Collapse
|
56
|
Trevisan B, Alcantara DM, Machado DJ, Marques FP, Lahr DJ. Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies. PeerJ 2019; 7:e7543. [PMID: 31565556 PMCID: PMC6746217 DOI: 10.7717/peerj.7543] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022] Open
Abstract
Global loss of biodiversity is an ongoing process that concerns both local and global authorities. Studies of biodiversity mainly involve traditional methods using morphological characters and molecular protocols. However, conventional methods are a time consuming and resource demanding task. The development of high-throughput sequencing (HTS) techniques has reshaped the way we explore biodiversity and opened a path to new questions and novel empirical approaches. With the emergence of HTS, sequencing the complete mitochondrial genome became more accessible, and the number of genome sequences published has increased exponentially during the last decades. Despite the current state of knowledge about the potential of mitogenomics in phylogenetics, this is still a relatively under-explored area for a multitude of taxonomic groups, especially for those without commercial relevance, non-models organisms and with preserved DNA. Here we take the first step to assemble and annotate the genomes from HTS data using a new protocol of genome skimming which will offer an opportunity to extend the field of mitogenomics to under-studied organisms. We extracted genomic DNA from specimens preserved in ethanol. We used Nextera XT DNA to prepare indexed paired-end libraries since it is a powerful tool for working with diverse samples, requiring a low amount of input DNA. We sequenced the samples in two different Illumina platform (MiSeq or NextSeq 550). We trimmed raw reads, filtered and had their quality tested accordingly. We performed the assembly using a baiting and iterative mapping strategy, and the annotated the putative mitochondrion through a semi-automatic procedure. We applied the contiguity index to access the completeness of each new mitogenome. Our results reveal the efficiency of the proposed method to recover the whole mitogenomes of preserved DNA from non-model organisms even if there are gene rearrangement in the specimens. Our findings suggest the potential of combining the adequate platform and library to the genome skimming as an innovative approach, which opens a new range of possibilities of its use to obtain molecular data from organisms with different levels of preservation.
Collapse
Affiliation(s)
- Bruna Trevisan
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Daniel M.C. Alcantara
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Denis Jacob Machado
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
- Department of Bioinformatics and Genomics / College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Fernando P.L. Marques
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Daniel J.G. Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| |
Collapse
|
57
|
Viruel J, Conejero M, Hidalgo O, Pokorny L, Powell RF, Forest F, Kantar MB, Soto Gomez M, Graham SW, Gravendeel B, Wilkin P, Leitch IJ. A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens. FRONTIERS IN PLANT SCIENCE 2019; 10:937. [PMID: 31396248 PMCID: PMC6667659 DOI: 10.3389/fpls.2019.00937] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 07/04/2019] [Indexed: 05/24/2023]
Abstract
Whole genome duplication (WGD) events are common in many plant lineages, but the ploidy status and possible occurrence of intraspecific ploidy variation are unknown for most species. Standard methods for ploidy determination are chromosome counting and flow cytometry approaches. While flow cytometry approaches typically use fresh tissue, an increasing number of studies have shown that recently dried specimens can be used to yield ploidy data. Recent studies have started to explore whether high-throughput sequencing (HTS) data can be used to assess ploidy levels by analyzing allelic frequencies from single copy nuclear genes. Here, we compare different approaches using a range of yam (Dioscorea) tissues of varying ages, drying methods and quality, including herbarium tissue. Our aims were to: (1) explore the limits of flow cytometry in estimating ploidy level from dried samples, including herbarium vouchers collected between 1831 and 2011, and (2) optimize a HTS-based method to estimate ploidy by considering allelic frequencies from nuclear genes obtained using a target-capture method. We show that, although flow cytometry can be used to estimate ploidy levels from herbarium specimens collected up to fifteen years ago, success rate is low (5.9%). We validated our HTS-based estimates of ploidy using 260 genes by benchmarking with dried samples of species of known ploidy (Dioscorea alata, D. communis, and D. sylvatica). Subsequently, we successfully applied the method to the 85 herbarium samples analyzed with flow cytometry, and successfully provided results for 91.7% of them, comprising species across the phylogenetic tree of Dioscorea. We also explored the limits of using this HTS-based approach for identifying high ploidy levels in herbarium material and the effects of heterozygosity and sequence coverage. Overall, we demonstrated that ploidy diversity within and between species may be ascertained from historical collections, allowing the determination of polyploidization events from samples collected up to two centuries ago. This approach has the potential to provide insights into the drivers and dynamics of ploidy level changes during plant evolution and crop domestication.
Collapse
Affiliation(s)
- Juan Viruel
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Laboratori de Botànica, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Barcelona, Spain
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Michael B. Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawai’i at Mânoa, Honolulu, HI, United States
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, BC, Canada
| | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, BC, Canada
| | - Barbara Gravendeel
- Naturalis Biodiversity Center, Endless Forms, Leiden, Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- Science and Technology Faculty, University of Applied Sciences Leiden, Leiden, Netherlands
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | |
Collapse
|
58
|
Tsai WL, Mota-Vargas C, Rojas-Soto O, Bhowmik R, Liang EY, Maley JM, Zarza E, McCormack JE. Museum genomics reveals the speciation history of Dendrortyx wood-partridges in the Mesoamerican highlands. Mol Phylogenet Evol 2019; 136:29-34. [DOI: 10.1016/j.ympev.2019.03.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/26/2019] [Accepted: 03/22/2019] [Indexed: 11/28/2022]
|
59
|
Forthman M, Miller CW, Kimball RT. Phylogenomic analysis suggests Coreidae and Alydidae (Hemiptera: Heteroptera) are not monophyletic. ZOOL SCR 2019. [DOI: 10.1111/zsc.12353] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Michael Forthman
- Entomology & Nematology Department University of Florida Gainesville Florida
| | - Christine W. Miller
- Entomology & Nematology Department University of Florida Gainesville Florida
| | | |
Collapse
|
60
|
Matos-Maraví P, Duarte Ritter C, Barnes CJ, Nielsen M, Olsson U, Wahlberg N, Marquina D, Sääksjärvi I, Antonelli A. Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies. PeerJ 2019; 7:e6727. [PMID: 31106048 PMCID: PMC6499058 DOI: 10.7717/peerj.6727] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 03/06/2019] [Indexed: 12/18/2022] Open
Abstract
Massively parallel DNA sequencing opens up opportunities for bridging multiple temporal and spatial dimensions in biodiversity research, thanks to its efficiency to recover millions of nucleotide polymorphisms. Here, we identify the current status, discuss the main challenges, and look into future perspectives on biodiversity genomics focusing on insects, which arguably constitute the most diverse and ecologically important group among all animals. We suggest 10 simple rules that provide a succinct step-by-step guide and best-practices to anyone interested in biodiversity research through the study of insect genomics. To this end, we review relevant literature on biodiversity and evolutionary research in the field of entomology. Our compilation is targeted at researchers and students who may not yet be specialists in entomology or molecular biology. We foresee that the genomic revolution and its application to the study of non-model insect lineages will represent a major leap to our understanding of insect diversity.
Collapse
Affiliation(s)
- Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Camila Duarte Ritter
- Department of Eukaryotic Microbiology, University of Duisburg-Essen, Essen, Germany
| | | | - Martin Nielsen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Urban Olsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Daniel Marquina
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Royal Botanical Garden, Kew, Richmond, Surrey, UK
| |
Collapse
|
61
|
Liu H, Wei J, Yang T, Mu W, Song B, Yang T, Fu Y, Wang X, Hu G, Li W, Zhou H, Chang Y, Chen X, Chen H, Cheng L, He X, Cai H, Cai X, Wang M, Li Y, Sahu SK, Yang J, Wang Y, Mu R, Liu J, Zhao J, Huang Z, Xu X, Liu X. Molecular digitization of a botanical garden: high-depth whole-genome sequencing of 689 vascular plant species from the Ruili Botanical Garden. Gigascience 2019; 8:giz007. [PMID: 30689836 PMCID: PMC6441391 DOI: 10.1093/gigascience/giz007] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/30/2018] [Accepted: 01/11/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Genome sequencing has been widely used in plant research to construct reference genomes and provide evolutionary insights. However, few plant species have had their whole genome sequenced, thus restraining the utility of these data. We collected 1,093 samples of vascular plant species growing in the Ruili Botanical Garden, located in southwest China. Of these, we sequenced 761 samples and collected voucher specimens stored in the Herbarium of China National GeneBank. RESULTS The 761 sequenced samples represented 689 vascular plant species from 137 families belonging to 49 orders. Of these, 257 samples were identified to the species level and 504 to the family level, using specimen and chloroplast sequences. In total, we generated 54 Tb of sequencing data, with an average sequencing depth of 60X per species, as estimated from genome sizes. A reference phylogeny was reconstructed with 78 chloroplast genes for molecular identification and other possible applications. CONCLUSIONS The large dataset of vascular plant genomes generated in this study, which includes both high-depth whole-genome sequencing data and associated voucher specimens, is valuable for plant genome research and other applications. This project also provides insight into the feasibility and technical requirements for "planetary-scale" projects such as the 10,000 Plant Genomes Project and the Earth BioGenome Project.
Collapse
Affiliation(s)
- Huan Liu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jinpu Wei
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Ting Yang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Weixue Mu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Bo Song
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Tuo Yang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Yuan Fu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Xuebing Wang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Guohai Hu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Wangsheng Li
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Hongcheng Zhou
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Yue Chang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Xiaoli Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Hongyun Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Le Cheng
- BGI-Yunnan, No. 389 Haiyuan Road, High-tech Development Zone, Kunming, Yunnan 650106, China
| | - Xuefei He
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Hechen Cai
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Xianchu Cai
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Mei Wang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yang Li
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
| | - Sunil Kumar Sahu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jinlong Yang
- BGI-Yunnan, No. 389 Haiyuan Road, High-tech Development Zone, Kunming, Yunnan 650106, China
| | - Yu Wang
- BGI-Yunnan, No. 389 Haiyuan Road, High-tech Development Zone, Kunming, Yunnan 650106, China
| | - Ranchang Mu
- Forestry Bureau of Ruili, Yunnan Dehong, Ruili 678600, China
| | - Jie Liu
- Forestry Bureau of Ruili, Yunnan Dehong, Ruili 678600, China
| | - Jianming Zhao
- Forestry Bureau of Ruili, Yunnan Dehong, Ruili 678600, China
| | - Ziheng Huang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Xin Liu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen 518120, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| |
Collapse
|
62
|
Knyshov A, Gordon ERL, Weirauch C. Cost‐efficient high throughput capture of museum arthropod specimen
DNA
using
PCR
‐generated baits. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexander Knyshov
- Department of EntomologyUniversity of California Riverside Riverside California
| | - Eric R. L. Gordon
- Department of EntomologyUniversity of California Riverside Riverside California
| | - Christiane Weirauch
- Department of EntomologyUniversity of California Riverside Riverside California
| |
Collapse
|
63
|
Sablok G, Amiryousefi A, He X, Hyvönen J, Poczai P. Sequencing the Plastid Genome of Giant Ragweed ( Ambrosia trifida, Asteraceae) From a Herbarium Specimen. FRONTIERS IN PLANT SCIENCE 2019; 10:218. [PMID: 30873197 PMCID: PMC6403193 DOI: 10.3389/fpls.2019.00218] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 02/08/2019] [Indexed: 05/09/2023]
Abstract
We report the first plastome sequence of giant ragweed (Ambrosia trifida); with this new genome information, we assessed the phylogeny of Asteraceae and the transcriptional profiling against glyphosate resistance in giant ragweed. Assembly and genic features show a normal angiosperm quadripartite plastome structure with no signatures of deviation in gene directionality. Comparative analysis revealed large inversions across the plastome of giant ragweed and the previously sequenced members of the plant family. Asteraceae plastid genomes contain two inversions of 22.8 and 3.3 kb; the former is located between trnS-GCU and trnG-UCC genes, and the latter between trnE-UUC and trnT-GGU genes. The plastid genome sequences of A. trifida and the related species, Ambrosia artemisiifolia, are identical in gene content and arrangement, but they differ in length. The phylogeny is well-resolved and congruent with previous hypotheses about the phylogenetic relationship of Asteraceae. Transcriptomic analysis revealed divergence in the relative expressions at the exonic and intronic levels, providing hints toward the ecological adaptation of the genus. Giant ragweed shows various levels of glyphosate resistance, with introns displaying higher expression patterns at resistant time points after the assumed herbicide treatment.
Collapse
Affiliation(s)
- Gaurav Sablok
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Ali Amiryousefi
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Xiaolan He
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Péter Poczai
- Finnish Museum of Natural History (Botany Unit), University of Helsinki, Helsinki, Finland
- Organismal Evolution and Biology, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| |
Collapse
|
64
|
Bravo GA, Antonelli A, Bacon CD, Bartoszek K, Blom MPK, Huynh S, Jones G, Knowles LL, Lamichhaney S, Marcussen T, Morlon H, Nakhleh LK, Oxelman B, Pfeil B, Schliep A, Wahlberg N, Werneck FP, Wiedenhoeft J, Willows-Munro S, Edwards SV. Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics. PeerJ 2019; 7:e6399. [PMID: 30783571 PMCID: PMC6378093 DOI: 10.7717/peerj.6399] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 01/07/2019] [Indexed: 12/23/2022] Open
Abstract
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
Collapse
Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Alexandre Antonelli
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Gothenburg Botanical Garden, Göteborg, Sweden
| | - Christine D. Bacon
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Krzysztof Bartoszek
- Department of Computer and Information Science, Linköping University, Linköping, Sweden
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Stella Huynh
- Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Graham Jones
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Thomas Marcussen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Hélène Morlon
- Institut de Biologie, Ecole Normale Supérieure de Paris, Paris, France
| | - Luay K. Nakhleh
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Bengt Oxelman
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Bernard Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Alexander Schliep
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | | | - Fernanda P. Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisa da Amazônia, Manaus, AM, Brazil
| | - John Wiedenhoeft
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
- Department of Computer Science, Rutgers University, Piscataway, NJ, USA
| | - Sandi Willows-Munro
- School of Life Sciences, University of Kwazulu-Natal, Pietermaritzburg, South Africa
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| |
Collapse
|
65
|
Kistenich S, Halvorsen R, Schrøder-Nielsen A, Thorbek L, Timdal E, Bendiksby M. DNA Sequencing Historical Lichen Specimens. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
|
66
|
Couvreur TLP, Helmstetter AJ, Koenen EJM, Bethune K, Brandão RD, Little SA, Sauquet H, Erkens RHJ. Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes. FRONTIERS IN PLANT SCIENCE 2019; 9:1941. [PMID: 30687347 PMCID: PMC6334231 DOI: 10.3389/fpls.2018.01941] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/13/2018] [Indexed: 05/19/2023]
Abstract
Targeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. Annonaceae is a major pantropical plant family with 110 genera and ca. 2,450 species, occurring across all major and minor tropical forests of the world. Baits were designed by sequencing the transcriptomes of five species from two of the largest Annonaceae subfamilies. Orthologous loci were identified. The resulting baiting kit was used to reconstruct phylogenetic relationships at two different levels using concatenated and gene tree approaches: a family wide Annonaceae analysis sampling 65 genera and a species level analysis of tribe Piptostigmateae sampling 29 species with multiple individuals per species. DNA extraction was undertaken mainly on silicagel dried leaves, with two samples from herbarium dried leaves. Our kit targets 469 exons (364,653 bp of sequence data), successfully capturing sequences from across Annonaceae. Silicagel dried and herbarium DNA worked equally well. We present for the first time a nuclear gene-based phylogenetic tree at the generic level based on 317 supercontigs. Results mainly confirm previous chloroplast based studies. However, several new relationships are found and discussed. We show significant differences in branch lengths between the two large subfamilies Annonoideae and Malmeoideae. A new tribe, Annickieae, is erected containing a single African genus Annickia. We also reconstructed a well-resolved species-level phylogenetic tree of the Piptostigmteae tribe. Our baiting kit is useful for reconstructing well-supported phylogenetic relationships within Annonaceae at different taxonomic levels. The nuclear genome is mainly concordant with plastome information with a few exceptions. Moreover, we find that substitution rate heterogeneity between the two subfamilies is also found within the nuclear compartment, and not just plastomes and ribosomal DNA as previously shown. Our results have implications for understanding the biogeography, molecular dating and evolution of Annonaceae.
Collapse
Affiliation(s)
| | | | - Erik J. M. Koenen
- Institute of Systematic Botany, University of Zurich, Zurich, Switzerland
| | - Kevin Bethune
- IRD, UMR DIADE, Univ. Montpellier, Montpellier, France
| | - Rita D. Brandão
- Maastricht Science Programme, Maastricht University, Maastricht, Netherlands
| | - Stefan A. Little
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université-Paris Saclay, Orsay, France
| | - Hervé Sauquet
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université-Paris Saclay, Orsay, France
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Roy H. J. Erkens
- Maastricht Science Programme, Maastricht University, Maastricht, Netherlands
| |
Collapse
|
67
|
A simple strategy for recovering ultraconserved elements, exons, and introns from low coverage shotgun sequencing of museum specimens: Placement of the partridge genus Tropicoperdix within the galliformes. Mol Phylogenet Evol 2018; 129:304-314. [DOI: 10.1016/j.ympev.2018.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 07/23/2018] [Accepted: 09/06/2018] [Indexed: 11/19/2022]
|
68
|
Lopez JV, Kamel B, Medina M, Collins T, Baums IB. Multiple Facets of Marine Invertebrate Conservation Genomics. Annu Rev Anim Biosci 2018; 7:473-497. [PMID: 30485758 DOI: 10.1146/annurev-animal-020518-115034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Conservation genomics aims to preserve the viability of populations and the biodiversity of living organisms. Invertebrate organisms represent 95% of animal biodiversity; however, few genomic resources currently exist for the group. The subset of marine invertebrates includes the most ancient metazoan lineages and possesses codes for unique gene products and possible keys to adaptation. The benefits of supporting invertebrate conservation genomics research (e.g., likely discovery of novel genes, protein regulatory mechanisms, genomic innovations, and transposable elements) outweigh the various hurdles (rare, small, or polymorphic starting materials). Here we review best conservation genomics practices in the laboratory and in silico when applied to marine invertebrates and also showcase unique features in several case studies of acroporid corals, crown-of-thorns starfish, apple snails, and abalone. Marine conservation genomics should also address how diversity can lead to unique marine innovations, the impact of deleterious variation, and how genomic monitoring and profiling could positively affect broader conservation goals (e.g., value of baseline data for in situ/ex situ genomic stocks).
Collapse
Affiliation(s)
- Jose V Lopez
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, Florida 33004, USA;
| | - Bishoy Kamel
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, New Mexico 87131, USA;
| | - Mónica Medina
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; ,
| | - Timothy Collins
- Department of Biological Sciences, Florida International University, Miami, Florida 33199, USA;
| | - Iliana B Baums
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; ,
| |
Collapse
|
69
|
Kharouba HM, Lewthwaite JMM, Guralnick R, Kerr JT, Vellend M. Using insect natural history collections to study global change impacts: challenges and opportunities. Philos Trans R Soc Lond B Biol Sci 2018; 374:20170405. [PMID: 30455219 PMCID: PMC6282079 DOI: 10.1098/rstb.2017.0405] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2018] [Indexed: 11/12/2022] Open
Abstract
Over the past two decades, natural history collections (NHCs) have played an increasingly prominent role in global change research, but they have still greater potential, especially for the most diverse group of animals on Earth: insects. Here, we review the role of NHCs in advancing our understanding of the ecological and evolutionary responses of insects to recent global changes. Insect NHCs have helped document changes in insects' geographical distributions, phenology, phenotypic and genotypic traits over time periods up to a century. Recent work demonstrates the enormous potential of NHCs data for examining insect responses at multiple temporal, spatial and phylogenetic scales. Moving forward, insect NHCs offer unique opportunities to examine the morphological, chemical and genomic information in each specimen, thus advancing our understanding of the processes underlying species' ecological and evolutionary responses to rapid, widespread global changes.This article is part of the theme issue 'Biological collections for understanding biodiversity in the anthropocene'.
Collapse
Affiliation(s)
- Heather M Kharouba
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada K1N 9B4
| | - Jayme M M Lewthwaite
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Rob Guralnick
- Department of Natural History and the Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Jeremy T Kerr
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada K1N 9B4
| | - Mark Vellend
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1 K 2R1
| |
Collapse
|
70
|
Andrew C, Diez J, James TY, Kauserud H. Fungarium specimens: a largely untapped source in global change biology and beyond. Philos Trans R Soc Lond B Biol Sci 2018; 374:20170392. [PMID: 30455210 PMCID: PMC6282084 DOI: 10.1098/rstb.2017.0392] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2018] [Indexed: 11/12/2022] Open
Abstract
For several hundred years, millions of fungal sporocarps have been collected and deposited in worldwide collections (fungaria) to support fungal taxonomy. Owing to large-scale digitization programs, metadata associated with the records are now becoming publicly available, including information on taxonomy, sampling location, collection date and habitat/substrate information. This metadata, as well as data extracted from the physical fungarium specimens themselves, such as DNA sequences and biochemical characteristics, provide a rich source of information not only for taxonomy but also for other lines of biological inquiry. Here, we highlight and discuss how this information can be used to investigate emerging topics in fungal global change biology and beyond. Fungarium data are a prime source of knowledge on fungal distributions and richness patterns, and for assessing red-listed and invasive species. Information on collection dates has been used to investigate shifts in fungal distributions as well as phenology of sporocarp emergence in response to climate change. In addition to providing material for taxonomy and systematics, DNA sequences derived from the physical specimens provide information about fungal demography, dispersal patterns, and are emerging as a source of genomic data. As DNA analysis technologies develop further, the importance of fungarium specimens as easily accessible sources of information will likely continue to grow.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
Collapse
Affiliation(s)
- Carrie Andrew
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Jeffrey Diez
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
| |
Collapse
|
71
|
Dodsworth S, Guignard MS, Christenhusz MJM, Cowan RS, Knapp S, Maurin O, Struebig M, Leitch AR, Chase MW, Forest F. Potential of Herbariomics for Studying Repetitive DNA in Angiosperms. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
72
|
Villaverde T, Pokorny L, Olsson S, Rincón-Barrado M, Johnson MG, Gardner EM, Wickett NJ, Molero J, Riina R, Sanmartín I. Bridging the micro- and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above. THE NEW PHYTOLOGIST 2018; 220:636-650. [PMID: 30016546 DOI: 10.1111/nph.15312] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/04/2018] [Indexed: 05/20/2023]
Abstract
Reconstructing phylogenetic relationships at the micro- and macroevoutionary levels within the same tree is problematic because of the need to use different data types and analytical frameworks. We test the power of target enrichment to provide phylogenetic resolution based on DNA sequences from above species to within populations, using a large herbarium sampling and Euphorbia balsamifera (Euphorbiaceae) as a case study. Target enrichment with custom probes was combined with genome skimming (Hyb-Seq) to sequence 431 low-copy nuclear genes and partial plastome DNA. We used supermatrix, multispecies-coalescent approaches, and Bayesian dating to estimate phylogenetic relationships and divergence times. Euphorbia balsamifera, with a disjunct Rand Flora-type distribution at opposite sides of Africa, comprises three well-supported subspecies: western Sahelian sepium is sister to eastern African-southern Arabian adenensis and Macaronesian-southwest Moroccan balsamifera. Lineage divergence times support Late Miocene to Pleistocene diversification and climate-driven vicariance to explain the Rand Flora pattern. We show that probes designed using genomic resources from taxa not directly related to the focal group are effective in providing phylogenetic resolution at deep and shallow evolutionary levels. Low capture efficiency in herbarium samples increased the proportion of missing data but did not bias estimation of phylogenetic relationships or branch lengths.
Collapse
Affiliation(s)
- Tamara Villaverde
- Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014, Madrid, Spain
| | - Lisa Pokorny
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
| | - Sanna Olsson
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Ctra. de la Coruña km. 7.5, 28040, Madrid, Spain
| | | | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, 79409-43131, USA
- Department of Plant Science and Conservation, Chicago Botanical Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
| | | | - Norman J Wickett
- Department of Plant Science and Conservation, Chicago Botanical Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
- Program in Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Julià Molero
- Laboratori de Botànica, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia, Universitat de Barcelona, 08028, Barcelona, Spain
| | - Ricarda Riina
- Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014, Madrid, Spain
| | - Isabel Sanmartín
- Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014, Madrid, Spain
| |
Collapse
|
73
|
|
74
|
Abstract
Quantifying the age of recent species divergence events can be challenging in the absence of calibration points within many groups. The katydid species Neoconocephalus lyristes provides the opportunity to calibrate a post-Pleistocene, taxa specific mutation rate using a known biogeographic event, the Mohawk-Hudson Divide. DNA was extracted from pinned museum specimens of N. lyristes from both Midwest and Atlantic populations and the mitochondrial gene COI sequenced using primers designed from extant specimens. Coalescent analyses using both strict and relaxed molecular clock models were performed in BEAST v1.8.2. The assumption of a strict molecular clock could not be rejected in favor of the relaxed clock model as the distribution of the standard deviation of the clock rate strongly abutted zero. The strict molecular clock model resulted in an intraspecific calculated mutation rate of 14.4-17.3 %/myr, a rate substantially higher than the common rates of sequence evolution observed for insect mitochondrial DNA sequences. The rate, however, aligns closely with mutation rates estimated from other taxa with similarly recent lineage divergence times.
Collapse
Affiliation(s)
- Gideon Ney
- Department of Biological Sciences, University of Missouri, Columbia, Missouri, United States
| | - Katy Frederick
- Department of Biological Sciences, University of Missouri, Columbia, Missouri, United States
| | - Johannes Schul
- Department of Biological Sciences, University of Missouri, Columbia, Missouri, United States
| |
Collapse
|
75
|
Gruenstaeudl M, Gerschler N, Borsch T. Bioinformatic Workflows for Generating Complete Plastid Genome Sequences-An Example from Cabomba (Cabombaceae) in the Context of the Phylogenomic Analysis of the Water-Lily Clade. Life (Basel) 2018; 8:E25. [PMID: 29933597 PMCID: PMC6160935 DOI: 10.3390/life8030025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/11/2018] [Accepted: 06/19/2018] [Indexed: 12/13/2022] Open
Abstract
The sequencing and comparison of plastid genomes are becoming a standard method in plant genomics, and many researchers are using this approach to infer plant phylogenetic relationships. Due to the widespread availability of next-generation sequencing, plastid genome sequences are being generated at breakneck pace. This trend towards massive sequencing of plastid genomes highlights the need for standardized bioinformatic workflows. In particular, documentation and dissemination of the details of genome assembly, annotation, alignment and phylogenetic tree inference are needed, as these processes are highly sensitive to the choice of software and the precise settings used. Here, we present the procedure and results of sequencing, assembling, annotating and quality-checking of three complete plastid genomes of the aquatic plant genus Cabomba as well as subsequent gene alignment and phylogenetic tree inference. We accompany our findings by a detailed description of the bioinformatic workflow employed. Importantly, we share a total of eleven software scripts for each of these bioinformatic processes, enabling other researchers to evaluate and replicate our analyses step by step. The results of our analyses illustrate that the plastid genomes of Cabomba are highly conserved in both structure and gene content.
Collapse
Affiliation(s)
- Michael Gruenstaeudl
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, 14195 Berlin, Germany.
| | - Nico Gerschler
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, 14195 Berlin, Germany.
| | - Thomas Borsch
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, 14195 Berlin, Germany.
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, 14195 Berlin, Germany.
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), 14195 Berlin, Germany.
| |
Collapse
|
76
|
Saeidi S, McKain MR, Kellogg EA. Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens. J Vis Exp 2018:56837. [PMID: 29578505 PMCID: PMC5946958 DOI: 10.3791/56837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Herbaria are an invaluable source of plant material that can be used in a variety of biological studies. The use of herbarium specimens is associated with a number of challenges including sample preservation quality, degraded DNA, and destructive sampling of rare specimens. In order to more effectively use herbarium material in large sequencing projects, a dependable and scalable method of DNA isolation and library preparation is needed. This paper demonstrates a robust, beginning-to-end protocol for DNA isolation and high-throughput library construction from herbarium specimens that does not require modification for individual samples. This protocol is tailored for low quality dried plant material and takes advantage of existing methods by optimizing tissue grinding, modifying library size selection, and introducing an optional reamplification step for low yield libraries. Reamplification of low yield DNA libraries can rescue samples derived from irreplaceable and potentially valuable herbarium specimens, negating the need for additional destructive sampling and without introducing discernible sequencing bias for common phylogenetic applications. The protocol has been tested on hundreds of grass species, but is expected to be adaptable for use in other plant lineages after verification. This protocol can be limited by extremely degraded DNA, where fragments do not exist in the desired size range, and by secondary metabolites present in some plant material that inhibit clean DNA isolation. Overall, this protocol introduces a fast and comprehensive method that allows for DNA isolation and library preparation of 24 samples in less than 13 h, with only 8 h of active hands-on time with minimal modifications.
Collapse
Affiliation(s)
| | - Michael R McKain
- Donald Danforth Plant Science Center; Department of Biological Sciences, The University of Alabama;
| | | |
Collapse
|
77
|
McKain MR, Johnson MG, Uribe‐Convers S, Eaton D, Yang Y. Practical considerations for plant phylogenomics. APPLICATIONS IN PLANT SCIENCES 2018; 6:e1038. [PMID: 29732268 PMCID: PMC5895195 DOI: 10.1002/aps3.1038] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/13/2018] [Indexed: 05/10/2023]
Abstract
The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome-scale data from diverse lineages. The development of high-throughput sequencing and long-read technologies has ushered in the era of phylogenomics, where hundreds to thousands of nuclear genes and whole organellar genomes are routinely used to reconstruct evolutionary relationships. As a result, understanding which options are best suited for a particular set of questions can be difficult, especially for those just starting in the field. Here, we review the most recent advances in plant phylogenomic methods and make recommendations for project-dependent best practices and considerations. We focus on the costs and benefits of different approaches in regard to the information they provide researchers and the questions they can address. We also highlight unique challenges and opportunities in plant systems, such as polyploidy, reticulate evolution, and the use of herbarium materials, identifying optimal methodologies for each. Finally, we draw attention to lingering challenges in the field of plant phylogenomics, such as reusability of data sets, and look at some up-and-coming technologies that may help propel the field even further.
Collapse
Affiliation(s)
- Michael R. McKain
- Department of Biological SciencesThe University of AlabamaBox 870344TuscaloosaAlabama35487USA
| | - Matthew G. Johnson
- Department of Biological SciencesTexas Tech University2901 Main Street, Box 43131LubbockTexas79409USA
| | - Simon Uribe‐Convers
- Department of Ecology and Evolutionary BiologyUniversity of Michigan830 North UniversityAnn ArborMichigan48109USA
| | - Deren Eaton
- Department of Ecology, Evolution, and Environmental BiologyColumbia University1200 Amsterdam AvenueNew YorkNew York10027USA
| | - Ya Yang
- Department of Plant and Microbial BiologyUniversity of Minnesota–Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108USA
| |
Collapse
|
78
|
Díez-del-Molino D, Sánchez-Barreiro F, Barnes I, Gilbert MTP, Dalén L. Quantifying Temporal Genomic Erosion in Endangered Species. Trends Ecol Evol 2018; 33:176-185. [DOI: 10.1016/j.tree.2017.12.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 11/28/2017] [Accepted: 12/01/2017] [Indexed: 12/30/2022]
|
79
|
Valderrama E, Richardson JE, Kidner CA, Madriñán S, Stone GN. Transcriptome mining for phylogenetic markers in a recently radiated genus of tropical plants (Renealmia L.f., Zingiberaceae). Mol Phylogenet Evol 2018; 119:13-24. [DOI: 10.1016/j.ympev.2017.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/17/2017] [Accepted: 10/03/2017] [Indexed: 11/25/2022]
|
80
|
Abstract
With a million described species and more than half a billion preserved specimens, the large scale of insect collections is unequaled by those of any other group. Advances in genomics, collection digitization, and imaging have begun to more fully harness the power that such large data stores can provide. These new approaches and technologies have transformed how entomological collections are managed and utilized. While genomic research has fundamentally changed the way many specimens are collected and curated, advances in technology have shown promise for extracting sequence data from the vast holdings already in museums. Efforts to mainstream specimen digitization have taken root and have accelerated traditional taxonomic studies as well as distribution modeling and global change research. Emerging imaging technologies such as microcomputed tomography and confocal laser scanning microscopy are changing how morphology can be investigated. This review provides an overview of how the realization of big data has transformed our field and what may lie in store.
Collapse
Affiliation(s)
- Andrew Edward Z Short
- Department of Ecology and Evolutionary Biology; and Division of Entomology, Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA;
| | - Torsten Dikow
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA;
| | - Corrie S Moreau
- Department of Science and Education, Field Museum of Natural History, Chicago, Illinois 60605, USA;
| |
Collapse
|
81
|
Zeng CX, Hollingsworth PM, Yang J, He ZS, Zhang ZR, Li DZ, Yang JB. Genome skimming herbarium specimens for DNA barcoding and phylogenomics. PLANT METHODS 2018; 14:43. [PMID: 29928291 PMCID: PMC5987614 DOI: 10.1186/s13007-018-0300-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/20/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND The world's herbaria contain millions of specimens, collected and named by thousands of researchers, over hundreds of years. However, this treasure has remained largely inaccessible to genetic studies, because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. RESULTS As a practical test of routine recovery of rDNA and plastid genome sequences from herbarium specimens, we sequenced 25 herbarium specimens up to 80 years old from 16 different Angiosperm families. Paired-end reads were generated, yielding successful plastid genome assemblies for 23 species and nuclear rDNAs for 24 species, respectively. These data showed that genome skimming can be used to generate genomic information from herbarium specimens as old as 80 years and using as little as 500 pg of degraded starting DNA. CONCLUSIONS The routine plastome sequencing from herbarium specimens is feasible and cost-effective (compare with Sanger sequencing or plastome-enrichment approaches), and can be performed with limited sample destruction.
Collapse
Affiliation(s)
- Chun-Xia Zeng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | | | - Jing Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Zheng-Shan He
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| |
Collapse
|
82
|
Daru BH, Park DS, Primack RB, Willis CG, Barrington DS, Whitfeld TJS, Seidler TG, Sweeney PW, Foster DR, Ellison AM, Davis CC. Widespread sampling biases in herbaria revealed from large-scale digitization. THE NEW PHYTOLOGIST 2018; 217:939-955. [PMID: 29083043 DOI: 10.1111/nph.14855] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/18/2017] [Indexed: 05/19/2023]
Abstract
Nonrandom collecting practices may bias conclusions drawn from analyses of herbarium records. Recent efforts to fully digitize and mobilize regional floras online offer a timely opportunity to assess commonalities and differences in herbarium sampling biases. We determined spatial, temporal, trait, phylogenetic, and collector biases in c. 5 million herbarium records, representing three of the most complete digitized floras of the world: Australia (AU), South Africa (SA), and New England, USA (NE). We identified numerous shared and unique biases among these regions. Shared biases included specimens collected close to roads and herbaria; specimens collected more frequently during biological spring and summer; specimens of threatened species collected less frequently; and specimens of close relatives collected in similar numbers. Regional differences included overrepresentation of graminoids in SA and AU and of annuals in AU; and peak collection during the 1910s in NE, 1980s in SA, and 1990s in AU. Finally, in all regions, a disproportionately large percentage of specimens were collected by very few individuals. We hypothesize that these mega-collectors, with their associated preferences and idiosyncrasies, shaped patterns of collection bias via 'founder effects'. Studies using herbarium collections should account for sampling biases, and future collecting efforts should avoid compounding these biases to the extent possible.
Collapse
Affiliation(s)
- Barnabas H Daru
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
| | - Daniel S Park
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
| | | | - Charles G Willis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
| | - David S Barrington
- Pringle Herbarium, Plant Biology Department, University of Vermont, Torrey Hall, 27 Colchester Ave, Burlington, VT, 05405, USA
| | - Timothy J S Whitfeld
- Brown University Herbarium, Department of Ecology and Evolutionary Biology, Brown University, 34 Olive Street, Box G-B225, Providence, RI, 02912, USA
| | - Tristram G Seidler
- Biology Department, University of Massachusetts, 611 North Pleasant Street, Amherst, MA, 01003, USA
| | - Patrick W Sweeney
- Division of Botany, Peabody Museum of Natural History, Yale University, New Haven, CT, 06511, USA
| | - David R Foster
- Harvard Forest, Harvard University, 324 North Main Street, Petersham, MA, 01366, USA
| | - Aaron M Ellison
- Harvard Forest, Harvard University, 324 North Main Street, Petersham, MA, 01366, USA
- Tropical Forests & People Research Centre, University of the Sunshine Coast, Maroochydore, Qld, 4558, Australia
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
| |
Collapse
|
83
|
Sproul JS, Maddison DR. Cryptic species in the mountaintops: species delimitation and taxonomy of the Bembidion breve species group (Coleoptera: Carabidae) aided by genomic architecture of a century-old type specimen. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx076] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- John S Sproul
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - David R Maddison
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| |
Collapse
|
84
|
Kuzmina ML, Braukmann TWA, Fazekas AJ, Graham SW, Dewaard SL, Rodrigues A, Bennett BA, Dickinson TA, Saarela JM, Catling PM, Newmaster SG, Percy DM, Fenneman E, Lauron-Moreau A, Ford B, Gillespie L, Subramanyam R, Whitton J, Jennings L, Metsger D, Warne CP, Brown A, Sears E, Dewaard JR, Zakharov EV, Hebert PDN. Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada. APPLICATIONS IN PLANT SCIENCES 2017; 5:apps.1700079. [PMID: 29299394 PMCID: PMC5749818 DOI: 10.3732/apps.1700079] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/26/2017] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada. METHODS Our study examined 20,816 specimens representing 5076 of 5190 vascular plant species in Canada (98%). For 98% of the specimens, at least one of the DNA barcode regions was recovered from the plastid loci rbcL and matK and from the nuclear ITS2 region. We used beta regression to quantify the effects of age, type of preservation, and taxonomic affiliation (family) on DNA sequence recovery. RESULTS Specimen age and method of preservation had significant effects on sequence recovery for all markers, but influenced some families more (e.g., Boraginaceae) than others (e.g., Asteraceae). DISCUSSION Our DNA barcode library represents an unparalleled resource for metagenomic and ecological genetic research working on temperate and arctic biomes. An observed decline in sequence recovery with specimen age may be associated with poor primer matches, intragenomic variation (for ITS2), or inhibitory secondary compounds in some taxa.
Collapse
Affiliation(s)
- Maria L. Kuzmina
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Thomas W. A. Braukmann
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Aron J. Fazekas
- The Arboretum, University of Guelph, 50 Stone Road East, Ontario N1G 2W1, Canada
| | - Sean W. Graham
- Department of Botany, University of British Columbia, 3200-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Stephanie L. Dewaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Anuar Rodrigues
- Office of the Vice-Principal Academic and Dean, University of Toronto, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Bruce A. Bennett
- Yukon Conservation Data Centre (CDC), Whitehorse, Yukon Territory Y1A 2C6, Canada
| | - Timothy A. Dickinson
- Green Plant Herbarium (TRT), Department of Natural History, Royal Ontario Museum (ROM), 100 Queens Park, Toronto, Ontario M5S2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 27 King's College Circle, Toronto, Ontario M5S, Canada
| | - Jeffery M. Saarela
- Beaty Centre for Species Discovery and National Herbarium of Canada (CAN), Botany Section, Research and Collections, National Heritage Campus of the Canadian Museum of Nature, Gatineau, Québec J9J 3N7, Canada
| | - Paul M. Catling
- The Agriculture and Agri-Food Canada Collection of Vascular Plants (DAO), 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Steven G. Newmaster
- BIO Herbarium (OAC), University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1, Canada
| | - Diana M. Percy
- Natural History Museum, Cromwell Road, Kensington, London SW75BD, United Kingdom
| | - Erin Fenneman
- Department of Botany, University of British Columbia, 3200-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Aurélien Lauron-Moreau
- Institut de recherche en biologie végétale, Université de Montréal, 2900 Edouard Montpetit Boulevard, Montréal, Québec H3T 1J4, Canada
| | - Bruce Ford
- University of Manitoba Vascular Plant Herbarium (WIN), Department of Biological Sciences, University of Manitoba, 66 Chancellors Circle, Winnipeg, Manitoba R3T 2N2, Canada
| | - Lynn Gillespie
- Beaty Centre for Species Discovery and National Herbarium of Canada (CAN), Botany Section, Research and Collections, National Heritage Campus of the Canadian Museum of Nature, Gatineau, Québec J9J 3N7, Canada
| | - Ragupathy Subramanyam
- BIO Herbarium (OAC), University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1, Canada
| | - Jeannette Whitton
- Department of Botany, University of British Columbia, 3200-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Linda Jennings
- Department of Botany, University of British Columbia, 3200-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Deborah Metsger
- Green Plant Herbarium (TRT), Department of Natural History, Royal Ontario Museum (ROM), 100 Queens Park, Toronto, Ontario M5S2C6, Canada
| | - Connor P. Warne
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Allison Brown
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Elizabeth Sears
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Jeremy R. Dewaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| |
Collapse
|
85
|
Twyford AD, Ness RW. Strategies for complete plastid genome sequencing. Mol Ecol Resour 2017; 17:858-868. [PMID: 27790830 PMCID: PMC6849563 DOI: 10.1111/1755-0998.12626] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/14/2016] [Accepted: 10/21/2016] [Indexed: 12/01/2022]
Abstract
Plastid sequencing is an essential tool in the study of plant evolution. This high-copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss recent innovations and approaches for de novo plastid assembly that harness genomic tools. We focus on technical developments including low-cost sequence library preparation approaches for genome skimming, enrichment via hybrid baits and methylation-sensitive capture, sequence platforms with higher read outputs and longer read lengths, and automated tools for assembly. These developments allow for a much more streamlined assembly than via conventional short-range PCR. Although newer methods make complete plastid sequencing possible for any land plant or green alga, there are still challenges for producing finished plastomes particularly from herbarium material or from structurally divergent plastids such as those of parasitic plants.
Collapse
Affiliation(s)
- Alex D. Twyford
- Institute of Evolutionary BiologyAshworth LaboratoriesUniversity of EdinburghEdinburghEH9 3FLUK
| | - Rob W. Ness
- Department of BiologyUniversity of Toronto MississaugaMississaugaONCanada
| |
Collapse
|
86
|
Shepherd LD. A non-destructive DNA sampling technique for herbarium specimens. PLoS One 2017; 12:e0183555. [PMID: 28859137 PMCID: PMC5578499 DOI: 10.1371/journal.pone.0183555] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/07/2017] [Indexed: 11/18/2022] Open
Abstract
Herbarium specimens are an important source of DNA for plant research but current sampling methods require the removal of material for DNA extraction. This is undesirable for irreplaceable specimens such as rare species or type material. Here I present the first non-destructive sampling method for extracting DNA from herbarium specimens. DNA was successfully retrieved from robust leaves and/or stems of herbarium specimens up to 73 years old.
Collapse
Affiliation(s)
- Lara D Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| |
Collapse
|
87
|
Affiliation(s)
- Freek T. Bakker
- Biosystematics Group, Wageningen University, Wageningen, The Netherlands
| |
Collapse
|
88
|
Gutaker RM, Burbano HA. Reinforcing plant evolutionary genomics using ancient DNA. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:38-45. [PMID: 28160617 DOI: 10.1016/j.pbi.2017.01.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/07/2016] [Accepted: 01/13/2017] [Indexed: 05/11/2023]
Abstract
Improved understanding of ancient DNA (aDNA) biochemical properties coupled with application of next generation sequencing (NGS) methods enabled sequencing and authenticating genomes of historical samples. This advancement ignited a revolution in plant evolutionary genomics by allowing direct observations of past molecular diversity. Analyses of genomes sequenced from temporally distributed samples of Gossypium sp., Phytophthora infestans and Arabidopsis thaliana improved our understanding of the evolutionary rates and time scales at which genome remodeling takes place. Comparison of historical samples of barley (Hordeum vulgare) and maize (Zea mays ssp. mays) with their present-day counterparts enabled assessment of selection during different stages of domestication. These examples show how aDNA already improved our evolutionary inferences. Increasing quality and amount of sequencing data retrieved from historical plants will further advance our understanding of plant evolution.
Collapse
Affiliation(s)
- Rafal M Gutaker
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstr. 37-39, Tuebingen 72076, Germany
| | - Hernán A Burbano
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstr. 37-39, Tuebingen 72076, Germany.
| |
Collapse
|
89
|
Sproul JS, Maddison DR. Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded
DNA. Mol Ecol Resour 2017; 17:1183-1201. [DOI: 10.1111/1755-0998.12660] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 11/28/2022]
Affiliation(s)
- John S. Sproul
- Department of Integrative Biology Oregon State University 3029 Cordley Hall Corvallis OR 97331 USA
| | - David R. Maddison
- Department of Integrative Biology Oregon State University 3029 Cordley Hall Corvallis OR 97331 USA
| |
Collapse
|
90
|
Silva C, Besnard G, Piot A, Razanatsoa J, Oliveira RP, Vorontsova MS. Museomics resolve the systematics of an endangered grass lineage endemic to north-western Madagascar. ANNALS OF BOTANY 2017; 119:339-351. [PMID: 28028020 PMCID: PMC5314640 DOI: 10.1093/aob/mcw208] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 07/28/2016] [Accepted: 08/24/2016] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Recent developments in DNA sequencing, so-called next-generation sequencing (NGS) methods, can help the study of rare lineages that are known from museum specimens. Here, the taxonomy and evolution of the Malagasy grass lineage Chasechloa was investigated with the aid of NGS. METHODS Full chloroplast genome data and some nuclear sequences were produced by NGS from old herbarium specimens, while some selected markers were generated from recently collected Malagasy grasses. In addition, a scanning electron microscopy analysis of the upper floret and cross-sections of the rachilla appendages followed by staining with Sudan IV were performed on Chasechloa to examine the morphology of the upper floret and the presence of oils in the appendages. KEY RESULTS Chasechloa was recovered within tribe Paniceae, sub-tribe Boivinellinae, contrary to its previous placement as a member of the New World genus Echinolaena (tribe Paspaleae). Chasechloa originated in Madagascar between the Upper Miocene and the Pliocene. It comprises two species, one of them collected only once in 1851. The genus is restricted to north-western seasonally dry deciduous forests. The appendages at the base of the upper floret of Chasechloa have been confirmed as elaiosomes, an evolutionary adaptation for myrmecochory. CONCLUSIONS Chasechloa is reinstated at the generic level and a taxonomic treatment is presented, including conservation assessments of its species. Our study also highlights the power of NGS technology to analyse relictual or probably extinct groups.
Collapse
Affiliation(s)
- Christian Silva
- Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Programa de Pós-graduação em Botânica, Av. Transnordestina s.n., Feira de Santana, Bahia 44036-900, Brazil
| | - Guillaume Besnard
- CNRS, Université de Toulouse, ENFA, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, 31062 Toulouse, France
| | - Anthony Piot
- CNRS, Université de Toulouse, ENFA, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, 31062 Toulouse, France
| | - Jacqueline Razanatsoa
- Herbier, Département Flore, Parc Botanique et Zoologique de Tsimbazaza, BP 4096, Antananarivo 101, Madagascar
| | - Reyjane P Oliveira
- Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Programa de Pós-graduação em Botânica, Av. Transnordestina s.n., Feira de Santana, Bahia 44036-900, Brazil
| | | |
Collapse
|
91
|
Mitogenomics of Hesperelaea, an extinct genus of Oleaceae. Gene 2016; 594:197-202. [DOI: 10.1016/j.gene.2016.09.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/02/2016] [Indexed: 11/21/2022]
|
92
|
Yeates DK, Zwick A, Mikheyev AS. Museums are biobanks: unlocking the genetic potential of the three billion specimens in the world's biological collections. CURRENT OPINION IN INSECT SCIENCE 2016; 18:83-88. [PMID: 27939715 DOI: 10.1016/j.cois.2016.09.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/23/2016] [Indexed: 05/25/2023]
Abstract
Museums and herbaria represent vast repositories of biological material. Until recently, working with these collections has been difficult, due to the poor condition of historical DNA. However, recent advances in next-generation sequencing technology, and subsequent development of techniques for preparing and sequencing historical DNA, have recently made working with collection specimens an attractive option. Here we describe the unique technical challenges of working with collection specimens, and innovative molecular methods developed to tackle them. We also highlight possible applications of collection specimens, for taxonomy, ecology and evolution. The application of next-generation sequencing methods to museum and herbaria collections is still in its infancy. However, by giving researchers access to billions of specimens across time and space, it holds considerable promise for generating future discoveries across many fields.
Collapse
Affiliation(s)
- David K Yeates
- Australian National Insect Collection, CSIRO National Research Collections Australia, PO Box 1700, Canberra, ACT 2601, Australia.
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, PO Box 1700, Canberra, ACT 2601, Australia
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun 904-0412, Japan
| |
Collapse
|
93
|
Yahr R, Schoch CL, Dentinger BTM. Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150336. [PMID: 27481788 PMCID: PMC4971188 DOI: 10.1098/rstb.2015.0336] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2016] [Indexed: 11/15/2022] Open
Abstract
The fungal kingdom is a hyperdiverse group of multicellular eukaryotes with profound impacts on human society and ecosystem function. The challenge of documenting and describing fungal diversity is exacerbated by their typically cryptic nature, their ability to produce seemingly unrelated morphologies from a single individual and their similarity in appearance to distantly related taxa. This multiplicity of hurdles resulted in the early adoption of DNA-based comparisons to study fungal diversity, including linking curated DNA sequence data to expertly identified voucher specimens. DNA-barcoding approaches in fungi were first applied in specimen-based studies for identification and discovery of taxonomic diversity, but are now widely deployed for community characterization based on sequencing of environmental samples. Collectively, fungal barcoding approaches have yielded important advances across biological scales and research applications, from taxonomic, ecological, industrial and health perspectives. A major outstanding issue is the growing problem of 'sequences without names' that are somewhat uncoupled from the traditional framework of fungal classification based on morphology and preserved specimens. This review summarizes some of the most significant impacts of fungal barcoding, its limitations, and progress towards the challenge of effective utilization of the exponentially growing volume of data gathered from high-throughput sequencing technologies.This article is part of the themed issue 'From DNA barcodes to biomes'.
Collapse
Affiliation(s)
- Rebecca Yahr
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, UK
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Bryn T M Dentinger
- Royal Botanic Gardens Kew, Richmond, Surrey, UK Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Cledwyn Building, Penglais, Aberystwyth SY23 3DD, UK
| |
Collapse
|
94
|
Jiang GF, Hinsinger DD, Strijk JS. Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads. Sci Rep 2016; 6:31473. [PMID: 27558458 PMCID: PMC4997344 DOI: 10.1038/srep31473] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/20/2016] [Indexed: 11/18/2022] Open
Abstract
Cycads are among the most threatened plant species. Increasing the availability of genomic information by adding whole chloroplast data is a fundamental step in supporting phylogenetic studies and conservation efforts. Here, we assemble a dataset encompassing three taxonomic levels in cycads, including ten genera, three species in the genus Cycas and two individuals of C. debaoensis. Repeated sequences, SSRs and variations of the chloroplast were analyzed at the intraspecific, interspecific and intergeneric scale, and using our sequence data, we reconstruct a phylogenomic tree for cycads. The chloroplast was 162,094 bp in length, with 133 genes annotated, including 87 protein-coding, 37 tRNA and 8 rRNA genes. We found 7 repeated sequences and 39 SSRs. Seven loci showed promising levels of variations for application in DNA-barcoding. The chloroplast phylogeny confirmed the division of Cycadales in two suborders, each of them being monophyletic, revealing a contradiction with the current family circumscription and its evolution. Finally, 10 intraspecific SNPs were found. Our results showed that despite the extremely restricted distribution range of C. debaoensis, using complete chloroplast data is useful not only in intraspecific studies, but also to improve our understanding of cycad evolution and in defining conservation strategies for this emblematic group.
Collapse
Affiliation(s)
- Guo-Feng Jiang
- Plant Ecophysiology and Evolution Group, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Forestry, Guangxi University, Nanning, Guangxi 530004, China
| | - Damien Daniel Hinsinger
- Plant Ecophysiology and Evolution Group, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Forestry, Guangxi University, Nanning, Guangxi 530004, China
| | - Joeri Sergej Strijk
- Plant Ecophysiology and Evolution Group, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and College of Forestry, Guangxi University, Nanning, Guangxi 530004, China
| |
Collapse
|
95
|
Blaimer BB, Lloyd MW, Guillory WX, Brady SG. Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens. PLoS One 2016; 11:e0161531. [PMID: 27556533 PMCID: PMC4996520 DOI: 10.1371/journal.pone.0161531] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/08/2016] [Indexed: 01/15/2023] Open
Abstract
Obtaining sequence data from historical museum specimens has been a growing research interest, invigorated by next-generation sequencing methods that allow inputs of highly degraded DNA. We applied a target enrichment and next-generation sequencing protocol to generate ultraconserved elements (UCEs) from 51 large carpenter bee specimens (genus Xylocopa), representing 25 species with specimen ages ranging from 2-121 years. We measured the correlation between specimen age and DNA yield (pre- and post-library preparation DNA concentration) and several UCE sequence capture statistics (raw read count, UCE reads on target, UCE mean contig length and UCE locus count) with linear regression models. We performed piecewise regression to test for specific breakpoints in the relationship of specimen age and DNA yield and sequence capture variables. Additionally, we compared UCE data from newer and older specimens of the same species and reconstructed their phylogeny in order to confirm the validity of our data. We recovered 6-972 UCE loci from samples with pre-library DNA concentrations ranging from 0.06-9.8 ng/μL. All investigated DNA yield and sequence capture variables were significantly but only moderately negatively correlated with specimen age. Specimens of age 20 years or less had significantly higher pre- and post-library concentrations, UCE contig lengths, and locus counts compared to specimens older than 20 years. We found breakpoints in our data indicating a decrease of the initial detrimental effect of specimen age on pre- and post-library DNA concentration and UCE contig length starting around 21-39 years after preservation. Our phylogenetic results confirmed the integrity of our data, giving preliminary insights into relationships within Xylocopa. We consider the effect of additional factors not measured in this study on our age-related sequence capture results, such as DNA fragmentation and preservation method, and discuss the promise of the UCE approach for large-scale projects in insect phylogenomics using museum specimens.
Collapse
Affiliation(s)
- Bonnie B. Blaimer
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
| | - Michael W. Lloyd
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
| | - Wilson X. Guillory
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Seán G. Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
| |
Collapse
|
96
|
Benson EE, Harding K, Mackenzie-dodds J. A new quality management perspective for biodiversity conservation and research: Investigating Biospecimen Reporting for Improved Study Quality (BRISQ) and the Standard PRE-analytical Code (SPREC) using Natural History Museum and culture collections as case studies. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1201167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Erica E. Benson
- Damar Research Scientists, Damar, Drum Road, Cuparmuir, Fife, Scotland KY15 5RJ, UK
| | - Keith Harding
- Damar Research Scientists, Damar, Drum Road, Cuparmuir, Fife, Scotland KY15 5RJ, UK
| | - Jacqueline Mackenzie-dodds
- Molecular Collections, Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| |
Collapse
|
97
|
Jaksch K, Eschner A, Rintelen TV, Haring E. DNA analysis of molluscs from a museum wet collection: a comparison of different extraction methods. BMC Res Notes 2016; 9:348. [PMID: 27430899 PMCID: PMC4950716 DOI: 10.1186/s13104-016-2147-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 07/01/2016] [Indexed: 11/25/2022] Open
Abstract
Background DNA isolation and PCR amplification from molluscan taxa is considered as problematic because polysaccharides in tissue and mucus presumably co-precipitate with the DNA and inhibit the activity of DNA polymerase. In the present study we tested two common extraction methods on specimens from the mollusc collection of the Natural History Museum Vienna (NHMW). We analysed a broad variety of taxa covering a large temporal span (acquisition years 1877 to 1999), which distinguishes our study from previous ones where mostly fresh material was used. We also took other factors into account: effects of sample age, effects of formaldehyde treatment and taxon-specific problems. We used several primer combinations to amplify amplicons of different lengths of two mitochondrial genes: cytochrome c oxidase subunit 1 (COI) and 16S rRNA gene (16S). Results Overall PCR success was 43 % in the 576 extractions (including all primer combinations). The smallest amplicon (~240 bp) showed the best results (49 % positive reactions), followed by the 400 bp amplicon (40.5 %). Both short sections yielded significantly better results than the 700 bp long amplicon (27 %). Comparatively, the Gen-ial-First, All-tissue DNA-Kit—extraction method performed significantly better than Promega-Tissue and Hair Extraction Kit. Generally, PCR success is age-dependent. Nonetheless, we were able to obtain the longest amplicon even from 137-year-old material. Importantly, formaldehyde traces did not totally inhibit amplification success, although very high concentrations did. Conclusions Museum material has gained importance for DNA analysis in recent years, especially for DNA barcoding projects. In some cases, however, the amplification of the standard barcoding region (partial sequence of the COI) is problematic with old material. Our study clearly shows that the COI barcoding region could be amplified in up to 49 % of PCRs (varying with amplicon length), which is, for museum samples, quite a high percentage. The difference between extraction methods was minimal and we recommend using an established kit for a first attempt because experience and routine in handling might be more important than slight performance differences of the various kits. Finally, we identify fixation, storage, sample conservation and documentation of the specimens’ history rather than the DNA extraction method to be the most crucial factors for PCR success. Electronic supplementary material The online version of this article (doi:10.1186/s13104-016-2147-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Katharina Jaksch
- Central Research Laboratories, Natural History Museum Vienna, Burgring 7, 1010, Vienna, Austria. .,Department of Integrative Zoology, University of Vienna, Althanstraße 14, 1090, Vienna, Austria.
| | - Anita Eschner
- Third Zoological Department, Natural History Museum Vienna, Burgring 7, 1010, Vienna, Austria
| | - Thomas V Rintelen
- Leibniz Institute for Research on Evolution and Biodiversity, Museum für Naturkunde, Invalidenstraße 43, 10115, Berlin, Germany
| | - Elisabeth Haring
- Central Research Laboratories, Natural History Museum Vienna, Burgring 7, 1010, Vienna, Austria.,Department of Integrative Zoology, University of Vienna, Althanstraße 14, 1090, Vienna, Austria
| |
Collapse
|
98
|
Weiß CL, Schuenemann VJ, Devos J, Shirsekar G, Reiter E, Gould BA, Stinchcombe JR, Krause J, Burbano HA. Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160239. [PMID: 27429780 PMCID: PMC4929915 DOI: 10.1098/rsos.160239] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/24/2016] [Indexed: 05/04/2023]
Abstract
Herbaria archive a record of changes of worldwide plant biodiversity harbouring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation and nucleotide misincorporation by analysing 86 herbarium samples spanning the last 300 years using Illumina shotgun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66 × 10(-4) per year, which is six times faster than the rate estimated for ancient bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar to what has been found analysing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine to thymine substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.
Collapse
Affiliation(s)
- Clemens L. Weiß
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - Verena J. Schuenemann
- Institute of Archaeological Sciences, University of Tübingen, Tuebingen 72076, Germany
| | - Jane Devos
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - Gautam Shirsekar
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - Ella Reiter
- Institute of Archaeological Sciences, University of Tübingen, Tuebingen 72076, Germany
| | - Billie A. Gould
- Department of Ecology and Evolutionary Biology, Toronto, Ontario, CanadaM5S
| | - John R. Stinchcombe
- Department of Ecology and Evolutionary Biology, Toronto, Ontario, CanadaM5S
- University of Toronto, Toronto, Ontario, CanadaM5S
| | - Johannes Krause
- Institute of Archaeological Sciences, University of Tübingen, Tuebingen 72076, Germany
- Departments of Paleoanthropology and Archaeogenetics, Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tuebingen 72076, Germany
- Max Planck Institute for the Science of Human History, Jena 07743, Germany
| | - Hernán A. Burbano
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
- Author for correspondence: Hernán A. Burbano e-mail:
| |
Collapse
|
99
|
The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae). Mol Phylogenet Evol 2016; 99:16-33. [DOI: 10.1016/j.ympev.2016.02.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/26/2016] [Accepted: 02/28/2016] [Indexed: 11/17/2022]
|
100
|
Tedersoo L, Liiv I, Kivistik PA, Anslan S, Kõljalg U, Bahram M. Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens. MycoKeys 2016. [DOI: 10.3897/mycokeys.13.8140] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
|