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Haarsma AJ, Jongejans E, Duijm E, van der Graaf C, Lammers Y, Sharma M, Siepel H, Gravendeel B. Female pond bats hunt in other areas than males and consume lighter prey when pregnant. J Mammal 2023; 104:1191-1204. [PMID: 38059006 PMCID: PMC10697422 DOI: 10.1093/jmammal/gyad096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 09/07/2023] [Indexed: 12/08/2023] Open
Abstract
Animals with large energy requirements are forced to optimize their hunting strategy, which may result in differentiation of the diet between sexes and across seasons. Here, we examined spatiotemporal variation in the diet of both sexes of the Pond Bat Myotis dasycneme, a species known to have spatial segregation of sexes when the young are born and lactating. Fecal pellets were collected from live animals for a period of 15 years at various locations in the Netherlands. A total of 535 pellets were successfully analyzed by microscopy and an additional 160 pellets by DNA metabarcoding. Morphological and molecular analyses showed that the diet of pregnant and lactating pond bats differed significantly from the diet of females with no reproductive investment. Further analyses of the data showed that pregnant female pond bats are highly dependent on small prey and pupae, mainly nonbiting midges and mosquitoes (Diptera: Chironomidae and Culicidae). These insects can be found in large quantities in peatlands intersected with shallow waterways, the habitat type in which female pond bats were observed more often than males. Our results suggest that during pregnancy the spatial segregation of sexes coincides with sex-specific diets, which might reflect habitat selection based on energy requirements, in addition to lowered intraspecific competition.
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Affiliation(s)
- Anne-Jifke Haarsma
- Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Naturalis Biodiversity Center, Evolutionary Ecology Group, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Eelke Jongejans
- Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Netherlands Institute of Ecology, Department of Animal Ecology, Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Elza Duijm
- Naturalis Biodiversity Center, Evolutionary Ecology Group, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Carolien van der Graaf
- Bat Research Consultancy Vroegvlieger, Ellekomstraat 70, 2573 XG Den Haag, The Netherlands
| | - Youri Lammers
- Naturalis Biodiversity Center, Evolutionary Ecology Group, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Milan Sharma
- Naturalis Biodiversity Center, Evolutionary Ecology Group, Darwinweg 2, 2333 CR Leiden, The Netherlands
- HZ University of Applied Sciences, Life Sciences cluster, Edisonweg 4, 4382 NW Vlissingen, The Netherlands
| | - Henk Siepel
- Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Barbara Gravendeel
- Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Naturalis Biodiversity Center, Evolutionary Ecology Group, Darwinweg 2, 2333 CR Leiden, The Netherlands
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Ter Steege H, Fortes EA, Rozendaal DMA, Erkens RHJ, Sabatier D, Aymard G, Duijm E, Eurlings M, Grewe F, Pombo MM, Gomes VF, de Mansano VF, de Oliveira SM. Molecular phylogeny and evolution of inflorescence types in Eperua. Am J Bot 2023; 110:e16229. [PMID: 37661805 DOI: 10.1002/ajb2.16229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 09/05/2023]
Abstract
PREMISE The Amazonian hyperdominant genus Eperua (Fabaceae) currently holds 20 described species and has two strongly different inflorescence and flower types, with corresponding different pollination syndrome. The evolution of these vastly different inflorescence types within this genus was unknown and the main topic in this study. METHODS We constructed a molecular phylogeny, based on the full nuclear ribosomal DNA and partial plastome, using Bayesian inference and maximum likelihood methods, to test whether the genus is monophyletic, whether all species are monophyletic and if the shift from bat to bee pollination (or vice versa) occurred once in this genus. RESULTS All but two species are well supported by the nuclear ribosomal phylogeny. The plastome phylogeny, however, shows a strong geographic signal suggesting strong local hybridization or chloroplast capture, rendering chloroplast barcodes meaningless in this genus. CONCLUSIONS With our data, we cannot fully resolve the backbone of the tree to clarify sister genera relationships and confirm monophyly of the genus Eperua. Within the genus, the shift from bat to bee and bee to bat pollination has occurred several times but, with the bee to bat not always leading to a pendant inflorescence.
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Affiliation(s)
- Hans Ter Steege
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Quantitative Biodiversity Dynamics, Dept. of Biology, Utrecht, Utrecht University, The Netherlands
| | - Elenice A Fortes
- Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Danaë M A Rozendaal
- Plant Production Systems Group, Wageningen University, P.O. Box 430, Wageningen, 6700 AK, the Netherlands
- Centre for Crop Systems Analysis, Wageningen University, P.O. Box 430, Wageningen, 6700 AK, the Netherlands
| | - Roy H J Erkens
- Maastricht Science Programme, Faculty of Science and Engineering, Maastricht University, P.O. Box 616. 6200 MD, Maastricht, The Netherlands
| | - Daniel Sabatier
- AMAP, IRD, Cirad, CNRS, INRA, Université de Montpellier, Montpellier, F-34398, France
| | - Gerardo Aymard
- UNELLEZ-Guanare, Programa de Ciencias del Agro y del Mar, Herbario Universitario (PORT), Mesa de Cavacas, estado Portuguesa, 3350, Venezuela
- Compensation International Progress S.A. Ciprogress-Greenlife, Bogotá D.C., Colombia
| | - Elza Duijm
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | - Felix Grewe
- Grainger Bioinformatics Center, Field Museum, 1400 S. Lake Shore Drive, Chicago, 60605-2496, IL, USA
| | - Maihyra M Pombo
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia - INPA, Av. André Araújo, 2936, Manaus, 69067-375, AM, Brazil
| | - Vitor F Gomes
- Escola de Negócios Tecnologia e Inovação, Centro Universitário do Pará, Belém, PA, Brazil
- Universidade Federal do Pará, Rua Augusto Corrêa 01, Belém, 66075-110, PA, Brazil
| | - Vidal F de Mansano
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão, 915, Rio de Janeiro, 22460-030, RJ, Brazil
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Mota de Oliveira S, Duijm E, Stech M, Ruijgrok J, Polling M, Barbosa CGG, Cerqueira GR, Nascimento AHM, Godoi RHM, Taylor PE, Wolff S, Weber B, Kesselmeier J. Life is in the air: An expedition into the Amazonian atmosphere. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.789791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Biological particles suspended in the atmosphere have a crucial role in the dynamics of the biosphere underneath. Although much attention is paid for the chemical and physical properties of these particles, their biological taxonomic identity, which is relevant for ecological research, remains little studied. We took air samples at 300 meters above the forest in central Amazonia, in seven periods of 7 days, and used high-throughput DNA sequencing techniques to taxonomically identify airborne fungal and plant material. The use of a molecular identification technique improved taxonomic resolution when compared to morphological identification. This first appraisal of airborne diversity showed that fungal composition was strikingly different from what has been recorded in anthropogenic regions. For instance, basidiospores reached 30% of the OTUs instead of 3–5% as found in the literature; and the orders Capnodiales and Eurotiales—to which many allergenic fungi and crop pathogens belong—were much less frequently recorded than Pleosporales, Polyporales, and Agaricales. Plant OTUs corresponded mainly to Amazonian taxa frequently present in pollen records such as the genera Helicostilys and Cecropia and/or very abundant in the region such as Pourouma and Pouteria. The origin of extra-Amazonian plant material is unknown, but they belong to genera of predominantly wind-pollinated angiosperm families such as Poaceae and Betulaceae. Finally, the detection of two bryophyte genera feeds the debate about the role of long distance dispersal in the distribution of these plants.
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Macher JN, Wideman JG, Girard EB, Langerak A, Duijm E, Jompa J, Sadekov A, Vos R, Wissels R, Renema W. First report of mitochondrial COI in foraminifera and implications for DNA barcoding. Sci Rep 2021; 11:22165. [PMID: 34772985 PMCID: PMC8589990 DOI: 10.1038/s41598-021-01589-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/28/2021] [Indexed: 01/04/2023] Open
Abstract
Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in many marine environments and play a major role in global carbon cycling. Species recognition in Foraminifera is mainly based on morphological characters and nuclear 18S ribosomal RNA barcoding. The 18S rRNA contains variable sequence regions that allow for the identification of most foraminiferal species. Still, some species show limited variability, while others contain high levels of intragenomic polymorphisms, thereby complicating species identification. The use of additional, easily obtainable molecular markers other than 18S rRNA will enable more detailed investigation of evolutionary history, population genetics and speciation in Foraminifera. Here we present the first mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences ("barcodes") of Foraminifera. We applied shotgun sequencing to single foraminiferal specimens, assembled COI, and developed primers that allow amplification of COI in a wide range of foraminiferal species. We obtained COI sequences of 49 specimens from 17 species from the orders Rotaliida and Miliolida. Phylogenetic analysis showed that the COI tree is largely congruent with previously published 18S rRNA phylogenies. Furthermore, species delimitation with ASAP and ABGD algorithms showed that foraminiferal species can be identified based on COI barcodes.
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Affiliation(s)
- Jan-Niklas Macher
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands.
| | - Jeremy G Wideman
- Biodesign Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Elsa B Girard
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Anouk Langerak
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | - Elza Duijm
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | | | - Aleksey Sadekov
- ARC Centre of Excellence for Coral Reef Studies, Ocean Graduate School, The University of Western Australia, Crawley, Australia
| | - Rutger Vos
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Richard Wissels
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | - Willem Renema
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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Macher JN, Kayal E, Duijm E, van der Hoorn B, Montano S, Speksnijder A. The mitochondrial genome of Nemalecium lighti (Hydrozoa, Leptothecata). Mitochondrial DNA B Resour 2021; 6:3196-3198. [PMID: 34660901 PMCID: PMC8519520 DOI: 10.1080/23802359.2021.1989335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The hydrozoan species Nemalecium lighti (Hargitt, 1924) is widely distributed in tropical marine waters around the world. Here we report the complete linear mitochondrial genome of N. lighti from Sint Eustatius (Lesser Antilles). The mitochondrial genome with a length of 14,320 bp encodes for 13 protein-coding genes, two tRNA genes, and two rRNA genes. Gene arrangement differs from that found in other species of the same taxonomic order and a phylogenetic analysis shows that based on mitochondrial genes, N. lighti clusters outside of the Leptothecata, rendering the order paraphyletic.
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Affiliation(s)
- Jan-Niklas Macher
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | - Ehsan Kayal
- Université de Caen Normandie, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Caen, France
| | - Elza Duijm
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | - Berry van der Hoorn
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands.,Inholland University of Applied Sciences, Delft, The Netherlands
| | - Simone Montano
- University of Milano-Bicocca, Department of Earth and Environmental Sciences (DISAT), Milano, Italy
| | - Arjen Speksnijder
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands.,University of Applied Sciences Leiden, Leiden, The Netherlands
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Wall-Palmer D, Mekkes L, Ramos-Silva P, Dämmer LK, Goetze E, Bakker K, Duijm E, Peijnenburg KTCA. The impacts of past, present and future ocean chemistry on predatory planktonic snails. R Soc Open Sci 2021; 8:202265. [PMID: 34386247 PMCID: PMC8334855 DOI: 10.1098/rsos.202265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
The atlantid heteropods represent the only predatory, aragonite shelled zooplankton. Atlantid shell production is likely to be sensitive to ocean acidification (OA), and yet we know little about their mechanisms of calcification, or their response to changing ocean chemistry. Here, we present the first study into calcification and gene expression effects of short-term OA exposure on juvenile atlantids across three pH scenarios: mid-1960s, ambient and 2050 conditions. Calcification and gene expression indicate a distinct response to each treatment. Shell extension and shell volume were reduced from the mid-1960s to ambient conditions, suggesting that calcification is already limited in today's South Atlantic. However, shell extension increased from ambient to 2050 conditions. Genes involved in protein synthesis were consistently upregulated, whereas genes involved in organismal development were downregulated with decreasing pH. Biomineralization genes were upregulated in the mid-1960s and 2050 conditions, suggesting that any deviation from ambient carbonate chemistry causes stress, resulting in rapid shell growth. We conclude that atlantid calcification is likely to be negatively affected by future OA. However, we also found that plentiful food increased shell extension and shell thickness, and so synergistic factors are likely to impact the resilience of atlantids in an acidifying ocean.
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Affiliation(s)
- Deborah Wall-Palmer
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Lisette Mekkes
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Paula Ramos-Silva
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Linda K. Dämmer
- Department of Ocean Systems, Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands
- Environmental Geology, Department of Geology, Institute of Geosciences, University of Bonn, Bonn, Germany
| | - Erica Goetze
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Karel Bakker
- Department of Ocean Systems, Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands
| | - Elza Duijm
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Katja T. C. A. Peijnenburg
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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7
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Gomes SIF, van Bodegom PM, van Agtmaal M, Soudzilovskaia NA, Bestman M, Duijm E, Speksnijder A, van Eekeren N. Microbiota in Dung and Milk Differ Between Organic and Conventional Dairy Farms. Front Microbiol 2020; 11:1746. [PMID: 32849375 PMCID: PMC7399162 DOI: 10.3389/fmicb.2020.01746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 07/03/2020] [Indexed: 12/29/2022] Open
Abstract
Organic farming is increasingly promoted as a means to reduce the environmental impact of artificial fertilizers, pesticides, herbicides, and antibiotics in conventional dairy systems. These factors potentially affect the microbial communities of the production stages (soil, silage, dung, and milk) of the entire farm cycle. However, understanding whether the microbiota representative of different production stages reflects different agricultural practices - such as conventional versus organic farming - is unknown. Furthermore, the translocation of the microbial community across production stages is scarcely studied. We sequenced the microbial communities of soil, silage, dung, and milk samples from organic and conventional dairy farms in the Netherlands. We found that community structure of soil fungi and bacteria significantly differed among soil types, but not between organic versus conventional farming systems. The microbial communities of silage also did not differ among conventional and organic systems. Nevertheless, the dung microbiota of cows and the fungal communities in the milk were significantly structured by agricultural practice. We conclude that, while the production stages of dairy farms seem to be disconnected in terms of microbial transfer, certain practices specific for each agricultural system, such as the content of diet and the use of antibiotics, are potential drivers of shifts in the cow's microbiota, including the milk produced. This may reflect differences in farm animal health and quality of dairy products depending on farming practices.
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Affiliation(s)
- Sofia I F Gomes
- Institute of Environmental Sciences, Leiden University, Leiden, Netherlands
| | | | | | | | | | - Elza Duijm
- Naturalis Biodiversity Center, Leiden, Netherlands
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8
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Affiliation(s)
| | - E. Duijm
- Naturalis Biodiversity Center, Leiden, The Netherlands
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9
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Groenenberg DSJ, Harl J, Duijm E, Gittenberger E. The complete mitogenome of Orcula dolium (Draparnaud, 1801); ultra-deep sequencing from a single long-range PCR using the Ion-Torrent PGM. Hereditas 2017; 154:7. [PMID: 28396619 PMCID: PMC5379511 DOI: 10.1186/s41065-017-0028-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/23/2017] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND With the increasing capacity of present-day next-generation sequencers the field of mitogenomics is rapidly changing. Enrichment of the mitochondrial fraction, is no longer necessary for obtaining mitogenomic data. Despite the benefits, shotgun sequencing approaches also have disadvantages. They do not guarantee obtaining the complete mitogenome, generally require larger amounts of input DNA and coverage is low compared to sequencing with enrichment strategies. If the mitogenome could be amplified in a single amplification, additional time and costs for sample preparation might outweigh these disadvantages. RESULTS A sequence of the complete mitochondrial genome of the pupilloid landsnail Orcula dolium is presented. The mitogenome was amplified in a single long-range (LR) PCR and sequenced on an Ion Torrent PGM (Life Technologies). The length is 14,063 nt and the average depth of coverage is 1112 X. This is the first published mitogenome for a member of the family Orculidae. It has the typical metazoan makeup of 13 protein coding genes (PCGs), 2 ribosomal RNAs (12S and 16S) and 22 transfer RNAs (tRNAs). Orcula is positioned between Pupilla and the Vertiginidae as the sister-group of Gastrocopta and Vertigo, together. An ancestral gene order reconstruction shows that Orthurethra in contrast to other Stylommatophora, have tRNA-H before tRNA-G and that the gene order in the 'non-achatinoid' clade is identical to that of closely related non-stylommatophoran taxa. CONCLUSIONS We show it is feasible to ultra-deep sequence a mitogenome from a single LR-PCR. This approach is particularly relevant to studies that have low concentrations of input DNA. It results in a more efficient use of NGS capacity (only the targeted fraction is sequenced) and is an effective selection against nuclear mitochondrial inserts (NUMTS). In contrast to previous studies based in particular on 28S, our results indicate that phylogeny reconstructions based on complete mitogenomes might be more suitable to resolve deep relationships within Stylommatophora. Ancestral gene order reconstructions reveal rearrangements that characterize systematic groups.
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Affiliation(s)
| | - J. Harl
- Central Research Laboratories, Museum of Natural History Vienna, Vienna, Austria
- Department of Biology, Shinshu University, Matsumoto, Japan
| | - E. Duijm
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - E. Gittenberger
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
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Voelker G, Tobler M, Prestridge HL, Duijm E, Groenenberg D, Hutchinson MR, Martin AD, Nieman A, Roselaar CS, Huntley JW. Three new species of Stiphrornis (Aves: Muscicapidae) from the Afro-tropics, with a molecular phylogenetic assessment of the genus. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1226978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Gary Voelker
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Heather L. Prestridge
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Elza Duijm
- Naturalis Biodiversity Center, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Dick Groenenberg
- Naturalis Biodiversity Center, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Mark R. Hutchinson
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Alyssa D. Martin
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Aline Nieman
- Naturalis Biodiversity Center, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Cees S. Roselaar
- Naturalis Biodiversity Center, Vertebrate Department, PO Box 9517, 2300 RA Leiden, the Netherlands
| | - Jerry W. Huntley
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
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Wielstra B, Duijm E, Lagler P, Lammers Y, Meilink WRM, Ziermann JM, Arntzen JW. Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform. Mol Ecol Resour 2014; 14:1080-9. [PMID: 24571307 PMCID: PMC4285185 DOI: 10.1111/1755-0998.12242] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/15/2014] [Accepted: 02/19/2014] [Indexed: 11/28/2022]
Abstract
Next-generation sequencing is a fast and cost-effective way to obtain sequence data for nonmodel organisms for many markers and for many individuals. We describe a protocol through which we obtain orthologous markers for the crested newts (Amphibia: Salamandridae: Triturus), suitable for analysis of interspecific hybridization. We use transcriptome data of a single Triturus species and design 96 primer pairs that amplify c. 180 bp fragments positioned in 3-prime untranslated regions. Next, these markers are tested with uniplex PCR for a set of species spanning the taxonomical width of the genus Triturus. The 52 markers that consistently show a single band of expected length at gel electrophoreses for all tested crested newt species are then amplified in five multiplex PCRs (with a plexity of ten or eleven) for 132 individual newts: a set of 84 representing the seven (candidate) species and a set of 48 from a presumed hybrid population. After pooling multiplexes per individual, unique tags are ligated to link amplicons to individuals. Subsequently, individuals are pooled equimolar and sequenced on the Ion Torrent next-generation sequencing platform. A bioinformatics pipeline identifies the alleles and recodes these to a genotypic format. Next, we test the utility of our markers. baps allocates the 84 crested newt individuals representing (candidate) species to their expected (candidate) species, confirming the markers are suitable for species delineation. newhybrids, a hybrid index and hiest confirm the 48 individuals from the presumed hybrid population to be genetically admixed, illustrating the potential of the markers to identify interspecific hybridization. We expect the set of markers we designed to provide a high resolving power for analysis of hybridization in Triturus.
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Affiliation(s)
- B Wielstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300, RA Leiden, The Netherlands; Department of Animal and Plant Sciences, University of Sheffield, S10 2TN, Sheffield, UK
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Gravendeel L, Kouwenhoven M, Gevaert O, de Rooi J, Stubbs A, Duijm E, Daemen A, Bleeker F, Bralten L, Kloosterhof N, de Moor B, Eilers P, van der Spek P, Kros JM, Smitt PS, van den Bent M, French P. Abstract 808: Intrinsic gene expression profiles of gliomas are a better predictor of survival than histology. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Gliomas are the most common primary brain tumors with heterogeneous morphology and variable prognosis. Treatment decisions in patients rely mainly on histological classification and clinical parameters. However, differences between histological subclasses and grades are subtle, and classifying gliomas is subject to a large inter-observer variability. To improve current classification standards, we have performed gene expression profiling on a large cohort of glioma samples of all histological subtypes and grades. We identified seven distinct molecular subgroups that correlate with survival. These include two favorable prognostic subgroups (median survival >4.7 years), two with intermediate prognosis (median survival 1-4 years), two with poor prognosis (median survival <1 year), and one control group. The intrinsic molecular subtypes of glioma are different from histological subgroups and correlate better to patient survival. The prognostic value of molecular subgroups was validated on five independent sample cohorts (TCGA, REMBRANDT, GSE12907, GSE4271, and Li et al.). The power of intrinsic subtyping is demonstrated by its ability to identify a subset of prognostically favorable tumors within an external dataset that contains only histologically confirmed glioblastomas. Specific genetic changes (EGFR amplification, IDH1 mutation, 1p/19q LOH) segregate in distinct molecular subgroups. We identified a subgroup with molecular features associated with secondary glioblastoma, suggesting that different genetic changes drive gene expression profiles. Finally, we assessed response to treatment in molecular subgroups. Our data provides compelling evidence that expression profiling is a more accurate and objective method to classify gliomas than histological classification. Molecular classification therefore may aid diagnosis and can guide clinical decision making.
Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 808.
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French PJ, Peeters J, Horsman S, Duijm E, Siccama I, van den Bent MJ, Luider TM, Kros JM, van der Spek P, Sillevis Smitt PA. Identification of differentially regulated splice variants and novel exons in glial brain tumors using exon expression arrays. Cancer Res 2007; 67:5635-42. [PMID: 17575129 DOI: 10.1158/0008-5472.can-06-2869] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Aberrant splice variants are involved in the initiation and/or progression of glial brain tumors. We therefore set out to identify splice variants that are differentially expressed between histologic subgroups of gliomas. Splice variants were identified using a novel platform that profiles the expression of virtually all known and predicted exons present in the human genome. Exon-level expression profiling was done on 26 glioblastomas, 22 oligodendrogliomas, and 6 control brain samples. Our results show that Human Exon arrays can identify subgroups of gliomas based on their histologic appearance and genetic aberrations. We next used our expression data to identify differentially expressed splice variants. In two independent approaches, we identified 49 and up to 459 exons that are differentially spliced between glioblastomas and oligodendrogliomas, a subset of which (47% and 33%) were confirmed by reverse transcription-PCR (RT-PCR). In addition, exon level expression profiling also identified >700 novel exons. Expression of approximately 67% of these candidate novel exons was confirmed by RT-PCR. Our results indicate that exon level expression profiling can be used to molecularly classify brain tumor subgroups, can identify differentially regulated splice variants, and can identify novel exons. The splice variants identified by exon level expression profiling may help to detect the genetic changes that cause or maintain gliomas and may serve as novel treatment targets.
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Affiliation(s)
- Pim J French
- Department of Neurology, Erasmus MC, Rotterdam, the Netherlands.
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Schutte M, Elstrodt F, Bralten LBC, Nagel JHA, Duijm E, Hollestelle A, Vuerhard MJ, Wasielewski M, Peeters JK, van der Spek P, Sillevis Smitt PA, French PJ. Exon expression arrays as a tool to identify new cancer genes. PLoS One 2007; 3:e3007. [PMID: 18688287 PMCID: PMC2500185 DOI: 10.1371/journal.pone.0003007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Accepted: 07/31/2008] [Indexed: 12/12/2022] Open
Abstract
Background Identification of genes that are causally implicated in oncogenesis is a major goal in cancer research. An estimated 10–20% of cancer-related gene mutations result in skipping of one or more exons in the encoded transcripts. Here we report on a strategy to screen in a global fashion for such exon-skipping events using PAttern based Correlation (PAC). The PAC algorithm has been used previously to identify differentially expressed splice variants between two predefined subgroups. As genetic changes in cancer are sample specific, we tested the ability of PAC to identify aberrantly expressed exons in single samples. Principal Findings As a proof-of-principle, we tested the PAC strategy on human cancer samples of which the complete coding sequence of eight cancer genes had been screened for mutations. PAC detected all seven exon-skipping mutants among 12 cancer cell lines. PAC also identified exon-skipping mutants in clinical cancer specimens although detection was compromised due to heterogeneous (wild-type) transcript expression. PAC reduced the number of candidate genes/exons for subsequent mutational analysis by two to three orders of magnitude and had a substantial true positive rate. Importantly, of 112 randomly selected outlier exons, sequence analysis identified two novel exon skipping events, two novel base changes and 21 previously reported base changes (SNPs). Conclusions The ability of PAC to enrich for mutated transcripts and to identify known and novel genetic changes confirms its suitability as a strategy to identify candidate cancer genes.
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Affiliation(s)
- Mieke Schutte
- Department of Medical Oncology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- * E-mail: (MS); (PF)
| | - Fons Elstrodt
- Department of Medical Oncology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Linda B. C. Bralten
- Department of Neurology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jord H. A. Nagel
- Department of Medical Oncology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Elza Duijm
- Department of Neurology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Antoinette Hollestelle
- Department of Medical Oncology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Maartje J. Vuerhard
- Department of Neurology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marijke Wasielewski
- Department of Medical Oncology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Justine K. Peeters
- Department of Bioinformatics, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Peter van der Spek
- Department of Bioinformatics, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Peter A. Sillevis Smitt
- Department of Neurology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Pim J. French
- Department of Neurology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- * E-mail: (MS); (PF)
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