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Abstract
The analysis of transcriptome data from non-model organisms contributes to our understanding of diverse aspects of evolutionary biology, including developmental processes, speciation, adaptation, and extinction. Underlying this diversity is one shared feature, the generation of enormous amounts of sequence data. Data availability requirements in most journals oblige researchers to make their raw transcriptome data publicly available, and the databases housed at the National Center for Biotechnology Information (NCBI) are a popular choice for data deposition. Unfortunately, the successful submission of raw sequences to the Sequence Read Archive (SRA) and transcriptome assemblies to the Transcriptome Shotgun Assembly (TSA) can be challenging for novice users, significantly delaying data availability and publication. Here we present two comprehensive protocols for submitting RNA-Seq data to NCBI databases, accompanied by an easy-to-use website that facilitates the timely submission of data by researchers of any experience level. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Wiebke Feindt
- ITZ, Division of Ecology and Evolution, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Sara J Oppenheim
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
| | - Robert DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
| | - Shaadi Mehr
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York.,Multiple Myeloma Research Foundation, Norwalk, Connecticut
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Oppenheim SJ, Feindt W, DeSalle R, Goldstein PZ. De Novo characterization of transcriptomes from two North American Papaipema stem-borers (Lepidoptera: Noctuidae). PLoS One 2018; 13:e0191061. [PMID: 29364900 PMCID: PMC5783364 DOI: 10.1371/journal.pone.0191061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 12/27/2017] [Indexed: 11/19/2022] Open
Abstract
Stem-borers in the genus Papaipema (Lepidoptera: Noctuidae) range from highly polyphagous agricultural pests to specialists on more than 20 families of flowering plants, many of them highly toxic. Papaipema is the largest genus of noctuids endemic to North America and provides an excellent study system for the evolution of noctuid host plant use. To improve the availability of genomic resources for such investigations, we performed de novo transcriptome sequencing and assembly for two specialist Papaipema with unusual larval hosts: P. speciosissima, which is associated with ferns, and the undescribed P. “sp. 4,” which is associated with bamboo. The resulting transcriptomes were similar in terms of completeness, gene count, and gene identity, but we identified some 8,000 genes (~17% of each transcriptome) not shared between the two species. While some of these have identifiable orthologs in other Lepidoptera, ~5% of each transcriptome consists of species-specific genes. We examine the function of these genes and find that almost half have retrotransposon-related functional domains. The potential role of species-specific genes is discussed, and the expansion of certain retrotransposon families in Papaipema is examined.
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Affiliation(s)
- Sara J. Oppenheim
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- * E-mail:
| | - Wiebke Feindt
- Stiftung Tierärztliche Hochschule Hannover, ITZ, Division of Ecology and Evolution, Hannover, Germany
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Paul Z. Goldstein
- Systematic Entomology Laboratory, USDA, National Museum of Natural History, Washington DC, United States of America
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Feindt W, Oppenheim SJ, DeSalle R, Goldstein PZ, Hadrys H. Transcriptome profiling with focus on potential key genes for wing development and evolution in Megaloprepus caerulatus, the damselfly species with the world's largest wings. PLoS One 2018; 13:e0189898. [PMID: 29329292 PMCID: PMC5766104 DOI: 10.1371/journal.pone.0189898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/04/2017] [Indexed: 11/20/2022] Open
Abstract
The evolution, development and coloration of insect wings remains a puzzling subject in evolutionary research. In basal flying insects such as Odonata, genomic research regarding bauplan evolution is still rare. Here we focus on the world's largest odonate species-the "forest giant" Megaloprepus caerulatus, to explore its potential for looking deeper into the development and evolution of wings. A recently discovered cryptic species complex in this genus previously considered monotypic is characterized by morphological differences in wing shape and color patterns. As a first step toward understanding wing pattern divergence and pathways involved in adaptation and speciation at the genomic level, we present a transcriptome profiling of M. caerulatus using RNA-Seq and compare these data with two other odonate species. The de novo transcriptome assembly consists of 61,560 high quality transcripts and is approximately 93% complete. For almost 75% of the identified transcripts a possible function could be assigned: 48,104 transcripts had a hit to an InterPro protein family or domain, and 28,653 were mapped to a Gene Ontology term. In particular, we focused on genes related to wing development and coloration. The comparison with two other species revealed larva-specific genes and a conserved 'core' set of over 8,000 genes forming orthologous clusters with Ischnura elegans and Ladona fulva. This transcriptome may provide a first point of reference for future research in odonates addressing questions surrounding the evolution of wing development, wing coloration and their role in speciation.
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Affiliation(s)
- Wiebke Feindt
- University of Veterinary Medicine Hannover, ITZ—Division of Ecology and Evolution, Hannover, Germany
- Leibniz University Hannover, Hannover, Germany
| | - Sara J. Oppenheim
- American Museum of Natural History, Sackler Institute for Comparative Genomics, New York, NY, United States of America
| | - Robert DeSalle
- American Museum of Natural History, Sackler Institute for Comparative Genomics, New York, NY, United States of America
| | - Paul Z. Goldstein
- Systematic Entomology Laboratory (USDA-ARS), National Museum of Natural History, Washington, DC, United States of America
| | - Heike Hadrys
- University of Veterinary Medicine Hannover, ITZ—Division of Ecology and Evolution, Hannover, Germany
- American Museum of Natural History, Sackler Institute for Comparative Genomics, New York, NY, United States of America
- Yale University, Department of Ecology & Evolutionary Biology, New Haven, Connecticut, United States of America
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Herzog R, Osigus H, Feindt W, Schierwater B, Hadrys H. The complete mitochondrial genome of the emperor dragonfly Anax imperator LEACH, 1815 (Odonata : Aeshnidae) via NGS sequencing. Mitochondrial DNA B Resour 2016; 1:783-786. [PMID: 33473626 PMCID: PMC7799497 DOI: 10.1080/23802359.2016.1186523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 05/03/2016] [Accepted: 05/03/2016] [Indexed: 11/05/2022] Open
Abstract
Here we report the complete mitochondrial genome of the emperor dragonfly, Anax imperator (Odonata: Aeshnidae) as the first of its genus. Data were generated via next generation sequencing (NGS) and assembled using an iterative approach. The typical metazoan set of 37 genes (13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes) was detected in the same gene order as in other odonate mitogenomes. However, only three intergenic spacer regions are present in A. imperator lacking the distinct s5 spacer, which was regarded as informative feature of the odonate suborder Anisoptera (dragonflies) but absent in Zygoptera (damselflies). With 16,087 bp, it is the longest anisopteran mitogenome to date, mainly due to the long A + T-rich control region of 1291 bp.
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Affiliation(s)
- Rebecca Herzog
- Division of Ecology and Evolution, ITZ, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Hans − Jürgen Osigus
- Division of Ecology and Evolution, ITZ, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Wiebke Feindt
- Division of Ecology and Evolution, ITZ, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Bernd Schierwater
- Division of Ecology and Evolution, ITZ, University of Veterinary Medicine Hannover, Hannover, Germany
- EEB, Yale University, New Haven, CT, USA
| | - Heike Hadrys
- Division of Ecology and Evolution, ITZ, University of Veterinary Medicine Hannover, Hannover, Germany
- EEB, Yale University, New Haven, CT, USA
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Feindt W, Herzog R, Osigus HJ, Schierwater B, Hadrys H. Short read sequencing assembly revealed the complete mitochondrial genome of Ischnura elegans Vander Linden, 1820 (Odonata: Zygoptera). Mitochondrial DNA B Resour 2016; 1:574-576. [PMID: 33473559 PMCID: PMC7800176 DOI: 10.1080/23802359.2016.1192510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 05/11/2016] [Accepted: 05/18/2016] [Indexed: 11/23/2022] Open
Abstract
Damselflies of the genus Ischnura emerge as organisms with high potential in ecological, evolutionary and developmental research at the base of flying insects. Ischnura elegans and Ischnura hastata are for example one of the few odonate species where a complete life cycle over generations can be reared under laboratory conditions. We here report the complete mitochondrial genome of Ischnura elegans as a valuable genomic resource for future eco-evo-devo studies at the base of flying insects. The genome has a total length of 15,962 bp and displays all typical features of Odonata (dragonflies and damselflies) mitochondrial genomes in gene content and order as well as A + T content. Start and stop codons of all protein-coding genes are consistent. Most interestingly, we found four intergenic spacer regions and a long A + T rich (control) region of 1196 bp, which is almost double the size of the close relative Ischnura pumilio. We assume that the adequate insert size and iterative mapping may be more efficient in assembling this duplicated and repetitive region.
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Affiliation(s)
- Wiebke Feindt
- ITZ – Forschungsstätte ‘Alter Bahnhof Schapen’ Braunschweig, University of Veterinary Medicine Hannover, Hannover/Braunschweig, Germany
| | - Rebecca Herzog
- ITZ – Forschungsstätte ‘Alter Bahnhof Schapen’ Braunschweig, University of Veterinary Medicine Hannover, Hannover/Braunschweig, Germany
| | - Hans-Jürgen Osigus
- ITZ – Forschungsstätte ‘Alter Bahnhof Schapen’ Braunschweig, University of Veterinary Medicine Hannover, Hannover/Braunschweig, Germany
| | - Bernd Schierwater
- ITZ – Forschungsstätte ‘Alter Bahnhof Schapen’ Braunschweig, University of Veterinary Medicine Hannover, Hannover/Braunschweig, Germany
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Heike Hadrys
- ITZ – Forschungsstätte ‘Alter Bahnhof Schapen’ Braunschweig, University of Veterinary Medicine Hannover, Hannover/Braunschweig, Germany
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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Feindt W, Osigus HJ, Herzog R, Mason CE, Hadrys H. The complete mitochondrial genome of the neotropical helicopter damselfly Megaloprepus caerulatus (Odonata: Zygoptera) assembled from next generation sequencing data. Mitochondrial DNA B Resour 2016; 1:497-499. [PMID: 33473533 PMCID: PMC7800115 DOI: 10.1080/23802359.2016.1192504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 05/03/2016] [Revised: 05/03/2016] [Accepted: 05/18/2016] [Indexed: 11/23/2022] Open
Abstract
Odonata (dragonflies and damselflies) is a small order at the base of flying insects (Pterygota). Resolving family-level phylogenetic relationships within this order receives great attention. Hereby, genetic data already resulted in various changes, which are however still under discussion. Mitochondrial genomes may further enhance such phylogenies. This study presents the complete mitochondrial genome of the Neotropical damselfly Megaloprepus caerulatus based on next generation sequencing (NGS) data on total genomic DNA. The total length comprises 16,094 bp and includes the standard metazoan set of 37 genes together with a 1376 bp long A + T rich (control) region. Gene content, gene arrangement and base frequency are consistent with other odonate mitochondrial genomes. It further contains four intergenic spacer regions, indicating a possible family specific feature for the Coenagrionidae and its close relatives.
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Affiliation(s)
- Wiebke Feindt
- ITZ, Division of Ecology and Evolution, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Hans-Jürgen Osigus
- ITZ, Division of Ecology and Evolution, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Rebecca Herzog
- ITZ, Division of Ecology and Evolution, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Christopher E. Mason
- The Department of Physiology and Biophysics, The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY, USA
| | - Heike Hadrys
- ITZ, Division of Ecology and Evolution, University of Veterinary Medicine Hannover, Hannover, Germany
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
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Feindt W, Fincke O, Hadrys H. Still a one species genus? Strong genetic diversification in the world’s largest living odonate, the Neotropical damselfly Megaloprepus caerulatus. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0554-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Neisel F, von Manikowsky S, Schümann M, Feindt W, Hoppe HW, Melchiors U. [Human biomonitoring of polychlorinated biphenyls in 130 exposed elementary school children]. Gesundheitswesen 1999; 61:137-49. [PMID: 10226386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
In the classroom air on a primary school polychlorinated biphenyls were present in a wide range extending to 10.220 ng/cbm; in a side room even 19.550 ng/cbm were measured. The school was closed down, a flame retardant paint was detected to be the main source of this contamination. 130 differently exposed persons gave blood specimens for measurement of PCB concentrations. Compared with a comparative reference collective of equal age reported by the analysing laboratory, the PCB blood concentrations of 92 actual pupils were even lower. A comparison with five near-representative child collectives of South Germany did not show any obvious difference. The reference values of the German Human Biomonitoring Commission were exceeded by 4 of 92 pupils for PCB 138, by 6 pupils for PCB 153 and by 6 pupils for PCB 180. In a group of 9 teachers and 1 cleaning person the median values of reference collectives of equal age reported by the analysing laboratory were exceeded by 8 persons for PCB 138, 7 persons for PCB 153 and 8 persons for PCB 180. The 95. Percentiles of these reference collectives and the reference values of the German Human Biomonitoring Commission were not exceeded. In bivariate and multiple regression analyses the data of 92 actual pupils showed positive associations between blood levels of PCB and age as well as nursing period, a negative association between PCB blood concentrations and body-mass index and a weak influence by gender (boys had lower blood concentrations). In addition, the results of multiple regression analyses showed (with the exception of the analyses of PCB 180 without controlling for gender) a significant influence of PCB concentrations in indoor air on PCB blood concentrations. This association could not be detected in bivariate analyses, and in comparison to the mentioned main influence variables it was obviously weaker. But basing on the results of the multiple regression analyses one can calculate an increase of PCB blood concentration by 3% multiplicatively if PCB indoor concentrations increase by 1000 ng/cbm.
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Affiliation(s)
- F Neisel
- Niedersächsisches Landesgesundheitsamt, Hannover
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Feindt W. Röntgenologischer Nachweis eines partiellen Sekretionsausfalles der Niere bei Harnleiterkonkrement und gedoppelter Ureterenanlage. ROFO-FORTSCHR RONTG 1950. [DOI: 10.1055/s-0029-1231741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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