Ole Seberg

Ole Seberg
University of Copenhagen · Natural History Museum of Denmark

Ph. D., Dr. Science

About

202
Publications
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Publications

Publications (202)
Article
Full-text available
The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the ‘plant island syndrome’, include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractylo...
Article
Full-text available
Open access to sequence data is a cornerstone of biology and biodiversity research, but has created tension under the United Nations Convention on Biological Diversity (CBD). Policy decisions could compromise research and development, unless a practical multilateral solution is implemented. Ensuring international benefit-sharing from sequence data...
Article
Full-text available
Mistletoes (Viscum) and close relatives are unique among flowering plants in having a drastically altered electron transport chain. Lack of complex I genes has previously been reported for the mitochondrial genome, and here we report an almost complete absence of nuclear-encoded complex I genes in the transcriptome of Viscum album. Compared to Arab...
Preprint
Full-text available
The profound absence of mitochondrial complex I (NADH-ubiquinone oxidoreductase) genes from the mitogenome of Viscum spp. and the rapid rates of molecular evolution characterizing most of their remaining mitochondrial genes raise questions regarding the possible transfer of the entire nad gene set to the nucleus, as well as for the functionality of...
Article
A phylogenetic hypothesis for the genus Dendrochilum s.l. (including Bracisepalum) is based on nucleotide sequences of the nuclear ribosomal ITS and two plastid regions (matK, ycf1). The trees based on parsimony analysis of the nrITS and plastid partitions, respectively, are largely congruent, the only strongly supported conflict being the exact po...
Article
Full-text available
Background Parasitic plants rely on their host to cover their nutritional requirements either for their entire life or a smaller part of it. Depending on the level of parasitism, a proportional reduction on the plastid genome has been found. However, knowledge on gene loss and evolution of the mitogenome of parasitic plants is only available for fo...
Article
Full-text available
European natural history collections are a critical infrastructure for meeting the most important challenge humans face over the next 30 years – creating a sustainable future for ourselves and the natural systems on which we depend – and for answering fundamental scientific questions about ecological, evolutionary, and geological processes. Since 2...
Article
Full-text available
The aim of the Global Genome Biodiversity Network (GGBN, http://www.ggbn.org) is to foster collaboration among biodiversity biobanks on a global scale in order to further compliance with standards, best practices, and to secure interoperability and exchange of material in accordance with national and international legislation and conventions. Thus,...
Article
Full-text available
The variety of molecular methods used to analyze biosamples is continuously increasing, as is the need for the standardized deposition, documentation and citation of both the samples as well as the methods applied to them. Global initiatives such as the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), Barcode...
Article
Full-text available
Genomic science is revolutionizing and accelerating biodiversity research. For collections-based institutions to continue to lead and support biodiversity research, they must adapt to this new reality. Simultaneously, “big data” is accumulating so rapidly that we have unprecedented capacity to plan strategically to use genomics to advance basic and...
Article
Full-text available
GGBN, the Global Genome Biodiversity Network, is a consortium of virtually linked biodiversity biobanks that provide unified open access to their sample data through a web portal (www.ggbn.org), together improve best practices and develop standards. Since its inception in 2011, GGBN has largely been supported by external grants and in-kind support...
Article
Full-text available
Most successful research programs depend on easily accessible and standardized research infrastructures. Until recently, access to tissue or DNA samples with standardized metadata and of a sufficiently high quality, has been a major bottleneck for genomic research. The Global Geonome Biodiversity Network (GGBN) fills this critical gap by offering s...
Article
Full-text available
With a reduced need for photosynthesis the plastome of parasitic and mycoheterotrophic plants degrades. In the tiny, fully mycoheterotrophic plant Sciaphila thaidanica we find one of the smallest plastomes yet encountered. Its size is just 12,780 bp and it contains only 20 potentially functional housekeeping genes. Thus S. thaidanica fits the propo...
Article
Using the "Seidenfaden collection" in Copenhagen as an example, we address the common view that botanical garden collections of orchids are important for conservation. Seidenfaden collected live orchids all over Thailand from 1957 to 1983 and created a traditional collection for taxonomic research, characterized by high taxonomic diversity and low...
Article
Full-text available
Higher phytase activity in food and feedstuffs is desirable in order to counter the antinutritional effects of phytate. The most promising platform where this might be achieved through plant breeding is wheat and its Triticeae relatives. They already accumulate notable amounts of phytase in the grains and higher expression of the responsible PAPhy_...
Article
Full-text available
The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mit...
Data
Sequence reads and coverage. Total number of reads from 454 and Illumina sequencing, number of reads mapped to the mitogenomes and mean coverage of reads. (DOCX)
Data
Gene content in mitogenomes of five representatives of Alismatales. The length of coding sequences in kb. Z = Zostera. Ψ = pseudogene or fragment. CP = tRNA gene located in region of plastid origin. (DOCX)
Data
Inserts of plastid origin in the mitogenomes of Stratiotes aloides, Butomus umbellatus and Zostera marina. (DOCX)
Data
Similarity and phylogenetic relationship of plastid gene fragments located in mitochondrial genomes of Butomus umbellatus, Zostera marina and Stratiotes aloides. BLASTN and phylogenetic analyses are done using matrices from Ross et al. [23] including ca. 150 taxa mostly from the Alismatales. (DOCX)
Data
Reference mitogenome and plastome sequences from GenBank. = indicates that the same species was used. (DOCX)
Data
Sequence similarity between the mitochondrial and nuclear genome of Zostera marina. (DOCX)
Data
Repeated sequence in Stratiotes aloides and Zostera marina. (DOCX)
Article
Full-text available
Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs t...
Article
Full-text available
Loss of introns in plant mitochondrial genes is commonly explained by retroprocessing. Under this model, an mRNA is reverse transcribed and integrated back into the genome, simultaneously affecting the contents of introns and edited sites. To evaluate the extent to which retroprocessing explains intron loss, we analyzed patterns of intron content a...
Article
Background: Genomic research depends upon access to DNA or tissue collected and preserved according to high-quality standards. At present, the collections in most natural history museums do not sufficiently address these standards, making them often hard or impossible to use for whole-genome sequencing or transcriptomics. In response to these chal...
Article
Full-text available
Parasitism is a successful survival strategy across all kingdoms and has evolved repeatedly in angiosperms. Parasitic plants obtain nutrients from other plants and some are agricultural pests. Obligate parasites, which cannot complete their lifecycle without a host, may lack functional photosystems (holoparasites), or have retained photosynthesis (...
Article
Past phylogenetic studies of the monocot order Alismatales left several higher-order relationships unresolved. We addressed these uncertainties using a nearly complete genus-level sampling of whole plastid genomes (gene sets representing 83 protein-coding and ribosomal genes) from members of the core alismatid families, Tofieldiaceae and additional...
Article
Full-text available
Santalales is an order of plants consisting almost entirely of parasites. Some, like Osyris, are facultative root parasites whereas others, like Viscum, are obligate stem parasitic mistletoes. Here, we report the complete plastome sequences of one species of Osyris and three species of Viscum, and we investigate the evolutionary aspects of structur...
Article
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The global herbal products market has grown in recent years, making regulation of these products paramount for public healthcare. For instance, the common horsetail (Equisetum arvense L.) is used in numerous herbal products, but it can be adulterated with closely related species, especially E. palustre L. that can produce toxic alkaloids. As morpho...
Article
A phylogenetic analysis of the early branching lineages of the monocotyledons is performed using data from two plastid genes (rbcL and matK), five mitochondrial genes (atp1, ccmB, cob, mttB and nad5) and morphology. The complete matrix includes 93 terminals representing Acorus, the 14 families currently recognized within Alismatales, and numerous l...
Article
"An overview of 31 previously published papers with a Danish summary" Incluye bibliografía
Article
Full-text available
The Cymodoceaceae is a small family of five genera (Amphibolis, Cymodocea, Halodule, Syringodium, Thalassodendron) that are easily recognizable when reproductive organs are present. To test monophyly of the five genera and clarify relationships among them, a phylogenetic analysis was conducted on data from two plastid genes and four mitochondrial g...
Article
For over 150 years, the correct spelling of the genus name Ripogonum (Rhipogonum) and the derived family name Ripogonaceae (Rhipogonaceae) has been the subject of uncertainty. The different spellings in use are due to transliterations of the Greek letter " ρ " (rho with spiritus asper) into Latin as either " r " or " rh ". As neither of Ripogonum o...
Article
Full-text available
In order to study the evolution of mitochondrial genomes in the early branching lineages of the monocotyledons, i.e., the Acorales and Alismatales, we are sequencing complete genomes from a suite of key taxa. As a starting point the present paper describes the mitochondrial genome of Butomus umbellatus (Butomaceae) based on next-generation sequenci...
Article
Full-text available
The Global Genome Biodiversity Network (GGBN) was formed in 2011 with the principal aim of making high-quality well-documented and vouchered collections that store DNA or tissue samples of biodiversity, discoverable for research through a networked community of biodiversity repositories. This is achieved through the GGBN Data Portal (http://data.gg...
Article
For over 150 years, the correct spelling of the genus name Ripogonum (Rhipogonum) and the derived family name Ripogonaceae ( Rhipogonaceae) has been the subject of uncertainty. The different spellings in use are due to transliterations of the Greek letter “ρ” (rho with spiritus asper) into Latin as either “r” or “rh”. As neither of Ripogonum or Rhi...
Article
Full-text available
According to their respective charters, both the European, Middle Eastern, and African Society for Biopreservation & Biobanking (ESBB) and the International Society for Biological and Environmental Repositories (ISBER) focus a sizeable share of their activities on repositories involving nonhuman material. Those specific collections may unfortunatel...
Article
AbstractA phylogenetic analysis of the monocot order Liliales was performed using sequence data from three mitochondrial (atp1, cob, nad5) and two plastid genes (rbcL, ndhF). The complete data matrix includes 46 terminals representing all 10 families currently included in Liliales. The two major partitions, mitochondrial and plastid data, were cong...
Data
Repeated sequences >50 bp in the mitochondrial genome of Butomus umbellatus. (DOCX)
Data
Sequence variation and species identification ability of eight plastid regions in Crocus series Crocus. Crocus series Crocus is monophyletic (see figure S1) and includes nine species (C. sativus L., C. cartwrightianus Herb., C. hadriaticus Herb., C. thomasii Ten., C. oreocreticus B. L. Burtt, C. asumaniae B. Mathew & T. Baytop, C. mathewii Kernd. &...
Data
Predicted edited sites in protein coding genes in the mitochondrial genome of Butomus umbellatus . (DOCX)
Article
Full-text available
Microfilamentous green algae in the Ulvellaceae are notoriously difficult to identify and classify. We revised Ulvella based on the morphology of 46 unialgal culture isolates, including several from type localities, and we were guided by a phylogenetic reconstruction based on chloroplast-encoded tufA gene sequences. Species previously referred to A...
Article
Full-text available
A phylogenetic analysis of 62 species (32 genera) of the Palaearctic millipede family Julidae, including the aberrant alpine genus Pteridoiulus Verhoeff, 1913, was made based on partial sequences of the mitochondrial 16S rRNA (16S) gene and the nuclear 28S rRNA (28S) gene, respectively. The two datasets (16S rDNA and 28S rDNA) were analysed in comb...
Article
Full-text available
Premise of the study: The Asparagales, with ca. 40% of all monocotyledons, include a host of commercially important ornamentals in families such as Orchidaceae, Alliaceae, and Iridaceae, and several important crop species in genera such as Allium, Aloe, Asparagus, Crocus, and Vanilla. Though the order is well defined, the number of recognized fami...
Article
Full-text available
RNA-mediated gene duplication has been proposed to create processed paralogs in the plant mitochondrial genome. A processed paralog may retain signatures left by the maturation process of its RNA precursor, such as intron removal and no need of RNA editing. Whereas it is well documented that an RNA intermediary is involved in the transfer of mitoch...
Data
Plant specimens, specimen information and mean DNA yield. (DOCX)
Data
Real-time PCR primers and performance of standard curves. (DOCX)
Data
Titanium fusion primers used for 454-sequencing. (DOCX)
Data
Mean DNA yield and mean gene copy numbers for plastid, mitochondrial and nuclear DNA regions. (DOCX)
Data
PCR primers and corresponding amplification targets. (DOCX)
Data
Copy numbers of chloroplast, mitochondrial and nuclear gene amplicons in fresh and herbarium tissues. (DOCX)
Data
ANOVA on average number of miscoding lesions (per 106 total nucleotides) for each substitution type across fresh and herbarium DNA. Separate analyses were performed for plastid, mitochondrial and nuclear DNA. (DOCX)
Article
Full-text available
Dried plant herbarium specimens are potentially a valuable source of DNA. Efforts to obtain genetic information from this source are often hindered by an inability to obtain amplifiable DNA as herbarium DNA is typically highly degraded. DNA post-mortem damage may not only reduce the number of amplifiable template molecules, but may also lead to the...
Article
A phylogenetic analysis of the genus Colchicum (including Bulbocodium and Merendera) is presented. The phylogeny includes all but four of the 100 species and all subspecies currently recognized in the genus, two insufficiently known species (C. mirzoevae, C. stenopetalum), and one cultivated specimen (C. laetum hort.) probably of hybrid origin. The...
Article
Direct optimization was used to reconstruct the phylogeny of the 26 diploid taxa included in the genus Hordeum. The total data set was composed of 16 nucleotide sequence regions from the nuclear as well as the plastid genome. The nine nuclear regions were from single-copy, protein coding genes located on six of the seven chromosome pairs in the dip...