Publications by authors named "Ole Seberg"

32 Publications

Genes from oxidative phosphorylation complexes II-V and two dual-function subunits of complex I are transcribed in Viscum album despite absence of the entire mitochondrial holo-complex I.

Mitochondrion 2022 01 2;62:1-12. Epub 2021 Nov 2.

Department of Molecular Biology and Genetics, Aarhus University, DK-4200 Slagelse, Denmark.

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 Arabidopsis with approximately 40 nuclear complex I genes, we recover only transcripts of two dual-function genes: gamma carbonic anhydrase and L-galactono-1,4-lactone dehydrogenase. The complement of genes belonging to complexes II-V of the oxidative phosphorylation pathway appears to be in accordance with other vascular plants. Additionally, transcripts encoding alternative NAD(P)H dehydrogenases and alternative oxidase were found. Despite sequence divergence, structural modeling suggests that the encoded proteins are structurally conserved. Complex I loss is a special feature in Viscum species and relatives, as all other parasitic flowering plants investigated to date seem to have a complete OXPHOS system. Hence, Viscum offers a unique system for specifically investigating molecular consequences of complex I absence, such as the role of complex I subunits involved in secondary functions.
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http://dx.doi.org/10.1016/j.mito.2021.10.006DOI Listing
January 2022

Mitochondrial genome evolution in parasitic plants.

BMC Evol Biol 2019 04 8;19(1):87. Epub 2019 Apr 8.

The Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Sølvgade 83, opg. S, DK-1307, Copenhagen K, Denmark.

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 four hemiparasitic Viscum species (Viscaceae), which lack many of the mitochondrial genes, while the remaining genes exhibit very fast molecular evolution rates. In this study, we include another genus, Phoradendron, from the Viscaceae, as well as 10 other hemiparasitic or holoparasitic taxa from across the phylogeny of the angiosperms to investigate how fast molecular evolution works on their mitogenomes, and the extent of gene loss.

Results: Our observations from Viscum were replicated in Phoradendron liga, whereas the remaining parasitic plants in the study have a complete set of the core mitochondrial genes and exhibit moderate or only slightly raised substitution rates compared to most autotrophic taxa, without any statistically significant difference between the different groups (autotrophs, hemiparasites and holoparasites). Additionally, further evidence is provided for the placement of Balanophoraceae within the order Santalales, while the exact placement of Cynomoriaceae still remains elusive.

Conclusions: We examine the mitochondrial gene content of 11 hemiparasitic and holoparasitic plants and confirm previous observations in Viscaceae. We show that the remaining parasitic plants do not have significantly higher substitution rates than autotrophic plants in their mitochondrial genes. We provide further evidence for the placement of Balanophoraceae in the Santalales.
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http://dx.doi.org/10.1186/s12862-019-1401-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454704PMC
April 2019

Genome Reports: Contracted Genes and Dwarfed Plastome in Mycoheterotrophic Sciaphila thaidanica (Triuridaceae, Pandanales).

Genome Biol Evol 2018 03;10(3):976-981

Natural History Museum of Denmark, University of Copenhagen, Denmark.

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 proposed model of gene loss in achlorophyllous plants. The most astonishing feature of the plastome is its extremely compact nature, with more than half of the genes having overlapping reading frames. Additionally, intergenic sequences have been reduced to a bare minimum, and the retained genes have been reduced in length both compared with the orthologous genes in another mycoheterotrophic species of Sciaphila and in the autotrophic relative Carludovica.
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http://dx.doi.org/10.1093/gbe/evy064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5952968PMC
March 2018

Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes.

PLoS One 2017 17;12(5):e0177606. Epub 2017 May 17.

Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.

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 mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant. Using a broad sample of the Alismatales, the evolutionary history of ribosomal protein gene loss is analyzed. In Zostera almost all ribosomal protein genes are lost from the mitogenome, but only some can be found in the nucleus.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177606PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5435185PMC
September 2017

Localized Retroprocessing as a Model of Intron Loss in the Plant Mitochondrial Genome.

Genome Biol Evol 2016 08 3;8(7):2176-89. Epub 2016 Aug 3.

Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark

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 and predicted RNA editing for whole mitochondrial genomes of 30 species in the monocot order Alismatales. In this group, we found an unusually high degree of variation in the intron content, even expanding the hitherto known variation among angiosperms. Some species have lost some two-third of the cis-spliced introns. We found a strong correlation between intron content and editing frequency, and detected 27 events in which intron loss is consistent with the presence of nucleotides in an edited state, supporting retroprocessing. However, we also detected seven cases of intron loss not readily being explained by retroprocession. Our analyses are also not consistent with the entire length of a fully processed cDNA copy being integrated into the genome, but instead indicate that retroprocessing usually occurs for only part of the gene. In some cases, several rounds of retroprocessing may explain intron loss in genes completely devoid of introns. A number of taxa retroprocessing seem to be very common and a possibly ongoing process. It affects the entire mitochondrial genome.
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http://dx.doi.org/10.1093/gbe/evw148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987113PMC
August 2016

Plastid phylogenomics and molecular evolution of Alismatales.

Cladistics 2016 Apr 23;32(2):160-178. Epub 2015 Nov 23.

Department of Botany, 6270 University Boulevard, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.

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 taxa (Araceae and other angiosperms). Parsimony and likelihood analyses inferred generally highly congruent phylogenetic relationships within the order, and several alternative likelihood partitioning schemes had little impact on patterns of clade support. All families with multiple genera were resolved as monophyletic, and we inferred strong bootstrap support for most inter- and intrafamilial relationships. The precise placement of Tofieldiaceae in the order was not well supported. Although most analyses inferred Tofieldiaceae to be the sister-group of the rest of the order, one likelihood analysis indicated a contrasting Araceae-sister arrangement. Acorus (Acorales) was not supported as a member of the order. We also investigated the molecular evolution of plastid NADH dehydrogenase, a large enzymatic complex that may play a role in photooxidative stress responses. Ancestral-state reconstructions support four convergent losses of a functional NADH dehydrogenase complex in Alismatales, including a single loss in Tofieldiaceae.
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http://dx.doi.org/10.1111/cla.12133DOI Listing
April 2016

Phylogeny of the Alismatales (Monocotyledons) and the relationship of Acorus (Acorales?).

Cladistics 2016 Apr 16;32(2):141-159. Epub 2015 Apr 16.

Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.

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 lineages of monocotyledons and other angiosperms. Total evidence analysis results in an almost completely resolved strict consensus tree, but all data partitions, genomic as well as morphological, are incongruent. The effects of RNA editing and potentially processed paralogous sequences are explored and discussed. Despite a decrease in incongruence length differences after exclusion of edited sites, the major data partitions remain significantly incongruent. The 14 families of Alismatales are all found to be monophyletic, but Acorus is found to be included in Alismatales rather than being the sister group to all other monocotyledons. The placement is strongly supported by the mitochondrial data, atp1 in particular, but it cannot be explained as an artifact caused by patterns of editing or by sampling of processed paralogues.
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http://dx.doi.org/10.1111/cla.12120DOI Listing
April 2016

Plastome Evolution in Hemiparasitic Mistletoes.

Genome Biol Evol 2015 Aug 29;7(9):2520-32. Epub 2015 Aug 29.

Natural History Museum of Denmark, University of Copenhagen, Denmark.

Santalales is an order of plants consisting almost entirely of parasites. Some, such as Osyris, are facultative root parasites whereas others, such as 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 structural changes and changes in gene content in relation to parasitism. Compared with typical angiosperms plastomes, the four Santalales plastomes are all reduced in size (10-22% compared with Vitis), and they have experienced rearrangements, mostly but not exclusively in the border areas of the inverted repeats. Additionally, a number of protein-coding genes (matK, infA, ccsA, rpl33, and all 11 ndh genes) as well as two transfer RNA genes (trnG-UCC and trnV-UAC) have been pseudogenized or completely lost. Most of the remaining plastid genes have a significantly changed selection pattern compared with other dicots, and the relaxed selection of photosynthesis genes is noteworthy. Although gene loss obviously reduces plastome size, intergenic regions were also shortened. As plastome modifications are generally most prominent in Viscum, they are most likely correlated with the increased nutritional dependence on the host compared with Osyris.
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http://dx.doi.org/10.1093/gbe/evv165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4607522PMC
August 2015

Identification of common horsetail (Equisetum arvense L.; Equisetaceae) using Thin Layer Chromatography versus DNA barcoding.

Sci Rep 2015 Jul 13;5:11942. Epub 2015 Jul 13.

Evolutionary Genomics Section, Natural History Museum of Denmark, Sølvgade 83S, Copenhagen, DK-1307, Denmark.

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 morphology-based identification is often difficult or impossible, the identification of processed material can be aided by molecular techniques. In this study, we explore two molecular identification techniques as methods of testing the purity of these products: a Thin Layer Chromatography approach (TLC-test) included in the European Pharmacopoeia and a DNA barcoding approach, used in recent years to identify material in herbal products. We test the potential of these methods for distinguishing and identifying these species using material from herbarium collections and commercial herbal products. We find that both methods can discriminate between the two species and positively identify E. arvense. The TLC-test is more cost- and time-efficient, but DNA barcoding is more powerful in determining the identity of adulterant species. Our study shows that, although DNA barcoding presents certain advantages, other established laboratory methods can perform as well or even better in confirming species' identity in herbal products.
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http://dx.doi.org/10.1038/srep11942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499799PMC
July 2015

Evolution of Asparagus L. (Asparagaceae): Out-of-South-Africa and multiple origins of sexual dimorphism.

Mol Phylogenet Evol 2015 Nov 14;92:25-44. Epub 2015 Jun 14.

Natural History Museum of Denmark, Sølvgade 83, Opg. S, K-1307 Copenhagen K, Denmark. Electronic address:

In the most comprehensive study to date we explored the phylogeny and evolution of the genus Asparagus, with emphasis on the southern African species. We included 211 accessions, representing 77 (92%) of the southern African, 6 (17%) of the tropical African, 10 (56%) of the strictly European and 6 (9%) of the Eurasian species. We analyzed DNA sequences from three plastid regions (trnH-psbA, trnD-T, ndhF) and from the nuclear region phytochrome C (PHYC) with parsimony and maximum likelihood methods, and recovered a monophyletic Asparagus. The phylogeny conflicts with all previous infra-generic classifications. It has many strongly supported clades, corroborated by morphological characters, which may provide a basis for a revised taxonomy. Additionally, the phylogeny indicates that many of the current species delimitations are problematic. Using biogeographic analyses that account for phylogenetic uncertainty (S-DIVA) and take into account relative branch lengths (Lagrange) we confirm the origin of Asparagus in southern Africa, and find no evidence that the dispersal of Asparagus follow the Rand flora pattern. We find that all truly dioecious species of Asparagus share a common origin, but that sexual dimorphism has arisen independently several times.
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http://dx.doi.org/10.1016/j.ympev.2015.06.002DOI Listing
November 2015

Recent initiatives in biodiversity biobanking: summary of presentations from the ESBB 2012 Conference.

Biopreserv Biobank 2013 Jun;11(3):182-8

1 Molecular Collections Facility , Natural History Museum, London, United Kingdom .

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http://dx.doi.org/10.1089/bio.2013.0018DOI Listing
June 2013

The Global Genome Biodiversity Network (GGBN) Data Portal.

Nucleic Acids Res 2014 Jan 16;42(Database issue):D607-12. Epub 2013 Oct 16.

Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Berlin 14195, Germany, National Museum of Natural History Smithsonian Institution, Washington DC 20013, USA, Zoological Research Museum Alexander Koenig, Bonn 53113, Germany, Wildlife & Environment Society of South Africa, Pretoria 0001, South Africa, National Herbarium of Victoria, Royal Botanic Gardens Melbourne, South Yarra, VIC 3141, Australia, Molecular Systematics Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK, Systematic Botany, Justus-Liebig-Universität, Giessen 35392, Germany, Global Biodiversity Information Facility (GBIF), Copenhagen Ø DK-2100, Denmark, Department of Zoology, The Natural History Museum, London SW7 5BD, UK, Natural History Museum of Denmark, Copenhagen K DK-1307, Denmark and Smithsonian Tropical Research Institute, Balboa Ancon, Unit 0948, Panama.

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.ggbn.org), which links globally distributed databases and bridges the gap between biodiversity repositories, sequence databases and research results. Advances in DNA extraction techniques combined with next-generation sequencing technologies provide new tools for genome sequencing. Many ambitious genome sequencing projects with the potential to revolutionize biodiversity research consider access to adequate samples to be a major bottleneck in their workflow. This is linked not only to accelerating biodiversity loss and demands to improve conservation efforts but also to a lack of standardized methods for providing access to genomic samples. Biodiversity biobank-holding institutions urgently need to set a standard of collaboration towards excellence in collections stewardship, information access and sharing and responsible and ethical use of such collections. GGBN meets these needs by enabling and supporting accessibility and the efficient coordinated expansion of biodiversity biobanks worldwide.
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http://dx.doi.org/10.1093/nar/gkt928DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965106PMC
January 2014

Phylogeny of the Liliales (Monocotyledons) with special emphasis on data partition congruence and RNA editing.

Cladistics 2013 Jun 3;29(3):274-295. Epub 2012 Oct 3.

L. H. Bailey Hortorium and Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA.

A 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 congruent, and parsimony analysis resulted in 50 equally parsimonious trees and a well resolved consensus tree confirming monophyly of all families. Mitochondrial genes are known to include RNA edited sites, and in some cases unprocessed genes are replaced by retro-processed gene copies, that is processed paralogs. To test the effects on phylogeny reconstruction of predicted edited sites and potentially unintentionally sampled processed paralogs, a number of analyses were performed using subsets of the complete data matrix. In general, predicted edited sites were more homoplasious than the other characters and increased incongruence among most data partitions. The predicted edited sites have a non-random phylogenetic signal in conflict with the signal of the non-edited sites. The potentially misleading signal was caused partially by the apparent presence of processed paralogs in Galanthus (Amaryllidaceae), part of the outgroup, but also by a deviating evolutionary pattern of predicted edited sites in Liliaceae compared with the remainder of the Liliales. Despite the problems that processed paralogs may cause, we argue that they should not a priori be excluded from phylogenetic analysis.
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http://dx.doi.org/10.1111/j.1096-0031.2012.00427.xDOI Listing
June 2013

The complete sequence of the mitochondrial genome of Butomus umbellatus--a member of an early branching lineage of monocotyledons.

PLoS One 2013 24;8(4):e61552. Epub 2013 Apr 24.

Botanical Garden, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark.

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 sequencing data. The genome was assembled into a circular molecule, 450,826 bp in length. Coding sequences cover only 8.2% of the genome and include 28 protein coding genes, four rRNA genes, and 12 tRNA genes. Some of the tRNA genes and a 16S rRNA gene are transferred from the plastid genome. However, the total amount of recognized plastid sequences in the mitochondrial genome is only 1.5% and the amount of DNA transferred from the nucleus is also low. RNA editing is abundant and a total of 557 edited sites are predicted in the protein coding genes. Compared to the 40 angiosperm mitochondrial genomes sequenced to date, the GC content of the Butomus genome is uniquely high (49.1%). The overall similarity between the mitochondrial genomes of Butomus and Spirodela (Araceae), the closest relative yet sequenced, is low (less than 20%), and the two genomes differ in size by a factor 2. Gene order is also largely unconserved. However, based on its phylogenetic position within the core alismatids Butomus will serve as a good reference point for subsequent studies in the early branching lineages of the monocotyledons.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0061552PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634813PMC
December 2013

Phylogeny of the Asparagales based on three plastid and two mitochondrial genes.

Am J Bot 2012 May 26;99(5):875-89. Epub 2012 Apr 26.

Botanical Garden, Natural History Museum of Denmark, Sølvgade 83, Copenhagen K, Denmark.

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 families, their circumscription, and relationships are somewhat controversial.

Methods: Phylogenetic analyses of Asparagales were based on parsimony and maximum likelihood using nucleotide sequence variation in three plastid genes (matK, ndhF, and rbcL) and two mitochondrial genes (atp1 and cob). Branch support was assessed using both jackknife analysis implementing strict-consensus (SC) and bootstrap analysis implementing frequency-within-replicates (FWR). The contribution of edited sites in the mitochondrial genes to topology and branch support was investigated.

Key Results: The topologies recovered largely agree with previous results, though some clades remain poorly resolved (e.g., Ruscaceae). When the edited sites were included in the analysis, the plastid and mitochondrial genes were highly incongruent. However, when the edited sites were removed, the two partitions became congruent.

Conclusions: Some deeper nodes in the Asparagales tree remain poorly resolved or unresolved as do the relationships of certain monogeneric families (e.g., Aphyllanthaceae, Ixioliriaceae, Doryanthaceae), whereas support for many families increases. However, the increased support is dominated by plastid data, and the potential influence of mitochondrial and biparentially inherited single or low-copy nuclear genes should be investigated.
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http://dx.doi.org/10.3732/ajb.1100468DOI Listing
May 2012

Genes and processed paralogs co-exist in plant mitochondria.

J Mol Evol 2012 Apr 7;74(3-4):158-69. Epub 2012 Apr 7.

Botanical Garden, Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83 Opg. S, 1307, Copenhagen K, Denmark.

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 mitochondrial genes to the nucleus, no direct evidence exists for insertion of processed paralogs in the mitochondria (i.e., processed and un-processed genes have never been found simultaneously in the mitochondrial genome). In this study, we sequenced a region of the mitochondrial gene nad1, and identified a number of taxa were two different copies of the region co-occur in the mitochondria. The two nad1 paralogs differed in their (a) presence or absence of a group II intron, and (b) number of edited sites. Thus, this work provides the first evidence of co-existence of processed paralogs and their precursors within the plant mitochondrial genome. In addition, mapping the presence/absence of the paralogs provides indirect evidence of RNA-mediated gene duplication as an essential process shaping the mitochondrial genome in plants.
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http://dx.doi.org/10.1007/s00239-012-9496-1DOI Listing
April 2012

DNA damage in plant herbarium tissue.

PLoS One 2011 5;6(12):e28448. Epub 2011 Dec 5.

Biosystematics Group, Wageningen University, Wageningen, The Netherlands.

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 generation of erroneous sequence information. A qualitative and quantitative assessment of DNA post-mortem damage is essential to determine the accuracy of molecular data from herbarium specimens. In this study we present an assessment of DNA damage as miscoding lesions in herbarium specimens using 454-sequencing of amplicons derived from plastid, mitochondrial, and nuclear DNA. In addition, we assess DNA degradation as a result of strand breaks and other types of polymerase non-bypassable damage by quantitative real-time PCR. Comparing four pairs of fresh and herbarium specimens of the same individuals we quantitatively assess post-mortem DNA damage, directly after specimen preparation, as well as after long-term herbarium storage. After specimen preparation we estimate the proportion of gene copy numbers of plastid, mitochondrial, and nuclear DNA to be 2.4-3.8% of fresh control DNA and 1.0-1.3% after long-term herbarium storage, indicating that nearly all DNA damage occurs on specimen preparation. In addition, there is no evidence of preferential degradation of organelle versus nuclear genomes. Increased levels of C→T/G→A transitions were observed in old herbarium plastid DNA, representing 21.8% of observed miscoding lesions. We interpret this type of post-mortem DNA damage-derived modification to have arisen from the hydrolytic deamination of cytosine during long-term herbarium storage. Our results suggest that reliable sequence data can be obtained from herbarium specimens.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028448PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230621PMC
July 2012

Phylogenetic relationships in the millipede family Julidae.

Cladistics 2011 Dec 17;27(6):606-616. Epub 2011 May 17.

Natural History Museum of Denmark, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark.

A phylogenetic analysis of 40 species (22 genera) of the Palaearctic millipede family Julidae was made based on partial sequences of the mitochondrial 16S rRNA (16S) gene and the nuclear 28S rRNA (28S) gene, respectively. The two data sets (16S rDNA and 28S rDNA) were analysed individually and in combination using direct optimization as implemented in POY. The 16S rDNA and the 28S rDNA sequences vary from 410 to 449 bp and from 467 to 525 bp in length, respectively. All searches were performed under six different gap opening costs, an extension gap cost of 1, and a substitution cost of 2. Incongruence length difference values were used to select the preferred tree. The order Julida was recovered as monophyletic under all weight sets. The family Julidae was recovered as monophyletic except under one weight set where the genus Nepalmatoiulus is sister to all other Julida. Within Julidae, a clade of Paectophyllini + Calyptophyllini is sister to all others on the preferred tree but this relationship is not robust. A hitherto unrecognized clade of (South) east Asian genera (Anaulaciulus and Nepalmatoiulus) was recovered under five weight sets. Another "new" robust clade (Oncoiulini + Schizophyllini) is congruent with a hitherto unrecognized complex morphological character. Further clades recovered within the Julidae partly conflict with the accepted classification, which is only to a limited extent based on phylogenetic arguments.
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http://dx.doi.org/10.1111/j.1096-0031.2011.00360.xDOI Listing
December 2011

When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae).

Cladistics 2011 Aug 1;27(4):428-446. Epub 2011 Feb 1.

Botanical Garden and Museum, Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83 opg. S, DK-1307 Copenhagen, Denmark.

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 diploid H. vulgare genome. The seven plastid regions comprise protein coding genes as well as intergenic regions. Studies of character congruence between data partitions showed no correlation between chromosomal location and congruence among the nuclear sequences and a level of congruence among the plastid sequences comparable with the level among the nuclear sequences. Combined analysis of all data resolved the phylogeny completely with most clades being robust and well supported. However, due to incongruence among data partitions some relationships are still and likely to remain ambiguously inferred. Rather than adding still more genes to the phylogenetic analyses, patterns of incongruence may be better explored by adding data from multiple specimens per taxon. For some species relationships the plastid data appear positively misleading, emphasizing the need for caution if plastid data are the only or dominant type of data used for phylogenetic reconstruction and subsequent re-classification. © The Willi Hennig Society 2011.
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http://dx.doi.org/10.1111/j.1096-0031.2011.00347.xDOI Listing
August 2011

Are substitution rates and RNA editing correlated?

BMC Evol Biol 2010 Nov 11;10:349. Epub 2010 Nov 11.

The Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83 Opg, S, DK-1307 Copenhagen C, Denmark.

Background: RNA editing is a post-transcriptional process that, in seed plants, involves a cytosine to uracil change in messenger RNA, causing the translated protein to differ from that predicted by the DNA sequence. RNA editing occurs extensively in plant mitochondria, but large differences in editing frequencies are found in some groups. The underlying processes responsible for the distribution of edited sites are largely unknown, but gene function, substitution rate, and gene conversion have been proposed to influence editing frequencies.

Results: We studied five mitochondrial genes in the monocot order Alismatales, all showing marked differences in editing frequencies among taxa. A general tendency to lose edited sites was observed in all taxa, but this tendency was particularly strong in two clades, with most of the edited sites lost in parallel in two different areas of the phylogeny. This pattern is observed in at least four of the five genes analyzed. Except in the groups that show an unusually low editing frequency, the rate of C-to-T changes in edited sites was not significantly higher that in non-edited 3rd codon positions. This may indicate that selection is not actively removing edited sites in nine of the 12 families of the core Alismatales. In all genes but ccmB, a significant correlation was found between frequency of change in edited sites and synonymous substitution rate. In general, taxa with higher substitution rates tend to have fewer edited sites, as indicated by the phylogenetically independent correlation analyses. The elimination of edited sites in groups that lack or have reduced levels of editing could be a result of gene conversion involving a cDNA copy (retroprocessing). If so, this phenomenon could be relatively common in the Alismatales, and may have affected some groups recurrently. Indirect evidence of retroprocessing without a necessary correlation with substitution rate was found mostly in families Alismataceae and Hydrocharitaceae (e.g., groups that suffered a rapid elimination of all their edited sites, without a change in substitution rate).

Conclusions: The effects of substitution rate, selection, and/or gene conversion on the dynamics of edited sites in plant mitochondria remain poorly understood. Although we found an inverse correlation between substitution rate and editing frequency, this correlation is partially obscured by gene retroprocessing in lineages that have lost most of their edited sites. The presence of processed paralogs in plant mitochondria deserves further study, since most evidence of their occurrence is circumstantial.
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http://dx.doi.org/10.1186/1471-2148-10-349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2989974PMC
November 2010

Alignment, clade robustness and fungal phylogenetics- Crepidotaceae and sister families revisited.

Cladistics 2010 Feb 1;26(1):62-71. Epub 2009 Sep 1.

The Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83 opg. S, DK-1307 Copenhagen K, Denmark.

The circumscription and delimitation of the agaric family Crepidotaceae and related families in the Agaricales have been analysed using nLSU sequence data and direct optimization. The influence of alignment parameters on clade robustness has been explored, and many clades are found to have a low robustness. Nevertheless, based on clades with a high or moderately high robustness to increased gap costs, a few taxonomic changes are suggested: Crepidotaceae has been amended to include Crepidotus, Episphaeria, Simocybe, Pleuroflammula and Inocybe, the latter genus adding the homoplasious character mycorrhization to the family, Pellidiscus is included in Crepidotus, a position supported by micromorphology, two other genera formerly included in the family, Chromocyphella and Phaeosolenia, are excluded, and a new family, Chromocyphellaceae fam. nov., is erected for them based on fruit body shape, microcharacters, and sequences. Monophyly of Tubariaceae as recently circumscribed was not recovered, but tentatively we accept the genera Tubaria and Phaeomarasmius as members of the family. © The Willi Hennig Society 2009.
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http://dx.doi.org/10.1111/j.1096-0031.2009.00279.xDOI Listing
February 2010

Stowaway MITEs in Hordeum (Poaceae): evolutionary history, ancestral elements and classification.

Cladistics 2009 Apr 25;25(2):198-208. Epub 2009 Feb 25.

Laboratory of Molecular Systematics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.

Given the lack of direct observational data relating to transposition of Stowaway miniature inverted repeat transposable elements, phylogenetic methods may provide a means of generating data that adds to our knowledge of these elements. In a phylogenetic framework the evolutionary history of homologous elements may be traced, and the nucleotide sequence of elements at or close to the time of insertion can be reconstructed. Based on a phylogeny of the diploid species of the genus Hordeum we explore evolutionary aspects of four non-homologous groups of Stowaway elements inserted into three nuclear genes: nucellin, xylose isomerase, and barley leucine zipper 1. The data illustrate how elements starting from a high degree of sequence similarity between terminal inverted repeat regions gradually degrade, and confirm previous notions about preferential insertion at particular TA target sites. It is shown how creation of consensus sequences as estimates of ancestral elements may be positively misleading. The Stowaway family of transposable elements is often further divided into subfamilies based on sequence similarity between elements. Sequence similarity data from the elements discovered in the xylose isomerase gene, and other elements found through BLAST searches in GenBank, reveal inconsistency in the rules used for classification. In order to reflect natural groups, a classification of transposable elements must be based on phylogenetic evidence rather than raw similarity. © The Willi Hennig Society 2009.
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http://dx.doi.org/10.1111/j.1096-0031.2008.00245.xDOI Listing
April 2009

How many loci does it take to DNA barcode a crocus?

PLoS One 2009 25;4(2):e4598. Epub 2009 Feb 25.

Laboratory of Molecular Systematics, Natural History Museum of Denmark, Copenhagen, Denmark.

Background: DNA barcoding promises to revolutionize the way taxonomists work, facilitating species identification by using small, standardized portions of the genome as substitutes for morphology. The concept has gained considerable momentum in many animal groups, but the higher plant world has been largely recalcitrant to the effort. In plants, efforts are concentrated on various regions of the plastid genome, but no agreement exists as to what kinds of regions are ideal, though most researchers agree that more than one region is necessary. One reason for this discrepancy is differences in the tests that are used to evaluate the performance of the proposed regions. Most tests have been made in a floristic setting, where the genetic distance and therefore the level of variation of the regions between taxa is large, or in a limited set of congeneric species.

Methodology And Principal Findings: Here we present the first in-depth coverage of a large taxonomic group, all 86 known species (except two doubtful ones) of crocus. Even six average-sized barcode regions do not identify all crocus species. This is currently an unrealistic burden in a barcode context. Whereas most proposed regions work well in a floristic context, the majority will--as is the case in crocus--undoubtedly be less efficient in a taxonomic setting. However, a reasonable but less than perfect level of identification may be reached--even in a taxonomic context.

Conclusions/significance: The time is ripe for selecting barcode regions in plants, and for prudent examination of their utility. Thus, there is no reason for the plant community to hold back the barcoding effort by continued search for the Holy Grail. We must acknowledge that an emerging system will be far from perfect, fraught with problems and work best in a floristic setting.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0004598PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643479PMC
April 2009

Phylogenetic relationships of Triticum and Aegilops and evidence for the origin of the A, B, and D genomes of common wheat (Triticum aestivum).

Mol Phylogenet Evol 2006 Apr 28;39(1):70-82. Epub 2006 Feb 28.

Botanical Garden and Museum, The Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83, DK-1307 Copenhagen K, Denmark.

Common wheat (Triticum aestivum) has for decades been a textbook example of the evolution of a major crop species by allopolyploidization. Using a sophisticated extension of the PCR technique, we have successfully isolated two single-copy nuclear genes, DMC1 and EF-G, from each of the three genomes found in hexaploid wheat (BA(u)D) and from the two genomes of the tetraploid progenitor Triticum turgidum (BA(u)). By subjecting these sequences to phylogenetic analysis together with sequences from representatives of all the diploid Triticeae genera we are able for the first time to provide simultaneous and strongly supported evidence for the D genome being derived from Aegilops tauschii, the A(u) genome being derived from Triticum urartu, and the hitherto enigmatic B genome being derived from Aegilops speltoides. Previous problems of identifying the B genome donor may be associated with a higher diversification rate of the B genome compared to the A(u) genome in the polyploid wheats. The phylogenetic hypothesis further suggests that neither Triticum, Aegilops, nor Triticum plus Aegilops are monophyletic.
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http://dx.doi.org/10.1016/j.ympev.2006.01.023DOI Listing
April 2006

Sequence length variation, indel costs, and congruence in sensitivity analysis.

Cladistics 2005 Feb;21(1):15-30

Botanical Institute, University of Copenhagen, Gothersgade 140, DK-1123 Copenhagen K, Denmark.

The behavior of two topological and four character-based congruence measures was explored using different indel treatments in three empirical data sets, each with different alignment difficulties. The analyses were done using direct optimization within a sensitivity analysis framework in which the cost of indels was varied. Indels were treated either as a fifth character state, or strings of contiguous gaps were considered single events by using linear affine gap cost. Congruence consistently improved when indels were treated as single events, but no congruence measure appeared as the obviously preferable one. However, when combining enough data, all congruence measures clearly tended to select the same alignment cost set as the optimal one. Disagreement among congruence measures was mostly caused by a dominant fragment or a data partition that included all or most of the length variation in the data set. Dominance was easily detected, as the character-based congruence measures approached their optimal value when indel costs were incremented. Dominance of a fragment or data partition was overwhelmed when new sequence length-variable fragments or data partitions were added.
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http://dx.doi.org/10.1111/j.1096-0031.2005.00053.xDOI Listing
February 2005

Investigation of genetic and morphological variation in the sago palm (Metroxylon sagu; Arecaceae) in Papua New Guinea.

Ann Bot 2004 Jul 21;94(1):109-17. Epub 2004 May 21.

Department of Systematic Botany, University of Aarhus, Nordlandsvej 68, DK-8240 Risskov, Denmark.

Background And Aims: The genetic and morphological variation in the sago palm (Metroxylon sagu, Arecaceae) in Papua New Guinea (PNG) was investigated.

Methods: Amplified fragment length polymorphism (AFLP) was used to investigate the genetic structure of 76 accessions of M. sagu, collected in seven wild and semi-wild stands in PNG.

Key Results: An analysis of ten quantitative morphological variables revealed that most of these were mutually correlated. Principal component analyses of the same morphological variables showed that neither armature (presence or absence of spines) nor geographical separation was reflected clearly in the quantitative morphological variation. Similarity matrices of genetic, quantitative morphological, geographical and armature data were tested for pair-wise correlations, using Mantel's test. The results only showed a significant correlation between genetic and geographical distances. Visual inspection of principal component analyses plots and a neighbour-joining dendrogram based on genetic distances supported this trend, whereas armature showed no relation with genetic distances.

Conclusions: Geographical distribution defines some weak patterns in the genetic variation, whereas the genetic variation does not reflect any patterns in the morphological variation, including armature. The present study supports the accepted taxonomy of M. sagu, recognizing only one species of M. sagu in PNG.
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http://dx.doi.org/10.1093/aob/mch112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4242368PMC
July 2004

An empirical test of the treatment of indels during optimization alignment based on the phylogeny of the genus Secale (Poaceae).

Mol Phylogenet Evol 2004 Mar;30(3):733-42

Botanical Institute, University of Copenhagen, Gothersgade 140, DK-1123 Copenhagen K, Denmark.

The ability of the program POY, implementing optimization alignment, to deal with major indels is explored and discussed in connection with a phylogenetic analysis of the genus Secale based on partial Adh1 sequences. The Adh1 sequences used span exon 2-4. Nearly all variation is found in intron 2 and intron 3, which form the basis for the phylogenetic analyses. Both in some ingroup and outgroup taxa intron 3 has a major duplication. Previous phylogenetic analyses have repeatedly confirmed monophyly of both Secale and Hordeum, the latter being part of the outgroup. However, optimization alignment only recovers both genera as monophyletic when knowledge of the duplication is incorporated in the analysis. The phylogenetic relationships within Secale are not clearly resolved. Subspecific taxa of Secale strictum have identical sequences and they are confined to a monophyletic group. However, the two subspecific taxa of Secale cereale do not form a monophyletic group, and the position of Secale sylvestre is uncertain.
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http://dx.doi.org/10.1016/S1055-7903(03)00206-9DOI Listing
March 2004

Molecular evolution and phylogenetic application of DMC1.

Mol Phylogenet Evol 2002 Jan;22(1):43-50

Botanical Institute, University of Copenhagen, Gothersgade 140, DK-1123 Copenhagen K, Denmark.

The protein encoded by the single-copy nuclear gene DMC1 belongs to the recA-like group of proteins involved in meiosis. Partial nucleotide sequence, spanning exon 10 to exon 15, was used to test the applicability of the gene to phylogenetic studies in higher plants and used to assess its molecular evolution. The sequences produced from the Triticeae (Poaceae) show that most of the variation is confined to the introns. If a wider taxon sampling is used, alignment problems may be predicted. Comparisons including four complete coding sequences from GenBank reveal that the exons are more than twice as variable as rbcL, but easy to align, and hence may be valuable at higher taxonomic levels. Substitution rates are variable within the Triticeae, though local subclades show rate constancy. The relationships between exon variation and predicted protein structure are briefly discussed. In general, none of the observed nucleotide substitutions can be predicted to cause major structural or functional changes.
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http://dx.doi.org/10.1006/mpev.2001.1011DOI Listing
January 2002
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