Publications
NIBIOs employees contribute to several hundred scientific articles and research reports every year. You can browse or search in our collection which contains references and links to these publications as well as other research and dissemination activities. The collection is continously updated with new and historical material.
2019
Authors
N. Feau Dario Isidro Ojeda Alayon S. Beauseigle G. J. Bilodeau A. Brar S. Cervantes-Arango A. L. Dale B. Dhillon C. Hammett P. Herath S. F. Shamoun C. K. M. Tsui P. Tanguay R. C. HamelinAbstract
Early detection provides the best way to prevent introduction and establishment of alien plant pathogens. Amplification of DNA by PCR has revolutionized the detection and monitoring of plant pathogens. Most of those assays rely on the amplification of a fraction of the genome of the targeted species. With the availability of whole genomes for a growing number of fungi and oomycetes it is becoming possible to compare genomes and discover regions that are unique to a target organism. This study has applied this pipeline to develop a set of hierarchical TaqMan real‐time PCR detection assays targeting DNA of all four Phytophthora ramorum lineages, and a closely related species, P. lateralis. Nine assays were generated: three targeting DNA of all P. ramorum lineages, one for each lineage of P. ramorum, one for P. lateralis and one targeting DNA of P. ramorum and P. lateralis. These assays were very accurate and sensitive, ranging from 98.7% to 100% detection accuracy of 2–10 gene copies of the targeted taxa from pure cultures or inoculated tissues. This level of sensitivity is within the lowest theoretical limit of detection of DNA. It is expected that these assays will be useful because of their high level of specificity and the ease with which they can be multiplexed because of the inherent flexibility in primer and probe design afforded by their lack of conservation in non‐target species.
Authors
Dario Isidro Ojeda Alayon Erik Koenen Sandra Cervantes Manuel de la Estrella Eulalia Banguera-Hinestroza Steven B. Janssens Jérémy Migliore Boris B. Demenou Anne Bruneau Félix Forest Olivier J. HardyAbstract
Detarioideae is well known for its high diversity of floral traits, including flower symmetry, number of organs, and petal size and morphology. This diversity has been characterized and studied at higher taxonomic levels, but limited analyses have been performed among closely related genera with contrasting floral traits due to the lack of fully resolved phylogenetic relationships. Here, we used four representative transcriptomes to develop an exome capture (target enrichment) bait for the entire subfamily and applied it to the Anthonotha clade using a complete data set (61 specimens) representing all extant floral diversity. Our phylogenetic analyses recovered congruent topologies using ML and Bayesian methods. Anthonotha was recovered as monophyletic contrary to the remaining three genera (Englerodendron, Isomacrolobium and Pseudomacrolobium), which form a monophyletic group sister to Anthonotha. We inferred a total of 35 transitions for the seven floral traits (pertaining to flower symmetry, petals, stamens and staminodes) that we analyzed, suggesting that at least 30% of the species in this group display transitions from the ancestral condition reconstructed for the Anthonotha clade. The main transitions were towards a reduction in the number of organs (petals, stamens and staminodes). Despite the high number of transitions, our analyses indicate that the seven characters are evolving independently in these lineages. Petal morphology is the most labile floral trait with a total of seven independent transitions in number and seven independent transitions to modification in petal types. The diverse petal morphology along the dorsoventral axis of symmetry within the flower is not associated with differences at the micromorphology of petal surface, suggesting that in this group all petals within the flower might possess the same petal identity at the molecular level. Our results provide a solid evolutionary framework for further detailed analyses of the molecular basis of petal identity.
Abstract
On the basis of a new phylogeny of the Detarioideae, with a particular focus on Englerodendron Harms, Anthonotha P.Beauv. and related genera, the possible options for delimiting monophyletic genera are discussed. As a result, Isomacrolobium Aubrév. & Pellegr. and Pseudomacrolobium Hauman are synonymised under Englerodendron. The following 12 new combinations are formed within the expanded Englerodendron: E. brachyrhachis (Breteler) Estrella & Ojeda, E. explicans (Baill.) Estrella & Ojeda, E. graciliflorum (Harms) Estrella & Ojeda, E. hallei (Aubrév.) Estrella & Ojeda, E. isopetalum (Harms) Breteler & Wieringa, E. lebrunii (J.Léonard) Estrella & Ojeda, E. leptorrhachis (Harms) Estrella & Ojeda, E. mengei (De Wild.) Estrella & Ojeda, E. nigericum (Baker f.) Estrella & Ojeda, E. obanense (Baker f.) Estrella & Ojeda, E. triplisomere (Pellegr.) Estrella & Ojeda and E. vignei (Hoyle) Estrella & Ojeda. A key to identification of the 17 species now recognised within Englerodendron is presented.
Authors
Dario Isidro Ojeda Alayon Tiina M. Mattila Tom Ruttink Sonja T. Kujala Katri Kärkkäinen Jukka-Pekka Verta Tanja PyhäjärviAbstract
Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies for short-reads data, including the utility of haploid megagametophyte tissue during de novo assembly as single-allele guides, for six individuals and five different tissues in Pinus sylvestris. We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity.
Authors
Magne SætersdalAbstract
No abstract has been registered
Authors
Nick Hodgetts Marta Cálix Eve Englefield Nicholas Fettes M. García Criado Lea Patin Ana Nieto Ariel Bergamini Irene Bisang Elvira Baisheva Patrizio Campisi A Cogoni Tomas Hallingbäck Nadya A. Konstantinova Neil Lochhart Marko Sabovljevic Norbert Schnyder Christian Schröck Cecília Sérgio Manuela Sim-Sim Jaroslav Vrba Catarina C. Ferreira Olga M. Afonina T.L. Blockeel Hans Blom Steffen Caspari Rosalina Gabriel Cesar Garcia Ricardo Garilleti J González Mancebo Irina Goldberg Lars Hedenäs David T. Holyoak Vincent Hugonnot Sanna Huttunen Mikhail S. Ignatov Elena A. Ignatova Marta Infante Riikka Juutinen Thomas Kiebacher Heribert Köckinger Jan Kucera Niklas Lönnell Michael Lüth Anabela Martins Oleg Maslovsky Beata Papp Ron Porley Gordon Rothero Lars Söderström Sorin Ştefǎnuţ Kimmo Syrjänen Alain Untereiner Jíri Vána Alain Vanderpoorten Kai Vellak Michele Aleffi J. W. Bates Neil Bell Montserrat Brugués Nils Cronberg Jo Denyer J.G. Duckett Heinjo During Johannes Enroth Vladimir E. Fedosov Kjell Ivar Flatberg Anna Ganeva Piotr Gorski Urban Gunnarsson Kristian Hassel Helena Hespanhol Mark O. Hill Rory Hodd Kristoffer Hylander Nele Ingerpuu Sanna Laaka-Lindberg Francisco Lara Vicente Mazimpaka Anna Mežaka Frank Müller Jose David Orgaz Jairo Patiño Sharon Pilkington Felisa Puche Rosa Maria Ros Fred Rumsey José Gabriel Segarra-Moragues Ana Séneca Adam Stebel Risto Virtanen Henrik Weibull Jo Wilbraham Jan ZarnowiecAbstract
No abstract has been registered
Abstract
We distinguish five Xanthomendoza species in Norway, viz., X. borealis, X. fallax, X. fulva, X. oregana, and X. ulophyllodes, based on morphology and molecular evidence. This paper gives an updated taxonomy of the Norwegian species of Xanthomendoza, and addresses previous misconceptions. Xanthomendoza ulophyllodes is reported as occurring in Norway. The species was previously misunderstood in Norway and removed from the Nordic checklist. We show that the nuclear internal transcribed spacer (nrITS) is a useful barcode marker for the treated species. We provide a key and short descriptions of the species, with notes on specific issues, ecology, geographic distribution, illustrations, maps, and a DNA reference library (DNA barcoding).
Abstract
No abstract has been registered
Abstract
The genus Scapania comprises a group of leafy liverworts distributed throughout many bryophytic assemblages. While many Scapania species grow widely, some are assessed as endangered and appear to be specialists with distinct niche environments. Several are found only in alpine forest communities, inhabiting decaying logs in streams, typical of an environment that is threatened by both logging activity and changes to watercourses. Another species, S. nimbosa, has an unusual Oceanic-Montane distribution across Ireland, Scotland, Norway, China and Nepal. Since gemmae and sexual reproduction are absent the species is hypothesized to be primarily dispersed by fragmentation. In Norway S. nimbosa occupies an area of only 13 x 20 km, at altitudes between 300-980 m, and is frequently found with another more abundant asexual species, S. ornithopodioides. This makes S. nimbosa susceptible to local extinction through climate change or perhaps interspecific competition. Genomics is being increasingly used to infer demography and the evolutionary history of a species. Ascertaining levels of genetic variation can also contribute towards an effective conservation management plan. Besides, very little is known about the genomic organization and sexual determination in leafy liverworts. To generate new knowledge about the genus Scapania we sequenced the genomes of the sexual species S. nemorea (both male and female isolates), S. undulata (a single isolate), and several asexual S. ornithopodiodes and S. nimbosa isolates. Illumina paired-end (2x 300 bp) and Oxford Nanopore long reads were used to create genomic references. Initially organellar genomes were assembled, annotated and genetic variation was discovered. This revealed that variation is indeed present even for S. nimbosa and S. ornithopodioides at Norwegian sites. Next we focussed on creating a high quality nuclear reference genome for S. nemorea using the SPAdes assembler (v3.13). Qualities of each assembly and isolate were assessed with QUAST and BUSCO. While one assembly spans 202.6 Mb (10930 scaffolds; N50 of 66 Kb), other isolates of S. nemorea show larger assembled genome sizes and different Kmer distributions, consistent with the expected alternative sexual chromosome complement. We further analyse genomic synteny and diversity, but emphasize that difficulties in extracting DNA from herbarium specimens really hamper analysis.
2018
Abstract
The long-term success of sites selected for species conservation depends on the persistence of target species. Red List species or threatened species lists are frequently defined as target species, but when Red Lists are updated, their species composition may change. Here we investigate the effects of Red List updates on the long-term robustness of fine-scale site selection. We used records of red-listed species (vascular plants, bryophytes, macrolichens, and polypore fungi) recorded in 1997–1998 in 1058 sample plots (50 × 50 m) from six forest landscapes in Norway, and four consecutive issues of the Norwegian Red List for species (1998, 2006, 2010, 2015). Sites were selected based on the first issue (1998) using both a scoring (“hotspot”) approach and a complementarity approach, and the ability of selected sites to include red-listed species of later issues was measured. In four boreal forests the mean proportion of red-listed species included in selected sites were reduced by18% during the study period, whereas no such effect was found in two hemiboreal forests, where increased clustering of red-listed species in sites compensated for target species changes. Changing target species adds to earlier documented challenges caused by population dynamics, and we suggest that alternatives to using occurrences of target species in site selection should be considered, and particularly at finer spatial scales.