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.
2020
Authors
Erik J. M. Koenen Dario Isidro Ojeda Alayon Freek T. Bakker Jan J. Wieringa Catherine Kidner Olivier J. Hardy R. Toby Pennington Patrick S. Herendeen Anne Bruneau Colin E. HughesAbstract
The consequences of the Cretaceous–Paleogene (K–Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic. [Allopolyploidy; Cretaceous–Paleogene (K–Pg) boundary; Fabaceae, Leguminosae; paleopolyploidy; phylogenomics; whole genome duplication events]
Authors
N.G. Hodgetts Lars Söderström T.L. Blockeel S. Caspari M.S. Ignatov N.A. Konstantinova N. Lockhart B. Papp C. Schröck M. Sim-Sim D. Bell N.E. Bell Hans Blom M.A. Bruggeman-Nannenga M. Brugués J. Enroth Kjell Ivar Flatberg R. Garilleti L. Hedenäs D.T. Holyoak V. Hugonnot I. Kariyawasam H. Köckinger J. Kučera F. Lara R.D. PorleyAbstract
Introduction. Following on from work on the European bryophyte Red List, the taxonomically and nomenclaturally updated spreadsheets used for that project have been expanded into a new checklist for the bryophytes of Europe. Methods. A steering group of ten European bryologists was convened, and over the course of a year, the spreadsheets were compared with previous European checklists, and all changes noted. Recent literature was searched extensively. A taxonomic system was agreed, and the advice and expertise of many European bryologists sought. Key results. A new European checklist of bryophytes, comprising hornworts, liverworts and mosses, is presented. Fifteen new combinations are proposed. Conclusions. This checklist provides a snapshot of the current European bryophyte flora in 2019. It will already be out-of-date on publication, and further research, particularly molecular work, can be expected to result in many more changes over the next few years.
Authors
L.T. Ellis Olga M. Afonina I.V. Czernyadjeva L.A. Konoreva A.D. Potemkin V.M. Kotkova M. Alataş Hans Blom M. Boiko R.A. Cabral S. Jimenez D. Dagnino C. Turcato L. Minuto P. Erzberger T. Ezer Olga Galanina N. Hodgetts M.S. Ignatov Elena A. Ignatova S.G. Kazanovsky T. Kiebacher H. Köckinger E.O. Korolkova J. Larraín A.I. Maksimov D. Maity A. Martins M. Sim-Sim F. Monteiro L. Catarino R. Medina M. Nobis Arkadiusz Nowak Ryszard Ochyra I. Parnikoza V. Ivanets V. Plášek M. Philippe P. Saha Md. N. Aziz A.V. Shkurko S. Ştefănuţ G.M. Suárez A. Uygur K. Erkul M. Wierzgoń A. GraulichAbstract
No abstract has been registered
Authors
L. T. Ellis M. Kh. Alikhadzhiev R. S. Erzhapova Hans Blom H. Bednarek-Ochyra M. Burghart M. J. Cano I.V. Czernyadjeva E. Yu. Kuzmina A. D. Potemkin G. Ya. Doroshina D. Dagnino C. Turcato L. Minuto P. Drapela M. V. Dulin E. Fuertes A. Graulich Kristian Hassel Lars Hedenäs Tom Hellik Hofton Torbjørn Høitomt I. Jukonienė M. Kırmacı N. E. Koroleva Ł. Krajewski M. Kropik H. Kürschner E. V. Kushnevskaya J. Larraín M. Lebouvier A. I. Maksimov O. Yu. Pisarenko V. Plášek Z. Skoupá S. Yu. Popov V. E. Fedosov M. Puglisi A Stebel S. Ştefănut G. Vončina M. Wierzgoń S.-L. GuoAbstract
No abstract has been registered
Abstract
Pythium species are ubiquitous organisms known to be pathogens to terrestrial plants and marine algae. While several Pythium species (hereafter, Pythium) are described as pathogens to marine red algae, little is known about the pathogenicity of Pythium on marine green algae. A strain of a Pythium was isolated from a taxonomically unresolved filamentous Ulva collected in an intertidal area of Oslo fjord. Its pathogenicity to a euryhaline Ulva intestinalis collected in the same area was subsequently tested under salinities of 0, 15, and 30 parts per thousand (ppt). The Pythium isolate readily infected U. intestinalis and decimated the filaments at 0 ppt. Mycelium survived on U. intestinalis filaments for at least 2 weeks at 15 and 30 ppt, but the infection did not progress. Sporulation was not observed in the infected algal filaments at any salinity. Conversely, Pythium sporulated on infected grass pieces at 0, 15, and 30 ppt. High salinity retarded sporulation, but did not prevent it. Our Pythium isolate produced filamentous non-inflated sporangia. The sexual stage was never observed and phylogenetic analysis using internal transcribed spacer suggest this isolate belongs to the clade B2. We conclude that the Pythium found in the Oslo fjord was a pathogen of U. intestinalis under low salinity.
2019
Abstract
No abstract has been registered
Abstract
The pine-dominated forests of Western Norway have been found to harbour viable populations of woodpeckers, including the highly specialized White-backed Woodpecker Dendrocopos leucotos. The aim of this study was to investigate to what extent there were any changes in frequencies of woodpeckers, in particular the White-backed Woodpecker and the Grey-headed Woodpecker Picus canus, by resurveying 60 plots (each 1 km2 ) originally surveyed during 1994/1995. The resurvey was performed in 2013/2014. The White-backed Woodpecker was found to be the most common woodpecker species in both time periods. The Grey-headed Woodpecker was found to have a statistically significant decline from 27% of the 60 plots in 1994/95 to only 12% in 2013/14. The other four species all increased in frequency; although none of those increased frequencies were found to be statistically significant. We discuss possible explanations to why pine forests in Western Norway constitute a valuable habitat for the White-backed Woodpecker at the same time as it has drastically declined in other parts of Norway and Western Europe. In general, the reduced frequency of Grey-headed Woodpecker is not fully understood, although we suggest that cold winters during the years prior to the surveys in 2013/14 may be an important factor.
Authors
Mohamed Neji Anais Gorel Dario Isidro Ojeda Alayon Jerome Duminil Chedly Kastally Kathy Steppe Adeline Fayolle Olivier J. HardyAbstract
With the ongoing climate change, African rainforests are expected to experience severe drought events in the future. In Africa, the tropical genus Erythrophleum (Fabaceae) includes two forest sister timber tree species displaying contrasting geographical distributions. Erythrophleum ivorense is adapted to wet evergreen Guineo-Congolian forests, whereas E. suaveolens occurs in a wider range of climates, being found in moist dense forests but also in gallery forests under a relatively drier climate. This geographical distribution pattern suggests that the two species might cope differently to drought at the genomic level. Yet, the genetic basis of tolerance response to drought stress in both species is still uncharacterized. To bridge this gap, we performed an RNA-seq approach on seedlings from each species to monitor their transcriptional responses at different levels of drought stress (0, 2 and 6 weeks after stopping watering seedlings). Monitoring of wilting symptoms revealed that E. suaveolens displayed an earlier phenotypic response to drought stress than E. ivorense. At the transcriptomic level, results revealed 2020 (1204 down-regulated/816 up-regulated) and 1495 differentially expressed genes (DEGs) in response to drought stress from a total of 67,432 and 66,605 contigs assembled in E. ivorense and E. suaveolens, respectively. After identifying 30,374 orthologs between species, we found that only 7 of them were DEGs shared between species, while 587 and 458 were differentially expressed only in E. ivorense or E. suaveolens, respectively. GO and KEGG enrichment analysis revealed that the two species differ in terms of significantly regulated pathways as well as the number and expression profile of DEGs (Up/Down) associated with each pathway in the two stress stages. Our results suggested that the two studied species react differently to drought. E. suaveolens seems displaying a prompt response to drought at its early stage strengthened by the down-regulation of many DEGs encoding for signaling and metabolism-related pathways. A considerable up-regulation of these pathways was also found in E. ivorense at the late stage of drought, suggesting this species may be a late responder. Overall, our data may serve as basis for further understanding the genetic control of drought tolerance in tropical trees and favor the selection of crucial genes for genetically enhancing drought resistance.
Authors
CKM Tsui S Beauseigle Dario Isidro Ojeda Alayon AV Rice JEK Cooke FAH Sperling AD Roe RC HamelinAbstract
No abstract has been registered
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.