Taxonomy of the order Mononegavirales : update 2016
Afonso, Claudio L. ; Amarasinghe, Gaya K. ; Bányai, Krisztián ; Bào, Yīmíng ; Basler, Christopher F. ; Bavari, Sina ; Bejerman, Nicolás ; Blasdell, Kim R. ; Briand, François Xavier ; Briese, Thomas ; Bukreyev, Alexander ; Calisher, Charles H. ; Chandran, Kartik ; Chéng, Jiāsēn ; Clawson, Anna N. ; Collins, Peter L. ; Dietzgen, Ralf G. ; Dolnik, Olga ; Domier, Leslie L. ; Dürrwald, Ralf ; Dye, John M. ; Easton, Andrew J. ; Ebihara, Hideki ; Farkas, Szilvia L. ; Freitas-Astúa, Juliana ; Formenty, Pierre ; Fouchier, Ron A.M. ; Fù, Yànpíng ; Ghedin, Elodie ; Goodin, Michael M. ; Hewson, Roger ; Horie, Masayuki ; Hyndman, Timothy H. ; Jiāng, Dàohóng ; Kitajima, Elliot W. ; Kobinger, Gary P. ; Kondo, Hideki ; Kurath, Gael ; Lamb, Robert A. ; Lenardon, Sergio ; Leroy, Eric M. ; Li, Ci Xiu ; Lin, Xian Dan ; Liú, Lìjiāng ; Longdon, Ben ; Marton, Szilvia ; Maisner, Andrea ; Mühlberger, Elke ; Netesov, Sergey V. ; Nowotny, Norbert ; Patterson, Jean L. ; Payne, Susan L. ; Paweska, Janusz T. ; Randall, Rick E. ; Rima, Bertus K. ; Rota, Paul ; Rubbenstroth, Dennis ; Schwemmle, Martin ; Shi, Mang ; Smither, Sophie J. ; Stenglein, Mark D. ; Stone, David M. ; Takada, Ayato ; Terregino, Calogero ; Tesh, Robert B. ; Tian, Jun Hua ; Tomonaga, Keizo ; Tordo, Noël ; Towner, Jonathan S. ; Vasilakis, Nikos ; Verbeek, Martin ; Volchkov, Viktor E. ; Wahl-Jensen, Victoria ; Walsh, John A. ; Walker, Peter J. ; Wang, David ; Wang, Lin Fa ; Wetzel, Thierry ; Whitfield, Anna E. ; Xiè, Jiǎtāo ; Yuen, Kwok Yung ; Zhang, Yong Zhen ; Kuhn, Jens H. - \ 2016
Archives of Virology 161 (2016)8. - ISSN 0304-8608 - p. 2351 - 2360.
In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
TRY - a global database of plant traits
Kattge, J. ; Diaz, S. ; Lavorel, S. ; Prentices, I.C. ; Leadley, P. ; Bönisch, G. ; Garnier, E. ; Westobys, M. ; Reich, P.B. ; Wrights, I.J. ; Cornelissen, C. ; Violle, C. ; Harisson, S.P. ; Bodegom, P.M. van; Reichstein, M. ; Enquist, B.J. ; Soudzilovskaia, N.A. ; Ackerly, D.D. ; Anand, M. ; Atkin, O. ; Bahn, M. ; Baker, T.R. ; Baldochi, D. ; Bekker, R. ; Blanco, C.C. ; Blonders, B. ; Bond, W.J. ; Bradstock, R. ; Bunker, D.E. ; Casanoves, F. ; Cavender-Bares, J. ; Chambers, J.Q. ; Chapin III, F.S. ; Chave, J. ; Coomes, D. ; Cornwell, W.K. ; Craine, J.M. ; Dobrin, B.H. ; Duarte, L. ; Durka, W. ; Elser, J. ; Esser, G. ; Estiarte, M. ; Fagan, W.F. ; Fang, J. ; Fernadez-Mendez, F. ; Fidelis, A. ; Finegan, B. ; Flores, O. ; Ford, H. ; Frank, D. ; Freschet, T. ; Fyllas, N.M. ; Gallagher, R.V. ; Green, W.A. ; Gutierrez, A.G. ; Hickler, T. ; Higgins, S.I. ; Hodgson, J.G. ; Jalili, A. ; Jansen, S. ; Joly, C.A. ; Kerkhoff, A.J. ; Kirkup, D. ; Kitajima, K. ; Kleyer, M. ; Klotz, S. ; Knops, J.M.H. ; Kramer, K. ; Kühn, I. ; Kurokawa, H. ; Laughlin, D. ; Lee, T.D. ; Leishman, M. ; Lens, F. ; Lewis, S.L. ; Lloyd, J. ; Llusia, J. ; Louault, F. ; Ma, S. ; Mahecha, M.D. ; Manning, P. ; Massad, T. ; Medlyn, B.E. ; Messier, J. ; Moles, A.T. ; Müller, S.C. ; Nadrowski, K. ; Naeem, S. ; Niinemets, Ü. ; Nöllert, S. ; Nüske, A. ; Ogaya, R. ; Oleksyn, J. ; Onipchenko, V.G. ; Onoda, Y. ; Ordonez Barragan, J.C. ; Ozinga, W.A. ; Poorter, L. - \ 2011
Global Change Biology 17 (2011)9. - ISSN 1354-1013 - p. 2905 - 2935.
relative growth-rate - tropical rain-forest - hawaiian metrosideros-polymorpha - litter decomposition rates - leaf economics spectrum - old-field succession - sub-arctic flora - functional traits - wide-range - terrestrial biosphere
Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.
Global patterns of leaf mechanical properties
Onoda, Y. ; Westoby, M. ; Adler, N.E. ; Choong, A.M.L. ; Clissold, F.J. ; Cornelissen, J.H.C. ; Diaz, S. ; Dominy, N.J. ; Elgart, A. ; Markesteijn, L. ; Poorter, L. ; Kitajima, K. - \ 2011
Ecology Letters 14 (2011)3. - ISSN 1461-023X - p. 301 - 312.
fracture-toughness - life-span - latitudinal variation - economics spectrum - leaves - plants - traits - shade - photosynthesis - biomechanics
Leaf mechanical properties strongly influence leaf lifespan, plant-herbivore interactions, litter decomposition and nutrient cycling, but global patterns in their interspecific variation and underlying mechanisms remain poorly understood. We synthesize data across the three major measurement methods, permitting the first global analyses of leaf mechanics and associated traits, for 2819 species from 90 sites worldwide. Key measures of leaf mechanical resistance varied c. 500-800-fold among species. Contrary to a long-standing hypothesis, tropical leaves were not mechanically more resistant than temperate leaves. Leaf mechanical resistance was modestly related to rainfall and local light environment. By partitioning leaf mechanical resistance into three different components we discovered that toughness per density contributed a surprisingly large fraction to variation in mechanical resistance, larger than the fractions contributed by lamina thickness and tissue density. Higher toughness per density was associated with long leaf lifespan especially in forest understory. Seldom appreciated in the past, toughness per density is a key factor in leaf mechanical resistance, which itself influences plant-animal interactions and ecosystem functions across the globe
Tissue-level leaf toughness, but not lamina thickness, predicts sapling leaf lifespan and shade tolerance of tropical tree species
Kitajima, K. ; Poorter, L. - \ 2010
New Phytologist 186 (2010). - ISSN 0028-646X - p. 708 - 721.
trade-offs - mechanical-properties - woody-plants - biomechanical properties - economics spectrum - fracture-toughness - light requirements - functional traits - forest - leaves
Leaf toughness is thought to enhance physical defense and leaf lifespan. Here, we evaluated the relative importance of tissue-level leaf traits vs lamina thickness, as well as their ontogenetic changes, for structure-level leaf toughness and regeneration ecology of 19 tropical tree species. We measured the fracture toughness of the laminas and veins of sapling leaves with shearing tests, and used principal component analysis and structural equation modeling to evaluate the multivariate relationships among traits that contribute to leaf toughness and their links to ecological performance traits. Tissue traits (density and fracture toughness of lamina and vein) were correlated positively with each other, but independent of lamina thickness. The tissue traits and lamina thickness contributed additively to the structure-level toughness (leaf mass per area and work-to-shear). Species with dense and tough leaves as saplings also had dense and tough leaves as seedlings and adults. The patterns of ontogenetic change in trait values differed between the seedling-to-sapling and sapling-to-adult transitions. The fracture toughness and tissue density of laminas and veins, but not the lamina thickness, were correlated positively with leaf lifespan and sapling survival, and negatively with herbivory rate and sapling regeneration light requirements, indicating the importance of tissue-level leaf traits.
Resprouting as a persistence strategy of tropical forest trees: relations with carbohydrate storage and shade tolerance
Poorter, L. ; Kitajima, K. ; Mercado, P. ; Chubina, J. ; Melgar, I. ; Prins, H.H.T. - \ 2010
Ecology 91 (2010). - ISSN 0012-9658 - p. 2613 - 2627.
life-history variation - rain-forest - dry forest - interspecific variation - light requirements - functional traits - seedling survival - leaf traits - growth - allocation
Resprouting is an important persistence strategy for woody species and represents a dominant pathway of regeneration in many plant communities with potentially large consequences for vegetation dynamics, community composition and species coexistence. Most of our knowledge on resprouting strategies comes from fire-prone systems, but this can not readily applied to other systems were disturbances are less intense. In this study we evaluated sapling responses to stem snapping for 49 moist forest species and 36 dry forest species from two Bolivian tropical forests. To this end we compared in a field experiment the survival and height growth of clipped and control saplings for a two-year period, and related this to the shade tolerance, carbohydrate reserves, and the morphological traits (wood density, leaf size) of the species. Nearly all saplings resprouted readily after stem damage, although dry forest species realized, on average, a better survival and growth after stem damage compared to moist forest species. Shade-tolerant species were better at resprouting than light-demanding species in moist forest. This resprouting ability is an important prerequisite for successful regeneration in the shaded understory, where saplings frequently suffer from damage by falling debris. Survival after stem damage was, surprisingly, only modestly related to stem reserves, and much stronger related to wood density, possibly because a high wood density enables plants to resist fungi and pathogens and to reduce stem decay. Correlations between sapling performance and functional traits were similar for the two forest types and for phylogenetically independent contrasts and for cross-species analyses. The consistency of these results suggests that tropical forest species face similar trade-offs in different sites and converge on similar sets of solutions. A high resprouting ability, investments in stem defense and storage reserves form part of a suite of co-evolved traits that underlies the growth-survival trade-off, and contributes to light gradient partitioning and species coexistence. These links with shade tolerance are important in the moist evergreen forest which casts a deep, more persistent shade, but tend to diminish in dry deciduous forest where light is a less limiting resource
|Functional basis for resource niche partitioning by tropical trees
Kitajima, K. ; Poorter, L. - \ 2008
In: Tropical forest community ecology / Carson, W.P., Schnitzer, S.A., Oxford : Blackwell Publishing - ISBN 9781405118972 - p. 160 - 181.
Carbohydrate storage and light requirements of tropical moist and dry forest tree species
Poorter, L. ; Kitajima, K. - \ 2007
Ecology 88 (2007)4. - ISSN 0012-9658 - p. 1000 - 1011.
seedling survival - leaf traits - growth-rate - shade - allocation - patterns - ecology - size - acclimatization - regeneration
In many plant communities, there is a negative interspecific correlation between relative growth rates and survival of juveniles. This negative correlation is most likely caused by a trade-off between carbon allocation to growth vs. allocation to defense and storage. Nonstructural carbohydrates (NSC) stored in stems allow plants to overcome periods of stress and should enhance survival. In order to assess how species differ in carbohydrate storage in relation to juvenile light requirements, growth, and survival, we quantified NSC concentrations and pool sizes in sapling stems of 85 woody species in moist semi-evergreen and dry deciduous tropical forests in the rainy season in Bolivia. Moist forest species averaged higher NSC concentrations than dry forest species. Carbohydrate concentrations and pool sizes decreased with the light requirements of juveniles of the species in the moist forest but not in the dry forest. Combined, these results suggest that storage is especially important for species that regenerate in persistently shady habitats, as in the understory of moist evergreen forests. For moist forest species, sapling survival rates increased with NSC concentrations and pool sizes while growth rates declined with the NSC concentrations and pool sizes. No relationships were found for dry forest species. Carbon allocation to storage contributes to the growth¿ survival trade-off through its positive effect on survival. And, a continuum in carbon storage strategies contributes to a continuum in light requirements among species. The link between storage and light requirements is especially strong in moist evergreen forest where species sort out along a light gradient, but disappears in dry deciduous forest where light is a less limiting resource and species sort out along drought and fire gradients. Key words: Bolivia; growth¿survival trade-off; shade tolerance; starch; sugar; total nonstructural carbohydrates (NSC); tropical forest.
|Diversity of tospoviruses in Brazil.
Avila, A.C. ; Pozzer, L. ; Bezerra, I. ; Kormelink, R. ; Prins, M. ; Peters, D. ; Kitajima, E.W. ; Resende, R. - \ 1998
In: 4th International Symposium on Tospoviruses and Thrips in Floral and Vegetable Crops, Wageningen, The Netherlands - p. 32 - 34.
|Tomato spotted wilt virus defective interfering RNAs: important features of their generation and survival.
Inoue-Nagate, A. ; Kormelink, R. ; Sgro, J.Y. ; Nagata, T. ; Kitajima, E.W. ; Goldbach, R. ; Peters, D. - \ 1998
In: 4th International Symposium on Tospoviruses and Thrips in Floral and Vegetable Crops, Wageningen, The Netherlands - p. 4 - 5.
Molecular characterization of tomato spotted wilt virus defective interfering RNAs and detection of truncated L proteins.
Inoue Nagata, A.K. ; Kormelink, R. ; Sgro, J.Y. ; Nagata, T. ; Kitajima, E.W. ; Goldbach, R. ; Peters, D. - \ 1998
Virology 248 (1998). - ISSN 0042-6822 - p. 342 - 356.
|Effects of temperature and host on the generation of tomato spotted wilt virus defective interfering RNA.
Inoue-Nagata, A.K. ; Kormelink, R. ; Nagata, T. ; Kitajima, E.W. ; Goldbach, R. ; Peters, D. - \ 1997
Phytopathology 87 (1997). - ISSN 0031-949X - p. 1168 - 1173.
Generation and characterization of mutants of tomato spotted wilt virus
Oliveira Resende, R. de - \ 1993
Agricultural University. Promotor(en): R.W. Goldbach. - S.l. : De Oliveira Resende - 115
tomatenbronsvlekkenvirus - virologie - moleculaire biologie - tomato spotted wilt virus - virology - molecular biology
In nature, tospoviruses like tomato spotted wilt virus (TSWV) are exclusively transmitted by thrips species (Sakimura, 1962) producing numerous enveloped virions during infection, which accumulate in the cisternae of the endoplasmatic. reticulum. system (Kitajima, 1965; Milne, 1970; Ie, 1971). Under experimental conditions however, it is common practice to maintain the virus by mechanical inoculation onto susceptible host plants.
Repeated passages of animal viruses, certainly at high inoculum densities results in the generation of defective mutants which co-replicate with the wild type virus interfering in their multiplication (Lazzarini et al ., 1981). This phenomenon is reported for only a few plant viruses (Morris & Knorr, 1990). As defective viral mutants lack one or more genetic functions but are still capable to co-replicate, they may constitute useful tools to study viral genes and viral protein functions.
This thesis reports studies aimed to generate and characterize defective forms of TSWV by their biological, serological and genetic properties. The understanding of these characteristics indeed, can help the elucidation the multiple events which take place during the infection process, and ultimately provide new ways to control the virus.
The first attempts to characterize TSWV defective forms showed that non-enveloped virus isolates are generated upon mechanical inoculation (Ie, 1982). These mechanically transmitted isolates were considered to represent morphologically defective forms of TSWV, lacking the lipid envelope though still being infectious (Ie, 1982). Further analysis revealed that these morphologically defective isolates failed to produce detectable amounts of the envelope glycoproteins G1 and G2 (Verkleij & Peters, 1983).
The results reported in this thesis show that during a series of mechanical transfers of TSWV, actually two distinct types of mutants are generated (Chapter 4). Firstly, starting with a wild type, the Dutch isolate of TSWV NL-04, a morphologically-defective isolate was obtained, which had lost its ability to produce the membrane-glycoproteins and, as a consequence, was not able to form enveloped particles. The appearance of such isolates could be followed by ELISA tests and readily detected by electron microscopy (Chapter 3 and 4). Secondly, starting from various TSWV wild type-isolates, defective mutants were obtained that had accumulated deleted forms of the large (L) RNA segment that most likely represented defective interfering (DI) RNAs, since they replicated more rapidly than full-length L RNA and their appearance was often associated with symptom attenuation in host plants (Chapter 4).
After elucidation of the nucleotide sequence of the M RNA of two tospoviruses, i.e. TSWV and Impatiens necrotic spot virus (INSV) (Kormelink et al ., 1992; Law et al. , 1992), the genetic nature of the morphological defectiveness of the envelope-deficient isolates could be identified by comparing their M RNA sequences with those of wild type isolates (Chapter 6). Comparison of (partial) M RNA sequences of several TSWV and INSV isolates revealed that the accumulation of point mutations in the G2/G1 ORF in this RNA may have been the causal event that led to the generation of envelopedeficient isolates during mechanical transmission. It was found that an envelope-deficient isolate (US-01) of INSV had acquired an extra nucleotide in this gene, causing a frameshift and consequently the loss of the putative signal peptide of the glycoprotein precursor (Chapter 6). In this case, the envelope deficiency may be explained by a blockage of the trans-membrane transport, and hence further maturation of the glycoprotein precursor. For the isolate NL-04 of TSWV the morphological defect seems to be caused by the accumulation of point mutations in the glycoprotein precursor rather than deletion of the hydrophobic signal sequence. The accumulation of point mutations in these isolates may either result in dysfunctional glycoproteins which do not become inserted in viral envelopes, or in stop codons though not detected in the sequenced part of the G2/G1 gene, but which are possibly present (further downstream), in the non analyzed part of this gene. The presence of these stop codons would then lead to premature termination of the G2/G1 precursor.
The generation and characterization of the envelope-deficient isolate of TSWV NL-04 has already lead to two important conclusions, with respect of the possible involvement of the glycoproteins during the tospovirus infection cycle. First, it has been observed that this defective-isolate is still able to infect leaf tissues at a similar rate as to that of wild type infection. Thus the glycoproteins (and lipid envelope) are neither essential for cellto-cell movement of the virus, nor for long-distance transport in the plant. The conclusion seems therefore to justify that tospoviruses, during the development of infection, are transported mainly as free nucleocapsid complexes. Secondly, the presence of lipid enveloped (and glycoproteins) appeared to be essential for successful thrips transmission, since sofar, the envelope-deficient isolate of NL-04 fails to show vector transmissibility (Wijkamp, personal communication). This finding strongly suggests a role of G1 and/or G2 glycoproteins in the virus-vector interactions. It is noteworthy in this context, that the primary structure of these proteins contain a so-called "cell attachment site (RGD) at the N- terminus of G2 (Kormelink et al. , 1992) which may be involved in the recognition of a receptor in the thrips midgut.
The results reported in this thesis also show that, tospoviruses generate DI RNAs during sequential passages of the virus at high multiplicity of infection (Chapters 4 and 5). DI RNAs have frequently been described in either positive or negative-stranded
Short repeated nucleotide sequences were identified at the junction sites of various DI molecules and a possible model for their generation is proposed, in which the viral polymerase can jump across secondary structures where these repeated internal sequences are located.
Alternatively, transgenic DI-expressing plant systems could be used, not only to study the viral RNA replication process, but also as an approach towards engineered protection of host plants against virus infection. Due to their features, transgenetically
Since DI RNAs of tospoviruses may be generated in any host system that permits the growth of the wild type virus, it is likely that they are not only generated under laboratory conditions, but also in natural infections. The presence of such molecules in enveloped particles (Chapter 4), indeed indicates that tospovirus DI RNAs can potentially be transmitted by thrips vectors and hence, "survive" in nature. If DI RNAs indeed do occur in natural infections, their presence during virus infection may serve to attenuate the pathogenic effects of the parental virus infection. Their occurrence may also have been advantageous for the evolution of tospovirus and for the establishment of their current, impressive host range.
Distinct levels of relationships between tospovirus isolates.
Avila, A.C. de; Haan, P. de; Smeets, M.L.L. ; O. Resende, R. de; Kormelink, R. ; Kitajima, E.W. ; Goldbach, R.W. ; Peters, D. - \ 1993
Archives of Virology 128 (1993). - ISSN 0304-8608 - p. 211 - 227.
|Comparative cytological and immunogold labelling studies on different isolates of tomato spotted wilt virus.
Kitajima, E.W. ; Avila, A.C. de; O. Resende, R. de; Goldbach, R.W. ; Peters, D. - \ 1992
Journal of submicroscopic cytology and pathology 24 (1992). - ISSN 1122-9497 - p. 1 - 14.
Immuno-electron microscopical detection of tomato spotted wilt virus and its nucleocapsids in crude plant extracts.
Kitajima, E.W. ; O. Resende, R. de; Avila, A.C. de; Goldbach, R.W. ; Peters, D. - \ 1992
Journal of Virological Methods 38 (1992). - ISSN 0166-0934 - p. 313 - 322.
Characterization of a distinct isolate of tomato spotted wilt virus (TSWV) from Impatiens sp. in The Netherlands.
Avila, A.C. de; Haan, P. de; Kitajima, E.W. ; Kormelink, R. ; O. Resende, R. de; Goldbach, R.W. ; Peters, D. - \ 1992
Journal of Phytopathology 134 (1992). - ISSN 0931-1785 - p. 133 - 151.
Generation of envelope and defective interfering RNA mutants of tomato spotted wilt virus by mechanical passage.
O. Resende, R. de; Haan, P. de; Avila, A.C. de; Kitajima, E.W. ; Kormelink, R. ; Goldbach, R.W. ; Peters, D. - \ 1991
Journal of General Virology 72 (1991). - ISSN 0022-1317 - p. 2375 - 2383.
|An overview of tomato spotted wilt virus.
Peters, D. ; Kitajima, E. ; Haan, P. de; Avila, A.C. de; Goldbach, R.W. - \ 1991
In: Virus-thrips-plant interactions of tomato spotted wilt virus - p. 1 - 14.
|The nonstructural protein (NSs) encoded by the ambisense S RNA segment of tomato spotted wilt virus is associated with fibrous structures in infected plant cells.
Kormelink, R. ; Kitajima, E.W. ; Haan, P. de; Zuidema, D. ; Peters, D. ; Goldbach, R.W. - \ 1991
Virology 181 (1991). - ISSN 0042-6822 - p. 459 - 468.
|Defective isolates of tomato spotted wilt virus.
O. Resende, R. de; Avila, A.C. de; Kitajima, E. ; Goldbach, R.W. ; Peters, D. - \ 1991
In: Virus-thrips-plant interactions of tomato spotted wilt virus - p. 71 - 76.