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1. Fusarium: more than a node or a foot-shaped basal cell.

Author

Crous, PW, Lombard, L, Sandoval-Denis, M, Seifert, KA, Schroers, H-J, Chaverri, P, Gené, J, Guarro, J, Hirooka, Y, Bensch, K, Kema, GHJ, Lamprecht, SC, Cai, L, Rossman, AY, Stadler, M, Summerbell, RC, Taylor, JW, Ploch, S, Visagie, CM, Yilmaz, N, Frisvad, JC, Abdel-Azeem, AM, Abdollahzadeh, J, Abdolrasouli, A, Akulov, A, Alberts, JF, Araújo, JPM, Ariyawansa, HA, Bakhshi, M, Bendiksby, M, Ben Hadj Amor, A, Bezerra, JDP, Boekhout, T, Câmara, MPS, Carbia, M, Cardinali, G, Castañeda-Ruiz, RF, Celis, A, Chaturvedi, V, Collemare, J, Croll, D, Damm, U, Decock, CA, de Vries, RP, Ezekiel, CN, Fan, XL, Fernández, NB, Gaya, E, González, CD, Gramaje, D, Groenewald, JZ, Grube, M, Guevara-Suarez, M, Gupta, VK, Guarnaccia, V, Haddaji, A, Hagen, F, Haelewaters, D, Hansen, K, Hashimoto, A, Hernández-Restrepo, M, Houbraken, J, Hubka, V, Hyde, KD, Iturriaga, T, Jeewon, R, Johnston, PR, Jurjević, Ž, Karalti, I, Korsten, L, Kuramae, EE, Kušan, I, Labuda, R, Lawrence, DP, Lee, HB, Lechat, C, Li, HY, Litovka, YA, Maharachchikumbura, SSN, Marin-Felix, Y, Matio Kemkuignou, B, Matočec, N, McTaggart, AR, Mlčoch, P, Mugnai, L, Nakashima, C, Nilsson, RH, Noumeur, SR, Pavlov, IN, Peralta, MP, Phillips, AJL, Pitt, JI, Polizzi, G, Quaedvlieg, W, Rajeshkumar, KC, Restrepo, S, Rhaiem, A, Robert, J, Robert, V, and Rodrigues, AM

Subjects
Apiognomonia platani (Lév.) L. Lombard, Atractium ciliatum Link, Atractium pallidum Bonord., Calloria tremelloides (Grev.) L. Lombard, Cephalosporium sacchari E.J. Butler, Cosmosporella cavisperma (Corda) Sand.-Den., L. Lombard & Crous, Cylindrodendrum orthosporum (Sacc. & P. Syd.) L. Lombard, Dialonectria volutella (Ellis & Everh.) L. Lombard & Sand.-Den., Fusarium aeruginosum Delacr., Fusarium agaricorum Sarrazin, Fusarium albidoviolaceum Dasz., Fusarium aleyrodis Petch, Fusarium amentorum Lacroix, Fusarium annuum Leonian, Fusarium arcuatum Berk. & M.A. Curtis, Fusarium aridum O.A. Pratt, Fusarium armeniacum (G.A. Forbes et al.) L.W. Burgess & Summerell, Fusarium arthrosporioides Sherb., Fusarium asparagi Delacr., Fusarium batatas Wollenw., Fusarium biforme Sherb., Fusarium buharicum Jacz. ex Babajan & Teterevn.-Babajan, Fusarium cactacearum Pasin. & Buzz.-Trav., Fusarium cacti-maxonii Pasin. & Buzz.-Trav., Fusarium caudatum Wollenw., Fusarium cavispermum Corda, Fusarium cepae Hanzawa, Fusarium cesatii Rabenh., Fusarium citriforme Jamal., Fusarium citrinum Wollenw., Fusarium citrulli Taubenh., Fusarium clavatum Sherb., Fusarium coccinellum Kalchbr., Fusarium cromyophthoron Sideris, Fusarium cucurbitae Taubenh., Fusarium cuneiforme Sherb., Fusarium delacroixii Sacc., Fusarium dimerum var. nectrioides Wollenw., Fusarium echinatum Sand.-Den. & G.J. Marais, Fusarium epicoccum McAlpine, Fusarium eucheliae Sartory, R. Sartory & J. Mey., Fusarium fissum Peyl, Fusarium flocciferum Corda, Fusarium gemmiperda Aderh., Fusarium genevense Dasz., Fusarium graminearum Schwabe, Fusarium graminum Corda, Fusarium heterosporioides Fautrey, Fusarium heterosporum Nees & T. Nees, Fusarium idahoanum O.A. Pratt, Fusarium juruanum Henn., Fusarium lanceolatum O.A. Pratt, Fusarium lateritium Nees, Fusarium loncheceras Sideris, Fusarium longipes Wollenw. & Reinking, Fusarium lyarnte J.L. Walsh, Sangal., L.W. Burgess, E.C.Y. Liew & Summerell, Fusarium malvacearum Taubenh., Fusarium martii f. phaseoli Burkh., Fusarium muentzii Delacr., Fusarium nigrum O.A. Pratt, Fusarium oxysporum var. asclerotium Sherb., Fusarium palczewskii Jacz., Fusarium palustre W.H. Elmer & Marra, Fusarium polymorphum Matr., Fusarium poolense Taubenh., Fusarium prieskaense G.J. Marais & Sand.-Den., Fusarium prunorum McAlpine, Fusarium pusillum Wollenw., Fusarium putrefaciens Osterw., Fusarium redolens Wollenw., Fusarium reticulatum Mont., Fusarium rhizochromatistes Sideris, Fusarium rhizophilum Corda, Fusarium rhodellum McAlpine, Fusarium roesleri Thüm., Fusarium rostratum Appel & Wollenw., Fusarium rubiginosum Appel & Wollenw., Fusarium rubrum Parav., Fusarium samoense Gehrm., Fusarium scirpi Lambotte & Fautrey, Fusarium secalis Jacz., Fusarium spinaciae Hungerf., Fusarium sporotrichioides Sherb., Fusarium stercoris Fuckel, Fusarium stilboides Wollenw., Fusarium stillatum De Not. ex Sacc., Fusarium sublunatum Reinking, Fusarium succisae Schröt. ex Sacc., Fusarium tabacivorum Delacr., Fusarium trichothecioides Wollenw., Fusarium tritici Liebman, Fusarium tuberivorum Wilcox & G.K. Link, Fusarium tumidum var. humi Reinking, Fusarium ustilaginis Kellerm. & Swingle, Fusarium viticola Thüm., Fusarium werrikimbe J.L. Walsh, L.W. Burgess, E.C.Y. Liew & B.A. Summerell, Fusarium willkommii Lindau, Fusarium xylarioides Steyaert, Fusarium zygopetali Delacr., Fusicolla meniscoidea L. Lombard & Sand.-Den., Fusicolla quarantenae J.D.P. Bezerra, Sand.-Den., Crous & Souza-Motta, Fusicolla sporellula Sand.-Den. & L. Lombard, Fusisporium andropogonis Cooke ex Thüm., Fusisporium anthophilum A. Braun, Fusisporium arundinis Corda, Fusisporium avenaceum Fr., Fusisporium clypeaster Corda, Fusisporium culmorum Wm.G. Sm., Fusisporium didymum Harting, Fusisporium elasticae Thüm., Fusisporium episphaericum Cooke & Ellis, Fusisporium flavidum Bonord., Fusisporium hordei Wm.G. Sm., Fusisporium incarnatum Roberge ex Desm., Fusisporium lolii Wm.G. Sm., Fusisporium pandani Corda, Gibberella phyllostachydicola W. Yamam., Hymenella aurea (Corda) L. Lombard, Hymenella spermogoniopsis (Jul. Müll.) L. Lombard & Sand.-Den., Luteonectria Sand.-Den., L. Lombard, Schroers & Rossman, Luteonectria albida (Rossman) Sand.-Den. & L. Lombard, Luteonectria nematophila (Nirenberg & Hagedorn) Sand.-Den. & L. Lombard, Macroconia bulbipes Crous & Sand.-Den., Macroconia phlogioides Sand.-Den. & Crous, Menispora penicillata Harz, Multi-gene phylogeny, Mycotoxins, Nectriaceae, Neocosmospora, Neocosmospora epipeda Quaedvl. & Sand.-Den., Neocosmospora floridana (T. Aoki et al.) L. Lombard & Sand.-Den., Neocosmospora merkxiana Quaedvl. & Sand.-Den., Neocosmospora neerlandica Crous & Sand.-Den., Neocosmospora nelsonii Crous & Sand.-Den., Neocosmospora obliquiseptata (T. Aoki et al.) L. Lombard & Sand.-Den., Neocosmospora pseudopisi Sand.-Den. & L. Lombard, Neocosmospora rekana (Lynn & Marinc.) L. Lombard & Sand.-Den., Neocosmospora tuaranensis (T. Aoki et al.) L. Lombard & Sand.-Den., Nothofusarium Crous, Sand.-Den. & L. Lombard, Nothofusarium devonianum L. Lombard, Crous & Sand.-Den., Novel taxa, Pathogen, Scolecofusarium L. Lombard, Sand.-Den. & Crous, Scolecofusarium ciliatum (Link) L. Lombard, Sand.-Den. & Crous, Selenosporium equiseti Corda, Selenosporium hippocastani Corda, Selenosporium sarcochroum Desm, Selenosporium urticearum Corda., Setofusarium (Nirenberg & Samuels) Crous & Sand.-Den., Setofusarium setosum (Samuels & Nirenberg) Sand.-Den. & Crous., Sphaeria sanguinea var. cicatricum Berk., Sporotrichum poae Peck., Stylonectria corniculata Gräfenhan, Crous & Sand.-Den., Stylonectria hetmanica Akulov, Crous & Sand.-Den., Taxonomy, Mycology & Parasitology, Microbiology
Abstract

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).

Published
2021

3. Comparison of light- and SST-based geolocation with satellite telemetry in free-ranging albatrosses

Author

Shaffer, Scott A, Tremblay, Y, Awkerman, J A, Henry, R W, Teo, SLH, Anderson, D J, Croll, D A, Block, B A, and Costa, D P

Subjects
biologging, telemetry, tracking, SST, albatross, seabird, Laysan, black-footed, geolocation, archival tag
Abstract

Light-based archival tags are increasingly being used on free- ranging marine vertebrates to study their movements using geolocation estimates. These methods use algorithms that incorporate threshold light techniques to determine longitude and latitude. More recently, researchers have begun using sea surface temperature (SST) to determine latitude in temperate regions. The accuracy and application of these algorithms have not been validated on free-ranging birds. Errors in both geolocation methods were quantified by double-tagging Laysan (Phoebastria immutabilis Rothschild) and black-footed (P. nigripes Audubon) albatrosses with both leg-mounted archival tags that measured SST and ambient light, and satellite transmitters. Laysan albatrosses were captured and released from breeding colonies on Tern Island, northwestern Hawaiian Islands (23 degrees 52'N, 166 degrees 17'W) and Guadalupe Island, Mexico (28 degrees 31'N, 118 degrees 10'W) and black-footed albatrosses from Tern Island. Studies were carried out between December 2002 and March 2003. For all birds combined, the mean +/- SD great circle (GC) distance between light-based locations and satellite-derived locations was 400 +/- 298 km (n=131). Errors in geolocation positions were reduced to 202 +/- 171 km (n=154) when light-based longitude and SST-based latitude (i.e. SST/light) were used to establish locations. The SST/light method produced comparable results for two Laysan albatross populations that traveled within distinctly different oceanic regions (open ocean vs more coastal) whereas light-based methods produced greater errors in the coastal population. Archival tags deployed on black-footed albatrosses returned a significantly higher proportion of lower-quality locations, which was attributed to interference of the light sensor on the tag. Overall, the results demonstrate that combining measures of light-based longitude and SST-based latitude significantly reduces the error in location estimates for albatrosses and can provide valid latitude estimates during the equinoxes, when light-based latitude measurements are indeterminate.

Published
2005

5. Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population

Author

Çilingir, F G; https://orcid.org/0000-0002-4575-1487, A’Bear, L, Hansen, D, Davis, L R, Bunbury, N, Ozgul, A, Croll, D; https://orcid.org/0000-0002-2072-380X, Grossen, Christine; https://orcid.org/0000-0003-4157-1910, Çilingir, F G; https://orcid.org/0000-0002-4575-1487, A’Bear, L, Hansen, D, Davis, L R, Bunbury, N, Ozgul, A, Croll, D; https://orcid.org/0000-0002-2072-380X, and Grossen, Christine; https://orcid.org/0000-0003-4157-1910

Abstract

The Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two giant tortoise species left in the world. The species is endemic to Aldabra Atoll in Seychelles and is considered vulnerable due to its limited distribution and threats posed by climate change. Genomic resources for A. gigantea are lacking, hampering conservation efforts focused on both wild and ex-situ populations. A high-quality genome would also open avenues to investigate the genetic basis of the exceptionally long lifespan. Here, we produced the first chromosome-level de novo genome assembly of A. gigantea using PacBio High-Fidelity sequencing and high-throughput chromosome conformation capture (Hi-C). We produced a 2.37 Gbp assembly with a scaffold N50 of 148.6 Mbp and a resolution into 26 chromosomes. RNAseq-assisted gene model prediction identified 23,953 protein-coding genes and 1.1 Gbp of repetitive sequences. Synteny analyses among turtle genomes revealed high levels of chromosomal collinearity even among distantly related taxa. We also performed a low-coverage re-sequencing of 30 individuals from wild populations and two zoo individuals. Our genome-wide population structure analyses detected genetic population structure in the wild and identified the most likely origin of the zoo-housed individuals. The high-quality chromosome-level reference genome for A. gigantea is one of the most complete turtle genomes available. It is a powerful tool to assess the population structure in the wild population and reveal the geographic origins of ex-situ individuals relevant for genetic diversity management and rewilding efforts.

Published
2022

8. Fusarium: more than a node or a foot-shaped basal cell

Author

Crous, P. W., Lombard, L., Sandoval-Denis, M., Seifert, K. A., Schroers, H. J., Chaverri, P., Gené, J., Guarro, J., Hirooka, Y., Bensch, K., Kema, G. H.J., Lamprecht, S. C., Cai, L., Rossman, A. Y., Stadler, M., Summerbell, R. C., Taylor, J. W., Ploch, S., Visagie, C. M., Yilmaz, N., Frisvad, J. C., Abdel-Azeem, A. M., Abdollahzadeh, J., Abdolrasouli, A., Akulov, A., Alberts, J. F., Araújo, J. P.M., Ariyawansa, H. A., Bakhshi, M., Bendiksby, M., Ben Hadj Amor, A., Bezerra, J. D.P., Boekhout, T., Câmara, M. P.S., Carbia, M., Cardinali, G., Castañeda-Ruiz, R. F., Celis, A., Chaturvedi, V., Collemare, J., Croll, D., Damm, U., Decock, C. A., de Vries, R. P., Ezekiel, C. N., Fan, X. L., Fernández, N. B., Gaya, E., González, C. D., Gramaje, D., Groenewald, J. Z., Grube, M., Guevara-Suarez, M., Gupta, V. K., Guarnaccia, V., Haddaji, A., Hagen, F., Haelewaters, D., Hansen, K., Hashimoto, A., Hernández-Restrepo, M., Houbraken, J., Hubka, V., Hyde, K. D., Iturriaga, T., Jeewon, R., Johnston, P. R., Jurjević, Karalti, Korsten, L., Kuramae, E. E., Kušan, I., Labuda, R., Lawrence, D. P., Lee, H. B., Lechat, C., Li, H. Y., Litovka, Y. A., Maharachchikumbura, S. S.N., Marin-Felix, Y., Matio Kemkuignou, B., Matočec, N., McTaggart, A. R., Mlčoch, P., Mugnai, L., Nakashima, C., Nilsson, R. H., Noumeur, S. R., Pavlov, I. N., Peralta, M. P., Phillips, A. J.L., Pitt, J. I., Polizzi, G., Quaedvlieg, W., Rajeshkumar, K. C., Restrepo, S., Rhaiem, A., Robert, J., Robert, V., Rodrigues, A. M., Salgado-Salazar, C., Samson, R. A., Santos, A. C.S., Shivas, R. G., Souza-Motta, C. M., Sun, G. Y., Swart, W. J., Szoke, S., Tan, Y. P., Taylor, J. E., Taylor, P. W.J., Tiago, P. V., Váczy, K. Z., van de Wiele, N., van der Merwe, N. A., Verkley, G. J.M., Vieira, W. A.S., Vizzini, A., Weir, B. S., Wijayawardene, N. N., Xia, J. W., Yáñez-Morales, M. J., Yurkov, A., Zamora, J. C., Zare, R., Zhang, C. L., Thines, M., Crous, P. W., Lombard, L., Sandoval-Denis, M., Seifert, K. A., Schroers, H. J., Chaverri, P., Gené, J., Guarro, J., Hirooka, Y., Bensch, K., Kema, G. H.J., Lamprecht, S. C., Cai, L., Rossman, A. Y., Stadler, M., Summerbell, R. C., Taylor, J. W., Ploch, S., Visagie, C. M., Yilmaz, N., Frisvad, J. C., Abdel-Azeem, A. M., Abdollahzadeh, J., Abdolrasouli, A., Akulov, A., Alberts, J. F., Araújo, J. P.M., Ariyawansa, H. A., Bakhshi, M., Bendiksby, M., Ben Hadj Amor, A., Bezerra, J. D.P., Boekhout, T., Câmara, M. P.S., Carbia, M., Cardinali, G., Castañeda-Ruiz, R. F., Celis, A., Chaturvedi, V., Collemare, J., Croll, D., Damm, U., Decock, C. A., de Vries, R. P., Ezekiel, C. N., Fan, X. L., Fernández, N. B., Gaya, E., González, C. D., Gramaje, D., Groenewald, J. Z., Grube, M., Guevara-Suarez, M., Gupta, V. K., Guarnaccia, V., Haddaji, A., Hagen, F., Haelewaters, D., Hansen, K., Hashimoto, A., Hernández-Restrepo, M., Houbraken, J., Hubka, V., Hyde, K. D., Iturriaga, T., Jeewon, R., Johnston, P. R., Jurjević, Karalti, Korsten, L., Kuramae, E. E., Kušan, I., Labuda, R., Lawrence, D. P., Lee, H. B., Lechat, C., Li, H. Y., Litovka, Y. A., Maharachchikumbura, S. S.N., Marin-Felix, Y., Matio Kemkuignou, B., Matočec, N., McTaggart, A. R., Mlčoch, P., Mugnai, L., Nakashima, C., Nilsson, R. H., Noumeur, S. R., Pavlov, I. N., Peralta, M. P., Phillips, A. J.L., Pitt, J. I., Polizzi, G., Quaedvlieg, W., Rajeshkumar, K. C., Restrepo, S., Rhaiem, A., Robert, J., Robert, V., Rodrigues, A. M., Salgado-Salazar, C., Samson, R. A., Santos, A. C.S., Shivas, R. G., Souza-Motta, C. M., Sun, G. Y., Swart, W. J., Szoke, S., Tan, Y. P., Taylor, J. E., Taylor, P. W.J., Tiago, P. V., Váczy, K. Z., van de Wiele, N., van der Merwe, N. A., Verkley, G. J.M., Vieira, W. A.S., Vizzini, A., Weir, B. S., Wijayawardene, N. N., Xia, J. W., Yáñez-Morales, M. J., Yurkov, A., Zamora, J. C., Zare, R., Zhang, C. L., and Thines, M.

Abstract

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In

Published
2021

9. Genome-scale phylogenies reveal relationships among Parastagonospora species infecting domesticated and wild grasses

Author

Croll, D., Crous, P.W. (Pedro Willem), Pereira, D., Mordecai, E.A., McDonald, B.A., Brunner, P.C., Croll, D., Crous, P.W. (Pedro Willem), Pereira, D., Mordecai, E.A., McDonald, B.A., and Brunner, P.C.

Abstract

Several plant pathogenic Parastagonospora species have been identified infecting wheat and other cereals over the past 50 years. As new lineages were discovered, naming conventions grew unwieldy and the relationships with previously recognized species remained unclear. We used genome sequencing to clarify relationships among these species and provided new names for most of these species. Six of the nine described Parastagonospora species were recovered from wheat, with five of these species coming from Iran. Genome sequences revealed that three strains thought to be hybrids between P. nodorum and P. pseudonodorum were not actually hybrids, but rather represented rare gene introgressions between those species. Our data are consistent with the hypothesis that P. nodorum originated as a pathogen of wild grasses in the Fertile Crescent, then emerged as a wheat pathogen via host-tracking during the domestication of wheat in the same region. The discovery of a diverse array of Parastagonospora species infecting wheat in Iran suggests that new wheat pathogens could emerge from this region in the future.

Published
2021
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10. Fusarium: more than a node or a foot-shaped basal cell

Author

Sub Molecular Microbiology, Sub Molecular Plant Physiology, Sub Ecology and Biodiversity, Molecular Microbiology, Molecular Plant Physiology, Ecology and Biodiversity, Crous, P. W., Lombard, L., Sandoval-Denis, M., Seifert, K. A., Schroers, H. J., Chaverri, P., Gené, J., Guarro, J., Hirooka, Y., Bensch, K., Kema, G. H.J., Lamprecht, S. C., Cai, L., Rossman, A. Y., Stadler, M., Summerbell, R. C., Taylor, J. W., Ploch, S., Visagie, C. M., Yilmaz, N., Frisvad, J. C., Abdel-Azeem, A. M., Abdollahzadeh, J., Abdolrasouli, A., Akulov, A., Alberts, J. F., Araújo, J. P.M., Ariyawansa, H. A., Bakhshi, M., Bendiksby, M., Ben Hadj Amor, A., Bezerra, J. D.P., Boekhout, T., Câmara, M. P.S., Carbia, M., Cardinali, G., Castañeda-Ruiz, R. F., Celis, A., Chaturvedi, V., Collemare, J., Croll, D., Damm, U., Decock, C. A., de Vries, R. P., Ezekiel, C. N., Fan, X. L., Fernández, N. B., Gaya, E., González, C. D., Gramaje, D., Groenewald, J. Z., Grube, M., Guevara-Suarez, M., Gupta, V. K., Guarnaccia, V., Haddaji, A., Hagen, F., Haelewaters, D., Hansen, K., Hashimoto, A., Hernández-Restrepo, M., Houbraken, J., Hubka, V., Hyde, K. D., Iturriaga, T., Jeewon, R., Johnston, P. R., Jurjević, Karalti, Korsten, L., Kuramae, E. E., Kušan, I., Labuda, R., Lawrence, D. P., Lee, H. B., Lechat, C., Li, H. Y., Litovka, Y. A., Maharachchikumbura, S. S.N., Marin-Felix, Y., Matio Kemkuignou, B., Matočec, N., McTaggart, A. R., Mlčoch, P., Mugnai, L., Nakashima, C., Nilsson, R. H., Noumeur, S. R., Pavlov, I. N., Peralta, M. P., Phillips, A. J.L., Pitt, J. I., Polizzi, G., Quaedvlieg, W., Rajeshkumar, K. C., Restrepo, S., Rhaiem, A., Robert, J., Robert, V., Rodrigues, A. M., Salgado-Salazar, C., Samson, R. A., Santos, A. C.S., Shivas, R. G., Souza-Motta, C. M., Sun, G. Y., Swart, W. J., Szoke, S., Tan, Y. P., Taylor, J. E., Taylor, P. W.J., Tiago, P. V., Váczy, K. Z., van de Wiele, N., van der Merwe, N. A., Verkley, G. J.M., Vieira, W. A.S., Vizzini, A., Weir, B. S., Wijayawardene, N. N., Xia, J. W., Yáñez-Morales, M. J., Yurkov, A., Zamora, J. C., Zare, R., Zhang, C. L., Thines, M., Sub Molecular Microbiology, Sub Molecular Plant Physiology, Sub Ecology and Biodiversity, Molecular Microbiology, Molecular Plant Physiology, Ecology and Biodiversity, Crous, P. W., Lombard, L., Sandoval-Denis, M., Seifert, K. A., Schroers, H. J., Chaverri, P., Gené, J., Guarro, J., Hirooka, Y., Bensch, K., Kema, G. H.J., Lamprecht, S. C., Cai, L., Rossman, A. Y., Stadler, M., Summerbell, R. C., Taylor, J. W., Ploch, S., Visagie, C. M., Yilmaz, N., Frisvad, J. C., Abdel-Azeem, A. M., Abdollahzadeh, J., Abdolrasouli, A., Akulov, A., Alberts, J. F., Araújo, J. P.M., Ariyawansa, H. A., Bakhshi, M., Bendiksby, M., Ben Hadj Amor, A., Bezerra, J. D.P., Boekhout, T., Câmara, M. P.S., Carbia, M., Cardinali, G., Castañeda-Ruiz, R. F., Celis, A., Chaturvedi, V., Collemare, J., Croll, D., Damm, U., Decock, C. A., de Vries, R. P., Ezekiel, C. N., Fan, X. L., Fernández, N. B., Gaya, E., González, C. D., Gramaje, D., Groenewald, J. Z., Grube, M., Guevara-Suarez, M., Gupta, V. K., Guarnaccia, V., Haddaji, A., Hagen, F., Haelewaters, D., Hansen, K., Hashimoto, A., Hernández-Restrepo, M., Houbraken, J., Hubka, V., Hyde, K. D., Iturriaga, T., Jeewon, R., Johnston, P. R., Jurjević, Karalti, Korsten, L., Kuramae, E. E., Kušan, I., Labuda, R., Lawrence, D. P., Lee, H. B., Lechat, C., Li, H. Y., Litovka, Y. A., Maharachchikumbura, S. S.N., Marin-Felix, Y., Matio Kemkuignou, B., Matočec, N., McTaggart, A. R., Mlčoch, P., Mugnai, L., Nakashima, C., Nilsson, R. H., Noumeur, S. R., Pavlov, I. N., Peralta, M. P., Phillips, A. J.L., Pitt, J. I., Polizzi, G., Quaedvlieg, W., Rajeshkumar, K. C., Restrepo, S., Rhaiem, A., Robert, J., Robert, V., Rodrigues, A. M., Salgado-Salazar, C., Samson, R. A., Santos, A. C.S., Shivas, R. G., Souza-Motta, C. M., Sun, G. Y., Swart, W. J., Szoke, S., Tan, Y. P., Taylor, J. E., Taylor, P. W.J., Tiago, P. V., Váczy, K. Z., van de Wiele, N., van der Merwe, N. A., Verkley, G. J.M., Vieira, W. A.S., Vizzini, A., Weir, B. S., Wijayawardene, N. N., Xia, J. W., Yáñez-Morales, M. J., Yurkov, A., Zamora, J. C., Zare, R., Zhang, C. L., and Thines, M.

Published
2021

11. Fusarium: more than a node or a foot-shaped basal cell

Author

Crous, P.W., Lombard, L., Sandoval-Denis, M., Seifert, K.A., Schroers, H.-J., Chaverri, P., Gené, J., Guarro, J., Hirooka, Y., Bensch, K., Kema, G.H.J., Lamprecht, S.C., Cai, L., Rossman, A.Y., Stadler, M., Summerbell, R.C., Taylor, J.W., Ploch, S., Visagie, C.M., Yilmaz, N., Frisvad, J.C., Abdel-Azeem, A.M., Abdollahzadeh, J., Abdolrasouli, A., Akulov, A., Alberts, J.F., Araújo, J.P.M., Ariyawansa, H.A., Bakhshi, M., Bendiksby, M., Amor, A. Ben Hadj, Bezerra, J.D.P., Boekhout, T., Câmara, M.P.S., Carbia, M., Cardinali, G., Castañeda-Ruiz, R.F., Celis, A., Chaturvedi, V., Collemare, J., Croll, D., Damm, U., Decock, C.A., Vries, R.P. de, Ezekiel, C.N., Fan, X.L., Fernández, N.B., Gaya, E., González, C.D., Gramaje, D., Groenewald, J.Z., Grube, M., Guevara-Suarez, M., Gupta, V.K., Guarnaccia, V., Haddaji, A., Hagen, F., Haelewaters, D., Hansen, K., Hashimoto, A., Hernández-Restrepo, M., Houbraken, J., Hubka, V., Hyde, K.D., Iturriaga, T., Jeewon, R., Johnston, P.R., Jurjević, Ž., Karalti, İ., Korsten, L., Kuramae, E.E., Kušan, I., Labuda, R., Lawrence, D.P., Lee, H.B., Lechat, C., Li, H.Y., Litovka, Y.A., Maharachchikumbura, S.S.N., Marin-Felix, Y., Kemkuignou, B. Matio, Matočec, N., McTaggart, A.R., Mlčoch, P., Mugnai, L., Nakashima, C., Nilsson, R.H., Noumeur, S.R., Pavlov, I.N., Peralta, M.P., Phillips, A.J.L., Pitt, J.I., Polizzi, G., Quaedvlieg, W., Rajeshkumar, K.C., Restrepo, S., Rhaiem, A., Robert, J., Robert, V., Rodrigues, A.M., Salgado-Salazar, C., Samson, R.A., Santos, A.C.S., Shivas, R.G., Souza-Motta, C.M., Sun, G.Y., Swart, W.J., Szoke, S., Tan, Y.P., Taylor, J.E., Taylor, P.W.J., Tiago, P.V., Váczy, K.Z., Wiele, N. van de, Merwe, N.A. van der, Verkley, G.J.M., Vieira, W.A.S., Vizzini, A., Weir, B.S., Wijayawardene, N.N., Xia, J.W., Yáñez-Morales, M.J., Yurkov, A., Zamora, J.C., Zare, R., Zhang, C.L., Thines, M., Crous, P.W., Lombard, L., Sandoval-Denis, M., Seifert, K.A., Schroers, H.-J., Chaverri, P., Gené, J., Guarro, J., Hirooka, Y., Bensch, K., Kema, G.H.J., Lamprecht, S.C., Cai, L., Rossman, A.Y., Stadler, M., Summerbell, R.C., Taylor, J.W., Ploch, S., Visagie, C.M., Yilmaz, N., Frisvad, J.C., Abdel-Azeem, A.M., Abdollahzadeh, J., Abdolrasouli, A., Akulov, A., Alberts, J.F., Araújo, J.P.M., Ariyawansa, H.A., Bakhshi, M., Bendiksby, M., Amor, A. Ben Hadj, Bezerra, J.D.P., Boekhout, T., Câmara, M.P.S., Carbia, M., Cardinali, G., Castañeda-Ruiz, R.F., Celis, A., Chaturvedi, V., Collemare, J., Croll, D., Damm, U., Decock, C.A., Vries, R.P. de, Ezekiel, C.N., Fan, X.L., Fernández, N.B., Gaya, E., González, C.D., Gramaje, D., Groenewald, J.Z., Grube, M., Guevara-Suarez, M., Gupta, V.K., Guarnaccia, V., Haddaji, A., Hagen, F., Haelewaters, D., Hansen, K., Hashimoto, A., Hernández-Restrepo, M., Houbraken, J., Hubka, V., Hyde, K.D., Iturriaga, T., Jeewon, R., Johnston, P.R., Jurjević, Ž., Karalti, İ., Korsten, L., Kuramae, E.E., Kušan, I., Labuda, R., Lawrence, D.P., Lee, H.B., Lechat, C., Li, H.Y., Litovka, Y.A., Maharachchikumbura, S.S.N., Marin-Felix, Y., Kemkuignou, B. Matio, Matočec, N., McTaggart, A.R., Mlčoch, P., Mugnai, L., Nakashima, C., Nilsson, R.H., Noumeur, S.R., Pavlov, I.N., Peralta, M.P., Phillips, A.J.L., Pitt, J.I., Polizzi, G., Quaedvlieg, W., Rajeshkumar, K.C., Restrepo, S., Rhaiem, A., Robert, J., Robert, V., Rodrigues, A.M., Salgado-Salazar, C., Samson, R.A., Santos, A.C.S., Shivas, R.G., Souza-Motta, C.M., Sun, G.Y., Swart, W.J., Szoke, S., Tan, Y.P., Taylor, J.E., Taylor, P.W.J., Tiago, P.V., Váczy, K.Z., Wiele, N. van de, Merwe, N.A. van der, Verkley, G.J.M., Vieira, W.A.S., Vizzini, A., Weir, B.S., Wijayawardene, N.N., Xia, J.W., Yáñez-Morales, M.J., Yurkov, A., Zamora, J.C., Zare, R., Zhang, C.L., and Thines, M.

Abstract

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In th

Published
2021

12. Fusarium: more than a node or a foot-shaped basal cell

Author

Universitat Rovira i Virgili, Crous, P. W.; Lombard, L.; Sandoval-Denis, M.; Seifert, K. A.; Schroers, H-J; Chaverri, P.; Gene, J.; Guarro, J.; Hirooka, Y.; Bensch, K.; Kema, G. H. J.; Lamprecht, S. C.; Cai, L.; Rossman, A. Y.; Stadler, M.; Summerbell, R. C.; Taylor, J. W.; Ploch, S.; Visagie, C. M.; Yilmaz, N.; Frisvad, J. C.; Abdel-Azeem, A. M.; Abdollahzadeh, J.; Abdolrasouli, A.; Akulov, A.; Alberts, J. F.; Araujo, J. P. M.; Ariyawansa, H. A.; Bakhshi, M.; Bendiksby, M.; Amor, A. Ben Hadj; Bezerra, J. D. P.; Boekhout, T.; Camara, M. P. S.; Carbia, M.; Cardinali, G.; Castaneda-Ruiz, R. F.; Celis, A.; Chaturvedi, V; Collemare, J.; Croll, D.; Damm, U.; Decock, C. A.; de Vries, R. P.; Ezekiel, C. N.; Fan, X. L.; Fernandez, N. B.; Gaya, E.; Gonzalez, C. D.; Gramaje, D.; Groenewald, J. Z.; Grube, M.; Guevara-Suarez, M.; Gupta, V. K.; Guarnaccia, V; Haddaji, A.; Hagen, F.; Haelewaters, D.; Hansen, K.; Hashimoto, A.; Hernandez-Restrepo, M.; Houbraken, J.; Hubka, V; Hyde, K. D.; Iturriaga, T.; Jeewon, R.; Johnston, P. R.; Jurjevic, Z.; Karalti, I; Korsten, L.; Kuramae, E. E.; Kusan, I; Labuda, R.; Lawrence, D. P.; Lee, H. B.; Lechat, C.; Li, H. Y.; Litovka, Y. A.; Maharachchikumbura, S. S. N.; Marin-Felix, Y.; Kemkuignou, B. Matio; Matocec, N.; McTaggart, A. R.; Mlcoch, P.; Mugnai, L.; Nakashima, C.; Nilsson, R. H.; Noumeur, S. R.; Pavlov, I. N.; Peralta, M. P.; Phillips, A. J. L.; Pitt, J., I; Polizzi, G.; Quaedvlieg, W.; Rajeshkumar, K. C.; Restrepo, S.; Rhaiem, A.; Robert, J.; Robert, V; Rodrigues, A. M.; Salgado-Salazar, C.; Samson, R. A.; Santos, A. C. S.; Shivas, R. G.; Souza-Motta, C. M.; Sun, G. Y.; Swart, W. J.; Szoke, S.; Tan, Y. P.; Taylor, J. E.; Taylor, P. W. J.; Tiago, P., V; Vaczy, K. Z.; van de Wiele, N.; van der Merwe, N. A.; Verkley, G. J. M.; Vieira, W. A. S.; Vizzini, A.; Weir, B. S., Universitat Rovira i Virgili, and Crous, P. W.; Lombard, L.; Sandoval-Denis, M.; Seifert, K. A.; Schroers, H-J; Chaverri, P.; Gene, J.; Guarro, J.; Hirooka, Y.; Bensch, K.; Kema, G. H. J.; Lamprecht, S. C.; Cai, L.; Rossman, A. Y.; Stadler, M.; Summerbell, R. C.; Taylor, J. W.; Ploch, S.; Visagie, C. M.; Yilmaz, N.; Frisvad, J. C.; Abdel-Azeem, A. M.; Abdollahzadeh, J.; Abdolrasouli, A.; Akulov, A.; Alberts, J. F.; Araujo, J. P. M.; Ariyawansa, H. A.; Bakhshi, M.; Bendiksby, M.; Amor, A. Ben Hadj; Bezerra, J. D. P.; Boekhout, T.; Camara, M. P. S.; Carbia, M.; Cardinali, G.; Castaneda-Ruiz, R. F.; Celis, A.; Chaturvedi, V; Collemare, J.; Croll, D.; Damm, U.; Decock, C. A.; de Vries, R. P.; Ezekiel, C. N.; Fan, X. L.; Fernandez, N. B.; Gaya, E.; Gonzalez, C. D.; Gramaje, D.; Groenewald, J. Z.; Grube, M.; Guevara-Suarez, M.; Gupta, V. K.; Guarnaccia, V; Haddaji, A.; Hagen, F.; Haelewaters, D.; Hansen, K.; Hashimoto, A.; Hernandez-Restrepo, M.; Houbraken, J.; Hubka, V; Hyde, K. D.; Iturriaga, T.; Jeewon, R.; Johnston, P. R.; Jurjevic, Z.; Karalti, I; Korsten, L.; Kuramae, E. E.; Kusan, I; Labuda, R.; Lawrence, D. P.; Lee, H. B.; Lechat, C.; Li, H. Y.; Litovka, Y. A.; Maharachchikumbura, S. S. N.; Marin-Felix, Y.; Kemkuignou, B. Matio; Matocec, N.; McTaggart, A. R.; Mlcoch, P.; Mugnai, L.; Nakashima, C.; Nilsson, R. H.; Noumeur, S. R.; Pavlov, I. N.; Peralta, M. P.; Phillips, A. J. L.; Pitt, J., I; Polizzi, G.; Quaedvlieg, W.; Rajeshkumar, K. C.; Restrepo, S.; Rhaiem, A.; Robert, J.; Robert, V; Rodrigues, A. M.; Salgado-Salazar, C.; Samson, R. A.; Santos, A. C. S.; Shivas, R. G.; Souza-Motta, C. M.; Sun, G. Y.; Swart, W. J.; Szoke, S.; Tan, Y. P.; Taylor, J. E.; Taylor, P. W. J.; Tiago, P., V; Vaczy, K. Z.; van de Wiele, N.; van der Merwe, N. A.; Verkley, G. J. M.; Vieira, W. A. S.; Vizzini, A.; Weir, B. S.

Abstract

Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, P. Bag X20, Hatfield, 0028, Pretoria, South Africa; 20Department of Biotechnology and Biomedicine, DTU-Bioengineering, Technical University of Denmark, 2800, Kongens Lyngby, Denmark; 21Systematic Mycology Lab., Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt; 22Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj, Iran; 23Department of Medical Microbiology, King's College Hospital, London, UK;24Department of Infectious Diseases, Imperial College London, London, UK;25Department of Mycology and Plant Resistance, V. N. Karazin Kharkiv National University, Maidan Svobody 4, 61022, Kharkiv, Ukraine; 26Department of Food Science and Technology, Cape Peninsula University of Technology, P.O. Box 1906, Bellville, 7535, South Africa; 27School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA; 28Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, No.1, Sec.4, Roosevelt Road, Taipei, 106, Taiwan, ROC

Published
2021

18. Wheat blast: from its origins in South America to its emergence as a global threat

Author

CERESINI. P. C., CASTROAGUDÍN, V. L., RODRIGUES, F. A., RIOS, J. A., AUCIQUE-PÉREZ, C. E., MOREIRA, S. I., CROLL, D., ALVES, E., CARVALHO, G. de, MACIEL, J. L. N., MCDONALD, B. A., PAULO CEZAR CERESINI, USP ILHA SOLTEIRA, VANINA LILI?AN CASTROAGUDÍN, USP ILHA SOLTEIRA, FABRÍCIO ÁVILA RODRIGUES, UFV, JONAS ALBERTO RIOS, UFV, CARLOS EDUARDO AUCIQUE-PÉREZ, UFV, SILVINO INTRA MOREIRA, ESALQ, DANIEL CROLL, UNIVERSITY OF NEUCHATEL, SWITZERLAND, EDUARDO ALVES, USP ILHA SOLTEIRA, GISELLE DE CARVALHO, USP ILHA SOLTEIRA, JOAO LEODATO NUNES MACIEL, CNPT, and BRUCE ALAN MCDONALD, Swiss Federal Institute of Technology, Zurich, Switzerland.

Subjects
Brusone, Pyricularia, Wheat, Plant diseases and disorders, Doença de Planta, Trigo
Abstract

Made available in DSpace on 2019-04-16T00:43:07Z (GMT). No. of bitstreams: 1 ID445622019v20N2p155MolecularPlantPathol.pdf: 1416148 bytes, checksum: 9c6fc23c22e11bb5463c390d682fbc55 (MD5) Previous issue date: 2019

Published
2019

20. Globally important islands where eradicating invasive mammals will benefit highly threatened vertebrates

Author

Holmes, N, Spatz, D, Oppel, S, Tershy, B, Croll, D, Keitt, B, Genovesi, P, Burfield, I, Will, D, Bond, A, Wegmann, A, Aguirre-Munoz, A, Raine, A, Knapp, C, Hung, C-H, Wingate, D, Hagen, E, Mendez-Sanchez, F, Rocamora, G, Yuan, H-W, Fric, J, Millett, J, Russell, J, Liske-Clark, J, Vidal, E, Jourdan, H, Campbell, K, Springer, K, Swinnerton, K, Gibbons-Decherong, L, Langrand, O, Brooke, MDL, McMinn, M, Bunbury, N, Oliviera, N, Sposimo, P, Geraldes, P, McClelland, P, Hodum, P, Ryan, P, Borroto-Paez, R, Griffiths, R, Fisher, R, Wanless, R, Pasachnik, S, Cranwell, S, Micol, T, Butchard, S, Holmes, N, Spatz, D, Oppel, S, Tershy, B, Croll, D, Keitt, B, Genovesi, P, Burfield, I, Will, D, Bond, A, Wegmann, A, Aguirre-Munoz, A, Raine, A, Knapp, C, Hung, C-H, Wingate, D, Hagen, E, Mendez-Sanchez, F, Rocamora, G, Yuan, H-W, Fric, J, Millett, J, Russell, J, Liske-Clark, J, Vidal, E, Jourdan, H, Campbell, K, Springer, K, Swinnerton, K, Gibbons-Decherong, L, Langrand, O, Brooke, MDL, McMinn, M, Bunbury, N, Oliviera, N, Sposimo, P, Geraldes, P, McClelland, P, Hodum, P, Ryan, P, Borroto-Paez, R, Griffiths, R, Fisher, R, Wanless, R, Pasachnik, S, Cranwell, S, Micol, T, and Butchard, S

Abstract

Invasive alien species are a major threat to native insular species. Eradicating invasive mammals from islands is a feasible and proven approach to prevent biodiversity loss. We developed a conceptual framework to identify globally important islands for invasive mammal eradications to prevent imminent extinctions of highly threatened species using biogeographic and technical factors, plus a novel approach to consider socio-political feasibility. We applied this framework using a comprehensive dataset describing the distribution of 1,184 highly threatened native vertebrate species (i.e. those listed as Critically Endangered or Endangered on the IUCN Red List) and 184 non-native mammals on 1,279 islands worldwide. Based on extinction risk, irreplaceability, severity of impact from invasive species, and technical feasibility of eradication, we identified and ranked 292 of the most important islands where eradicating invasive mammals would benefit highly threatened vertebrates. When socio-political feasibility was considered, we identified 169 of these islands where eradication planning or operation could be initiated by 2020 or 2030 and would improve the survival prospects of 9.4% of the Earth’s most highly threatened terrestrial insular vertebrates (111 of 1,184 species). Of these, 107 islands were in 34 countries and territories and could have eradication projects initiated by 2020. Concentrating efforts to eradicate invasive mammals on these 107 islands would benefit 151 populations of 80 highly threatened vertebrates and make a major contribution towards achieving global conservation targets adopted by the world’s nations.

Published
2019

22. Comparative Genomics of Smut Pathogens: Insights From Orphans and Positively Selected Genes Into Host Specialization

Author

Benevenuto, J., Texeira-Silva, N.S., Kuramae, E.E., Croll, D., Vitorello, C.B.M., Benevenuto, J., Texeira-Silva, N.S., Kuramae, E.E., Croll, D., and Vitorello, C.B.M.

Abstract

Host specialization is a key evolutionary process for the diversification and emergence of new pathogens. However, the molecular determinants of host range are poorly understood. Smut fungi are biotrophic pathogens that have distinct and narrow host ranges based on largely unknown genetic determinants. Hence, we aimed to expand comparative genomics analyses of smut fungi by including more species infecting different hosts and to define orphans and positively selected genes to gain further insights into the genetics basis of host specialization. We analyzed nine lineages of smut fungi isolated from eight crop and non-crop hosts: maize, barley, sugarcane, wheat, oats, Zizania latifolia (Manchurian rice), Echinochloa colona (a wild grass), and Persicaria sp. (a wild dicot plant). We assembled two new genomes: Ustilago hordei (strain Uhor01) isolated from oats and U. tritici (strain CBS 119.19) isolated from wheat. The smut genomes were of small sizes, ranging from 18.38 to 24.63 Mb. U. hordei species experienced genome expansions due to the proliferation of transposable elements and the amount of these elements varied among the two strains. Phylogenetic analysis confirmed that Ustilago is not a monophyletic genus and, furthermore, detected misclassification of the U. tritici specimen. The comparison between smut pathogens of crop and non-crop hosts did not reveal distinct signatures, suggesting that host domestication did not play a dominant role in shaping the evolution of smuts. We found that host specialization in smut fungi likely has a complex genetic basis: different functional categories were enriched in orphans and lineage-specific selected genes. The diversification and gain/loss of effector genes are probably the most important determinants of host specificity.

Published
2018

24. Comparative transcriptomic analyses of Zymoseptoria tritici strains show complex lifestyle transitions and intraspecific variability in transcription profiles

Author

Palma-Guerrero, J., Torriani, S. F. F., Zala, M., Carter, D., Courbot, M., Rudd, J. J., Mcdonald, B. A., and Croll, D.

Subjects
Plant Sciences, food and beverages
Abstract

Zymoseptoria tritici causes Septoria tritici blotch (STB) on wheat. The disease interaction is characterized by clearly defined temporal phases of infection, ultimately resulting in the death of host tissue. Zymoseptoria tritici is a highly polymorphic species with significant intraspecific variation in virulence profiles. We generated a deep transcriptomic sequencing dataset spanning the entire time course of an infection using a previously uncharacterized, highly virulent Z. tritici strain isolated from a Swiss wheat field. We found that seven clusters of gene transcription profiles explained the progression of the infection. The earliest highly up-regulated genes included chloroperoxidases, which may help the fungus cope with plant defences. The onset of necrotrophy was characterized by a concerted up-regulation of proteases, plant cell wall-degrading enzymes and lipases. Functions related to nutrition and growth characterized late necrotrophy and the transition to saprotrophic growth on dead plant tissue. We found that the peak up-regulation of genes essential for mating coincided with the necrotrophic phase. We performed an intraspecies comparative transcriptomics analysis using a comparable time course infection experiment of the genome reference isolate IPO323. Major components of the fungal infection transcriptome were conserved between the two strains. However, individual small, secreted proteins, proteases and cell wall-degrading enzymes showed strongly differentiated transcriptional profiles between isolates. Our analyses illustrate that successful STB infections involve complex transcriptomic remodelling to up-regulate distinct gene functions. Heterogeneity in transcriptomes among isolates may explain some of the considerable variation in virulence and host specialization found within the species.

Published
2016

25. Anthropogenic Threats and Conservation Needs of Blue Whales, Balaenoptera musculus indica, around Sri Lanka

Author

de Vos, A., Brownell, R. L.Jr., Tershy, B., and Croll, D.

Subjects
Article Subject
Abstract

Blue whales in the Northern Indian Ocean are a morphologically and acoustically distinct population restricted to these waters. Off Sri Lanka a portion of the population concentrates near shore where they are exposed to a range of anthropogenic threats. We review available data to determine anthropogenic threats/stressors faced by this population and assign subjective rankings for the population-level severity of each threat/stressor based on severity, scope, and immediacy. With the cessation of direct illegal catches on this population in the late 1960s, we ranked ship strike as the most important population-level threat. Incidental catch, which includes entanglement and bycatch, is also important as it can result in death. Other less important stressors that may negatively impact this population include threats resulting from oil and gas development and pollution. However, some stressors can have a long-term cumulative impact that is difficult to assess. The most important research needed for the conservation of these whales is to obtain an estimate of the size of the population using photo-identification methods.

Published
2016
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31. Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex

Author

Grossen C., Keller L., Biebach I., Zhang W., Tosser-Klopp G., Ajmone P., Amills M., Boitard S., Chen W., Cheng S., Dong Y., Faraut T., Faruque O., Heuven H., Jinshan Z., Jun L., Lenstra H., Li X., Liu X., Moreno C., Mulsant P., Pan S., Poli M.A., Ren L., Rui S., Rupp R., Cristobal M.S., Sayre B.L., Servin B., Shi P., Song C., Stella A., Valentini A., Xianglong L., XU X., Yanjun Z., Ye C., Yu J., Zhang B., Zhao S., Croll D., Department of Zoology, Auburn University (AU), Institute of Evolutionary Biology and Environmental Studies, Universität Zürich [Zürich] = University of Zurich (UZH), Kunming Institute of Zoology, State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences [Changchun Branch] (CAS), University of British Columbia (UBC), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Chinese Academy of Sciences (CAS), Swiss National Science Foundation [PBLAP3-14584, PA00P3_145360], Swiss Federal Office for the Environment, University of Zurich, and Grossen, Christine

Subjects
Evolutionary Genetics, 0106 biological sciences, haplotype, Cancer Research, Introgression, [SDV]Life Sciences [q-bio], HLA-DR beta-Chains, Balancing selection, 01 natural sciences, Linkage Disequilibrium, Major Histocompatibility Complex, Natural Selection, 1306 Cancer Research, chromosome, Genome Evolution, Phylogeny, Genetics (clinical), Genetics, Evolutionary Theory, 0303 health sciences, biology, Goats, loci, Chromosomal region, 590 Animals (Zoology), Research Article, Gene Flow, 2716 Genetics (clinical), Evolutionary Processes, Capra ibex, intron, lcsh:QH426-470, chèvre, Immunology, complexe majeur d'histocompatibilité, Locus (genetics), 010603 evolutionary biology, 10127 Institute of Evolutionary Biology and Environmental Studies, 03 medical and health sciences, 1311 Genetics, Genetic variation, 1312 Molecular Biology, Animals, Allele, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Evolutionary Biology, Polymorphism, Genetic, Base Sequence, Genetic Drift, Haplotype, Biology and Life Sciences, Computational Biology, allèle, Sequence Analysis, DNA, DNA sequence, genetic association, biology.organism_classification, lcsh:Genetics, 1105 Ecology, Evolution, Behavior and Systematics, Haplotypes, Genetic Polymorphism, 570 Life sciences, Clinical Immunology, Population Genetics, Microsatellite Repeats
Abstract

The major histocompatibility complex (MHC) is a crucial component of the vertebrate immune system and shows extremely high levels of genetic polymorphism. The extraordinary genetic variation is thought to be ancient polymorphisms maintained by balancing selection. However, introgression from related species was recently proposed as an additional mechanism. Here we provide evidence for introgression at the MHC in Alpine ibex (Capra ibex ibex). At a usually very polymorphic MHC exon involved in pathogen recognition (DRB exon 2), Alpine ibex carried only two alleles. We found that one of these DRB alleles is identical to a DRB allele of domestic goats (Capra aegagrus hircus). We sequenced 2489 bp of the coding and non-coding regions of the DRB gene and found that Alpine ibex homozygous for the goat-type DRB exon 2 allele showed nearly identical sequences (99.8%) to a breed of domestic goats. Using Sanger and RAD sequencing, microsatellite and SNP chip data, we show that the chromosomal region containing the goat-type DRB allele has a signature of recent introgression in Alpine ibex. A region of approximately 750 kb including the DRB locus showed high rates of heterozygosity in individuals carrying one copy of the goat-type DRB allele. These individuals shared SNP alleles both with domestic goats and other Alpine ibex. In a survey of four Alpine ibex populations, we found that the region surrounding the DRB allele shows strong linkage disequilibria, strong sequence clustering and low diversity among haplotypes carrying the goat-type allele. Introgression at the MHC is likely adaptive and introgression critically increased MHC DRB diversity in the genetically impoverished Alpine ibex. Our finding contradicts the long-standing view that genetic variability at the MHC is solely a consequence of ancient trans-species polymorphism. Introgression is likely an underappreciated source of genetic diversity at the MHC and other loci under balancing selection., PLoS Genetics, 10 (6), ISSN:1553-7390, ISSN:1553-7404

Published
2014

32. Genetic diversity and host plant preferences revealed by simple sequence repeat and mitochondrial markers in a population of the arbuscular mycorrhizal fungus Glomus intraradices

Author

Croll, D., Wille, L., Gamper, H.A., Mathimaran, N., Lammers, P.J., Corradi, N., Sanders, I.R., Croll, D., Wille, L., Gamper, H.A., Mathimaran, N., Lammers, P.J., Corradi, N., and Sanders, I.R.

Abstract

Arbuscular mycorrhizal fungi (AMF) are important symbionts of plants that improve plant nutrient acquisition and promote plant diversity. Although within-species genetic differences among AMF have been shown to differentially affect plant growth, very little is actually known about the degree of genetic diversity in AMF populations. This is largely because of difficulties in isolation and cultivation of the fungi in a clean system allowing reliable genotyping to be performed. - A population of the arbuscular mycorrhizal fungus Glomus intraradices growing in an in vitro cultivation system was studied using newly developed simple sequence repeat (SSR), nuclear gene intron and mitochondrial ribosomal gene intron markers. - The markers revealed a strong differentiation at the nuclear and mitochondrial level among isolates. Genotypes were nonrandomly distributed among four plots showing genetic subdivisions in the field. Meanwhile, identical genotypes were found in geographically distant locations. AMF genotypes showed significant preferences to different host plant species (Glycine max, Helianthus annuus and Allium porrum) used before the fungal in vitro culture establishment. - Host plants in a field could provide a heterogeneous environment favouring certain genotypes. Such preferences may partly explain within-population patterns of genetic diversity., Arbuscular mycorrhizal fungi (AMF) are important symbionts of plants that improve plant nutrient acquisition and promote plant diversity. Although within-species genetic differences among AMF have been shown to differentially affect plant growth, very little is actually known about the degree of genetic diversity in AMF populations. This is largely because of difficulties in isolation and cultivation of the fungi in a clean system allowing reliable genotyping to be performed. - A population of the arbuscular mycorrhizal fungus Glomus intraradices growing in an in vitro cultivation system was studied using newly developed simple sequence repeat (SSR), nuclear gene intron and mitochondrial ribosomal gene intron markers. - The markers revealed a strong differentiation at the nuclear and mitochondrial level among isolates. Genotypes were nonrandomly distributed among four plots showing genetic subdivisions in the field. Meanwhile, identical genotypes were found in geographically distant locations. AMF genotypes showed significant preferences to different host plant species (Glycine max, Helianthus annuus and Allium porrum) used before the fungal in vitro culture establishment. - Host plants in a field could provide a heterogeneous environment favouring certain genotypes. Such preferences may partly explain within-population patterns of genetic diversity.

Published
2008

33. Multilocus genotyping of arbuscular mycorrhizal fungi and marker suitability for population genetics

Author

Croll, D., Corradi, N., Gamper, H.A., Sanders, I.R., Croll, D., Corradi, N., Gamper, H.A., and Sanders, I.R.

Abstract

No Abstract [KEYWORDS: arbuscular mycorrhizal fungi (AMF) • Glomus intraradices • microsatellites • multilocus genotyping • population genetics • simple sequence repeats (SSR)], No Abstract [KEYWORDS: arbuscular mycorrhizal fungi (AMF) • Glomus intraradices • microsatellites • multilocus genotyping • population genetics • simple sequence repeats (SSR)]

Published
2008

35. The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont

Author

Tisserant, E., primary, Kohler, A., additional, Dozolme‐Seddas, P., additional, Balestrini, R., additional, Benabdellah, K., additional, Colard, A., additional, Croll, D., additional, Da Silva, C., additional, Gomez, S. K., additional, Koul, R., additional, Ferrol, N., additional, Fiorilli, V., additional, Formey, D., additional, Franken, Ph., additional, Helber, N., additional, Hijri, M., additional, Lanfranco, L., additional, Lindquist, E., additional, Liu, Y., additional, Malbreil, M., additional, Morin, E., additional, Poulain, J., additional, Shapiro, H., additional, van Tuinen, D., additional, Waschke, A., additional, Azcón‐Aguilar, C., additional, Bécard, G., additional, Bonfante, P., additional, Harrison, M. J., additional, Küster, H., additional, Lammers, P., additional, Paszkowski, U., additional, Requena, N., additional, Rensing, S. A., additional, Roux, C., additional, Sanders, I. R., additional, Shachar‐Hill, Y., additional, Tuskan, G., additional, Young, J. P. W., additional, Gianinazzi‐Pearson, V., additional, and Martin, F., additional

Published
2011
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38. The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont.

Author

Tisserant, E., Kohler, A., Dozolme-Seddas, P., Balestrini, R., Benabdellah, K., Colard, A., Croll, D., Da Silva, C., Gomez, S. K., Koul, R., Ferrol, N., Fiorilli, V., Formey, D., Franken, Ph., Helber, N., Hijri, M., Lanfranco, L., Lindquist, E., Liu, Y., and Malbreil, M.

Subjects
GENETIC transcription, VESICULAR-arbuscular mycorrhizas, GLOMUS intraradices, SYMBIOSIS, GENOMES, GENE expression
Abstract

Summary [ABSTRACT FROM AUTHOR]

Published
2012
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40. Novel Indolylindazolylmaleimides as Inhibitors of Protein Kinase C-β:  Synthesis, Biological Activity, and Cardiovascular Safety

Author

Zhang, H.-C., Derian, C. K., McComsey, D. F., White, K. B., Ye, H., Hecker, L. R., Li, J., Addo, M. F., Croll, D., Eckardt, A. J., Smith, C. E., Li, Q., Cheung, W.-M., Conway, B. R., Emanuel, S., Demarest, K. T., Andrade-Gordon, P., Damiano, B. P., and Maryanoff, B. E.

Abstract

Novel indolylindazolylmaleimides were synthesized and examined for kinase inhibition. We identified low-nanomolar inhibitors of PKC-β with good to excellent selectivity vs other PKC isozymes and GSK-3β. In a cell-based functional assay, 8f and 8i effectively blocked IL-8 release induced by PKC-βII (IC50 = 20−25 nM). In cardiovascular safety assessment, representative lead compounds bound to the hERG channel with high affinity, potently inhibited ion current in a patch-clamp experiment, and caused a dose-dependent increase of QTc in guinea pigs.

Published
2005

42. Validation of deuterium incorporation against sterol balance for measurement of human cholesterol biosynthesis.

Author

Jones, P J, Ausman, L M, Croll, D H, Feng, J Y, Schaefer, E A, and Lichtenstein, A H

Abstract

To examine the validity of the deuterium (D) incorporation technique for measurement of human cholesterol synthesis rates, D uptake from D2O into cholesterol was compared to sterol balance in 13 subjects each under three controlled diet settings. Subjects (age 62 +/- 3.6 yr, body weight 74 +/- 4.0 kg, BMI 27 +/- 1.4) consumed weight maintenance diets enriched in either corn oil, beef tallow, or stick corn oil margarine over a 5-week period. During the final week of the study period, subjects were given 1.2 g/D2O per kg body water. D enrichment was measured in plasma water and total cholesterol over 24 h. Also, during the final week, dietary intake and fecal elimination rates of cholesterol were assessed over one 6-day period to calculate sterol balance. There was no significant difference (t = 0.858, P = 0.397) between D incorporation into cholesterol (1,183 +/- 92 mg/day) and sterol balance (1,316 +/- 125 mg/day). Among diets, net cholesterol biosynthesis measured by D incorporation agreed (r = 0.745, P = 0.0001) with values derived from sterol balance. The degree of association between methods was not influenced by the wide range of fatty acid composition of the diet fat. These data demonstrate the utility of the simple, non-restrictive deuterium incorporation method as a reliable means of determining cholesterol biosynthesis in free-living humans.

Published
1998

44. Highly Recombinant VGII Cryptococcus gattii Population Develops Clonal Outbreak Clusters through both Sexual Macroevolution and Asexual Microevolution

Author

Heitman, J., Mieczkowski, P., Billmyre, R. B., Li, W., Croll, D., Carter, D. A., Kronstad, J. W., and Cuomo, C. A.

Subjects
3. Good health
Abstract

An outbreak of the fungal pathogen Cryptococcus gattii began in the Pacific Northwest (PNW) in the late 1990s. This outbreak consists of three clonal subpopulations: VGIIa/major, VGIIb/minor, and VGIIc/novel. Both VGIIa and VGIIc are unique to the PNW and exhibit increased virulence. In this study, we sequenced the genomes of isolates from these three groups, as well as global isolates, and analyzed a total of 53 isolates. We found that VGIIa/b/c populations show evidence of clonal expansion in the PNW. Whole-genome sequencing provided evidence that VGIIb originated in Australia, while VGIIa may have originated in South America, and these were likely independently introduced. Additionally, the VGIIa outbreak lineage may have arisen from a less virulent clade that contained a mutation in the MSH2 ortholog, but this appears to have reverted in the VGIIa outbreak strains, suggesting that a transient mutator phenotype may have contributed to adaptation and evolution of virulence in the PNW outbreak. PNW outbreak isolates share genomic islands, both between the clonal lineages and with global isolates, indicative of sexual recombination. This suggests that VGII C.gattii has undergone sexual reproduction, either bisexual or unisexual, in multiple locales contributing to the production of novel, virulent subtypes. We also found that the genomes of two basal VGII isolates from HIV+ patients contain an introgression tract spanning three genes. Introgression substantially contributed to intra-VGII polymorphism and likely occurred through sexual reproduction with VGI. More broadly, these findings illustrate how both microevolution and sexual reproduction play central roles in the development of infectious outbreaks from avirulent or less virulent progenitors.IMPORTANCECryptococcus gattii is the causative agent responsible for ongoing infections in the Pacific Northwest of the United States and western Canada. The incidence of these infections increased dramatically in the 1990s and remains elevated. These infections are attributable to three clonal lineages of C.gattii, VGIIa, VGIIb, and VGIIc, with only VGIIa identified once previously in the Pacific Northwest prior to the start of the outbreak, albeit in a less virulent form. This study addresses the origin and emergence of this outbreak, using whole-genome sequencing and comparison of both outbreak and global isolates. We show that VGIIa arose mitotically from a less virulent clonal group, possibly via the action of a mutator phenotype, while VGIIb was likely introduced from Australia, and VGIIc appears to have emerged in the United States or in an undersampled locale via sexual reproduction. This work shows that multiple processes can contribute to the emergence of an outbreak.

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