Artículo

Rochi, L.; Diéguez, M.J.; Burguener, G.; Darino, M.A.; Pergolesi, M.F.; Ingala, L.R.; Cuyeu, A.R.; Turjanski, A.; Kreff, E.D.; Sacco, F. "Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust" (2018) Fungal Genetics and Biology. 112:31-39
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Abstract:

Rust fungi are one of the most devastating pathogens of crop plants. The biotrophic fungus Puccinia sorghi Schwein (Ps) is responsible for maize common rust, an endemic disease of maize (Zea mays L.) in Argentina that causes significant yield losses in corn production. In spite of this, the Ps genomic sequence was not available. We used Illumina sequencing to rapidly produce the 99.6 Mb draft genome sequence of Ps race RO10H11247, derived from a single-uredinial isolate from infected maize leaves collected in the Argentine Corn Belt Region during 2010. High quality reads were obtained from 200 bp paired-end and 5000 bp mate-paired libraries and assembled in 15,722 scaffolds. A pipeline which combined an ab initio program with homology-based models and homology to in planta enriched ESTs from four cereal pathogenic fungus (the three sequenced wheat rusts and Ustilago maydis) was used to identify 21,087 putative coding sequences, of which 1599 might be part of the Ps RO10H11247 secretome. Among the 458 highly conserved protein families from the euKaryotic Orthologous Groups (KOG) that occur in a wide range of eukaryotic organisms, 97.5% have at least one member with high homology in the Ps assembly (TBlastN, E-value ⩽ e−10) covering more than 50% of the length of the KOG protein. Comparative studies with the three sequenced wheat rust fungus, and microsynteny analysis involving Puccinia striiformis f. sp. tritici (Pst, wheat stripe rust fungus), support the quality achieved. The results presented here show the effectiveness of the Illumina strategy for sequencing dikaryotic genomes of non-model organisms and provides reliable DNA sequence information for genomic studies, including pathogenic mechanisms of this maize fungus and molecular marker design. © 2016 Elsevier Inc.

Registro:

Documento: Artículo
Título:Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust
Autor:Rochi, L.; Diéguez, M.J.; Burguener, G.; Darino, M.A.; Pergolesi, M.F.; Ingala, L.R.; Cuyeu, A.R.; Turjanski, A.; Kreff, E.D.; Sacco, F.
Filiación:Instituto de Genética “Ewald A. Favret”, CICVyA-INTA CC25 (1712) Castelar, Buenos Aires, Argentina
Plataforma Bioinformática Argentina, FCEyN-UBA, Intendente Güiraldes 2160 (C1428EGA), Buenos Aires, Argentina
cPioneer Hi-Bred International, Inc., Ruta Nacional 178 km 11 Pergamino, Buenos Aires, Argentina
Palabras clave:Genomic sequence; Maize; Maize common rust; Plant pathogens; Puccinia sorghi; Secretome; fungal protein; Article; comparative study; controlled study; DNA sequence; expressed sequence tag; fungal genome; Illumina sequencing; microsynteny; multigene family; nonhuman; priority journal; Puccinia; Puccinia graminis f. sp. tritici; Puccinia sorghi; Puccinia striiformis f. sp. tritici; Puccinia triticina; sequence analysis; sequence homology; synteny; transposon; Ustilago maydis; Argentina; Basidiomycetes; biology; genetics; high throughput sequencing; isolation and purification; maize; microbiology; molecular genetics; plant disease; plant leaf; Argentina; Basidiomycota; Computational Biology; Genome, Fungal; High-Throughput Nucleotide Sequencing; Molecular Sequence Annotation; Plant Diseases; Plant Leaves; Sequence Analysis, DNA; Zea mays
Año:2018
Volumen:112
Página de inicio:31
Página de fin:39
DOI: http://dx.doi.org/10.1016/j.fgb.2016.10.001
Título revista:Fungal Genetics and Biology
Título revista abreviado:Fungal Genet. Biol.
ISSN:10871845
CODEN:FGBIF
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_10871845_v112_n_p31_Rochi

Referencias:

  • Anderson, P.A., Tyler, B.M., Pryor, A., Genome complexity of the maize rust fungus, Puccinia sorghi (1992) Exp. Mycol., 16, pp. 302-307
  • Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., Lesin, V.M., Pevzner, P.A., SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing (2012) J. Comput. Biol., 19 (5), pp. 455-477
  • Bakkeren, G., Joly, D.L., Duplessis, S., Editorial: genomics research on non-model plant pathogens: delivering novel insights into rust fungus biology (2016) Front. Plant Sci., 7, p. 216
  • Backlund, J.E., Szabo, L.J., Physical characteristics of the genome of the phytopathogenic fungus Puccinia graminis (1993) Curr. Genet., 24, pp. 89-93
  • Blanco, E., Parra, G., Guigó, R., Using geneid to Identify Genes (2007) Curr. Protocols Bioinform., , 18:4.3:4.3.1–4.3.28
  • Boetzer, M., Henkel, C.V., Jansen, H.J., Butler, D., Pirovano, W., Scaffolding pre-assembled contigs using SSPACE (2011) Bioinformatics, 27 (4), pp. 578-579
  • Bruce, M., Neugebauer, K.A., Joly, D.L., Migeon, P., Cuomo, C.A., Wang, S., Akhunov, E., Fellers, J.P., Using transcription of six Puccinia triticina races to identify the effective secretome during infection of wheat (2014) Front. Plant Sci., 4, p. 520
  • Cantu, D., Govindarajulu, M., Kozik, A., Wang, M., Chen, X., Kojima, K.K., Jurka, J., Dubcovsky, J., Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust (2011) PLoS One, 6 (8), p. e24230
  • Cantu, D., Segovia, V., MacLean, D., Bayles, R., Chen, X., Kamoun, S., Dubcovsky, J., Uauy, C., Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors (2013) BMC Genom., 14, p. 270
  • Carver, T.J., Rutherford, K.M., Berriman, M., Rajandream, M.A., Barrell, B.G., Parkhill, J., ACT: the Artemis Comparison Tool (2005) Bioinformatics, 21 (16), pp. 3422-3423
  • Cummins, G.B., Hiratsuka, Y., Illustrated Genera of Rust Fungi (2003), third ed. APS Press St Paul, MN, USA; Cuomo, C.A., Bakkeren, G., Khalil, H.B., Panwar, V., Joly, D., Linning, R., Sakthikumar, S., Fellers, J.P., (2016), http://biorxiv.org/content/early/2016/06/24/060665.abstract, Comparative analysis highlights variable genome content of wheat rusts and divergence of the mating loci; Darino, M.A., Rochi, L., Lia, V.V., Kreff, E.D., Pergolesi, M.F., Ingala, L.R., Diéguez, M.J., Sacco, F., Virulence characterization and identification of resistant maize lines to Puccinia sorghi Schwein present in the Argentine Corn Belt Region (2016) Plant Dis., 100 (4), pp. 770-776
  • Dodds, P.N., Rafiqi, M., Gan, P.H.P., Hardham, A.R., Jones, D.A., Ellis, J.G., Effectors of biotrophic fungi and oomycetes – pathogenicity factors and triggers of host resistance (2009) New Phytol., 183, pp. 993-1000
  • Duplessis, S., Cuomo, C.A., Lin, Y.C., Aerts, A., Tisserant, E., Obligate biotrophy features unraveled by the genomic analysis of rust fungi (2011) Proc. Natl. Acad. Sci. USA, 108 (22), pp. 9166-9171
  • Duplessis, S., Bakkeren, G., Joly, D.L., (2016) Genomics Research on Non-model Plant Pathogens: Delivering Novel Insights into Rust Fungus Biology, , Frontiers Media Lausanne
  • Eilam, T., Bushnell, W.R., Anikster, Y., Relative DNA content of rust fungi estimated by flow cytometry of propidium iodide-stained pycniospores (1994) Phytopathology, 84, pp. 728-735
  • Emanuelsson, O., Brunak, S., von Heijne, G., Nielsen, H., Locating proteins in the cell using TargetP, SignalP and related tools (2007) Nat. Protocols, 2, pp. 953-971
  • Enright, A.J., Van Dongen, S., Ouzounis, C.A., An efficient algorithm for large-scale detection of protein families (2002) Nucl. Acids Res., 30, pp. 1575-1584
  • Finn, R.D., Coggill, P., Eberhardt, R.Y., Eddy, S.R., Mistry, J., Mitchell, A.L., Potter, S.C., Bateman, A., The Pfam protein families database: towards a more sustainable future (2016) Nucl. Acids Res., 44, pp. D279-D285
  • Flutre, T., Duprat, E., Feuillet, C., Quesneville, H., Considering transposable element diversification in De Novo annotation approaches (2011) PLoS ONE, 6 (1), p. e16526
  • Goloboff, P.A., Catalano, S.A., TNT version 1.5, including a full implementation of phylogenetic morphometrics (2016) Cladistics, 32, pp. 221-238
  • Godoy, E.F., Bruni, O., Ciclo evolutivo de las royas del lino (Melampsora lini) y del maíz (Puccinia sorghi) en la Argentina (1952) Rev. Argentina Agron., 19, pp. 21-34
  • Gonzalez, M., First report of virulence in Argentine populations of Puccinia sorghi to Rp resistance genes in corn (2000) Plant Dis., 84, p. 921
  • Gonzalez, M., Caracterización de factores de resistencia y virulencia en la interacción Zea mays – Puccinia sorghi (2007), PhD dissertation Universidad Nacional de Córdoba, Facultad de Ciencias Agropecuarias Córdoba, Argentina; Grigoriev, I.V., Nikitin, R., Haridas, S., Kuo, A., Ohm, R., Otillar, R., Riley, R., Shabalov, I., MycoCosm portal: gearing up for 1000 fungal genomes (2014) Nucl. Acids Res., 42 (1), pp. D699-D704
  • Hooker, A.L., Corn and sorghum rusts (1985) The Cereal Rust, pp. 207-236. , A. Roelfs W. Bushnell Academic Press New York
  • Hulbert, S.H., Structure and evolution of the rp1 complex conferring rust resistance in maize (1997) Annu. Rev. Phytopathol., 35, pp. 293-310
  • Juncker, A.S., Willenbrock, H., von Heijne, G., Nielsen, H., Brunak, S., Krogh, A., Prediction of lipoprotein signal peptides in Gram-negative bacteria (2003) Protein Sci., 12 (8), pp. 1652-1662
  • Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E.L.L., Predicting transmembrane protein topology with a hidden markov model: application to complete genomes (2001) J. Mol. Biol., 305, pp. 567-580
  • Kullman, B., Tamm, H., Kullman, K., (2005), http://www.zbi.ee/fungal-genomesize, Fungal Genome Size Database. <>; Lagesen, K., Hallin, P.F., Rødland, E., Stærfeldt, H.H., Rognes, T., Ussery, D.W., RNAmmer: consistent annotation of rRNA genes in genomic sequences (2007) Nucl. Acids Res., 35 (9), pp. 3100-3108
  • Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Higgins, D.G., Clustal W and Clustal X version 2.0 (2007) Bioinformatics, 23, pp. 2947-2948
  • Lawrence, C.J., Seigfried, T.E., Brendel, V., MaizeGDB – the community resource for access to diverse maize data (2005) Plant Physiol., 138, pp. 55-58
  • Lowe, T.M., Eddy, S.R., TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence (1997) Nucl. Acids Res., 25, pp. 955-964
  • McCarthy, E.M., McDonald, J.F., LTR_STRUC: a novel search and identification program for LTR retrotransposons (2003) Bioinformatics, 19, pp. 362-367
  • Nawrocki, E.P., Eddy, S.R., Infernal 1.1: 100-fold faster RNA homology searches (2013) Bioinformatics, 29 (22), pp. 2933-2935
  • Parra, G., Bradnam, K., Korf, I., CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes (2007) Bioinformatics, 23, pp. 1061-1067
  • Pataky, J.K., Quantitative relationship between sweet corn yield and common rust, Puccinia sorghi (1987) Phytopathology, 77, pp. 1066-1071
  • Petersen, T.N., Brunak, S., von Heijne, G., Nielsen, H., SignalP 4.0: discriminating signal peptides from transmembrane regions (2011) Nat. Meth., 8, pp. 785-786
  • Petre, B., Joly, D.L., Duplessis, S., Effector proteins of rust fungi (2014) Front. Plant Sci., 5, p. 416
  • Proost, S., Fostier, J., De Witte, D., Dhoedt, B., Demeester, P., I-ADHoRe 3.0–fast and sensitive detection of genomic homology in extremely large data sets (2012) Nucl. Acids Res., 40, p. e11
  • Saunders, D.G.O., Win, J., Cano, L.M., Szabo, L.J., Kamoun, S., Using hierarchical clustering of secreted protein families to classify and rank candidate effectors of rust fungi (2012) PLoS ONE, 7 (1), p. e29847
  • Suzek, B.E., Wang, Y., Huang, H., McGarvey, P.B., Wu, C.H., UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches (2015) Bioinformatics, 31 (6), pp. 926-932
  • Talavera, G., Castresana, J., Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments (2007) System. Biol., 56, pp. 564-577
  • Tan, M.-K., Collins, D., Chen, Z., Englezou, A., Wilkins, M.R., A brief overview of the size and composition of the myrtle rust genome and its taxonomic status (2014) Mycology, 5 (2), pp. 52-63
  • Tavares, S., Ramos, A.P., Pires, A.S., Azinheira, H.G., Caldeirinha, P., Link, T., Abranches, R., Talhinhas, P., Genome size analyses of Pucciniales reveal the largest fungal genomes (2014) Front. Plant Sci., 5, p. 422
  • Vallega, J., (1942), pp. 14-16. , Observaciones preliminares sobre especialización fisiológica de Puccinia sorghi en Argentina. In: Vallega, J. (Ed.), Anales del Instituto Fitotécnico de Santa Catalina. Universidad de la Plata; Zheng, W., Huang, L., Huang, J., Wang, X., Chen, X., Zhao, J., High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus (2013) Nat. Commun., 4, p. 2673

Citas:

---------- APA ----------
Rochi, L., Diéguez, M.J., Burguener, G., Darino, M.A., Pergolesi, M.F., Ingala, L.R., Cuyeu, A.R.,..., Sacco, F. (2018) . Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust. Fungal Genetics and Biology, 112, 31-39.
http://dx.doi.org/10.1016/j.fgb.2016.10.001
---------- CHICAGO ----------
Rochi, L., Diéguez, M.J., Burguener, G., Darino, M.A., Pergolesi, M.F., Ingala, L.R., et al. "Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust" . Fungal Genetics and Biology 112 (2018) : 31-39.
http://dx.doi.org/10.1016/j.fgb.2016.10.001
---------- MLA ----------
Rochi, L., Diéguez, M.J., Burguener, G., Darino, M.A., Pergolesi, M.F., Ingala, L.R., et al. "Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust" . Fungal Genetics and Biology, vol. 112, 2018, pp. 31-39.
http://dx.doi.org/10.1016/j.fgb.2016.10.001
---------- VANCOUVER ----------
Rochi, L., Diéguez, M.J., Burguener, G., Darino, M.A., Pergolesi, M.F., Ingala, L.R., et al. Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust. Fungal Genet. Biol. 2018;112:31-39.
http://dx.doi.org/10.1016/j.fgb.2016.10.001