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2. JCVI: A versatile toolkit for comparative genomics analysis.

Author

Tang, Haibao, Krishnakumar, Vivek, Zeng, Xiaofei, Xu, Zhougeng, Taranto, Adam, Lomas, Johnathan S., Zhang, Yixing, Huang, Yumin, Wang, Yibin, Yim, Won Cheol, Zhang, Jisen, and Zhang, Xingtan

Subjects
COMPARATIVE genomics, LIFE cycles (Biology), COMPARATIVE method, MODULAR design, QUALITY control, DATA modeling
Abstract

The life cycle of genome builds spans interlocking pillars of assembly, annotation, and comparative genomics to drive biological insights. While tools exist to address each pillar separately, there is a growing need for tools to integrate different pillars of a genome project holistically. For example, comparative approaches can provide quality control of assembly or annotation; genome assembly, in turn, can help to identify artifacts that may complicate the interpretation of genome comparisons. The JCVI library is a versatile Python‐based library that offers a suite of tools that excel across these pillars. Featuring a modular design, the JCVI library provides high‐level utilities for tasks such as format parsing, graphics generation, and manipulation of genome assemblies and annotations. Supporting genomics algorithms like MCscan and ALLMAPS are widely employed in building genome releases, producing publication‐ready figures for quality assessment and evolutionary inference. Developed and maintained collaboratively, the JCVI library emphasizes quality and reusability. Highlights: JCVI is a Python‐based library that enables genomic workflows through a collection of simple reusable tools.The JCVI library is modular with basic functionalities separated into bioinformatics format parsing, assembly and annotation‐related tools, comparative genomics, and graphics generation.Embedded algorithms like MCscan, ALLMAPS, and other tools within JCVI are now widely used in the community and power a wide array of use cases. [ABSTRACT FROM AUTHOR]

Published
2024
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6. Transposon-Mediated Horizontal Transfer of the Host-Specific Virulence Protein ToxA between Three Fungal Wheat Pathogens

Author

McDonald, Megan, Taranto, Adam, Hill, Erin, Schwessinger, Benjamin, Liu, Zhaohui, Simpfendorfer, Steven, Milgate, Andrew, Solomon, Peter, McDonald, Megan, Taranto, Adam, Hill, Erin, Schwessinger, Benjamin, Liu, Zhaohui, Simpfendorfer, Steven, Milgate, Andrew, and Solomon, Peter

Abstract

Most known examples of horizontal gene transfer (HGT) between eukaryotes are ancient. These events are identified primarily using phylogenetic methods on coding regions alone. Only rarely are there examples of HGT where noncoding DNA is also reported. The gene encoding the wheat virulence protein ToxA and the surrounding 14 kb is one of these rare examples. ToxA has been horizontally transferred between three fungal wheat pathogens (Parastagonospora nodorum, Pyrenophora tritici-repentis, and Bipolaris sorokiniana) as part of a conserved ∼14 kb element which contains coding and noncoding regions. Here we used long-read sequencing to define the extent of HGT between these three fungal species. Construction of near-chromosomal-level assemblies enabled identification of terminal inverted repeats on either end of the 14 kb region, typical of a type II DNA transposon. This is the first description of ToxA with complete transposon features, which we call ToxhAT. In all three species, ToxhAT resides in a large (140-to-250 kb) transposon-rich genomic island which is absent in isolates that do not carry the gene (annotated here as toxa−). We demonstrate that the horizontal transfer of ToxhAT between P. tritici-repentis and P. nodorum occurred as part of a large (∼80 kb) HGT which is now undergoing extensive decay. In B. sorokiniana, in contrast, ToxhAT and its resident genomic island are mobile within the genome. Together, these data provide insight into the noncoding regions that facilitate HGT between eukaryotes and into the genomic processes which mask the extent of HGT between these species.

Published
2019

8. Additional file 8: of Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

Author

Deng, Cecilia, Plummer, Kim, Jones, Darcy, Mesarich, Carl, Shiller, Jason, Taranto, Adam, Robinson, Andrew, Kastner, Patrick, Hall, Nathan, Templeton, Matthew, and Bowen, Joanna

Abstract

The predicted proteins belonging to OrthoMCL clusters present in the secretomes of five Venturia isolates. The coloured horizontal bars represent proportions of predicted proteins (scale at bottom of figure) that have been annotated according to the key at the top of the figure, that are present in the secretomes indicated by grey boxes to the left of the figure (white boxes indicate lack of similar proteins). S: indicates singleton proteins. Numbers in the boxes are numbers of proteins. The order of the categories in the key is the same as that in the horizontal bars. For example: the core secretome is represented by the top-most horizontal bar; there are similar proteins present in each of the secretomes (5 grey boxes), of which 15% (77 proteins) are classified as SSPs between 200 and 500 amino acids in length with 2 or more cysteines. (PPTX 56 kb)

Published
2017
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9. Additional file 6: of Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

Author

Deng, Cecilia, Plummer, Kim, Jones, Darcy, Mesarich, Carl, Shiller, Jason, Taranto, Adam, Robinson, Andrew, Kastner, Patrick, Hall, Nathan, Templeton, Matthew, and Bowen, Joanna

Abstract

Pipeline of programmes used to identify the in silico-predicted secretome of each isolate. (DOCX 147 kb)

Published
2017
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10. Additional file 13: of Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

Author

Deng, Cecilia, Plummer, Kim, Jones, Darcy, Mesarich, Carl, Shiller, Jason, Taranto, Adam, Robinson, Andrew, Kastner, Patrick, Hall, Nathan, Templeton, Matthew, and Bowen, Joanna

Subjects
food and beverages
Abstract

Small, secreted protein (SSP) family 07 members. Sequence logo of members of A. family 07 from Vi1 and B. family 07 from all isolates. (DOCX 221 kb)

Published
2017
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11. Bioconda: A sustainable and comprehensive software distribution for the life sciences

Author

Grüning, Björn, primary, Dale, Ryan, additional, Sjödin, Andreas, additional, Chapman, Brad A., additional, Rowe, Jillian, additional, Tomkins-Tinch, Christopher H., additional, Valieris, Renan, additional, Caprez, Adam, additional, Batut, Bérénice, additional, Haudgaard, Mathias, additional, Cokelaer, Thomas, additional, Beauchamp, Kyle A., additional, Pedersen, Brent S, additional, Hoogstrate, Youri, additional, Bretaudeau, Anthony, additional, Ryan, Devon, additional, Corguillé, Gildas Le, additional, Yusuf, Dilmurat, additional, Luna-Valero, Sebastian, additional, Kirchner, Rory, additional, Brinda, Karel, additional, Wollmann, Thomas, additional, Raden, Martin, additional, Heeringen, Simon J. van, additional, Soranzo, Nicola, additional, Pantano, Lorena, additional, Charlop-Powers, Zachary, additional, Unneberg, Per, additional, Smet, Matthias De, additional, Martin, Marcel, additional, Kuster, Greg Von, additional, Antao, Tiago, additional, Miladi, Milad, additional, Thornton, Kevin, additional, Brueffer, Christian, additional, Beek, Marius van den, additional, Maticzka, Daniel, additional, Blank, Clemens, additional, Will, Sebastian, additional, Gravouil, K´evin, additional, Wolff, Joachim, additional, Holtgrewe, Manuel, additional, Fallmann, Jörg, additional, Piro, Vitor C., additional, Shlyakhter, Ilya, additional, Yousif, Ayman, additional, Mabon, Philip, additional, Zhang, Xiao-Ou, additional, Shen, Wei, additional, Cabral, Jennifer, additional, Thomas, Cristel, additional, Enns, Eric, additional, Brown, Joseph, additional, Boekel, Jorrit, additional, Hollander, Mattias de, additional, Kelleher, Jerome, additional, Turaga, Nitesh, additional, Ruiter, Julian R. de, additional, Bouvier, Dave, additional, Gladman, Simon, additional, Choudhary, Saket, additional, Harding, Nicholas, additional, Eggenhofer, Florian, additional, Kratz, Arne, additional, Fang, Zhuoqing, additional, Kleinkauf, Robert, additional, Timm, Henning, additional, Cock, Peter J. A., additional, Seiler, Enrico, additional, Brislawn, Colin, additional, Nguyen, Hai, additional, Stovner, Endre Bakken, additional, Ewels, Philip, additional, Chambers, Matt, additional, Johnson, James E., additional, Hägglund, Emil, additional, Ye, Simon, additional, Guimera, Roman Valls, additional, Pruesse, Elmar, additional, Dunn, W. Augustine, additional, Parsons, Lance, additional, Patro, Rob, additional, Koppstein, David, additional, Grassi, Elena, additional, Wohlers, Inken, additional, Reynolds, Alex, additional, Cornwell, MacIntosh, additional, Stoler, Nicholas, additional, Blankenberg, Daniel, additional, He, Guowei, additional, Bargull, Marcel, additional, Junge, Alexander, additional, Farouni, Rick, additional, Freeberg, Mallory, additional, Singh, Sourav, additional, Bogema, Daniel R., additional, Cumbo, Fabio, additional, Wang, Liang-Bo, additional, Larson, David E, additional, Workentine, Matthew L., additional, Devisetty, Upendra Kumar, additional, Laurent, Sacha, additional, Roger, Pierrick, additional, Garnier, Xavier, additional, Agren, Rasmus, additional, Khan, Aziz, additional, Eppley, John M, additional, Li, Wei, additional, Stöcker, Bianca Katharina, additional, Rausch, Tobias, additional, Taylor, James, additional, Wright, Patrick R., additional, Taranto, Adam P., additional, Chicco, Davide, additional, Sennblad, Bengt, additional, Baaijens, Jasmijn A., additional, Gopez, Matthew, additional, Abdennur, Nezar, additional, Milne, Iain, additional, Preussner, Jens, additional, Pinello, Luca, additional, Srivastava, Avi, additional, Chande, Aroon T., additional, Kensche, Philip Reiner, additional, Pirola, Yuri, additional, Knudsen, Michael, additional, Bruijn, Ino de, additional, Blin, Kai, additional, Gonnella, Giorgio, additional, Enache, Oana M., additional, Rai, Vivek, additional, Waters, Nicholas R., additional, Hiltemann, Saskia, additional, Bendall, Matthew L., additional, Stahl, Christoph, additional, Miles, Alistair, additional, Boursin, Yannick, additional, Perez-Riverol, Yasset, additional, Schmeier, Sebastian, additional, Clarke, Erik, additional, Arvai, Kevin, additional, Jung, Matthieu, additional, Domenico, Tom´as Di, additional, Seiler, Julien, additional, Rasche, Eric, additional, Kornobis, Etienne, additional, Beisser, Daniela, additional, Rahmann, Sven, additional, Mikheyev, Alexander S, additional, Tran, Camy, additional, Capellades, Jordi, additional, Schröder, Christopher, additional, Salatino, Adrian Emanuel, additional, Dirmeier, Simon, additional, Webster, Timothy H., additional, Moskalenko, Oleksandr, additional, Stephen, Gordon, additional, and Köster, Johannes, additional

Published
2017
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12. Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

Author

Deng, Cecilia H., primary, Plummer, Kim M., additional, Jones, Darcy A. B., additional, Mesarich, Carl H., additional, Shiller, Jason, additional, Taranto, Adam P., additional, Robinson, Andrew J., additional, Kastner, Patrick, additional, Hall, Nathan E., additional, Templeton, Matthew D., additional, and Bowen, Joanna K., additional

Published
2017
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15. Fungal phytopathogens encode functional homologues of plant rapid alkalinization factor (RALF) peptides

Author

Thynne, Elisha, primary, Saur, Isabel M. L., additional, Simbaqueba, Jaime, additional, Ogilvie, Huw A., additional, Gonzalez-Cendales, Yvonne, additional, Mead, Oliver, additional, Taranto, Adam, additional, Catanzariti, Ann-Maree, additional, McDonald, Megan C., additional, Schwessinger, Benjamin, additional, Jones, David A., additional, Rathjen, John P., additional, and Solomon, Peter S., additional

Published
2016
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16. A large family of AvrLm6-like genes in the apple and pear scab pathogens, Venturia inaequalis and venturia pirina

Author

Shiller, J, Van de Wouw, A P, Taranto, Adam, Bowen, J K, Dubois, D, Robinson, A, Deng, C H, Plummer, K M, Shiller, J, Van de Wouw, A P, Taranto, Adam, Bowen, J K, Dubois, D, Robinson, A, Deng, C H, and Plummer, K M

Abstract

Venturia inaequalis and V. pirina are Dothideomycete fungi that cause apple scab and pear scab disease, respectively. Whole genome sequencing of V. inaequalis and V. pirina isolates has revealed predicted proteins with sequence similarity to AvrLm6, a Leptosphaeria maculans effector that triggers a resistance response in Brassica napus and B. juncea carrying the resistance gene, Rlm6. AvrLm6-like genes are present as large families (>15 members) in all sequenced strains of V. inaequalis and V. pirina, while in L. maculans, only AvrLm6 and a single paralog have been identified. The Venturia AvrLm6-like genes are located in gene-poor regions of the genomes, and mostly in close proximity to transposable elements, which may explain the expansion of these gene families. An AvrLm6-like gene from V. inaequalis with the highest sequence identity to AvrLm6 was unable to trigger a resistance response in Rlm6-carrying B. juncea. RNA-seq and qRT-PCR gene expression analyses, of in planta- and in vitro-grown V. inaequalis, has revealed that many of the AvrLm6-like genes are expressed during infection. An AvrLm6 homolog from V. inaequalis that is up-regulated during infection was shown (using an eYFP-fusion protein construct) to be localized to the sub-cuticular stroma during biotrophic infection of apple hypocotyls.

Published
2015

18. Fungal phytopathogens encode functional homologues of plant rapid alkalinization factor (RALF) peptides.

Author

Thynne, Elisha, Saur, Isabel M. L., Simbaqueba, Jaime, Ogilvie, Huw A., Gonzalez‐Cendales, Yvonne, Mead, Oliver, Taranto, Adam, Catanzariti, Ann‐Maree, McDonald, Megan C., Schwessinger, Benjamin, Jones, David A., Rathjen, John P., and Solomon, Peter S.

Subjects
PATHOGENIC microorganisms, FUSARIUM diseases of plants, FUSARIUM genetics, FUSARIUM disease of plants prevention, FUSARIUM, ALKALINIZATION
Abstract

In this article, we describe the presence of genes encoding close homologues of an endogenous plant peptide, rapid alkalinization factor (RALF), within the genomes of 26 species of phytopathogenic fungi. Members of the RALF family are key growth factors in plants, and the sequence of the RALF active region is well conserved between plant and fungal proteins. RALF1-like sequences were observed in most cases; however, RALF27-like sequences were present in the Sphaerulina musiva and Septoria populicola genomes. These two species are pathogens of poplar and, interestingly, the closest relative to their respective RALF genes is a poplar RALF27-like sequence. RALF peptides control cellular expansion during plant development, but were originally defined on the basis of their ability to induce rapid alkalinization in tobacco cell cultures. To test whether the fungal RALF peptides were biologically active in plants, we synthesized RALF peptides corresponding to those encoded by two sequenced genomes of the tomato pathogen Fusarium oxysporum f. sp. lycopersici. One of these peptides inhibited the growth of tomato seedlings and elicited responses in tomato and Nicotiana benthamiana typical of endogenous plant RALF peptides (reactive oxygen species burst, induced alkalinization and mitogen-activated protein kinase activation). Gene expression analysis confirmed that a RALF-encoding gene in F. oxysporum f. sp. lycopersici was expressed during infection on tomato. However, a subsequent reverse genetics approach revealed that the RALF peptide was not required by F. oxysporum f. sp. lycopersici for infection on tomato roots. This study has demonstrated the presence of functionally active RALF peptides encoded within phytopathogens that harbour an as yet undetermined role in plant-pathogen interactions. [ABSTRACT FROM AUTHOR]

Published
2017
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20. Proteogenomic Analysis of the Venturia pirina(Pear Scab Fungus) Secretome Reveals Potential Effectors

Author

Cooke, Ira R., Jones, Dan, Bowen, Joanna K., Deng, Cecilia, Faou, Pierre, Hall, Nathan E., Jayachandran, Vignesh, Liem, Michael, Taranto, Adam P., Plummer, Kim M., and Mathivanan, Suresh

Abstract

A proteogenomic analysis is presented for Venturia pirina, a fungus that causes scab disease on European pear (Pyrus communis). V. pirinais host-specific, and the infection is thought to be mediated by secreted effector proteins. Currently, only 36 V. pirinaproteins are catalogued in GenBank, and the genome sequence is not publicly available. To identify putative effectors, V. pirinawas grown in vitro on and in cellophane sheets mimicking its growth in infected leaves. Secreted extracts were analyzed by tandem mass spectrometry, and the data (ProteomeXchange identifier PXD000710) was queried against a protein database generated by combining in silico predicted transcripts with six frame translations of a whole genome sequence of V. pirina(GenBank Accession JEMP00000000). We identified 1088 distinct V. pirinaprotein groups (FDR 1%) including 1085 detected for the first time. Thirty novel (not in silico predicted) proteins were found, of which 14 were identified as potential effectors based on characteristic features of fungal effector protein sequences. We also used evidence from semitryptic peptides at the protein N-terminus to corroborate in silico signal peptide predictions for 22 proteins, including several potential effectors. The analysis highlights the utility of proteogenomics in the study of secreted effectors.

Published
2014
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