Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi

Published on Dec 1, 2018in Scientific Reports 4.12
· DOI :10.1038/s41598-018-24301-6
Ning Zhang23
Estimated H-index: 23
(Rutgers University),
Guohong Cai12
Estimated H-index: 12
(United States Department of Agriculture)
+ 12 AuthorsDebashish Bhattacharya64
Estimated H-index: 64
(Rutgers University)
Abstract
The rice blast fungus Pyricularia oryzae (syn. Magnaporthe oryzae, Magnaporthe grisea), a member of the order Magnaporthales in the class Sordariomycetes, is an important plant pathogen and a model species for studying pathogen infection and plant-fungal interaction. In this study, we generated genome sequence data from five additional Magnaporthales fungi including non-pathogenic species, and performed comparative genome analysis of a total of 13 fungal species in the class Sordariomycetes to understand the evolutionary history of the Magnaporthales and of fungal pathogenesis. Our results suggest that the Magnaporthales diverged ca. 31 millon years ago from other Sordariomycetes, with the phytopathogenic blast clade diverging ca. 21 million years ago. Little evidence of inter-phylum horizontal gene transfer (HGT) was detected in Magnaporthales. In contrast, many genes underwent positive selection in this order and the majority of these sequences are clade-specific. The blast clade genomes contain more secretome and avirulence effector genes, which likely play key roles in the interaction between Pyricularia species and their plant hosts. Finally, analysis of transposable elements (TE) showed differing proportions of TE classes among Magnaporthales genomes, suggesting that species-specific patterns may hold clues to the history of host/environmental adaptation in these fungi.
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References61
Published on May 14, 2004in BMC Bioinformatics 2.21
Ian Korf37
Estimated H-index: 37
(Wellcome Trust Sanger Institute)
Background Computational gene prediction continues to be an important problem, especially for genomes with little experimental data.
748 Citations Source Cite
Published on Feb 9, 2006in BMC Bioinformatics 2.21
Mario Stanke36
Estimated H-index: 36
(University of Göttingen),
Oliver Schöffmann1
Estimated H-index: 1
(University of Göttingen)
+ 1 AuthorsStephan Waack16
Estimated H-index: 16
(University of Göttingen)
Background In order to improve gene prediction, extrinsic evidence on the gene structure can be collected from various sources of information such as genome-genome comparisons and EST and protein alignments. However, such evidence is often incomplete and usually uncertain. The extrinsic evidence is usually not sufficient to recover the complete gene structure of all genes completely and the available evidence is often unreliable. Therefore extrinsic evidence is most valuable when it is balanced ...
348 Citations Source Cite
Published on Aug 19, 2004in BMC Bioinformatics 2.21
Robert C. Edgar17
Estimated H-index: 17
(University of California, Berkeley)
Background In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reported to date on four alignment accuracy benchmarks. Here we present a more complete discussion of the algorithm, describing several previously unpublished techniques that improve biological accuracy and / or computational complexity. We introduce a new option, MUSCLE-fast, designed f...
4,154 Citations Source Cite
Published on Jan 1, 2007in Advances in Genetics 4.69
Jin-Rong Xu50
Estimated H-index: 50
(Purdue University),
Xinhua Zhao9
Estimated H-index: 9
(Purdue University),
Ralph A. Dean44
Estimated H-index: 44
(North Carolina State University)
Abstract Magnaporthe oryzae is the most destructive fungal pathogen of rice worldwide and because of its amenability to classical and molecular genetic manipulation, availability of a genome sequence, and other resources it has emerged as a leading model system to study host–pathogen interactions. This chapter reviews recent progress toward elucidation of the molecular basis of infection‐related morphogenesis, host penetration, invasive growth, and host–pathogen interactions. Related information...
48 Citations Source Cite
Published on Jun 1, 1999in Nature 41.58
Thomas N. Taylor46
Estimated H-index: 46
,
Hagen Hass21
Estimated H-index: 21
,
Hans Kerp34
Estimated H-index: 34
112 Citations Source Cite
Published on Dec 1, 2015in Genome Biology 13.21
David Emms8
Estimated H-index: 8
(University of Oxford),
Steven L. Kelly54
Estimated H-index: 54
(University of Oxford)
Identifying homology relationships between sequences is fundamental to biological research. Here we provide a novel orthogroup inference algorithm called OrthoFinder that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy. Using real benchmark datasets we demonstrate that OrthoFinder is more accurate than other orthogroup inference methods by between 8 % and 33 %. Furthermore, we demonstrate the utility of OrthoFinder by pro...
377 Citations Source Cite
Published on Dec 1, 2011in Journal of Phytopathology 0.82
Alfredo S. Urashima10
Estimated H-index: 10
(Federal University of São Carlos),
Cristina P. Silva4
Estimated H-index: 4
(University of Western Australia)
Blast caused by Magnaporthe grisea (Pyricularia grisea) is a disease that occurs in many important gramineous plants in Brazil such as rice, wheat, triticale and barley. In 2005, the presence of this disease was reported on black oat (Avena strigosa) at different locations of Parana state. Due to little information of M. grisea that is infecting this host, this work aimed to characterize it at molecular, sexual and pathogenic level. DNA analysis showed that M. grisea from black oat formed a homo...
7 Citations Source Cite
Published on Oct 4, 2013in Science 41.06
Arne Weiberg8
Estimated H-index: 8
(University of California, Riverside),
Ming Wang8
Estimated H-index: 8
(University of California, Riverside)
+ 5 AuthorsHailing Jin39
Estimated H-index: 39
(University of California, Riverside)
Plant microbial pathogens often work through protein effectors that are delivered into the plant cells to disrupt critical cellular functions. Weiberg et al. (p. [118][1]; see the Perspective by [Baulcombe][2] ) have now found that small RNAs (sRNAs) of the fungus Botrytis cinerea can play a similar role. After fungal infection of tomato or Arabidopsis leaves, the plant cells contained a suite of fungal-derived sRNAs. Three sRNAs were found to bind to the plant's own Argonaute protein, thereby s...
326 Citations Source Cite
Published on Jan 26, 1996in Science 41.06
Russell F. Doolittle66
Estimated H-index: 66
(University of California, San Diego),
Da-Fei Feng14
Estimated H-index: 14
(University of California, San Diego)
+ 2 AuthorsElizabeth Little3
Estimated H-index: 3
(University of California, San Diego)
Amino acid sequence data from 57 different enzymes were used to determine the divergence times of the major biological groupings. Deuterostomes and protostomes split about 670 million years ago and plants, animals, and fungi last shared a common ancestor about a billion years ago. With regard to these protein sequences, plants are slightly more similar to animals than are the fungi. In contrast, phylogenetic analysis of the same sequences indicates that fungi and animals shared a common ancestor...
467 Citations Source Cite
Published on Jan 1, 2014in Biophysical Journal 3.50
Sathish Thiyagarajan4
Estimated H-index: 4
(Columbia University),
Zhou Zhou2
Estimated H-index: 2
(Columbia University)
+ 2 AuthorsBen O'Shaughnessy20
Estimated H-index: 20
(Columbia University)
In fungi and metazoans, cytokinesis involves constriction of a contractile actomyosin ring. The role of the ring remains unclear: it is unknown if it sets the constriction rate or has some other function. We combined mathematical modelling and quantitative image analysis of experimental septum measurements to study the interaction between the constricting ring and septation, the growth of new cell wall in the wake of the constricting ring. We hypothesize local mechanosensitivity of the Bgs compl...
2 Citations Source Cite