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Comparative genomics of Taphrina fungi causing varying degrees of tumorous deformity in plants.

Tsai IJ, Tanaka E, Masuya H, Tanaka R, Hirooka Y, Endoh R, Sahashi N, Kikuchi T - Genome Biol Evol (2014)

Bottom Line: High levels of gene synteny within Taphrina species were observed, and our comparative analysis further revealed that these fungi may utilize multiple strategies in coping with the host environment that are also found in some specialized dimorphic species.We also identified species differences in plant hormone biosynthesis pathways, which may contribute to varying degree of disease symptoms.The genomes provide a rich resource for investigation into Taphrina biology and evolutionary studies across the basal ascomycetes clade.

View Article: PubMed Central - PubMed

Affiliation: Division of Parasitology, Faculty of Medicine, University of Miyazaki, Japan.

ABSTRACT
Taphrina fungi are biotrophic plant pathogens that cause plant deformity diseases. We sequenced the genomes of four Taphrina species-Taphrina wiesneri, T. deformans, T. flavorubra, and T. populina-which parasitize Prunus, Cerasus, and Populus hosts with varying severity of disease symptoms. High levels of gene synteny within Taphrina species were observed, and our comparative analysis further revealed that these fungi may utilize multiple strategies in coping with the host environment that are also found in some specialized dimorphic species. These include species-specific aneuploidy and clusters of highly diverged secreted proteins located at subtelomeres. We also identified species differences in plant hormone biosynthesis pathways, which may contribute to varying degree of disease symptoms. The genomes provide a rich resource for investigation into Taphrina biology and evolutionary studies across the basal ascomycetes clade.

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Taphrina infection symptoms and phylogeny. (A) Leaf curl (a), witches’ broom (b), leaf spots (c), and deformed fruits (d) that were caused by four different Taphrina species indicated by arrows. (a) Image no. 5435623: Yuan-Min Shen, Taichung District Agricultural Research and Extension Station, Bugwood.org; (c) image no. 3046084: Theodor D. Leininger, USDA Forest Service, Bugwood.org. (B) A maximum-likelihood phylogeny of four Taphrina species and seven other fungi from 75 single copy orthologs. Blue dots indicate 100% bootstrap support.
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evu067-F1: Taphrina infection symptoms and phylogeny. (A) Leaf curl (a), witches’ broom (b), leaf spots (c), and deformed fruits (d) that were caused by four different Taphrina species indicated by arrows. (a) Image no. 5435623: Yuan-Min Shen, Taichung District Agricultural Research and Extension Station, Bugwood.org; (c) image no. 3046084: Theodor D. Leininger, USDA Forest Service, Bugwood.org. (B) A maximum-likelihood phylogeny of four Taphrina species and seven other fungi from 75 single copy orthologs. Blue dots indicate 100% bootstrap support.

Mentions: The nuclear genomes of T. wiesneri, T. deformans, T. populina, and T. flavorubra were selected for sequencing on the basis of the very different symptoms exhibited by their many Prunus, Cerasus, and Populus hosts worldwide (fig. 1A, supplementary table S1, Supplementary Material online). The Taphrina genomes were sequenced using Illumina technology with up to 450 × depth of coverage obtained. CEGMA analysis suggests that assemblies are 98.4–98.8% complete. The assemblies range from 12.0 to 15.7 Mb (table 1), similar to the 12.5-Mb genome of fission yeast S. pombe. Using transcriptomic evidence such as RNA Illumina sequenced reads and ESTs to guide de novo gene prediction, we identified 6,403–7,563 putative gene models per genome (table 2). Our T. deformans assembly is on average 99.7% identical with the published genome sequence of T. deformans PYCC5710 (Cissé et al. 2013) but is twice as contiguated. Similarly, the Taphrina mitochondrial genomes were assembled into single scaffolds ranging from 56 to 60 kb (supplementary fig. S1, Supplementary Material online), which is bigger than that reported for S. pombe (19.4 kb) (Bullerwell et al. 2003) but still smaller than Sa. cerevisiae (85.8 kb) (Foury et al. 1998). In the most contiguated case of T. wiesneri, the mitochondrial genome was assembled into a single sequence of 58,215 bp without any gaps, containing 39 genes (supplementary fig. S1A, Supplementary Material online), consisting of 14 proteins, 2 ribosomal RNAs, and 23 transfer RNAs. Our mitochondrial assembly of T. deformans is 56,006 bp in size, which is 20 kb bigger and identified 16 more tRNA genes than previously reported (Cissé et al. 2013). The gene orders of the four mitochondrial genomes are in almost perfect synteny to each other, with only minor differences in the order of tRNAs (supplementary fig. S1B, Supplementary Material online). Together these assemblies allow us to build upon what is already known about Taphrina species using a comparative genomics approach.Fig. 1.—


Comparative genomics of Taphrina fungi causing varying degrees of tumorous deformity in plants.

Tsai IJ, Tanaka E, Masuya H, Tanaka R, Hirooka Y, Endoh R, Sahashi N, Kikuchi T - Genome Biol Evol (2014)

Taphrina infection symptoms and phylogeny. (A) Leaf curl (a), witches’ broom (b), leaf spots (c), and deformed fruits (d) that were caused by four different Taphrina species indicated by arrows. (a) Image no. 5435623: Yuan-Min Shen, Taichung District Agricultural Research and Extension Station, Bugwood.org; (c) image no. 3046084: Theodor D. Leininger, USDA Forest Service, Bugwood.org. (B) A maximum-likelihood phylogeny of four Taphrina species and seven other fungi from 75 single copy orthologs. Blue dots indicate 100% bootstrap support.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4007546&req=5

evu067-F1: Taphrina infection symptoms and phylogeny. (A) Leaf curl (a), witches’ broom (b), leaf spots (c), and deformed fruits (d) that were caused by four different Taphrina species indicated by arrows. (a) Image no. 5435623: Yuan-Min Shen, Taichung District Agricultural Research and Extension Station, Bugwood.org; (c) image no. 3046084: Theodor D. Leininger, USDA Forest Service, Bugwood.org. (B) A maximum-likelihood phylogeny of four Taphrina species and seven other fungi from 75 single copy orthologs. Blue dots indicate 100% bootstrap support.
Mentions: The nuclear genomes of T. wiesneri, T. deformans, T. populina, and T. flavorubra were selected for sequencing on the basis of the very different symptoms exhibited by their many Prunus, Cerasus, and Populus hosts worldwide (fig. 1A, supplementary table S1, Supplementary Material online). The Taphrina genomes were sequenced using Illumina technology with up to 450 × depth of coverage obtained. CEGMA analysis suggests that assemblies are 98.4–98.8% complete. The assemblies range from 12.0 to 15.7 Mb (table 1), similar to the 12.5-Mb genome of fission yeast S. pombe. Using transcriptomic evidence such as RNA Illumina sequenced reads and ESTs to guide de novo gene prediction, we identified 6,403–7,563 putative gene models per genome (table 2). Our T. deformans assembly is on average 99.7% identical with the published genome sequence of T. deformans PYCC5710 (Cissé et al. 2013) but is twice as contiguated. Similarly, the Taphrina mitochondrial genomes were assembled into single scaffolds ranging from 56 to 60 kb (supplementary fig. S1, Supplementary Material online), which is bigger than that reported for S. pombe (19.4 kb) (Bullerwell et al. 2003) but still smaller than Sa. cerevisiae (85.8 kb) (Foury et al. 1998). In the most contiguated case of T. wiesneri, the mitochondrial genome was assembled into a single sequence of 58,215 bp without any gaps, containing 39 genes (supplementary fig. S1A, Supplementary Material online), consisting of 14 proteins, 2 ribosomal RNAs, and 23 transfer RNAs. Our mitochondrial assembly of T. deformans is 56,006 bp in size, which is 20 kb bigger and identified 16 more tRNA genes than previously reported (Cissé et al. 2013). The gene orders of the four mitochondrial genomes are in almost perfect synteny to each other, with only minor differences in the order of tRNAs (supplementary fig. S1B, Supplementary Material online). Together these assemblies allow us to build upon what is already known about Taphrina species using a comparative genomics approach.Fig. 1.—

Bottom Line: High levels of gene synteny within Taphrina species were observed, and our comparative analysis further revealed that these fungi may utilize multiple strategies in coping with the host environment that are also found in some specialized dimorphic species.We also identified species differences in plant hormone biosynthesis pathways, which may contribute to varying degree of disease symptoms.The genomes provide a rich resource for investigation into Taphrina biology and evolutionary studies across the basal ascomycetes clade.

View Article: PubMed Central - PubMed

Affiliation: Division of Parasitology, Faculty of Medicine, University of Miyazaki, Japan.

ABSTRACT
Taphrina fungi are biotrophic plant pathogens that cause plant deformity diseases. We sequenced the genomes of four Taphrina species-Taphrina wiesneri, T. deformans, T. flavorubra, and T. populina-which parasitize Prunus, Cerasus, and Populus hosts with varying severity of disease symptoms. High levels of gene synteny within Taphrina species were observed, and our comparative analysis further revealed that these fungi may utilize multiple strategies in coping with the host environment that are also found in some specialized dimorphic species. These include species-specific aneuploidy and clusters of highly diverged secreted proteins located at subtelomeres. We also identified species differences in plant hormone biosynthesis pathways, which may contribute to varying degree of disease symptoms. The genomes provide a rich resource for investigation into Taphrina biology and evolutionary studies across the basal ascomycetes clade.

Show MeSH
Related in: MedlinePlus