Limits...
Species limits in Diaporthe: molecular re-assessment of D. citri, D. cytosporella, D. foeniculina and D. rudis.

Udayanga D, Castlebury LA, Rossman AY, Hyde KD - Persoonia (2014)

Bottom Line: Diaporthe cytosporella is found on Citrus in Europe and California (USA).Newly designed primers are introduced to optimise the amplification and sequencing of calmodulin and actin genes in Diaporthe.A discussion is provided of the utility of genes and the need for multi-gene phylogenies when distinguishing species of Diaporthe or describing new species.

View Article: PubMed Central - PubMed

Affiliation: Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, 20705 USA; ; Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand. ; School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand.

ABSTRACT
Species of Diaporthe are important plant pathogens of a wide range of hosts worldwide. In the present study the species causing melanose and stem end rot diseases of Citrus spp. are revised. Three species of Diaporthe occurring on Citrus are characterised, including D. citri, D. cytosporella and D. foeniculina. Morphology and phylogenetic analyses of the complete nuclear ribosomal internal transcribed spacer regions and partial sequences of actin, beta-tubulin, calmodulin and translation elongation factor 1-α were used to resolve species on Citrus and related Diaporthe species. Diaporthe citri occurs on Citrus throughout the Citrus-growing regions of the world. Diaporthe cytosporella is found on Citrus in Europe and California (USA). Diaporthe foeniculina, including the synonym D. neotheicola, is recognised as a species with an extensive host range including Citrus. Diaporthe medusaea, a name widely used for D. citri, was determined to be a synonym of D. rudis, a species with a broad host range. Diaporthe citri is delimited based on molecular phylogenetic analysis with the inclusion of the conserved ex-type and additional collections from different geographic locations worldwide. Diaporthe cytosporella, D. foeniculina and D. rudis are epitypified, fully described and illustrated with a review of all synonyms based on molecular data and morphological studies. Newly designed primers are introduced to optimise the amplification and sequencing of calmodulin and actin genes in Diaporthe. A discussion is provided of the utility of genes and the need for multi-gene phylogenies when distinguishing species of Diaporthe or describing new species.

No MeSH data available.


Related in: MedlinePlus

One of the 45 equally parsimonious trees generated from the analysis of the ITS sequence alignment. MP/RAxML bootstrap values/Bayesian posterior probabilities ≥ 70 % are displayed above or below each branch. Ex-type and ex-epitype culture numbers are in bold. GenBank accessions are given for downloaded sequences and isolate codes for the newly generated sequences annotated with host and location. Isolates from Citrus are indicated in green. ITS sequences obtained from GenBank verified as D. cytosporella, D. foeniculina and D. rudis are indicated with an asterisk. The tree is rooted with D. helianthi (CBS 592.81).
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Figure 1: One of the 45 equally parsimonious trees generated from the analysis of the ITS sequence alignment. MP/RAxML bootstrap values/Bayesian posterior probabilities ≥ 70 % are displayed above or below each branch. Ex-type and ex-epitype culture numbers are in bold. GenBank accessions are given for downloaded sequences and isolate codes for the newly generated sequences annotated with host and location. Isolates from Citrus are indicated in green. ITS sequences obtained from GenBank verified as D. cytosporella, D. foeniculina and D. rudis are indicated with an asterisk. The tree is rooted with D. helianthi (CBS 592.81).

Mentions: Complete failure of amplification of the isolates in the D. foeniculina clade (Fig. 1) and evidence of non-specific priming in the sequences of the CAL gene region was observed when using the CAL-228F/CAL-737R (Carbone & Kohn 1999) or CL1/CL2A (O’Donnell et al. 2000) primer sets. Additionally frequent failures of sequencing when using ACT-512F/ACT-783R (Carbone & Kohn 1999) were encountered in this clade. On closer inspection of ACT and CAL multiple sequence alignments for Diaporthe, non-specific binding sites were observed for both ACT-783R and CAL-228F primers (Carbone & Kohn 1999).


Species limits in Diaporthe: molecular re-assessment of D. citri, D. cytosporella, D. foeniculina and D. rudis.

Udayanga D, Castlebury LA, Rossman AY, Hyde KD - Persoonia (2014)

One of the 45 equally parsimonious trees generated from the analysis of the ITS sequence alignment. MP/RAxML bootstrap values/Bayesian posterior probabilities ≥ 70 % are displayed above or below each branch. Ex-type and ex-epitype culture numbers are in bold. GenBank accessions are given for downloaded sequences and isolate codes for the newly generated sequences annotated with host and location. Isolates from Citrus are indicated in green. ITS sequences obtained from GenBank verified as D. cytosporella, D. foeniculina and D. rudis are indicated with an asterisk. The tree is rooted with D. helianthi (CBS 592.81).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150081&req=5

Figure 1: One of the 45 equally parsimonious trees generated from the analysis of the ITS sequence alignment. MP/RAxML bootstrap values/Bayesian posterior probabilities ≥ 70 % are displayed above or below each branch. Ex-type and ex-epitype culture numbers are in bold. GenBank accessions are given for downloaded sequences and isolate codes for the newly generated sequences annotated with host and location. Isolates from Citrus are indicated in green. ITS sequences obtained from GenBank verified as D. cytosporella, D. foeniculina and D. rudis are indicated with an asterisk. The tree is rooted with D. helianthi (CBS 592.81).
Mentions: Complete failure of amplification of the isolates in the D. foeniculina clade (Fig. 1) and evidence of non-specific priming in the sequences of the CAL gene region was observed when using the CAL-228F/CAL-737R (Carbone & Kohn 1999) or CL1/CL2A (O’Donnell et al. 2000) primer sets. Additionally frequent failures of sequencing when using ACT-512F/ACT-783R (Carbone & Kohn 1999) were encountered in this clade. On closer inspection of ACT and CAL multiple sequence alignments for Diaporthe, non-specific binding sites were observed for both ACT-783R and CAL-228F primers (Carbone & Kohn 1999).

Bottom Line: Diaporthe cytosporella is found on Citrus in Europe and California (USA).Newly designed primers are introduced to optimise the amplification and sequencing of calmodulin and actin genes in Diaporthe.A discussion is provided of the utility of genes and the need for multi-gene phylogenies when distinguishing species of Diaporthe or describing new species.

View Article: PubMed Central - PubMed

Affiliation: Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, 20705 USA; ; Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand. ; School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand.

ABSTRACT
Species of Diaporthe are important plant pathogens of a wide range of hosts worldwide. In the present study the species causing melanose and stem end rot diseases of Citrus spp. are revised. Three species of Diaporthe occurring on Citrus are characterised, including D. citri, D. cytosporella and D. foeniculina. Morphology and phylogenetic analyses of the complete nuclear ribosomal internal transcribed spacer regions and partial sequences of actin, beta-tubulin, calmodulin and translation elongation factor 1-α were used to resolve species on Citrus and related Diaporthe species. Diaporthe citri occurs on Citrus throughout the Citrus-growing regions of the world. Diaporthe cytosporella is found on Citrus in Europe and California (USA). Diaporthe foeniculina, including the synonym D. neotheicola, is recognised as a species with an extensive host range including Citrus. Diaporthe medusaea, a name widely used for D. citri, was determined to be a synonym of D. rudis, a species with a broad host range. Diaporthe citri is delimited based on molecular phylogenetic analysis with the inclusion of the conserved ex-type and additional collections from different geographic locations worldwide. Diaporthe cytosporella, D. foeniculina and D. rudis are epitypified, fully described and illustrated with a review of all synonyms based on molecular data and morphological studies. Newly designed primers are introduced to optimise the amplification and sequencing of calmodulin and actin genes in Diaporthe. A discussion is provided of the utility of genes and the need for multi-gene phylogenies when distinguishing species of Diaporthe or describing new species.

No MeSH data available.


Related in: MedlinePlus