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

The single most parsimonious tree generated from the analysis of the EF1-α 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. The tree is rooted with D. helianthi (CBS 592.81)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4150081&req=5

Figure 2: The single most parsimonious tree generated from the analysis of the EF1-α 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. The tree is rooted with D. helianthi (CBS 592.81)

Mentions: The rooted gene genealogies resulting from each of the single gene analyses of ACT, CAL, EF1-α, ITS and TUB were submitted to the genealogical sorting index (gsi) parallel computing resource (http://www.genealogicalsorting.org/) for analysis. The gsi estimates the degree of exclusive ancestry of individuals in labelled predefined groups in a rooted tree (Cummings et al. 2008). Values range from 0 to 1 with 0 corresponding to a lack of genealogical divergence from other groups and 1 corresponding to monophyly for the predetermined clade (or species). Each isolate was assigned to a predetermined species based on Genealogical Concordance Phylogenetic Species Recognition (GCPSR) and the gsi was calculated for the best tree selected in parsimony analysis and for all trees using 10 000 permutations (Cummings et al. 2008). The assignment of each tip to groups representing the recognised species was identical for the EF1-α and combined phylogenetic trees (Fig. 2, 3). Taxa in the ITS tree that were not present in EF1-α and combined trees were not included in the calculation of gsi. The gsi and each of the probability values (P) corresponding to the species represented by more than one isolate were tabulated (Table 3). Species with one representative isolate including the outgroup were not subjected to gsi analysis. The ensemble genealogical sorting index (gsiT) is the sum of the gsi values calculated for all individual gene trees (Table 3).


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)

The single most parsimonious tree generated from the analysis of the EF1-α 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. 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 2: The single most parsimonious tree generated from the analysis of the EF1-α 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. The tree is rooted with D. helianthi (CBS 592.81)
Mentions: The rooted gene genealogies resulting from each of the single gene analyses of ACT, CAL, EF1-α, ITS and TUB were submitted to the genealogical sorting index (gsi) parallel computing resource (http://www.genealogicalsorting.org/) for analysis. The gsi estimates the degree of exclusive ancestry of individuals in labelled predefined groups in a rooted tree (Cummings et al. 2008). Values range from 0 to 1 with 0 corresponding to a lack of genealogical divergence from other groups and 1 corresponding to monophyly for the predetermined clade (or species). Each isolate was assigned to a predetermined species based on Genealogical Concordance Phylogenetic Species Recognition (GCPSR) and the gsi was calculated for the best tree selected in parsimony analysis and for all trees using 10 000 permutations (Cummings et al. 2008). The assignment of each tip to groups representing the recognised species was identical for the EF1-α and combined phylogenetic trees (Fig. 2, 3). Taxa in the ITS tree that were not present in EF1-α and combined trees were not included in the calculation of gsi. The gsi and each of the probability values (P) corresponding to the species represented by more than one isolate were tabulated (Table 3). Species with one representative isolate including the outgroup were not subjected to gsi analysis. The ensemble genealogical sorting index (gsiT) is the sum of the gsi values calculated for all individual gene trees (Table 3).

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