@ARTICLE{TreeBASE2Ref26999,
author = {Shawn Christopher Kenaley},
title = {First report of Puccinia coronata var. coronata s.s. infecting alder buckthorn in the United States},
year = {2017},
keywords = {Crown rust; Fragula alnus; Pucciniales},
doi = {},
url = {http://},
pmid = {},
journal = {Plant Health Progress},
volume = {},
number = {},
pages = {},
abstract = {The raw DNA sequences produced from the suspected Puccinia sp. on alder buckthorn collected in Storrs, Connecticut were edited in CodonCode Aligner v5.1.5 (CodonCode Corporation,Dedham, MA) to address ambiguous base calls. Alignments were constructed using Clustal X v2.1 (Larkin et al. 2007) and adjusted by eye in Geneious v.9.0.5 (Biomatters Ltd., Auckland, New Zealand) to correct ambiguously aligned sites and erroneous gaps.
Phylogenetic analyses integrated two approaches: maximum-likelihood (ML) and maximum parsimony (MP). ML and MP analyses were performed using PAUP* (Swofford 2003). For the ML analyses, the best model of sequence evolution for each alignment (gene region) was selected by the Akaike Information Criterion (AIC; Akaike 1974) implemented in jModelTest 2.1.10 (Darriba et al. 2012). A heuristic search was performed with 1000 random-addition-sequence (RAS) replicates, tree bisection-reconnection (TBR) branch swapping, and MULTREES in effect. All nucleotides were included in the phylogenetic analysis. Branch support was evaluated using 1000 bootstrap replicates and 100 RAS per pseudo-replicate. MP analysis was conducted with the heuristic search option with 1000 RAS replicates and TBR as the branch-swapping algorithm. The robustness of the most parsimonious trees was evaluated by 1000 bootstrap replicates.}
}
Citation for Study 20727
Citation title:
"First report of Puccinia coronata var. coronata s.s. infecting alder buckthorn in the United States".
Study name:
"First report of Puccinia coronata var. coronata s.s. infecting alder buckthorn in the United States".
This study is part of submission 20727
(Status: Published).
Citation
Kenaley S.C. 2017. First report of Puccinia coronata var. coronata s.s. infecting alder buckthorn in the United States. Plant Health Progress, .
Authors
-
Kenaley S.C.
(submitter)
607-339-7366
Abstract
The raw DNA sequences produced from the suspected Puccinia sp. on alder buckthorn collected in Storrs, Connecticut were edited in CodonCode Aligner v5.1.5 (CodonCode Corporation,Dedham, MA) to address ambiguous base calls. Alignments were constructed using Clustal X v2.1 (Larkin et al. 2007) and adjusted by eye in Geneious v.9.0.5 (Biomatters Ltd., Auckland, New Zealand) to correct ambiguously aligned sites and erroneous gaps.
Phylogenetic analyses integrated two approaches: maximum-likelihood (ML) and maximum parsimony (MP). ML and MP analyses were performed using PAUP* (Swofford 2003). For the ML analyses, the best model of sequence evolution for each alignment (gene region) was selected by the Akaike Information Criterion (AIC; Akaike 1974) implemented in jModelTest 2.1.10 (Darriba et al. 2012). A heuristic search was performed with 1000 random-addition-sequence (RAS) replicates, tree bisection-reconnection (TBR) branch swapping, and MULTREES in effect. All nucleotides were included in the phylogenetic analysis. Branch support was evaluated using 1000 bootstrap replicates and 100 RAS per pseudo-replicate. MP analysis was conducted with the heuristic search option with 1000 RAS replicates and TBR as the branch-swapping algorithm. The robustness of the most parsimonious trees was evaluated by 1000 bootstrap replicates.
Keywords
Crown rust; Fragula alnus; Pucciniales
External links
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S20727
- Other versions:
Nexus
NeXML
- Show BibTeX reference
@ARTICLE{TreeBASE2Ref26999,
author = {Shawn Christopher Kenaley},
title = {First report of Puccinia coronata var. coronata s.s. infecting alder buckthorn in the United States},
year = {2017},
keywords = {Crown rust; Fragula alnus; Pucciniales},
doi = {},
url = {http://},
pmid = {},
journal = {Plant Health Progress},
volume = {},
number = {},
pages = {},
abstract = {The raw DNA sequences produced from the suspected Puccinia sp. on alder buckthorn collected in Storrs, Connecticut were edited in CodonCode Aligner v5.1.5 (CodonCode Corporation,Dedham, MA) to address ambiguous base calls. Alignments were constructed using Clustal X v2.1 (Larkin et al. 2007) and adjusted by eye in Geneious v.9.0.5 (Biomatters Ltd., Auckland, New Zealand) to correct ambiguously aligned sites and erroneous gaps.
Phylogenetic analyses integrated two approaches: maximum-likelihood (ML) and maximum parsimony (MP). ML and MP analyses were performed using PAUP* (Swofford 2003). For the ML analyses, the best model of sequence evolution for each alignment (gene region) was selected by the Akaike Information Criterion (AIC; Akaike 1974) implemented in jModelTest 2.1.10 (Darriba et al. 2012). A heuristic search was performed with 1000 random-addition-sequence (RAS) replicates, tree bisection-reconnection (TBR) branch swapping, and MULTREES in effect. All nucleotides were included in the phylogenetic analysis. Branch support was evaluated using 1000 bootstrap replicates and 100 RAS per pseudo-replicate. MP analysis was conducted with the heuristic search option with 1000 RAS replicates and TBR as the branch-swapping algorithm. The robustness of the most parsimonious trees was evaluated by 1000 bootstrap replicates.}
}
- Show RIS reference
TY - JOUR
ID - 26999
AU - Kenaley,Shawn Christopher
T1 - First report of Puccinia coronata var. coronata s.s. infecting alder buckthorn in the United States
PY - 2017
KW - Crown rust; Fragula alnus; Pucciniales
UR - http://dx.doi.org/
N2 - The raw DNA sequences produced from the suspected Puccinia sp. on alder buckthorn collected in Storrs, Connecticut were edited in CodonCode Aligner v5.1.5 (CodonCode Corporation,Dedham, MA) to address ambiguous base calls. Alignments were constructed using Clustal X v2.1 (Larkin et al. 2007) and adjusted by eye in Geneious v.9.0.5 (Biomatters Ltd., Auckland, New Zealand) to correct ambiguously aligned sites and erroneous gaps.
Phylogenetic analyses integrated two approaches: maximum-likelihood (ML) and maximum parsimony (MP). ML and MP analyses were performed using PAUP* (Swofford 2003). For the ML analyses, the best model of sequence evolution for each alignment (gene region) was selected by the Akaike Information Criterion (AIC; Akaike 1974) implemented in jModelTest 2.1.10 (Darriba et al. 2012). A heuristic search was performed with 1000 random-addition-sequence (RAS) replicates, tree bisection-reconnection (TBR) branch swapping, and MULTREES in effect. All nucleotides were included in the phylogenetic analysis. Branch support was evaluated using 1000 bootstrap replicates and 100 RAS per pseudo-replicate. MP analysis was conducted with the heuristic search option with 1000 RAS replicates and TBR as the branch-swapping algorithm. The robustness of the most parsimonious trees was evaluated by 1000 bootstrap replicates.
L3 -
JF - Plant Health Progress
VL -
IS -
ER -
Go to search
Citation
Taxa
Matrices
Trees
Analyses
