Computational reclassification of resistance gene analogs in Rosaceae based on the NBS-LRR domain.

Angela M. Baldo; Suren Samuelian; Courtney A. Weber

Computational reclassification of resistance gene analogs in Rosaceae based on the NBS-LRR domain.

Angela M. Baldo, Suren Samuelian, Courtney A. Weber

Research output: Book chapter/Published conference paper › Conference paper › peer-review

Abstract

Plant R genes are known to confer resistance to a variety of pathogens in a gene-for-gene mode. One hundred and ninety-five Rosaceae putative resistance gene analog (RGA) sequences containing conserved NBS-LRR domains were downloaded from the public domain. An additional seventy-six RGAs were amplified and sequenced from red raspberry Rubus idaeus cv 'Latham' using degenerate primers. Sequences were aligned using Hidden Markov Models and clustered with Neighbor-Joining. There are eleven TIR and ten non-TIR sequence clusters containing two or more genera with a bootstrap greater than 50%. This classification will be used to help identify novel RGAs found in the USDA-ARS apple and cherry germplasm collections in Geneva, NY.

Original language	English
Title of host publication	Plant and Animal Genome XV Conference
Place of Publication	USA
Publisher	Plant and Animal Genome?
Pages	157 (P224)
Publication status	Published - 2007
Event	Plant and Animal Genome XV Conference - San Diego, USA, New Zealand Duration: 13 Jan 2007 → 17 Jan 2007

Conference

Conference	Plant and Animal Genome XV Conference
Country	New Zealand
Period	13/01/07 → 17/01/07

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@inproceedings{77baed30e32c4394a90d0599ae349150,

title = "Computational reclassification of resistance gene analogs in Rosaceae based on the NBS-LRR domain.",

abstract = "Plant R genes are known to confer resistance to a variety of pathogens in a gene-for-gene mode. One hundred and ninety-five Rosaceae putative resistance gene analog (RGA) sequences containing conserved NBS-LRR domains were downloaded from the public domain. An additional seventy-six RGAs were amplified and sequenced from red raspberry Rubus idaeus cv 'Latham' using degenerate primers. Sequences were aligned using Hidden Markov Models and clustered with Neighbor-Joining. There are eleven TIR and ten non-TIR sequence clusters containing two or more genera with a bootstrap greater than 50%. This classification will be used to help identify novel RGAs found in the USDA-ARS apple and cherry germplasm collections in Geneva, NY.",

author = "Baldo, {Angela M.} and Suren Samuelian and Weber, {Courtney A.}",

note = "Imported on 03 May 2017 - DigiTool details were: publisher = USA: Plant and Animal Genome?, 2007. Event dates (773o) = 13-17 Jan, 2007; Parent title (773t) = Plant and Animal Genome XV Conference.; Plant and Animal Genome XV Conference ; Conference date: 13-01-2007 Through 17-01-2007",

year = "2007",

language = "English",

pages = "157 (P224)",

booktitle = "Plant and Animal Genome XV Conference",

publisher = "Plant and Animal Genome?",

}

TY - GEN

T1 - Computational reclassification of resistance gene analogs in Rosaceae based on the NBS-LRR domain.

AU - Baldo, Angela M.

AU - Samuelian, Suren

AU - Weber, Courtney A.

N1 - Imported on 03 May 2017 - DigiTool details were: publisher = USA: Plant and Animal Genome?, 2007. Event dates (773o) = 13-17 Jan, 2007; Parent title (773t) = Plant and Animal Genome XV Conference.

PY - 2007

Y1 - 2007

N2 - Plant R genes are known to confer resistance to a variety of pathogens in a gene-for-gene mode. One hundred and ninety-five Rosaceae putative resistance gene analog (RGA) sequences containing conserved NBS-LRR domains were downloaded from the public domain. An additional seventy-six RGAs were amplified and sequenced from red raspberry Rubus idaeus cv 'Latham' using degenerate primers. Sequences were aligned using Hidden Markov Models and clustered with Neighbor-Joining. There are eleven TIR and ten non-TIR sequence clusters containing two or more genera with a bootstrap greater than 50%. This classification will be used to help identify novel RGAs found in the USDA-ARS apple and cherry germplasm collections in Geneva, NY.

AB - Plant R genes are known to confer resistance to a variety of pathogens in a gene-for-gene mode. One hundred and ninety-five Rosaceae putative resistance gene analog (RGA) sequences containing conserved NBS-LRR domains were downloaded from the public domain. An additional seventy-six RGAs were amplified and sequenced from red raspberry Rubus idaeus cv 'Latham' using degenerate primers. Sequences were aligned using Hidden Markov Models and clustered with Neighbor-Joining. There are eleven TIR and ten non-TIR sequence clusters containing two or more genera with a bootstrap greater than 50%. This classification will be used to help identify novel RGAs found in the USDA-ARS apple and cherry germplasm collections in Geneva, NY.

M3 - Conference paper

SP - 157 (P224)

BT - Plant and Animal Genome XV Conference

PB - Plant and Animal Genome?

CY - USA

T2 - Plant and Animal Genome XV Conference

Y2 - 13 January 2007 through 17 January 2007

ER -