Identifying host molecular features strongly linked with responses to huanglongbing disease in citrus leaves

Tiziano Caruso, Federico Martinelli, Bipin Balan, Ana M. Ibáñez, Abhaya M. Dandekar

Risultato della ricerca: Article

3 Citazioni (Scopus)

Abstract

A bioinformatic analysis of previously published RNA-Seq studies on Huanglongbing (HLB) response and tolerance in leaf tissues was performed. The aim was to identify genes commonly modulated between studies and genes, pathways and gene set categories strongly associated with this devastating Citrus disease. Bioinformatic analysis of expression data of four datasets present in NCBI provided 46–68 million reads with an alignment percentage of 72.95–86.76%. Only 16 HLB-regulated genes werecommonlyidentifiedbetweenthethreeleafdatasets.Amongthemwerekeygenes encoding proteins involved in cell wall modification such as CESA8, pectinesterase, expansin8, expansin beta 3.1, and a pectate lyase. Fourteen HLB-regulated genes were in common between all four datasets. Gene set enrichment analysis showed some different gene categories affected by HLB disease. Although sucrose and starch metabolism was highly linked with disease symptoms, different genes were significantly regulated depending on leaf growth and infection stages and experimental conditions. Histone-related transcription factors were highly affected by HLB in the analyzed RNA-Seq datasets. HLB tolerance was linked with induction of proteins involved in detoxification. Protein–protein interaction (PPI) network analysis confirmed a possible role for heat shock proteins in curbing disease progression.
Lingua originaleEnglish
pagine (da-a)1-13
Numero di pagine13
RivistaFrontiers in Plant Science
Volume9
Stato di pubblicazionePublished - 2018

All Science Journal Classification (ASJC) codes

  • Plant Science

Cita questo

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title = "Identifying host molecular features strongly linked with responses to huanglongbing disease in citrus leaves",
abstract = "A bioinformatic analysis of previously published RNA-Seq studies on Huanglongbing (HLB) response and tolerance in leaf tissues was performed. The aim was to identify genes commonly modulated between studies and genes, pathways and gene set categories strongly associated with this devastating Citrus disease. Bioinformatic analysis of expression data of four datasets present in NCBI provided 46–68 million reads with an alignment percentage of 72.95–86.76{\%}. Only 16 HLB-regulated genes werecommonlyidentifiedbetweenthethreeleafdatasets.Amongthemwerekeygenes encoding proteins involved in cell wall modification such as CESA8, pectinesterase, expansin8, expansin beta 3.1, and a pectate lyase. Fourteen HLB-regulated genes were in common between all four datasets. Gene set enrichment analysis showed some different gene categories affected by HLB disease. Although sucrose and starch metabolism was highly linked with disease symptoms, different genes were significantly regulated depending on leaf growth and infection stages and experimental conditions. Histone-related transcription factors were highly affected by HLB in the analyzed RNA-Seq datasets. HLB tolerance was linked with induction of proteins involved in detoxification. Protein–protein interaction (PPI) network analysis confirmed a possible role for heat shock proteins in curbing disease progression.",
author = "Tiziano Caruso and Federico Martinelli and Bipin Balan and Ib{\'a}{\~n}ez, {Ana M.} and Dandekar, {Abhaya M.}",
year = "2018",
language = "English",
volume = "9",
pages = "1--13",
journal = "Frontiers in Plant Science",
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TY - JOUR

T1 - Identifying host molecular features strongly linked with responses to huanglongbing disease in citrus leaves

AU - Caruso, Tiziano

AU - Martinelli, Federico

AU - Balan, Bipin

AU - Ibáñez, Ana M.

AU - Dandekar, Abhaya M.

PY - 2018

Y1 - 2018

N2 - A bioinformatic analysis of previously published RNA-Seq studies on Huanglongbing (HLB) response and tolerance in leaf tissues was performed. The aim was to identify genes commonly modulated between studies and genes, pathways and gene set categories strongly associated with this devastating Citrus disease. Bioinformatic analysis of expression data of four datasets present in NCBI provided 46–68 million reads with an alignment percentage of 72.95–86.76%. Only 16 HLB-regulated genes werecommonlyidentifiedbetweenthethreeleafdatasets.Amongthemwerekeygenes encoding proteins involved in cell wall modification such as CESA8, pectinesterase, expansin8, expansin beta 3.1, and a pectate lyase. Fourteen HLB-regulated genes were in common between all four datasets. Gene set enrichment analysis showed some different gene categories affected by HLB disease. Although sucrose and starch metabolism was highly linked with disease symptoms, different genes were significantly regulated depending on leaf growth and infection stages and experimental conditions. Histone-related transcription factors were highly affected by HLB in the analyzed RNA-Seq datasets. HLB tolerance was linked with induction of proteins involved in detoxification. Protein–protein interaction (PPI) network analysis confirmed a possible role for heat shock proteins in curbing disease progression.

AB - A bioinformatic analysis of previously published RNA-Seq studies on Huanglongbing (HLB) response and tolerance in leaf tissues was performed. The aim was to identify genes commonly modulated between studies and genes, pathways and gene set categories strongly associated with this devastating Citrus disease. Bioinformatic analysis of expression data of four datasets present in NCBI provided 46–68 million reads with an alignment percentage of 72.95–86.76%. Only 16 HLB-regulated genes werecommonlyidentifiedbetweenthethreeleafdatasets.Amongthemwerekeygenes encoding proteins involved in cell wall modification such as CESA8, pectinesterase, expansin8, expansin beta 3.1, and a pectate lyase. Fourteen HLB-regulated genes were in common between all four datasets. Gene set enrichment analysis showed some different gene categories affected by HLB disease. Although sucrose and starch metabolism was highly linked with disease symptoms, different genes were significantly regulated depending on leaf growth and infection stages and experimental conditions. Histone-related transcription factors were highly affected by HLB in the analyzed RNA-Seq datasets. HLB tolerance was linked with induction of proteins involved in detoxification. Protein–protein interaction (PPI) network analysis confirmed a possible role for heat shock proteins in curbing disease progression.

UR - http://hdl.handle.net/10447/286470

UR - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5836289/

M3 - Article

VL - 9

SP - 1

EP - 13

JO - Frontiers in Plant Science

JF - Frontiers in Plant Science

SN - 1664-462X

ER -