Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection

Stanford Kwenda, Paul R. J. Birch, Lucy N. Moleleki (Lead / Corresponding author)

Research output: Contribution to journalArticle

15 Citations (Scopus)
37 Downloads (Pure)

Abstract

BACKGROUND: Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression in both mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of long intergenic nocoding RNAs (lincRNAs) in plant defence responses are yet to be fully explored.

RESULTS: In this study, we used strand-specific RNA sequencing to identify 1113 lincRNAs in potato (Solanum tuberosum) from stem tissues. The lincRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lincRNAs possess single exons. A time-course RNA-seq analysis between a tolerant and a susceptible potato cultivar showed that 559 lincRNAs are responsive to Pectobacterium carotovorum subsp. brasiliense challenge compared to mock-inoculated controls. Moreover, coexpression analysis revealed that 17 of these lincRNAs are highly associated with 12 potato defence-related genes.

CONCLUSIONS: Together, these results suggest that lincRNAs have potential functional roles in potato defence responses. Furthermore, this work provides the first library of potato lincRNAs and a set of novel lincRNAs implicated in potato defences against P. carotovorum subsp. brasiliense, a member of the soft rot Enterobacteriaceae phytopathogens.

Original languageEnglish
Article number614
Pages (from-to)1-14
Number of pages14
JournalBMC Genomics
Volume17
DOIs
Publication statusPublished - 11 Aug 2016

Fingerprint

Pectobacterium carotovorum
Long Noncoding RNA
Solanum tuberosum
Genome
RNA
Infection
Mammals
Plant RNA
RNA Sequence Analysis
Chromosomes, Human, Pair 12
Gene Expression Regulation
Enterobacteriaceae
Libraries
Exons

Keywords

  • Journal article
  • Noncoding RNA
  • Potato
  • Pectobacterium
  • lincRNA
  • Plant defence
  • Soft rot bacteria
  • Solanum tuberosum
  • Entereobacteria

Cite this

@article{2e893e14bffd4714b5ed219d5752b4b7,
title = "Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection",
abstract = "BACKGROUND: Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression in both mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of long intergenic nocoding RNAs (lincRNAs) in plant defence responses are yet to be fully explored.RESULTS: In this study, we used strand-specific RNA sequencing to identify 1113 lincRNAs in potato (Solanum tuberosum) from stem tissues. The lincRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lincRNAs possess single exons. A time-course RNA-seq analysis between a tolerant and a susceptible potato cultivar showed that 559 lincRNAs are responsive to Pectobacterium carotovorum subsp. brasiliense challenge compared to mock-inoculated controls. Moreover, coexpression analysis revealed that 17 of these lincRNAs are highly associated with 12 potato defence-related genes.CONCLUSIONS: Together, these results suggest that lincRNAs have potential functional roles in potato defence responses. Furthermore, this work provides the first library of potato lincRNAs and a set of novel lincRNAs implicated in potato defences against P. carotovorum subsp. brasiliense, a member of the soft rot Enterobacteriaceae phytopathogens.",
keywords = "Journal article, Noncoding RNA, Potato, Pectobacterium, lincRNA, Plant defence , Soft rot bacteria, Solanum tuberosum , Entereobacteria",
author = "Stanford Kwenda and Birch, {Paul R. J.} and Moleleki, {Lucy N.}",
note = "We thank the National Research Foundation (NRF), South Africa for funding this work through Thuthuka grant number 69362; Research Development Grant for Y Rated Researchers 93357; Bioinformatics and Functional Genomics (BFG 93685) and The Genomics Research Institute, University of Pretoria.",
year = "2016",
month = "8",
day = "11",
doi = "10.1186/s12864-016-2967-9",
language = "English",
volume = "17",
pages = "1--14",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "Springer Verlag",

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Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection. / Kwenda, Stanford; Birch, Paul R. J.; Moleleki, Lucy N. (Lead / Corresponding author).

In: BMC Genomics, Vol. 17, 614, 11.08.2016, p. 1-14.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection

AU - Kwenda, Stanford

AU - Birch, Paul R. J.

AU - Moleleki, Lucy N.

N1 - We thank the National Research Foundation (NRF), South Africa for funding this work through Thuthuka grant number 69362; Research Development Grant for Y Rated Researchers 93357; Bioinformatics and Functional Genomics (BFG 93685) and The Genomics Research Institute, University of Pretoria.

PY - 2016/8/11

Y1 - 2016/8/11

N2 - BACKGROUND: Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression in both mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of long intergenic nocoding RNAs (lincRNAs) in plant defence responses are yet to be fully explored.RESULTS: In this study, we used strand-specific RNA sequencing to identify 1113 lincRNAs in potato (Solanum tuberosum) from stem tissues. The lincRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lincRNAs possess single exons. A time-course RNA-seq analysis between a tolerant and a susceptible potato cultivar showed that 559 lincRNAs are responsive to Pectobacterium carotovorum subsp. brasiliense challenge compared to mock-inoculated controls. Moreover, coexpression analysis revealed that 17 of these lincRNAs are highly associated with 12 potato defence-related genes.CONCLUSIONS: Together, these results suggest that lincRNAs have potential functional roles in potato defence responses. Furthermore, this work provides the first library of potato lincRNAs and a set of novel lincRNAs implicated in potato defences against P. carotovorum subsp. brasiliense, a member of the soft rot Enterobacteriaceae phytopathogens.

AB - BACKGROUND: Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression in both mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of long intergenic nocoding RNAs (lincRNAs) in plant defence responses are yet to be fully explored.RESULTS: In this study, we used strand-specific RNA sequencing to identify 1113 lincRNAs in potato (Solanum tuberosum) from stem tissues. The lincRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lincRNAs possess single exons. A time-course RNA-seq analysis between a tolerant and a susceptible potato cultivar showed that 559 lincRNAs are responsive to Pectobacterium carotovorum subsp. brasiliense challenge compared to mock-inoculated controls. Moreover, coexpression analysis revealed that 17 of these lincRNAs are highly associated with 12 potato defence-related genes.CONCLUSIONS: Together, these results suggest that lincRNAs have potential functional roles in potato defence responses. Furthermore, this work provides the first library of potato lincRNAs and a set of novel lincRNAs implicated in potato defences against P. carotovorum subsp. brasiliense, a member of the soft rot Enterobacteriaceae phytopathogens.

KW - Journal article

KW - Noncoding RNA

KW - Potato

KW - Pectobacterium

KW - lincRNA

KW - Plant defence

KW - Soft rot bacteria

KW - Solanum tuberosum

KW - Entereobacteria

U2 - 10.1186/s12864-016-2967-9

DO - 10.1186/s12864-016-2967-9

M3 - Article

C2 - 27515663

VL - 17

SP - 1

EP - 14

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

M1 - 614

ER -