Deep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L.

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Deep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L. / Bisaga, M.; Lowe, Matthew; Hegarty, Matthew; Abberton, M.; Ravagnani, A.

In: Frontiers in Plant Science, Vol. 8, 213, 23.02.2017.

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@article{1b9b22f6f0b3431685e7fcc8d61f86a4,
title = "Deep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L.",
abstract = "BackgroundWhite clover is a short-lived perennial whose persistence is greatly affected by abiotic stresses, particularly drought. An understanding of its molecular response to water deficit and recovery following re-hydration is of paramount importance to identify targets for the breeding of tolerant varieties.ResultsWe created a white clover reference transcriptome of 16,193 contigs by de novo and reference-based assembly of Illumina reads from four SSH libraries (forward and reverse libraries for each treatment) constructed from leaf material of white clover at the onset of drought and recovery. Reads from individual libraries were then mapped to the reference transcriptome and processed comparing expression level data to generate four robust sets of transcripts induced and repressed in the leaves subjected to and recovering from water stress. The differentially expressed transcripts were functionally annotated and mapped to biological processes and pathways.ConclusionsThe work presented in this paper provides a simple pipeline for the processing of data generated by deep sequencing of SSH libraries and the first large scale molecular analysis of the white clover response to drought stress and recovery.",
keywords = "white clover, drought, recovery, SSH libraries, MiSeq",
author = "M. Bisaga and Matthew Lowe and Matthew Hegarty and M. Abberton and A. Ravagnani",
year = "2017",
month = feb,
day = "23",
doi = "10.3389/fpls.2017.00213",
language = "English",
volume = "8",
journal = "Frontiers in Plant Science",
issn = "1664-462X",
publisher = "Frontiers Media",

}

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TY - JOUR

T1 - Deep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L.

AU - Bisaga, M.

AU - Lowe, Matthew

AU - Hegarty, Matthew

AU - Abberton, M.

AU - Ravagnani, A.

PY - 2017/2/23

Y1 - 2017/2/23

N2 - BackgroundWhite clover is a short-lived perennial whose persistence is greatly affected by abiotic stresses, particularly drought. An understanding of its molecular response to water deficit and recovery following re-hydration is of paramount importance to identify targets for the breeding of tolerant varieties.ResultsWe created a white clover reference transcriptome of 16,193 contigs by de novo and reference-based assembly of Illumina reads from four SSH libraries (forward and reverse libraries for each treatment) constructed from leaf material of white clover at the onset of drought and recovery. Reads from individual libraries were then mapped to the reference transcriptome and processed comparing expression level data to generate four robust sets of transcripts induced and repressed in the leaves subjected to and recovering from water stress. The differentially expressed transcripts were functionally annotated and mapped to biological processes and pathways.ConclusionsThe work presented in this paper provides a simple pipeline for the processing of data generated by deep sequencing of SSH libraries and the first large scale molecular analysis of the white clover response to drought stress and recovery.

AB - BackgroundWhite clover is a short-lived perennial whose persistence is greatly affected by abiotic stresses, particularly drought. An understanding of its molecular response to water deficit and recovery following re-hydration is of paramount importance to identify targets for the breeding of tolerant varieties.ResultsWe created a white clover reference transcriptome of 16,193 contigs by de novo and reference-based assembly of Illumina reads from four SSH libraries (forward and reverse libraries for each treatment) constructed from leaf material of white clover at the onset of drought and recovery. Reads from individual libraries were then mapped to the reference transcriptome and processed comparing expression level data to generate four robust sets of transcripts induced and repressed in the leaves subjected to and recovering from water stress. The differentially expressed transcripts were functionally annotated and mapped to biological processes and pathways.ConclusionsThe work presented in this paper provides a simple pipeline for the processing of data generated by deep sequencing of SSH libraries and the first large scale molecular analysis of the white clover response to drought stress and recovery.

KW - white clover

KW - drought

KW - recovery

KW - SSH libraries

KW - MiSeq

UR - http://hdl.handle.net/2160/44596

U2 - 10.3389/fpls.2017.00213

DO - 10.3389/fpls.2017.00213

M3 - Article

C2 - 28280499

VL - 8

JO - Frontiers in Plant Science

JF - Frontiers in Plant Science

SN - 1664-462X

M1 - 213

ER -

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