PMID- 25728802
OWN - NLM
STAT- MEDLINE
DCOM- 20160408
LR  - 20221005
IS  - 1469-8137 (Electronic)
IS  - 0028-646X (Print)
IS  - 0028-646X (Linking)
VI  - 207
IP  - 1
DP  - 2015 Jul
TI  - Modular organization of the white spruce (Picea glauca) transcriptome reveals 
      functional organization and evolutionary signatures.
PG  - 172-187
LID - 10.1111/nph.13343 [doi]
AB  - Transcript profiling has shown the molecular bases of several biological 
      processes in plants but few studies have developed an understanding of overall 
      transcriptome variation. We investigated transcriptome structure in white spruce 
      (Picea glauca), aiming to delineate its modular organization and associated 
      functional and evolutionary attributes. Microarray analyses were used to: 
      identify and functionally characterize groups of co-expressed genes; investigate 
      expressional and functional diversity of vascular tissue preferential genes which 
      were conserved among Picea species, and identify expression networks underlying 
      wood formation. We classified 22 857 genes as variable (79%; 22 coexpression 
      groups) or invariant (21%) by profiling across several vegetative tissues. 
      Modular organization and complex transcriptome restructuring among vascular 
      tissue preferential genes was revealed by their assignment to coexpression groups 
      with partially overlapping profiles and partially distinct functions. Integrated 
      analyses of tissue-based and temporally variable profiles identified secondary 
      xylem gene networks, showed their remodelling over a growing season and 
      identified PgNAC-7 (no apical meristerm (NAM), Arabidopsis transcription 
      activation factor (ATAF) and cup-shaped cotyledon (CUC) transcription factor 007 
      in Picea glauca) as a major hub gene specific to earlywood formation. Reference 
      profiling identified comprehensive, statistically robust coexpressed groups, 
      revealing that modular organization underpins the evolutionary conservation of 
      the transcriptome structure.
CI  - (c) 2015 The Authors. New Phytologist (c) 2015 New Phytologist Trust.
FAU - Raherison, Elie S M
AU  - Raherison ESM
AD  - Center for Forest Research and Institute for Integrative and Systems Biology, 
      Universite Laval, Quebec, QC, G1V 0A6, Canada.
FAU - Giguere, Isabelle
AU  - Giguere I
AD  - Center for Forest Research and Institute for Integrative and Systems Biology, 
      Universite Laval, Quebec, QC, G1V 0A6, Canada.
FAU - Caron, Sebastien
AU  - Caron S
AD  - Center for Forest Research and Institute for Integrative and Systems Biology, 
      Universite Laval, Quebec, QC, G1V 0A6, Canada.
FAU - Lamara, Mebarek
AU  - Lamara M
AD  - Center for Forest Research and Institute for Integrative and Systems Biology, 
      Universite Laval, Quebec, QC, G1V 0A6, Canada.
FAU - MacKay, John J
AU  - MacKay JJ
AD  - Department of Plant Sciences, University of Oxford, OX1 3RB, Oxford, UK.
LA  - eng
SI  - GENBANK/BT101047
SI  - GENBANK/BT102049
SI  - GENBANK/BT103744
SI  - GENBANK/BT104565
SI  - GENBANK/BT104876
SI  - GENBANK/BT104881
SI  - GENBANK/BT105806
SI  - GENBANK/BT106274
SI  - GENBANK/BT106749
SI  - GENBANK/BT107150
SI  - GENBANK/BT107836
SI  - GENBANK/BT108414
SI  - GENBANK/BT109195
SI  - GENBANK/BT112527
SI  - GENBANK/BT113137
SI  - GENBANK/BT114680
SI  - GENBANK/BT114833
SI  - GENBANK/BT115870
SI  - GENBANK/BT116286
SI  - GENBANK/BT117400
SI  - GENBANK/BT117952
SI  - GENBANK/CO235762
SI  - GENBANK/DR574449
SI  - GENBANK/DR591085
SI  - GENBANK/DR594044
SI  - GENBANK/EX329848
SI  - GENBANK/GSE51884
SI  - GENBANK/GSE60277
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20150227
PL  - England
TA  - New Phytol
JT  - The New phytologist
JID - 9882884
RN  - 0 (Propanols)
RN  - 0F897O3O4M (1-phenylpropanol)
RN  - 9005-53-2 (Lignin)
SB  - IM
MH  - *Biological Evolution
MH  - Cell Wall/metabolism
MH  - Conserved Sequence
MH  - Gene Expression Regulation, Developmental
MH  - *Gene Expression Regulation, Plant
MH  - Gene Ontology
MH  - *Gene Regulatory Networks
MH  - Genes, Plant
MH  - Lignin/metabolism
MH  - Meristem/genetics
MH  - Molecular Sequence Annotation
MH  - Molecular Sequence Data
MH  - Picea/*genetics
MH  - Propanols/metabolism
MH  - Seasons
MH  - Species Specificity
MH  - Time Factors
MH  - Transcriptome/*genetics
MH  - Wood/growth & development
MH  - Xylem/genetics
PMC - PMC5024012
OTO - NOTNLM
OT  - conifers
OT  - modular organization
OT  - tissue differentiation
OT  - transcriptional network
OT  - transcriptome
OT  - white spruce (Picea glauca)
EDAT- 2015/03/03 06:00
MHDA- 2016/04/09 06:00
PMCR- 2016/09/15
CRDT- 2015/03/03 06:00
PHST- 2014/08/27 00:00 [received]
PHST- 2015/01/18 00:00 [accepted]
PHST- 2015/03/03 06:00 [entrez]
PHST- 2015/03/03 06:00 [pubmed]
PHST- 2016/04/09 06:00 [medline]
PHST- 2016/09/15 00:00 [pmc-release]
AID - NPH13343 [pii]
AID - 10.1111/nph.13343 [doi]
PST - ppublish
SO  - New Phytol. 2015 Jul;207(1):172-187. doi: 10.1111/nph.13343. Epub 2015 Feb 27.