title: Transcriptome profiling of peanut gynophores revealed global reprogramming of gene expression during early pod development in darkness.
abstract: BACKGROUND
  After the zygote divides few times, the development of peanut pre-globular embryo and fruit is arrested under white or red light. Embryo development could be resumed in dark condition after gynophore is buried in soil. It is interesting to study the mechanisms of gynophore development and pod formation in peanut.
  
  
  RESULTS
  In this study, transcriptome analysis of peanut gynophore was performed using Illumina HiSeq™ 2000 to understand the mechanisms of geocarpy. More than 13 million short sequences were assembled into 72527 unigenes with average size of 394 bp. A large number of genes that were not identified previously in peanut EST projects were identified in this study, including most genes involved in plant circadian rhythm, intra-cellular transportation, plant spliceosome, eukaryotes basal transcription factors, genes encoding ribosomal proteins, brassinosteriod biosynthesis, light-harvesting chlorophyll protein complex, phenylpropanoid biosynthesis and TCA cycle. RNA-seq based gene expression profiling results showed that before and after gynophore soil penetration, the transcriptional level of a large number of genes changed significantly. Genes encoding key enzymes for hormone metabolism, signaling, photosynthesis, light signaling, cell division and growth, carbon and nitrogen metabolism as well as genes involved in stress responses were high lighted.
  
  
  CONCLUSIONS
  Transcriptome analysis of peanut gynophore generated a large number of unigenes which provide useful information for gene cloning and expression study. Digital gene expression study suggested that gynophores experience global changes and reprogram from light to dark grown condition to resume embryo and fruit development.
authors.forename: Han
authors.initials: H
authors.lastname: Xia
authors.forename: Chuanzhi
authors.initials: C
authors.lastname: Zhao
authors.forename: Lei
authors.initials: L
authors.lastname: Hou
authors.forename: Aiqin
authors.initials: A
authors.lastname: Li
authors.forename: Shuzhen
authors.initials: S
authors.lastname: Zhao
authors.forename: Yuping
authors.initials: Y
authors.lastname: Bi
authors.forename: Jing
authors.initials: J
authors.lastname: An
authors.forename: Yanxiu
authors.initials: Y
authors.lastname: Zhao
authors.forename: Shubo
authors.initials: S
authors.lastname: Wan
authors.forename: Xingjun
authors.initials: X
authors.lastname: Wang
mesh_terms: D010367:Arachis / Q000235:genetics*; D003624:Darkness; D005638:Fruit / Q000254:growth & development; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D058977:Molecular Sequence Annotation; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D018749:RNA, Plant
references.citation: Plant Cell. 2012 Jan;24(1):163-77
references.pmid: 22294619
references.citation: Plant J. 2008 Dec;56(6):922-34
references.pmid: 18702668
references.citation: Plant Cell. 2012 Feb;24(2):589-607
references.pmid: 22327741
references.citation: BMC Genomics. 2013 Jun 22;14:415
references.pmid: 23799877
references.citation: Mol Plant. 2013 Jan;6(1):5-7
references.pmid: 22973064
references.citation: Plant Cell. 1998 Jul;10(7):1083-94
references.pmid: 9668129
references.citation: Genome Res. 2010 Feb;20(2):265-72
references.pmid: 20019144
references.citation: Plant Cell. 1992 Nov;4:1425-33
references.pmid: 11538167
references.citation: Plant Biotechnol J. 2013 Jan;11(1):115-27
references.pmid: 23130888
references.citation: Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):10134-9
references.pmid: 16777956
references.citation: Plant Cell. 2002 Dec;14(12):3119-32
references.pmid: 12468731
references.citation: Plant Cell. 2003 Dec;15(12):2966-78
references.pmid: 14615593
references.citation: Development. 2003 Jul;130(14):3283-95
references.pmid: 12783798
references.citation: Genome Biol. 2005;6(5):220
references.pmid: 15892880
references.citation: Plant Physiol. 1985 Jun;78(2):370-3
references.pmid: 16664247
references.citation: Cell. 1992 Nov 27;71(5):791-801
references.pmid: 1423630
references.citation: Genes Dev. 2010 Oct 1;24(19):2127-32
references.pmid: 20889713
references.citation: Plant Physiol. 2010 Feb;152(2):904-17
references.pmid: 20007445
references.citation: Plant J. 2010 May 1;62(4):653-62
references.pmid: 20202166
references.citation: Extremophiles. 2004 Feb;8(1):1-11
references.pmid: 15064984
references.citation: Tree Physiol. 2003 Aug;23(12):815-23
references.pmid: 12865247
references.citation: J Exp Bot. 2009;60(5):1523-32
references.pmid: 19321650
references.citation: EMBO J. 1999 Apr 15;18(8):2066-73
references.pmid: 10205161
references.citation: Plant Cell. 2002;14 Suppl:S207-25
references.pmid: 12045278
references.citation: Plant J. 2002 Feb;29(4):405-15
references.pmid: 11846874
references.citation: Plant Cell. 2007 Mar;19(3):890-903
references.pmid: 17351116
references.citation: Nature. 2002 Jun 6;417(6889):618-24
references.pmid: 12050657
references.citation: Science. 1996 Aug 16;273(5277):948-50
references.pmid: 8688077
references.citation: Plant Physiol. 2010 Jun;153(2):773-84
references.pmid: 20388662
references.citation: Plant J. 2009 Apr;58(2):318-32
references.pmid: 19207215
references.citation: Methods. 2001 Dec;25(4):402-8
references.pmid: 11846609
references.citation: Plant Cell. 2009 Oct;21(10):3041-62
references.pmid: 19880793
references.citation: Plant Cell. 2002 Jul;14(7):1621-33
references.pmid: 12119379
references.citation: Trends Plant Sci. 2012 Oct;17(10):584-93
references.pmid: 22705257
references.citation: Ann Bot. 1999 Mar;83(3):235-42
references.pmid: 11541548