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International Journal of Agriculture, Environment and Biotechnology

Citation: IJAEB: 8(2): 295-302 June 2015

DOI Number: 10.5958/2230-732X.2015.00036.4

GENETICS

Gene Expression Study of Arachis Hypogaea L.

SagarȱPatel 1* ,ȱDiptiȱShah 1 ȱandȱHetalkumarȱPanchal 2

1 G.H. Patel Post Graduate Department of Computer Science and Technology, Sardar Patel University, Vallabh Vidyanagar,

Gujarat-388120, India.

2 Gujarat Agricultural Biotechnology Institute, Navsari Agricultural University, Surat, Gujarat- 395007, India.

*Corresponding author: sgr308@gmail.com

Paper No. 320

Received: 25 August 2014

Accepted: 28 April 2015

Published: 29 June 2015

Abstract

Arachis hypogaea ȱL.ȱ(Theȱpeanut)ȱisȱanȱimportantȱoilseedȱcropȱinȱtropicalȱandȱsubtropicalȱregionsȱofȱ

theȱworld.ȱThisȱspeciesȱbelongsȱtoȱtheȱsubfamilyȱFabaceaeȱandȱfamilyȱLeguminosae.ȱDifferentȱpartsȱofȱ

theȱplantȱsuchȱasȱleavesȱandȱseedsȱareȱusedȱforȱmanyȱpurposesȱinȱIndia.ȱNext-generationȱsequencingȱ

technologyȱ(NGS)ȱsuchȱasȱRNA-seqȱhasȱprovidedȱaȱpowerfulȱapproachȱforȱanalyzingȱtheȱTranscriptomeȱ

accuratelyȱandȱcheaply.ȱThisȱstudyȱisȱfocusȱonȱgeneȱexpressionȱstudyȱofȱRNA-seqȱofȱ Arachis hypogaea

L.ȱ(Theȱpeanut);ȱThreeȱSRAȱfilesȱofȱBioProjectȱIDȱ243319ȱdownloadedȱfromȱNCBIȱdatabaseȱandȱgenomeȱ

ofȱ Arabidopsis thaliana ȱwasȱconsideredȱasȱreferenceȱgenomeȱforȱgeneȱexpressionȱstudy.ȱDataȱanalysisȱ

carriedȱoutȱwithȱmanyȱBioinformaticsȱtoolsȱsuchȱasȱTopHat2,ȱCufflinks,ȱCuffmerge,ȱCuffcompareȱandȱ

Cuffdiff.ȱCummeRbundȱtoolȱwasȱusedȱtoȱmanage,ȱvisualizeȱandȱintegrateȱallȱofȱtheȱdataȱproducedȱbyȱ

aȱCuffdiffȱtoolȱforȱgeneȱexpressionȱanalysis.ȱTheseȱdataȱreportedȱinȱtheȱcurrentȱstudyȱwillȱserveȱasȱaȱ

valuableȱgeneticȱresourceȱofȱtheȱ Arachis hypogaea ȱL..

Highlights

ȱ Geneȱ expressionȱ studyȱ ofȱ Arachisȱ hypogaeaȱ L.ȱ (Theȱ peanut)ȱ analyzedȱ withȱ threeȱ SRAȱ filesȱ ofȱ

BioProjectȱIDȱ243319.

ȱ DataȱanalysisȱdoneȱwithȱmanyȱBioinformaticsȱtoolsȱtoȱgetȱusefulȱresults.ȱ

ȱ Next-generationȱ sequenceȱ dataȱ analysisȱ ofȱ Arachisȱ hypogaeaȱ L.ȱ (Theȱ peanut)ȱ basedȱ onȱ Geneȱ

expressionȱstudyȱwillȱbeȱveryȱusefulȱforȱfurtherȱstudyȱorȱanalysisȱpurpose.ȱ

Keywords: Transcriptome,ȱgeneȱexpression,ȱbioinformatics,ȱ Arachis hypogaea ȱL.

Theȱ developmentȱ ofȱ theȱ peanutȱ seedȱ hasȱ beenȱ Transcriptomeȱ analysisȱ methodȱ isȱ fastȱ andȱ simpleȱ

studiedȱ intenselyȱ toȱ understandȱ theȱ physiological,ȱ becauseȱ itȱ doesȱ notȱ requireȱ cloningȱ ofȱ theȱ cDNAs.ȱ

biochemical,ȱ andȱ molecularȱ characteristicsȱ thatȱ DirectȱsequencingȱofȱtheseȱcDNAsȱcanȱgenerateȱshortȱ

determineȱ theȱ oilȱ qualityȱ andȱ theirȱ beneficialȱ readsȱatȱanȱextraordinaryȱdepth.ȱAfterȱsequencing,ȱ

nutritionalȱcontributions.ȱHowever,ȱtheȱdevelopmentȱ theȱresultingȱreadsȱcanȱbeȱassembledȱintoȱaȱgenome-

ofȱtheȱpeanutȱseedȱisȱaȱcomplexȱprocessȱinvolvingȱaȱ scaleȱtranscriptionȱprofile.ȱThisȱmethodȱisȱcheapȱasȱ

cascadeȱofȱbiochemicalȱchanges,ȱwhichȱinvolveȱtheȱ compareȱtoȱotherȱmethods.ȱItȱisȱaȱmoreȱcomprehensiveȱ

transcriptionalȱmodulationȱofȱmanyȱgenes,ȱyetȱlittleȱ andȱ efficientȱ wayȱ toȱ measureȱ Transcriptomeȱ

isȱ knownȱ aboutȱ theseȱ transcriptionalȱ changesȱ andȱ composition,ȱ obtainȱ RNAȱ expressionȱ patterns,ȱ andȱ

theirȱregulationȱ(Zhangȱ et al. 2012).

discoversȱ newȱ exonsȱ andȱ genesȱ (Mortazaviȱ et al.

2008,ȱWangȱ et al. ȱ2009).ȱ