Transcript Expression Level of White Kelampayan

Negotiative Explanation and Likeness Look Dissection of RNA-Seq Basis (via NGS) from Clear Kelampayan (Neolamarckia cadamba) using bioinformatics approach

  • Lim Leong Rui


Consideration of Contents



Applied Biosystems/Sequencing by Oligonucleotide Ligation and Detection


Complementary deoxyribonucleic distressing


Chromatin immunoprecipitation sequencing


Deoxyribonucleic distressing


Expressed continuity tags




Gene ontology




Standard organisms basisbase


National Center control Biotechnology Advice


Instant era sequencing


Polymerase fetter reaction


Ribonucleic distressing


Ribonucleic distressing sequencing


Reads per kb per pet reads


Serial dissection of gene look


Work Gene Ontology Explanation






Taxonomy of clear kelampayan tree symbol



Neolamarckia cadamba or clear kelampayan is a pay growing tree symbol that generates economic benefits in 8 to 10 years. There are brace objectives contrivanceed in the examine: to specify negotiative explanation of RNA-Seq basis from clear kelampayan; to fulfill and analyse likeness look flatten of the RNA-Seq basis from the kelampayan tree. The provision antecedently dissection such as scantling assembly, RNA self-containedness, cDNA library fabrication, sequencing and mapping are manufactured. Later, dissection marchs including Blaze2Go program impression, WEGO impression, statistics on proportions proof and corrected p-compute are mentioned. Negotiative explanation of RNA-Seq basis from clear kelampayan is expected to be specifyd and vivid in a suspend or pie charts controlmat. Meanwhile, the likeness look flatten of each scantling basis of the xylem and leaves make is expected to be measured and compared to each other respectively. Haughty-throughput developments from the exemplification impart haughty genome basis character of the kelampayan tree.

1.0 Introduction

Clear kelampayan or Neolamarckia cadamba is a pay growing tree symbol that generates stinted benefits to the intercourse in 8 to 10 years (Ho et al., 2014). The tree symbol delineates its superfluous role in meat and pamphlet origination, medical diligence, plywood diligence as polite as movables origination (Joker, 2000; Ho et al., 2014). Since the kelampayan tree imcompressiveness protracted stinted benefits, divers timber companies and scrutiny institutes roverification doing molecular scrutinyes on the kelampayan tree symbol to confront extinguished the restraintthcoming immanent of the kelampayan. However, short genetic advice scrutinyes enjoy been generated on the kelampayan tree.

Although actual plants such as Saccharomyces cerevisae and Arabidopsis thaliana were canvassd and thought-quenched via using instant era sequencing (NGS) technologies (Wang et al., 2010), there was no any NGS scrutiny on the kelampayan tree symbol. NGS is defenseless commercially in 2005 (Bubnoff, 2008) and is an opinion restraintm to reresolve the seasonations faced by Sanger sequencing such as haughty require, era abverification and frequent-sided verification. There are sepaadmonish controlms and impressions of NGS widely verificationd nowadays. NGS technologies such as 454 sequencing technology, Illumina sequencing and ABI/SOLiD sequencing regularity are applied floating the scrutinyers in open, opportunity impressions of NGS are RNA-Sequencing (RNA-Seq), genomic sequencing and epigenetic impressions (Morozova & Marra, 2008; Perdacher, 2011).

In this examine, RNA-Seq basis via Illumina sequencing obtain be applied to canvass the likeness look flatten of clear kelampayan tree symbol. The likeness look

flatten obtain be congenial and compared statistically (Zheng et al., 2012). Other than that, the negotiative explanation of the clear kelampayan symbol obtain be muscular and categorized in three compressiveness: biological government, molecular exercise and cellular element by applying gene ontology (GO) via Blaze2GO program (Blast2GO® – Software control biologists, 2011; Xiong, 2006).

Therefore, the objectives of the examine are:

  1. To specify the negotiative explanation of RNA-Seq basis from clear kelampayan in message of gene ontology via Blaze2GO program.
  2. To individualize and analyse likeness look flatten of RNA-Seq basis from clear kelampayan.
  1. Literature Review
    1. Clear kelampayan

Clear kelampayan or philosophicalally disclosed as Neolamarckia cadamba, is a pay growing tree symbol. It is widely distributed in some East Asia countries such as India, Thailand, Malaysia and Papua New Guinea (Joker, 2000). The taxonomy of the tree symbol is shown as the succeedingcited (Dubey et al., 2011):

Consideration 1.1 Taxonomy of clear kelampayan tree symbol












Neolamarckia cadamba

Kelampayan is normally applied control redintegration in weather-beaten areas (Joker, 2000). Besides, twain leaves and suspendk of the kelampayan delineate superfluous role in medical globe. The leaves are quoteed to subsubserve as perforation absterge, opportunity the dried suspendk is verificationd to succor brglaze (Globe Agroforestry Centre, as cited in Ho et al., 2014). Aidmore, other compressiveness of the kelampayan such as stock and branches are as-well verificationd in meat and pamphlet diligence and movables diligence (Joker, 2000). In India, there has some scrutiny shown that the perfection of the kelampayan can be quoteed extinguished to amount superfluous glaze, which can be aid amountd as Indian perfumes with sandalwood infamous (Krisnawati et al., 2011).

  1. Instant Era Sequencing (NGS)

Instant era sequencing (NGS) is an opinion restraintm to overpower seasonations of the earliest era sequencing, Sanger sequencing. It was earliestly introduced in 2005 (Morozova & Marra, 2008), and this imcompressiveness a gigantic contact to the computational biology globe.

It brings considerable advantages compared to Sanger sequencing in message of era power and require. According to Bubnoff (2008, p.721), he periodical that “NGS technology is up to 200 eras payer and cheaper than the unwritten Sanger sequencing.” He as-well mentioned that NGS technologies facilitate the bacterial cloning government.

There are three controlms of NGS technologies, which are 454 sequencing technology, Illumina sequencing and ABI/SOLiD sequencing regularity (Bubnoff, 2008; Morozova & Marra, 2008; Perdacher, 2011). These three technologies enjoy a similar indication where the DNA can be amplified via polymerase fetter reaction (PCR) withextinguished applying any bacterial cloning government (Bubnoff, 2008). Aidmore, there are sepaadmonish impressions verificationd in NGS technology such as likenessome sequencing or RNA-Sequencing (RNA-Seq), genomic sequencing and epigenetic impressions which verification CHIP-Seq and methylation profiling to achievement extinguished dissection on interaction in among proteins and DNA and dissection on prevalent chromatin make respectively (Perdacher, 2011).

  1. RNA-Sequencing (RNA-Seq)

RNA-Seq, disclosed as Whole Likenessome Shotgun Sequencing, is “a revolutionary utensil control likenessomes” (Perdacher, 2011; Wang et al., 2010, p. 57). It has been applied in some thought-quenched objects such as Saccharomyces cerevisae, Schizosaccharomyces pombe, Arabidopsis thaliana, moverification and rational cells (Wang et al., 2010).

RNA-Seq is widely applied in philosophical examine becaverification it can impart a clearer and over reason picture abextinguished likenessomes compared to DNA microarray and serial dissection of gene look (SAGE) admission. Comparing to these fashions, the RNA-Seq is cheaper, over servile and over era fruitful. There are the benefits of RNA-Seq catalogueed as the succeedingciteds (Getting rouseed with RNA-Seq basis dissection, 2011; Nagalakshmi et al., 2010; Perdacher, 2011; Wang et al., 2010) :

  1. Species- and likeness-specific probes are not attribuconsideration attribuconsideration attribuconsideration attribuconsideration attribuconsideration attribuconsideration attribuconsideration attribuconsideration attribuconsideration required in the RNA-Seq fashion and thus, the development basis abextinguished the truth of the transciptomes is not attribuconsideration attribuconsideration attribuconsideration attribuconsideration attribuconsideration attribuconsideration attribuconsideration attribuconsideration attribuconsideration be amply affected by earlier impudence.
  2. A hypothesis-free exemplification can be speedy and created.
  3. Symbol with sunk partition of genome explanation can be canvassd in a haughty throughput restraintm.
  4. Transcription roverification codon and boundaries can be amply located and signed, opportunity exon look and splicing variants can be measured in pointed.
  5. Undefined genome continuitys from non-standard organisms such as centipedes can be thought-quenched and muscular via RNA-Seq.
  1. Functional explanation and Gene ontology
    1. Negotiative explanation

Negotiative explanation is a message where the advice abextinguished a gene’s personality such as biological government, cellular element and molecular element is attentive, analyzed and vivid by referring controlled vocabularies, that is gene ontology (GO)(Berardini et al., 2010).

2.3.2 Gene ontology (GO)

GO is a fashion where the uncertain vocabularies abextinguished biological government, cellular element and molecular exercises are standardized via consortium of standard organisms basisinfamous (MODs) (Xiong, 2006). He as-well periodical that three compressiveness of GO: biological government, cellular element and molecular exercises are vivid in a hierarchy restraintm, in which the specificity of a negotiative gene is vivid from open (summit flatten) to over ascertained (sunk flatten).

  1. Reads per kb per pet reads (RPKM) and Blaze2GO® program
    1. RPKM

The RPKM is a fashion where the controlethought of gene look is not attribuconsideration attribuconsideration attribuconsideration attribuconsideration attribuconsideration attribuconsideration attribuconsideration attribuconsideration attribuconsideration influenced by the gene extension and sequencing difference (Zheng et al., 2012). The co-ordination of gene look among scantlings can be at-uninterruptedly muscular uninterruptedly RPKM is verificationd.

  1. Blast2GO® program

Blast2GO, a software utensil, was familiar in 2005. It was familiar to overpower seasonations faced in applying gene ontology (GO) messages such as sunk throughput continuity explanation, sunk visualization class and haughty exclusion to annotated continuitys from national basisbase. The software utensil is trained by 5 governmentes: Blaze minute from national basisinfamous such as NCBI, mapping to quote GO messages, impression of explanation government in explanation march, statistical dissection which performs in suspend or pie charts and lastly, visualization government. There are divers indications solicitous from the program: vocabularies, basis mining, haughty extinguishedline, haughty-throughput, verificationr-friendly and sunk subsistence.

  1. WEGO Utensil

WEGO, or Work Gene Ontology Explanation, is a verificationful work utensil delineateing its role in graph plotting, visualization and co-ordination. By using the WEGO, a histogram with GO explanation developments is created via frequenteded acyclic graph (DAG) make.. According to Ye et al. (2006), the WEGO utensil has been widely applied in rice genome contrivance and silkworm genome contrivance. They as-well mentioned that the work utensil is verificationr –friendly and operating regularity dogged, which allows verificationr gentle to touch the GO explanation disposal graph plotting.

  1. Methodology

Developing xylem and leaves makes were attentive from a 2-years pristine kelampayan tree. RNA was quoteed from the attentive makes and aid speedy control cDNA library fabrication (Ho et al., 2014). cDNA libraries were sham by using ScriptSeqTM Complete Kit (Epicentre, USA) and Illumina HiSeq 2500 (Illumina Inc. USA) was applied to convey extinguished sequencing. Succeeding sequencing, using CLC Genomics Achievementbench 7.5 (Qiagen, Denmark), sunk character reads and unwanted adaptors were removed by character versatile government with the parameters: character season = 0.01 and equivocal season = 2. Amiable character of the sequencing reads were obtained succeeding versatile.

The sequencing reads were mapped to the regard likenessome. Using Blaze2GO program (BioBam Bioinformatics S.L., Spain), the regard likenessome was created by assembling the ESTs and likenesss of the kelampayan tree (BioGentle Sdn Bhd, 2014). The continuity similarities were signed by comparing regard likenessome to NCBI non-reductant protein basisbase. Sepaadmonish parameters were interposed in blaze minute government: confluence compute and strike calculate thresholds (Conesa et al., 2005). Then, the regard likenessome was mapped to the Gene Ontology messages by referring continuity similarities. During mapping, Blaze strike gene identifiers and gene accessions were interposed in retrieving GO messages control the strike continuitys with experienceimony codes (Conesa et al., 2005). Assembly of a established of canvasser explanations and explanations fountain was manufactured succeeding mapping.

Explanation government (AR) obtain be applied to the Gene ontologies of each canvasser explanation. Besides, explanation mandible (AS), including frequented message and AT of the explanation government obtain be congenial control each canvasser explanation (Conesa et al., 2005). Statistics on gene ontology of canvasser explanation obtain be carried on by applying Fischer Exact Proof associating with muscular sham solution admonish (FDR) punishment (Blüthgen et al. as cited in Conesa et al., 2005). In specification, a catalogue of coercioncible GO messages obtain be created via corrected P-values. Suspend or pie charts obtain be verificationd in describing developments statistically. The proficiency in the explanation government control each continuity obtain be visualized by observing complexion changes of nodes in the visualization graph. A work utensil, WEGO (Ye et al., 2006) obtain be applied in plotting the disposal of GO explanations developments into a histogram.

Using CLC Genomics Achievementbench 7.5 (Qiagen, Denmark), RNA-Seq dissection obtain be chosen to course in a Batch sequence. There obtain be 2 controlms of amiable character sequencing reads basis obtain be chosen antecedently analyzing government. Besides, regard likenessome obtain be chosen. The parameters control the dissection such as mismatch require, extension division and co-ordination division obtain be established as delinquency. Look compute obtain be congenial by normalization of the sequencing reads in reads per kilo infamous per pet (RPKM). Succeeding that, an exemplification on likeness look flatten obtain be established up, where the controlms of scantlings preference, exemplification controlm limitation and assignation of assembly names obtain be considered and interposed. Then, a footprint catalogue control the likeness look flatten obtain be created. One of three statistical analyses, “On Proportions”, obtain be applied in measuring likeness look flatten.

On proportions dissection, in-particular Z proof (Kal et al., 1999), indecent columns (“Proportions difference”, “Fpristine Change”, “Proof statistics” and “P-value”) obtain be created and added to the exemplification consideration control each analyzed assemblys pairs: Xylem and leaves make assemblys. The corrected p-values obtain be established with delinquency controlethoughts: Bonferroni corrected p-values or FDR corrected p-values. Look dissection of scantlings obtain be observed and narrative. Developments of statistical dissection on likeness look flatten obtain be visualized in volcano plots with CLC Genomics Achievementbench 7.5 (Qiagen, Denmark).

4.0 Expected Extinguishedcomes

The negotiative explanation of RNA-seq basis from clear kelampayan obtain be expected to be specifyd in message of gene ontology via Blaze2GO program. The likeness look flatten of RNA-Seq basis from clear kelampayan’s xylem and leaves obtain be expected to be muscular and analyzed. Haughty throughput dissection basis obtain be obtained in prescribe to amend genetic basis character and likenessome personality of kelampayan tree.

  1. Achievement Schedule

Contrivance Activities













Basis minute and assembly


Proposal agreement and presentation


Scantling assembly and RNA self-containedness


Illumina Sequencing Technology


Proficiency report


Basis Dissection


Report agreement and presentation

  1. References

Lim Leong Rui 36728 13

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