Building And Utilization Of Pineapple Gene Database

Pineapple(Anana comosusMerrs.)is the third important tropical fruit tree in the world and is also an important tropical fruit trees in China.It possesses high market value,which can be consumedas fresh or processed food and can be used for bromelain extraction.It also has high research value,which is CAM plant,forms a collective fruit and has ethylene-sensitive flower bud induction characteristics.As the development of sequencing technology,highthrough-put data of pineapple grew at a fast pace.It can be noticed by the publish of its genome and a huge number of pineapple transcriptome sequencing project.These data contain high value for integrated analysis and utilization.However,no related work focusing on a similar project has been reported.In the present study,we collected all available pineapple transcriptome sequencing data,built a robust analysis pipeline and conducted the analysis as bellowed:1.tranformated the pineapple genome sequences(25 LGs and 3,108 scaffolds)and gene sequences(27,024 locus);built a pineapple genome browser based on JBrowse and improved its gene-name search function.2.compared different data analysis softwares and built a analysis pipeline: removed all adapters and low quality bases by using Trimmomtic;removedcontaminating rRNA reads with a home-made pipeline,PlantRNArm.pl;mapped back all reads to the pineapple genome and transcriptome with STAR;calculated raw read count with HTseq-count;used a home-made toolkit,TBtools,to utilize the resultant information.3.collected all available pineapple transcriptome sequencing data(102);used the pipeline described above to analyse the data and built a pineapple gene database based on RNAseqExpressionBrowser.The gene database contains 2,756,448 expression value,covering four organs of pineapple(root,leaf,flower and fruit),green part and white part of pineapple leaf at different time,pineapple bud before and after ethylene induction and pineapple plantlet before and after cold treatment.4.developed a toolkit(TBtools)for downstream data analysis,which could be run in command line mode and GUI mode on different operating system(Window,Linux and Mac).It can be used for sequences extraction,transformation,gene function analysis,table manipulation and data visualization.Till now,45 GUI tools have been opened for use.5.characterized pineapple organ-specific-expressing gene using the Z-score method.Totally,3,679 genes were identified,including 1,740 root-specific expressing genes,1,803 leaf-specific expressing genes,167 flower-specific expressing genes and 707 fruit-spefic expressing genes.6.predicted pineapple cold-regulated gene network using protein and protein interaction information on string database,which was found to have 214 nodes and 286 edges.This network coutains 116 differential expressing transcription factor classified in 36 families.According to the functions of transcription factor,the network could be divided into three sub-cluster.The sub-clusters were related to plant hormone signal transduction,cold domestication and ROS signal transduction.