Bioinformatics Analysis Of Patulin Degradation By Byssochlamys Nivea FF1-2 Based On RNA-Seq

Patulin(PAT)is a mycotoxin that poses a great threat to human health.Patulin has been identified in various fruits and fruit products commonly,especially in apples and its derived products.As a prospective method,using microorganisms to degrade patulin is economical,safe and efficient.In our previous study,we firstly screened and identified the first strain in Byssochlamys named Byssochlamys nivea FF1-2,which could degrade patulin efficiently.And the patulin degradation features of this strain were also conducted.However,the mechanism of the patulin degradation by B.nivea FF1-2 has not yet been clarified,which severely restricts its application in apple processing industry for controlling and degrading patulin.To solve this situation,in the present study,transcriptomes of B.nivea FF1-2 with different times of patulin degradation were sequenced using RNA-sequencing technology,transcriptome databases of B.nivea FF1-2 were established after de novo assembly.Based on transcriptome sequencing,functional annotation and pathway analysis against protein databases including NCBI non-redudant protein NR,Swiss-Prot,Gene Ontology(GO),Clusters of Orthologous Groups for Eukaryotic Complete Genomes(KOG)and Kyoto Encyclopedia of Genes and Genomes(KEGG)were perfomed;By means of differential screening,differentially expressed genes possibly related to patulin degradation were analyzed and the mechanisms involved in degradation were explored.In addition,simple sequence repeat(SSR)locis of the B.nivea FF1-2 transcription data were mined using MISA.The results of the present study are as follow:1.RNA samples of B.nivea FF1-2 with different time of patulin degradation were subjected to pair-end read sequencing with the Illumina Hiseq 2500 platform.Approximately 271.22 million paired-end clean reads were obtained.After de novo assembly,27,214 unigenes with a total length of 36,019,203 bp,and N50 length of 2722 bp were obtained.A total of 22,075(about 81.12%of the assembled unigenes)unigenes were successfully annotated to one or more databases using the publically available protein database incluing NR,Swiss-Prot,GO,KOG and KEGG A total of 12,900 unigenes had homologous genes in KOG database and could be classified into 25 categories according to their predicted functions.Results of the GO classification showed that a total of 15,498 unigens could be classified into 63 categories,accounting for 56.95 percentages.Pathway enrichment analysis classified all 5364 unigenes into 215 metabolic pathyways.2.Differential gene expression analysis was performed for comparisons among B.nivea FF1-2 different degrees of patulin degradation.The fold change cut-off was set at twofold with FDR?0.05.A total of 1680 differentially expressed unigenes were detected consisted of up-and 655 down-regulated unigenes between the Ck and D3 libraries;There were 1454 differentially expressed unigenes between Ck and D5 libraries of which 894 and 560 unigenes were up-regulated and down-regulated respectively;For D3 and D5 libraries,there were 2247 differentially expressed unigenes including 1228 up-regulated unigenes and 1019 down-regulated unigenes.3.GO and KEGG pathway enrichment of differentially expressed unigenes revealed that these unigenes were predominately involved in oxidoreductase activity and methyltransferase activity,biotin metabolism,metabolism of xenobiotics by cytochrome P450 and other physiological metabolic process.4.75 SSR motifs and 3909 SSRs were searched in 27,214 unigenes with the occurrence frequency of 14.36%using MIS A software.Among unigenes containing SSR locis,3040 were successfully designed with the PCR primers by Primer 3,with the successfully rate of 82.27%.Based on the transcriptome data of B.nivea FF1-2 and previous studies about patulin degradation by microorganisms,we discussed the molecular mechanism of patulin degradation.Further study should be conducted to verify the exact regulatory mechanism.This research for the first time explores the molecular mechanism of toxins degrading by B.nivea FF1-2 using the next-generation sequencing technology and bioinformatics analysis.It provides a reference for clarifying the mechanism of toxins degradation by microorganisms and also lay the foundation for using this strain to solve the toxin contamination in apple processing industry.