Structural variation of differentially expressed genes in Zanthoxylum bungeanum Maxim.at different altitudes
[Objective]The effects of different altitudinal gradients on gene expression in Sichuan pepper(Zanthoxylum bungeanum Maxim.)were investigated to provide the basis for studying the genetic diversity and metabolic regulation of Sichuan pepper and its molecular mecha-nisms adapting to different altitudinal habitats stress.[Method]Using the leaves of Sichuan pepper from different altitudes(1054,821 and 645 meters)in Banguixiang of Zhenfeng county in Guizhou province as test materials,we employed bioinformatics methods of transcriptome sequencing to analyze alternative splicing(AS)and SNP/InDel variant sites of differentially expressed genes,thereby uncovering novel tran-scripts involved in the adaptation of Sichuan pepper to its environment.[Result]In the leaves of Sichuan pepper plants from three different altitudes,a total of 2619 genes underwent alternative splicing events,mainly consisting of two types of skipped exon(SE)and mutually ex-clusive exons(MXE)with SE being the most abundant.Additionally,a significant increase in alternative splicing events was observed in the high-altitude comparison group.Furthermore,a total of 748 331 SNPs and 87 402 InDel loci were identified,with a higher occurrence of SNP transitions than the transversion and a distribution of exonic SNPs accounting for 40.0％.InDel loci were predominantly found in intron-ic regions,reaching 28.6％.Moreover,9363 novel transcripts were discovered,with 5648 of them being annotated in 7 major databases.KEGG metabolic pathway analysis revealed that functional genes undergoing alternative splicing in Sichuan pepper leaves were mainly in-volved in metabolic pathways,biosynthesis of secondary metabolites and biosynthesis pathways of cofactors.On the other hand,novel tran-scripts were mainly enriched in pathways such as photosynthesis,phenylpropanoid biosynthesis,isoflavonoid biosynthesis,flavonoid biosyn-thesis and terpenoid biosynthesis.[Conclusion]The study enriches understanding of genetic structural variations of Sichuan pepper under dif-ferent altitudinal conditions and lays the foundation for subsequent research on genetic diversity,metabolic regulation and molecular mecha-nisms in response to environmental stress.
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