| RNA alternative splicing is not only prelavent in plants but also plays important roles in many biological functions.Ginseng(Panax ginseng C.A.Meyer)is one of the most important traditional medicinal herbs in China;however,it is unknown about how AS action charcateristics and functions in ginseng,especially in ginsenoside biosynthesis,the most important chemical compoments effective for human health and medicine.The knowledge is also limited for a single plant in other species.Here,we systematically studied the AS action charcteristics in differet organs of a single ginseng plant at the flowering and fruiting stage using the transcriptomes of 14 organs of a four-year-old ginseng plant with the ginseng genome sequence as a reference.Moreover,we further exmined the potential roles of AS in the ginsenoside biosynthesis in ginseng using the transcriptome of the adventitious roots treated with methyl jasmonate(Me JA)that is widely used to induce in vitro ginsenoside biosynthesis in ginseng.Sumarized are the major findings of this study:1.Analysis of the transcriptomes of 14 organs of a four-year-old ginseng plant identified that a total of 13,863 genes(AS genes)were subjected to 30,801 AS events.The probability of AS events for a gene was significantly associated with the number of its exons.2.Five AS mechanisms were responsible for these AS events in the plant,including skipped exon(SE),retained intron(RI),alternative 5' splice site(A5SS),alternative 3' splice site(A3SS)and mutually exclusive exon(MXE).Of the five AS mechanisms,SE was the most prevalent(53%)and approximately 68% of the AS genes were subjected to only one of them.3.The frequency and mechanism of AS events varied substantially across organs,but the genes expressed across organs were subjected to more AS events than those organ-specifically expressed genes.Furthermore,At the 3' ends of AS introns,most splicing sites are the AG;at the 5' end,a majority of splicing sites are the GU,but a small fractions are also the GC.There were no obvious different sequence patterns at the splicing sites between AS and non-AS.Over 500 GO(gene ontology)terms were enriched for AS genes in the plant,while the number of AS gene-enriched GO terms varied across organs.4.Correlation analysis identified 24 AS genes whose expressions were significantly correlated with ginsenoside contents,thus suggesting that they were involved in ginsenoside biosynthesis.The number of AS genes were significantly up-enriched in the process and they were more likely to form a co-expression network,suggesting their functions and correlations in ginsenoside biosynthesis.5.The correlation between AS and ginsenoside synthesis was further confirmed through analysis of the transcriptomes of ginseng adventitious roots treated by Me JA for 0-48 hours.The result showed that a total of 11,182 AS genes were subjected to 23,240 AS events in the Me JA-treated adventitious roots.Gene differential expression analysis showed that of the AS genes differentially expressed between the adventitious roots treated and not treated with Me JA,15 were the genes encoding the enzyme's key to ginseoside biosynthesis.13 of the 15 genes were in the 24 AS genes whose expressions were significantly correlated with ginsenoside contents identified above and significantly correlated with the contents of protopanaxadiol saponins,Rb1 and Rd.This result was consistent with the previous finding that Me JA positively regulates the biosynthesis of protopanaxadiol saponins,thus further demonstrating the important roles of AS in ginsenoside biosynthesis.In summary,AS is prevalent in plants,but its occurrence and underlying mechanisms varied across organs and in association with the number of exons that a gene contains,its expression across organs and Me JA treatment.Both AS and non-AS genes were involved in ginsenoside biosynthesis,but the AS genes were significantly up-enriched in the process.These findings provide new and comprehensive insights into the action characteristics and functions of AS in a plant. |
PDF Full Text Request