Annotation And Data Mining Of The Plant Genome

As one of the oldest seed plants available,Ginkgo biloba is widely regarded as a "living fossil" among plants.Because of its unique morphological and physiological characteristics,together with the debate on its phylogenetic position among seed plants,ginkgo has played a very important role in evolutionary studies.In addition to this,ginkgo has very high medicinal value,mainly including its very important secondary metabolites,flavonoids and terpenoids.In this study,we took the important metabolites of G.biloba as a breakthrough,combined with multi-omics data such as genome,transcriptome and metabolome,and mainly investigated the alternative splicing of genes related to ginkgo genome and secondary metabolites,and the changes of metabolites in ginkgo leaves across different periods.We wish that these results will be useful for the study of the synthesis and regulatory mechanisms of secondary metabolites.The main findings are listed below.1.Based on the high-quality genome of G.biloba,the alternative splicing events of the ginkgo genome were analyzed,and the genome-wide landscape of the AS pattern was revealed by a comprehensive analysis of multiple tissues at different developmental stages.Compared with other plants,intron retention was the predominant AS type in all tissues,its frequency was much lower,and the functional enrichment of genes associated with different AS types showed great differences.In addition,the AS patterns of important secondary metabolites in G.biloba,including flavonoids and terpenoids,were also analyzed in depth.2.To further investigate the detailed differences in metabolism and gene function at different time periods,mature leaves of G.biloba were collected from three time points(June,August and October)where metabolic changes were most pronounced,and their metabolites were identified separately.Seven hundred and eighty metabolites,including 133 flavonoid compounds(69 flavonoids,41 flavonols and 23 flavanones),5 terpenoids and 72 organic acids and their derivatives,were successfully isolated by UPLC-MS/MS.Of all 133 flavonoid compounds detected,83 were not available in the KEGG database,and these newly discovered metabolites will be a good addition to secondary metabolite studies.The results suggest that although the major components of flavonoids are not essential for G.biloba,its co-occurring metabolites,stilbenes,can play an important role in resisting environmental changes and plant diseases.The combination analysis between differential genes and metabolites revealed a total of 2,523 single genes and 203 metabolites that were strongly linked,and this information will facilitate subsequent studies on the molecular mechanisms of secondary metabolites in G.biloba.