Genome-wide Identification And Evolutionary Analysis Of Duplicated Genes In Pear And Other Sequenced Plants

Duplicated genes can be generated by different modes of gene duplication,which is very common in fungi,animals and plants.Gene duplication provides substantial raw materials for genetic novelty,adaptive evolution and biodiversity.The sharp increase in the number of sequenced plant genomes empowers investigation of evolution and retention mechanisms of duplicated genes.In this study,we used bioinformatics approaches to identify the different modes of duplicated genes in pear('Dangshansuli')and other sequenced plant genomes.Integrated large-scale genome,transcriptome and methylome datasets were used to investigate the evolution and retention mechanisms of duplicated genes.In addition,the contribution of gene duplication to biological innovation was evaluated by investigating the expansion patterns of gene families involved in key fruit traits.The main results are as follows:1.Genome-wide identification and evolutionary analysis of duplicated genes in pearIn this study,we identified the different modes of gene duplication in pear.Duplicate genes derived from WGD,tandem,proximal,retrotransposed,DNA-based transposed or dispersed duplication differ in genomic distribution,gene features,selection pressure,expression divergence,regulatory divergence and biological roles.Widespread sequence,expression and regulatory divergence have occurred between duplicate genes in pear.In contrast with other modes of duplicated genes,the retrotransposed genes show relatively higher expression and regulatory divergence than other gene duplication modes.However,WGD genes have slower evolutionary rate and show relatively lower expression and regulatory divergence.TD and PD largely account for the extensive expansion of gene families involved in the sorbitol metabolism pathway in pear.The gene family expansion found in the sucrose metabolism pathway was largely attributed to the WGD and DSD.In addition,WGD play important roles in the expansion of Hsf gene family.2.Investigation of evolution and retention mechanisms of duplicated genes based on transcriptome and methylome datasets in pearThe MCScanX-transposed package was updated to version 2,and was used to automatically identify the different modes of gene duplication in pear.We estimated the evolutionary dates of two rounds of WGD events occurred in pear genome based on the gaussian mixture model.The time of these two WGD events were dated to?16 Mya and?111 Mya,respectively.The duplicated gene pairs derived from the recent and ancient WGD were identified respectively,and the evolutionary fate of these two sets of duplicated genes was investigated.The asymmetric expression level between duplicated genes were unraveled in pear based on the transcriptome datasets,that is,one gene copy has higher expression level than the other copy.When the expression difference is more than 2-fold,5-fold or 10-fold,the highly expressed duplicates showed higher levels of CG methylation and lower levels of CHG methylation than the lowly expressed duplicates within the gene body region.The divergence of CG or CHG methylation between paralogs increased with the increasing expression level difference.For different modes of gene duplication,the highly expressed duplicates have qualitatively smaller Ka/Ks ratios,and experienced stronger purifying selection than the lowly expressed duplicates.The expression reduction in both copies within a duplicated pair is very common in plants.We also observed the asymmetric expression reduction between duplicated genes,in which one gene copy evolved toward elevated expression relative to the progenitor gene while the other copy has lower expression than the progenitor gene.In addition,we used newly developed IDGRM algorithm to infer the retention mechanisms of duplicated genes.The important roles of asymmetric subfunctionalization,asymmetric neofunctionalization,and expression specialization were revealed.3.Identifying duplicated genes in 141 sequenced plants and revealing the mechanisms underlying duplicate gene evolutionIn this study,we identified the different modes of duplicated genes in 141 sequenced plant genomes.Genes derived from whole-genome(WGD),tandem(TD),proximal(PD),transposed(TRD)or dispersed(DSD)duplication differ in abundance,selection pressure,expression divergence,and gene conversion rate among genomes.The number of WGDderived duplicate genes decrease exponentially with increasing antiquity of duplication events--in parallel,the exponential decrease over time was also found in TRD-and DSDderived genes.The majority of duplicated genes evolve under the purifying selection although PD-derived genes experienced stronger positive selection.Widespread expression divergence occurred following gene duplication.The rate of gene conversion among WGD-derived gene pairs declined over time compared with shortly after polyploidization.Despite rich opportunity for functional divergence,only?0.4%of genes in these 141 plant genomes are in species-specific families-232 ancient gene families present in all 141 plants are enriched in biological processes related to actin filament-based movement,formation of multiple cellular components,and biological regulation and signal transduction.4.Asymmetric evolution between duplicated genes in plantsThe widespread asymmetric evolution patterns between duplicated genes were unraveled in plants based on the large-scale genome,transcriptome and methylome datasets.Based on the transcriptome analysis,we found that 59%-69%WGD-,66%-75%TD-,61%-79%PD-,66%-78%TRD-,and 66%-74%DSD-derived gene pairs show asymmetric expression level in plants.The asymmetric CG and CHG methylation patterns between the highly and lowly expressed genes within duplicated gene pairs were found in different plants.Moreover,the asymmetric evolutionary rate between the highly and lowly expressed gene duplicates was also found in different plants.The lowly expressed duplicates have qualitatively higher Ka/Ks ratios,and experienced rapider sequence mutations than the highly expressed duplicates.The expression reduction in both copies within a duplicated pair is very common in plants.Those duplicated gene pairs with expression reduction in only one of the two gene copies evolved under the absolute dosage balance constraints,while those duplicated gene pairs with expression reduction in both copies evolve under dosage subfunctionalization constraints.