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CAGE:A case study of gene cluster evolution  

2013-08-07 17:28:23|  分类: 文献学习 |  标签: |举报 |字号 订阅

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        Much important evolutionary activity occurs in gene clusters, where a copy of a gene may be free to acquire new functions. Current computational methods to extract evolutionary information from sequence data for such clusters are suboptimal, in part because accurate sequence data are often lacking in these genomic regions, making existing methods difficult to apply. We describe a new method for reconstructing the recent evolutionary history of gene clusters, and evaluate its performance on both simulated data and actual human gene clusters.

CAGE:A case study of gene cluster evolution - 喜欢吃桃子 - wangyufeng的博客
Simulation results to evaluate detection of duplications. (a) Total numbers of reconstructed events and (b) fraction of true events detected correctly. (c) Simulation results of duplication detection for gene clusters in two species; each bar has three numbers: events before speciation, events in species 1 after speciation, and events in species 2 after speciation, for n true events of each type (i.e., 3n duplications in total) for n = 5, 10, 15, 20, 25. (d) Observed breakpoint reuse rate by the duplications in the human gene clusters.
 

       Functional gene clusters, containing two or more genes encoding different enzymes for the same pathway, are sometimes observed in plant genomes, most often when the genes specify the synthesis of specialized defensive metabolites. Here, we show that a cluster of genes in tomato (Solanum lycopersicum; Solanaceae) contains genes for terpene synthases (TPSs) that specify the synthesis of monoterpenes and diterpenes from cis-prenyl diphosphates, substrates that are synthesized by enzymes encoded by cis-prenyl transferase (CPT) genes also located within the same cluster. The monoterpene synthase genes in the cluster likely evolved from a diterpene synthase gene in the cluster by duplication and divergence. In the orthologous cluster in Solanum habrochaites, a new sesquiterpene synthase gene was created by a duplication event of a monoterpene synthase followed by a localized gene conversion event directed by a diterpene synthase gene. The TPS genes in the Solanum cluster encoding cis-prenyl diphosphate–utilizing enzymes are closely related to a tobacco (Nicotiana tabacum; Solanaceae) diterpene synthase encoding Z-abienol synthase (Nt-ABS). Nt-ABS uses the substrate copal-8-ol diphosphate, which is made from the all-trans geranylgeranyl diphosphate by copal-8-ol diphosphate synthase (Nt-CPS2). The Solanum gene cluster also contains an ortholog of Nt-CPS2, but it appears to encode a nonfunctional protein. Thus, the Solanum functional gene cluster evolved by duplication and divergence of TPS genes, together with alterations in substrate specificity to utilize cis-prenyl diphosphates and through the acquisition of CPTgenes.

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