Genome-wide analyses of phenylpropanoid-related genes in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa:: the Populus lignin toolbox and conservation and diversification of angiosperm gene families
Genome-wide analyses of phenylpropanoid-related genes in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa:: the Populus lignin toolbox and conservation and diversification of angiosperm gene families
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DOI：
10.1139/b07-098
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发表时间：
2007-12-01
期刊：
影响因子：
--
通讯作者：
Douglas, Carl J.
中科院分区：
文献类型：
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作者：
Hamberger, Bjoern;Ellis, Margaret;Douglas, Carl J.
完成的杨大果杨（托。& A. Gray）（白杨）基因组序列提供了一个机会，研究完整的基因组家族在第三个完全测序的被子植物（后拟南芥和水稻），并进行比较基因组学研究的被子植物基因家族进化。我们集中在基因家族编码类苯丙烷和类苯丙烷酶，并确定和注释的全套基因编码这些和相关酶的白杨基因组。我们使用了类似的方法，以确定一组类似的基因从水稻基因组和生成系统发育树的9个苯丙素类基因家族对齐白杨，拟南芥，水稻预测的蛋白质序列。这使我们能够确定可能的全套真正的白杨木质素相关的苯丙素类基因（白杨“木质化工具箱”）明显在所有系统发育树中明确的分支。对白杨基因表达数据的分析证实并细化了木质素相关基因的注释，这些基因通常在木材形成组织中表现出高表达。从白杨和拟南芥的表达数据进行推断的生化和生物学功能的苯丙烷类基因与未知的功能。比较的方法也提供了深入了解被子植物苯丙烷类基因家族的进化，说明谱系特定的分支，以及古老的分支含有明显的保守功能的基因。
The completion of the Populus trichocarpa (Torr. & A. Gray) (poplar) genome sequence offers an opportunity to study complete genome families in a third fully sequenced angiosperm (after Arabidopsis and rice) and to conduct comparative genomics studies of angiosperm gene family evolution. We focussed on gene families encoding phenylpropanoid and phenylpropanoid-like enzymes, and identified and annotated the full set of genes encoding these and related enzymes in the poplar genome. We used a similar approach to identify an analogous set of genes from the rice genome and generated phylogenetic trees for nine phenylpropanoid gene families from aligned poplar, Arabidopsis, and rice predicted protein sequences. This enabled us to identify the likely full set of bona fide poplar lignin-related phenylpropanoid genes (poplar "lignification toolbox") apparent within well-defined clades in all phylogenetic trees. Analysis of expression data for poplar genes confirmed and refined annotations of lignin-related genes, which generally showed high expression in wood-forming tissues. Expression data from both poplar and Arabidopsis were used to make inferences regarding biochemical and biological functions of phenylpropanoid-like genes with unknown functions. The comparative approach also provided insights into the evolution of angiosperm phenylpropanoid-like gene families, illustrating lineage-specific clades as well as ancient clades containing genes with apparent conserved function.