Placing paleopolyploidy in relation to taxon divergence: A phylogenetic analysis in legumes using 39 gene families
Placing paleopolyploidy in relation to taxon divergence: A phylogenetic analysis in legumes using 39 gene families
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DOI：
10.1080/10635150590945359
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发表时间：
2005-06-01
影响因子：
6.5
通讯作者：
Doyle, JJ
中科院分区：
文献类型：
--
作者：
Pfeil, BE;Schlueter, JA;Doyle, JJ
年轻的多倍体事件很容易被各种方法诊断，但较老的多倍体事件变得越来越难以识别，因为染色体重排、串联基因或部分染色体重复、重复基因之间替换率的变化、假基因或位点丢失以及基因间相互作用使推断过去的遗传事件的手段变得复杂。基因组数据提供了许多物种多倍体历史的有价值的信息，但它们本身无法显示相关物种是否分享特定的多倍体事件，每个物种都有多倍体历史。系统发生学方法为确定这一点提供了一种强有力的方法，但许多过程可能会误导调查人员。这些过程可以影响单个基因树，但很可能不会影响所有基因，而且几乎可以肯定不会以同样的方式影响所有基因。因此，多基因方法结合了基因组学的大规模方面和系统发育学的解决方案，具有克服这些困难的能力，并使我们能够比其他方法更深入地推断过去的基因组事件。之前利用物种内基因对之间的同义距离进行的研究表明，豆科植物大豆和紫花苜蓿存在大规模复制的证据。我们提供了一个案例研究，使用39个基因家族，每个家族有三到四个成员在G.max和假定的同源物在根茎拟南芥。我们测试了这些豆科植物的基因复制是在它们分化后在每个谱系中单独发生(假设1)，还是它们共享一轮基因复制(假设2)。更多的基因家族拓扑支持假设2而不是假设1(分别为11和2)，即使在同义距离分析显示一些拓扑提供了误导性的结果之后。只有33%左右的基因支持这两种假说，这有力地表明，单基因家族的方法在用核DNA研究古代事件时可能是不够的。我们的结果表明，G.max和M.truncatula，以及来自同一分支的大约7000种其他豆科植物，共享一轮古老的基因复制，要么是由于多倍体，要么是由于某些其他过程。
Young polyploid events are easily diagnosed by various methods, but older polyploid events become increasingly difficult to identify as chromosomal rearrangements, tandem gene or partial chromosome duplications, changes in substitution rates among duplicated genes, pseudogenization or locus loss, and interlocus interactions complicate the means of inferring past genetic events. Genomic data have provided valuable information about the polyploid history of numerous species, but on their own fail to show whether related species, each with a polyploid past, share a particular polyploid event. A phylogenetic approach provides a powerful method to determine this but many processes may mislead investigators. These processes can affect individual gene trees, but most likely will not affect all genes, and almost certainly will not affect all genes in the same way. Thus, a multigene approach, which combines the large-scale aspect of genomics with the resolution of phylogenetics, has the power to overcome these difficulties and allow us to infer genomic events further into the past than would otherwise be possible. Previous work using synonymous distances among gene pairs within species has shown evidence for large-scale duplications in the legumes Glycine max and Medicago truncatula. We present a case study using 39 gene families, each with three or four members in G. max and the putative orthologues in M. truncatula, rooted using Arabidopsis thaliana. We tested whether the gene duplications in these legumes occurred separately in each lineage after their divergence ( Hypothesis 1), or whether they share a round of gene duplications ( Hypothesis 2). Many more gene family topologies supported Hypothesis 2 over Hypothesis 1 ( 11 and 2, respectively), even after synonymous distance analysis revealed that some topologies were providing misleading results. Only ca. 33% of genes examined support either hypothesis, which strongly suggests that single gene family approaches may be insufficient when studying ancient events with nuclear DNA. Our results suggest that G. max and M. truncatula, along with approximately 7000 other legume species from the same clade, share an ancient round of gene duplications, either due to polyploidy or to some other process.