Extracting functional trends from whole genome duplication events using comparative genomics.
Extracting functional trends from whole genome duplication events using comparative genomics.
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DOI：
10.1186/s12575-016-0041-2
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发表时间：
2016
影响因子：
6.4
通讯作者：
Liberles DA
中科院分区：
文献类型：
--
作者：
Hermansen RA;Hvidsten TR;Sandve SR;Liberles DA
拥有完整基因组的物种数量，包括那些有证据表明最近发生了全基因组复制事件的物种数量，已经激增。最近测序的大西洋鲑鱼基因组已经经历了两轮全基因组复制，因为硬骨鱼从导致鲑鱼的谱系分化。这种潜在基因数量的四极化导致了基因家族之间复杂的保留和丢失模式。已经开发了方法来表征跨全基因组复制事件和另外的较小规模复制事件两者的重复基因保留过程的相互作用。此外，基因表达趋异数据已成为可用的，以及大西洋鲑鱼和密切相关的，前全基因组复制派克和方法来描述表达趋异。描述了这些方法用于表征已应用于鲑鱼的重复基因保留和基因表达趋异。随着可用基因组和功能数据的增长，使用比较方法从大规模重复中提取功能推断的机会急剧增加。最近开发的方法，进一步这种推断重复基因已被描述。本文的在线版本（doi：10.1186/s12575-016-0041-2）包含补充材料，可供授权用户使用。
The number of species with completed genomes, including those with evidence for recent whole genome duplication events has exploded. The recently sequenced Atlantic salmon genome has been through two rounds of whole genome duplication since the divergence of teleost fish from the lineage that led to amniotes. This quadrupoling of the number of potential genes has led to complex patterns of retention and loss among gene families. Methods have been developed to characterize the interplay of duplicate gene retention processes across both whole genome duplication events and additional smaller scale duplication events. Further, gene expression divergence data has become available as well for Atlantic salmon and the closely related, pre-whole genome duplication pike and methods to describe expression divergence are also presented. These methods for the characterization of duplicate gene retention and gene expression divergence that have been applied to salmon are described. With the growth in available genomic and functional data, the opportunities to extract functional inference from large scale duplicates using comparative methods have expanded dramatically. Recently developed methods that further this inference for duplicated genes have been described. The online version of this article (doi:10.1186/s12575-016-0041-2) contains supplementary material, which is available to authorized users.