2x genomes--depth does matter.
2x genomes--depth does matter.
复制标题
DOI：
10.1186/gb-2010-11-2-r16
复制
发表时间：
2010
期刊：
影响因子：
12.3
通讯作者：
Gabaldón T
中科院分区：
文献类型：
--
作者：
Milinkovitch MC;Helaers R;Depiereux E;Tzika AC;Gabaldón T
在比较进化分析中使用低覆盖率的基因组会扭曲对基因获得和损失的估计。鉴于全基因组序列的可用性，绘制进化过程中的基因获得，复制和丢失在理论上应该是简单的。然而，这一奋进受到过度强调检测保守基因组特征的影响，这反过来又导致对具有低覆盖度的多个真兽目基因组进行测序，而不是更少的具有高覆盖度和更均匀分布的基因组。虽然与低覆盖率基因组分析相关的限制被认识到，但它们尚未被量化。在这里，使用最近开发的比较基因组应用系统，我们评估的影响，低覆盖率的基因组的推断有关的基因的获得和损失时，通过基因复制分析真核生物基因组进化。我们证明，在进行基因组内容进化的推断时，低覆盖率基因组不仅产生大量的假基因丢失，而且在基因复制推断中也产生惊人的伪像，特别是在低覆盖率基因组的最近共同祖先处。我们表明，人为的收益是由低覆盖率的基因组序列本身，而不是由增加分类单元采样在一个有偏见的一部分的物种树。我们认为，这将仍然很难区分文物的模式和克里思的基因组进化的真正变化，直到有更好的同质性在两个分类单元的采样和高覆盖率测序。这对于将全基因组数据的效用扩大到进化生物学家社区是重要的，因为他们的兴趣远远超出了广泛保守的生理学和发育模式，因为他们试图了解生物多样性的生成机制。
The use of low coverage genomes in comparative evolutionary analyses skews estimates of gene gains and losses. Given the availability of full genome sequences, mapping gene gains, duplications, and losses during evolution should theoretically be straightforward. However, this endeavor suffers from overemphasis on detecting conserved genome features, which in turn has led to sequencing multiple eutherian genomes with low coverage rather than fewer genomes with high-coverage and more even distribution in the phylogeny. Although limitations associated with analysis of low coverage genomes are recognized, they have not been quantified. Here, using recently developed comparative genomic application systems, we evaluate the impact of low-coverage genomes on inferences pertaining to gene gains and losses when analyzing eukaryote genome evolution through gene duplication. We demonstrate that, when performing inference of genome content evolution, low-coverage genomes generate not only a massive number of false gene losses, but also striking artifacts in gene duplication inference, especially at the most recent common ancestor of low-coverage genomes. We show that the artifactual gains are caused by the low coverage of genome sequence per se rather than by the increased taxon sampling in a biased portion of the species tree. We argue that it will remain difficult to differentiate artifacts from true changes in modes and tempo of genome evolution until there is better homogeneity in both taxon sampling and high-coverage sequencing. This is important for broadening the utility of full genome data to the community of evolutionary biologists, whose interests go well beyond widely conserved physiologies and developmental patterns as they seek to understand the generative mechanisms underlying biological diversity.
登录
查看更多内容
影响因子：
12.3
作者：
Gabaldón T
通讯作者：
Gabaldón T
影响因子：
7
作者：
Bashir, A;Ye, C;Bafna, V
通讯作者：
Bafna, V
人类的前线。
影响因子：
12.3
作者：
通讯作者：
--
影响因子：
6.8
作者：
AKAIKE, H
通讯作者：
AKAIKE, H
影响因子：
3.1
作者：
Haussler, David;O'Brien, Stephen J.;Turner, Steve
通讯作者：
Turner, Steve