Department for Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany.
BMC Evol Biol. 2011 Aug 15;11:239. doi: 10.1186/1471-2148-11-239.
The recent sequencing of nematode genomes has laid the basis for comparative genomics approaches to study the impact of horizontal gene transfer (HGT) on the adaptation to new environments and the evolution of parasitism. In the beetle associated nematode Pristionchus pacificus HGT events were found to involve cellulase genes of microbial origin and Diapausin genes that are known from beetles, but not from other nematodes. The insect-to-nematode horizontal transfer is of special interest given that P. pacificus shows a tight association with insects.
In this study we utilized the observation that horizontally transferred genes often exhibit codon usage patterns more similar to that of the donor than that of the acceptor genome. We introduced GC-normalized relative codon frequencies as a measure to detect characteristic features of P. pacificus orphan genes that show no homology to other nematode genes. We found that atypical codon usage is particularly prevalent in P. pacificus orphans. By comparing codon usage profiles of 71 species, we detected the most significant enrichment in insect-like codon usage profiles. In cross-species comparisons, we identified 509 HGT candidates that show a significantly higher similarity to insect-like profiles than genes with nematode homologs. The most abundant gene family among these genes are non-LTR retrotransposons. Speculating that retrotransposons might have served as carriers of foreign genetic material, we found a significant local clustering tendency of orphan genes in the vicinity of retrotransposons.
Our study combined codon usage bias, phylogenetic analysis, and genomic colocalization into a general picture of the computational archaeology of the P. pacificus genome and suggests that a substantial fraction of the gene repertoire is of insect origin. We propose that the Pristionchus-beetle association has facilitated HGT and discuss potential vectors of these events.
最近对线虫基因组的测序为比较基因组学方法研究水平基因转移（HGT）对新环境适应和寄生进化的影响奠定了基础。在与甲虫相关的线虫 Pristionchus pacificus 中，发现 HGT 事件涉及微生物来源的纤维素酶基因和 Diapausin 基因，这些基因已知存在于甲虫中，但不存在于其他线虫中。鉴于 P. pacificus 与昆虫紧密相关，昆虫到线虫的水平转移特别引人注目。
在本研究中，我们利用了这样一个观察结果，即水平转移的基因通常表现出与供体基因组而不是受体基因组更相似的密码子使用模式。我们引入了 GC 归一化相对密码子频率作为一种度量标准，以检测与其他线虫基因没有同源性的 P. pacificus 孤儿基因的特征。我们发现，非典型密码子使用在 P. pacificus 孤儿基因中尤为普遍。通过比较 71 个物种的密码子使用谱，我们检测到昆虫样密码子使用谱的显著富集。在种间比较中，我们鉴定了 509 个 HGT 候选基因，它们与昆虫样谱的相似性明显高于具有线虫同源物的基因。这些基因中最丰富的基因家族是非 LTR 反转录转座子。推测反转录转座子可能是外源遗传物质的载体，我们发现孤儿基因在反转录转座子附近存在显著的局部聚类趋势。
我们的研究将密码子使用偏性、系统发育分析和基因组共定位结合在一起，形成了 P. pacificus 基因组计算考古学的总体图景，并表明基因库的很大一部分具有昆虫起源。我们提出 Pristionchus-甲虫的共生关系促进了 HGT，并讨论了这些事件的潜在载体。
