Data from: A recently transferred cluster of bacterial genes in Trichomonas vaginalis –lateral gene transfer and the fate of acquired genes.

Background: Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A previously defined norm for LGTs in microbial eukaryotes states that the majority are genes involved in metabolism, the LGTs are typically localized one by one, surrounded by vertically inherited genes on the chromosome, and phylogenetics shows that a broad collection of bacterial lineages have contributed to the transferome. Results: A unique 34 kbp long fragment with 27 clustered genes (TvLF) of prokaryote origin was identified in the sequenced genome of the protozoan parasite Trichomonas vaginalis. Using a PCR based approach we confirmed the presence of the orthologous fragment in four additional T. vaginalis strains. Detailed sequence analyses unambiguously suggest that TvLF is the result of one single, recent LGT event. The proposed donor is a close relative to the firmicute bacterium Peptoniphilus harei. High nucleotide sequence similarity between T. vaginalis strains, as well as to P. harei, and the absence of homologs in other Trichomonas species, suggests that the transfer event took place after the radiation of the genus Trichomonas. Some genes have undergone pseudogenization and degradation, indicating that they may not be retained in the future. Functional annotations reveal that genes involved in informational processes are particularly prone to degradation. Conclusions: We conclude that, although the majority of eukaryote LGTs are single gene occurrences, they may be acquired in clusters of several genes that are subsequently cleansed of evolutionarily less advantageous genes.

背景：水平基因转移（Lateral Gene Transfer, LGT）近年来被认为是塑造部分真核生物蛋白质组的重要因素，但其在真核生物基因组中的获取与固定机制仍未明确。此前针对微生物真核生物LGT的研究共识提出，多数此类转移事件所涉及的基因均与代谢功能相关，LGT通常以单基因形式独立整合，在染色体上被垂直遗传的基因环绕；系统发育分析显示，广泛的细菌类群共同构成了真核生物的外源转移基因组（transferome）。
研究结果：在原生动物寄生虫阴道毛滴虫（Trichomonas vaginalis）的测序基因组中，我们鉴定出一段长34 kbp、包含27个成簇基因的原核生物起源独特片段（命名为TvLF）。通过聚合酶链式反应（Polymerase Chain Reaction, PCR）实验，我们在另外4株阴道毛滴虫菌株中均验证到该同源片段的存在。详细的序列分析明确证实，TvLF是单次近期LGT事件的产物。其潜在供体为厚壁菌门（Firmicutes）细菌Peptoniphilus harei的近缘类群。阴道毛滴虫各菌株间以及与P. harei之间的核苷酸序列相似性较高，且其他毛滴虫属物种中未检测到该片段的同源基因，表明该转移事件发生在毛滴虫属分化之后。部分基因已发生假基因化（pseudogenization）与降解，提示其未来可能无法被保留。功能注释结果显示，参与信息传递过程的基因尤其容易发生降解。
研究结论：我们认为，尽管多数真核生物的LGT事件均为单基因转移，但此类外源基因也可能以多基因簇的形式被整体获取，随后会通过进化过程清除那些进化适应性较差的基因。