Abstract：
Plasmids are extrachromosomal genetic elements that reside in prokaryotes. The acquisition of plasmids encoding beneficial traits can facilitate short-term survival in harsh environmental conditions or long-term adaptation of new ecological niches. Due to their ability to transfer between cells, plasmids are considered agents of gene transfer. Nonetheless, the frequency of DNA transfer between plasmids and chromosomes remains understudied. Using a novel approach for detection of homologous loci between genome pairs, we uncover gene sharing with the chromosome in 1,974 (66%) plasmids residing in 1,016 (78%) taxonomically diverse isolates. The majority of homologous loci correspond to mobile elements, which may be duplicated in the host chromosomes in tens of copies. Neighboring shared genes often encode similar functional categories, indicating the transfer of multigene functional units. Rare transfer events of antibiotics resistance genes are observed mainly with mobile elements. The frequent erosion of sequence similarity in homologous regions indicates that the transferred DNA is often devoid of function. DNA transfer between plasmids and chromosomes thus generates genetic variation that is akin to workings of endosymbiotic gene transfer in eukaryotic evolution. Our findings imply that plasmid contribution to gene transfer most often corresponds to transfer of the plasmid entity rather than transfer of protein-coding genes between plasmids and chromosomes.
摘要：
质粒是存在于原核生物中的染色体外遗传元件。获得编码有益性状的质粒可以促进在恶劣环境条件下的短期生存或新生态位的长期适应。由于它们在细胞之间转移的能力，质粒被认为是基因转移的试剂。尽管如此，质粒和染色体之间的DNA转移频率仍未得到充分研究。使用一种新的方法来检测基因组对之间的同源基因座，我们发现了1,974（66％）个质粒中与染色体共享的基因，这些质粒位于1,016（78％）个分类差异的分离株中。大多数同源基因座对应于移动元件，可以在宿主染色体中复制数十份。相邻的共享基因通常编码相似的功能类别，表明多基因功能单位的转移。抗生素抗性基因的罕见转移事件主要是通过移动元素观察到的。同源区域中序列相似性的频繁侵蚀表明转移的DNA通常缺乏功能。因此，质粒和染色体之间的DNA转移会产生类似于真核生物进化中内共生基因转移的遗传变异。我们的发现表明，质粒对基因转移的贡献通常对应于质粒实体的转移，而不是质粒和染色体之间蛋白质编码基因的转移。
