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摘要:
目的 研究河弧菌中可移动遗传元件的种类和分布，探究其对河弧菌适应性进化的意义。 方法 从公共数据库中获取170株河弧菌的基因组数据，使用MGEfinder软件识别河弧菌中的可移动遗传元件，并对其种类、插入活性、分布及毒力因子进行研究。 结果 170株河弧菌基因组中共识别到1 227个可移动遗传元件。 这些元件可归类为完整噬菌体、不完整噬菌体、插入序列、含有第二类内含子的元件、含有丝氨酸/酪氨酸重组酶的元件、含有末端重复序列和编码基因的元件、只含有编码基因的元件以及不含任何开放读码框的元件共8类。 317个代表性元件序列簇中有307个转座活性都较低，但高转座活性的可移动遗传元件在河弧菌中分布更广泛。 可移动遗传元件携带的编码基因的功能主要涉及基因复制、重组、修复，以及基因转录等。 可移动遗传元件在环境分离株和临床分离株的分布没有差异。 在插入序列、含有丝氨酸/酪氨酸重组酶的元件、含有末端重复序列和编码基因的元件以及只含有编码基因的元件这4种可移动遗传元件中识别到多种毒力因子，且不同的可移动遗传元件携带的毒力因子不同。 结论 河弧菌含有多种类型、多种功能的可移动遗传元件，表现出以高转座活性可移动遗传元件为主导的适应性进化特征。 Abstract:Objective To evaluate the types and distribution of mobile gene elements (MGEs) in the genome of Vibrio fluvialis and investigate their significance for the adaptive evolution of V. fluvialis. Methods The publicly available genomes of 170 V. fluvialis strains were downloaded from NCBI SRA database, and MGEfinder was used to identify the MGEs in the genomes of V. fluvialis, and the diversity, insertion activity, distribution and virulence genes of MGEs were studied. Results A total of 1 227 MGEs were identified in 170 strains of V. fluvialis, including intact phage, questionable/incomplete phage, insertion element (IS element), group II intron, serine/tyrosine recombinase, containing CDS and TIR, coding gene sequences (CDS) and open reading frame-free sequences (No CDS). Among the 317 unique insertion clusters, 307 had low transposition activity, but the MGEs with high transposition activity were distributed more widely in V. fluvialis. The functions of coding genes carried by MGEs mainly involved gene duplication, duplication, repair, and gene transcription. The distribution of MGEs had no difference between environmental and clinical isolates of V. fluvialis. A variety of virulence factors were identified in four MGEs, including insertion elements, serine/tyrosine recombinase, containing CDS and TIR, and coding gene sequences, and the virulence factors carried by different MGEs were different. Conclusion V. fluvialis possess various types and functions of MGEs and exhibits adaptive evolutionary characteristics dominated by MGEs with high transposition activity. -
Key words:
- Vibrio fluvialis /
- Mobile genetic elements /
- Horizontal gene transfer /
- Virulence /
- Survival
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图 1 MGEfinder识别的河弧菌中可移动遗传元件的G＋C含量和种类
注：A. 河弧菌可移动遗传元件与基因组的G＋C含量比较；B. 可移动遗传元件的分类；a. P<0.001
Figure 1. G＋C content and types of MGEs identified by MGEfinder workflow in V. fluvialis
图 2 河弧菌可移动遗传元件的转座活性
注：A. 代表性元件序列簇的转座活性；B. 不同转座活性的代表性元件序列簇的构成比例；C. 不同转座活性的代表性元件序列簇的序列长度；D. 不同转座活性的代表性元件序列簇在河弧菌中的分布；a. P<0.001
Figure 2. Transposition activity of mobile genetic elements in V. fluvialis
图 3 河弧菌泛基因组和可移动遗传元件编码基因的COG功能分类
注：A. 河弧菌泛基因组编码基因的COG功能分类；B. 河弧菌可移动遗传元件编码基因的COG功能分类
Figure 3. COG functional classifications of genes encoding pan-genome and mobile genetic elements in V. fluvialis
图 4 可移动遗传元件在河弧菌基因组中的分布
注：参考菌株ATCC33809使用箭头标示出
Figure 4. Distribution of mobile genetic elements in genome of V. fluvialis
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