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目的确定副溶血弧菌(Vibrio parahaemolyticus)RIMD2210633与霍乱弧菌(Vibrio cholerae)N16961菌株中超级整合子结构特点差异。方法 (1)使用Perl脚本搜寻RIMD2210633和N16961中superintegron(SI)中核心序列(core segment,CS)和反向核心序列(inverted core segment,ICS);(2)配对核心序列和反向核心序列,获得副溶血弧菌重复序列(V.parahaemolyticus repeat,VPR)及霍乱弧菌重复序列(V.cholerae repeat,VCR)基因组位置信息;(3)使用Perl语言脚本获得副溶血弧菌RIMD2210633以及霍乱弧菌N16961的SI中重复序列,并获得基因盒的构成和分布信息;(4)使用全局比对软件Clustal W将上一步获得的所有VPR和VCR序列进行多序列比对,使用Perl语言脚本处理比对结果以获得一致性序列;(5)使用MEGA 4.0查看多序列比对结果,并使用Perl脚本计算各位置的变异频率,据此结果来分析副溶血RIMD2210633和霍乱弧菌N16961中的弧菌重复序列以及基因盒分布的特点。结果在RIMD2210633的超级整合子鉴定了69个VPR,其核苷酸长度在91～125bp之间。在包含128个核苷酸的一致性序列中,15个为保守核苷酸位点,113个为可变核苷酸位点。在副溶血弧菌的SI中,共确定了64个基因盒,基因盒的长度范围是420～1 709bp,中位数是648bp。在霍乱弧菌N16961的超级整合子中鉴定了158个VCR,长度在117～124bp之间。在包含126个核苷酸的一致性序列中,37个为保守核苷酸位点,89个为可变核苷酸位点。N16961的SI中共存在146个基因盒,基因盒的长度范围是390～5924bp,中位数是1 518bp。结论与霍乱弧菌的VCR相比,副溶血弧菌的VPR可变区序列变异更大,与弧菌重复序列之间序列一致性高的特点不相吻合。
Objective To determine the differences in super integron structural characteristics between Vibrio parahaemolyticus RIMD2210633 and Vibrio cholerae N16961. Methods (1) Perl script was used to search core segment (CS) and inverted core segment (ICS) of superintegron (SI) in RIMD2210633 and N16961; (2) Paired core sequence and reverse core sequence, (VPR) and V. cholerae repeat (VCR) genome were obtained. (3) Vibrio parahaemolyticus RIMD2210633 and Vibrio cholerae were obtained by using Perl script N16961 and obtain the gene cassette configuration and distribution information; (4) Multiple alignment of all the VPR and VCR sequences obtained in the previous step was performed using the global alignment software Clustal W, and the alignment was performed using Perl script (5) Using MEGA 4.0 to examine the results of multiple alignment, and calculating the frequency of variation at each position using Perl script. Based on the results, the Vibrio repeat sequences in the hemolysin RIMD2210633 and V. cholerae N16961 As well as the gene cassette distribution characteristics. Results The super integron in RIMD2210633 identified 69 VPRs with nucleotide lengths between 91 and 125 bp. Of the 128 nucleotide consensus sequences, 15 are conserved nucleotide sites and 113 are variable nucleotide sites. In SI of V. parahaemolyticus, a total of 64 gene cassettes were identified. The length of the gene cassette ranged from 420 to 1 709 bp with a median of 648 bp. 158 VCRs were identified in the super integron of Vibrio cholerae N16961 and range in length from 117 to 124 bp. Of the 126 nucleotide consensus sequences, 37 are conserved nucleotide sites and 89 are variable nucleotide sites. There are 146 gene cassettes in SI of N16961, the length of gene cassette ranged from 390 to 5924 bp, and the median was 1 518 bp. Conclusion Compared with the VCR of Vibrio cholerae, Vibrio parahaemolyticus has more variation in the VPR variable region than the VCR of Vibrio cholerae, which is not consistent with the high sequence identity of Vibrio parahaemolyticus repeats.