Species identification and phylogenetic relationship in Siganidae based on DNA barcoding
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摘要: 为建立篮子鱼科鱼类物种快速鉴定方法,该研究扩增获得了篮子鱼科10种鱼类的46条线粒体COⅠ基因序列,结合从BOLD和GenBank上筛选出的12种27条篮子鱼科COⅠ基因序列,分析篮子鱼科鱼类的COⅠ基因片段序列特征、种间和种内遗传距离及分子系统进化关系。结果表明,19种73条篮子鱼科COⅠ基因序列的平均碱基组成为T:28.9%、C:28.7%、A:24.6%、G:17.8%。G+C的含量(46.5%)低于A+T的含量(53.5%),碱基组成表现出明显的偏倚性;篮子鱼科鱼类的种间平均遗传距离为0.098,是种内平均遗传距离(0.002)的49倍;基于19种篮子鱼科鱼类的COⅠ序列的系统进化分析结果显示,19种篮子鱼中仅单斑篮子鱼(Siganus unimaculatus)和狐篮子鱼(S. vulpinus)聚类在一起,形成1个分支,剩余17种(89.5%)篮子鱼相同种内个体各自聚为一支,形成17个独立的分支。结果表明基于COⅠ基因的DNA条形码技术可应用于篮子鱼科物种鉴定。Abstract: In order to establish a rapid and convenient method for fish species identification of Siganidae, we obtained 46 COⅠ genes from 10 species and downloaded 27 COⅠ genes from 12 species from BOLD and GenBank to study the COⅠ gene's genetic composition, intraspecific and interspecific genetic distance, codon characteristics and molecular phylogenetic tree. The results show that the average base composition of 73 COⅠ genes was T: 28.9%, C: 28.7%, A: 24.6% and G: 17.8%. The content of G+C (46.5%) was lower than the content of A+T (53.5%) and the base composition showed obvious bias. The average interspecific genetic distance was 0.098, which was 49 times the length of the genetic distance within the species (average: 0.002). The phylogenetic tree reveals that Siganus unimaculatus and S. vulpinus clustered into one branch among 19 species of basket fish. The other 17 species (89.5%) clustered in monophyletic groups at genus level. It is shown that the technology of DNA barcoding can be used for fish species identification of Siganidae.
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Key words:
- Siganidae /
- COⅠ gene /
- DNA barcoding
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图 1 NJ 法构建的篮子鱼科鱼类系统进化树
节点上数字显示1 000次重复的bootstrap验证分析中大于50%的支持率;标尺代表遗传距离单位为0.02·百万年–1
Figure 1. NJ tree resulting from analysis of COⅠ gene for 19 Siganidae species
Values higher than 50% bootstrap in 1 000 replications are shown on branches. The scale represents the genetic distance of 0.02 per million years.
表 1 本研究篮子鱼科19种鱼类COⅠ基本信息
Table 1. Information of COⅠ genes from 19 Siganidae species
序号
No.物种
species拉丁名
Latin name样品数目
number of samplesGenbank序列号
GenBank accession No.Gp1 银篮子鱼 Siganus argenteus 2 JQ350365, JQ350364 Gp2 长鳍篮子鱼 Siganus canaliculatus 12 MH469588~MH469599 Gp3 凹吻篮子鱼 Siganus corallinus 2 KP194212, KP194871 Gp4 大瓮篮子鱼 Siganus doliatus 3 KP194691, KF930440, RESIC044-11 Gp5 褐篮子鱼 Siganus fuscescens 3 KY372164, MH469600, MH469601 Gp6 星斑篮子鱼 Siganus guttatus 6 MH469574~MH469579 Gp7 爪哇篮子鱼 Siganus javus 2 KU692888, EU752210 Gp8 截尾篮子鱼 Siganus luridus 3 BIM342-13, BIM364-13, MF409629 Gp9 眼带篮子鱼 Siganus puellus 3 FJ584108, MH469572, MH469573 Gp10 暗体篮子鱼 Siganus punctatissimus 1 KP194669 Gp11 斑篮子鱼 Siganus punctatus 2 MH469570, MH469571 Gp12 金带篮子鱼 Siganus rivulatus 3 KM538561, KM538560, BIM363-13 Gp13 刺篮子鱼 Siganus spinus 5 KJ968266, KP193962, KF930443, MH469602, MH469603 Gp14 白点篮子鱼 Siganus sutor 3 MF409513, MF409582, MF409508 Gp15 单斑篮子鱼 Siganus unimaculatus 3 MH469558, MH469560, MH469561 Gp16 蓝带篮子鱼 Siganus virgatus 8 MH469580~MH469587 Gp17 狐篮子鱼 Siganus vulpinus 5 MH469562~MH469565, MH469557 Gp18 蠕纹篮子鱼 Siganus vermiculatus 3 KF715016.1, KF715017.1, KF715018.1 Gp19 大篮子鱼 Siganus magnificus 4 MH469566~MH469569 注:本研究基因序列为MH469557~MH469558、MH469560~MH469603 Note: The GenBank accession No. are MH469557−MH469558 and MH469560−MH469603 in this study. 表 2 种间/种内遗传距离小于“10×”的物种对
Table 2. Species of interspecific/intraspecific distance ratio less than “10×”
物种1 (种内遗传距离)
Species 1 (intraspecific distance)物种2 (种内遗传距离)
Species 2 (intraspecific distance)种间距离
interspecific distance种间/种内遗传距离比
intraspecific/intraspecific distance凹吻篮子鱼 S. corallinus (0.000) 大瓮篮子鱼 S. doliatus (0.004) 0.016 4.00 大瓮篮子鱼 S. doliatus (0.004) 蓝带篮子鱼 S. virgatus (0.001) 0.008 2.00 单斑篮子鱼 S. unimaculatus (0.002) 狐篮子鱼 S. vulpinus (0.003) 0.002 0.67 单斑篮子鱼 S. unimaculatus (0.002) 大篮子鱼 S. magnificus (0.000) 0.010 5.00 狐篮子鱼 S. vulpinus (0.003) 大篮子鱼 S. magnificus (0.000) 0.010 3.33 -
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