Species composition and distribution characteristic of fish eggs and larvae based on DNA barcoding technology of the Zhujiang River Estuary in spring
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摘要: 采用线粒体COⅠ和12S rRNA基因片段作为DNA条形码，分析珠江口春季鱼卵和仔稚鱼种类组成和分布特征，并探究两种条形码在鱼卵和仔稚鱼种类鉴定中的适用性。研究共扩增样本391个，成功鉴定的鱼卵和仔稚鱼共7目25科42属60种（2种未鉴定到种）。其中，以鲈形目（Perciformes）种类和数量最多，种类数占比为51.6%，数量占比为47.91%；其次为鲱形目（Clupeiformes），种类数占比为25%，数量占比为34.56%。优势种10种，其中凤鲚（Coilia mystus）优势度最高，为0.071；棘头梅童鱼（Collichthys lucidus）最低，为0.014。COⅠ和12S rRNA基因片段扩增结果显示，鱼卵和仔稚鱼12S rRNA基因片段扩增成功率（95.60%）明显高于COⅠ基因（43.22%）。遗传距离和ABGD分析显示，COⅠ基因种内遗传距离为0～0.005（平均0.003），种间遗传距离为0.061～0.376（平均0.253），两者间存在明显的“条形码间隙”，ABGD划分结果与数据库比对结果一致；12S rRNA基因种内遗传距离为0～0.011（平均0.007），种间遗传距离为0.007～0.487（平均0.283），龟鰉（Chelon haematocheila）和前鳞龟鰉（Chelon affinis）种间遗传距离与种内遗传距离不形成“条形码间隙”，ABGD将其划分为同一种。系统发育分析显示，在种的分类阶元，所有物种均能聚为独立分支，得到有效区分。综上，线粒体COⅠ和12S rRNA条形码可有效鉴定珠江口大多数鱼卵和仔稚鱼，但是COⅠ基因扩增成功率较低，12S rRNA基因部分近缘物种存在区分困难的情况，两种基因结合使用更能提高鱼卵和仔稚鱼种类鉴定的成功率和准确性。
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关键词:
- COⅠ基因 /
- 12S rRNA基因 /
- 鱼卵和仔稚鱼 /
- DNA条形码
Abstract: In order to improve the success rate and accuracy of species identification of fish eggs and larvae, fish eggs and larvae samples collected from the Zhujiang River Estuary in spring were identified by DNA barcoding technology based on the mitochondrial COⅠand 12S rRNA genes. A total of 391 samples were amplified and 60 species in 7 orders, 25 families, 42 genera were successfully identified (2 species were not identified). Among them, Perciformes had the most species and quantity accounting for 51.6% and 47.91% respectively, followed by Clupeiformes with 25% and 34.56% respectively. There were 10 dominant species, among which Coilia mystus had the highest dominance of 0.071, Collichthys lucidus had the lowest dominance of 0.014. The amplification results of COⅠand 12S rRNA gene fragments showed that the success rate of 12S rRNA gene amplification in eggs and larvae (95.60%) was significantly higher than that of COⅠgene (43.22%). Genetic distance and ABGD analysis showed that the intraspecies genetic distance of COⅠ gene was 0−0.005 (average was 0.003), and the interspecific genetic distance was 0.061−0.376 (average was 0.253), and there was an obvious “barcode gap” between them. The intraspecific genetic distance of 12S rRNA gene was 0−0.011 (average was 0.007), and the interspecific genetic distance was 0.007−0.487(average was 0.283). which do not form a “barcode gap” between the interspecific and intraspecies genetic distances. The Bayesian phylogenetic tree based on COⅠ and 12S rRNA genes showed that all species could be clustered into independent branches and can be effectively distinguished. The above results show that both COⅠ gene and 12S rRNA gene can be used for the identification of most fish eggs and larvae, but the success rate of COⅠ gene amplification is low, and it is difficult to distinguish some closely related species of 12S rRNA gene. The combined use of the two genes can improve the success rate and accuracy of species identification of fish eggs and larvae.-
Key words:
- COⅠgene /
- 12S rRNA gene /
- fish eggs and larvae /
- DNA barcoding
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图 2 ABGD方法对COⅠ序列（a）和12S rRNA序列（b）的划分结果
Fig. 2 Partition results of COⅠ sequence (a) and 12S rRNA sequence (b) by ABGD method
图 3 基于COⅠ序列构建的系统发育树
ABGD的DNA鉴定与比对鉴定物种数目一致，未用红点显示出
Fig. 3 Phylogenetic tree based on COⅠ sequences
The DNA identification from ABGD is consistent with the number of identified species and are not displayed through the red dot
图 4 基于12S rRNA序列构建的系统发育树
ABGD的DNA鉴定通过红色圆点显示在外围
Fig. 4 Phylogenetic tree based on 12S rRNA sequences
The DNA identification from ABGD is displayed on the periphery through the red dot
表 1 具体采样时间和站位
Tab. 1 Specific sampling time and stations
站位 采样时间 水深/m 表层盐度 D1 2020年4月3日 24 1.45 D2 2020年4月3日 15 7.85 D3 2020年4月2日 6 6.95 D4 2020年4月2日 10 25.6 D5 2020年4月1日 6.5 8 D6 2020年4月1日 9 23.57 D7 2020年4月1日 24 32.52 D8 2020年3月31日 13 28.82 D9 2020年3月31日 18 27.82 
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表 2 不同站位鱼卵及仔稚鱼种类和数量
Tab. 2 Species and quantity of eggs and larvae at different stations
站位 总扩增数 有效数 种类数 鱼卵 仔稚鱼 鱼卵 仔稚鱼 鱼卵 仔稚鱼 D1 42 4 42 4 5 3 D2 39 0 38 0 9 0 D3 31 17 28 17 14 7 D4 40 0 40 0 15 0 D5 40 8 40 8 14 4 D6 40 1 40 1 20 1 D7 42 0 42 0 18 0 D8 40 5 36 5 18 3 D9 38 4 37 4 10 4 总计 352 39 343 39 52 15
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表 3 珠江口春季鱼卵及仔稚鱼种类组成和数量分布
Tab. 3 Species composition and quantity distribution of fish eggs and larvae in Zhujiang River Estuary in spring
目 科 属 种 样本量/个 相似度/% 站位 12S rRNA COⅠ D1 D2 D3 D4 D5 D6 D7 D8 D9 鲱形目
Clupeiformes锯腹鳓科
Pristigasteridae鳓属
Ilisha鳓鱼
Ilisha elongata1 100 99.85 ─ ─ ─ ─ ─ ─ ─ ○ ─ 鳀科
Engraulidae棱鳀属
Thryssa黄吻棱鳀
Thryssa vitrirostris6 100 99.82 ○ ─ ─ ○ ─ ○ ─ ○ ─ 赤鼻棱鳀
Thryssa kammalensis6 100 ─ ─ ─ ─ ─ ─ ○ ◎ ─ ─ 杜氏棱鳀
Thryssa dussumieri4 100 99.85 ─ ─ ─ ─ ○ ○ ○ ─ ─ 汉氏棱鳀
Thryssa hamiltonii1 100 100 ─ ─ ─ ○ ─ ─ ─ ─ ─ 侧带小公鱼属
Stolephorus岛屿侧带小公鱼
Stolephorus insularis20 100 100 ─ ─ ○ ─ ○ ○ ◎ ◎ ─ 康氏侧带小公鱼
Stolephorus commersonnii1 100 99.40 ─ ─ ─ ○ ─ ─ ─ ─ ─ 鲚属
Coilia凤鲚
Coilia mystus61 100 100 ● ○ ◎ ─ ◎ ─ ─ ─ ─ 鲱科
Clupeidae小沙丁鱼属
Sardinella黄泽小沙丁鱼
Sardinella lemuru17 100 ─ ─ ─ ◎ ◎ ○ ○ ─ ○ ─ 隆背小沙丁鱼
Sardinella gibbosa4 100 ─ ─ ─ ─ ─ ─ ─ ○ ─ ─ 裘氏小沙丁鱼
Sardinella jussieu2 100 ─ ─ ─ ○ ─ ─ ─ ─ ─ ○ 斑鰶属
Konosirus斑鰶
Konosirus punctatus1 99 ─ ─ ─ ─ ─ ─ ○ ─ ─ ─ 海鰶属
Nematalosa日本海鰶
Nematalosa japonica2 100 100 ─ ─ ─ ─ ─ ─ ○ ─ ─ 高鼻海鰶
Nematalosa nasus1 100 100 ─ ─ ─ ○ ─ ─ ─ ─ ─ 鰶属
Clupanodon花鰶
Clupanodon thrissa5 100 ─ ○ ─ ○ ─ ─ ─ ─ ─ ─ 胡瓜鱼目
Osmeriformes胡瓜鱼科
Osmeridae银鱼属
Salanx居氏银鱼
Salanx cuvieri1 99 99.69 ○ ─ ─ ─ ─ ─ ─ ─ ─ 仙女鱼目
Aulopiformes狗母鱼科
Synodontidae蛇鲻属
Saurida多齿蛇鲻
Saurida tumbil2 100 99.84 ─ ─ ─ ─ ─ ○ ○ ─ ─ 龙头鱼属
Harpadon龙头鱼
Harpadon nehereus1 100 100 ─ ─ ─ ─ ─ ─ ○ ─ ─ 鲻形目
Mugiliformes鲻科
Mugilidae莫鲻属
Moolgarda长鳍莫鲻
Moolgarda cunnesius6 100 100 ─ ─ ○ ─ ─ ○ ─ ○ ○ 龟鰉属
Chelon龟鰉
Chelon haematocheila9 100 100 ○ ◎ ─ ─ ─ ─ ─ ─ ─ 前鳞龟鰉
Chelon affinis1 100 100 ─ ─ ─ ─ ─ ─ ─ ─ ○ 鲉形目Scorpaeniformes 鲉科
Scorpaenidae鬼鲉属
Inimicus日本鬼鲉
Inimicus japonicus1 100 99.84 ─ ─ ─ ○ ─ ─ ─ ─ ─ 鲬科
Platycephalidae鳄鲬属
Cociella鳄鲬
Cociella crocodilus2 100 100 ─ ─ ─ ─ ○ ─ ─ ○ ─ 瞳鲬属
Inegocia日本瞳鲬
Inegocia japonica9 100 100 ─ ─ ○ ─ ─ ─ ◎ ─ ─ 鲈形目
Perciformes双边鱼科
Ambassidae双边鱼属
Ambassis裸头双边鱼
Ambassis gymnocephalus11 100 100 ○ ○ ─ ◎ ─ ─ ─ ─ ─ 鮨科
Serranidae石斑鱼属
Epinephelus斑带石斑鱼
Epinephelus fasciatomaculosus3 100 ─ ─ ─ ─ ─ ─ ○ ─ ○ ─ 天竺鲷科
Apogonidae天竺鲷属
Apogon宽条天竺鲷
Apogon fasciatus1 100 100 ─ ─ ─ ─ ─ ─ ─ ○ ─ 鱚科
Sillaginidae鱚属
Sillago多鳞鱚
Sillago sihama5 100 100 ─ ○ ─ ─ ○ ○ ─ ○ ○ 少鳞鱚
Sillago japonica1 100 100 ─ ─ ─ ─ ─ ○ ─ ─ ─ 鲾科
Leiognathidae项鲾属
Nuchequula项斑项鲾
Nuchequula nuchalis18 100 100 ─ ○ ○ ◎ ○ ○ ○ ◎ ○ 光胸鲾属
Photopectoralis黄斑光胸鲾
Photopectoralis bindus4 100 100 ─ ○ ─ ○ ─ ─ ─ ─ ─ 银鲈科
Gerreidae银鲈属
Gerres红尾银鲈
Gerres erythrourus6 100 100 ─ ○ ─ ○ ─ ○ ─ ○ ─ 仿石鲈科
Haemulidae少棘胡椒鲷属
Diagramma密點少棘胡椒鲷
Diagramma picta8 100 100 ─ ─ ─ ─ ○ ○ ○ ─ ─ 矶鲈属
Parapristipoma三线矶鲈
Parapristipoma trilineatum2 100 100 ─ ─ ─ ─ ○ ─ ○ ─ ─ 金线鱼科
Nemipteridae金线鱼属
Nemipterus日本金线鱼
Nemipterus japonicus28 100 100 ─ ─ ○ ─ ○ ○ ○ ─ ● 鲷科
Sparidae棘鲷属
Acanthopagrus灰鳍棘鲷
Acanthopagrus berda1 100 100 ─ ─ ─ ─ ─ ─ ─ ○ ─ 黑棘鲷
Acanthopagrus schlegelii4 100 100 ─ ─ ○ ○ ○ ─ ─ ─ ─ 太平洋棘鲷
Acanthopagrus pacificus12 99 100 ─ ─ ○ ○ ○ ○ ─ ─ ○ 石首鱼科
Sciaenidae3 87.5 ─ ─ ─ ○ ○ ○ ─ ─ ─ ─ 牙鱛属
Otolithes红牙鱛
Otolithes ruber3 100 99.64 ─ ─ ○ ─ ─ ─ ─ ○ ○ 黄姑鱼属
Nibea黄姑鱼
Nibea albiflora3 100 100 ─ ─ ─ ─ ─ ─ ─ ○ ○ 梅童鱼属
Collichthys棘头梅童鱼
Collichthys lucidus24 100 100 ○ ● ─ ─ ─ ─ ─ ─ ─ 白姑鱼属
Pennahia截尾白姑鱼
Pennahia anea1 99 ─ ─ ─ ─ ─ ─ ─ ○ ─ ─ 叫姑鱼属
Johnius叫姑鱼
Johnius grypotus18 100 ─ ─ ○ ○ ─ ◎ ○ ─ ○ ─ 卡氏叫姑鱼
Johnius carouna4 100 99.83 ─ ─ ○ ─ ─ ○ ─ ○ ─ 皮氏叫姑鱼
Johnius belangerii5 100 ─ ─ ─ ─ ○ ─ ─ ○ ○ ─ 屈氏叫姑鱼
Johnius trewavasae3 100 ─ ─ ─ ─ ─ ○ ─ ○ ○ ─ 枝鳔石首鱼属
Dendrophysa勒氏枝鳔石首鱼
Dendrophysa russelii1 100 99.85 ─ ─ ─ ○ ─ ─ ─ ─ ─ 隆头鱼科
Labridae海猪鱼属
Halichoeres黑带海猪鱼
Halichoeres nigrescens4 100 100 ─ ─ ─ ─ ─ ─ ─ ○ ○ 鳚科
Blenniidae宽颌鳚属
Laiphognathus长棘宽颌鳚
Laiphognathus longispinis1 100 100 ─ ─ ─ ─ ─ ─ ─ ─ ○ 肩鳃鳚属
Omobranchus斑头肩鳃鳚
Omobranchus fasciolatoceps1 100 99.69 ─ ─ ○ ─ ─ ─ ─ ─ ─ 斑點肩鰓鳚
Omobranchus punctatus1 ─ 99.84 ─ ─ ─ ─ ─ ─ ─ ─ ○ 鴨科
Callionymidae斜棘鴨属
Repomucenus斜棘鴨属未定种
Repomucenus sp.1 100 100 ─ ─ ○ ─ ─ ─ ─ ─ ─ 虾虎鱼科
Gobiidae狼牙虾虎鱼属
Odontamblyopus红狼牙虾虎鱼
Odontamblyopus rubicundus5 100 ─ ─ ─ ○ ─ ○ ─ ─ ─ ─ 鲳科
Stromateidae鲳属
Pampus灰鲳
Pampus cinereus1 100 ─ ─ ─ ─ ─ ─ ○ ─ ─ ─ 鲽形目
Pleuronectiformes鳎科
Soleidae鳎属
Solea卵鳎
Solea ovata12 100 100 ─ ─ ○ ◎ ─ ○ ○ ─ ○ 舌鳎科
Cynoglossidae舌鳎属
Cynoglossus中华舌鳎
Cynoglossus sinicus14 100 ─ ─ ─ ○ ─ ○ ◎ ─ ○ ─ 长体舌鳎
Cynoglossus lingua1 100 ─ ─ ─ ─ ─ ─ ─ ○ ─ ─ 斑头舌鳎
Cynoglossus puncticeps1 100 ─ ─ ─ ─ ─ ─ ─ ○ ─ ─ 巨鳞舌鳎
Cynoglossus macrolepidotus7 100 100 ─ ─ ─ ─ ─ ○ ─ ○ ◎ 注：●表示本种类在本站位数量占比为50%～100%；◎表示本种类在本站位数量占比为10%～50%；○表示本种类在本站位数量占比为0～10%（不包括0）；─表示未扩增成功或本种类在本站位无。
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