MOLECULAR PHYLOGENY OF ACIPENSERIFORMES BASED ON COMPLETE MITOCHONDRIAL GENOME SEQUENCE
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摘要: 为厘清鲟形目鱼类的系统发育, 研究新测定了中华鲟(Acipenser sinensis)、长江鲟(A. dabryanus)、短吻鲟(A. brevirostrum)、纳氏鲟(A. naccarii)、鳇(Huso dauricus)和匙吻鲟(Polyodon spathula)共6种鲟类的线粒体全基因组序列。联合已测的17种鲟类的线粒体基因组数据, 利用最大似然法和贝叶斯法重建了鲟形目鱼类的分子系统发育关系, 并采用似然值检验对不同的树拓扑结构进行了评价。结果表明, 6种新测鲟类的线粒体基因组大小为16521—16766 bp, 编码13个蛋白质编码基因、22个转运RNA基因和2个核糖体基因, 与大多数已测的鲟类的线粒体基因组结构高度相似。基于23种鲟形目鱼类线粒体基因组数据, 系统发育分析的结果表明: (1)鲟形目的两个科, 匙吻鲟科(Polyodontidae)和鲟科(Acipenseridae)均为单系; (2)鲟科的内部亲缘关系复杂, 鲟属和鳇属的物种均不构成单系群。鲟科鱼类按分子系统发育重建结果可以分为3个类群: 尖吻鲟类(A. sturio - A. oxyrinchus clade)、大西洋鲟类(Atlantic clade)和太平洋鲟类(Pacific clade)。树拓扑结构的检验结果表明, 鲟科的系统发育关系为(尖吻鲟类(太平洋鲟类, 大西洋鲟类))。铲鲟属(Scaphirhynchus)是大西洋鲟类的基部类群。研究也说明线粒体基因组数据在鲟形目鱼类系统与进化研究方面具有重要应用价值。Abstract: In this study, six complete mitochondrial genomes of Acipenseriforemes (Acipenser sinensis, A. dabryanus, A. brevirostrum, A. naccarii, Huso dauricus and Polyodon spathula) were successfully assembled. Based on 6 novel mitogenomes and 17 previously published mitogenomes of sturgeons and paddlefishes, the molecular phylogeny of Acipenseriformes was constructed by maximum likelihood and Bayesian method, and the tree topologies were evaluated by likelihoods value test. The results showed that the length of entire mitochondrial genomes of the six species were 16521—16766 bp, encoding 13 protein-coding genes, 22 tRNA genes and two rRNA gene, which were similar to those of other sturgeons and paddlefishes. Molecular phylogenetic analyses showed that (i) the Acipenseriformes contained two monophyly families (Polyodontidae and Acipenseridae); (ii) genus Huso and Acipenser were demonstrated as non-monophyletic and the family Acipenseridae can be divided into 3 subgroups: A. sturio-A. oxyrinchus clade, Atlantic clade and Pacific clade. Tree topology tests indicated that the phylogenetic relationship of the subfamily Acipenseridae is [A. sturio-A. oxyrinchus clade (Pacific clade, Atlantic clade)]. The species of genus Scaphirhynchus has occupied the basal position of the Atlantic clade in Acipenseridae. This study showed that mitochondrial genome data has important application value in the systematic and evolutionary study of Acipenseriformes.
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Keywords:
- Mitochondrial genome /
- Acipenseriformes /
- Phylogeny /
- Maximum likelihood /
- Bayesian method /
- Tree topology test
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图 1 基于23种鲟形目鱼类的线粒体全基因组(Com_Mito)构建的贝叶斯法和最大似然法的系统发育树(节点前数字表示BI后验支持率及ML自展数)
Figure 1. Baysian and ML phylogenetic tree based on 23 complete mitochondrial genomes nucleotide sequences
表 1 新测6种鲟形目鱼类的线粒体基因组长度及碱基组成
Table 1 Total length and base composition of mitochondrial genomes of six sequenced Acipenseriforme fishes
物种名
SpeciesGenBank登录号
GenBank accession number总长
Total length (bp)GC含量
GC content (%)AT-
偏斜
AT-skewGC-
偏斜
GC-skew中华鲟Acipenser sinensis MK078261 16,524 45.98 0.117 −0.284 长江鲟A. dabryanus MK078262 16,439 46.07 0.120 −0.287 短吻鲟A. brevirostrum MK078263 16,596 45.63 0.112 −0.285 纳氏鲟A. naccarii MK078265 16,759 45.23 0.109 −0.285 鳇Huso dauricus MK078264 16,766 45.26 0.113 −0.290 匙吻鲟Polyodon spathula MK078260 16,521 45.36 0.126 −0.316 
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表 2 不同数据集、不同方法获得的鲟形目鱼类的系统发育结果
Table 2 Phylogenetic relationships within order Acipenseriforme based on different dataset
系统发育关系Phylogenetic topology Pro AA Pro_2 rRNA 2 rRNA Com_Mito BI ML BI ML BI ML BI ML BI ML 匙吻鲟科是单系群Polyodontidae is a monophyletic subfamily 1.00 100 1.00 100 1.00 100 1.00 100 1.00 100 鲟科是单系群Acipenseridae is a monophyletic subfamily 1.00 100 1.00 100 1.00 100 1.00 100 1.00 100 鲟属是单系群Acipenser is a monophyletic genus — — — — — — — — — — 鳇属是单系群Huso is a monophyletic genus — — — — — — — — — — 铲鲟属是单系群Scaphirhynchus is a monophyletic genus 1.00 100 1.00 100 1.00 100 1.00 99 1.00 100 尖吻鲟类是单系群A. sturio-A. oxyrinchus cluster is a monophyletic group 1.00 100 1.00 100 1.00 100 1.00 100 1.00 100 尖吻鲟类是鲟科的基部类群A. sturio-A. oxyrinchus cluster is the basal lineage of Acipenseridae 1.00 100 1.00 100 1.00 100 — — 1.00 100 铲鲟属是鲟科的基部类群Scaphirhynchus is the basal lineage of Acipenseridae — — — — — — 1.00 100 — — 大西洋鲟类是单系群Atlantic clade is a monophyletic group 1.00 86 1.00 87 1.00 96 — — 1.00 99 太平洋鲟类是单系群Pacific clade is one monophyletic group 1.00 100 1.00 95 1.00 100 0.98 78 1.00 100 铲鲟属是大西洋鲟类的基部类群Scaphirhynchus is the basal group of Atlantic clade 1.00 86 — — 1.00 96 — — 1.00 99 (大西洋鲟类, 太平洋鲟类)(A. sturio-A. oxyrinchus cluster, Pacific clade) 0.99 70 0.98 54 0.97 71 0.31 36 0.96 79 闪光鲟是大西洋鲟类基部类群A. stellatus is the basal group of Atlantic clade — — 1.00 — — — — — — — (H. dauricus (A. medirostris, A. mikadoi))(A. dabryanus, A. sinensis) (A. transmontanus, A. schrenckii) 1.00 100 1.00 95 1.00 100 0.98 78 1.00 100 ((A. nudiventris, A. ruthenus) A. stellatus) (A. fulvescens (A. brevirostrum (A. baerii (A. naccarii, A. gueldenstaedtii)))) 1.00 — — — 1.00 100 — — 1.00 100
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表 3 系统发育树拓扑结构检验结果
Table 3 Results of topological tests for five phylogenetic trees
数据集Dataset 拓扑结构Treetopology −ln
likelihoodSH WKH WSH AU Pro Com_Mitogenome_BI+ML −42355.2 0.83 0.31 0.72 0.28 Pro_ML −42352.8 1.00 0.69 0.96 0.72 AA_BI −42559.2 0 0 0 0 AA_ML −42514.7 0 0 0 0 2 rRNA_BI+ML −42503.5 0 0 0 0 AA Com_Mitogenome_BI+ML −14865.7 0.48 0.17 0.52 0.06 Pro_ML −14862.9 0.61 0.34 0.71 0.39 AA_BI −14857.9 1.00 0.53 0.79 0.65 AA_ML −14859.3 0.78 0.47 0.78 0.47 2 rRNA_BI+ML −14888.5 0.03 0.02 0.04 0 Pro_2 rRNA Com_Mitogenome_BI+ML −52330.1 1 0.94 1 0.96 Pro_ML −52336.9 0.67 0.06 0.20 0.04 AA_BI −52608.3 0 0 0 0.02 AA _ML −52546.3 0 0 0 0.01 2 rRNA_BI+ML −52465.9 0 0 0 0 2 rRNA Com_Mitogenome_BI+ML −5930.6 0.37 0.14 0.32 0.09 Pro_ML −5935.6 0.21 0.04 0.10 0 AA _BI −5981.2 0 0 0 0 AA _ML −5975.5 0 0 0 0 2 rRNA_BI+ML −5920.4 1.00 0.87 0.97 0.94 Com_Mito Com_Mitogenome_BI+ML −57626.0 1.00 0.95 1.00 0.94 Pro_ML −57633.6 0.68 0.05 0.15 0.06 AA _BI −57913.2 0 0 0 0 AA _ML −57853.5 0 0 0 0 2rRNA_BI+ML −57763.6 0 0 0 0
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