地山雀、黄腹山雀和红头长尾山雀线粒体全基因组序列测定和分析
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摘要
基于长距PCR扩增及保守引物步移法测定并注释了地山雀(Pseudopodoces humilis)、黄腹山雀(Parus venustulus)和红头长尾山雀(Aegithalos concinnus)线粒体全基因组序列,并联合GenBank已收录的鸟类线粒体全基因组的数据和本室已测5种雀形目鸟类,以线粒体蛋白质编码基因作为分子标记,研究了雀形目鸟类的系统发育关系,并探讨不同数据集对系统发育关系的有效性。主要结果如下：
1、地山雀、黄腹山雀和红头长尾山雀线粒体全基因组长度分别为16809 bp、16780 bp和17926 bp；均编码13个蛋白质基因(COⅠ-Ⅲ、Cyt b、ATP8、ATP6、ND1-4和(ND4L),22个tRNA基因,2个rRNA和1-2个A+T富集区,其中地山雀与黄腹山雀为一个A+T富集区,而红头长尾山雀则含有两个A+T富集区。
2、3种鸟类线粒体全基因组的碱基组成A+T偏向性无明显统计学差异。其中,红头长尾山雀A+T偏向性程度最高,A+T含量为54.1%,黄腹山雀最低,A+T含量为52%,地山雀居中,为52.9%。
3、3种鸟类起始密码子方面：除地山雀和红头长尾山雀的COⅠ基因起始密码子为GTG外,3种鸟类的其余蛋白编码基因起始密码子均为典型的ATG；终止密码子方面：除COⅢ和ND4基因为不完全的终止密码子T外,其他蛋白编码基因均为完整的终止密码子,并且为典型的鸟类终止密码子TAA,AGG,AGA和TAG。
4、3种鸟类的tRNASer(AGN)基因均缺失DHU臂,其余均能形成典型三叶草型二级结构。3种鸟的tRNA二级结构中均有一定数目碱基错配的现象发生,大部分为G-U错配。
5、3和鸟的srRNA和lrRNA基因全序列的二级结构预测发现,rRNA的二级结构十分保守：srRNA二级结构均包含四个结构域,47个茎区；lrRNA二级结构均包含六个结构域,60个茎区。
6、对17种鸟类线粒体ND3基因序列174位点进行了比对分析研究,发现13种雀形目鸟类线粒体ND3基因174位点处均无碱基胞嘧啶的插入。
7、确定了13种雀形目鸟类的AT富集区的中央保守区,同时对CSB-1结构域进行了分析,发现雀形目鸟类控制区CSB-1结构域较红原鸡相比均多出一段长度为18-20bp的插入序列。
8、将线粒体全基因组中蛋白质编码基因分成3个数据集对雀形目鸟类进行了系统发育分析：所得结果支持将鸟类分成鸣禽亚目和亚鸣禽亚目两大类；支持将鸣禽亚目划分成鸦小目和雀小目；支持将长尾山雀属单列为科；确定莺总科并非为单系；建议将琴鸟科归为鸣禽亚目的鸦小目；验证地山雀并非与鸦科亲缘关系较近。
The complete sequence of Pseudopodoces humilis, Parus venustulus and Aegithalos concinnus mitochondrial genomes were determined by using long PCR and conserved primers walking approaches. The three new complete mitochondrial genomes combined with others included in GenBank, as well as other two Passeriformes complete mitochondrial genomes were accomplished in our laboratory, were used to phylogenomic analysis for Passeriformes based on protein conding genes and investigated phylogenetic utility in every data sets.
1. The complete mitochondrial genomes of Pseudopodoces humilis, Parus venustulus and Aegithalos concinnus are 16809 bp,16780 bp and 17926 bp in length, respectively, and encode 13 protein genes (COI--Ⅲ、Cytb、ATP8、ATP6、ND1—4 and ND4L),22 tRNA genes,2 rRNA genes, and 1-2 A+T rich regions。
2. The A+T content of Pseudopodoces humilis, Parus venustulus and Aegithalos concinnus mitochondrial genome has not significently biased statistically. The highest A+T biase is found in Aegithalos concinnus which is only 54.1%, the lowest found in Parus venustulus which is only 52% too, the value of Pseudopodoces humilis is 52.9%.
3. For start codons, except COI in Pseudopodoces humilis and Aegithalos concinnus with GTG, the other protein genes in three Aves are all with the typical start codons ATG; for stop codons, except the COⅢand ND4 genes had shorttened stop codons T, the other genes are all have the typical stop codons TAA, AGG, AGA or TAG.
4. All the tRNA genes of Pseudopodoces humilis, Parus venustulus and Aegithalos concinnus mitochondrial genomes have the typical clover leaf structure except the tRNA Ser(AGN) gene, which is lack of the DHU arm in their secondary structure. There are some G-U mispair from the secondary structure in all three Aves.
5. The secondary structures of complete rRNAs have been predicted for Pseudopodoces humilis, Parus venustulus and Aegithalos concinnus. Most parts of the secondary structure are conserved in the three aves species, the main differences took place in terminal regions.
6. Through analyzing the aligned the 174 site of the ND3 gene in 17 Aves, we found the 13 species from Passeriformes involved in this paper all do not have the C base insert.
7. Through analyzing the aligned A+T-rich regions, we determined the central conserved region, and found that the CSB-1 region in all 13 Passeriformes have 18-20 bp sequence insert compared with Gallus gallus.
8. The protein coding genes were partitioned into three data sets and applied to reconstruct the phylogenetic relationships of Passeriformes. The phylogenetic trees from different methods and data sets agreed that Passeriformes divide two groups Passeri and Tyranni, and Passeri include the Corvida and Passerida. The result also support Aegithalos as a section level separately, Menuridae belongs to Corvida, Sylvioidea is not a monophyletic group; Pseudopodoces humilis have not closely relationships with species of Corvidae.
1、地山雀、黄腹山雀和红头长尾山雀线粒体全基因组长度分别为16809 bp、16780 bp和17926 bp；均编码13个蛋白质基因(COⅠ-Ⅲ、Cyt b、ATP8、ATP6、ND1-4和(ND4L),22个tRNA基因,2个rRNA和1-2个A+T富集区,其中地山雀与黄腹山雀为一个A+T富集区,而红头长尾山雀则含有两个A+T富集区。
2、3种鸟类线粒体全基因组的碱基组成A+T偏向性无明显统计学差异。其中,红头长尾山雀A+T偏向性程度最高,A+T含量为54.1%,黄腹山雀最低,A+T含量为52%,地山雀居中,为52.9%。
3、3种鸟类起始密码子方面：除地山雀和红头长尾山雀的COⅠ基因起始密码子为GTG外,3种鸟类的其余蛋白编码基因起始密码子均为典型的ATG；终止密码子方面：除COⅢ和ND4基因为不完全的终止密码子T外,其他蛋白编码基因均为完整的终止密码子,并且为典型的鸟类终止密码子TAA,AGG,AGA和TAG。
4、3种鸟类的tRNASer(AGN)基因均缺失DHU臂,其余均能形成典型三叶草型二级结构。3种鸟的tRNA二级结构中均有一定数目碱基错配的现象发生,大部分为G-U错配。
5、3和鸟的srRNA和lrRNA基因全序列的二级结构预测发现,rRNA的二级结构十分保守：srRNA二级结构均包含四个结构域,47个茎区；lrRNA二级结构均包含六个结构域,60个茎区。
6、对17种鸟类线粒体ND3基因序列174位点进行了比对分析研究,发现13种雀形目鸟类线粒体ND3基因174位点处均无碱基胞嘧啶的插入。
7、确定了13种雀形目鸟类的AT富集区的中央保守区,同时对CSB-1结构域进行了分析,发现雀形目鸟类控制区CSB-1结构域较红原鸡相比均多出一段长度为18-20bp的插入序列。
8、将线粒体全基因组中蛋白质编码基因分成3个数据集对雀形目鸟类进行了系统发育分析：所得结果支持将鸟类分成鸣禽亚目和亚鸣禽亚目两大类；支持将鸣禽亚目划分成鸦小目和雀小目；支持将长尾山雀属单列为科；确定莺总科并非为单系；建议将琴鸟科归为鸣禽亚目的鸦小目；验证地山雀并非与鸦科亲缘关系较近。
The complete sequence of Pseudopodoces humilis, Parus venustulus and Aegithalos concinnus mitochondrial genomes were determined by using long PCR and conserved primers walking approaches. The three new complete mitochondrial genomes combined with others included in GenBank, as well as other two Passeriformes complete mitochondrial genomes were accomplished in our laboratory, were used to phylogenomic analysis for Passeriformes based on protein conding genes and investigated phylogenetic utility in every data sets.
1. The complete mitochondrial genomes of Pseudopodoces humilis, Parus venustulus and Aegithalos concinnus are 16809 bp,16780 bp and 17926 bp in length, respectively, and encode 13 protein genes (COI--Ⅲ、Cytb、ATP8、ATP6、ND1—4 and ND4L),22 tRNA genes,2 rRNA genes, and 1-2 A+T rich regions。
2. The A+T content of Pseudopodoces humilis, Parus venustulus and Aegithalos concinnus mitochondrial genome has not significently biased statistically. The highest A+T biase is found in Aegithalos concinnus which is only 54.1%, the lowest found in Parus venustulus which is only 52% too, the value of Pseudopodoces humilis is 52.9%.
3. For start codons, except COI in Pseudopodoces humilis and Aegithalos concinnus with GTG, the other protein genes in three Aves are all with the typical start codons ATG; for stop codons, except the COⅢand ND4 genes had shorttened stop codons T, the other genes are all have the typical stop codons TAA, AGG, AGA or TAG.
4. All the tRNA genes of Pseudopodoces humilis, Parus venustulus and Aegithalos concinnus mitochondrial genomes have the typical clover leaf structure except the tRNA Ser(AGN) gene, which is lack of the DHU arm in their secondary structure. There are some G-U mispair from the secondary structure in all three Aves.
5. The secondary structures of complete rRNAs have been predicted for Pseudopodoces humilis, Parus venustulus and Aegithalos concinnus. Most parts of the secondary structure are conserved in the three aves species, the main differences took place in terminal regions.
6. Through analyzing the aligned the 174 site of the ND3 gene in 17 Aves, we found the 13 species from Passeriformes involved in this paper all do not have the C base insert.
7. Through analyzing the aligned A+T-rich regions, we determined the central conserved region, and found that the CSB-1 region in all 13 Passeriformes have 18-20 bp sequence insert compared with Gallus gallus.
8. The protein coding genes were partitioned into three data sets and applied to reconstruct the phylogenetic relationships of Passeriformes. The phylogenetic trees from different methods and data sets agreed that Passeriformes divide two groups Passeri and Tyranni, and Passeri include the Corvida and Passerida. The result also support Aegithalos as a section level separately, Menuridae belongs to Corvida, Sylvioidea is not a monophyletic group; Pseudopodoces humilis have not closely relationships with species of Corvidae.
引文
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