The complete mitochondrial genome of the raccoon dog
The complete mitochondrial genome of the raccoon dog
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DOI：
10.3109/19401736.2010.490835
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发表时间：
2010-06
影响因子：
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通讯作者：
Honghai Zhang;Lei Chen
中科院分区：
文献类型：
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作者：
Honghai Zhang;Lei Chen
采用引物步移法和长片段精确PCR技术，在ABI 3730 xl上首次对浣熊犬线粒体基因组进行了全序列测定。从中国内蒙古达赉湖自然保护区捕获的一只雌性浣熊犬中获得肝脏样本。线粒体基因组是一个环状双链DNA序列，长16，713 bp，包括13个蛋白质编码基因、2个rRNA基因、22个tRNA基因和1个控制区（表I）。将精确注释的线粒体基因组序列提交至GenBank，登录号为NC_013700。多个基因的排列与其他犬科动物（Nowak 1991; Kim et al. 1998; Inoue et al. 2007; Meng et al. 2009）和大多数哺乳动物（洛佩斯et al. 1996; Ursing and Arnason 1998;吉西et al. 1998; Gu et al. 2007; Peng et al. 2007; Wei et al. 2009）一致。蛋白质编码基因序列的总长度为11，396 bp。除了ND 2、ND 3和ND 5以ATA开始开始外，大多数蛋白质编码基因以ATG开始。8个蛋白质编码基因以TAA终止，而ND 2基因以TAG终止，Cytb基因以阿加终止。在ND 3、COXIII和ND 4中使用不完全终止密码子（TA_和T_）。在蛋白质编码基因中观察到第三密码子位置对G的强烈偏好。CTA（Leu）、ATA（Ile）和TTC（Phe）密码子频率较高。tRNA基因的长度从60到74 bp不等。除tRNA-Ser（AGY）缺少完整的二氢尿苷臂外，其余21个氨基酸均能折叠成典型的三叶草二级结构。大多数浣熊狗线粒体基因编码的H链，除了ND 6基因和8个tRNA基因，这是L链编码。发现了一些阅读帧间隔和重叠，其中最典型的是在ATP 8和ATP 6之间。L链复制起点（OL）位于WANCY区域内，包含5个tRNA基因（tRNA-Trp、tRNA-Ala、tRNA-Asn、tRNA-Cys、tRNA-Pro）。该区域长33 bp，具有折叠成稳定的茎环二级结构的潜力。浣熊犬线粒体基因组总碱基组成为A（32.1%）。T（27.0%）。C（26.7%）。G（14.2%）。碱基组成存在明显的A-T偏斜，以16 SrRNA和tRNA基因最为明显。浣熊狗线粒体基因组的控制区位于tRNA-Pro和tRNA-Phe基因之间，仅包含复制和转录的启动子和调控序列，而不包含结构基因。在浣熊狗线粒体基因组控制区中定义了三个结构域（Sbisà et al.1997）：扩展终止相关序列（ETAS）结构域、中央保守结构域和保守序列块（CSB）结构域。在CSB结构域中发现三个CBS，它们分别位于16，093 - 16，119、16，445 - 16，463和16，509 - 16，520位。仅找到ETAS 1，其位于位置15，532 - 15，585。此外，仅发现一个重复序列区域（RS3），其位于
In the present paper, the complete mitochondrial genome of the raccoon dog was sequenced for the first time on ABI 3730xl using a primer-walking strategy and the long and accurate PCR, with 5 pairs of long-PCR primers and 11 pairs of sub-PCR primers. A liver sample was obtained from a female raccoon dog captured from the Dalai Lake Nature Reserve in Inner Mongolia, China. The mitochondrial genome is a circular doublestranded DNA sequence that is 16,713 bp long including 13 protein-coding genes, two rRNA genes, 22 tRNA genes and one control region (Table I). The accurate annotated mitochondrial genome sequence was submitted to GenBank with accession number NC_013700. The arrangement of the multiple genes is in line with other canine animals (Nowak 1991; Kim et al. 1998; Inoue et al. 2007; Meng et al. 2009) and most mammals (Lopez et al. 1996; Ursing and Arnason 1998; Gissi et al. 1998; Gu et al. 2007; Peng et al. 2007; Wei et al. 2009). The total length of the protein-coding gene sequences is 11,396 bp. Most protein-coding genes initiate with ATG except for ND2, ND3 and ND5, which begin with ATA. Eight protein-coding genes terminate with TAAwhereas theND2 gene terminates with TAG and the Cytb gene terminates with AGA. The incomplete stop codons (TA_ and T_) are used in ND3, COXIII andND4. A strong bias against G at the third codon position is observed in the protein-coding genes. The frequencies of CTA (Leu), ATA (Ile) and TTC (Phe) are higher than those of other codons. The length of tRNA genes vary from 60 to 74 bp. Twenty-one of them could be folded into the typical cloverleaf secondary structure except the tRNA-Ser (AGY), whose complete dihydrouridine arm is lacking. Most raccoon dog mitochondrial genes are encoded on the H strand, except for the ND6 gene and eight tRNA genes, which are encoded on the L strand. Some reading frame intervals and overlaps are found. One of the most typical is between ATP8 and ATP6. The L-strand replication origin (OL) is located within the WANCY region containing five tRNA genes (tRNA-Trp, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Pro). This region is 33 bp long and has the potential to fold into a stable stem-loop secondary structure. The total base composition of raccoon dog mitochondrial genome is A (32.1%) . T (27.0%) . C (26.7%) . G (14.2%). The base compositions present clearly the A–T skew, which is most obviously in the 16S rRNA gene and tRNA genes. The control region of the raccoon dog mitochondrial genome is located between the tRNA-Pro and tRNA-Phe genes, and contains only promoters and regulatory sequences for replication and transcription, but no structural genes. Three domains are defined in the raccoon dog mitochondrial genome control region (Sbisà et al. 1997): the extended terminationassociated sequence (ETAS) domain, the central conserved domain and the conserved sequence block (CSB) domain. Three CBSs are found in the CSB domain and they are located in positions 16,093– 16,119, 16,445–16,463 and 16,509–16,520, respectively. Only ETAS1 is found, which is located in the position 15,532–15,585. Also only one repetitive sequence region (RS3) is found, which is located