The complete mitochondrial genome and phylogenetic analysis of the giant panda (Ailuropoda melanoleuca)

Peng, Rui; Zeng, Bo; Meng, Xiuxiang; Yue, Bisong; Zhang, Zhihe; Zou, Fangdong

doi:10.1016/j.gene.2007.04.009

Cited by 81 publications

(42 citation statements)

References 44 publications

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“…Three types of incomplete stop codons were determined in the red fox mitochondrial genome. The phenomenon of terminating with incomplete stop codons was also found in other mammals (Gissi et al, 1998;Kim et al, 1998;Ursing & Arnason et al, 1998;Xu et al, 1996;Peng et al, 2007;Gu et al, 2007). Codon bias and degeneration which occur in both nuclear and mitochondrial genome were found.…”

Section: Mitochondrial Genome Evolutionmentioning

confidence: 57%

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Complete Mitochondrial Genome of the Red Fox (<I>Vuples vuples</I>) and Phylogenetic Analysis with Other Canid Species

Zhong

Zhang²,

Sha³

et al. 2010

Zoological Research

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Abstract:The whole mitochondrial genome sequence of red fox (Vuples vuples) was determined. It had a total length of 16 723 bp. As in most mammal mitochondrial genome, it contained 13 protein coding genes, two ribosome RNA genes, 22 transfer RNA genes and one control region. The base composition was 31.3% A, 26.1% C, 14.8% G and 27.8% T, respectively. The codon usage of red fox, arctic fox, gray wolf, domestic dog and coyote followed the same pattern except for an unusual ATT start codon, which initiates the NADH dehydrogenase subunit 3 gene in the red fox. A long tandem repeat rich in AC was found between conserved sequence block 1 and 2 in the control region. In order to confirm the phylogenetic relationships of red fox to other canids, phylogenetic trees were reconstructed by neighbor-joining and maximum parsimony methods using 12 concatenated heavy-strand protein-coding genes. The result indicated that arctic fox was the sister group of red fox and they both belong to the red fox-like clade in family Canidae, while gray wolf, domestic dog and coyote belong to wolf-like clade. The result was in accordance with existing phylogenetic results.

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Section: Mitochondrial Genome Evolutionmentioning

confidence: 57%

“…The unusual ATT start codon was also observed in fur seal (Lin et al, 2002) and giant panda (Peng, 2007). Three types of incomplete stop codons were determined in the red fox mitochondrial genome.…”

Section: Mitochondrial Genome Evolutionmentioning

confidence: 91%

Complete Mitochondrial Genome of the Red Fox (<I>Vuples vuples</I>) and Phylogenetic Analysis with Other Canid Species

Zhong

Zhang²,

Sha³

et al. 2010

Zoological Research

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“…Unlike the other 21 tRNA genes, the tRNA Ser(GCU) gene cannot form a typical cloverleaf structure because it lacks the appropriate sequence to form the dihydrouridine arm and loop. This unusual secondary structure is also found in many mt genomes from other vertebrates, including bear, coyote, dogs, Eurasian otter, and wild camel (Peng et al, 2007;Hou et al, 2007;Cui et al, 2007;Hwang et al, 2008 Leu(UAG) ], which may be restored through RNA-editing mechanisms.…”

Section: Ribosomal and Transfer Rna Genesmentioning

confidence: 94%

Complete mitochondrial genome sequence of Marmota himalayana (Rodentia: Sciuridae) and phylogenetic analysis within Rodentia

Chao¹,

Li²,

Geng³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. This is the first report of a complete mitochondrial genome sequence from Himalayan marmot (Marmota himalayana, class Marmota). We determined the M. himalayana mitochondrial (mt) genome sequence by using long-PCR methods and a primerwalking sequencing strategy with genus-specific primers. The complete mt genome of M. himalayana was 16,443 bp in length and comprised 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a typical control region (CR). Gene order and orientation were identical to those in mt genomes of most vertebrates. The heavy strand showed an overall A+T content of 63.49%. AT and GC skews for the mt genome of the M. himalayana were 0.012 and -0.300, respectively, indicating a nucleotide bias against T and G. The control region was 997 bp in size and displayed some unusual features, including absence of repeated motifs and two conserved sequence blocks (CSB2 and CSB3), which is consistent with observations from two other rodent species, Sciurus vulgaris and Myoxus glis. Phylogenetic analysis of complete mt DNA sequences without the control region including 30 taxa of Rodentia was performed with Maximum-Likelihood (ML) and Bayesian Inference (BI) methods and provided strong support for Sciurognathi polyphyly and Hystricognathi monophyly. This analysis also provided evidence that M. himalayana mt DNA was closely related to that from Sciurus vulgaris (Sciuridae) and was similar to mt DNA from Myoxus glis.

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“…Five incomplete stop codons T(--) were found in the ND1, ND2, Cox3, ND4, and cytb genes. Incomplete stop codons have been observed in many other mammals (Peng et al 2007). Several pairs of genes overlapped: ATPase8 and ATPase6, ATPase6 and Cox3, and ND4L and ND4 (Table 1).…”

Section: Mitogenome Announcementmentioning

confidence: 96%

The complete mitochondrial genome of the Tamarisk gerbil, Meriones tamariscinus (Rodentia: Muridae)

Wang

Yan

et al. 2016

Mitochondrial DNA Part B

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The complete mitochondrial genome and phylogenetic analysis of the giant panda (Ailuropoda melanoleuca)

Cited by 81 publications

References 44 publications

Complete Mitochondrial Genome of the Red Fox (<I>Vuples vuples</I>) and Phylogenetic Analysis with Other Canid Species

Complete Mitochondrial Genome of the Red Fox (<I>Vuples vuples</I>) and Phylogenetic Analysis with Other Canid Species

Complete mitochondrial genome sequence of Marmota himalayana (Rodentia: Sciuridae) and phylogenetic analysis within Rodentia

The complete mitochondrial genome of the Tamarisk gerbil, Meriones tamariscinus (Rodentia: Muridae)

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