| Literature DB >> 16144518 |
Shu Qing Xu1, Ying Zhong Yang, Jun Zhou, Guo En Jing, Yun Tian Chen, Jun Wang, Huan Ming Yang, Jian Wang, Jun Yu, Xiao Guang Zheng, Ri Li Ge.
Abstract
To investigate genetic mechanisms of high altitude adaptations of native mammals on the Tibetan Plateau, we compared mitochondrial sequences of the endangered Pantholops hodgsonii with its lowland distant relatives Ovis aries and Capra hircus, as well as other mammals. The complete mitochondrial genome of P. hodgsonii (16,498 bp) revealed a similar gene order as of other mammals. Because of tandem duplications, the control region of P. hodgsonii mitochondrial genome is shorter than those of O. aries and C. hircus, but longer than those of Bos species. Phylogenetic analysis based on alignments of the entire cytochrome b genes suggested that P. hodgsonii is more closely related to O. aries and C. hircus, rather than to species of the Antilopinae subfamily. The estimated divergence time between P. hodgsonii and O. aries is about 2.25 million years ago. Further analysis on natural selection indicated that the COXI (cytochrome c oxidase subunit I) gene was under positive selection in P. hodgsonii and Bos grunniens. Considering the same climates and environments shared by these two mammalian species, we proposed that the mitochondrial COXI gene is probably relevant for these native mammals to adapt the high altitude environment unique to the Tibetan Plateau.Entities:
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Year: 2005 PMID: 16144518 PMCID: PMC5172476 DOI: 10.1016/s1672-0229(05)03003-2
Source DB: PubMed Journal: Genomics Proteomics Bioinformatics ISSN: 1672-0229 Impact factor: 7.691
Fig. 1Annotation of the Pantholops hodgsonii mitochondrial genome. The original figure was from Bae et al. (. ND1 to ND6 refer to NADH subunits; COXI, COXII, COXIII refer to cytochrome c oxidase subunits; ATP6 and ATP8 refer to ATPase6 and ATPase8; the tRNA genes are denoted by shade and are noted accordingly; Origin refers to Origin of L-strand replication. The ATPase8 and ATPase6 genes are overlapped for 40 bp. Some bases between genes are too few to be denoted in the figure.
Components of P. hodgsonii Mitochondrial Genome
| Gene | Direction | Nucleotide number | Start codon | Stop codon |
|---|---|---|---|---|
| tRNA Phe | F | 1–69 | ||
| 12S rRNA | F | 70–1,026 | ||
| tRNA Val | F | 1,027–1,093 | ||
| 16S rRNA | F | 1,094–2,659 | ||
| tRNA Leu | F | 2,663–2,737 | ||
| NADH1 | F | 2,740–3,694 | ATG | TAa |
| tRNA Ile | F | 3,696–3,764 | ||
| tRNA Gln | R | 3,762–3,833 | ||
| tRNA Met | F | 3,836–3,904 | ||
| NADH2 | F | 3,905–4,946 | ATA | Taa |
| tRNA Trp | F | 4,947–5,013 | ||
| tRNA Ala | R | 5,015–5,083 | ||
| tRNA Asn | R | 5,085–5,157 | ||
| Origin of L-strand replication | R | 5,158–5,189 | ||
| tRNA Cys | R | 5,190–5,256 | ||
| tRNA Tyr | R | 5,257–5,324 | ||
| COXI | F | 5,326–6,870 | ATG | TAA |
| tRNA Ser | R | 6,868–6,936 | ||
| tRNA Asp | F | 6,944–7,011 | ||
| COXII | F | 7,013–7,696 | ATG | TAA |
| tRNA Lys | F | 7,700–7,767 | ||
| ATPase8 | F | 7,769–7,969 | ATG | TAA |
| ATPase6 | F | 7,930–8,610 | ATG | Taa |
| COXIII | F | 8,610–9,393 | ATG | Taa |
| tRNA Gly | F | 9,394–9,462 | ||
| NADH3 | F | 9,463–9,809 | ATA | TAa |
| tRNA Arg | F | 9,810–9,878 | ||
| NADH4L | F | 9,879–10,175 | ATG | TAA |
| NADH4 | F | 10,169–11,546 | ATG | Taa |
| tRNA His | F | 11,547–11,616 | ||
| tRNA Ser | F | 11,617–11,676 | ||
| tRNA Leu | F | 11,678–11,747 | ||
| NADH5 | F | 11,748–13,568 | ATA | TAA |
| NADH6 | R | 13,555–14,081 | ATG | TAA |
| tRNA Glu | R | 14,080–14,148 | ||
| Cytochrome b | F | 14,153–15,292 | ATG | AGA |
| tRNA Thr | F | 15,296–15,366 | ||
| tRNA Pro | R | 15,366–15,431 | ||
| Control region | 15,432–16,498 |
Number of Polymorphic Sites at Protein Coding Genes and RNA Genes
| Location | Gene | Number of mutations | |||
|---|---|---|---|---|---|
| All | |||||
| 1 | tRNA-Phe | 9 | 4 | 2 | 1 |
| 70 | 12s rRNA | 101 | 39 | 29 | 31 |
| 1,027 | tRNA-Val | 10 | 5 | 3 | 2 |
| 1,094 | 16s rRNA | 160 | 53 | 56 | 45 |
| 2,663 | tRNA-Leu | 4 | 4 | ||
| 2,740 | NU1M | 149 | 53 | 48 | 42 |
| 3,762 | tRNA-Gln (L) | 1 | 1 | ||
| 3,836 | tRNA-Met | 1 | 1 | ||
| 3,905 | NU2M | 168 | 59 | 63 | 43 |
| 4,947 | tRNA-Trp | 3 | 3 | ||
| 5,015 | tRNA-Ala (L) | 4 | 1 | 1 | 2 |
| 5,085 | tRNA-Asn (L) | 4 | 2 | 2 | |
| 5,190 | tRNA-Cys (L) | 1 | 1 | ||
| 5,257 | tRNA-Tyr (L) | 4 | 2 | 1 | 1 |
| 5,326 | COXI | 241 | 100 | 65 | 71 |
| 6,868 | tRNA-Ser (L) | 4 | 1 | 3 | |
| 6,944 | tRNA-Asp | 3 | 1 | 1 | 1 |
| 7,013 | COXII | 106 | 35 | 36 | 32 |
| 7,700 | tRNA-Lys | 12 | 4 | 3 | 4 |
| 7,769 | ATP8 | 39 | 13 | 12 | 11 |
| 7,930 | ATP6 | 131 | 44 | 45 | 39 |
| 8,610 | COXIII | 148 | 59 | 56 | 30 |
| 9,394 | tRNA-Gly | 4 | 1 | 2 | |
| 9,463 | NU3M | 57 | 25 | 13 | 17 |
| 9,810 | tRNA-Arg | 5 | 1 | 3 | 1 |
| 9,879 | NU4L | 45 | 10 | 10 | 23 |
| 10,169 | NU4M | 273 | 101 | 74 | 90 |
| 11,547 | tRNA-His | 8 | 3 | 4 | |
| 11,617 | tRNA-Ser | 10 | 5 | 2 | 3 |
| 11,678 | tRNA-Leu | 2 | 2 | ||
| 11,748 | NU5M | 365 | 126 | 110 | 121 |
| 13,555 | NU6M (L) | 69 | 19 | 25 | 24 |
| 14,080 | tRNA-Glu (L) | 6 | 3 | 2 | 1 |
| 14,153 | CYB | 185 | 60 | 62 | 57 |
| 15,296 | tRNA-Thr | 11 | 6 | 4 | 1 |
| 15,366 | tRNA-Pro (L) | 5 | 4 | 1 | |
Number of polymorphic sites at protein coding genes and RNA genes in the mitochondrial genomes of P. hodgsonii, C. hircus and O. aries. The column “All” refers to the number of sites at which all three species are different; the column “P. hodgsonii” refers to number of the sites at which P. hodgsonii is different from the other two species.
Amino Acid Mutations of the COXI Gene
| Species | Mutation | E/B | Neighbor rigidity | Rigidity | Volume change | Charge change | Polarity change |
|---|---|---|---|---|---|---|---|
| V155I | 64 | −0.2351483 | −0.34353 | 26.7 | 0 | 0 | |
| A308T | 5 | −0.2854679 | −0.4675 | 27.5 | 0 | 0 | |
| N512S | 80 | 2.12195984 | 2.659928 | −114.1 | 0 | −2 | |
| F8Y | 136 | 0.2337137 | −0.0661 | 3.7 | 0 | 0 | |
| D407T | 76 | 0.63863865 | 0.801412 | 5 | 1 | −1 | |
| M449V | 129 | 0.05870691 | 1.199486 | −22.9 | 0 | 0 | |
| L467V | 34 | 0.18495316 | 0.683123 | −26.7 | 0 | 0 | |
| T509V | 52 | −0.2661298 | −0.22177 | 23.9 | 0 | −1 | |
| Y440S | 108 | −0.3272085 | 0.142943 | −193.6 | 0 | 0 | |
| S441P | 5 | 0.35454652 | −0.54554 | 112.7 | 0 | 1 | |
| I453V | 51 | 0.1775126 | −0.22684 | −26.7 | 0 | 0 | |
| F476L | 96 | 0.08862233 | 0.404623 | −23.2 | 0 | 0 |
Amino acid mutations of the COXI gene for C. hircus, P. hodgsonii, and B. grunniens, as compared with B. taurus. The influences of these mutations are predicted by the methods referred from Mirkovic et al. (.
Fig. 2Alignment of amino acid sequences of the COXI gene using CLUSTAL W1.83. The species included were Bos taurus (P00396), Bubalus bubalis (YP_087084), Bos grunniens (YP_133786), Pantholops hodgsonii, Sus scrofa (NP_008636), Ovis aries(NP_008408), Muntiacus muntjak (AY225986), Canis familiaris (NP_008473), Equus caballus (NP_007162), Mus musculus (NP_904330), Capra hircus (NP_877405), Homo sapiens (NP_536845), Eschrichtius robustus (NP_944635), Ursus arctos (Q8SJI5), Ursus maritimus (Q8SJH3), Xenopus laevis (P00398), Shinisaurus crocodilurus (NC_005959), Gallus gallus (P18943), Anser albifrons (NP_777304), Brachydanio rerio (Q9MIY8), and Takifugu rubripes (NP_694917). Mutations of P. hodgsonii were highlighted as bold letters.
Fig. 3Neighbor-joining tree based on the complete cytochrome b genes of some Bovidae species. The tree was constructed by using PAUP*(4b10), with parameters estimated by MODELTEST3.6 and with Giraffe camelopardalis as the outgroup. Number of bootstrap replication is 1000. Bootstrap values over 50% are shown on the branches.
Molecular Divergence and Estimated Divergence Time Between Native Mammals on the Tibetan Plateau and Their Lowland Relatives
| Species | Molecular divergence | Divergence time |
|---|---|---|
| 0.124 | 2.22 | |
| 0.126 | 2.25 | |
| 0.124 | 2.21 | |
| 0.089 | 1.59 |
Based on complete sequences of mitochondrial cytochrome b and a substitution rate of 0.056 per site per million years between two mammalian taxa.
Fig. 4The COXI gene was used to analyze N/S ratio of each branch within Artiodactyla mammals. Phylogeny was inferred with PAUP*(4b10). Numbers on the branches are mutation of nonsynonymous/synonymous for protein coding region of the COXI gene, as obtained with codeml in PAML package. * Fisher test P-value < 0.001. Take other branches (except B. grunniens and P. hodgsonii branches) as background for testing. The difference between the B. grunniens and P. hodgsonii branches is not significant (Fisher test P-value > 0.1).