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A Complete Mitochondrial Genome Sequence of the Wild Two-Humped Camel (Camelus Bactrianus Ferus): An Evolutionary History of Camelidae

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A Complete Mitochondrial Genome Sequence of the Wild Two-Humped Camel (Camelus Bactrianus Ferus): An Evolutionary History of Camelidae

Peng Cui et al. BMC Genomics.

Abstract

Background: The family Camelidae that evolved in North America during the Eocene survived with two distinct tribes, Camelini and Lamini. To investigate the evolutionary relationship between them and to further understand the evolutionary history of this family, we determined the complete mitochondrial genome sequence of the wild two-humped camel (Camelus bactrianus ferus), the only wild survivor of the Old World camel.

Results: The mitochondrial genome sequence (16,680 bp) from C. bactrianus ferus contains 13 protein-coding, two rRNA, and 22 tRNA genes as well as a typical control region; this basic structure is shared by all metazoan mitochondrial genomes. Its protein-coding region exhibits codon usage common to all mammals and possesses the three cryptic stop codons shared by all vertebrates. C. bactrianus ferus together with the rest of mammalian species do not share a triplet nucleotide insertion (GCC) that encodes a proline residue found only in the nd1 gene of the New World camelid Lama pacos. This lineage-specific insertion in the L. pacos mtDNA occurred after the split between the Old and New World camelids suggests that it may have functional implication since a proline insertion in a protein backbone usually alters protein conformation significantly, and nd1 gene has not been seen as polymorphic as the rest of ND family genes among camelids. Our phylogenetic study based on complete mitochondrial genomes excluding the control region suggested that the divergence of the two tribes may occur in the early Miocene; it is much earlier than what was deduced from the fossil record (11 million years). An evolutionary history reconstructed for the family Camelidae based on cytb sequences suggested that the split of bactrian camel and dromedary may have occurred in North America before the tribe Camelini migrated from North America to Asia.

Conclusion: Molecular clock analysis of complete mitochondrial genomes from C. bactrianus ferus and L. pacos suggested that the two tribes diverged from their common ancestor about 25 million years ago, much earlier than what was predicted based on fossil records.

Figures

Figure 1
Figure 1
The mitochondrial genome of C. bactrianus ferus (16,680 bp). Protein-coding genes (black) and rRNA genes (light-gray) are identified by arrows. The gene nd6 is transcribed in the opposite direction as relative to the rest in the cluster. tRNA genes are depicted with their corresponding amino acids.
Figure 2
Figure 2
Predicted secondary structures of 22 mitochondrial tRNA sequences from the wild camel. All tRNAs were folded into secondary structures based on the "least free energy" principle. (A) 21 tRNAs exhibit cloverleaf structures and possess anticodons. The secondary structure of tRNAAsn was shown (bold) as an example for the cloverleaf structure that usually has 7 bp in the aminoacyl stems, 4 bp or 5 bp in the TψC and anticodon stems, and 4 bp or 3 bp in the DHU stems. tRNA stem regions include some non-complementary and T:G base pairings. (B) tRNAser can not form the appropriate dihydrouridine loop and does not possess the anticodon for AGN.
Figure 3
Figure 3
Alignment of termination-associated sequences (TAS) and eight putative conserved sequence blocks of CBS (1–3) and CBS (B-F). The bactrian camel sequence was used as the consensus sequence, orientated from 5' to 3' on the heavy strand. Dots, dashes, and numbers indicate nucleotide identity, indels, and positions of the first and the last nucleotide for each identified region, respectively.
Figure 4
Figure 4
The phylogenic relationship between bactrian camel and alpaca based on maximum likelihood analysis (without the control regions). To estimate the divergence time, cow and pig were taken as an ingroup calibration point, while the mouse and rat were taken as an outgroup calibration point. All nodes were supported by the bootstrap value (1000 replications) and posterior probability on the nodes (above the branch is the bootstrap value, and below the branch is posterior probability). The scale bar indicates 0.1 substitutions.
Figure 5
Figure 5
Phylogeny of the Camelidae species based on maximum likelihood analysis of cytb sequences. To estimate the divergence time, pairwise comparisons of cow-pig and mouse-rat were taken as the ingroup and outgroup calibration points, respectively. All nodes were supported by the bootstrap value (1000 replications) on the nodes.

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