Genome sequences of wild and domestic bactrian camels

Abstract

Bactrian camels serve as an important means of transportation in the cold desert regions of China and Mongolia. Here we present a 2.01 Gb draft genome sequence from both a wild and a domestic bactrian camel. We estimate the camel genome to be 2.38 Gb, containing 20,821 protein-coding genes. Our phylogenomics analysis reveals that camels shared common ancestors with other even-toed ungulates about 55-60 million years ago. Rapidly evolving genes in the camel lineage are significantly enriched in metabolic pathways, and these changes may underlie the insulin resistance typically observed in these animals. We estimate the genome-wide heterozygosity rates in both wild and domestic camels to be 1.0 × 10(-3). However, genomic regions with significantly lower heterozygosity are found in the domestic camel, and olfactory receptors are enriched in these regions. Our comparative genomics analyses may also shed light on the genetic basis of the camel's remarkable salt tolerance and unusual immune system.

Figure 1. Genomic comparison between bactrian camel and other animals.

(a) Proportion of shared orthologs between bactrian camel and animals in Vertebrata (chicken and zebrafish; NCBI genome accession codes GCF_000002315.3 and GCF_000002035.4), Mammalia (human, chimpanzee, mouse and rat; NCBI genome accession codes GCF_000001405.21, GCF_000001515.5, GCF_000001635.20 and GCF_000001895.4), Laurasiatheria (dog and horse; NCBI genome accession codes GCF_000002285.3 and GCF_000002305.2) and Artiodactyla (cattle and pig; NCBI genome accession codes GCF_000003055.4 and GCF_000003025.5). (b) Length of syntenic regions on each scaffold (Mb, million base pairs). Coverage is calculated as the length of syntenic region divided by the length of scaffold. Scaffolds with coverage >75%, >50% and <50% are represented by red, green and grey dots, respectively. (c) Supertree inference for nine mammals. The topology was evaluated by input tree bootstrap percentages. Distances are shown in millions of years. (d) Points represent pairs of medians of dN/dS ratios in camels and in cattle by KEGG pathways. Pathways in which rapidly evolving genes are significantly enriched (FDR<0.05) in camels and cattle are coloured in red and green, respectively. MAPK, mitogen-activated protein kinase; mTOR, mammalian target of rapamycin; TCA, tricarboxylic acid cycle.

Figure 2. Comparison of genetic diversity between wild and domestic bactrian camels.

(a) Heterozygosity rate in coding and non-coding regions. The heterozygosity rate is calculated as the number of heterozygous SNPs divided by the length of corresponding genomic regions. (b) A genomic region where the heterozygosity of the domestic camel is significantly lower than that of the wild one. The region also contains a cluster of olfactory receptors (OR10J1, olfactory receptor 10J1). Genes and gene intervals are represented by solid and dash lines, respectively. Exons are shown in blue blocks and transcriptional directions are indicated by arrows. The locations of SNPs are marked in black. Sequencing depth in the region is also shown, with white lines indicating the average sequencing depth. (c) Enrichment of molecular function for genes with low heterozygosity in the domestic camel. The hierarchy of the Gene Ontology is displayed. The size of the circle is proportional to the number of genes in the genome, and the colour indicates the odds ratio of the enrichment.

Figure 3. Biological findings from the genome analysis.

(a) The type II diabetes mellitus and insulin signalling pathway. The rapidly evolving genes in camels (shown in red) are identified in the pathway. Abbreviations, annotations and connexions are presented in accordance with KEGG standards: solid lines represent direct relationships among proteins (boxes) and metabolites (circular nodes), dashed lines represent indirect relationships, lines with arrowheads denote activation, and lines with the crossing mean inhibition. (b) The pathway of arachidonate synthesis and conversion. Arachidonate is synthesized from lecithin by PLA2G (EC: 3.1.1.4), and converted into 19(S)-hydroxyeicosatetraenoic acid (19(S)-HETE) by CYP2E and CYP2J (expansion in camel), or transformed into 20-hydroxyeicosatetraenoic acid (20-HETE) by CYP4A and CYP4F (contraction in camel). (c) The schematic diagram of IgH loci in the camel genome inferred from a complete V-D-J-C gene cluster in scaffold 355.1.