Estimating the Population Mutation Rate from a de novo Assembled Bactrian Camel Genome and Cross-Species Comparison with Dromedary ESTs

Abstract

The Bactrian camel (Camelus bactrianus) and the dromedary (Camelus dromedarius) are among the last species that have been domesticated around 3000–6000 years ago. During domestication, strong artificial (anthropogenic) selection has shaped the livestock, creating a huge amount of phenotypes and breeds. Hence, domestic animals represent a unique resource to understand the genetic basis of phenotypic variation and adaptation. Similar to its late domestication history, the Bactrian camel is also among the last livestock animals to have its genome sequenced and deciphered. As no genomic data have been available until recently, we generated a de novo assembly by shotgun sequencing of a single male Bactrian camel. We obtained 1.6 Gb genomic sequences, which correspond to more than half of the Bactrian camel’s genome. The aim of this study was to identify heterozygous single-nucleotide polymorphisms (SNPs) and to estimate population parameters and nucleotide diversity based on an individual camel. With an average 6.6-fold coverage, we detected over 116 000 heterozygous SNPs and recorded a genome-wide nucleotide diversity similar to that of other domesticated ungulates. More than 20 000 (85%) dromedary expressed sequence tags successfully aligned to our genomic draft. Our results provide a template for future association studies targeting economically relevant traits and to identify changes underlying the process of camel domestication and environmental adaptation.

During the process of domestication and breed formation, farm animals have encountered both natural and artificial selections. This created a huge diversity of phenotypes among domesticated species. Moreover, this has triggered marked genetic adaptation to different environmental and anthropogenic, very specific, conditions. Livestock and other domestic animals therefore represent a unique resource to understand the genetic bases of phenotypic variation and genetic adaptation (Andersson and Georges 2004). The development of “next-generation” sequencing technologies and high-throughput genotyping platforms tremendously advanced whole-genome analysis in domestic animals and nonmodel species (Nawy 2012). Just as new advances in sequencing methodologies have made it possible to identify the basic changes during the transformation from a wild species to a domesticated animal. This has been investigated in chicken (Rubin et al. 2010), dog (vonHoldt et al. 2010), pig (Larson et al. 2010), and sheep (Kijas et al. 2009).

One of the key technologies in the genomic analyses of domestic animals are high-density single-nucleotide polymorphism (SNP) arrays. These usually biallelic markers are distributed over the entire genome and have been found to occur every 100–300bp in humans (Brown 2002). With a proper coverage to discriminate genuine polymorphisms from sequencing errors (Nielsen et al. 2011), these SNPs have been highly useful to reveal some of the genetic factors underlying human disease (Hirschhorn and Daly 2005). For domestic animals, the characterization of SNPs can be used to determine the genotype associated with specific favored phenotypes, for example, in genome-wide association studies as done in pigs (Amaral et al. 2009), cattle (Eck et al. 2009; Kawahara-Miki et al. 2011) and chicken (Marklund and Carlborg 2010; Wenbo et al. 2011). Beyond, the evolution of particular species, their domestication, breed formation, and genetic divergence can be investigated using population-wide SNP data (vonHoldt et al. 2010; Amaral et al. 2011). Finally, new methods and markers for selective breeding can be developed with a reduced amount of labor-intensive laboratory work.

While for other livestock animals the complete genomes are already sequenced (cattle, sheep, pig, and chicken; summarized in Fan et al. 2010) or under way (alpaca; dromedary, Al-Swailem et al. 2010), nuclear genomic data about the domestic Bactrian camel (Camelus bactrianus) have not been made publicly available yet. Although recently published (Jirimutu et al. 2012), in the DDBJ/EMBL/GenBank project (accession number PRJNA76177), only wild camel (Camelus ferus) sequences have been released. Still, there is an increasing need for high-density SNP maps of domestic animals’ genomes as animal breeders progressively rely on marker-assisted breeding. This holds also true for dromedary and Bactrian camels, where the selection for specific traits has not been extensively explored until now. Being among the last livestock species that have been domesticated, camels have been utilized as a multipurpose animal for transport, milk, wool, and meat production (Bulliet 1990; Grigson 2012). Since their domestication around 3000–6000 years ago (Peters and von den Driesch 1997; Uerpmann and Uerpmann 2002), only little selection into breeds has been observed, apart from grouping individuals according to coat colors (Al-Swailem et al. 2010; Abdussamad et al. 2012). In view of increasing desertification and the demand of sustainable resources for human nutrition, the potential of dromedary and Bactrian camels has been recognized and their economic value is greater than ever. This has also challenged research efforts in the past few years like the sequencing of expressed sequence taqs (ESTs) in dromedaries (Al-Swailem et al. 2010), the application of camelid immunoglobulins in nanobody technology (Muyldermans et al. 2009), or the usage of camel milk in diabetes therapy (Agrawal et al. 2011). Summarized, camels harbor specific biological characteristics, which make them highly interesting not only for their economic value but also for human medicine.

Now, it is more important than ever to understand the genetic basis underlying phenotypic traits important for future selective breeding; especially interesting is the identification of genetic bases of adaptation to hot environments in the context of global climate change and increasing desertification. Here, we assemble de novo a draft of one individual Bactrian camel genome and compare the new contigs with dromedary ESTs (Al-Swailem et al. 2010). Based on the detected heterozygous SNPs, we estimate population parameters and demonstrate that the nucleotide diversity in Bactrian camels is comparable with that of other domestic ungulates.

Material and Methods

We performed whole-genome shotgun sequencing of a single male Bactrian camel for the identification of heterozygous SNPs and the estimation of populations parameters and sequencing error rate. Genomic DNA (5–10 µg) was extracted from two ethylene diamine tetra-acetic acid blood samples of a single male Bactrian camel originating from the Austrian Zoo Herberstein using the DNeasy blood & tissue kit (Qiagen; Vienna, Austria). Sequencing library preparation (Genomic DNA Sample Prep Kit; Illumina) was performed according to the manufacturer’s protocol. The shotgun sequencing of paired-end (PE) reads (2×101bp) was carried out with an Illumina Genome Analyzer IIx. In the shotgun sequencing method, the DNA is sheared into fragments, which are randomly distributed over the entire genome. The assembly of large genomes with many repetitive sequences such as in mammals (Ridley 1996; Alkan et al. 2011) is challenging and therefore PE sequencing with predefined insert sizes of 400–600bp were used for the assembly process (Jaffe et al. 2003).

We trimmed the raw reads with a modified Mott algorithm implemented in the PoPoolation software package (Kofler et al. 2011), where low-quality bases with a Q_PHRED score below 20 at the ends of the reads are removed (Table 1). Using FastQC (Babraham bioinformatics; Cambridge, UK; www.bioinformatics.babraham.ac.uk), we performed an additional quality check of the trimmed reads. As there is no domestic Bactrian camel reference genome available, we generated a de novo assembly with CLC Assembly Cell 4.0.1beta (CLC bio; Aarhus, Denmark; www.clcbio.com/): In a first step, we created contig sequences by assembling all the trimmed reads using the paired-end information to resolve longer repeats. Second, we aligned the PE reads with BWA 0.5.7 (Li and Durbin 2009) using the de novo assembled Bactrian camel contig sequences as reference. We applied the following filtering steps on the resulting alignment: we removed 1) reads with a mapping quality Q_PHRED score lower than 20 and 2) reads that did not map in proper pairs. For downstream analysis, we consequently kept only those reads that mapped uniquely and in proper pairs (Table 1). Identification of heterozygous SNPs was carried out with BCFtools (http://samtools.sourceforge.net/samtools.shtml) implemented in SAMtools 0.1.14 (Li et al. 2009). To be conservative and to avoid false SNPs in repetitive regions, we employed Repeatmasker 3.2.8 (http://repeatmasker.org) to detect repetitive regions in the de novo-assembled Bactrian camel genome and removed SNPs overlapping with these regions using BEDTools 2.15.0 (Quinlan and Hall 2010). Finally we calculated exact two-sided 95% confidence intervals on the remaining set of SNPs using the Clopper-Pearson interval method (Clopper and Pearson 1934) based on the assumption that each SNP is drawn from a binomial distribution. We removed SNPs whose allele frequency was outside the limits of the confidence intervals. To determine the within-individual genetic diversity π (Nei and Li 1979; Nei and Kumar 2000), we jointly estimated the scaled mutation rate θ = 4N_eμ (Johnson and Slatkin 2006; where N_e is the effective population size and μ is the mutation rate per generation per nucleotide) and the sequencing error rate ε, using the software mlRho (Haubold et al. 2010). This program computes the maximum likelihood (ML) estimators of θ, ε, and ρ (recombination rate) based on the heterozygous polymorphisms obtained through shotgun sequencing of single diploid individuals. Using this approach, joint estimates for θ_π and ε can be calculated without an external (possibly inaccurate) assumption of a sequencing error rate (Lynch 2008). A critical point in the estimation of π is the coverage of sites; it is essential that both nucleotides at a heterozygous locus are sequenced at least twice, so there is sufficient information to distinguish between genuine polymorphisms and sequencing errors. Therefore, we considered only positions with a minimum 4-fold coverage for the ML estimations. In the mlRho program, confidence intervals are determined by calculating the values of an estimator where the likelihood is 2 log units below the maximum (Haubold et al. 2010). For a comparative genomic analysis between the two Old World camelid species, we used BLAT (Kent 2002) to align the available dromedary ESTs (Al-Swailem et al. 2010; Otu, H. personal communication; http://camel.kacst.edu.sa) with the Bactrian camel contig sequences. Finally, we plotted and edited our results with the R software package version 2.11.1 (Hornik 2011).

Table 1.

Summary of read and mapping statistics

Number of untrimmed reads in pairs	115 328 191
Number of trimmed reads in pairs	93 705 190	81.3%
Number of trimmed single readsa	15 663 023	13.6%
Average length of trimmed reads (bp)	88.94
Total number of PE reads used for mapping	187 410 380
Total number of reads mappedb	115 870 996	61.8%
Total number of reads mappedb in proper pairs	114 746 608	61.2%

^aOne read of the PE reads (given in boldface) was removed due to low quality; note that the trimmed reads in pairs and single do not sum up to 100% because those PE reads that have been discarded as a pair during the trimming process are missing in the count.

^bAfter applying a filtering step for a minimum mapping quality of Q_PHRED 20.

Results and Discussion

Whole-genome shotgun sequencing was used to detect heterozygous SNPs and to estimate population parameters in a single male Bactrian camel. For this purpose, we generated 20 Gb of raw reads by PE read sequencing (2×101bp) on an Illumina Genome Analyzer IIx. After the trimming process, most of the reads displayed a length between 97 and 101bp (Figure 1a), and the average read length was 88.9bp (Table 1). The quality Q_PHRED scores across all bases of the trimmed reads were generally high ranging from 30 to 38, with a decrease to 28 toward the end of the reads (Figure 1b). A summary statistics of the trimming and mapping results is given in Table 1. In absence of a species-specific reference genome, we created a de novo assembly and obtained 1.57 Gb of genomic sequence, which corresponds to more than half of the Bactrian camel genome assuming an average mammalian genome size of 3 Gb. The Bactrian camel de novo genome assembly consisted of 781 462 contigs with a minimum and maximum contig size of 500 and 36 400bp, respectively, and an average GC content of 39.6% as shown in Table 2. The N50, which describes that 50% of the assembly consists of contigs equal or larger than this value, was 2814bp. The distribution of the contig lengths is displayed in Figure 2. The complete assembly containing all contigs in fasta format has been submitted to the European Nucleotide Archive project (accession number PRJEB407).

Figure 1.

Length and quality distribution of trimmed reads. (A) After trimming, most of the reads showed a length between 97 and 101bp. (B) The per base quality of the trimmed reads ranged above a Q_PHRED score of 20. For each position a Box-and-Whisker plot was calculated with FastQC. The upper line displays the median value, while the central line represents the mean quality per base.

Table 2.

Summary of the Bactrian camel assembly statistics

Total contig basesa	1 568 773 587bp (1.57 Gb)
Number of contigs	781 462
Number of contigs >1 kb	510 192 (65.3%)
Shortest contig	500 bp
Longest contig	36 400 bp
Average contig length	2008 bp
N50 contig length	2814 bp
N90 contig length	897 bp
Average read depthb	6.56-fold

N50/90 refers to a length-weighted median such that 50/90% of the genome is contained in contigs of the indicated size or greater.

^aHere we present the total number of bases in the assembly with a base quality Q_PHRED score greater than 20 (>Q_PHRED 20).

^bThe average read depth was calculated using reads up to a maximal coverage of 15.

Figure 2.

Distribution of the contig length. While 34.7% of the contigs’ lengths are below 1kb, the length-weighted median N50 (Table 1) demonstrates that 50% of the assembly consists of contigs with a length equal to or greater than 2814bp.

Paired-end read mapping against the de novo-generated reference assembly resulted in 114.7 million reads (61.1%) that were uniquely mapped in proper pairs. This seemingly moderate mapping result might be due to the stringent filtering criteria, that is, only reads with a minimum mapping quality of 20 were used (Figure 3). In addition, we have to consider the high frequency of repetitive sequences in the mammalian genome (Charlesworth et al. 1994; Ridley 1996) that renders the mapping of the reads more difficult. Here, we show the number of reads mapping to a contig proportional to the contig lengths (Figure 4). On average, we reached a 6.6-fold coverage of the Bactrian camel genome including only positions up to a coverage of 15-fold (adjusted to approximately twice the average read depth). We used these stringent criteria to account for gene duplications and copy number variations. Applying the same rigorous conditions for SNP calling and using only sites with maximum coverage of 15-fold, we detected 116 313 heterozygous SNPs, whose major allele frequencies lay within a two-sided 95% confidence interval (see Material and Methods). Recently, 2 129 442 heterozygous SNPs have been described in the domestic Bactrian camel genome (Jirimutu et al. 2012). However, as these sequences have not been made publicly accessible, we could not cross-check our data. Therefore, we compared our results with other domesticated ungulates for which SNP data are available. Whole-genome resequencing of a single Bos taurus animal for SNP detection (Eck et al. 2009) resulted in 749 091 heterozygous and 1 694 546 homozygous polymorphisms in comparison with the cattle reference genome bosTau 4.0 (Elsik et al. 2009). The comparatively lower numbers of heterozygous SNPs in the Bactrian camel analyzed in this study and in the single Fleckvieh cattle (Eck et al. 2009) might be due to the fact that little more than a half of the Bactrian genome has been sequenced and to the low genome sequencing depths of 6.6- and 7.4-fold, respectively. It has been estimated that a 20- to 30-fold coverage is necessary to discriminate 99% of the heterozygous variants (Li et al. 2008). For sites with a low coverage, the probability of sampling just one of the parental chromosomes is relatively high, which consequently would lead to an underestimation of the heterozygosity and nucleotide diversity (Lynch 2008). Also, both sequenced individuals were male and therefore missing the X-chromosomal heterozygous polymorphisms.

Figure 3.

Distribution of the mapping quality. Only PE reads with a minimum mapping quality (q) of 20 and mapped in proper pairs were used for the analyses. 91.5% of the PE reads show q = 60. The slightly increased number of reads with q between 20 and 30 are due to mapping hits in repetitive regions (data not shown).

Figure 4.

Number of mapped reads distributed over the contig lengths. The number of reads mapped to a contig increases with the length of the contigs.

To catalog the genomic diversity within a single individual, we used the program mlRho (Haubold et al. 2010) and obtained a likelihood estimation of the population mutation rate θ = 4N_eμ of 1.29×10^–3 (CI: 1.28×10^–3; 1.29×10^–3). As the calculations of the estimators are based on assembled shotgun reads, we used only positions with a minimum 4-fold coverage (Haubold et al. 2010). Second-generation sequencing techniques are prone to error rates, possibly in the order of the targeted genetic diversity. Therefore, this software additionally computes a likelihood estimation of the sequencing error rate ε. In the case of the shotgun-sequenced Bactrian camel genome ε equaled 6.64×10^–4, which was 10 times less than the genuine polymorphisms. The nucleotide diversity π, also known as the average pairwise nucleotide differences in a sample of DNA sequences (Nei and Li 1979; Nei and Kumar 2000), is a measure of the average genome-wide heterozygosity and can be used as an estimator of the scaled mutation rate θ = 4N_eμ, assuming random mating and the infinite sites mutation model (Hamilton 2009). In mlRho, π is interpreted as θ without any numerical changes (Haubold et al. 2010). At low coverages, the ML estimates can be downwardly biased (Lynch 2008); therefore, we calculated the nucleotide diversity also with a minimum coverage of 6-, 8-, and 10-fold. However, we saw only a slight increase of θ at higher coverages, while the estimated error rates remained stable (Figure 5), rendering our results of the within-individual nucleotide diversity as robust. Moreover, our results are comparable to the heterozygosity (1.0×10^–3) estimated across the whole genome of a domestic Bactrian camel (Jirimutu et al. 2012). Individual-based estimates of heterozygosity can provide information on relative levels of inbreeding in nonrandom mating populations (Lynch 2008). We observed that compared with other domesticated ungulates, the nucleotide diversity in a single Bactrian camel is higher than that in cattle (9.4×10^–4; Eck et al. 2009) but similar to pig (1.1–2.1×10^–3; Amaral et al. 2009).

Figure 5.

Average ML estimates for the nucleotide diversity (θ) and sequencing error rate (ε). The values for θ and ε calculated with a minimum coverage of 4-, 6-, 8-, and 10-fold do not display a downward bias of θ at lower sequencing depths apart from a slight increase at 10-fold coverage, while ε remains stable throughout the different estimates.

To gain comparative genome-wide information within the Old World camelids, we used the available dromedary ESTs (AL-Swailem et al. 2010; Otu, H. personal communication; http://camel.kacst.edu.sa), which were already assembled in contigs corresponding to genes. We aligned these EST contigs against the Bactrian camel contig sequences and found an overlap of 20 014 (84.8%; see online supplementary Table 1) out of 23 602 genes (Al-Swailem et al. 2010), suggesting that most of the homologos genes are recovered in our genome assembly. Further analyses will be necessary to identify one-to-one ortholog pairs.

In this study, we estimated heterozygous SNPs and population mutation parameters from an individual Bactrian camel and show that the predicted genetic diversity within a single individual matches the population-wide computations in other domestic ungulates. Moreover, we present a first comparative genomic alignment between the Old World camelid species, the dromedary and the Bactrian camel. Our results provide a template for future genome-wide association and comparative studies to define underlying genotypes of specific favored phenotypes. Subsequent individual-based more detailed analysis will have the purpose of locating regions with unusual high or low levels of nucleotide diversity that hint to loci and genomic regions under selection during the process of camel domestication.

Supplementary Material

Supplementary material can be found at http://www.jhered.oxfordjournals.org/.

Funding

Austrian Programme for Advanced Research and Technology- fellowship of the Austrian Academy of Sciences (11506) to P.B.;Austrian Science Fund FWF (P21084-B17) to P.B.