A whole-genome assembly of the domestic cow, Bos taurus

Abstract

Background: The genome of the domestic cow, Bos taurus, was sequenced using a mixture of hierarchical and whole-genome shotgun sequencing methods.

Results: We have assembled the 35 million sequence reads and applied a variety of assembly improvement techniques, creating an assembly of 2.86 billion base pairs that has multiple improvements over previous assemblies: it is more complete, covering more of the genome; thousands of gaps have been closed; many erroneous inversions, deletions, and translocations have been corrected; and thousands of single-nucleotide errors have been corrected. Our evaluation using independent metrics demonstrates that the resulting assembly is substantially more accurate and complete than alternative versions.

Conclusions: By using independent mapping data and conserved synteny between the cow and human genomes, we were able to construct an assembly with excellent large-scale contiguity in which a large majority (approximately 91%) of the genome has been placed onto the 30 B. taurus chromosomes. We constructed a new cow-human synteny map that expands upon previous maps. We also identified for the first time a portion of the B. taurus Y chromosome.

Figure 1

Chromosome (Chr) lengths (in base pairs) based on amount of sequence in the B. taurus assembly placed on each chromosome.

Figure 2

Cumulative plot of the N statistic for both the UMD2 (blue) and BCM4 (red) assemblies. Each point (X, Y) in the plot shows the contig size Y such that X% of the genome is contained in contigs of length Y or larger, for a genome of size 2.5 Gbp. For example, the N50 size for each assembly corresponds to the value of Y at X = 50; for UMD2 this value is 93,156 and for BCM4 it is 81,627.

Figure 3

Examples of large-scale disagreements between UMD2 and BCM4. (a) Dot-plot alignment of the region between 15 Mbp and 25 Mbp of chromosome 26 showing a large inversion in BCM4 compared to UMD2; (b) positions of Cmap markers for the same region of chromosome 26, plotted against their positions in UMD2 (blue) and BCM4 (red), showing that Cmap supports the UMD2 assembly. (c) Alignment of 7 Mbp of chromosome 27, showing a large inversion in BCM4 compared to UMD2; (d) positions of Cmap markers for the same region of chromosome 27, showing as in (b) that Cmap is in much closer agreement with the UMD2 assembly.

Figure 4

Assembly comparison by gene mapping. (a) Number of RefSeq mRNA sequences (out of 8,689) that can be aligned to each genome assembly at varying coverage cutoffs (horizontal axis) with at least 95% sequence identity. (b) Difference in the number of mRNAs mapping to the two assemblies at different levels of coverage, plotted as UMD2 minus BCM4. Negative values indicate that BCM4 has more genes at a given level, while positive values indicate that UMD2 has more. For example, at 0-5% coverage, 104 more mRNAs map to BCM4 than to UMD2. At 95-100% coverage, 275 more mRNAs map to UMD2. Blue, UMD2 assembly; red, BCM4 assembly.

Figure 5

Aligment of B. taurus chromosome X to human chromosome X, showing regions of large-scale synteny. Most of the two chromosomes is shared in the five large blocks evident in the figure. Red: sequences are aligned in the same orientation; blue: sequences are aligned, but one is in the reverse complement orientation. The inverted (blue) block at approximately 25 Mbp in B. taurus, although small at this scale, spans over 800 Kbp.