Abstract
BackgroundThe cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals. Currently, there are two cattle genome sequence assemblies (UMD3.1 and Btau4.6) from groups using dissimilar assembly algorithms, which were complemented by genetic and physical map resources. However, past comparisons between these assemblies revealed substantial differences. Consequently, such discordances have engendered ambiguities when using reference sequence data, impacting genomic studies in cattle and motivating construction of a new optical map resource--BtOM1.0--to guide comparisons and improvements to the current sequence builds. Accordingly, our comprehensive comparisons of BtOM1.0 against the UMD3.1 and Btau4.6 sequence builds tabulate large-to-immediate scale discordances requiring mediation.ResultsThe optical map, BtOM1.0, spanning the B. taurus genome (Hereford breed, L1 Dominette 01449) was assembled from an optical map dataset consisting of 2,973,315 (439 X; raw dataset size before assembly) single molecule optical maps (Rmaps; 1 Rmap = 1 restriction mapped DNA molecule) generated by the Optical Mapping System. The BamHI map spans 2,575.30 Mb and comprises 78 optical contigs assembled by a combination of iterative (using the reference sequence: UMD3.1) and de novo assembly techniques. BtOM1.0 is a high-resolution physical map featuring an average restriction fragment size of 8.91 Kb. Comparisons of BtOM1.0 vs. UMD3.1, or Btau4.6, revealed that Btau4.6 presented far more discordances (7,463) vs. UMD3.1 (4,754). Overall, we found that Btau4.6 presented almost double the number of discordances than UMD3.1 across most of the 6 categories of sequence vs. map discrepancies, which are: COMPLEX (misassembly), DELs (extraneous sequences), INSs (missing sequences), ITs (Inverted/Translocated sequences), ECs (extra restriction cuts) and MCs (missing restriction cuts).ConclusionAlignments of UMD3.1 and Btau4.6 to BtOM1.0 reveal discordances commensurate with previous reports, and affirm the NCBI’s current designation of UMD3.1 sequence assembly as the “reference assembly” and the Btau4.6 as the “alternate assembly.” The cattle genome optical map, BtOM1.0, when used as a comprehensive and largely independent guide, will greatly assist improvements to existing sequence builds, and later serve as an accurate physical scaffold for studies concerning the comparative genomics of cattle breeds.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1823-7) contains supplementary material, which is available to authorized users.
Highlights
The cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals
The cattle genome was originally selected for sequencing due to its unique biology and economic importance, virtues that are strengthened by its role as a model organism for understanding other ruminants, or mammals
Optical map dataset Genomic DNA was prepared from L1 Dominette 014490 blood samples, after separation of white blood cells, and BamHI restriction mapped using our Optical Mapping pipeline (Materials and Methods)
Summary
The cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals. Domestic cattle comprise more than 800 breeds and are grouped taxonomically into two species—Bos taurus (taurine) and B. indicus (indicine)—which were evolved from the ancestral species of B. primigenius. Given this large and venerable resource of cattle breeds, cattle research efforts have greatly contributed to our knowledge of genetics, endocrine function, fertilization, growth, lactation and mammalian biology. The cattle genome was originally selected for sequencing due to its unique biology and economic importance, virtues that are strengthened by its role as a model organism for understanding other ruminants, or mammals
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