Zhou Shiguo, Goldstein Steve, Place Michael, Bechner Michael, Patino Diego, Potamousis Konstantinos, Ravindran Prabu, Pape Louise, Rincon Gonzalo, Hernandez-Ortiz Juan, Medrano Juan F, Schwartz David C
Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA.
Departamento de Materiales, Facultad de Minas, Universidad Nacional de Colombia, Sede Medellin, Calle 75 # 79A-51, Bloque M17, Medellin, Colombia, SA.
BMC Genomics. 2015 Aug 28;16(1):644. doi: 10.1186/s12864-015-1823-7.
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. 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.
The 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).
Alignments 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.
由于牛（Bos taurus）在经济上的重要性以及其作为理解其他反刍动物或哺乳动物的模式生物所具有的独特生物学特性，其基因组最初被选定进行测序。目前，有两组使用不同组装算法得到的牛基因组序列组装结果（UMD3.1和Btau4.6），并辅以遗传和物理图谱资源。然而，过去对这些组装结果的比较显示出显著差异。因此，在使用参考序列数据时，这种不一致性产生了模糊性，影响了牛的基因组研究，并促使构建新的光学图谱资源——BtOM1.0——以指导对当前序列构建的比较和改进。因此，我们将BtOM1.0与UMD3.1和Btau4.6序列构建进行了全面比较，列出了需要调解的从大到直接规模的不一致性。
光学图谱BtOM1.0覆盖了牛（赫里福德品种，L1 Dominette 01449）的基因组，它是由光学图谱数据集组装而成的，该数据集包含由光学图谱系统生成的2,973,315个（439倍；组装前的原始数据集大小）单分子光学图谱（Rmaps；1个Rmap = 1个经限制性酶切图谱分析的DNA分子）。BamHI图谱跨度为2,575.30 Mb，由78个光学重叠群组成，这些重叠群通过迭代（使用参考序列：UMD3.1）和从头组装技术相结合的方式组装而成。BtOM1.0是一个高分辨率的物理图谱，其平均限制性片段大小为8.91 Kb。BtOM1.0与UMD3.1或Btau4.6的比较显示，Btau4.6与UMD3.1（4,754个）相比呈现出更多的不一致性（7,463个）。总体而言，我们发现在序列与图谱差异的6个类别中的大多数类别中，Btau4.6呈现出的不一致性数量几乎是UMD3.1的两倍，这6个类别分别是：COMPLEX（错误组装）、DELs（外来序列）、INSs（缺失序列）、ITs（倒位/易位序列）、ECs（额外的限制性酶切位点）和MCs（缺失的限制性酶切位点）。
UMD3.1和Btau4.6与BtOM1.0的比对揭示了与先前报告相符的不一致性，并确认了NCBI目前将UMD3.1序列组装指定为“参考组装”以及将Btau4.6指定为“替代组装”。牛基因组光学图谱BtOM1.0在用作全面且基本独立的指导时，将极大地有助于改进现有的序列构建，并随后作为牛品种比较基因组学研究的准确物理支架。
