Analysis of recent segmental duplications in the bovine genome

Abstract

Background: Duplicated sequences are an important source of gene innovation and structural variation within mammalian genomes. We performed the first systematic and genome-wide analysis of segmental duplications in the modern domesticated cattle (Bos taurus). Using two distinct computational analyses, we estimated that 3.1% (94.4 Mb) of the bovine genome consists of recently duplicated sequences (>or= 1 kb in length, >or= 90% sequence identity). Similar to other mammalian draft assemblies, almost half (47% of 94.4 Mb) of these sequences have not been assigned to cattle chromosomes.

Results: In this study, we provide the first experimental validation large duplications and briefly compared their distribution on two independent bovine genome assemblies using fluorescent in situ hybridization (FISH). Our analyses suggest that the (75-90%) of segmental duplications are organized into local tandem duplication clusters. Along with rodents and carnivores, these results now confidently establish tandem duplications as the most likely mammalian archetypical organization, in contrast to humans and great ape species which show a preponderance of interspersed duplications. A cross-species survey of duplicated genes and gene families indicated that duplication, positive selection and gene conversion have shaped primates, rodents, carnivores and ruminants to different degrees for their speciation and adaptation. We identified that bovine segmental duplications corresponding to genes are significantly enriched for specific biological functions such as immunity, digestion, lactation and reproduction.

Conclusion: Our results suggest that in most mammalian lineages segmental duplications are organized in a tandem configuration. Segmental duplications remain problematic for genome and assembly and we highlight genic regions that require higher quality sequence characterization. This study provides insights into mammalian genome evolution and generates a valuable resource for cattle genomics research.

Figure 1

Comparison of bovine segmental duplications predicted by the WGAC and WSSD algorithms. We initially identified 328.0 (red) and 75.8 Mb (blue) as putative duplications using the WGAC and WSSD analysis, respectively. The overlapping relationship of these two predictions is shown in a Venn diagram. We defined segmental duplications based on the union of significant WGAC hits with less than 94% sequence identity (18.6 Mb, shaded red) and WSSD results (75.8 Mb, shaded blue).

Figure 2

Bovine segmental duplication landscape (≥ 5 kb in legnth, ≥ 90% sequence identity). Intrachromosomal (blue, with connecting lines) and interchromosomal (red bars, without connecting lines) duplications are shown on Batu_4.0. White bars represent gaps in the genome assembly. A local tandem distribution pattern is predominant in bovine segmental duplications. With few exceptions, most intrachromosomal duplications are organized as clusters of tandem or inverted duplications within close proximity (1 Mb). A total of 21 large regions (each ≥ 300 kb in length, total ~12.6 Mb of sequence) are shown as gold bars. Twelve of these duplication blocks (labeled A to L) correspond to known genes (A:LAD1; B:GBP6; C:WC1.1, WC1.2, CD163L1, SYT1; D:WC1.3; E: T-cell receptor alpha clusters; F: T-cell receptor delta clusters; G:ANKRD26, FBXO18; H:Zinc finger protein clusters, ACTR2; I: Zinc finger protein clusters; J: β-defensins 2, 4,7,8, and 10; K: β-defensins 1 and 5; L: VAMP7). For more detail, including sequence identity and pairwise relationships of all duplications and alignments, see http://bfgl.anri.barc.usda.gov/cattleSD/. For details about patterns of interchromosomal duplications, see Additional file 1: Fig. S1.

Figure 3

The distribution of length and percent identity for high-confidence segmental duplication detected by WGAC and WSSD. Panel A shows the length distributions while panel B shows the pairwise sequence identity distribution for the segmental duplications. Red, interchromosomal segmental duplications; blue, intrachromosomal segmental duplications.

Figure 4

The intrachromosomal duplication patterns in mammalian genomes: human and mouse (> 20 kb, > 94%) and dog and cattle (> 10 kb, > 94%). The human genome displays interspersed pattern of recent duplications as compared to the tandem clusters in the mouse, dog and cattle genomes. Based on UCSC Genome Browser Human Net tracks, chrX is syntenic among these mammals. Human chr17 is syntenic to mouse chr11, dog chr9 and chr5 and cattle chr19. Human chr7 is syntenic to mouse chr6 and chr5, dog chr14, chr16, chr18 and chr6 and cattle chr4 and chr25.

Figure 5

FISH confirmation. Examples of metaphase and interphase FISH hybridization with duplicated BAC clones and their associated genes. A. 154H9 (LYZ1: lysozyme 1), B. 170G20 (PDE5A: cGMP-specific phosphodiesterase 5A), C. 27N13 (STX7: syntaxin 7), and D. 303B2 (ZFP2: zinc finger protein 2 homolog). The results of all FISH experiments are available online at http://bfgl.anri.barc.usda.gov/cattleSD/.