Instruct: Identify the main category of Biorxiv papers based on the titles and abstracts
Query: Bovine pangenome reveals trait-associated structural variation from diverse assembly inputs Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. We generated haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT was sufficient to produce two haplotype-resolved assemblies meeting the standards set by the Vertebrate Genome Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrated significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identified 90 thousand structural variants including 931 overlapping with coding sequences; this approach revealed variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46, and GC that have potential to affect phenotype.
28
The categories of this paper are: communication
22
The categories of this paper are: physiology
31
The categories of this paper are: paleontology
14
The categories of this paper are: biophysics
5
The categories of this paper are: cell
32
The categories of this paper are: zoology
27
The categories of this paper are: pathology
23
The categories of this paper are: immunology
29
The categories of this paper are: education
10
The categories of this paper are: and
18
The categories of this paper are: systems
2
The categories of this paper are: biology
12
The categories of this paper are: behavior
30
The categories of this paper are: scientific
4
The categories of this paper are: neuroscience
11
The categories of this paper are: cognition