Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome

The
sequence of cattle genome provided a valuable opportunity to systematically
link genetic and metabolic traits of cattle. The objectives of this study were 1)
to reconstruct genome-scale cattle-specific metabolic pathways based on the
most recent and updated cattle genome build and 2) to identify duplicated
metabolic genes in the cattle genome for better understanding of metabolic
adaptations in cattle. A bioinformatic pipeline of an organism for amalgamating
genomic annotations from multiple sources was updated. Using this, an amalgamated
cattle genome database based on UMD_3.1, was created. The amalgamated cattle
genome database is composed of a total of 33,292 genes: 19,123 consensus genes
between NCBI and Ensembl databases, 8,410 and 5,493 genes only found in NCBI or
Ensembl, respectively, and 266 genes from NCBI scaffolds. A metabolic
reconstruction of the cattle genome and cattle pathway genome database (PGDB)
was also developed using Pathway Tools, followed by an intensive manual
curation. The manual curation filled or revised 68 pathway holes, deleted 36
metabolic pathways, and added 23 metabolic pathways. Consequently, the curated
cattle PGDB contains 304 metabolic pathways, 2,460 reactions including 2,371
enzymatic reactions, and 4,012 enzymes. Furthermore, this study identified eight
duplicated genes
in 12 metabolic pathways in the cattle genome compared to human and mouse. Some of these
duplicated genes are related with specific hormone biosynthesis and
detoxifications. The updated
genome-scale metabolic reconstruction is a useful tool for
understanding biology and metabolic characteristics in cattle. There has been significant improvements
in the quality of cattle genome annotations and the MetaCyc database. The duplicated metabolic genes in the cattle
genome compared to human and mouse implies evolutionary
changes in the cattle genome and
provides a useful information for further research on understanding
metabolic adaptations
of cattle.