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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...

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Autores principales: Kim, Woonsu, Park, Hyesun, Seo, Seongwon
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4798299/
https://www.ncbi.nlm.nih.gov/pubmed/26992093
http://dx.doi.org/10.1371/journal.pone.0150974
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author Kim, Woonsu
Park, Hyesun
Seo, Seongwon
author_facet Kim, Woonsu
Park, Hyesun
Seo, Seongwon
author_sort Kim, Woonsu
collection PubMed
description 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.
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spelling pubmed-47982992016-03-23 Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome Kim, Woonsu Park, Hyesun Seo, Seongwon PLoS One Research Article 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. Public Library of Science 2016-03-18 /pmc/articles/PMC4798299/ /pubmed/26992093 http://dx.doi.org/10.1371/journal.pone.0150974 Text en © 2016 Kim et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Kim, Woonsu
Park, Hyesun
Seo, Seongwon
Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome
title Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome
title_full Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome
title_fullStr Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome
title_full_unstemmed Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome
title_short Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome
title_sort global metabolic reconstruction and metabolic gene evolution in the cattle genome
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4798299/
https://www.ncbi.nlm.nih.gov/pubmed/26992093
http://dx.doi.org/10.1371/journal.pone.0150974
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