Reconstruction of metabolic pathways for the cattle genome

Seo, Seongwon; Lewin, Harris A.

doi:10.1186/1752-0509-3-33

Cited by 37 publications

(48 citation statements)

References 86 publications

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“…Metabolic reconstruction or reconstruction of metabolic pathways of a genome is a process of linking known enzymatic reactions and pathways to annotated genes of the genome (Seo and Lewin, 2009). There have been many attempts to reconstruct metabolic pathways for a wide variety of organisms, and various bioinformatic tools are available for reconstructing metabolic pathways automatically (see the review by Pitkä nen et al (2010)).…”

Section: Linking Cattle Genome To Ruminant Metabolismmentioning

confidence: 99%

“…For example, Seo and Lewin (2009) found that 53% of pathways in the initial automated reconstruction for cattle needed to be deleted or modified, and manually modified or created 66 mammalian-specific metabolic pathways from the reference pathways in MetaCyc. Accumulated knownledge about mammalian enzymatic reactions and metabolic pathways and deposition of these information in biological databases (e.g.…”

Section: Linking Cattle Genome To Ruminant Metabolismmentioning

confidence: 99%

“…Metabolic reconstruction of the cattle genome Seo and Lewin (2009) reconstructed metabolic pathways of the cattle genome and developed cattle-specific PGDB based on Btau_3.1, named as CattleCyc. For the metabolic reconstruction, an amalgamated cattle genome database that incorporated all the available functional annotation information for cattle genes and proteins from multiple sources of biological databases, for instance, NCBI (http://www.ncbi.nlm.nih.gov), Ensembl (http:// www.ensembl.org), UniProt (www.uniprot.org) and KEGG (www.genome.jp/kegg/).…”

Section: Linking Cattle Genome To Ruminant Metabolismmentioning

confidence: 99%

“…Metabolic pathways encoded in the cattle genome were then identified using Pathway Tools, followed by comprehensive manual curation based on scientific literature. To identify unpredicted metabolic pathways and fill the gaps of functional annotation of cattle genes due to lack of experimental evidence, a comparative and metabolic-centered approach was used (Seo and Lewin, 2009).…”

Section: Linking Cattle Genome To Ruminant Metabolismmentioning

confidence: 99%

“…Metabolic pathways encoded in the cattle genome have been reconstructed for the first time in a farm animal (Seo and Lewin, 2009), and a web-based cattle-specific pathway genome database and tool, CattleCyc, has been developed providing a platform for studying cattle metabolism using a systems biology approach. This will facilitate the functional analysis of various 'omics' data (e.g.…”

Section: Introductionmentioning

confidence: 99%

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Cattle genomics and its implications for future nutritional strategies for dairy cattle

Seo

Larkin

Loor

2013

Animal

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The recently sequenced cattle (Bos taurus) genome unraveled the unique genomic features of the species and provided the molecular basis for applying a systemic approach to systematically link genomic information to metabolic traits. Comparative analysis has identified a variety of evolutionary adaptive features in the cattle genome, such as an expansion of the gene families related to the rumen function, large number of chromosomal rearrangements affecting regulation of genes for lactation, and chromosomal rearrangements that are associated with segmental duplications and copy number variations. Metabolic reconstruction of the cattle genome has revealed that core metabolic pathways are highly conserved among mammals although five metabolic genes are deleted or highly diverged and seven metabolic genes are present in duplicate in the cattle genome compared to their human counter parts. The evolutionary loss and gain of metabolic genes in the cattle genome may reflect metabolic adaptations of cattle. Metabolic reconstruction also provides a platform for better understanding of metabolic regulation in cattle and ruminants. A substantial body of transcriptomics data from dairy and beef cattle under different nutritional management and across different stages of growth and lactation are already available and will aid in linking the genome with metabolism and nutritional physiology of cattle. Application of cattle genomics has great potential for future development of nutritional strategies to improve efficiency and sustainability of beef and milk production. One of the biggest challenges is to integrate genomic and phenotypic data and interpret them in a biological and practical platform. Systems biology, a holistic and systemic approach, will be very useful in overcoming this challenge.

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Section: Linking Cattle Genome To Ruminant Metabolismmentioning

confidence: 99%

Section: Linking Cattle Genome To Ruminant Metabolismmentioning

confidence: 99%

Section: Linking Cattle Genome To Ruminant Metabolismmentioning

confidence: 99%

Section: Linking Cattle Genome To Ruminant Metabolismmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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