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Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.

Qi M, Wang P, O'Toole N, Barboza PS, Ungerfeld E, Leigh MB, Selinger LB, Butler G, Tsang A, McAllister TA, Forster RJ - PLoS ONE (2011)

Bottom Line: These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies.The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes.This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes.

View Article: PubMed Central - PubMed

Affiliation: Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada.

ABSTRACT

Background: Herbivores rely on digestive tract lignocellulolytic microorganisms, including bacteria, fungi and protozoa, to derive energy and carbon from plant cell wall polysaccharides. Culture independent metagenomic studies have been used to reveal the genetic content of the bacterial species within gut microbiomes. However, the nature of the genes encoded by eukaryotic protozoa and fungi within these environments has not been explored using metagenomic or metatranscriptomic approaches.

Methodology/principal findings: In this study, a metatranscriptomic approach was used to investigate the functional diversity of the eukaryotic microorganisms within the rumen of muskoxen (Ovibos moschatus), with a focus on plant cell wall degrading enzymes. Polyadenylated RNA (mRNA) was sequenced on the Illumina Genome Analyzer II system and 2.8 gigabases of sequences were obtained and 59129 contigs assembled. Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies.

Conclusions/significance: The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes. This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes.

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Related in: MedlinePlus

Phylogenetic distribution of muskoxen rumen metatranscriptome putative protein encoding reads (a total of 21.1 million) based on MEGAN analysis of top BLASTX hits against the NRMO database.The percentages of the major phylogenetic groups were indicated.
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pone-0020521-g002: Phylogenetic distribution of muskoxen rumen metatranscriptome putative protein encoding reads (a total of 21.1 million) based on MEGAN analysis of top BLASTX hits against the NRMO database.The percentages of the major phylogenetic groups were indicated.

Mentions: The first BLASTX match was used to estimate the possible origin of each putative protein coding RNA reads, according to MEGAN analysis (Figure 2). About 6.6 million reads (31%) showed highest similarity to proteins from the Eukaryota kingdom. Among these, Rumen anaerobic fungi, which belong to the phylum Neocallimastigomycota [28], were represented by 1.4 million reads. Rumen ciliate protozoa, which belong to the Litostomatea class of Alveolata group, were represented by 1.1 million reads. At the genus level, the most represented genera were known rumen/anaerobic species, including Entodinium, Piromyces, Neocallimastix, Trichomonas, Orpinomyces, Entamoeba, and Epidinium, that were represented by over 100,000 reads each (Figure S3). A total of 0.7 million reads (3.4%) and 0.02 million reads (0.1%) were binned to Bacteria and Archaea kingdoms, respectively.


Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.

Qi M, Wang P, O'Toole N, Barboza PS, Ungerfeld E, Leigh MB, Selinger LB, Butler G, Tsang A, McAllister TA, Forster RJ - PLoS ONE (2011)

Phylogenetic distribution of muskoxen rumen metatranscriptome putative protein encoding reads (a total of 21.1 million) based on MEGAN analysis of top BLASTX hits against the NRMO database.The percentages of the major phylogenetic groups were indicated.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3105075&req=5

pone-0020521-g002: Phylogenetic distribution of muskoxen rumen metatranscriptome putative protein encoding reads (a total of 21.1 million) based on MEGAN analysis of top BLASTX hits against the NRMO database.The percentages of the major phylogenetic groups were indicated.
Mentions: The first BLASTX match was used to estimate the possible origin of each putative protein coding RNA reads, according to MEGAN analysis (Figure 2). About 6.6 million reads (31%) showed highest similarity to proteins from the Eukaryota kingdom. Among these, Rumen anaerobic fungi, which belong to the phylum Neocallimastigomycota [28], were represented by 1.4 million reads. Rumen ciliate protozoa, which belong to the Litostomatea class of Alveolata group, were represented by 1.1 million reads. At the genus level, the most represented genera were known rumen/anaerobic species, including Entodinium, Piromyces, Neocallimastix, Trichomonas, Orpinomyces, Entamoeba, and Epidinium, that were represented by over 100,000 reads each (Figure S3). A total of 0.7 million reads (3.4%) and 0.02 million reads (0.1%) were binned to Bacteria and Archaea kingdoms, respectively.

Bottom Line: These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies.The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes.This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes.

View Article: PubMed Central - PubMed

Affiliation: Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada.

ABSTRACT

Background: Herbivores rely on digestive tract lignocellulolytic microorganisms, including bacteria, fungi and protozoa, to derive energy and carbon from plant cell wall polysaccharides. Culture independent metagenomic studies have been used to reveal the genetic content of the bacterial species within gut microbiomes. However, the nature of the genes encoded by eukaryotic protozoa and fungi within these environments has not been explored using metagenomic or metatranscriptomic approaches.

Methodology/principal findings: In this study, a metatranscriptomic approach was used to investigate the functional diversity of the eukaryotic microorganisms within the rumen of muskoxen (Ovibos moschatus), with a focus on plant cell wall degrading enzymes. Polyadenylated RNA (mRNA) was sequenced on the Illumina Genome Analyzer II system and 2.8 gigabases of sequences were obtained and 59129 contigs assembled. Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies.

Conclusions/significance: The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes. This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes.

Show MeSH
Related in: MedlinePlus