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Metagenomic analysis of the turkey gut RNA virus community.

Day JM, Ballard LL, Duke MV, Scheffler BE, Zsak L - Virol. J. (2010)

Bottom Line: High-throughput nucleic acid pyrosequencing is a powerful diagnostic technology capable of determining the full genomic repertoire present in a complex environmental sample.This approach yielded numerous sequences homologous to viruses in the BLAST nr protein database, many of which have not been described in turkeys.Our analysis of this turkey gut RNA metagenome focuses in particular on the turkey-origin members of the Picornavirales, the Caliciviridae, and the turkey Picobirnaviruses.

View Article: PubMed Central - HTML - PubMed

Affiliation: Southeast Poultry Research Laboratory Agricultural Research Service United States Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA. michael.day@ars.usda.gov

ABSTRACT
Viral enteric disease is an ongoing economic burden to poultry producers worldwide, and despite considerable research, no single virus has emerged as a likely causative agent and target for prevention and control efforts. Historically, electron microscopy has been used to identify suspect viruses, with many small, round viruses eluding classification based solely on morphology. National and regional surveys using molecular diagnostics have revealed that suspect viruses continuously circulate in United States poultry, with many viruses appearing concomitantly and in healthy birds. High-throughput nucleic acid pyrosequencing is a powerful diagnostic technology capable of determining the full genomic repertoire present in a complex environmental sample. We utilized the Roche/454 Life Sciences GS-FLX platform to compile an RNA virus metagenome from turkey flocks experiencing enteric disease. This approach yielded numerous sequences homologous to viruses in the BLAST nr protein database, many of which have not been described in turkeys. Our analysis of this turkey gut RNA metagenome focuses in particular on the turkey-origin members of the Picornavirales, the Caliciviridae, and the turkey Picobirnaviruses.

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MEGAN tree with taxonomic assignments. The blastx output of the total contigs was assembled using the gsAssembler software. Circles located next to taxa are proportional to the total number of contigs identified in the pyrosequencing run and subsequent assembly (see Materials and Methods).
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Figure 1: MEGAN tree with taxonomic assignments. The blastx output of the total contigs was assembled using the gsAssembler software. Circles located next to taxa are proportional to the total number of contigs identified in the pyrosequencing run and subsequent assembly (see Materials and Methods).

Mentions: The initial pyrosequencing runs produced in excess of 139,000,000 bases of high quality nucleotide sequence with an average read length of 362. The sequence data was used to assemble 6526 contigs ranging in size from 97 to 2578 bp, with the majority of contigs falling in the range of approximately 250 to 450 bp. 4563 contigs produced no hits in the nr protein database using the blastx search parameters and the MEGAN default settings. 724 contigs had similarity to sequences from cellular organisms, including bacteria, fungi and avian species. 788 contigs had similarity to RNA viral sequences, including sequences from the dsRNA viruses (Reoviridae and Picobirnaviruses), and the ssRNA viruses (Caliciviridae, Leviviridae, Picornavirales, and Astroviridae) (Figure 1). The number of cellular sequences in the present dataset are likely due to the use of intestinal homogenates, which included intestinal tissue in order to ensure the discovery of cell-associated viruses in the submitted samples. The tblastx search output produced a MEGAN taxon tree similar to the one presented in Figure 1 and revealed that many of the unassigned contigs were similar to avian sequences.


Metagenomic analysis of the turkey gut RNA virus community.

Day JM, Ballard LL, Duke MV, Scheffler BE, Zsak L - Virol. J. (2010)

MEGAN tree with taxonomic assignments. The blastx output of the total contigs was assembled using the gsAssembler software. Circles located next to taxa are proportional to the total number of contigs identified in the pyrosequencing run and subsequent assembly (see Materials and Methods).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2991317&req=5

Figure 1: MEGAN tree with taxonomic assignments. The blastx output of the total contigs was assembled using the gsAssembler software. Circles located next to taxa are proportional to the total number of contigs identified in the pyrosequencing run and subsequent assembly (see Materials and Methods).
Mentions: The initial pyrosequencing runs produced in excess of 139,000,000 bases of high quality nucleotide sequence with an average read length of 362. The sequence data was used to assemble 6526 contigs ranging in size from 97 to 2578 bp, with the majority of contigs falling in the range of approximately 250 to 450 bp. 4563 contigs produced no hits in the nr protein database using the blastx search parameters and the MEGAN default settings. 724 contigs had similarity to sequences from cellular organisms, including bacteria, fungi and avian species. 788 contigs had similarity to RNA viral sequences, including sequences from the dsRNA viruses (Reoviridae and Picobirnaviruses), and the ssRNA viruses (Caliciviridae, Leviviridae, Picornavirales, and Astroviridae) (Figure 1). The number of cellular sequences in the present dataset are likely due to the use of intestinal homogenates, which included intestinal tissue in order to ensure the discovery of cell-associated viruses in the submitted samples. The tblastx search output produced a MEGAN taxon tree similar to the one presented in Figure 1 and revealed that many of the unassigned contigs were similar to avian sequences.

Bottom Line: High-throughput nucleic acid pyrosequencing is a powerful diagnostic technology capable of determining the full genomic repertoire present in a complex environmental sample.This approach yielded numerous sequences homologous to viruses in the BLAST nr protein database, many of which have not been described in turkeys.Our analysis of this turkey gut RNA metagenome focuses in particular on the turkey-origin members of the Picornavirales, the Caliciviridae, and the turkey Picobirnaviruses.

View Article: PubMed Central - HTML - PubMed

Affiliation: Southeast Poultry Research Laboratory Agricultural Research Service United States Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA. michael.day@ars.usda.gov

ABSTRACT
Viral enteric disease is an ongoing economic burden to poultry producers worldwide, and despite considerable research, no single virus has emerged as a likely causative agent and target for prevention and control efforts. Historically, electron microscopy has been used to identify suspect viruses, with many small, round viruses eluding classification based solely on morphology. National and regional surveys using molecular diagnostics have revealed that suspect viruses continuously circulate in United States poultry, with many viruses appearing concomitantly and in healthy birds. High-throughput nucleic acid pyrosequencing is a powerful diagnostic technology capable of determining the full genomic repertoire present in a complex environmental sample. We utilized the Roche/454 Life Sciences GS-FLX platform to compile an RNA virus metagenome from turkey flocks experiencing enteric disease. This approach yielded numerous sequences homologous to viruses in the BLAST nr protein database, many of which have not been described in turkeys. Our analysis of this turkey gut RNA metagenome focuses in particular on the turkey-origin members of the Picornavirales, the Caliciviridae, and the turkey Picobirnaviruses.

Show MeSH
Related in: MedlinePlus