Limits...
Analysis and functional classification of transcripts from the nematode Meloidogyne incognita.

McCarter JP, Mitreva MD, Martin J, Dante M, Wylie T, Rao U, Pape D, Bowers Y, Theising B, Murphy CV, Kloek AP, Chiapelli BJ, Clifton SW, Bird DM, Waterston RH - Genome Biol. (2003)

Bottom Line: Molecular characterization of these species as well as the development of new techniques for control can benefit from genomic approaches.In addition to identifying putative nematode-specific and Tylenchida-specific genes, sequencing revealed previously uncharacterized horizontal gene transfer candidates in Meloidogyne with high identity to rhizobacterial genes including homologs of nodL acetyltransferase and novel cellulases.With sequencing from plant parasitic nematodes accelerating, the approaches to transcript characterization described here can be applied to more extensive datasets and also provide a foundation for more complex genome analyses.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genome Sequencing Center, Department of Genetics, Box 8501, Washington University School of Medicine, St, Louis, MO 63108, USA. jmccarte@watson.wustl.edu

ABSTRACT

Background: Plant parasitic nematodes are major pathogens of most crops. Molecular characterization of these species as well as the development of new techniques for control can benefit from genomic approaches. As an entrée to characterizing plant parasitic nematode genomes, we analyzed 5,700 expressed sequence tags (ESTs) from second-stage larvae (L2) of the root-knot nematode Meloidogyne incognita.

Results: From these, 1,625 EST clusters were formed and classified by function using the Gene Ontology (GO) hierarchy and the Kyoto KEGG database. L2 larvae, which represent the infective stage of the life cycle before plant invasion, express a diverse array of ligand-binding proteins and abundant cytoskeletal proteins. L2 are structurally similar to Caenorhabditis elegans dauer larva and the presence of transcripts encoding glyoxylate pathway enzymes in the M. incognita clusters suggests that root-knot nematode larvae metabolize lipid stores while in search of a host. Homology to other species was observed in 79% of translated cluster sequences, with the C. elegans genome providing more information than any other source. In addition to identifying putative nematode-specific and Tylenchida-specific genes, sequencing revealed previously uncharacterized horizontal gene transfer candidates in Meloidogyne with high identity to rhizobacterial genes including homologs of nodL acetyltransferase and novel cellulases.

Conclusions: With sequencing from plant parasitic nematodes accelerating, the approaches to transcript characterization described here can be applied to more extensive datasets and also provide a foundation for more complex genome analyses.

Show MeSH

Related in: MedlinePlus

Distribution of contigs by size of longest ORF. Solid line, contigs with any database homology by BLASTX (1,445). Dotted line, contigs without database homology (353).
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC154577&req=5

Figure 4: Distribution of contigs by size of longest ORF. Solid line, contigs with any database homology by BLASTX (1,445). Dotted line, contigs without database homology (353).

Mentions: The 20% of contigs (353) that had no homology may contain novel or diverged amino-acid coding sequences that are specific to Meloidogyne species or even to M. incognita only. Alternatively, clusters which containing mostly 3' or 5' untranslated regions (UTRs) would lack BLASTX homology because they are non-coding or contain too short a coding sequence to result in significant homology. To examine this latter possibility contig consensus sequences with and without BLASTX homology were examined to determine their longest open reading frame (ORF). The distribution of ORF sizes indicates that clusters without homology contain two populations; one population of novel protein-coding sequences with a similar distribution of ORF sizes to that found in sequences with homology, and a second population of UTR sequences containing random or generally short ORFs (Figure 4). The combined distribution is bimodal (relatively high left shoulder) with a mean ORF size of 140 amino acids versus a mean ORF size of 172 amino acids for sequences with homology. A further characterization of novel M. incognita genes could begin by examining those with longer ORFs as these are most likely to be real coding regions.


Analysis and functional classification of transcripts from the nematode Meloidogyne incognita.

McCarter JP, Mitreva MD, Martin J, Dante M, Wylie T, Rao U, Pape D, Bowers Y, Theising B, Murphy CV, Kloek AP, Chiapelli BJ, Clifton SW, Bird DM, Waterston RH - Genome Biol. (2003)

Distribution of contigs by size of longest ORF. Solid line, contigs with any database homology by BLASTX (1,445). Dotted line, contigs without database homology (353).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC154577&req=5

Figure 4: Distribution of contigs by size of longest ORF. Solid line, contigs with any database homology by BLASTX (1,445). Dotted line, contigs without database homology (353).
Mentions: The 20% of contigs (353) that had no homology may contain novel or diverged amino-acid coding sequences that are specific to Meloidogyne species or even to M. incognita only. Alternatively, clusters which containing mostly 3' or 5' untranslated regions (UTRs) would lack BLASTX homology because they are non-coding or contain too short a coding sequence to result in significant homology. To examine this latter possibility contig consensus sequences with and without BLASTX homology were examined to determine their longest open reading frame (ORF). The distribution of ORF sizes indicates that clusters without homology contain two populations; one population of novel protein-coding sequences with a similar distribution of ORF sizes to that found in sequences with homology, and a second population of UTR sequences containing random or generally short ORFs (Figure 4). The combined distribution is bimodal (relatively high left shoulder) with a mean ORF size of 140 amino acids versus a mean ORF size of 172 amino acids for sequences with homology. A further characterization of novel M. incognita genes could begin by examining those with longer ORFs as these are most likely to be real coding regions.

Bottom Line: Molecular characterization of these species as well as the development of new techniques for control can benefit from genomic approaches.In addition to identifying putative nematode-specific and Tylenchida-specific genes, sequencing revealed previously uncharacterized horizontal gene transfer candidates in Meloidogyne with high identity to rhizobacterial genes including homologs of nodL acetyltransferase and novel cellulases.With sequencing from plant parasitic nematodes accelerating, the approaches to transcript characterization described here can be applied to more extensive datasets and also provide a foundation for more complex genome analyses.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genome Sequencing Center, Department of Genetics, Box 8501, Washington University School of Medicine, St, Louis, MO 63108, USA. jmccarte@watson.wustl.edu

ABSTRACT

Background: Plant parasitic nematodes are major pathogens of most crops. Molecular characterization of these species as well as the development of new techniques for control can benefit from genomic approaches. As an entrée to characterizing plant parasitic nematode genomes, we analyzed 5,700 expressed sequence tags (ESTs) from second-stage larvae (L2) of the root-knot nematode Meloidogyne incognita.

Results: From these, 1,625 EST clusters were formed and classified by function using the Gene Ontology (GO) hierarchy and the Kyoto KEGG database. L2 larvae, which represent the infective stage of the life cycle before plant invasion, express a diverse array of ligand-binding proteins and abundant cytoskeletal proteins. L2 are structurally similar to Caenorhabditis elegans dauer larva and the presence of transcripts encoding glyoxylate pathway enzymes in the M. incognita clusters suggests that root-knot nematode larvae metabolize lipid stores while in search of a host. Homology to other species was observed in 79% of translated cluster sequences, with the C. elegans genome providing more information than any other source. In addition to identifying putative nematode-specific and Tylenchida-specific genes, sequencing revealed previously uncharacterized horizontal gene transfer candidates in Meloidogyne with high identity to rhizobacterial genes including homologs of nodL acetyltransferase and novel cellulases.

Conclusions: With sequencing from plant parasitic nematodes accelerating, the approaches to transcript characterization described here can be applied to more extensive datasets and also provide a foundation for more complex genome analyses.

Show MeSH
Related in: MedlinePlus