I would like to inform the worm community that more than 3,000 GenBank entries attributed to Caenorhabditis (C. angaria and C. remanei) do not belong to Nematoda.
Bioinformatic evidence indicates that the purported Caenorhabditis sequences actually belong to a novel bacterial species (Leucobacter sp. AEAR), which has been unintentionally sequenced together with its eukaryotic host . A near complete genome of the bacterium has been obtained by targeted assembly of Caenorhabditis reads.
Details on the identification of the contaminating DNA and a description of a bacterial species which is thought to establish a symbiotic relationship with Caenorhabditis can be found in the newly published paper: http://la-press.com/article.php?article_id=3557
Best regards,
Riccardo Percudani
Department of Biosciences,
University of Parma,
Italy
Do you have by chance the regions of potential contamination of the C.remanei and C.angaria? Then we could import them, mark them up and if necessary change the genome sequence and annotation.
Such information was supposed to be included as supplementary data, but I see that it is still missing from the journal web site. Please find below the links to the files in a Google drive.
Lsp41_contigs.fa Velvet contigs – optimized bacterial assembly
Lsp41_scaffolds.fa Bambus scaffolds + unlinked contigs (>1000 bp.)
Lsp41_reads.fa.gz C. angaria (Illumina) and C. remanei (Sanger) reads in the bacterial assembly
Lsp41_ncRNAs.fa 16S rRNA, 23S rRNA, 5S rRNA, 44 tRNAs
Lsp41_annotated.fa 2778 annotated protein sequences
C_remanei_refseq.blasttable 75 C. remanei Refseq entries with >95% id. over >100 bp.
C_remanei_wgs.blasttable 229 C. remanei wgs entries with >95% id. over >100 bp.
C_angaria_wgs.blasttable 3069 C. angaria wgs entries with >95% id. over >100 bp.