how and why dna barcodes underestimate the diversity of microbial eukaryotes如何以及为什么真核生物dna条形码低估微生物的多样性.pdfVIP

How and Why DNA Barcodes Underestimate the Diversity of Microbial Eukaryotes 1,2 3 1,2 ´ 1,2 Gwenael Piganeau *, Adam Eyre-Walker , Nigel Grimsley , Herve Moreau ´ ´ 1 UPMC Univ Paris 06, UMR 7232, Observatoire Oceanologique, Banyuls-sur-Mer, France, 2 CNRS, UMR 7232, Observatoire Oceanologique, Banyuls-sur-Mer, France, 3 School of Life Sciences, Sussex University, Brighton, United Kingdom Abstract Background: Because many picoplanktonic eukaryotic species cannot currently be maintained in culture, direct sequencing of PCR-amplified 18S ribosomal gene DNA fragments from filtered sea-water has been successfully used to investigate the astounding diversity of these organisms. The recognition of many novel planktonic organisms is thus based solely on their 18S rDNA sequence. However, a species delimited by its 18S rDNA sequence might contain many cryptic species, which are highly differentiated in their protein coding sequences. Principal Findings: Here, we investigate the issue of species identification from one gene to the whole genome sequence. Using 52 whole genome DNA sequences, we estimated the global genetic divergence in protein coding genes between organisms from different lineages and compared this to their ribosomal gene sequence divergences. We show that this relationship between proteome divergence and 18S divergence is lineage dependant. Unicellular lineages have especially low 18S divergences relative to their protein sequence divergences, suggesting that 18S ribosomal genes are too conservative to assess planktonic eukaryotic diversity. W