Skip to main content

Advertisement

Table 4 Taxonomic distribution of unigene blastx hits in the nr database

From: De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum

  Best blastx hit Lowest common ancestor for blastx hits
Taxonomic category Number of unigenes Percent of unigenes with hits Number of unigenes Percent of Unigenes with hits
Eukaryotes 33,776 97.2% 32,059 92.3%
   Green plants 33,406 96.2% 31,373 90.3%
"Green algae" 175 0.5% 78 0.2%
Land plants 33,231 95.7% 30,822 88.7%
"Bryophytes" 394 1.1% 2,197 6.3%
Vascular plants 32,837 94.5% 16,731 48.2%
Lycophytes 74 0.2% 13 0.0%
Ferns 928 2.7% 435 1.3%
Seed plants 31,835 91.6% 16,015 46.1%
Gymnosperms 8,000 23.0% 866 2.5%
Angiosperms 23,835 68.6% 10,572 30.4%
   Animals 288 0.8% 63 0.2%
   Fungi 0 0.0% 4 0.0%
   Other eukaryotes 77 0.2% 12 0.0%
Bacteria 22 0.1% 91 0.3%
Artificial sequences, hits don't pass threshold, or taxon not assigned 20 0.1% 216 0.6%
  1. Unigenes were searched in the NCBI nr protien database using blastx with an e-value threshold of 1e-10, keeping the best ten hits. Of the 56,256 unigenes, 34,740 (61.8%) had a positive hit. The lowest common ancestor (LCA) assignment for a sequence was calculated using the LCA algorithm implemented in MEGAN v3.9 [61] based on at least three blastx hits with a bitscore greater than 75 and within 10% of the best bitscore. Note: the predicted proteins from Selaginella moellendorffii are not currently included in the nr database and thus are not reflected in these results.