Skip to main content

Table 5 Data obtained from MISA (SSR), Blast2GO (GO) and RepeatMasker (RM)

From: Developing molecular tools and insights into the Penstemon genome using genomic reduction and next-generation sequencing

    Penstemonspecies
    P. cyananthus P. dissectus P. davidsonii P. fruticosus
SSR Total SSRs1 97 113 49 58
SSRs/Assembly Length 2.1E-05 (~1/48000) 4.3E-05 (~1/23000) 2.1E-05 (~1/48000) 2.5E-05 (~1/40000)
Repeat Type di- 44.3% 40.7% 46.9% 48.3%
tri- 45.4% 43.4% 44.9% 41.4%
tetra- 10.3% 15.9% 8.2% 10.3%
GO Contigs Analyzed 9,714 5,364 4,882 4,777
Blast Hits Found2 1,899 1,125 1,121 1,091
Annotated Hits 1,430 844 388 826
% Blast Hits 19.5% 21.0% 23.0% 22.8%
% Annotated 14.7% 15.7% 7.9% 17.3%
RM Masked Repeat Elements 28.5% 16.8% 17.4% 16.1%
Retroelements (LTR) 7.8% 3.0% 4.9% 4.6%
DNA Transposons 0.3% 0.9% 1.0% 1.0%
Other Repeats3 20.4% 12.9% 11.6% 10.5%
  1. 1 For MISA, “unmasked” individual species assemblies were used.
  2. 2 Sequence compared to the GenBank refseq-protein database e-value threshold of <1.0e-15.
  3. 3 Other Repeats includes: lines, unclassified repeats, satellites, simple repeats, and low complexity sequence.