Journal: PLoS ONE

Article Title: Extensive Pyrosequencing Reveals Frequent Intra-Genomic Variations of Internal Transcribed Spacer Regions of Nuclear Ribosomal DNA

doi: 10.1371/journal.pone.0043971

Figure Lengend Snippet: (A) Pairs of variants are linked using red and blue lines at 100% and 95% identities, respectively. Each open box represents a single variant with relative variant abundance (RVA) over 1%, and each solid box represents the variants with RVA less than 1%. The rulers show the RVA in percentage. (B) The Neighbor-Joining tree of ITS2 in Araliaceae. Numbers are bootstrap values (<50% not shown). One minor variant of ITS2 in Eleutherococcus giraldii showed close affinity to the ITS2 variants of Panax ginseng and was clustered with them. Based on a fossil calibration of the split between Dendropanax and Merrilliopanax at 45 million year ago (MYA), divergence dates among Panax species and among Eleutherococcus species were estimated o be 52 MYA and 25 MYA, respectively.

Article Snippet: A database of full-length ITS2 sequences from the investigated species was compiled using our full-length-match ITS2 pyrosequencing reads (if we obtained more than 50 reads from that sample), and sequences obtained according to standard query sequences using BLAST hits with E-values less than 10 −20 .

Techniques: Variant Assay

Journal: PLoS ONE

Article Title: Extensive Pyrosequencing Reveals Frequent Intra-Genomic Variations of Internal Transcribed Spacer Regions of Nuclear Ribosomal DNA

doi: 10.1371/journal.pone.0043971

Figure Lengend Snippet: Identification efficiency at species level for ITS2 variants from 207 samples of 153 species in 51 genera using best BLAST hit.

Article Snippet: A database of full-length ITS2 sequences from the investigated species was compiled using our full-length-match ITS2 pyrosequencing reads (if we obtained more than 50 reads from that sample), and sequences obtained according to standard query sequences using BLAST hits with E-values less than 10 −20 .

Techniques:

Journal: PLoS ONE

Article Title: Extensive Pyrosequencing Reveals Frequent Intra-Genomic Variations of Internal Transcribed Spacer Regions of Nuclear Ribosomal DNA

doi: 10.1371/journal.pone.0043971

Figure Lengend Snippet: Identification efficiency at species level for ITS2 variants among each of 51 genera using best BLAST hit.

Article Snippet: A database of full-length ITS2 sequences from the investigated species was compiled using our full-length-match ITS2 pyrosequencing reads (if we obtained more than 50 reads from that sample), and sequences obtained according to standard query sequences using BLAST hits with E-values less than 10 −20 .

Techniques:

Journal: PLoS ONE

Article Title: Extensive Pyrosequencing Reveals Frequent Intra-Genomic Variations of Internal Transcribed Spacer Regions of Nuclear Ribosomal DNA

doi: 10.1371/journal.pone.0043971

Figure Lengend Snippet: (A) Comparison of the genetic distances for intra-genomic and intra-specific ITS2 variants (95 dots total). (B) Comparison of the genetic distances for intra-genomic and inter-specific ITS2 variants (207 dots total).

Article Snippet: A database of full-length ITS2 sequences from the investigated species was compiled using our full-length-match ITS2 pyrosequencing reads (if we obtained more than 50 reads from that sample), and sequences obtained according to standard query sequences using BLAST hits with E-values less than 10 −20 .

Techniques: Comparison