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Nuclear Ribosomal Internal Transcribed Spacer Sublocus Termini
in the Amanitaceae

Version 24 - 22 April 2016 
This page records the observed terminal motifs for the 3' end of the 18S rDNA locus, the 5' and 3' ends of the 5.8S rDNA locus, and the 5' end of the 28S rDNA locus.  In Amanita these terminal motifs often have a few adjacent bases [in either ITS1 or ITS2] that appear to be somewhat stable within one or more sections of the genus.  Using the sequences that we have certified as based on vouchers revised in either the Yang or Tulloss laboratories, we have explored:
  • the rDNA terminal motifs

  • the terminal sequences of ITS1 and ITS2
On this page we catalog our findings.

Below there is a drawing showing the order of the components in fungal nuclear ribosomal DNA.  The drawing is followed by outlined blocks providing examples of the (relatively) conserved terminal motifs of the 18S, 5.8S, and 28S segments (pale purple background in the outlined blocks) and the adjacent sequences of bases found at the termini of the ITS1 and ITS2 segments (black background in the outlined blocks).

5'... 18S (SSU)  ITS1  5.8S  ITS2  28S (LSU) ...3'

The ordering (top to bottom) of blocks follows 5' to 3' ordering of elements in the nrDNA.  Motifs and other strings are supplied without alignments and are based on character count.  

18S highly conserved 3' terminal motif

5'... 18S (SSU)  ITS1  5.8S  ITS2  28S (LSU) ...3'

This data is based on 75 sequences representing 21 taxa.

[20 species (73 seq)]a 5'... GGATCATTA 3'
[A. inculta (1 seq)] 5'... AGATCATTA 3'
[A. inculta (1 seq)] 5'... GGGTCATTA 3'

  Notes:

  1. A. albocreata (7 seq), A. aprica (2 seq), A. breckonii (1 seq), A. concentrica (1 seq), A. cruzii (2 seq), A. fibrillopes (1 seq), A. frostiana (5 seq), A. grandis (2 seq), A. ibotengutake (12 seq), A. levistriata (11 seq), A. muscaria (2 seq), A. oleosa (3 seq), A. parcivolvata (3 seq), A. pseudoinculta (4 seq), A. regalis (3 seq), A. roseitincta (3 seq), A. sinensis (2 seq), A. sp-N60 (4 seq), A. subglobosa (2 seq) and A. wellsii (3 seq).

ITS1 observed 5' terminal strings

5'... 18S (SSU)  ITS1  5.8S  ITS2  28S (LSU) ...3'

ITS1 observed 3' terminal strings

5'... 18S (SSU)  ITS1  5.8S  ITS2  28S (LSU) ...3'

5.8S largely conserved 5' terminal motifs

5'... 18S (SSU)  ITS1  5.8S  ITS2  28S (LSU) ...3'

This data is based on 134 sequences representing 39 species.

5' ACAACTTTCAACAAT ...3' [25 species (87 seq)]a
5' ACAACTTTCAACAAC ...3' [12 species (45 seq)]b
5' ATAACTTTCAACAAT ...3' [A. madagascariensis (1 seq)]
5' ATAACTTTCAACAAC ...3' [A. trygonion (1 seq)]

  Notes:

  1. A. albiceps (1 seq), A. arenicola (7 seq), A. basiana (1 seq), A. crassiputamen (1 seq), A. drummondii (6 seq), A. friabilis (4 seq), A. homolalittenii (4 seq), A. lippiae (1 seq), A. liquii (1 seq), A. minnesorora (2 seq), A. mortenii (3 seq), A. olivaceogrisea (4 seq), A. pahasapaensis (2 seq), A. populiphila (12 seq), A. protecta (5 seq), A. pseudovaginata (1 seq), A. punctata sensu A. E. Wood (1 seq), A. sp-58 (1 seq), A. sp-Arora 01-555 (1 seq), A. sp-GSM05 (1 seq), A. sp-MO04 (1 seq), A. subnigra (3 seq), A. texasorora (16 seq), A. variicolor (1 seq), and A. xanthomitra (7 seq).

  2. A. atrofusca (1 seq), A. fulva (7 seq), A. griseofolia (1 seq), A. orientifulva (1 seq), A. penetratrix (7 seq), A. rhacopus (17 seq), A. sp-GSM03 (1 seq), A. sp-GSM04 (6 seq), A. sp-GSM07 (1 seq), A. sp-N48 (1 seq), A. sp-NW04 (1 seq), and A. supravolvata (1 seq).

5.8S somewhat conserved 3' terminal motifs

5'... 18S (SSU)  ITS1  5.8S  ITS2  28S (LSU) ...3'

ITS2 observed 5' terminal strings

5'... 18S (SSU)  ITS1  5.8S  ITS2  28S (LSU) ...3'

ITS2 observed 3' terminal strings

5'... 18S (SSU)  ITS1  5.8S  ITS2  28S (LSU) ...3'

28S rRNA highly conserved 5' terminus motif

5'... 18S (SSU)  ITS1  5.8S  ITS2  28S (LSU) ...3'