Premium
STRUCTURAL AND SEQUENCE SIGNATURES OF NUCLEAR SSU RRNA DEFINE TAXONOMIC LEVELS WITHIN THE RHODOPHYTA
Author(s) -
Müller K. M.,
Sheath R. G.,
Sherwood A.R.,
Madabusi L.V.,
Can J.J.,
Subashchandran S.,
Lin N.,
Gutell R.R.
Publication year - 2000
Publication title -
journal of phycology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.85
H-Index - 127
eISSN - 1529-8817
pISSN - 0022-3646
DOI - 10.1046/j.1529-8817.1999.00001-148.x
Subject(s) - biology , phylogenetic tree , ribosomal rna , archaea , sequence (biology) , genetics , nucleic acid sequence , evolutionary biology , gene
Over 400 nuclear SSU rRNA sequences representing all orders of the Rhodophyta were aligned and analyzed using comparative sequence analysis. Numerous nucleotide positions and structural elements were found that delineated various taxonomic groups. The 1245 region ( E. coli numbering) contained a loop that differed in size between two conserved helices and clearly separated the Florideophyceae [3 nt (>95% of 268 sequences)], Bangiales [13 to 14 nt (100% of 116 sequences)] and remaining Bangiophyceae including the Cryptophyta nucleomorphs [four to eight nt (100% of 32 sequences)]. In addition, members of the Thoreaceae were found to have additional helices in the 650 and 1139 region of which a corresponding structure was not present in any other red algal SSU rRNA gene sequence. Base‐pair and nucleotide signatures differentiated the Bangiales, Florideophyceae, Bangiophyceae (not including Bangiales) and Hildenbrandiales at three levels of comparison: within the Rhodophyta (>400 sequences), the Eukaryota (not including Rhodophyta;> 1300 sequences) and three kingdom (Archaea, Bacteria, 2 organelles, Eukaryota;> 7000 sequences). For example, all members of the Hildenbrandiales have a change in the base‐pair 512:539 that is a region of functional importance. Sequences from the Eukaryota, Archaea, Bacteria and two organelles have a C:G or a U:A in this position whereas the Hildenbrandiales have a C:A pair. This analysis raises the possibility of utilizing structural features of nuclear SSU rRNA and sequence signatures to support and delineate phylogenetic clades within the Rhodophyta.