Compilation of small ribosomal subunit RNA sequences

TLDR: The set of 452 different sequences comprises all sequences that to the authors' knowledge had been published or were available from the sequence library file servers as of December 1, 1990, and that are either complete or cover a minimum of about 70% of the complete sequence.

Abstract: Table 1 lists data on 455 small ribosomal subunit RNA (further abbreviated as srRNA) sequences (references 1 —452) that have been published or submitted to the EMBL or GenBank nucleotide sequence libraries and that are presently stored in aligned form in our data base. The number identifying each sequence in the first column of Table 1 corresponds with the literature reference. If two or more closely related species share the same sequence, they bear the same number, followed by a different lower case character, and the common sequence is listed only once in our alignment. The set of 452 different sequences consists of 97 eukaryotic cytoplasmic, 19 archaebacterial, 276 eubacterial, 16 plastidial, and 44 mitochondrial srRNAs. It comprises all sequences that to our knowledge had been published or were available from the sequence library file servers as of December 1, 1990, and that are either complete or cover a minimum of about 70% of the complete sequence. Partial sequences are included because some of the methods now frequently used for srRNA sequencing preclude the determination of the structure at one or both of the termini. One such method consists of reverse transcription of the srRNA by means of primers complementary to conserved areas in the primary structure (453). In this case the 3'-terminal sequence cannot be found. Another approach (55, 328) involves amplification of the rDNA by means of the polymerase chain reaction (454), using primers binding to conserved areas near the termini, but within the sequence coding for the mature small subunit RNA. In this case both terminal sequences remain unknown. Both methods allow to establish a continuous sequence covering more than 95% of the structure, provided that a sufficient number of primers complementary to internal conserved areas is used. Some authors (e.g. 455), however, use a more limited set of primers and publish sequences that are not only partial but also discontinuous.