Aufsatz in einer Fachzeitschrift
Using GenBank data for plant identification: possibilities and limitations using the ITS 1 of Asteraceae species belonging to the tribes Lactuceae and Anthemideae
Details zur Publikation
Autor(inn)en: | Gemeinholzer, B.; Oberprieler, C.; Bachmann, K. |
Verlag: | INT ASSOC PLANT TAXONOMY-IAPT |
Publikationsjahr: | 2006 |
Zeitschrift: | Taxon |
Seitenbereich: | 173-187 |
Jahrgang/Band : | 55 |
Heftnummer: | 1 |
Erste Seite: | 173 |
Letzte Seite: | 187 |
Seitenumfang: | 15 |
ISSN: | 0040-0262 |
eISSN: | 1996-8175 |
DOI-Link der Erstveröffentlichung: |
Zusammenfassung, Abstract
As a contribution to establish taxonomic identification methods using DNA sequence data, we evaluate to which extent the present set-up of the nucleotide databases (NCBI, EBI, GenomeNet) allows to use them for reliable routine plant identification applying the implemented sequence similarity and homology search tools. We screened newly determined ITS 1 sequences from Asteraceae (tribes Lactuceae, Anthemideae) against the molecular nucleotide databases where sequences from that exact species, from other species of the same genus, or only from other genera of the same family had already been published. With the present set up of the BLAST (R) algorithms [MEGABLAST, BLASTN] 100% correct family, 99% correct tribe, and 98% precise genus affiliation could be achieved in Lactuceae representatives and 100% correct family, 100% correct tribe, and 95% precise genus affiliation in Anthemideae. Correct species detection varied between 86% accuracy for Lactuceae and 91% in Anthemideae. Necessary optimization criteria are proposed as well as further requirements for a standardized molecular identification system.
As a contribution to establish taxonomic identification methods using DNA sequence data, we evaluate to which extent the present set-up of the nucleotide databases (NCBI, EBI, GenomeNet) allows to use them for reliable routine plant identification applying the implemented sequence similarity and homology search tools. We screened newly determined ITS 1 sequences from Asteraceae (tribes Lactuceae, Anthemideae) against the molecular nucleotide databases where sequences from that exact species, from other species of the same genus, or only from other genera of the same family had already been published. With the present set up of the BLAST (R) algorithms [MEGABLAST, BLASTN] 100% correct family, 99% correct tribe, and 98% precise genus affiliation could be achieved in Lactuceae representatives and 100% correct family, 100% correct tribe, and 95% precise genus affiliation in Anthemideae. Correct species detection varied between 86% accuracy for Lactuceae and 91% in Anthemideae. Necessary optimization criteria are proposed as well as further requirements for a standardized molecular identification system.
Schlagwörter
Asteraccae, DNA taxonomy, ITS, molecular marker, plant identification
