Using GenBank data for plant identification: possibilities and limitations using the ITS 1 of Asteraceae species belonging to the tribes Lactuceae and Anthemideae

Taxon - Tập 55 Số 1 - Trang 173-187 - 2006
Birgit Gemeinholzer1, Christoph Oberprieler2, Konrad Bachmann3
1Botanic Garden and Botanical Museum Berlin-Dahlem (FU-Berlin), Königin-Luise-Straße 6–8 D-14191 Berlin Germany
2Institute of Botany, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
3Institute for Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3 D-06466 Gatersleben Germany

Tóm tắt

AbstractAs 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® 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.

Từ khóa


Tài liệu tham khảo

10.1016/S0022-2836(05)80360-2

10.1038/ng0294-119

10.1016/S1055-7903(03)00208-2

10.1093/bioinformatics/14.4.349

Babcock E. B., 1947, The Genus Crepis. Part II. Systematic Treatment

Babcock E. B., 1938, The American Species of Crepis.

10.1016/S0169-5347(03)00101-0

10.2307/2399880

Baldwin B. G., 2002, Nuclear rDNA evidence for major lineages of helenioid Heliantheae (Compositae), Syst. Bot, 27, 161

10.1016/1055-7903(92)90021-8

Bremer K., 1994, Asteraceae Cladistics & Classification

Bryant D., 2002, Algorithms in Bioinformatics, Second International Workshop, WABI, 375, 10.1007/3-540-45784-4_28

10.1093/aob/mch027

10.1007/s00606-004-0272-6

Gish W.1996-2004.blast.wustl.edu.

10.2307/4135441

Hallett M. T., 2001, Proceedings of the Fifth Annual International Conference on Computational Biology (RECOMB01), 149, 10.1145/369133.369188

10.1093/bioinformatics/14.1.68

10.1007/BF00985439

10.2307/2419648

10.1007/s00606-003-0003-4

10.1007/BF00986191

Lee J., 2003, Phylogenetic Relationships among the primarily north-American genera of Cichorieae (Compositae) based on analysis of 18S-26S nuclear rDNA ITS and ETS sequences, Syst. Bot, 28, 616

Linder C. R., 2003, Phylogenetic Networks: Generation, Comparison, and Reconstruction

10.3732/ajb.91.10.1700

Liston A., 1995, Internal transcribed spacer sequences of conifers: There is a fungus among us, Inoculum, 46, 26

Mallet J., 2003, Taxonomy: renaissance or Tower of Babel? Trends Ecol., Evol, 82, 57

10.2307/1223705

10.1046/j.1095-8339.2002.00030.x

Oberprieler C., 2004, On the taxonomic status and the phy-logenetic relationships of some unispecific Mediterranean genera of Compositae-Anthemideae. I, Brocchia Vis., Endopappus Sch. Bip., and Heliocauta Humphries. -Willdenowia, 34, 39

Oberprieler C., 2004, On the taxonomic status and the phy-logenetic relationships of some unispecific Mediterranean genera of Compositae-Anthemideae. II, Daveaua Willk. ex Mariz, Leucocyclus Boiss., and Nananthea DC. -Willdenowia, 34, 341

10.1007/BF00985465

10.1016/0076-6879(90)83007-V

10.1073/pnas.85.8.2444

10.1093/jhered/esg027

10.1093/oxfordjournals.molbev.a003725

10.1006/mpev.1997.0422

Thông tin
Thông tin xuất bản

Taxon

Tập 55 Số 1

173-187

Thông tin tác giả