THE IMPORTANCE OF trnL/trnF IGS REGION IN THE TAXONOMY OF THE GENUS Potentilla L.
This study was performed to determine the phylogenetic relationships in the genus Potentilla L. and to assess the importance of the trnL/trnF intergenic spacer (IGS) region. The selection of DNA barcoding region to provide for more effective, accurate and consistent results in the analysis is one of...
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| Format: | Article |
| Language: | English |
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Trakya University
2023-04-01
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| Series: | Trakya University Journal of Natural Sciences |
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| Online Access: | https://dergipark.org.tr/en/download/article-file/2960083 |
| _version_ | 1797633887731449856 |
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| author | Aykut Yılmaz |
| author_facet | Aykut Yılmaz |
| author_sort | Aykut Yılmaz |
| collection | DOAJ |
| description | This study was performed to determine the phylogenetic relationships in the genus Potentilla L. and to assess the importance of the trnL/trnF intergenic spacer (IGS) region. The selection of DNA barcoding region to provide for more effective, accurate and consistent results in the analysis is one of the most important points in success of the study. For this purpose, 71 Potentilla taxa were examined based on trnL/trnF IGS sequence data of chloroplast DNA acquired from the National Center for Biotechnology Information (NCBI) and a Maximum Parsimony (MP) dendrogram was drawn. The trnL/trnF IGS region has the convenient sequence length for barcoding region, and it is also proposed the use of this region which has highly variable and parsimony informative sites. When the probabilities of substitutions from one base to another base for trnL/trnF IGS region were examined, it was assigned that the rate of transitional substitutions with 57.13% is higher than the transversional substitutions. The MP dendrogram revealed that the studies taxa were placed in six groups as Fragarioides, Reptans, Anserina, Alba, Himalayan and Argentea. Phylogenetic relationships within the Argentea clade, represented by the highest species number in this study, were observed as quite confusing compared to other clades. In order to get the most accurate results, it is necessary to determine the regions giving the best results, and then to use these regions together with as many taxa as possible. In conclusion, the using of trnL/trnF IGS sequence information that have high variable sites and grouping ability for studies taxa is strongly recommended. |
| first_indexed | 2024-03-11T12:00:59Z |
| format | Article |
| id | doaj.art-a3f76d44ab96487fbb09101702abd26f |
| institution | Directory Open Access Journal |
| issn | 2528-9691 |
| language | English |
| last_indexed | 2024-03-11T12:00:59Z |
| publishDate | 2023-04-01 |
| publisher | Trakya University |
| record_format | Article |
| series | Trakya University Journal of Natural Sciences |
| spelling | doaj.art-a3f76d44ab96487fbb09101702abd26f2023-11-08T07:27:55ZengTrakya UniversityTrakya University Journal of Natural Sciences2528-96912023-04-01241717610.23902/trkjnat.125298069THE IMPORTANCE OF trnL/trnF IGS REGION IN THE TAXONOMY OF THE GENUS Potentilla L.Aykut Yılmaz0UŞAK ÜNİVERSİTESİThis study was performed to determine the phylogenetic relationships in the genus Potentilla L. and to assess the importance of the trnL/trnF intergenic spacer (IGS) region. The selection of DNA barcoding region to provide for more effective, accurate and consistent results in the analysis is one of the most important points in success of the study. For this purpose, 71 Potentilla taxa were examined based on trnL/trnF IGS sequence data of chloroplast DNA acquired from the National Center for Biotechnology Information (NCBI) and a Maximum Parsimony (MP) dendrogram was drawn. The trnL/trnF IGS region has the convenient sequence length for barcoding region, and it is also proposed the use of this region which has highly variable and parsimony informative sites. When the probabilities of substitutions from one base to another base for trnL/trnF IGS region were examined, it was assigned that the rate of transitional substitutions with 57.13% is higher than the transversional substitutions. The MP dendrogram revealed that the studies taxa were placed in six groups as Fragarioides, Reptans, Anserina, Alba, Himalayan and Argentea. Phylogenetic relationships within the Argentea clade, represented by the highest species number in this study, were observed as quite confusing compared to other clades. In order to get the most accurate results, it is necessary to determine the regions giving the best results, and then to use these regions together with as many taxa as possible. In conclusion, the using of trnL/trnF IGS sequence information that have high variable sites and grouping ability for studies taxa is strongly recommended.https://dergipark.org.tr/en/download/article-file/2960083mp dendrogramdna barcodingphylogenetic relationships |
| spellingShingle | Aykut Yılmaz THE IMPORTANCE OF trnL/trnF IGS REGION IN THE TAXONOMY OF THE GENUS Potentilla L. Trakya University Journal of Natural Sciences mp dendrogram dna barcoding phylogenetic relationships |
| title | THE IMPORTANCE OF trnL/trnF IGS REGION IN THE TAXONOMY OF THE GENUS Potentilla L. |
| title_full | THE IMPORTANCE OF trnL/trnF IGS REGION IN THE TAXONOMY OF THE GENUS Potentilla L. |
| title_fullStr | THE IMPORTANCE OF trnL/trnF IGS REGION IN THE TAXONOMY OF THE GENUS Potentilla L. |
| title_full_unstemmed | THE IMPORTANCE OF trnL/trnF IGS REGION IN THE TAXONOMY OF THE GENUS Potentilla L. |
| title_short | THE IMPORTANCE OF trnL/trnF IGS REGION IN THE TAXONOMY OF THE GENUS Potentilla L. |
| title_sort | importance of trnl trnf igs region in the taxonomy of the genus potentilla l |
| topic | mp dendrogram dna barcoding phylogenetic relationships |
| url | https://dergipark.org.tr/en/download/article-file/2960083 |
| work_keys_str_mv | AT aykutyılmaz theimportanceoftrnltrnfigsregioninthetaxonomyofthegenuspotentillal AT aykutyılmaz importanceoftrnltrnfigsregioninthetaxonomyofthegenuspotentillal |