Internal Transcribed Spacer (ITS) Fails Barcoding of the Genus Neotinea Rchb.f. (Orchidaceae)
Internal Transcribed Spacer (ITS) is one of the most used barcoding regions for the molecular phylogenetics and barcoding of orchids. Our aim in this study is to test the reliability of ITS on barcoding of closely related Neotinea spp., including Neotinea tridentata, Neotinea ustulata subsp. ustulat...
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| Language: | English |
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Ankara University
2021-03-01
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| Series: | Journal of Agricultural Sciences |
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| Online Access: | https://dergipark.org.tr/tr/download/article-file/865704 |
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| author | Kaan Hürkan Kemal Melih Taşkın |
| author_facet | Kaan Hürkan Kemal Melih Taşkın |
| author_sort | Kaan Hürkan |
| collection | DOAJ |
| description | Internal Transcribed Spacer (ITS) is one of the most used barcoding regions for the molecular phylogenetics and barcoding of orchids. Our aim in this study is to test the reliability of ITS on barcoding of closely related Neotinea spp., including Neotinea tridentata, Neotinea ustulata subsp. ustulata and Neotinea ustulata subsp. aestivalis, by comparing it to the accD-psaI intergenic spacer of the plastid DNA. Both ITS and accD-psaI regions were amplified by specific primer sets and sequenced. Phylogenetic trees were regenerated by using Maximum Parsimony approach. The results showed that ITS separated some N. tridentata samples of Turkish, Greek, Hungarian and Croatian samples from the others on the phylogenetic trees due to the incomplete lineage sorting. In contrast to ITS, the accD-psaI marker could successfully separate N. tridentata and N. ustulata samples according to a priori species classification. Our findings refer to a hybridisation story between some N. tridentata and N. ustulata. We propose not to use ITS sequences directly as a barcode and to reconstruct the phylogeny of the Neotinea group. Instead, the inclusion of other nuclear regions such as LFY, ADH, etc., or utilisation of whole genome sequencing could give better barcoding results. |
| format | Article |
| id | doaj-art-c467cd363d3a42568cbdea5b071e7f74 |
| institution | OA Journals |
| issn | 1300-7580 2148-9297 |
| language | English |
| publishDate | 2021-03-01 |
| publisher | Ankara University |
| record_format | Article |
| series | Journal of Agricultural Sciences |
| spelling | doaj-art-c467cd363d3a42568cbdea5b071e7f742025-08-20T02:02:36ZengAnkara UniversityJournal of Agricultural Sciences1300-75802148-92972021-03-01271697510.15832/ankutbd.61584845Internal Transcribed Spacer (ITS) Fails Barcoding of the Genus Neotinea Rchb.f. (Orchidaceae)Kaan Hürkan0Kemal Melih Taşkın1IĞDIR ÜNİVERSİTESİ, IĞDIR ZİRAAT FAKÜLTESİÇANAKKALE ONSEKİZ MART ÜNİVERSİTESİ, FEN VE EDEBİYAT FAKÜLTESİInternal Transcribed Spacer (ITS) is one of the most used barcoding regions for the molecular phylogenetics and barcoding of orchids. Our aim in this study is to test the reliability of ITS on barcoding of closely related Neotinea spp., including Neotinea tridentata, Neotinea ustulata subsp. ustulata and Neotinea ustulata subsp. aestivalis, by comparing it to the accD-psaI intergenic spacer of the plastid DNA. Both ITS and accD-psaI regions were amplified by specific primer sets and sequenced. Phylogenetic trees were regenerated by using Maximum Parsimony approach. The results showed that ITS separated some N. tridentata samples of Turkish, Greek, Hungarian and Croatian samples from the others on the phylogenetic trees due to the incomplete lineage sorting. In contrast to ITS, the accD-psaI marker could successfully separate N. tridentata and N. ustulata samples according to a priori species classification. Our findings refer to a hybridisation story between some N. tridentata and N. ustulata. We propose not to use ITS sequences directly as a barcode and to reconstruct the phylogeny of the Neotinea group. Instead, the inclusion of other nuclear regions such as LFY, ADH, etc., or utilisation of whole genome sequencing could give better barcoding results.https://dergipark.org.tr/tr/download/article-file/865704accd-psai markerorchidsdna barcodingphylogenetic incongruence |
| spellingShingle | Kaan Hürkan Kemal Melih Taşkın Internal Transcribed Spacer (ITS) Fails Barcoding of the Genus Neotinea Rchb.f. (Orchidaceae) Journal of Agricultural Sciences accd-psai marker orchids dna barcoding phylogenetic incongruence |
| title | Internal Transcribed Spacer (ITS) Fails Barcoding of the Genus Neotinea Rchb.f. (Orchidaceae) |
| title_full | Internal Transcribed Spacer (ITS) Fails Barcoding of the Genus Neotinea Rchb.f. (Orchidaceae) |
| title_fullStr | Internal Transcribed Spacer (ITS) Fails Barcoding of the Genus Neotinea Rchb.f. (Orchidaceae) |
| title_full_unstemmed | Internal Transcribed Spacer (ITS) Fails Barcoding of the Genus Neotinea Rchb.f. (Orchidaceae) |
| title_short | Internal Transcribed Spacer (ITS) Fails Barcoding of the Genus Neotinea Rchb.f. (Orchidaceae) |
| title_sort | internal transcribed spacer its fails barcoding of the genus neotinea rchb f orchidaceae |
| topic | accd-psai marker orchids dna barcoding phylogenetic incongruence |
| url | https://dergipark.org.tr/tr/download/article-file/865704 |
| work_keys_str_mv | AT kaanhurkan internaltranscribedspaceritsfailsbarcodingofthegenusneotinearchbforchidaceae AT kemalmelihtaskın internaltranscribedspaceritsfailsbarcodingofthegenusneotinearchbforchidaceae |