18S rDNA phylogeny of Pseudo-nitzschia (Bacillariophyceae) inferred from sequence-structure information
We explored the 18S rDNA sequences of Pseudo-nitzschia and its close relatives, together with their individual secondary structure information to reconstruct phylogenies. Forty-eight taxa classified in the Bacillariaceae and Achnanthaceae were analyzed by character-based (maximum parsimony and maxim...
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| Format: | Article |
| Language: | English |
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Allen Press Publishing Services
2016
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| Online Access: | http://ir.unimas.my/id/eprint/12454/ http://ir.unimas.my/id/eprint/12454/1/18S%20rDNA.pdf |
| _version_ | 1848837201236852736 |
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| author | Lim, H.C. Teng, S.T. Lim, P.T. Wolf, M. Leaw, CP |
| author_facet | Lim, H.C. Teng, S.T. Lim, P.T. Wolf, M. Leaw, CP |
| author_sort | Lim, H.C. |
| building | UNIMAS Institutional Repository |
| collection | Online Access |
| description | We explored the 18S rDNA sequences of Pseudo-nitzschia and its close relatives, together with their individual secondary structure information to reconstruct phylogenies. Forty-eight taxa classified in the Bacillariaceae and Achnanthaceae were analyzed by character-based (maximum parsimony and maximum likelihood) and distance-based (neighbour-joining) methods. Three raphid diatoms from the Eunotiaceae were used as out-groups. The sequencestructure alignment was generated by 4SALE (i.e. a one-letter encoded alignment that contained the individual secondary structure information) and applied to the character-based phylogeny reconstruction. All analyses highly support Pseudonitzschia + Fragilariopsis as monophyletic. The Pseudo-nitzschia/Fragilariopsis clade is further divided into three subclades. One clade comprises members in the P. seriata and P. americana complexes and species of Fragilariopsis; the second and third clades constitute members in P. pseudodelicatissima and P. delicatissima complexes. Among all analyses, the distance-based method yielded a more highly resolved phylogenetic framework for the Pseudo-nitzschia/Fragilariopsis clade than did the character-based analyses. Other than those currently known genetic markers, 18S rDNA was also useful in exploring the intrageneric relationships. |
| first_indexed | 2025-11-15T06:35:53Z |
| format | Article |
| id | unimas-12454 |
| institution | Universiti Malaysia Sarawak |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T06:35:53Z |
| publishDate | 2016 |
| publisher | Allen Press Publishing Services |
| recordtype | eprints |
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| spelling | unimas-124542022-05-30T06:27:41Z http://ir.unimas.my/id/eprint/12454/ 18S rDNA phylogeny of Pseudo-nitzschia (Bacillariophyceae) inferred from sequence-structure information Lim, H.C. Teng, S.T. Lim, P.T. Wolf, M. Leaw, CP Q Science (General) SH Aquaculture. Fisheries. Angling We explored the 18S rDNA sequences of Pseudo-nitzschia and its close relatives, together with their individual secondary structure information to reconstruct phylogenies. Forty-eight taxa classified in the Bacillariaceae and Achnanthaceae were analyzed by character-based (maximum parsimony and maximum likelihood) and distance-based (neighbour-joining) methods. Three raphid diatoms from the Eunotiaceae were used as out-groups. The sequencestructure alignment was generated by 4SALE (i.e. a one-letter encoded alignment that contained the individual secondary structure information) and applied to the character-based phylogeny reconstruction. All analyses highly support Pseudonitzschia + Fragilariopsis as monophyletic. The Pseudo-nitzschia/Fragilariopsis clade is further divided into three subclades. One clade comprises members in the P. seriata and P. americana complexes and species of Fragilariopsis; the second and third clades constitute members in P. pseudodelicatissima and P. delicatissima complexes. Among all analyses, the distance-based method yielded a more highly resolved phylogenetic framework for the Pseudo-nitzschia/Fragilariopsis clade than did the character-based analyses. Other than those currently known genetic markers, 18S rDNA was also useful in exploring the intrageneric relationships. Allen Press Publishing Services 2016 Article PeerReviewed text en http://ir.unimas.my/id/eprint/12454/1/18S%20rDNA.pdf Lim, H.C. and Teng, S.T. and Lim, P.T. and Wolf, M. and Leaw, CP (2016) 18S rDNA phylogeny of Pseudo-nitzschia (Bacillariophyceae) inferred from sequence-structure information. Phycologia, 55 (2). pp. 134-146. ISSN 00318884 https://www.scopus.com/inward/record.uri?eid=2-s2.0-84963548424&partnerID=40&md5=4130b59b80c36439f4c37ea9845e1286 DOI: 10.2216/15-78.1 |
| spellingShingle | Q Science (General) SH Aquaculture. Fisheries. Angling Lim, H.C. Teng, S.T. Lim, P.T. Wolf, M. Leaw, CP 18S rDNA phylogeny of Pseudo-nitzschia (Bacillariophyceae) inferred from sequence-structure information |
| title | 18S rDNA phylogeny of Pseudo-nitzschia (Bacillariophyceae) inferred from sequence-structure information |
| title_full | 18S rDNA phylogeny of Pseudo-nitzschia (Bacillariophyceae) inferred from sequence-structure information |
| title_fullStr | 18S rDNA phylogeny of Pseudo-nitzschia (Bacillariophyceae) inferred from sequence-structure information |
| title_full_unstemmed | 18S rDNA phylogeny of Pseudo-nitzschia (Bacillariophyceae) inferred from sequence-structure information |
| title_short | 18S rDNA phylogeny of Pseudo-nitzschia (Bacillariophyceae) inferred from sequence-structure information |
| title_sort | 18s rdna phylogeny of pseudo-nitzschia (bacillariophyceae) inferred from sequence-structure information |
| topic | Q Science (General) SH Aquaculture. Fisheries. Angling |
| url | http://ir.unimas.my/id/eprint/12454/ http://ir.unimas.my/id/eprint/12454/ http://ir.unimas.my/id/eprint/12454/ http://ir.unimas.my/id/eprint/12454/1/18S%20rDNA.pdf |