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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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Main Authors: Lim, H.C., Teng, S.T., Lim, P.T., Wolf, M., Leaw, CP
Format: Article
Language:English
Published: Allen Press Publishing Services 2016
Subjects:
Q Science (General)
SH Aquaculture. Fisheries. Angling
Online Access:http://ir.unimas.my/id/eprint/12454/1/18S%20rDNA.pdf
http://ir.unimas.my/id/eprint/12454/
https://www.scopus.com/inward/record.uri?eid=2-s2.0-84963548424&partnerID=40&md5=4130b59b80c36439f4c37ea9845e1286
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spelling my.unimas.ir.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
institution Universiti Malaysia Sarawak
building Centre for Academic Information Services (CAIS)
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Malaysia Sarawak
content_source UNIMAS Institutional Repository
url_provider http://ir.unimas.my/
language English
topic Q Science (General)
SH Aquaculture. Fisheries. Angling
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
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.
format Article
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.
title 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_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_sort 18s rdna phylogeny of pseudo-nitzschia (bacillariophyceae) inferred from sequence-structure information
publisher Allen Press Publishing Services
publishDate 2016
url http://ir.unimas.my/id/eprint/12454/1/18S%20rDNA.pdf
http://ir.unimas.my/id/eprint/12454/
https://www.scopus.com/inward/record.uri?eid=2-s2.0-84963548424&partnerID=40&md5=4130b59b80c36439f4c37ea9845e1286
_version_ 1734303755843665920
score 13.211869

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