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Citation for Study 1540

Citation title: "Intragenomic nucleotide polymorphism among SSU rDNA paralogs in the diatom genus Skeletonema".

This study was previously identified under the legacy study ID S1485 (Status: Published).

Citation

Alverson A., & Kolnick L. 2005. Intragenomic nucleotide polymorphism among SSU rDNA paralogs in the diatom genus Skeletonema. Journal of Phycology, 41: 1248-1257.

Authors

• Alverson A.
• Kolnick L.

Abstract

Morphological features of the siliceous cell wall traditionally have been used to diagnose and classify species of diatoms, though an increasing number of studies distinguish new species, in part, by phylogenetic analysis of rDNA sequences. Intragenomic sequence variation is common among the hundreds to thousands of rDNA cistrons present within a genome, and this variation has strong potential to obscure species boundaries based on rDNA sequences. We screened six Skeletonema culture strains for intragenomic nucleotide polymorphisms in the SSU rDNA gene and found that all strains had polymorphic sites, with proportions ranging from 0.571.81%. In all cases, transitions accounted for more than 70% of nucleotide differences at polymorphic sites. Polymorphic sites were split nearly evenly in the SSU rRNA molecule between the base-paired regions of helices (52%) and the unpaired regions of loops and bulges (48%). Phylogenetic analysis showed that SSU rDNA genotypes were monophyletic for two of the six culture strains examined. Genotypes from the other four culture strains either showed little or no phylogenetic structure compared to genotypes of other conspecific culture strains, or had phylogenetic structure that was incongruent with existing species boundaries. Moderate to strong support for monophyly was recovered for four of the seven species included in the analysis. Phylogenetic results combined with the low sequence divergence of SSU rDNA genotypes within species suggest that concerted evolution has not proceeded to completion in these species, and/or that the rate at which variation is being generated exceeds the rate at which concerted evolution is expunging variation.

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1540
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref14540,
  	 author = {Andrew J  Alverson and Leanne  Kolnick},
  	 title = {Intragenomic nucleotide polymorphism among SSU rDNA paralogs in the diatom genus Skeletonema},
  	 year = {2005},
  	 keywords = {},
  	 doi = {},
  	 url = {},
  	 pmid = {},
  	 journal = {Journal of Phycology},
  	 volume = {41},
  	 number = {},
  	 pages = {1248--1257},
  	 abstract = {Morphological features of the siliceous cell wall traditionally have been used to diagnose and classify species of diatoms, though an increasing number of studies distinguish new species, in part, by phylogenetic analysis of rDNA sequences. Intragenomic sequence variation is common among the hundreds to thousands of rDNA cistrons present within a genome, and this variation has strong potential to obscure species boundaries based on rDNA sequences. We screened six Skeletonema culture strains for intragenomic nucleotide polymorphisms in the SSU rDNA gene and found that all strains had polymorphic sites, with proportions ranging from 0.571.81%. In all cases, transitions accounted for more than 70% of nucleotide differences at polymorphic sites. Polymorphic sites were split nearly evenly in the SSU rRNA molecule between the base-paired regions of helices (52%) and the unpaired regions of loops and bulges (48%). Phylogenetic analysis showed that SSU rDNA genotypes were monophyletic for two of the six culture strains examined. Genotypes from the other four culture strains either showed little or no phylogenetic structure compared to genotypes of other conspecific culture strains, or had phylogenetic structure that was incongruent with existing species boundaries. Moderate to strong support for monophyly was recovered for four of the seven species included in the analysis. Phylogenetic results combined with the low sequence divergence of SSU rDNA genotypes within species suggest that concerted evolution has not proceeded to completion in these species, and/or that the rate at which variation is being generated exceeds the rate at which concerted evolution is expunging variation.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 14540
  AU  - Alverson,Andrew J 
  AU  - Kolnick,Leanne 
  T1  - Intragenomic nucleotide polymorphism among SSU rDNA paralogs in the diatom genus Skeletonema
  PY  - 2005
  UR  - 
  N2  - Morphological features of the siliceous cell wall traditionally have been used to diagnose and classify species of diatoms, though an increasing number of studies distinguish new species, in part, by phylogenetic analysis of rDNA sequences. Intragenomic sequence variation is common among the hundreds to thousands of rDNA cistrons present within a genome, and this variation has strong potential to obscure species boundaries based on rDNA sequences. We screened six Skeletonema culture strains for intragenomic nucleotide polymorphisms in the SSU rDNA gene and found that all strains had polymorphic sites, with proportions ranging from 0.571.81%. In all cases, transitions accounted for more than 70% of nucleotide differences at polymorphic sites. Polymorphic sites were split nearly evenly in the SSU rRNA molecule between the base-paired regions of helices (52%) and the unpaired regions of loops and bulges (48%). Phylogenetic analysis showed that SSU rDNA genotypes were monophyletic for two of the six culture strains examined. Genotypes from the other four culture strains either showed little or no phylogenetic structure compared to genotypes of other conspecific culture strains, or had phylogenetic structure that was incongruent with existing species boundaries. Moderate to strong support for monophyly was recovered for four of the seven species included in the analysis. Phylogenetic results combined with the low sequence divergence of SSU rDNA genotypes within species suggest that concerted evolution has not proceeded to completion in these species, and/or that the rate at which variation is being generated exceeds the rate at which concerted evolution is expunging variation.
  L3  - 
  JF  - Journal of Phycology
  VL  - 41
  IS  - 
  SP  - 1248
  EP  - 1257
  ER  -