Phylogeny of Alariaceae, Laminariaceae, and Lessoniaceae (Phaeophyceae) Based on Plastid-Encoded RuBisCo Spacer and Nuclear-Encoded ITS Sequence Comparisons

Yoon, Hwan Su; Lee, Ju‐Yeon; Boo, Sung Min; Bhattacharya, Debashish

doi:10.1006/mpev.2001.1009

Cited by 105 publications

(131 citation statements)

References 36 publications

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“…The few exceptions were generally concordant with the current phylogenies (Yoon et al, 2001;Lane et al, 2006). For example, two loci (rps14/atp8 and rpl31/rns) amplify in only one of the two Lessoniaceae species of the tested taxa, Ln and Mp, but both Yoon et al, (2001) and Lane et al, (2006) demonstrated that these are paraphyletic.…”

Section: Discussionsupporting

confidence: 67%

“…To compute diversity indices, insertion-deletions (gaps) were treated as independent (mutation) sites. For comparison, we also analysed two cytoplasmic loci, for which sequences from more than three of the panel species (or closely related, congeneric species according to Yoon et al, 2001) were available in GenBank. These were a mitochondrial coding region locus, nad6, and a chloroplastic intergenic region locus, the RuBisCO spacer.…”

Section: Sequence Analysismentioning

confidence: 99%

“…2), is suitable for phylogenetic studies at the family level, for which the chloroplast marker is frequently employed (e.g. Yoon et al, 2001). The faster rates of evolution of the second group provide markers that are more appropriate for lower taxonomic levels, e.g.…”

Section: Distribution Of Sequence Divergence Across Taxonomic Levelsmentioning

confidence: 99%

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Conservation and polymorphism of mitochondrial intergenic sequences in brown algae (Phaeophyceae)

Engel

Billard

Viard

2008

European Journal of Phycology

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Due to their haploid nature, uniparental inheritance and apparent absence of recombination, organellar DNA markers are ideal tools for studying both intraspecific and interspecific phylogenies. Although 'universal' cytoplasmic DNA primers have become available for both red and green seaweeds, they are not transferable to brown seaweeds. Thus, based on the sequence of mitochondrial genome of the kelp Laminaria digitata, we developed universal-type primers for seven intergenic spacer loci and one mononucleotide tandem repeat locus. We investigated the conservation and sequence variation of these loci among nine Laminarialean and three fucoid species, as well as intraspecific polymorphism within five of these species. Six loci were conserved in at least four of the five brown algal families tested and five were polymorphic within at least one species. Although overall levels of divergence were relatively homogenous ( ¼ 0.314 AE 0.031), a hierarchical analysis suggests there is variation in the rate of evolutionary change among the six intergenic spacers. Due to their high degree of transferability, versatility and to non-coding nature, we argue that these intergenic spacer loci are highly efficient markers for within-family phylogenetic studies and for intra-specific phylogeographic studies in brown seaweeds.

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Section: Discussionsupporting

confidence: 67%

Section: Sequence Analysismentioning

confidence: 99%

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Conservation and polymorphism of mitochondrial intergenic sequences in brown algae (Phaeophyceae)

Engel

Billard

Viard

2008

European Journal of Phycology

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“…Phylogenetic analyses showed that 'Ailunwan' firstly groups with Saccharina japonica. It indicated that 'Ailunwan' had a closer evolutionary relationship with Saccharina than Laminaria, supporting current taxonomic systems (Yoon et al 2001;Lane et al 2006). …”

supporting

confidence: 57%

Complete mitogenome of Saccharina cultivation variety ‘Ailunwan’(Saccharina japonica × latissima)

Zhang

Liu

Zhang

et al. 2016

Mitochondrial DNA Part B

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Complete mitogenome of Saccharina variety ‘Ailunwan’ ( Saccharina japonica × latissima ) was obtained in this work. Circular-mapping mitogenome was 37,657 bp with overall A + T content of 64.71%, encoding 3 rRNAs (23S, 16S and 5S), 25 tRNAs, 35 protein-coding genes and 3 open reading frames (ORFs). Gene content and genome organization of ‘Ailunwan’ mitogenome were identical to those Saccharina species. From the total alignment of ‘Ailunwan’ and another reported variety ‘Rongfu’ ( S. japonica × latissima ), 33 nucleotide substitutions were detected, and one intergenic region of 19 nucleotides insertion/deletion was found which located between rps 3 and rps 9. The phylogenetic analysis based on mitogenomes showed that ‘Ailunwan’ had a closer evolutionary relationship with Saccharina than Laminaria and validated the genus Saccharina and Laminaria were polyphyletic.

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“…All Laminariaceae species with complete mitogenomes available in the GenBank were selected to construct the phylogenetic tree by the Bayesian method. Phylogenetic analysis based on combined 35 protein-encoding genes exhibited the species were divided into two clades: Saccharina and Laminaria (Figure 1), supporting current taxonomic systems (Yoon et al 2001;Lane et al 2006). It also showed that 'Pingbancai' firstly groups with S. japonica and then with S. latissima and validated that the mitogenome was maternally inherited.…”

Section: Introductionsupporting

confidence: 53%

The complete mitogenome of ‘Pingbancai’, an important economic Saccharina cultivation variety

Zhang

Gao

Liu

et al. 2016

Mitochondrial DNA Part B

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Saccharina is one of the most important economic seaweed. We presented the complete mitogenome of Saccharina variety ‘Pingbancai’ ( Saccharina japonica × latissima ) in this work. Circular-mapping mitogenome was 37,658 bp in length with overall A + T content of 64.70%, encoding 3 rRNAs (23S, 16S and 5S), 25 tRNAs, 38 genes (including 3 open reading frames, ORFs). Gene arrangement and component of ‘Pingbancai’ mitogenome were identical to those Saccharina species and cultivation varieties, which show highly conservative evolution in mitochondrial genomes within Saccharina . The phylogenetic analysis based on mitogenomes showed that ‘Pingbancai’ had a closer evolutionary relationship with Saccharina japonica than Saccharina latissima and the supported mitogenome was maternally inherited.

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Phylogeny of Alariaceae, Laminariaceae, and Lessoniaceae (Phaeophyceae) Based on Plastid-Encoded RuBisCo Spacer and Nuclear-Encoded ITS Sequence Comparisons

Cited by 105 publications

References 36 publications

Conservation and polymorphism of mitochondrial intergenic sequences in brown algae (Phaeophyceae)

Conservation and polymorphism of mitochondrial intergenic sequences in brown algae (Phaeophyceae)

Complete mitogenome of Saccharina cultivation variety ‘Ailunwan’(Saccharina japonica × latissima)

The complete mitogenome of ‘Pingbancai’, an important economic Saccharina cultivation variety

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