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Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida.

Zhang L, Wang X, Liu T, Wang G, Chi S, Liu C, Wang H - PLoS ONE (2015)

Bottom Line: In the large brown algae branch, U. pinnatifida and S. japonica formed a sister clade with much closer relationship to Ectocarpus siliculosus than to Fucus vesiculosus.For the first time, the start codon ATT was identified in the plastid genome of large brown algae, in the atpA gene of U. pinnatifida.In addition, we found a gene-length change induced by a 3-bp repetitive DNA in ycf35 and ilvB genes of the U. pinnatifida plastid genome.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Genetics and Breeding of Marine Organism, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China.

ABSTRACT
In this study, we fully sequenced the circular plastid genome of a brown alga, Undaria pinnatifida. The genome is 130,383 base pairs (bp) in size; it contains a large single-copy (LSC, 76,598 bp) and a small single-copy region (SSC, 42,977 bp), separated by two inverted repeats (IRa and IRb: 5,404 bp). The genome contains 139 protein-coding, 28 tRNA, and 6 rRNA genes; none of these genes contains introns. Organization and gene contents of the U. pinnatifida plastid genome were similar to those of Saccharina japonica. There is a co-linear relationship between the plastid genome of U. pinnatifida and that of three previously sequenced large brown algal species. Phylogenetic analyses of 43 taxa based on 23 plastid protein-coding genes grouped all plastids into a red or green lineage. In the large brown algae branch, U. pinnatifida and S. japonica formed a sister clade with much closer relationship to Ectocarpus siliculosus than to Fucus vesiculosus. For the first time, the start codon ATT was identified in the plastid genome of large brown algae, in the atpA gene of U. pinnatifida. In addition, we found a gene-length change induced by a 3-bp repetitive DNA in ycf35 and ilvB genes of the U. pinnatifida plastid genome.

No MeSH data available.


Phylogenetic tree topologies based on 23 plastid protein-coding genes inferred using Bayesian methods.
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pone.0139366.g004: Phylogenetic tree topologies based on 23 plastid protein-coding genes inferred using Bayesian methods.

Mentions: The phylogenetic dataset included 23 protein-coding genes of plastid genomes from 41 algae and 2 land plants (Arabidopsis thaliana and Oryza sativa). The phylogenetic analysis was based on the whole concatenated alignment of 6,113 amino acids. Cyanophora paradoxa was assigned as an outgroup. The Bayesian inference (BI) and ML analyses yielded different topologies with little difference (Fig 4 and S1 Fig). Results of both analyses suggest that secondary plastid-containing groups of Chromalveolata, including Heterokontophyta, Haptophyta and Cryptophyta, are sister groups of Rhodophyta; however, results of the ML analysis suggest that Cryptophyta and Haptophyta are separate from the rest of Chromalveolata and formed a sister group with Rhodophyta. The phylogenetic relationships based on BI analysis were consistent with results of previous studies on plastid genomes of the three brown algae [24, 25], while the relationships based on ML analysis were consistent with phylogenetic results of previous studies on the two red algal species [26]. Here, we have only presented the phylogenetic tree based on BI analysis with posterior probabilities for illustration (Fig 4). Overall, all taxa were clearly divided into two distinct lineages. Branch A includes land plants, Charophyta, Chlorarachniophyta, and the green algae Chlorophyta. Within this branch, land plants and Charophyta formed one sub-branch and Mesostigma viride emerged at the base of this sub-branch with a posterior probability of 0.88. The other sub-branch of branch A consisted of Bigelowiella natans and green algae. Branch B and C formed the other main clade. All Rhodophyta algae were grouped in branch C, with strong support for Porphyridium purpureum as the basal member. Moreover, there was a split between Cyanidiaceae on the one hand and Florideophyceae and Bangiophyceae on the other hand at a higher support value (100%). Branch B consisted of two clades. In clade B1, Heterokontophyta, including two taxa from Pelagophyceae and six taxa from Bacillariophyceae, formed one main group, while in the other part of the lineage, U. pinnatifida and S. japonica had a relatively high support value as the closest branch to E. siliculosus, and were further grouped with F. vesiculosus. In clade B2, Emiliania huxleyi from Haptophyta was grouped together with two species from Cryptophyta. These results support the conclusion that the Alariaceae family, including Undaria, is a sister group of the Laminariaceae family, including Saccharina.


Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida.

Zhang L, Wang X, Liu T, Wang G, Chi S, Liu C, Wang H - PLoS ONE (2015)

Phylogenetic tree topologies based on 23 plastid protein-coding genes inferred using Bayesian methods.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591262&req=5

pone.0139366.g004: Phylogenetic tree topologies based on 23 plastid protein-coding genes inferred using Bayesian methods.
Mentions: The phylogenetic dataset included 23 protein-coding genes of plastid genomes from 41 algae and 2 land plants (Arabidopsis thaliana and Oryza sativa). The phylogenetic analysis was based on the whole concatenated alignment of 6,113 amino acids. Cyanophora paradoxa was assigned as an outgroup. The Bayesian inference (BI) and ML analyses yielded different topologies with little difference (Fig 4 and S1 Fig). Results of both analyses suggest that secondary plastid-containing groups of Chromalveolata, including Heterokontophyta, Haptophyta and Cryptophyta, are sister groups of Rhodophyta; however, results of the ML analysis suggest that Cryptophyta and Haptophyta are separate from the rest of Chromalveolata and formed a sister group with Rhodophyta. The phylogenetic relationships based on BI analysis were consistent with results of previous studies on plastid genomes of the three brown algae [24, 25], while the relationships based on ML analysis were consistent with phylogenetic results of previous studies on the two red algal species [26]. Here, we have only presented the phylogenetic tree based on BI analysis with posterior probabilities for illustration (Fig 4). Overall, all taxa were clearly divided into two distinct lineages. Branch A includes land plants, Charophyta, Chlorarachniophyta, and the green algae Chlorophyta. Within this branch, land plants and Charophyta formed one sub-branch and Mesostigma viride emerged at the base of this sub-branch with a posterior probability of 0.88. The other sub-branch of branch A consisted of Bigelowiella natans and green algae. Branch B and C formed the other main clade. All Rhodophyta algae were grouped in branch C, with strong support for Porphyridium purpureum as the basal member. Moreover, there was a split between Cyanidiaceae on the one hand and Florideophyceae and Bangiophyceae on the other hand at a higher support value (100%). Branch B consisted of two clades. In clade B1, Heterokontophyta, including two taxa from Pelagophyceae and six taxa from Bacillariophyceae, formed one main group, while in the other part of the lineage, U. pinnatifida and S. japonica had a relatively high support value as the closest branch to E. siliculosus, and were further grouped with F. vesiculosus. In clade B2, Emiliania huxleyi from Haptophyta was grouped together with two species from Cryptophyta. These results support the conclusion that the Alariaceae family, including Undaria, is a sister group of the Laminariaceae family, including Saccharina.

Bottom Line: In the large brown algae branch, U. pinnatifida and S. japonica formed a sister clade with much closer relationship to Ectocarpus siliculosus than to Fucus vesiculosus.For the first time, the start codon ATT was identified in the plastid genome of large brown algae, in the atpA gene of U. pinnatifida.In addition, we found a gene-length change induced by a 3-bp repetitive DNA in ycf35 and ilvB genes of the U. pinnatifida plastid genome.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Genetics and Breeding of Marine Organism, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China.

ABSTRACT
In this study, we fully sequenced the circular plastid genome of a brown alga, Undaria pinnatifida. The genome is 130,383 base pairs (bp) in size; it contains a large single-copy (LSC, 76,598 bp) and a small single-copy region (SSC, 42,977 bp), separated by two inverted repeats (IRa and IRb: 5,404 bp). The genome contains 139 protein-coding, 28 tRNA, and 6 rRNA genes; none of these genes contains introns. Organization and gene contents of the U. pinnatifida plastid genome were similar to those of Saccharina japonica. There is a co-linear relationship between the plastid genome of U. pinnatifida and that of three previously sequenced large brown algal species. Phylogenetic analyses of 43 taxa based on 23 plastid protein-coding genes grouped all plastids into a red or green lineage. In the large brown algae branch, U. pinnatifida and S. japonica formed a sister clade with much closer relationship to Ectocarpus siliculosus than to Fucus vesiculosus. For the first time, the start codon ATT was identified in the plastid genome of large brown algae, in the atpA gene of U. pinnatifida. In addition, we found a gene-length change induced by a 3-bp repetitive DNA in ycf35 and ilvB genes of the U. pinnatifida plastid genome.

No MeSH data available.