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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.


Comparison of four large brown algal plastid genomes by using the Geneious software.Letters A to E with two-header arrows correspond to the specified area of each species.
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pone.0139366.g002: Comparison of four large brown algal plastid genomes by using the Geneious software.Letters A to E with two-header arrows correspond to the specified area of each species.

Mentions: Detailed characteristics of gene order based on Geneious analyses for plastid genomes of all four large brown algae from Phaeophyceae are shown in Fig 2. The gene content and order were almost identical for U. pinnatifida and S. japonica, both of which belong to the order Laminariales, while F. vesiculosus and Ectocarpus siliculosus showed some differences compared with these two species. Nevertheless, there were two long and conserved gene clusters among the four plastid genomes, in which the gene order was almost exactly the same in the four species (area A and D in Fig 2). In addition, a gene cluster in area E of U. pinnatifida and S. japonica corresponded to the gene cluster located in area C of Ectocarpus siliculosus with the same gene content and order but in opposite direction. Furthermore, area B contained a short gene cluster identical in U. pinnatifida, S. japonica, and E. siliculosus. Overall, there was an extraordinary high linear relationship between U. pinnatifida and S. japonica, as they both had exactly the same gene content and gene order. E. siliculosus showed a higher linear relationship with these two species than with F. vesiculosus. The presence of two long gene clusters indicates a conserved evolutionary process for large brown algal plastid genes.


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)

Comparison of four large brown algal plastid genomes by using the Geneious software.Letters A to E with two-header arrows correspond to the specified area of each species.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139366.g002: Comparison of four large brown algal plastid genomes by using the Geneious software.Letters A to E with two-header arrows correspond to the specified area of each species.
Mentions: Detailed characteristics of gene order based on Geneious analyses for plastid genomes of all four large brown algae from Phaeophyceae are shown in Fig 2. The gene content and order were almost identical for U. pinnatifida and S. japonica, both of which belong to the order Laminariales, while F. vesiculosus and Ectocarpus siliculosus showed some differences compared with these two species. Nevertheless, there were two long and conserved gene clusters among the four plastid genomes, in which the gene order was almost exactly the same in the four species (area A and D in Fig 2). In addition, a gene cluster in area E of U. pinnatifida and S. japonica corresponded to the gene cluster located in area C of Ectocarpus siliculosus with the same gene content and order but in opposite direction. Furthermore, area B contained a short gene cluster identical in U. pinnatifida, S. japonica, and E. siliculosus. Overall, there was an extraordinary high linear relationship between U. pinnatifida and S. japonica, as they both had exactly the same gene content and gene order. E. siliculosus showed a higher linear relationship with these two species than with F. vesiculosus. The presence of two long gene clusters indicates a conserved evolutionary process for large brown algal plastid genes.

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.