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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.


The 3-bp repetitive DNA mutations in U. pinnatifida plastid genes.Colored letters are amino acid sequences corresponding to the nucleotide sequence of each gene for both U. pinnatifida and S. japonica, and “–” represents the deletion of a base.
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pone.0139366.g003: The 3-bp repetitive DNA mutations in U. pinnatifida plastid genes.Colored letters are amino acid sequences corresponding to the nucleotide sequence of each gene for both U. pinnatifida and S. japonica, and “–” represents the deletion of a base.

Mentions: We found that the ycf35 gene in the U. pinnatifida plastid genome was 3 bp shorter than that of S. japonica, because of an ATT repeat (Fig 3). However, the repetitive sequence neither affected the overall ORF structure nor caused any change to remaining rest amino acid sequences of the gene. Similar to the ycf35 gene, another 3-bp length mutation existed in the ilvB gene. The ilvB gene of S. japonica had one less AAA repeat than that of U. pinnatifida, which again did not cause a frame-shift (Fig 3). Both mutations occurred in the region close to the tri-nucleotide repeat enrichment area. There were four AAT repeats ahead of the ATT mutation in the ycf35 gene, and three GAA repeats followed the AAA mutation site in the ilvB gene. The presence of repetitive DNA may induce some genomic instability that causes minor sequence changes to occur.


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)

The 3-bp repetitive DNA mutations in U. pinnatifida plastid genes.Colored letters are amino acid sequences corresponding to the nucleotide sequence of each gene for both U. pinnatifida and S. japonica, and “–” represents the deletion of a base.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139366.g003: The 3-bp repetitive DNA mutations in U. pinnatifida plastid genes.Colored letters are amino acid sequences corresponding to the nucleotide sequence of each gene for both U. pinnatifida and S. japonica, and “–” represents the deletion of a base.
Mentions: We found that the ycf35 gene in the U. pinnatifida plastid genome was 3 bp shorter than that of S. japonica, because of an ATT repeat (Fig 3). However, the repetitive sequence neither affected the overall ORF structure nor caused any change to remaining rest amino acid sequences of the gene. Similar to the ycf35 gene, another 3-bp length mutation existed in the ilvB gene. The ilvB gene of S. japonica had one less AAA repeat than that of U. pinnatifida, which again did not cause a frame-shift (Fig 3). Both mutations occurred in the region close to the tri-nucleotide repeat enrichment area. There were four AAT repeats ahead of the ATT mutation in the ycf35 gene, and three GAA repeats followed the AAA mutation site in the ilvB gene. The presence of repetitive DNA may induce some genomic instability that causes minor sequence changes to occur.

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.