Limits...
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.


Gene map of the Undaria pinnatifida plastid genome.Genes on the outside of the map are transcribed counterclockwise and those on the inside of the map are transcribed clockwise. The innermost gray ring represents the GC content. The black arrow indicates the position of the stem-loop structure.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4591262&req=5

pone.0139366.g001: Gene map of the Undaria pinnatifida plastid genome.Genes on the outside of the map are transcribed counterclockwise and those on the inside of the map are transcribed clockwise. The innermost gray ring represents the GC content. The black arrow indicates the position of the stem-loop structure.

Mentions: The plastid DNA of U. pinnatifida was a circular molecule of 130,383 nucleotides (nt), with an overall A+T content of 69.38%. It consisted of four typical parts: LSC, SSC, IRa, and IRb. The size of LSC and SSC was 76,598 bp and 42,977 bp, respectively, while IRa and IRb were both 5,404 bp. The U. pinnatifida plastid genome encoded 139 proteins, 28 tRNAs, and 6 rRNAs, and none of these genes contained introns. All genes were distributed in both positive and negative strands, but there was no obvious rule regarding the direction of transcription (Fig 1). Four gene overlaps were identified: rpl23 overlapped with rpl4 by 8 nt, ftrB overlapped with ycf12 by 6 nt, ycf16 overlapped with ycf24 by 4 nt, and psbC overlapped with psbD by 53 nt. These overlaps are virtually identical to those found in the plastid genome of S. japonica. In an intergenic region at the demarcation point of two opposite transcriptional units, a long and stable stem-loop structure (84 bp) was identified in the plastid genome of U. pinnatifida. The secondary structure was a complete inverted repeat sequence between the psaL and rbcR genes (Fig 1).


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)

Gene map of the Undaria pinnatifida plastid genome.Genes on the outside of the map are transcribed counterclockwise and those on the inside of the map are transcribed clockwise. The innermost gray ring represents the GC content. The black arrow indicates the position of the stem-loop structure.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139366.g001: Gene map of the Undaria pinnatifida plastid genome.Genes on the outside of the map are transcribed counterclockwise and those on the inside of the map are transcribed clockwise. The innermost gray ring represents the GC content. The black arrow indicates the position of the stem-loop structure.
Mentions: The plastid DNA of U. pinnatifida was a circular molecule of 130,383 nucleotides (nt), with an overall A+T content of 69.38%. It consisted of four typical parts: LSC, SSC, IRa, and IRb. The size of LSC and SSC was 76,598 bp and 42,977 bp, respectively, while IRa and IRb were both 5,404 bp. The U. pinnatifida plastid genome encoded 139 proteins, 28 tRNAs, and 6 rRNAs, and none of these genes contained introns. All genes were distributed in both positive and negative strands, but there was no obvious rule regarding the direction of transcription (Fig 1). Four gene overlaps were identified: rpl23 overlapped with rpl4 by 8 nt, ftrB overlapped with ycf12 by 6 nt, ycf16 overlapped with ycf24 by 4 nt, and psbC overlapped with psbD by 53 nt. These overlaps are virtually identical to those found in the plastid genome of S. japonica. In an intergenic region at the demarcation point of two opposite transcriptional units, a long and stable stem-loop structure (84 bp) was identified in the plastid genome of U. pinnatifida. The secondary structure was a complete inverted repeat sequence between the psaL and rbcR genes (Fig 1).

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.