Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida

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.