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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.

Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida