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 b...
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doaj-43350e312e4440dbb6d419b33f4be1172021-03-03T19:58:51ZengPublic Library of Science (PLoS)PLoS ONE1932-62032015-01-011010e013936610.1371/journal.pone.0139366Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida.Lei ZhangXumin WangTao LiuGuoliang WangShan ChiCui LiuHaiyang WangIn 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.https://doi.org/10.1371/journal.pone.0139366 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Lei Zhang Xumin Wang Tao Liu Guoliang Wang Shan Chi Cui Liu Haiyang Wang |
spellingShingle |
Lei Zhang Xumin Wang Tao Liu Guoliang Wang Shan Chi Cui Liu Haiyang Wang Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida. PLoS ONE |
author_facet |
Lei Zhang Xumin Wang Tao Liu Guoliang Wang Shan Chi Cui Liu Haiyang Wang |
author_sort |
Lei Zhang |
title |
Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida. |
title_short |
Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida. |
title_full |
Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida. |
title_fullStr |
Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida. |
title_full_unstemmed |
Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida. |
title_sort |
complete plastid genome sequence of the brown alga undaria pinnatifida. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2015-01-01 |
description |
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. |
url |
https://doi.org/10.1371/journal.pone.0139366 |
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