Journal
MARINE GENOMICS
Volume 10, Issue -, Pages 1-9Publisher
ELSEVIER
DOI: 10.1016/j.margen.2012.12.002
Keywords
Photosynthetic heterokont; Saccharina japonica; Chloroplast; Phylogenomic; Molecular phylogenetics
Categories
Funding
- National High Tech 863 Project [2012AA10A406]
- NSFC [31272660, 30500383, 40976085]
- Project of Achievement Transformation of Agricultural Sci. Tech. [2011GB2491005]
- Key Laboratory of Experimental Marine Biology of CAS
- Key Laboratory of Feed Biotechnology of MOAPRC
- CAS
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The chloroplast genome sequence of one brown seaweed, Saccharina japonica, was fully determined. It is characterized by 130,584 base pairs (bp) with a large and a small single-copy region (LSC and SSC), separated by two copies of inverted repeats (IR1 and IR2). The inverted repeat is 5015 bp long, and the sizes of SSC and LSC are 43,174 bp and 77,378 bp, respectively. The chloroplast genome of S. japonica consists of 139 protein-coding genes, 29 tRNA genes, and 3 ribosomal RNA genes. One intron was found in one tRNA-Leu gene in the chloroplast genome of S. japonica. Four types of overlapping genes were identified, ycf24 overlapped with ycf16 by 4 nucleotides (nt), ftrB overlapped with ycf12 by 6 nt, rpl4 and rpl23 overlapped by 8 nt, finally, psbC overlapped with psbD by 53 tit With two sets of concatenated plastid protein data, 40-protein dataset and 26-protein dataset, the chloroplast phylogenetic relationship among S. japonica and the other photosynthetic species was evaluated. We found that the chloroplast genomes of haptophyte, cryptophyte and heterokont were not resolved into one cluster by the 40-protein dataset with amino acid composition bias, although it was recovered with strong support by the 26-protein dataset. (C) 2012 Elsevier B.V. All rights reserved.
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