http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2014.1003832

MITOGENOME ANNOUNCEMENT

Sequencing of complete mitochondrial genome of Saccharina latissima ye-C14 Shuai Wang1, Xiao Fan2, Zheng Guan1, Dong Xu2, Xiaowen Zhang2, Dongsheng Wang3, Yu Miao2, and Naihao Ye2 College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China, 2Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China, and 3Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, China

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Abstract

Keywords

The complete the mitochondrial DNA (mtDNA) of Saccharina latissima ye-C14 (37,659 bp) was determined using Illumina sequencing data. The genome contains 38 protein-coding genes (PCGs), 3 ribosomal RNA (rRNA), 25 transfer RNA (tRNA) genes that are typical of Saccharina mtDNA. A phylogenetic analysis based on the mitochondrial genome of brown algae and coxI gene indicated that S. latissima and S. coriacea are closely related a sister taxon, which strongly supports their close phylogenetic affinity.

Complete mitochondrial genome, Illumina sequencing data, Saccharina latissima

Saccharina latissima (Laminariales, Phaeophyceae) is cold-water species and geologically distributed in the North Atlantic (Adey et al., 2008). Saccharina latissima is known as an economic macro algal and a marine energy crop with respect to its carbohydrate-rich and fast-growing feature. Consequently, for the indispensable analysis on the molecular genetics in S. latissima, quick and effective molecular markers with high polymorphism are needed (Zhan et al., 2012). MtDNA sequences are extensively used for comparative and evolutionary genomics, molecular evolution, population genetics, species identification, and phylogenetic relationships at various taxonomic levels owing to abundance of mitochondria in cells, lack of recombination, maternal inheritance, absence of introns and higher evolutionary rates (Fan et al., 2013; Yuan et al., 2012). To date, four partial or complete mitochondrial genomes of Saccharina genus have been determined, including three partial mitochondrial genomes for S. latissima. Here, we first sequenced the complete mitochondrial genome of a wild strain (NO. KM675818) which was sampled in Germany. The strain was subsequently named Saccharina latissima ye-C14 based on the phylogenetic analysis with 13 complete brown algae mitochondrial genomes and 4 coxI genes. Modified phenol-chloro form procedure was used to extract the total genomic DNA (Greco et al., 2014). 4G PE100 reads in total

Correspondence: Naihao Ye, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China. Fax: +86-53285830360. E-mail: [email protected]

History Received 17 November 2014 Accepted 5 December 2014 Published online 28 January 2015

was produced by the second-generation Illumina sequencing. 45,368 reads were mapped to the Saccharina japonica mitochondrial genome using Genious (http://www.genious.com) and no gap region was found in the mapping result. BLAST (Altschul et al., 1997), DNAstar (Burland et al., 2000), DOGMA (http:// dogma.ccbb.utexas.edu), sequin (http://www.ncbi.nlm.nih.gov/ projects/Sequin/) were employed to annotate and submit the S. latissima mitochondrial genome. The length of complete Saccharina latissima ye-C14 is 37,659 bp and the genome contains 3 ribosomal RNA (rRNA) genes (5S rRNA, 16S rRNA and 23S rRNA), 25 transfer RNA (tRNA) genes, 38 protein-coding genes (atp6, atp8, atp9, cob, coxI-III, nad1-7, nad9, nad11, nad4L, ORF41, ORF130, ORF377, rpl2, rpl5, rpl6, rpl14, rpl16, rpl31, rps2-4, rps7-8, rps10-14, rpl19, tatC). The length of the rrnL, rrnS and rrn5 genes are 2749, 1537 and 133 bp, respectively. All the 25 typical tRNAs range from 72 to 84. All 38 protein-coding genes (PCGs) have typical initiation codons (ATG). All PCGs have complete termination codons (29 TAA, 4 TAG and 5 TGA). The overall AT content is well within the normal range of brown alga mitochondrial DNAs, which is 64.60%. Nucleotide frequency of the H-strand is as follows: A, 28.34%; T, 36.26%; G, 20.66%; C, 14.74%. Besides the stop codons, the mitogenome of S. latissima ye-C14 encodes 10, 639 amino acids. A phylogenetic analysis based on the mitochondrial genome of brown algae and coxI gene indicated that S. latissima and Saccharina coriacea are closely related as a sister taxon, which strongly supports their close phylogenetic affinity. This result is consistent with recent phylogenetic analyses and certain morphological characters. The complete mitochondrial genomes have enhanced the resolution and statistical confidence of inferred phylogenetic trees (Figure 1).

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Mitochondrial DNA, Early Online: 1–2

Figure 1. Phylogenetic tree of ML analyses based on complete mitochondrial nucleotide acid sequences of 13 brown algae and 4 coxI genes (sbu-tree in box). Pentagrams stand for the species studied in this work.

Declaration of interest This work was supported by National Natural Science Foundation of China (41306179), Special Scientific Research Funds for Central Nonprofit Institutes, Yellow Sea Fisheries Research Institutes (20603022012004), a project from Science and Technology Commission of Qingdao Shinan District (2012-5-008-SW), Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Fisheries Research Institute Grant (201213), Shandong Science and Technology plan project (2011GHY11528), the Hi-Tech Research and Development Program (863) of China (2012AA052103), National Natural Science Foundation of China (41176153,31200187), and Qingdao Municipal Science and Technology plan project (12-6-1-3-hy). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

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Sequencing of complete mitochondrial genome of Saccharina latissima ye-C14.

The complete the mitochondrial DNA (mtDNA) of Saccharina latissima ye-C14 (37,659 bp) was determined using Illumina sequencing data. The genome contai...
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