Abstract
Complete mitogenome of Saccharina variety ‘Ailunwan’ (Saccharina japonica × latissima) was obtained in this work. Circular-mapping mitogenome was 37,657 bp with overall A + T content of 64.71%, encoding 3 rRNAs (23S, 16S and 5S), 25 tRNAs, 35 protein-coding genes and 3 open reading frames (ORFs). Gene content and genome organization of ‘Ailunwan’ mitogenome were identical to those Saccharina species. From the total alignment of ‘Ailunwan’ and another reported variety ‘Rongfu’ (S. japonica × latissima), 33 nucleotide substitutions were detected, and one intergenic region of 19 nucleotides insertion/deletion was found which located between rps3 and rps9. The phylogenetic analysis based on mitogenomes showed that ‘Ailunwan’ had a closer evolutionary relationship with Saccharina than Laminaria and validated the genus Saccharina and Laminaria were polyphyletic.
Keywords: Ailunwan, genetic differentiation, mitogenome, phylogenetic relationship
Saccharina (Laminariales, Phaeophyceae) is an important economic seaweed with respect to both its economic importance and global distribution (Kain 1979). ‘Ailunwan’ is one of the most important commercially Saccharina varieties in China. Here, we obtained the complete mitogenome of ‘Ailunwan’ (specimen number: 201004476, collected from Li dao Bay, Shandong, China and stored at −80 °C in the Culture Collection of Seaweed at Ocean University of China) via primer walking and long PCR techniques and gave the comparison with that of ‘Rongfu’, as part of our work to understand genetic characteristics of different varieties at genomic level.
The complete mitogenome of ‘Ailunwan’ was characterized as a circular molecule of 37,657 bp (GenBank accession number KU556731). The nucleotide composition was as follows: A = 10,700 (28.41%), C = 5541 (14.71%), G = 7749 (20.58%) and T = 136,667 (36.29%). The mitogenome had an overall A + T content of 64.71%. Cumulative GC-skew (0.1661) and AT-skew (–0.1218) analysis of mitogenome reflected a slight bias towards G and T in nucleotide composition on H-strand. The total intergenic regions were 2445 bp, accounting for 6.49% of the whole mitogenome.
The mitogenome encoded 66 genes, including 3 rRNAs, 25 tRNAs, 35protein-coding genes and 3 open reading frames (ORFs). The gene arrangement and component were identical within Saccharina mitogenomes (Yotsukura et al. 2010; Zhang et al. 2011; 2013), showing highly conservative evolution. Excepting rpl2, rpl16, rps3, rps19, tatc and ORF130, 60 genes were encoded on H-strand. All protein-coding genes started with ATG codon. Approximately 68.42% of protein-coding genes terminated with TAA codon, higher than that for TAG (21.05%) and TGA (10.53%). There were 13 pairs of genes with overlapping by 1–16 bp, making full use of nucleotide and genetic information. One obvious gene cluster (rps8-rpl6-rps2-rps4) was conserved in Saccharina mitogenomes.
Total mitogenome sequences of ‘Ailunwan’ and ‘Rongfu’ were aligned to find useful DNA barcoding. 33 nucleotide substitutions and 19 nucleotides intergenic region located between rps3 and rps9 in ‘Ailunwan’ while lacked from ‘Rongfu’ were found. Bayesian analysis based on combined 35 protein-encoding genes shared by Laminariaceae species exhibited the species were divided into two clades: Saccharina and Laminaria (Figure 1). Phylogenetic analyses showed that ‘Ailunwan’ firstly groups with Saccharina japonica. It indicated that ‘Ailunwan’ had a closer evolutionary relationship with Saccharina than Laminaria, supporting current taxonomic systems (Yoon et al. 2001; Lane et al. 2006).
Figure 1.
Phylogenetic trees derived from Bayesian analysis constructed based on concatenated nucleotide sequences of 35 mtDNA protein-encoding genes.
Acknowledgments
Disclosure statement
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article.
This work was supported by the National Natural Science Foundation of China (Grant No. 31402300), the Fundamental Research Funds for the Central Universities (201562019) and TaiShan industrial Experts Programme.
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