Prof. Naihao Ye’s laboratory in Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, recently published an article entitled “Saccharina genomes provide novel insight into kelp biology” in Nature Communications on April 24, 2015. The S. japonica genome is the first sequenced reference genome from kelps, which provide novel insight into the evolutionary adaptation mechanisms of kelp and low genetic diversity within Saccharina cultivars. This paper represents an important advance toward improving yields and economic traits in Saccharina and provides an invaluable resource for plant genome studies.
The draft genome sequence of the female gametophytes of the artificially cultivated S. japonica strain Ja was obtained. The 537-Mb assembled genomic sequence covered 98.5% of the estimated genome, and 18,733 protein-coding genes are predicted and annotated. Comparative genomics revealed that expansion of the Saccharina genome was mainly due to large-scale amplification of gene families, and a total of 1,240 gene families were gained from the common ancestor of S. japonica and Ectocarpus siliculosus. After the divergence of these two species, gene families related to cell wall synthesis, halogen concentration, development and defense systems were expanded in S. japonica. The recent expansion and functional diversification of the mannuronan C-5-epimerase and vanadium-dependent haloperoxidase gene families provides insight into the evolutionary adaptation of polysaccharide biosynthesis, and iodine concentration and antioxidation mechanisms.
S. japonica has become the most economically important seaweed in China’s mariculture industry. The output of S. japonica reached 7.9-million tons (dry weight) and had a market value of more than US $1.3 billion in 2012. Despite its ecological and economic importance, years of interspecific hybridization and biomass yield-targeted artificial selections have not only compromised the economic characteristics of these kelps but also narrowed their genetic variation. In this paper, the resequencing of seven wild populations and nine representative cultivars of Saccharina species were also reported. All of the cultivars are descendants of a wild S. japonica accession showing limited admixture with S. longissima. An average of 0.94 M single nucleotide variations (SNVs) and 96 K small InDels in the cultivars and an average of 2.27 M SNVs and 274 K small InDels in the wild populations were identified. The results confirmed that the diversity between any pair of the collected wild individuals was greater than the diversity among all of the cultivars and that these cultivated individuals shared the same ancestor with the wild individual, indicating a restricted germplasm base and a very low genetic diversity within the principal Saccharina cultivars.
This work presents the first comprehensive resequencing data for wild and cultivated Saccharina individuals, providing the basic materials for evolution and population genetic studies. The obtained genomic information on wild Saccharina species can not only be used to increase the genetic diversity through hybridization, but also provide a large source of candidate genes for further functional studies aimed at improving quality and yield.
Associate Prof. Xiaowen Zhang and Assistant Prof. Xiao Fan in Yellow Sea Fisheries Research Institute, and Associate Prof. Miao Miao in College of Life Sciences, University of Chinese Academy of Sciences contributed equally to this work. Prof. Fangqing Zhao in Beijing Institutes of Life Science, Chinese Academy of Sciences and Prof. Ji Qi in Fudan University are the co-correspondence authors. This work was supported by the Hi-Tech Research and Development Program (863) of China (2012AA052103, 2014AA022003), the National Science & Technology Pillar Program (2013BAD23B01), and Qingdao Municipal Leading Talent project (13-CX-27) to N.Y., the National Natural Science Foundation of China Grant (91131013, 31100952), and the Fund of Beijing Institutes of Life Science, Chinese Academy of Sciences to F.Z., and the National Natural Science Foundation of China Grant (31272285) to M.M., the Ministry of Sciences and Technology of China 973 Program Grant (2012CB910503) to J.Q.
