Saccharina genomes provide novel insight into kelp biology

Abstract

Seaweeds are essential for marine ecosystems and have immense economic value. Here we present a comprehensive analysis of the draft genome of Saccharina japonica, one of the most economically important seaweeds. The 537-Mb assembled genomic sequence covered 98.5% of the estimated genome, and 18,733 protein-coding genes are predicted and annotated. Gene families related to cell wall synthesis, halogen concentration, development and defence systems were expanded. Functional diversification of the mannuronan C-5-epimerase and haloperoxidase gene families provides insight into the evolutionary adaptation of polysaccharide biosynthesis and iodine antioxidation. Additional sequencing of seven cultivars and nine wild individuals reveal that the genetic diversity within wild populations is greater than among cultivars. All of the cultivars are descendants of a wild S. japonica accession showing limited admixture with S. longissima. This study represents an important advance toward improving yields and economic traits in Saccharina and provides an invaluable resource for plant genome studies.

Characterization and physical mapping of nuclear ribosomal RNA (rRNA) genes in the haploid gametophytes of Saccharina japonica (Phaeophyta)

“…2). This finding was confirmed by searching against the recently released kelp genome database by Ye et al (2015). The IGSs detected in this study were deposited to NCBI (GenBank Accession Nos.…”

“…The copy number of rDNA in the kelp haploid genome was calculated using the following equation: Zagoskin et al 2010); where N r is the 18S rDNA or 5S rDNA copy number, C is the size of the S. japonica haploid genome (C = 0.5975 pg) as estimated by Ye et al (2015), N m is the experimentally determined initial amount of the 18S or 5S rRNA gene templates, N p is the same as earlier described, and k is the amount of genomic DNA template of the sample that was used in the Q-RT PCR.…”

“…The C T value of the S. japonica 18S rRNA gene in the haploid genome was also detected by Q-RT PCR (Table 2). By referring to the constructed standard curve and the recently reported genome size of S. japonica (Ye et al 2015), the copy number of 18S-5.8S-25S rRNA gene in S. japonica female and male gametophytes was evaluated (Table 2). The copy number ranged from 39 to 51 (mean ± SD = 45 ± 7, n = 9) and from 22 to 56 (mean ± SD = 41 ± 15, n = 9) per haploid genome of female and male gametophytes, respectively (Table 2).…”

Sequencing of complete mitochondrial genome of brown algal Saccharina sp. ye-C

“…However, in China S. japonica suffered close breeding for generations which have caused significant issues such as loss of genetic varieties, decreasing growth rate and massive mortality (Guan et al 2016). Recently, the genome of S. japonica has been sequenced (Ye et al 2015), which could strongly promote the genetic improvement of the species. In the study, genomes of several strains of Saccharina collected from different locations all over the world were re-sequenced.…”

Sequencing of complete mitochondrial genome of brown algal Saccharina sp. ye-C2

“…However, close breeding for generations in China caused loss of genetic variance in S. japonica (Zhan et al 2012). Thankfully, the genome of S. japonica has been sequenced (Ye et al 2015), which would powerfully push the genetic improvement of the species.…”