Development of 11 Ecklonia radicosa (Phaeophyceae, Laminariales) SSRs markers using next-generation sequencing and intra-genus amplification analysis

作者：Akita Shingo^*; Koiwai Keiichiro; Hanyuda Takeaki; Kato Syou; Nozaki Reiko; Uchino Tsubasa; Sakamoto Takashi; Kondo Hidehiro; Hirono Ikuo; Fujita Daisuke

来源：Journal of Applied Phycology, 2018, 30(3): 2111-2115.

DOI：10.1007/s10811-018-1406-5

• Ecklonia radicosa
• SSRs
• Microsatellite
• Phaeophyceae

Polymorphic simple sequence repeat (SSR) markers of Ecklonia radicosa were developed using Illumina MiSeq next-generation sequencing (NGS) analysis. In total, 3112 SSRs (di- to hexanucleotide motifs repeated more than six times) were identified from 61.5-Mb assembled genomic DNA using MISA perl script. Among the SSRs, di- (853 loci, 27.4%) and trinucleotides (1813 loci, 58.3%) were dominant, while tetra- (172 loci, 5.5%), penta- (175 loci, 5.6%), and hexanucleotides (99 loci, 3.2%) were not common. After specific amplification and polymorphic tests of 75 selected loci (tri- to hexanucleotide motifs repeated more than eight times), 11 SSR markers (Eradic01-11) were successfully developed. The range of the number of alleles, observed heterozygosity, and expected heterozygosity in the 11 markers was 3-13, 0.200-0.683, and 0.258-0.864, respectively. Polymorphic information content (PIC) analysis indicated that eight markers (Eradic01, 02, 04, 05, 06, 08, 09, and 11) were highly informative (PIC > 0.5) and the other three were reasonably informative (0.5 < PIC < 0.25). In addition, intra-genus amplification was obtained in all markers except for Eradic02, 08, and 11. These markers could help to reveal the genetic diversity and population structure of E. radicosa.

• 出版日期2018-6