Characterization of genome-wide microsatellites of <Emphasis Type="Italic">Saccharina japonica</Emphasis> based on a preliminary assembly of Illumina sequencing reads |
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| Authors: | Linan Zhang Jie Peng Xiaojie Li Cuiju Cui Juan Sun Guanpin Yang |
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| Institution: | 1.Marine Science and Engineering College,Qingdao Agriculture University,Qingdao,P. R. China;2.Shandong Oriental Ocean Sci-tech Co., Ltd; National Engineering and Technique Research and Development Center of Algae and Sea Cucumber of China,Provincial Key Laboratory of Genetic Improvement and Efficient Culture of Marine Algae of Shandong,Yantai,P. R. China;3.College of Marine Life Sciences,Ocean University of China,Qingdao,P. R. China |
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| Abstract: | Microsatellites or simple sequence repeats (SSR) function widely and locate dependently in genome. However, their characteristics are often ignored due to the lack of genomic sequences of most species. Kelp (Saccharina japonica), a brown macroalga, is extensively cultured in China. In this study, the genome of S. japonica was surveyed using an Illumina sequencing platform, and its microsatellites were characterized. The preliminarily assembled genome was 469.4 Mb in size, with a scaffold N50 of 20529 bp. Among the 128370 identified microsatellites, 90671, 25726 and 11973 were found in intergenic regions, introns and exons, averaging 339.3, 178.8 and 205.4 microsatellites per Mb, respectively. These microsatellites distributed unevenly in S. japonica genome. Mononucleotide motifs were the most abundant in the genome, while trinucleotide ones were the most prevalent in exons. The microsatellite abundance decreased significantly with the increase of motif repeat numbers, and the microsatellites with a small number of repeats accounted for a higher proportion of the exons than those of the intergenic regions and introns. C/G-rich motifs were more common in exons than in intergenic regions and introns. These characteristics of microsatellites in S. japonica genome may associate with their functions, and ultimately their adaptation and evolution. Among the 120140 pairs of designed microsatellite primers, approximately 75% were predicted to be able to amplify S. japonica DNA. These microsatellite markers will be extremely useful for the genetic breeding and population evolution studies of kelp. |
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