The lumpfish Cyclopterus lumpus is commercially exploited in numerous areas of its range in the North Atlantic Ocean, and is important in salmonid aquaculture as a biological agent for controlling sea lice. Despite the economic importance, few genetic resources for downstream applications, such as linkage mapping, parentage analysis, marker-assisted selection (MAS), quantitative trait loci (QTL) analysis, and assessing adaptive genetic diversity are currently available for the species. Here, we identify both genome- and transcriptome-derived microsatellites loci from C. lumpus to facilitate such applications. Across 2,346 genomic contigs, we detected a total of 3,067 microsatellite loci, of which 723 were the most suitable ones for primer design. From 116,555 transcriptomic unigenes, we identified a total of 231,556 microsatellite loci, which may indicate a high coverage of the available STRs. Out of these, primer pairs could only be designed for 6,203 loci. Dinucleotide repeats accounted for 89 percent and 52 percent of the genome- and transcriptome-derived microsatellites, respectively. The genetic composition of the dominant repeat motif types showed differences from other investigated fish species. In the genome-derived microsatellites AC/GT (67.8 percent), followed by AG/CT (15.1 percent) and AT/AT (5.6 percent) were the major motifs. Transcriptome-derived microsatellites showed also most dominantly the AC/GT repeat motif (33 percent), followed by A/T (26.6 percent) and AG/CT (11 percent). Functional annotation of microsatellite-containing transcriptomic sequences showed that the majority of the expressed sequence tags encode proteins involved in cellular and metabolic processes, binding activity and catalytic reactions. Importantly, STRs linked to genes involved in immune system process, growth, locomotion and reproduction were discovered in the present study. The extensive genomic marker information reported here will facilitate molecular ecology studies, conservation initiatives and will benefit many aspects of the breeding programmes of C. lumpus.

中文翻译：

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ump鱼Cyclopterus lumpus中基因组和转录组衍生的微卫星基因座：用于水产养殖，保护和渔业管理的分子工具。

ump鱼Cyclopterus ump在北大西洋的许多范围内都有商业用途，在鲑鱼养殖中作为控制海虱的生物剂很重要。尽管具有经济重要性，但目前对于该物种而言，用于下游应用的遗传资源很少，例如连锁作图，亲缘关系分析，标记辅助选择（MAS），数量性状基因座（QTL）分析和评估适应性遗传多样性。在这里，我们从C. lumpus确定基因组和转录组衍生的微卫星基因座，以促进此类应用。在2346个基因组重叠群中，我们检测到3067个微卫星基因座，其中723个最适合引物设计。从116,555个转录组单基因中，我们鉴定出总共231,556个微卫星基因座，这可能表明可用STR的覆盖率很高。其中，引物对只能用于6,203个基因座。双核苷酸重复分别占基因组和转录组微卫星的89％和52％。优势重复基序类型的遗传组成显示与其他调查鱼类不同。在基因组衍生的微卫星中，AC / GT（67.8％），其次是AG / CT（15.1％）和AT / AT（5.6％）。转录组衍生的微卫星还显示了AC / GT重复基序（33％），占主导地位，其次是A / T（26.6％）和AG / CT（11％）。含有微卫星的转录组序列的功能注释显示，大多数表达的序列标签编码参与细胞和代谢过程，结合活性和催化反应的蛋白质。重要的是，在本研究中发现了与免疫系统过程，生长，运动和繁殖相关基因相关的STR。此处报道的广泛的基因组标记信息将促进分子生态学研究，保护计划，并将有益于块茎。鱼育种计划的许多方面。