Data from: Using linkage maps as a tool to determine patterns of chromosome synteny in the genus Salvelinus

Next generation sequencing techniques have revolutionized the collection of genome and transcriptome data from non-model organisms. This manuscript details the application of restriction site associated DNA sequencing (RADseq) to generate a marker dense genetic map for Brook trout (Salvelinus fontinalis). The consensus map was constructed from three full-sib families totaling 176 F1 individuals. The map consisted of 42 linkage groups with a total female map size of 2502.5 cM, and a total male map size of 1863.8 cM. Synteny was confirmed with Atlantic salmon for 38 linkage groups, with Rainbow trout for 37 linkage groups, Arctic char for 36 linkage groups, and with a previously published Brook trout linkage map for 39 linkage groups. Comparative mapping confirmed the presence of eight metacentric and 34 acrocentric chromosomes in Brook trout. Six metacentric chromosomes seem to be conserved with Arctic char suggesting there have been at least two species specific fusion and fission events within the genus Salvelinus. In addition, the sex marker (sdY; sexually dimorphic on the Y chromosome) was mapped to Brook trout BC35, which is homologous with Atlantic salmon Ssa09qa, Rainbow trout Omy25, and Arctic char AC04q. Ultimately, this linkage map will be a useful resource for studies on the genome organization of Salvelinus, and facilitates comparisons of the Salvelinus genome with Salmo and Oncorhynchus.

下一代测序技术彻底革新了非模式生物的基因组与转录组数据采集工作。本研究详述了利用限制性酶切位点相关DNA测序（restriction site associated DNA sequencing，RADseq）为溪红点鲑（Salvelinus fontinalis）构建高标记密度遗传图谱的应用方案。该整合遗传图谱基于3个全同胞家系构建完成，共包含176个F1代个体。该图谱共包含42个连锁群，雌性连锁图谱总长度为2502.5厘摩（centimorgan，cM），雄性连锁图谱总长度为1863.8厘摩。通过与大西洋鲑、虹鳟、北极红点鲑以及已发表的溪红点鲑连锁图谱进行共线性分析，分别验证了38、37、36以及39个连锁群的共线性关系。比较基因组定位分析证实，溪红点鲑拥有8条中间着丝粒染色体（metacentric chromosome）与34条近端着丝粒染色体（acrocentric chromosome）。其中6条中间着丝粒染色体与北极红点鲑保守，这表明在红点鲑属（Salvelinus）内至少发生过2次物种特异性的染色体融合与断裂事件。此外，本研究将Y染色体性别二态性标记（sexually dimorphic on the Y chromosome，sdY）定位至溪红点鲑BC35连锁群，该连锁群与大西洋鲑Ssa09qa、虹鳟Omy25以及北极红点鲑AC04q具有同源性。综上，本研究所构建的连锁图谱可为红点鲑属的基因组结构研究提供宝贵资源，同时也为红点鲑属基因组与鲑属（Salmo）、大麻哈鱼属（Oncorhynchus）基因组的比较分析提供便利。