Data from: A genomic reference panel for Drosophila serrata

Here we describe a collection of re-sequenced inbred lines of Drosophila serrata, sampled from a natural population situated deep within the species endemic distribution in Brisbane, Australia. D. serrata is a member of the speciose montium group whose members inhabit much of south east Asia and has been well studied for aspects of climatic adaptation, sexual selection, sexual dimorphism, and mate recognition. We sequenced 110 lines that were inbred via 17-20 generations of full-sib mating at an average coverage of 23.5x with paired-end Illumina reads. 15,228,692 biallelic SNPs passed quality control after being called using the Joint Genotyper for Inbred Lines (JGIL). Inbreeding was highly effective and the average levels of residual heterozygosity (0.86%) were well below theoretical expectations. As expected, linkage disequilibrium decayed rapidly, with r2 dropping below 0.1 within 100 base pairs. With the exception of four closely related pairs of lines which may have been due to technical errors, there was no statistical support for population substructure. Consistent with other endemic populations of other Drosophila species, preliminary population genetic analyses revealed high nucleotide diversity and, on average, negative Tajima’s D values. A preliminary GWAS was performed on a cuticular hydrocarbon trait, 2-MeC28 revealing 4 SNPs passing Bonferroni significance residing in or near genes. One gene Cht9 may be involved in the transport of CHCs from the site of production (oenocytes) to the cuticle. Our panel will facilitate broader population genomic and quantitative genetic studies of this species and serve as an important complement to existing D. melanogaster panels that can be used to test for the conservation of genetic architectures across the Drosophila genus.本研究描述了一套锯缘果蝇（Drosophila serrata）的重测序近交系集合，该品系采集自澳大利亚布里斯班深处的该物种特有分布区内的自然种群。锯缘果蝇隶属于物种多样性丰富的montium种组，该种组的成员广泛栖息于东南亚大部分区域，且在气候适应、性选择、性二型以及配偶识别等方面已有充分研究。我们对110个经17-20代全同胞交配获得的近交系进行了测序，采用双端Illumina读段，平均测序深度为23.5×。使用近交系联合基因分型器（Joint Genotyper for Inbred Lines, JGIL）进行基因型鉴定后，共有15,228,692个双等位基因单核苷酸多态性位点（SNPs）通过质量控制。近交效果显著，平均残余杂合率为0.86%，远低于理论预期值。如预期所示，连锁不平衡（linkage disequilibrium, LD）衰减迅速，在100个碱基对（bp）范围内，r²值即降至0.1以下。除了4对亲缘关系极近的品系（可能由技术误差导致）外，未检测到种群亚结构的统计学支持。与其他果蝇物种的特有种群一致，初步种群遗传学分析显示其核苷酸多样性较高，且平均Tajima's D值为负值。针对表皮碳氢化合物（cuticular hydrocarbons, CHCs）性状2-MeC28开展了初步全基因组关联分析（Genome-Wide Association Study, GWAS），共鉴定出4个达到邦费罗尼显著性阈值的SNPs，这些位点位于基因内部或基因附近。其中一个名为Cht9的基因可能参与表皮碳氢化合物从合成位点（造蜡细胞oenocytes）向表皮的转运过程。本近交系面板将为该物种更广泛的种群基因组学和数量遗传学研究提供助力，并可作为现有黑腹果蝇（Drosophila melanogaster）品系面板的重要补充，用于验证果蝇属内遗传架构的保守性。