Temperature-dependent effects of house fly proto-Y chromosomes on gene expression

Code, commands, and data to perform analyses of house fly RNA-seq data. House fly has a stable polygenic sex determination system. The male determining factor (Mdmd) is commonly found on the Y chromosome (Y^M) or the third chromosome (III^M). These proto-Y chromosomes are clinally distributed, with Y^M found most commonly in northern latitudes and III^M most commonly found at southern latitudes, hinting at possible genotype-by-temperature interactions that maintain the polymorphism. If this distribution is maintained by temperature-dependent selection pressures, we expect the fitness of III^M and Y^M flies to vary across developmental temperatures. These temperature-dependent effects could be driven by differential gene expression in III^M and Y^M males at different temperatures. Here, we performed RNA-seq experiments to study how genotype-by-temperature interactions affect gene expression in male houseflies carrying different proto-Y chromosomes. We raised a Y^M strain known as IsoCS and a III^M strain known as CSrab at 18°C and 29°C for two generations. We dissected 5 heads and 15-20 pairs of testes for each of three replicates of each genotype-by-temperature combination. We carried out RNA-seq on these tissues. Data are available from NCBI Gene Expression Omnibus accession GSE136188.

本数据集包含用于家蝇（house fly）RNA测序（RNA-seq）数据分析的代码、命令与配套数据集。家蝇拥有稳定的多基因性别决定系统，其雄性决定因子（male determining factor, Mdmd）通常定位于Y染色体（Y^M）或三号染色体（III^M）上。此类原Y染色体呈纬度梯度分布：Y^M在北半球高纬度地区最为常见，III^M则多见于南半球低纬度地区，提示存在维持该遗传多态性的基因型×温度互作（genotype-by-temperature interactions）效应。若该分布由温度依赖性选择压力所维持，则III^M与Y^M品系家蝇的适合度（fitness）会随发育温度的变化产生差异。此类温度依赖性效应可能源于不同温度下III^M与Y^M雄性个体的差异基因表达（differential gene expression）。本研究开展RNA测序实验，以探究基因型×温度互作如何影响携带不同原Y染色体的雄性家蝇的基因表达模式。我们将命名为IsoCS的Y^M品系与命名为CSrab的III^M品系分别在18℃与29℃下连续饲养两代。针对每种基因型-温度组合的三个生物学重复样本，我们分别解剖了5个头部组织以及15~20对精巢，并对上述组织进行RNA测序。本数据集的相关数据可从NCBI基因表达汇编（Gene Expression Omnibus, GEO）登录号GSE136188获取。