Short intron sequence alignment of the 3R chromosome arm

We analyzed whole-genome data (Langley C. et al., accepted 2012) of D. melanogaster (Release 1.0) from a sample of six inbred Malawi isofemale lines from the 50 genomes Drosophila Population Genomics Project (DPGP) (http://www.dpgp.org/ ). We downloaded (http://genome.ucsc.edu/ ) aligned single sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Release 5) (Begun et al., 2007; Clark et al., 2007) and combined them with the five D. melanogaster sequences into a multiple alignment for all autosomes. We used position 8 to 30 in short introns (less than 66 bp) as these are thought to be the least constrained sites in the Drosophila genome (Halligan and Keightley, 2006; Parsch et al., 2010). We used the D. melanogaster Flybase annotation (release 5.31) to identify these sites. Introns, which overlapped with coding regions were excluded from the analyses. Python scripts were written to concatenate all 23 considered positions per short intron into one alignment file for each chromosome arm.我们分析了来自果蝇群体基因组计划（Drosophila Population Genomics Project, DPGP）50基因组项目的6个近交马拉维单雌品系的黑腹果蝇（Drosophila melanogaster, D. melanogaster）全基因组数据（版本1.0，Langley C.等，2012年已接收），数据来源网址为http://www.dpgp.org/。我们从http://genome.ucsc.edu/ 下载了拟暗果蝇（Drosophila simulans）、塞舌尔果蝇（Drosophila sechellia）、直立果蝇（Drosophila erecta）及雅库巴果蝇（Drosophila yakuba）的经比对单序列（版本5，Begun等，2007；Clark等，2007），并将其与5条黑腹果蝇序列整合，构建了所有常染色体的多序列比对集。我们选取了长度小于66 bp的短内含子中的第8至30位碱基，因为此前研究认为这类位点是果蝇基因组中选择约束最弱的区域（Halligan和Keightley，2006；Parsch等，2010）。我们利用黑腹果蝇果蝇数据库（Flybase）注释版本5.31定位上述位点，并剔除了与编码区重叠的内含子以用于后续分析。我们编写了Python脚本，将每个短内含子中纳入分析的全部23个位点拼接为单个比对文件，对应每条染色体臂。