Identified intermediate variants files for calling de-novo mutations in Colorado potato beetle.

Direct germline mutation rate estimates are scarce in insects, with none available for beetles (Coleoptera), the most speciose order including major pests. We sequenced genomes from 16 trios of Colorado potato beetle (<i>Leptinotarsa decemlineata</i>, CPB)—a pest evolving resistance to many insecticides. We sequenced the genomes of 16 trios derived from two familes and detected 69 <i>de novo</i> SNP mutations that affects a single site in a single offspring. This yields an estimated germline mutation rate of 5.2 × 10^-9 (95%CI: 4.0 × 10^-9, 6.6 × 10^-9) per site per generation, exceeding 1.6-fold of median mutation rates in other insects. The spectrum shows a transition ratio (Ts/Tv = 1.56) that is consistent with other insects.The files in the folders:Unique variants identified from GATK pipeline: Chr_all.flt.pass.AC1.vcf.gzUnique variants identified from MPILEIUP pipeline: joint.chr1-18.flt.AC1.vcf.gzConcensus variants: CPB-MA.concensus.vcfThe concensus variants were then used for identifying de novo mutations based on trio pedigree information.Raw data from Sanger-sequencing: SangerSequences.zip

昆虫的生殖系突变率直接估算数据本就稀缺，而作为物种丰富度最高的昆虫目类——鞘翅目（Coleoptera，甲虫），其中包含诸多重大农业害虫，目前仍无相关突变率估算结果。我们对源自两个家系的16个科罗拉多马铃薯甲虫（Leptinotarsa decemlineata，CPB）三联体样本进行了基因组测序——该物种是一种可对多种杀虫剂产生抗性的重要农业害虫。测序完成后，我们在单个子代的单个位点上检测到69个新生（de novo）单核苷酸多态性（SNP）突变。据此估算得到的生殖系突变率为每位点每世代5.2 × 10^-9（95%置信区间：4.0 × 10^-9，6.6 × 10^-9），是其他昆虫中位突变率的1.6倍以上。突变频谱的转换/颠换比值（Ts/Tv = 1.56）与其他昆虫的相关结果保持一致。
本次研究涉及的文件夹内文件如下：
1. 经GATK流程鉴定的独特变异文件：Chr_all.flt.pass.AC1.vcf.gz
2. 经MPILEUP流程鉴定的独特变异文件：joint.chr1-18.flt.AC1.vcf.gz
3. 共识变异文件：CPB-MA.concensus.vcf
随后研究人员基于三联体家系信息，利用上述共识变异位点鉴定新生突变。
桑格测序原始数据文件：SangerSequences.zip