Whole-genome re-sequencing of the wild accession HK104 (Caenorhabditis briggsae nematode) and two derived Mutation Accumulation Lines. HK104 and two MALs

This study contains whole-genome re-sequencing runs of three samples: HK104, MA211 and MA296.HK104 is a wild accession of the nematode Caenorhabditis briggsae.This accession has been used in different studies, notably to explore natural phenotypic variations and as a progenitor of mutation accumulation lines (Baer CF. et. al, PNAS 2005).Genomic DNA of HK104 was extracted in Dec. 2012 directly from stocks received from Charles Baer. This stock is the true progenitor line of a set of mutation accumulation lines and was kept frozen to avoid accumulation of spontaneous mutations and genetic drift.MA211 and MA296 are two independant mutation accumulation lines derived from HK104. The stocks sequenced in the present study have been passed through single-worm bottlenecks for 250 generations. Genomic DNA were also extracted in Dec. 2012 directly from stocks received from Charles Baer.Short-insert random libraries were prepared for each sample by BGI and sequenced by Illumina on a HiSeq 2000 sequencer with 100-bp paired-end reads. HK104 and MA296 have two sequencing runs of 10X target depth each (for both samples, the same library was used for the first run -in March 2013- and the second run -Nov. 2013). Only one run of target-depth 20X has been performed for sample MA211 in Nov. 2013. Quality scores of these raw reads are encoded old deprecated Phred+64 ASCII socres. This must be converted on Phred+33 encoding to ensure compatibility with most softwares for downstream analysis.

本研究包含3个样本的全基因组重测序数据，分别为HK104、MA211与MA296。HK104是线虫布氏隐杆线虫（Caenorhabditis briggsae）的野生株系，该株系曾被应用于多项研究，尤其用于探究自然表型变异，同时作为突变积累系的亲本株系（Baer CF 等，《美国国家科学院院刊》，2005）。HK104的基因组DNA于2012年12月直接从Charles Baer提供的原种提取，该株系是一组突变积累系的真实亲本株系，为避免自发突变积累与遗传漂变，该原种被冷冻保存。MA211与MA296是两个独立的、源自HK104的突变积累系；本研究中测序的株系经过了250代的单虫瓶颈传代，其基因组DNA同样于2012年12月直接从Charles Baer提供的原种提取。华大基因（BGI）为每个样本制备了短插入片段随机文库，并由Illumina公司采用HiSeq 2000测序仪完成测序，测序模式为100 bp双端读长。HK104与MA296各完成两轮测序，目标测序深度均为10×；两个样本的第一轮测序均于2013年3月完成，且均使用同一文库，第二轮测序于2013年11月完成。样本MA211仅于2013年11月完成一轮目标测序深度为20×的测序。上述原始reads的质量值采用已废弃的旧版Phred+64 ASCII编码格式，为适配多数下游分析软件，需将其转换为Phred+33编码格式。