Barrière Antoine, Yang Shiaw-Pyng, Pekarek Elizabeth, Thomas Cristel G, Haag Eric S, Ruvinsky Ilya
Department of Ecology and Evolution and Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois 60637, USA.
Genome Res. 2009 Mar;19(3):470-80. doi: 10.1101/gr.081851.108. Epub 2009 Feb 9.
The majority of nematodes are gonochoristic (dioecious) with distinct male and female sexes, but the best-studied species, Caenorhabditis elegans, is a self-fertile hermaphrodite. The sequencing of the genomes of C. elegans and a second hermaphrodite, C. briggsae, was facilitated in part by the low amount of natural heterozygosity, which typifies selfing species. Ongoing genome projects for gonochoristic Caenorhabditis species seek to approximate this condition by intense inbreeding prior to sequencing. Here we show that despite this inbreeding, the heterozygous fraction of the whole genome shotgun assemblies of three gonochoristic Caenorhabditis species, C. brenneri, C. remanei, and C. japonica, is considerable. We first demonstrate experimentally that independently assembled sequence variants in C. remanei and C. brenneri are allelic. We then present gene-based approaches for recognizing heterozygous regions of WGS assemblies. We also develop a simple method for quantifying heterozygosity that can be applied to assemblies lacking gene annotations. Consistently we find that approximately 10% and 30% of the C. remanei and C. brenneri genomes, respectively, are represented by two alleles in the assemblies. Heterozygosity is restricted to autosomes and its retention is accompanied by substantial inbreeding depression, suggesting that it is caused by multiple recessive deleterious alleles and not merely by chance. Both the overall amount and chromosomal distribution of heterozygous DNA is highly variable between assemblies of close relatives produced by identical methodologies, and allele frequencies have continued to change after strains were sequenced. Our results highlight the impact of mating systems on genome sequencing projects.
大多数线虫是雌雄异体（两性异体），具有明显的雄性和雌性性别，但研究得最透彻的物种秀丽隐杆线虫是一种能自我受精的雌雄同体。秀丽隐杆线虫和另一种雌雄同体的线虫——布氏隐杆线虫的基因组测序，部分得益于自然杂合度较低，这是自交物种的典型特征。正在进行的关于雌雄异体的秀丽隐杆线虫物种的基因组计划试图通过在测序前进行强烈的近亲繁殖来接近这种状况。在这里我们表明，尽管进行了这种近亲繁殖，但三种雌雄异体的秀丽隐杆线虫物种——布氏线虫、雷氏线虫和日本线虫的全基因组鸟枪法组装中的杂合部分仍然相当可观。我们首先通过实验证明，雷氏线虫和布氏线虫中独立组装的序列变体是等位基因。然后我们提出了基于基因的方法来识别全基因组测序组装中的杂合区域。我们还开发了一种简单的方法来量化杂合度，该方法可应用于缺乏基因注释的组装。我们一致发现，在组装中，雷氏线虫和布氏线虫基因组分别约有10%和30%由两个等位基因代表。杂合性仅限于常染色体，其保留伴随着严重的近亲繁殖衰退，这表明它是由多个隐性有害等位基因引起的，而不仅仅是偶然因素。通过相同方法产生的近亲组装之间，杂合DNA的总量和染色体分布都高度可变，并且在菌株测序后等位基因频率仍在继续变化。我们的结果突出了交配系统对基因组测序项目的影响。
