Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes
Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes
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DOI：
10.1101/gr.081851.108
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发表时间：
2009-03-01
期刊：
影响因子：
7
通讯作者：
Ruvinsky, Ilya
中科院分区：
文献类型：
--
作者：
Barriere, Antoine;Yang, Shiaw-Pyng;Ruvinsky, Ilya
大多数线虫都是雌雄异株的（雌雄异株），具有不同的雄性和雌性，但研究最多的物种秀丽隐杆线虫是一种自我受精的雌雄同体。对C. elegans和第二个雌雄同体的C. briggsae，促进了部分的自然杂合性，这是典型的自交物种的低量。正在进行的无性生殖小杆线虫物种的基因组计划试图在测序前通过强烈的近亲繁殖来接近这种情况。在这里，我们表明，尽管这种近亲繁殖，杂合子部分的全基因组鸟枪组装的三个gonochoristic小杆线虫物种，C。brenneri，C. remanei和C. japonica，是一个很大的。我们首先通过实验证明了C. remanei和C. brenneri是等位基因。然后，我们提出了基于基因的方法来识别WGS组件的杂合区域。我们还开发了一种简单的方法，用于定量杂合性，可应用于缺乏基因注释的组件。一致地，我们发现类似于10%和30%的C。remanei和C. Brenneri基因组分别由组装体中的两个等位基因表示。杂合性仅限于常染色体，它的保留伴随着大量的近交衰退，这表明它是由多个隐性有害等位基因引起的，而不仅仅是偶然的。杂合DNA的总量和染色体分布在通过相同方法产生的近亲组装体之间是高度可变的，并且等位基因频率在菌株测序后继续变化。我们的研究结果突出了交配系统对基因组测序项目的影响。
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 similar to 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.