Plant self-incompatibility (SI) is a genetic system that prevents selfing and enforces outcrossing. Because of strong balancing selection, the genes encoding SI are predicted to maintain extraordinarily high levels of polymorphism, both in terms of the number of functionally distinct S-alleles that segregate in SI species and in terms of their nucleotide sequence divergence. However, because of these two combined features, documenting polymorphism of these genes also presents important methodological challenges that have so far largely prevented the comprehensive analysis of complete allelic series in natural populations, and also precluded the obtention of complete genic sequences for many S-alleles. Here, we develop a powerful methodological approach based on a computationally optimized comparison of short Illumina sequencing reads from genomic DNA to a database of known nucleotide sequences of the extracellular domain of SRK (eSRK). By examining mapping patterns along the reference sequences, we obtain highly reliable predictions of S-genotypes from individuals collected from natural populations of Arabidopsis halleri. Furthermore, using a de novo assembly approach of the filtered short reads, we obtain full-length sequences of eSRK even when the initial sequence in the database was only partial, and we discover putative new SRK alleles that were not initially present in the database. When including those new alleles in the reference database, we were able to resolve the complete diploid SI genotypes of all individuals. Beyond the specific case of Brassicaceae S-alleles, our approach can be readily applied to other polymorphic loci, given reference allelic sequences are available.

中文翻译：

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从短读测序数据中发现在十字花科自交不亲和基因座的等位基因变体的基因分型和从头发现。

植物自交不亲和（SI）是一种防止自交并强制异交的遗传系统。由于有很强的平衡选择，无论是在SI物种中分离的功能不同的S等位基因的数目，还是在核苷酸序列的差异方面，编码SI的基因都有望保持异常高的多态性。然而，由于这两个特征的结合，记录这些基因的多态性也带来了重要的方法学挑战，迄今为止，这些挑战很大程度上阻止了对自然种群中完整等位基因系列的全面分析，并且还排除了获得许多S-等位基因完整基因序列的可能性。 。这里，SRK（eSRK）。通过检查沿参考序列的作图模式，我们从拟南芥自然种群中收集的个体获得了S基因型的高度可靠的预测。此外，使用过滤后的短读的从头组装方法，即使数据库中的初始序列只是部分序列，我们也可以获得eSRK的全长序列，并且发现了推定的新SRK数据库中最初不存在的等位基因。当将这些新等位基因包括在参考数据库中时，我们能够解析所有个体的完整二倍体SI基因型。除了十字花科S-等位基因的具体情况外，只要有参考等位基因序列可用，我们的方法也可以容易地应用于其他多态性基因座。