Whole-genome sequencing of non-model organisms is now widely accessible and has allowed a range of questions in the field of molecular ecology to be investigated with greater power. However, some genomic regions that are of high biological interest remain problematic for assembly and data-handling. Three such regions are the major histocompatibility complex (MHC), sex-determining regions (SDRs) and the plant self-incompatibility locus (S-locus). Using these as examples, we illustrate the challenges of both assembling and resequencing these highly polymorphic regions and how bioinformatic and technological developments are enabling new approaches to their study. Mapping short-read sequences against multiple alternative references improves genotyping comprehensiveness at the S-locus thereby contributing to more accurate assessments of allelic frequencies. Long-read sequencing, producing reads of several tens to hundreds of kilobase pairs in length, facilitates the assembly of such regions as single sequences can span the multiple duplicated gene copies of the MHC region, and sequence through repetitive stretches and translocations in SDRs and S-locus haplotypes. These advances are adding value to short-read genome resequencing approaches by allowing, for example, more accurate haplotype phasing across longer regions. Finally, we assessed further technical improvements, such as nanopore adaptive sequencing and bioinformatic tools using pangenomes, which have the potential to further expand our knowledge of a number of genomic regions that remain challenging to study with classical resequencing approaches.

中文翻译：

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全基因组测序和特别感兴趣的基因组区域：主要组织相容性复合体、性别决定和植物自交不亲和性的教训

非模式生物的全基因组测序现在可以广泛使用，并且可以更有效地研究分子生态学领域的一系列问题。然而，一些具有高度生物学意义的基因组区域对于组装和数据处理仍然存在问题。三个这样的区域是主要组织相容性复合体 (MHC)、性别决定区 (SDR) 和植物自交不亲和基因座 (S-基因座)。以这些为例，我们说明了组装和重新测序这些高度多态性区域的挑战，以及生物信息学和技术的发展如何为他们的研究提供新的方法。将短读序列与多个替代参考进行比对提高了 S 位点的基因分型综合性，从而有助于更准确地评估等位基因频率。长读长测序，产生几十到几百千碱基对长度的读长，有利于这些区域的组装，因为单个序列可以跨越 MHC 区域的多个重复基因拷贝，并通过 SDR 和 SDR 中的重复延伸和易位进行测序-基因座单倍型。这些进步为短读长基因组重测序方法增加了价值，例如，允许跨更长区域的更准确的单倍型定相。最后，我们评估了进一步的技术改进，例如使用泛基因组的纳米孔自适应测序和生物信息学工具，