The power of chromosome-scale, haplotype-resolved genomes
The power of chromosome-scale, haplotype-resolved genomes
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染色体规模、单倍型解析基因组的力量
DOI：
10.1016/j.molp.2022.02.010
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发表时间：
2022
期刊：
影响因子：
27.5
通讯作者：
Edger, Patrick P.
中科院分区：
文献类型：
--
作者：
Edger, Patrick P.
染色体规模和单倍型分辨参考基因组的组装现在更容易实现，这主要是由于组装算法和长距离测序技术的各种改进（见Michael和VanBuren最近的评论，2020）。由于这些技术进步，已经从使用高度近交的种质（在某些情况下为双单倍体）转变为组装重要参考基因型的基因组。例如，最近为重要的栽培花园草莓（Fragaria x ananassa）栽培品种皇家罗伊斯（Royce）组装了单倍型解析基因组，其不仅是高度杂合的，而且是二倍体（83）（Hardigan et al.，2021年）。类似地，已经为其他重要作物组装了单倍型定相的基因组，包括木薯（Manihot esculenta）（Hu et al. 2021）和马铃薯（Solanum tuberosum）（Hoopes等，2022年）。这导致了新的基因组资源的开发，其可以直接用于指导分子育种工作，而不用担心作物或物种内存在的基因存在-不存在变异（Golicz et al. 2016; Bayer等人，2021年）。具有重要栽培品种和/或基因型的参考基因组与来自高度近交系的参考基因组相比的额外益处在于，潜在地从单倍型中存在的遗传变体的分析获得的有价值的见解不会丢失，从而允许额外的见解。（2022）发表了荔枝（Litchi chinensis Sonn.）基因组，并提供了一个最好的例子研究如何分析和比较单倍型可以导致令人兴奋的新发现。对这两种单倍型的分析不仅为这种重要热带水果的驯化历史提供了新的见解，而且还为编码重要性状和杂种优势的潜在遗传学提供了新的见解（Hu等人，2022年）。这些发现不会从作为组装高度近交系的基因组的结果的单个单倍型的分析或从分解单倍型以形成单个主参考而揭示。
The assembly of chromosome-scale and haplotype-resolved reference genomes is now more easily attainable, largely due to various improvements in both assembly algorithms and longread sequencing technologies (see recent review by Michael and VanBuren, 2020). Due to these technological advancements, there has been a shift away from using highly inbred accessions, in some instances double haploids, to instead assembling the genomes of important reference genotypes. For example, a haplotype-resolved genome was recently assembled for an important cultivated garden strawberry (Fragaria x ananassa) cultivar Royal Royce, which is not only highly heterozygous but also octoploid (83)(Hardigan et al., 2021). Similarly, haplotype-phased genomes have been assembled for other important crops, including cassava (Manihot esculenta)(Hu et al., 2021) and potato (Solanum tuberosum)(Hoopes et al., 2022). This has resulted in the development of new genomic resources that can be directly used in guiding molecular breeding efforts, without worrying about the gene presence-absence variation that exists within a crop or species (Golicz et al., 2016; Bayer et al., 2021). An additional benefit of having a reference genome of an important cultivar and/or genotype, versus from a highly inbred line, is that valuable insights that are potentially gained from the analysis of genetic variants present among haplotypes are not lost, allowing for additional insights.Recently, Hu et al.(2022) published the lychee (Litchi chinensis Sonn.) genome and provided one of the best example studies to date of how analyzing and comparing haplotypes can result in exciting new discoveries. The analysis of both haplotypes provided novel insights not only into the domestication history of this important tropical fruit but also into the underlying genetics encoding important traits and heterosis (Hu et al., 2022). These findings would not have been revealed from the analysis of a single haplotype as a result of either assembling a genome of a highly inbred line or from collapsing haplotypes to form a single master reference.