Background Bananas and plantains (Musa spp.) are among the most important crops worldwide. The cultivated varieties are vegetatively propagated, so their genetic diversity is essentially fixed over time. M. acuminata, M. balbisiana and M. schizocarpa provided the named A, B and S subgenomes that predominantly constitute these varieties. We aimed to characterise intergenetic recombination and chromosomal imbalances between these A/B/S subgenomes, which often result in CNVs leading to changes in gene dosage and phenotype, in a diverse panel of bananas and plantains. This will allow us to characterise varietal lineages better and identify sources of genetic variation. Methods We delimited population structure and clonal lineages in a diversity panel of 188 banana and plantain accessions from the most common cultivars using admixture, principal component, and phylogenetic analyses. We used new scalable alignment-based methods, Relative Averaged Alignment (RAA) and Relative Coverage, to infer subgenome composition (AA, AAB, etc.) and interspecific recombination. Results In our panel, we identified ten varietal lineages composed of somatic clones, plus three groups of tetraploid accessions. We identified chromosomal exchanges resulting in gains/losses in chromosomal segments (CNVs), particularly in AAB and ABB varieties. Conclusions We demonstrated alignment-based RAA and Relative Coverage can identify subgenome composition and introgressions with similar results to more complex approaches based on SNP databases. These ab initio species-agnostic methods can be used without sequencing a panel of wild ancestors to find private SNPs, or in recently diverged pools where private SNPs are uncommon. The extensive A/B/S exchanges and the variation in the length of some introgressions between lineages further support multiple foundational events of hybridisation and residual backcrossing. Imbalances between A/B/S may have resulted in CNVs and gene dosage variation. Since most edible banana genomes are fixed on time, these CNVs are stable genetic variation likely associated with phenotypic variation for future genetic studies.

中文翻译：

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香蕉品种谱系中亚基因组重组和染色体失衡的特征

背景 香蕉和大蕉（Musa spp.）是世界上最重要的农作物之一。栽培品种是无性繁殖的，因此它们的遗传多样性随着时间的推移基本上是固定的。 M. acuminata、M. balbisiana 和 M. schizocarpa 提供了主要构成这些变种的命名为 A、B 和 S 的亚基因组。我们的目的是表征这些 A/B/S 亚基因组之间的基因间重组和染色体不平衡，这些亚基因组通常会导致 CNV，从而在不同的香蕉和大蕉组中导致基因剂量和表型的变化。这将使我们能够更好地描述品种谱系并确定遗传变异的来源。方法 我们使用混合物、主成分和系统发育分析，在由来自最常见品种的 188 个香蕉和大蕉品种组成的多样性小组中界定了种群结构和克隆谱系。我们使用新的基于可扩展比对的方法，即相对平均比对 (RAA) 和相对覆盖率，​​来推断亚基因组组成（AA、AAB 等）和种间重组。结果在我们的小组中，我们鉴定了十个由体细胞克隆组成的品种谱系，以及三组四倍体种质。我们发现染色体交换会导致染色体片段 (CNV) 的增加/丢失，特别是在 AAB 和 ABB 品种中。结论 我们证明基于比对的 RAA 和相对覆盖率可以识别亚基因组组成和基因渗入，其结果与基于 SNP 数据库的更复杂方法相似。这些从头开始与物种无关的方法可以在不对一组野生祖先进行测序的情况下使用来寻找私有SNP，或者在最近分歧的私有SNP不常见的库中使用。广泛的A/B/S交换和谱系之间一些基因渗入的长度变化进一步支持杂交和剩余回交的多个基础事件。 A/B/S 之间的不平衡可能导致 CNV 和基因剂量变化。由于大多数可食用香蕉基因组在时间上是固定的，因此这些 CNV 是稳定的遗传变异，可能与未来遗传研究的表型变异相关。