East African lake cichlids are one of the most impressive examples of an adaptive radiation. Independently in Lake Victoria, Tanganyika, and Malawi, several hundreds of species arose within the last 10 million to 100,000 years. Whereas most analyses in cichlids focused on nucleotide substitutions across species to investigate the genetic bases of this explosive radiation, to date, no study has investigated the contribution of structural variants (SVs) in the evolution of adaptive traits across the three Great Lakes of East Africa. Here, we annotate and characterize the repertoires and evolutionary potential of different SV classes (deletion, duplication, inversion, insertions and translocations) in four cichlid species: Haplochromis burtoni, Metriaclima zebra, Neolamprologus brichardi and Pundamilia nyererei. We investigate the patterns of gain and loss evolution for each SV type, enabling the identification of lineage specific events. Both deletions and inversions show a significant overlap with SINE elements, while inversions additionally show a limited, but significant association with DNA transposons. Inverted regions are enriched for genes regulating behaviour, or involved in skeletal and visual system development. We also find that duplicated regions show enrichment for genes associated with “antigen processing and presentation” and other immune related categories. Our pipeline and results were further tested by PCR validation of selected deletions and inversions, which confirmed respectively 7 out of 10 and 6 out of 9 events. Altogether, we provide the first comprehensive overview of rearrangement evolution in East African cichlids, and some important insights into their likely contribution to adaptation.

中文翻译：

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对四种非洲慈鲷的结构变异分析强调了与发育和免疫相关基因的关联。

东非湖慈鲷是适应性辐射最令人印象深刻的例子之一。独立地在维多利亚湖、坦噶尼喀和马拉维，在过去的 1000 万到 100,000 年间出现了数百种物种。尽管对慈鲷的大多数分析都集中在物种间的核苷酸替代上，以研究这种爆炸性辐射的遗传基础，但迄今为止，还没有研究调查结构变异 (SV) 在东非三大湖的适应性特征进化中的贡献. 在这里，我们对四种慈鲷物种（Haplochromis burtoni、Metriaclima zebra、Neolamprologus brichardi 和 Pundamilia nyererei）中不同 SV 类别（缺失、复制、倒置、插入和易位）的库和进化潜力进行了注释和描述。我们研究了每种 SV 类型的收益和损失演变模式，从而能够识别谱系特定事件。缺失和倒位都显示出与 SINE 元件的显着重叠，而倒位还显示出与 DNA 转座子有限但显着的关联。倒置区域富含调节行为的基因，或参与骨骼和视觉系统发育。我们还发现，重复区域显示出与“抗原加工和呈递”和其他免疫相关类别相关的基因富集。我们的流程和结果通过对选定删除和倒位的 PCR 验证进行了进一步测试，分别确认了 10 个事件中的 7 个和 9 个事件中的 6 个。总之，我们首次全面概述了东非慈鲷的重排进化，