Understanding the evolution of chromatin conformation among species is fundamental to elucidate the architecture and plasticity of genomes. Nonrandom interactions of linearly distant loci regulate gene function in species-specific patterns, affecting genome function, evolution, and, ultimately, speciation. Yet, data from nonmodel organisms are scarce. To capture the macroevolutionary diversity of vertebrate chromatin conformation, here we generate de novo genome assemblies for two cryptodiran (hidden-neck) turtles via Illumina sequencing, chromosome conformation capture, and RNA-seq: Apalone spinifera (ZZ/ZW, 2n = 66) and Staurotypus triporcatus (XX/XY, 2n = 54). We detected differences in the three-dimensional (3D) chromatin structure in turtles compared to other amniotes beyond the fusion/fission events detected in the linear genomes. Namely, whole-genome comparisons revealed distinct trends of chromosome rearrangements in turtles: (1) a low rate of genome reshuffling in Apalone (Trionychidae) whose karyotype is highly conserved when compared to chicken (likely ancestral for turtles), and (2) a moderate rate of fusions/fissions in Staurotypus (Kinosternidae) and Trachemys scripta (Emydidae). Furthermore, we identified a chromosome folding pattern that enables “centromere–telomere interactions” previously undetected in turtles. The combined turtle pattern of “centromere–telomere interactions” (discovered here) plus “centromere clustering” (previously reported in sauropsids) is novel for amniotes and it counters previous hypotheses about amniote 3D chromatin structure. We hypothesize that the divergent pattern found in turtles originated from an amniote ancestral state defined by a nuclear configuration with extensive associations among microchromosomes that were preserved upon the reshuffling of the linear genome.

中文翻译：

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具有 ZZ/ZW 和 XX/XY 性染色体的两只隐翅龟的从头基因组组装提供了对基因组重新洗牌模式的见解，并揭示了羊膜中新的三维基因组折叠


了解物种之间染色质构象的进化对于阐明基因组的结构和可塑性至关重要。线性距离位点的非随机相互作用以物种特异性模式调节基因功能，影响基因组功能、进化，并最终影响物种形成。然而，来自非模式生物的数据很少。为了捕获脊椎动物染色质构象的宏观进化多样性，我们在这里通过 Illumina 测序、染色体构象捕获和 RNA-seq 生成两种隐鳖（隐藏颈）龟的从头基因组组装：Apalone spinifera （ZZ/ZW， 2n = 66） 和 Staurotypus triporcatus （XX/XY， 2n= 54）。我们检测到海龟的三维 （3D） 染色质结构与其他羊膜动物相比的差异，超出了线性基因组中检测到的融合/裂变事件。也就是说，全基因组比较揭示了海龟染色体重排的不同趋势：（1） 与鸡（可能是海龟的祖先）相比，其核型高度保守的鲍鱼 （Trionychidae） 基因组重洗率较低，以及 （2） Staurotypus （Kinosternidae） 和 Trachemys scripta 的融合/裂变率适中（Emydidae）。此外，我们确定了一种染色体折叠模式，该模式使以前在海龟中未检测到的“着丝粒-端粒相互作用”成为可能。“着丝粒-端粒相互作用”（在此处发现）和“着丝粒聚集”（以前在蜥蜴科中报道过）的组合海龟模式对于羊膜动物来说是新颖的，它反驳了以前关于羊膜生物 3D 染色质结构的假设。 我们假设在海龟中发现的发散模式起源于羊膜祖先状态，该状态由核构型定义，在线性基因组重新洗牌时保留的微染色体之间存在广泛的关联。