Topological structures and syntenic conservation in sea anemone genomes.
Topological structures and syntenic conservation in sea anemone genomes.
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海葵基因组拓扑结构与同线保守性。
DOI：
10.1038/s41467-023-44080-7
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发表时间：
2023-12-13
影响因子：
16.6
通讯作者：
Technau, Ulrich
中科院分区：
文献类型：
--
作者：
Zimmermann, Bob;Montenegro, Juan D.;Robb, Sofia M. C.;Fropf, Whitney J.;Weilguny, Lukas;He, Shuonan;Chen, Shiyuan;Lovegrove-Walsh, Jessica;Hill, Eric M.;Chen, Cheng-Yi;Ragkousi, Katerina;Praher, Daniela;Fredman, David;Schultz, Darrin;Moran, Yehu;Simakov, Oleg;Genikhovich, Grigory;Gibson, Matthew C.;Technau, Ulrich
目前，关于早期分支动物的基因簇、基因组结构和核型的进化信息很少。缓慢进化的珊瑚虫刺胞动物可以特别提供有关这些基因组特征进化的信息。在这里，我们报告染色体水平的基因组组装的两个相关的珊瑚虫，海葵Nematostella vectensis和Scolanthus callimorphus。我们发现了一个强大的15条染色体，这两个物种之间有明确的一一对应关系。这两个基因组显示染色体保守，使我们能够重建祖先刺胞动物和后生动物的染色体块，分别由至少19和16个祖先连锁群。我们发现，在对比Bilateria，Hox和NK集群的调查刺胞动物在很大程度上解体，尽管存在交错的Hox/Gbx的表达在Nematostella。这种微共线性保守的损失可能是由顺式调控序列和它们的同源转录起始位点之间的较短距离促进的。我们没有发现拓扑相关域的明确证据，这表明与脊椎动物相比，在远程基因调控方面存在根本差异。这些数据表明，大套的祖先后生动物基因已被保留在祖先的连锁群的一些现存的血统，然而，高阶基因调控与相关的三维结构可能只进化后的刺胞动物bilaterian分裂。缓慢进化的刺胞动物是研究基因组结构的有用模型。本研究表明，海葵具有高度的染色体大同线性，但微同线性的保守性较差。这与小的基因组大小和顺式调控元件与基因的短距离相关。
There is currently little information about the evolution of gene clusters, genome architectures and karyotypes in early branching animals. Slowly evolving anthozoan cnidarians can be particularly informative about the evolution of these genome features. Here we report chromosome-level genome assemblies of two related anthozoans, the sea anemones Nematostella vectensis and Scolanthus callimorphus. We find a robust set of 15 chromosomes with a clear one-to-one correspondence between the two species. Both genomes show chromosomal conservation, allowing us to reconstruct ancestral cnidarian and metazoan chromosomal blocks, consisting of at least 19 and 16 ancestral linkage groups, respectively. We show that, in contrast to Bilateria, the Hox and NK clusters of investigated cnidarians are largely disintegrated, despite the presence of staggered hox/gbx expression in Nematostella. This loss of microsynteny conservation may be facilitated by shorter distances between cis-regulatory sequences and their cognate transcriptional start sites. We find no clear evidence for topologically associated domains, suggesting fundamental differences in long-range gene regulation compared to vertebrates. These data suggest that large sets of ancestral metazoan genes have been retained in ancestral linkage groups of some extant lineages; yet, higher order gene regulation with associated 3D architecture may have evolved only after the cnidarian-bilaterian split. Slowly evolving cnidarians are useful models to study genome architecture. This study shows that sea anemones have a high degree of chromosomal macrosynteny, but poor microsynteny conservation. This is correlated with a small genome size and short distances of cis-regulatory elements to genes.
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DOI：
10.1242/dev.108480
发表时间：
2014-10
期刊：
Development (Cambridge, England)
影响因子：
--
作者：
Anderson E;Devenney PS;Hill RE;Lettice LA
通讯作者：
Lettice LA
Hydra基因组的染色体尺度表观遗传图揭示了细胞态的保守调节剂。
影响因子：
7
作者：
Cazet, Jack F.;Siebert, Stefan;Little, Hannah Morris;Bertemes, Philip;Primack, Abby S.;Ladurner, Peter;Achrainer, Matthias;Fredriksen, Mark T.;Moreland, R. Travis;Singh, Sumeeta;Zhang, Suiyuan;Wolfsberg, Tyra G.;Schnitzler, Christine E.;Baxevanis, Andreas D.;Simakov, Oleg;Hobmayer, Bert;Juliano, Celina E.
通讯作者：
Juliano, Celina E.
影响因子：
4.9
作者：
Bao W;Kojima KK;Kohany O
通讯作者：
Kohany O
影响因子：
14.9
作者：
Adams, Matthew;McBroome, Jakob;Corbett-Detig, Russell B.
通讯作者：
Corbett-Detig, Russell B.
影响因子：
3.7
作者：
Cartwright P;Halgedahl SL;Hendricks JR;Jarrard RD;Marques AC;Collins AG;Lieberman BS
通讯作者：
Lieberman BS