Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes
Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes
复制标题
DOI：
10.1093/gigascience/giz030
复制
发表时间：
2019-04-01
期刊：
影响因子：
9.2
通讯作者：
Kocher, Thomas D.
中科院分区：
文献类型：
--
作者：
Conte, Matthew A.;Joshi, Rajesh;Kocher, Thomas D.
背景：非洲丽鱼以其快速的辐射而闻名，是研究进化过程的模式系统。在这里，我们比较多个，高质量的，染色体规模的基因组组件，以阐明慈鲷多样化的遗传机制，并研究基因组结构如何在快速辐射谱系的演变。结果：我们使用新的高密度遗传图谱重新锚定了我们最近组装的尼罗罗非鱼（Oreochromis niloticus）基因组。我们还开发了一个新的从头基因组组装马拉维湖慈鲷，Metriaclima斑马，使用高覆盖率的太平洋生物科学测序，并锚定重叠群的连锁群（LG）使用4个不同的遗传图谱。这些新的锚定组件允许非洲慈鲷基因组的第一个染色体规模的比较。物种间的染色体内结构差异很大（类似于2-28兆碱基对）是常见的，而染色体间的差异很罕见（
Background: African cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to elucidate the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages. Results: We re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We also developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage Pacific Biosciences sequencing, and anchored contigs to linkage groups (LGs) using 4 different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes. Large intra-chromosomal structural differences (similar to 2-28 megabase pairs) among species are common, while inter-chromosomal differences are rare (