Department of Biology, University of Maryland, College Park, MD 20742, USA.
Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Norway.
Gigascience. 2019 Apr 1;8(4). doi: 10.1093/gigascience/giz030.
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.
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 (∼2-28 megabase pairs) among species are common, while inter-chromosomal differences are rare (<10 megabase pairs total). Placement of the centromeres within the chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11, and LG20 are associated with reduced recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element insertions compared with O. niloticus, suggesting that several transposable element families have a higher rate of insertion in the haplochromine cichlid lineage.
This study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.
非洲慈鲷鱼类以其快速辐射而闻名，是研究进化过程的模式系统。在这里，我们比较了多个高质量的染色体尺度基因组组装，以阐明慈鲷多样性的遗传机制，并研究基因组结构如何在快速辐射的谱系中进化。
我们使用新的高密度遗传图谱重新锚定了我们最近对尼罗河罗非鱼（Oreochromis niloticus）基因组的组装。我们还使用高覆盖率的太平洋生物科学测序开发了新的马拉维湖慈鲷Metriaclima zebra 的从头基因组组装，并使用 4 种不同的遗传图谱将 contigs 锚定到连锁群（LGs）上。这些新的锚定组装允许首次对非洲慈鲷基因组进行染色体尺度的比较。物种之间的染色体内结构差异（约 2-28 兆碱基对）很大，但染色体间差异很少（总共<10 兆碱基对）。在染色体尺度组装中着丝粒的位置确定了许多种间核型差异的大结构差异。结构差异也与性染色体上独特的重组模式有关。LG9、LG11 和 LG20 上的结构差异与重组减少有关，这表明马拉维湖慈鲷的岩石栖和砂栖类群之间存在倒位。与 O. niloticus 相比，M. zebra 具有更多的近期转座元件插入，这表明几个转座元件家族在haplochromine 慈鲷谱系中具有更高的插入率。
本研究确定了东非慈鲷基因组之间的新型结构变异，并提供了一组新的基因组资源，以支持研究驱动慈鲷适应和物种形成的机制。
