Evolution of genomic structural variation and genomic architecture in the adaptive radiations of African cichlid fishes.
Evolution of genomic structural variation and genomic architecture in the adaptive radiations of African cichlid fishes.
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DOI：
10.3389/fgene.2014.00163
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发表时间：
2014
影响因子：
3.7
通讯作者：
Meyer A
中科院分区：
文献类型：
--
作者：
Fan S;Meyer A
非洲慈鲷是研究适应辐射中物种形成爆发率和多样性起源的理想系统。在过去的几百万年里，东非五大湖进化出了2000多种物种，这是脊椎动物中最大的适应性辐射。这些年轻的物种在颜色、形态和行为上表现出惊人的多样性。然而，人们对这种惊人多样性的基因组基础知之甚少。最近，研究人员对5种非洲鱼科鱼类的基因组进行了测序，其中包括尼罗河罗非鱼（Oreochromis niloticus）的基因组，这是一种相对中等多样化的基础谱系，以及适应辐射的4种代表性特有物种Neolamprologus brichardi， burtoni Astatotilapia， Metriaclima斑马和Pundamila nyererei的基因组。使用罗非鱼基因组作为参考基因组，我们生成了高分辨率的基因组变异图谱，包括单核苷酸多态性（SNPs）、短插入和缺失（indels）、反转和缺失。总共有大约18.8、17.7、17.0和1700万个snp， 230、220、140和190万个索引，262、306、162和154个反转，以及3509、2705、2710和2634个缺失被推断出分别在N. brichardi、A. burtoni、P. nyererei和M. zebra中进化。许多这些变异影响了基因组中注释的基因区域。在非洲慈鲷的适应辐射过程中发现了不同的遗传变异模式。在单核苷酸多态性方面，进化率最高的是N. brichardi、A. burtoni、P. nyererei和M. zebra的共同祖先。然而，对于反转和缺失的进化，我们发现终端分类群的比率明显高于祖先谱系的比率。高分辨率的地图为了解非洲慈鲷的适应性辐射的基因组基础提供了一个理想的机会。
African cichlid fishes are an ideal system for studying explosive rates of speciation and the origin of diversity in adaptive radiation. Within the last few million years, more than 2000 species have evolved in the Great Lakes of East Africa, the largest adaptive radiation in vertebrates. These young species show spectacular diversity in their coloration, morphology and behavior. However, little is known about the genomic basis of this astonishing diversity. Recently, five African cichlid genomes were sequenced, including that of the Nile Tilapia (Oreochromis niloticus), a basal and only relatively moderately diversified lineage, and the genomes of four representative endemic species of the adaptive radiations, Neolamprologus brichardi, Astatotilapia burtoni, Metriaclima zebra, and Pundamila nyererei. Using the Tilapia genome as a reference genome, we generated a high-resolution genomic variation map, consisting of single nucleotide polymorphisms (SNPs), short insertions and deletions (indels), inversions and deletions. In total, around 18.8, 17.7, 17.0, and 17.0 million SNPs, 2.3, 2.2, 1.4, and 1.9 million indels, 262, 306, 162, and 154 inversions, and 3509, 2705, 2710, and 2634 deletions were inferred to have evolved in N. brichardi, A. burtoni, P. nyererei, and M. zebra, respectively. Many of these variations affected the annotated gene regions in the genome. Different patterns of genetic variation were detected during the adaptive radiation of African cichlid fishes. For SNPs, the highest rate of evolution was detected in the common ancestor of N. brichardi, A. burtoni, P. nyererei, and M. zebra. However, for the evolution of inversions and deletions, we found that the rates at the terminal taxa are substantially higher than the rates at the ancestral lineages. The high-resolution map provides an ideal opportunity to understand the genomic bases of the adaptive radiation of African cichlid fishes.