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Evolution of genomic structural variation and genomic architecture in the adaptive radiations of African cichlid fishes.

Fan S, Meyer A - Front Genet (2014)

Bottom Line: Many of these variations affected the annotated gene regions in the genome.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.

View Article: PubMed Central - PubMed

Affiliation: Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz Konstanz, Germany.

ABSTRACT
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.

No MeSH data available.


The distribution of genomic variation in the African cichlid genomes. This figure shows an overview of the SNPs, indels, inversions, and deletions that were identified in this study. The most outer ring showed the chromosomal ideogram in a clockwise orientation. The panels from outside to inside summarized the SNP density, indel density, and the location of the inversions and deletions, which were identified in the N. brichardi (in red), A. burtoni (in green), P. nyererei (in blue), and M. zebra (in orange) genomes. The SNP and indel densities were scanned using a 50 kb sliding window. The histograms in the inversion and deletion panels represent the position of the inversion and deletion and the widths of the histograms show the size of the variations. The results were visualized using Circos (Krzywinski et al., 2009).
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Figure 1: The distribution of genomic variation in the African cichlid genomes. This figure shows an overview of the SNPs, indels, inversions, and deletions that were identified in this study. The most outer ring showed the chromosomal ideogram in a clockwise orientation. The panels from outside to inside summarized the SNP density, indel density, and the location of the inversions and deletions, which were identified in the N. brichardi (in red), A. burtoni (in green), P. nyererei (in blue), and M. zebra (in orange) genomes. The SNP and indel densities were scanned using a 50 kb sliding window. The histograms in the inversion and deletion panels represent the position of the inversion and deletion and the widths of the histograms show the size of the variations. The results were visualized using Circos (Krzywinski et al., 2009).

Mentions: Around 17 million SNPs were detected in the N. brichardi, A. burtoni, P. nyererei, and M. zebra genomes using the Tilapia genome as the reference genome (Table 1, Figure 1). Whereas most of the SNPs are located in the intergenic and intronic regions of the genomes (>70%), many SNPs (around 4%) are located the exonic regions of all four species (Table 1) and the ratio between non-synonymous and synonymous SNP is around 0.7 (Table 1). Of all 20 162 genes on the 22 linkage groups, we found around 77% of the genes with at least one non-synonymous SNP (data not shown). Except for the genes in the N. brichardi genome, the top 1% of the genes with highest proportion of the non-synonymous SNPs (normalized by the exon length) is significant enriched in the pathways related to immune response in the A. burtoni, P. nyererei, and M. zebra genomes.


Evolution of genomic structural variation and genomic architecture in the adaptive radiations of African cichlid fishes.

Fan S, Meyer A - Front Genet (2014)

The distribution of genomic variation in the African cichlid genomes. This figure shows an overview of the SNPs, indels, inversions, and deletions that were identified in this study. The most outer ring showed the chromosomal ideogram in a clockwise orientation. The panels from outside to inside summarized the SNP density, indel density, and the location of the inversions and deletions, which were identified in the N. brichardi (in red), A. burtoni (in green), P. nyererei (in blue), and M. zebra (in orange) genomes. The SNP and indel densities were scanned using a 50 kb sliding window. The histograms in the inversion and deletion panels represent the position of the inversion and deletion and the widths of the histograms show the size of the variations. The results were visualized using Circos (Krzywinski et al., 2009).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4042683&req=5

Figure 1: The distribution of genomic variation in the African cichlid genomes. This figure shows an overview of the SNPs, indels, inversions, and deletions that were identified in this study. The most outer ring showed the chromosomal ideogram in a clockwise orientation. The panels from outside to inside summarized the SNP density, indel density, and the location of the inversions and deletions, which were identified in the N. brichardi (in red), A. burtoni (in green), P. nyererei (in blue), and M. zebra (in orange) genomes. The SNP and indel densities were scanned using a 50 kb sliding window. The histograms in the inversion and deletion panels represent the position of the inversion and deletion and the widths of the histograms show the size of the variations. The results were visualized using Circos (Krzywinski et al., 2009).
Mentions: Around 17 million SNPs were detected in the N. brichardi, A. burtoni, P. nyererei, and M. zebra genomes using the Tilapia genome as the reference genome (Table 1, Figure 1). Whereas most of the SNPs are located in the intergenic and intronic regions of the genomes (>70%), many SNPs (around 4%) are located the exonic regions of all four species (Table 1) and the ratio between non-synonymous and synonymous SNP is around 0.7 (Table 1). Of all 20 162 genes on the 22 linkage groups, we found around 77% of the genes with at least one non-synonymous SNP (data not shown). Except for the genes in the N. brichardi genome, the top 1% of the genes with highest proportion of the non-synonymous SNPs (normalized by the exon length) is significant enriched in the pathways related to immune response in the A. burtoni, P. nyererei, and M. zebra genomes.

Bottom Line: Many of these variations affected the annotated gene regions in the genome.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.

View Article: PubMed Central - PubMed

Affiliation: Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz Konstanz, Germany.

ABSTRACT
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.

No MeSH data available.