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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.


Indel length distribution. The Y-axis is the proportion of the indels in the exon region (Red) and genome wide (Blue). The X-axis is binned by the length of the indel. (A–D) present in the indel length distribution in the N. brichardi, A. burtoni, P. nyererei, and M. zebra genomes.
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Figure 3: Indel length distribution. The Y-axis is the proportion of the indels in the exon region (Red) and genome wide (Blue). The X-axis is binned by the length of the indel. (A–D) present in the indel length distribution in the N. brichardi, A. burtoni, P. nyererei, and M. zebra genomes.

Mentions: The number of indels in these data sets ranges from 1,440,691 to 2,317,313 in these four species (Table 1). Proportionally, indels occur as frequently as SNPs in the intronic, intergenic, upstream and downstream regions, but are less common in the exonic regions (<1% vs. >4%, Table 1). Based on the gene annotation of the Tilapia genome, some of the exonic indels may have deleterious effects, such as causing frameshifts or the loss of start and stop codons. In comparison to the genome-wide indels, the exonic indels are enriched for sizes divisible by three, which indicates that those indel events may affect a whole codon (Figure 3).


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

Fan S, Meyer A - Front Genet (2014)

Indel length distribution. The Y-axis is the proportion of the indels in the exon region (Red) and genome wide (Blue). The X-axis is binned by the length of the indel. (A–D) present in the indel length distribution in the N. brichardi, A. burtoni, P. nyererei, and M. zebra genomes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Indel length distribution. The Y-axis is the proportion of the indels in the exon region (Red) and genome wide (Blue). The X-axis is binned by the length of the indel. (A–D) present in the indel length distribution in the N. brichardi, A. burtoni, P. nyererei, and M. zebra genomes.
Mentions: The number of indels in these data sets ranges from 1,440,691 to 2,317,313 in these four species (Table 1). Proportionally, indels occur as frequently as SNPs in the intronic, intergenic, upstream and downstream regions, but are less common in the exonic regions (<1% vs. >4%, Table 1). Based on the gene annotation of the Tilapia genome, some of the exonic indels may have deleterious effects, such as causing frameshifts or the loss of start and stop codons. In comparison to the genome-wide indels, the exonic indels are enriched for sizes divisible by three, which indicates that those indel events may affect a whole codon (Figure 3).

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.