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Comparative Study
. 2015 Mar 17;112(11):E1257-62.
doi: 10.1073/pnas.1501764112. Epub 2015 Mar 2.

Whole-genome Sequence of the Tibetan Frog Nanorana Parkeri and the Comparative Evolution of Tetrapod Genomes

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Free PMC article
Comparative Study

Whole-genome Sequence of the Tibetan Frog Nanorana Parkeri and the Comparative Evolution of Tetrapod Genomes

Yan-Bo Sun et al. Proc Natl Acad Sci U S A. .
Free PMC article

Abstract

The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia, and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs. 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged approximately 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multigenome synteny blocks further show that amphibians have fewer interchromosomal rearrangements than mammals but have a comparable rate of intrachromosomal rearrangements. Our analysis also identifies 11 Mb of anuran-specific highly conserved elements that will be useful for comparative genomic analyses of frogs. The Nanorana genome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies.

Keywords: chromosome rearrangement; de novo genome; highly conserved element; transposable elements.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Comparison of transposable elements (TEs) between N. parkeri and X. tropicalis. (A) Comparisons of the TEs in the two frogs. (B) Boxplot of divergence rates for different TE families for the two frogs. Divergence rate calculated from alignments of the TEs identified against entries in the Repbase library. Generally, the divergence of TEs in Nanorana is higher than in Xenopus. (C) Clustering results based on the distribution correlation within a 2-Mb sliding windows across genome; two TE families are more correlated (with same color) in distribution if they show more similar occurrences in amount. DNA, DNA transposon; LINE, long interspersed nuclear elements; LTR, long terminal repeat transposable elements.
Fig. 2.
Fig. 2.
Expansion and contraction in gene families (A) and whole-genome synteny between N. parkeri and X. tropicalis (B). (A) The phylogeny using one representative genome for each major vertebrate lineage and the dynamic evolution of gene families along each lineage (MRCA, most recent common ancestor). Divergence time between the two frog species was estimated to be 266 Ma. (B) Syntenic map between the large (>4 M) scaffolds of the genome of N. parkeri and the chromosomal map of X. tropicalis. Colors refer to the different chromosomes of Xenopus that hold scaffolds of N. parkeri. Gray bars indicate aligned scaffolds of X. tropicalis not incorporated into chromosomes of Xenopus.
Fig. 3.
Fig. 3.
Chromosome synteny blocks among human, chicken, N. parkeri, and X. tropicalis. (A) Homologous synteny blocks between human chr1 and other genomes. The homologous synteny blocks (HSBs; shaded areas) occur over the whole human chr1; gray and blue shadings are used to indicate different chromosomes/scaffolds. A light-blue triangle points to a Xenopus-specific break. (B) Homologous synteny blocks between chicken chr1 and other genomes. HSBs (shaded areas) occur across chicken chr1. Light blue triangles point to two breaks in Xenopus, one of which also occurs in Nanorana, indicating a common break in amphibians. (C) Homologous synteny blocks between chicken chr4 and other genomes. Light blue triangles point to two Xenopus-specific breaks, and the black triangle points to a chicken-specific fusion. (D) Homologous synteny blocks between chicken microchromosomes and other genomes. Light blue and white triangles point to amphibian- and human-specific breaks, respectively. (E) Homologous synteny blocks between the longest scaffold of Xenopus and the other genomes. The light blue triangle indicates an amniote fission.

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