Riadi G et al. (2016), Towards the bridging of molecular genetics data...

XB-ART-51924

BMC Genomics 2016 Mar 01;17:161. doi: 10.1186/s12864-016-2440-9.

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Towards the bridging of molecular genetics data across Xenopus species.

Riadi G , Ossandón F , Larraín J , Melo F .

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BACKGROUND: The clawed African frog Xenopus laevis has been one of the main vertebrate models for studies in developmental biology. However, for genetic studies, Xenopus tropicalis has been the experimental model of choice because it shorter life cycle and due to a more tractable genome that does not result from genome duplication as in the case of X. laevis. Today, although still organized in a large number of scaffolds, nearly 85% of X. tropicalis and 89% of X. laevis genomes have been sequenced. There is expectation for a comparative physical map that can be used as a Rosetta Stone between X. laevis genetic studies and X. tropicalis genomic research. RESULTS: In this work, we have mapped using coarse-grained alignment the 18 chromosomes of X. laevis, release 9.1, on the 10 reference scaffolds representing the haploid genome of X. tropicalis, release 9.0. After validating the mapping with theoretical data, and estimating reference averages of genome sequence identity, 37 to 44% between the two species, we have carried out a synteny analysis for 2,112 orthologous genes. We found that 99.6% of genes are in the same organization. CONCLUSIONS: Taken together, our results make possible to establish the correspondence between 62 and 65.5% of both genomes, percentage of identity, synteny and automatic annotation of transcripts of both species, providing a new and more comprehensive tool for comparative analysis of these two species, by allowing to bridge molecular genetics data among them.

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References [+] :

Altschul, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997, Pubmed

	Fig. 1. A chart summarizing the workflow from the two Xenopus assemblies to the map and the analyses
	Fig. 2. Dotplot alignments of each XLA9.1Â L and S chromosomes (y axis) to each XTR9.0 chromosome (x axis). A red dot represents a block alignment between X. laevis and X. tropicalis chromosomes. The alignments are not at the same scale
	Fig. 3. Maximum drop-off scores chart of X. laevis blocks on X. tropicalis. a bar-plot of the maximum drop-off score, X, per block position for chromosome 1. b Histogram of drop-off scores. c Table with the average maximum drop-off scores per chromosome calculated using all blocks, only the aligning blocks, and the coverage of the aligning blocks on X. tropicalis. The cells in grey show the most conserved chromosomes according each column
	Fig. 4. Three distances measured between the consecutive genes in X. laevis (XLA9.1), A and B as intergenic-distance, igd(A, B); between two consecutive genes in X. tropicalis (XTR9.0), Aâ and Bâ as igd(Aâ, Bâ) and; the distance between orthologous genes in both genomes d(B, Bâ)
	Fig. 5. Boxplot of the global and local alignment sequence identities of the 20,000 samples of pairs of blocks from all chromosomes. The box in the boxplot concentrates 50Â % of the data. The whiskers are 1.5x the length of the box. The red crosses represent outliers