Xenopus laevis genome v9.1 released

The Xenopus laevis genome v9.1 is available at chromosome scale.

It can be accessed via BLAST or by selecting the 9.1 version within GBrowse.

Click here to view on GBrowse.

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Version 8.0 is now retired. Version 8.0 used a lot of the “Dovetail” data to add to the Chromosome mapping by BAC Fish, to assemble chromosome scale “pseudomolecules”, but on subsequent examination, there were a large number of regions lost from the assembly.

Xenopus laevis (version 9.1) is now available, along with annotation, on the Xenbase server, in both browser and downloadable formats.  The assembly is a chromosome scale reassembly of version 7.1, any analysis previously done should, in principle, be able to be “lifted over” to the new coordinates. We recommend the use of X. laevis genome v9.1 instead of v8.0.

The X. laevis 9.1 assembly improves on previous version by capturing >90% of the assembled sequence into 18 pseudomolecules representing the 18 chromosomes of X. laevis. These have been named based off of their orthology to X. tropicalis and unique evolutionary history. The v7.2 assembly was improved by Dovetail, using their proprietary Chicago reads followed by Hi-C data to measure DNA-DNA interactions and assemble scaffolds large enough to be ordered/oriented by BAC-FISH and synteny to X. tropicalis. Regions with important genes that were affected by gaps were replaced by high quality BAC sequences.

A new X. tropicalis assembly is also available at Xenbase.

The new X. tropicalis v9.0 assembly improves on previous versions by utilizing Dovetail’s Chicago reads to reorient small segments of X. tropicalis chromosomes whose orientation could not be discerned by the genetic map. Additional extrachromosomal sequence has been assigned to chromosomes. Improvements to the X. laevis transcriptome, which is used as a sister taxon, have also improved models in the X. tropicalis genome.