We are pleased to announce that a new high quality chromosomal assembly is being released prior to publication. This assembly can be accessed through the following Genome Hub or the NCBI genome page.  Please see fair use statements below.

 The previous AmexG_v6 reported by Schloissnig et al 2021 and various data tracks can be accessed through the following genome hub link to the UCSC Genome Browser. Similarly the previous Amex_PQ.v4 chromosomal scale assembly reported by Smith et al 2019 can be accessed through the following genome hub link to the UCSC Genome Browser. Variant and SNP density track session from Timoshevskaya et al 2020 (read-only access to full text). Tracks on the new browser should also aid in cross referencing gene IDs between assembly and annotation versions.

EMBARGO/FAIR USE OF THESE DATA: his genome is being released pre-publication and we encourage others to use these data, but in doing so we also expect that they will respect our right to first presentation (including journal publications, pre-prints such as in bioRxiv, public conference talks, and press releases) of a genome-wide analysis of this assembly. This includes the use of genome-wide data for evolutionary and phylogenetic analyses, epigenetic analyses, and analysis of sex determination.

Exceptions to the policy are for analyses of either a single locus, or a single gene family, or a maximum of 5 gene loci or for mapping of independently-generated RNAseq datasets. This genome and associated datasets will be considered released from this embargo when they are expressly published. These expectations extend to tracks that are uploaded by us and others prior to publication (individually listed as listed as “unpublished: on the browser). For any queries about using the data, referencing/publishing analyses based on pre-publication data or interest in contributing to genome-scale analyses please contact This email address is being protected from spambots. You need JavaScript enabled to view it. and This email address is being protected from spambots. You need JavaScript enabled to view it..

We provide three assemblies for BLAST search of the A. mexicanum genome. To get search results faster, limit the number of sequences in your query and number of reported alignments (set smaller value for the -num_alignments parameter). When searching oligonucleotides (PCR primers, gRNAs) for off-target alignments, use the following command: word_size 11.

1. The AmexG_v6 database was built from a chromosomal scale assembly reported by Schloissnig et al 2021. This assembly was generated from DNA sequences obtained from a single white (d/d) male axolotl. The assembly also includes the mitochondrial genome.

2. The Amex_PQ.v4 database was built from a chromosomal scale assembly reported by Smith et al 2019.

Gene and EST Database

Assembly V4.0: The A. mexicanum transcriptome has been deep sequenced (15,000,000 Roche 454 short sequence reads and 50K Sanger reads) and assembled. The resulting assembly V4.0 can now be BLAST searched here. Approximately 89.9% of the 14 million high quality sequences were assembled into contigs with a total length of 542 Mb.

Gene Expression

The analysis of gene expression is being studied using microarray, quantitative-realtime PCR, RNA-Seq, and Nanostring. These resources include: