Ambystoma.org

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Welcome to Sal-Site

Sal-Site provides information to support research and educational efforts that use salamanders, and in particular the Mexican axolotl.
It also highlights some of the amazing characteristics of salamanders that endear them to scientists and naturalists around the world.
 

                                                                    

NEW! BLAST Axolotl Genome: This assembly represents a single individual from the AGSC and was generated using 600 Gb of HiSeq paired end reads and 640Gb of HiSeq mate pair reads. Reads were assembled using a modified version of SparseAssembler [Ye C, et al. 2012]. The resulting draft assembly covers 21Gb in 21M (21,007,744) scaffolds with N50/L50 of 27236/216411. For those interested in single-copy genes, these tend to be found on longer scaffolds, but we recommend caution in interpreting negative alignment results. Several analyses aimed at increasing megabase/chromosome-level contiguity and gap filling are ongoing and will be incorporated at a future date.

Disclaimer: This unpublished preliminary genome assembly is being made available as a community resource for the analyses of target genes and candidate genomic regions. Users may use data to analyze their own data (i.e. for development/analysis of mutagenesis constructs or as a reference database for transcriptional/proteomics analyses). The scientific community is expected to postpone publications of large-scale analyses of the data until consortia organized by the data producers can publish their initial large-scale analyses, in the spirit of the Ft. Lauderdale agreement. Inquires can be sent to  This e-mail address is being protected from spambots. You need JavaScript enabled to view it . Information about the BLAST server can be found here.

In the meantime, if you use this interim assembly for published analyses please cite the following papers that cover this data portal and a fraction of the underlying sequence data:

 1) Keinath MC, Timoshevskaya, NY, Timoshevskiy VA, Tsonis PA, Voss SR, Smith JJ. (2015) Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing. Scientific Reports5:16413.

 2) Smith JJ, Putta S, Walker JA, Kump DK, Samuels AK, Monaghan JR, Weisrock DW, Staben C, Voss SR. (2005) Sal-Site: Integrating new and existing ambystomatid salamander research and informational resources. BMC Genomics 6: 181.

 

About Salamanders ...

The axolotl (Ambystoma mexicanum) is a salamander native to Lake Xochimilco, Mexico. It belongs to the group of salamanders known as mole salamanders. Other members of this group include one of the axolotl's closest relatives, the tiger salamander (Ambystoma tigrinum). A more distant relative is the spotted salamander (Ambystoma maculatum). 

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Support

Sal-Site (R24-OD010435) and the Ambystoma Genetic nig
Stock Center (P40-OD019794) are funded by the Office
of the Director at
the National Institutes of Health.

                                           

 

Fun Facts

What’s the difference between a newt and an axolotl?

A newt is a salamander but not all salamanders are newts.

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