Genome assemblies
b...@bioinf.uni-leipzig.de
I have genomes downloaded from UCSC. I am working with a dataset that came
originally from genome assemblies of the ENSEMBL v62. I want to know if
these genome correspondences between UCSC and ENSEMBL are the same.
- ENSEMBL (UCSC)
- GRCh37 (hg19)
- CHIMP 2.1 (panTro3)
- gorGor3 (gorGor3)
- PPYG2 (ponAbe2)
- MMUL 1.0 (rheMac3)
- NCBI m37 (mm9)
Yours faithfully,
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Maria Beatriz Walter Costa
PhD Student
Bioinformatik/Universität Leipzig
Härtelstraße 16-18 D-04107 Leipzig, Germany
Jonathan Casper
Hello Maria,
Thank you for your question about genome correspondences between UCSC and Ensembl. Both UCSC and Ensembl provide genome assemblies after they have been submitted to Genbank, so the easiest way to discover which assemblies correspond is to check if they are both related to the same record. This information should be provided on the assembly description pages for both UCSC and Ensembl.
In the case of the human genome assembly, both UCSC hg19 and Emsembl GRCh37 point to the GRCh37 assembly released by the Genome Reference Consortium. Both assemblies should be updated to the most recent patch (p13). Note, however, that the UCSC description for the hg19 assembly (visible when you select the hg19 assembly on our genomes page at http://genome.ucsc.edu/cgi-bin/hgGateway) has a caveat: since the release of the UCSC hg19 assembly, the Homo sapiens mitochondrion sequence (represented as "chrM" in the Genome Browser) has been replaced in GenBank with the record NC_012920. We have not replaced the original sequence, NC_001807, in the hg19 Genome Browser. We have fixed this for the new hg38 human genome assembly.
Ensembl CHIMP 2.1 does not appear to be the same as UCSC panTro3 - note the March 2006 release date for CHIMP 2.1, while panTro3 references the Pan_troglodytes-2.1.3 entry at NCBI from 2010. Ensembl also has another chimpanzee assembly named Pan_troglodytes_2.1.3(Ensembl pre), which shares the 2010 release date.
Both UCSC and Ensembl provide the same NCBI identifier for their gorGor3 assemblies: GCA_000151905.1.
Ensembl PPYG2 points to the GCA_000001545.1 assembly, while UCSC ponAbe2 points to GCA_000001545.3 (which replaced .1). They are not the same.
The description of Ensembl MMUL 1.0 notes that it was derived from an Indian-origin rhesus monkey, while the UCSC rheMac3 entry notes that it is based on the genome of a five-year-old female originating from the South-West of China. The UCSC rheMac2 assembly, however, is also based on the Indian-origin rhesus monkey. Both Ensembl MMUL 1.0 and UCSC rheMac2 point to the Mmul_051212 assembly.
UCSC mm9, as noted on the description page, is a presentation of the version 37 build of the assembly from NCBI. This matches the assembly details provided by Ensembl at http://may2012.archive.ensembl.org/Mus_musculus/Info/Index (also accessible by visiting the Ensembl mouse genome page at http://www.ensembl.org/Mus_musculus/Info/Index and selecting "NCBI37" from the "other assemblies" section).
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Jonathan Casper
UCSC Genome Bioinformatics Group
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