[Bioc-devel] BSgenome changes

[Felix Ernst]

Hi Leonard, Hi Herve,

I followed your conversation, since I have noticed the same problem. Thanks, Herve, for the explanation of the recent changes on hg19.

The GRCh37.P13 report states in its last line:

MT	assembled-molecule	MT	Mitochondrion	J01415.2	=	NC_012920.1	non-nuclear	16569	chrM

Since the last name is called "UCSC-style-name", wouldn't that mean that chrM has to be renamed to MT and not chrMT?

Thanks again for the explanation.

Cheers,
Felix

-----Ursprüngliche Nachricht-----
Von: Bioc-devel <bioc-devel-bounces using r-project.org> Im Auftrag von Hervé Pagès
Gesendet: Freitag, 14. August 2020 01:08
An: Leonard Goldstein <goldstein.leonard using gene.com>; bioc-devel using r-project.org
Cc: charlotte.soneson using fmi.ch
Betreff: Re: [Bioc-devel] BSgenome changes

Hi Leonard,

On 8/12/20 15:22, Leonard Goldstein via Bioc-devel wrote:
> Dear Bioc team,
> 
> I'm following up on this recent GitHub issue 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ldg21
> _SGSeq_issues_5&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=n5bIFHTIgC1B4EdjWUDLIlVcRJdXScYvfbojaqTJZVg&s=Tfk-tDM99P63dnsvMydG2phv5WQPVbJzPk0hzi-_1SE&e= >. Please see the issue for more details and code examples.
> 
> It looks like changes in Bioc devel result in two copies of the 
> mitochondrial chromosome for BSgenome.Hsapiens.UCSC.hg19 -- one named 
> chrM like in previous package versions (length 16571) and one named 
> chrMT (length 16569).
> 
> When using seqlevelsStyle() to change chromosome names from UCSC to 
> NCBI format, this results in new behavior -- in the past chrM was 
> simply renamed MT, now the different sequence chrMT is used. Is this intended?

Absolutely intended.

There is a long story behind the unfortunate fate of the mitochondrial chromosome in hg19. I'll try to keep it short.

When the UCSC folks released the hg19 browser more than 10 years ago, they based it on assembly GRCh37:

   https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13

See sequence report for GRCh37:

 
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.13_GRCh37/GCF_000001405.13_GRCh37_assembly_report.txt

For some mysterious reason GRCh37 didn't include the mitochondrial chromosome so the UCSC folks decided to use mitochondrial sequence
NC_001807 and called it chrM.

However, UCSC has recently decided to base hg19 on GRCh37.p13 instead of GRCh37. A rather surprising move after many years of hg19 being based on the latter.

   https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25/

See sequence report for GRCh37.p13:

 
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_report.txt

Note that GRCh37.p13 does include the mitochondrial chromosome. It's called MT in the official sequence report above and chrMT in hg19.

At the same time the UCSC folks decided to keep chrM so now hg19 contains 2 mitochondrial sequences: chrM and chrMT. Previously it has only one: chrM.

So what you see in BioC devel in BSgenome.Hsapiens.UCSC.hg19 and with
seqlevelsStyle(genome) is only reflecting this. In particular
seqlevelsStyle(genome) <- "NCBI" now does the following:

   - Rename chrMT -> MT.

   - chrM does NOT get renamed. There is no point in renaming this sequence because it has no equivalent in GRCh37.p13.

Hope this helps,

H.

> 
> Leonard
> 
> 	[[alternative HTML version deleted]]
> 
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--
Hervé Pagès

Program in Computational Biology
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