Data Wrangling - Gene ID Extraction from P.generosa Genome GFF Using Methylation Machinery List

Per this GitHub Issue Steven asked that I take a list of gene names associated with DNA methylation and see if I could extract a list of Panopea generosa (Panopea generosa) gene IDs and corresponding BLAST e-values for each from our P.generosa genome annotation (see Genomic Resources wiki for more info).

Here’s the list of gene names provided:

dnmt1
dnmt3a
dnmt3b
dnmt3l
mbd1
mbd2
mbd3
mbd4
mbd5
mbd6
mecp2
Baz2a
Baz2b
UHRF1
UHRF2
Kaiso
zbtb4
zbtb38b
zfp57
klf4
egr1
wt1
ctcf
tet1
tet2
tet3

The operations were run in a Jupyter Notebook. All results are available in the notebook, as well as in the RESULTS section below.

Briefly, here’s how the process was run:

1. Use list of gene names to scan GenSAS Panopea-generosa-vv0.74.a4.gene.gff3

2. Use list of matches to scan both GenSAS BLAST results files:

• Panopea-generosa-vv0.74.a4.5d951a9b74287-blast_functional.tab

• Panopea-generosa-vv0.74.a4.5d951bcf45b4b-diamond_functional.tab

3. Extract e-values for any matches.

4. Print out tab-delimited table of P.generosa gene IDs, gene names, and both BLAST results e-values, if present.

Jupyter Notebook:

• GitHub: 20210226_pgen_methylation_gene_IDs.ipynb

• nbviewer: 20210226_pgen_methylation_gene_IDs.ipynb

---

RESULTS

Tab-delimited:

gene_ID          gene_name  BLASTp_evalue  DIAMOND_evalue
PGEN_.00g104080  Baz2b      1.05e-98       5.4e-102
PGEN_.00g104170  Baz2b      3.09e-96       1.2e-109
PGEN_.00g116950  mbd5       6.40e-21       2.8e-20
PGEN_.00g186870  ctcf       1.25e-116
PGEN_.00g192900  UHRF1      2.32e-19
PGEN_.00g202750  mbd2       9.46e-82       2.6e-63
PGEN_.00g209890  mbd2       4.37e-19       9.2e-09
PGEN_.00g209900  mbd4       3.14e-32       8.0e-29
PGEN_.00g243700  egr1       6.24e-58       2.2e-23
PGEN_.00g249090  egr1       4.19e-18       2.6e-06
PGEN_.00g283000  dnmt1      5.03e-10
PGEN_.00g283010  dnmt1      0.0            7.3e-224

Gene_ID	gene_name	BLASTp_evalue	DIAMOND_evalue
PGEN_.00g104080	Baz2b	1.05E-98	5.40E-102
PGEN_.00g104170	Baz2b	3.09E-96	1.20E-109
PGEN_.00g116950	mbd5	6.40E-21	2.80E-20
PGEN_.00g186870	ctcf	1.25E-116
PGEN_.00g192900	UHRF1	2.32E-19
PGEN_.00g202750	mbd2	9.46E-82	2.60E-63
PGEN_.00g209890	mbd2	4.37E-19	9.20E-09
PGEN_.00g209900	mbd4	3.14E-32	8.00E-29
PGEN_.00g243700	egr1	6.24E-58	2.20E-23
PGEN_.00g249090	egr1	4.19E-18	2.60E-06
PGEN_.00g283000	dnmt1	5.03E-10	8.20E-28
PGEN_.00g283010	dnmt1	0	7.30E-224