Overlapping 5.8S and 28S annotations in Eukaryotic rDNAs

[BartvdVossenberg]

Dear Torsten Seemann,

I am an enthusiastic user of the barrnap tool. I work with both plant parasitic prokaryotes and eukaryotes. I noticed that when annotating eukaryotic rDNA sequences, the 18S and 5.8S predictions are accurate, but the 28S gene is consequently predicted to start just before the 5.8S gene (see image attached). As a result, the ITS2 and correct start of the 28S gene have to be determined manually. I can imagine the prediction if difficult as the start of 5.8S and 28S have high sequence similarity and share some key conserved sequences.

Is there some way to overcome this inconvenience?

Hope to hear from you. Best wishes,
Bart

[ramiroricardo]

Hi all,

we are having a similar issue. Did you ever come up with a solution to this?

Thanks,

Ramiro

[BartvdVossenberg]

No, unfortunately we have not. Best wishes Bart Op ma 19 jun. 2023 18:59 schreef ramiroricardo ***@***.***>:

…

Hi all, we are having a similar issue. Did you ever come up with a solution to this? Thanks, Ramiro — Reply to this email directly, view it on GitHub <#47 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AN5KIRIH2YLWIUTPT4WB7HLXMCAO3ANCNFSM4TYNOIOA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[gbdias]

Hi @BartvdVossenberg , I was curious how do you determine the correct start of the 28S as well as the correct end of 5.8S.

[moshi4]

I recently developed pybarrnap, which reimplements the equivalent functionality of barrnap in python and updates the Rfam model profiles to the latest version.
In pybarrnap, no overlap occurs between eukaryotic 5.8S and 28S, so I think the old model profile in barrnap is the reason why it cannot accurately distinguish between 5.8S and 28S.

Example (barrnap vs pybarrnap)

Saccharomyces_cerevisiae.fna.gz

$ barrnap Saccharomyces_cerevisiae.fna -k euk -q # Overlap 5.8S and 28S
##gff-version 3
NC_001144.5	barrnap:0.9	rRNA	451796	455574	0	-	.	Name=28S_rRNA;product=28S ribosomal RNA
NC_001144.5	barrnap:0.9	rRNA	455418	455569	1.6e-36	-	.	Name=5_8S_rRNA;product=5.8S ribosomal RNA
NC_001144.5	barrnap:0.9	rRNA	455934	457731	0	-	.	Name=18S_rRNA;product=18S ribosomal RNA
NC_001144.5	barrnap:0.9	rRNA	459678	459795	3.1e-13	+	.	Name=5S_rRNA;product=5S ribosomal RNA
NC_001144.5	barrnap:0.9	rRNA	460933	464711	0	-	.	Name=28S_rRNA;product=28S ribosomal RNA
NC_001144.5	barrnap:0.9	rRNA	464555	464706	1.6e-36	-	.	Name=5_8S_rRNA;product=5.8S ribosomal RNA
NC_001144.5	barrnap:0.9	rRNA	465071	466868	0	-	.	Name=18S_rRNA;product=18S ribosomal RNA
NC_001144.5	barrnap:0.9	rRNA	468815	468930	5.4e-13	+	.	Name=5S_rRNA;product=5S ribosomal RNA
NC_001144.5	barrnap:0.9	rRNA	472467	472582	5.4e-13	+	.	Name=5S_rRNA;product=5S ribosomal RNA
NC_001144.5	barrnap:0.9	rRNA	482047	482162	5.4e-13	+	.	Name=5S_rRNA;product=5S ribosomal RNA
NC_001144.5	barrnap:0.9	rRNA	485699	485814	5.4e-13	+	.	Name=5S_rRNA;product=5S ribosomal RNA
NC_001144.5	barrnap:0.9	rRNA	489351	489468	3.1e-13	+	.	Name=5S_rRNA;product=5S ribosomal RNA
NC_001144.5	barrnap:0.9	rRNA	489766	490546	5.2e-189	-	.	Name=28S_rRNA;product=28S ribosomal RNA (partial);note=aligned only 26 percent of the 28S ribosomal RNA

$ pybarrnap Saccharomyces_cerevisiae.fna -k euk -q # No overlap 5.8S and 28S
##gff-version 3
NC_001144.5	pybarrnap:0.5.0	rRNA	451787	455177	0	-	.	Name=28S_rRNA;product=28S ribosomal RNA;Dbxref=RFAM:RF02543
NC_001144.5	pybarrnap:0.5.0	rRNA	455418	455570	8.0e-45	-	.	Name=5_8S_rRNA;product=5.8S ribosomal RNA;Dbxref=RFAM:RF00002
NC_001144.5	pybarrnap:0.5.0	rRNA	455934	457731	0	-	.	Name=18S_rRNA;product=18S ribosomal RNA;Dbxref=RFAM:RF01960
NC_001144.5	pybarrnap:0.5.0	rRNA	459678	459794	5.5e-16	+	.	Name=5S_rRNA;product=5S ribosomal RNA;Dbxref=RFAM:RF00001
NC_001144.5	pybarrnap:0.5.0	rRNA	460924	464314	0	-	.	Name=28S_rRNA;product=28S ribosomal RNA;Dbxref=RFAM:RF02543
NC_001144.5	pybarrnap:0.5.0	rRNA	464555	464707	8.0e-45	-	.	Name=5_8S_rRNA;product=5.8S ribosomal RNA;Dbxref=RFAM:RF00002
NC_001144.5	pybarrnap:0.5.0	rRNA	465071	466868	0	-	.	Name=18S_rRNA;product=18S ribosomal RNA;Dbxref=RFAM:RF01960
NC_001144.5	pybarrnap:0.5.0	rRNA	468815	468930	9.5e-16	+	.	Name=5S_rRNA;product=5S ribosomal RNA;Dbxref=RFAM:RF00001
NC_001144.5	pybarrnap:0.5.0	rRNA	472467	472582	9.5e-16	+	.	Name=5S_rRNA;product=5S ribosomal RNA;Dbxref=RFAM:RF00001
NC_001144.5	pybarrnap:0.5.0	rRNA	482047	482162	9.5e-16	+	.	Name=5S_rRNA;product=5S ribosomal RNA;Dbxref=RFAM:RF00001
NC_001144.5	pybarrnap:0.5.0	rRNA	485699	485814	9.5e-16	+	.	Name=5S_rRNA;product=5S ribosomal RNA;Dbxref=RFAM:RF00001
NC_001144.5	pybarrnap:0.5.0	rRNA	489351	489467	5.5e-16	+	.	Name=5S_rRNA;product=5S ribosomal RNA;Dbxref=RFAM:RF00001
NC_001144.5	pybarrnap:0.5.0	rRNA	489755	490547	1.7e-240	-	.	Name=28S_rRNA;product=28S ribosomal RNA (partial);Dbxref=RFAM:RF02543;Note=aligned only 27.23 percent of the 28S ribosomal RNA