From e2ce900e8290f4aaab11fb39eb47e9c090dc53bd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Zo=C3=A9=20Pochon?= <78050804+ZoePochon@users.noreply.github.com> Date: Fri, 7 Feb 2025 12:52:44 +0100 Subject: [PATCH 1/4] Add RodriguezVarela2024 samples One accession number is missing for a sample on ENA. First author has been contacted. --- .../samples/ancientsinglegenome-hostassociated_samples.tsv | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv index 2d68ef353..c053daa34 100644 --- a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv +++ b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv @@ -734,3 +734,9 @@ Fiddaman2023 2023 10.1126/science.adg2238 Naderi Tepe 38.01 57.02 Iran OL2267 Ga Fiddaman2023 2023 10.1126/science.adg2238 Castillo de Montsoriu 41.783 2.540 Spain OL1999 Gallus gallus 400 10.1126/science.adg2238 virus Gallid alphaherpesvirus 2 bone chromosome SRA raw PRJEB64489 ERS16164995 Fiddaman2023 2023 10.1126/science.adg2238 Kazan City 55.791 49.121 Russia OL1584 Gallus gallus 400 10.1126/science.adg2238 virus Gallid alphaherpesvirus 2 bone chromosome SRA raw PRJEB64489 ERS16164996 Fiddaman2023 2023 10.1126/science.adg2238 Cheboksary City 56.152 47.246 Russia OL1585 Gallus gallus 400 10.1126/science.adg2238 virus Gallid alphaherpesvirus 2 bone chromosome SRA raw PRJEB64489 ERS16164997 +RodriguezVarela2024 2024 10.1126/sciadv.adp8625 Las Gobas 42.675 -2.627 Spain ldo052 Homo sapiens 1200 10.1126/sciadv.adp8625 bacteria Streptococcus pneumoniae tooth chromosome ENA raw PRJEB72246 ERS20844405 +RodriguezVarela2024 2024 10.1126/sciadv.adp8625 Las Gobas 42.675 -2.627 Spain ldo267 Homo sapiens 1200 10.1126/sciadv.adp8625 bacteria Streptococcus pneumoniae tooth chromosome ENA raw PRJEB72247 +RodriguezVarela2024 2024 10.1126/sciadv.adp8625 Las Gobas 42.675 -2.627 Spain ldo060 Homo sapiens 1200 10.1126/sciadv.adp8625 bacteria Erysipelothrix rhusiopathiae tooth chromosome ENA raw PRJEB72248 ERS20844413 +RodriguezVarela2024 2024 10.1126/sciadv.adp8625 Las Gobas 42.675 -2.627 Spain ldo050 Homo sapiens 1200 10.1126/sciadv.adp8625 bacteria Erysipelothrix rhusiopathiae tooth chromosome ENA raw PRJEB72249 ERS20844404 +RodriguezVarela2024 2024 10.1126/sciadv.adp8625 Las Gobas 42.675 -2.627 Spain ldo042 Homo sapiens 1200 10.1126/sciadv.adp8625 bacteria Yersinia enterocolitica tooth chromosome ENA raw PRJEB72250 ERS20844396 +RodriguezVarela2024 2024 10.1126/sciadv.adp8625 Las Gobas 42.675 -2.627 Spain ldo049 Homo sapiens 1000 10.1126/sciadv.adp8625 virus Variola virus tooth chromosome ENA raw PRJEB72251 ERS20844403 From 81c19b0f3206003f3ba1b283689b7f9b7da05dbe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Zo=C3=A9=20Pochon?= <78050804+ZoePochon@users.noreply.github.com> Date: Fri, 7 Feb 2025 13:19:56 +0100 Subject: [PATCH 2/4] Update ancientsinglegenome-hostassociated_samples.tsv Add accession code for library ldo054 since both libraries of the same individual ldo054 and ldo267 have been merged into one FASTQ file on ENA. --- .../samples/ancientsinglegenome-hostassociated_samples.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv index c053daa34..d557beaa0 100644 --- a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv +++ b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv @@ -735,7 +735,7 @@ Fiddaman2023 2023 10.1126/science.adg2238 Castillo de Montsoriu 41.783 2.540 Spa Fiddaman2023 2023 10.1126/science.adg2238 Kazan City 55.791 49.121 Russia OL1584 Gallus gallus 400 10.1126/science.adg2238 virus Gallid alphaherpesvirus 2 bone chromosome SRA raw PRJEB64489 ERS16164996 Fiddaman2023 2023 10.1126/science.adg2238 Cheboksary City 56.152 47.246 Russia OL1585 Gallus gallus 400 10.1126/science.adg2238 virus Gallid alphaherpesvirus 2 bone chromosome SRA raw PRJEB64489 ERS16164997 RodriguezVarela2024 2024 10.1126/sciadv.adp8625 Las Gobas 42.675 -2.627 Spain ldo052 Homo sapiens 1200 10.1126/sciadv.adp8625 bacteria Streptococcus pneumoniae tooth chromosome ENA raw PRJEB72246 ERS20844405 -RodriguezVarela2024 2024 10.1126/sciadv.adp8625 Las Gobas 42.675 -2.627 Spain ldo267 Homo sapiens 1200 10.1126/sciadv.adp8625 bacteria Streptococcus pneumoniae tooth chromosome ENA raw PRJEB72247 +RodriguezVarela2024 2024 10.1126/sciadv.adp8625 Las Gobas 42.675 -2.627 Spain ldo054 Homo sapiens 1200 10.1126/sciadv.adp8625 bacteria Streptococcus pneumoniae tooth chromosome ENA raw PRJEB72247 ERS20844406 RodriguezVarela2024 2024 10.1126/sciadv.adp8625 Las Gobas 42.675 -2.627 Spain ldo060 Homo sapiens 1200 10.1126/sciadv.adp8625 bacteria Erysipelothrix rhusiopathiae tooth chromosome ENA raw PRJEB72248 ERS20844413 RodriguezVarela2024 2024 10.1126/sciadv.adp8625 Las Gobas 42.675 -2.627 Spain ldo050 Homo sapiens 1200 10.1126/sciadv.adp8625 bacteria Erysipelothrix rhusiopathiae tooth chromosome ENA raw PRJEB72249 ERS20844404 RodriguezVarela2024 2024 10.1126/sciadv.adp8625 Las Gobas 42.675 -2.627 Spain ldo042 Homo sapiens 1200 10.1126/sciadv.adp8625 bacteria Yersinia enterocolitica tooth chromosome ENA raw PRJEB72250 ERS20844396 From 987d397c8648d64a82a9c2f695a3a8c12382069f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Zo=C3=A9=20Pochon?= <78050804+ZoePochon@users.noreply.github.com> Date: Fri, 7 Feb 2025 13:54:56 +0100 Subject: [PATCH 3/4] Add RodriguezVarela2024 libraries In the libraries the author called the sample ldo054: ldo054+ldo267 but I only kept ldo054 for consistency. --- .../ancientsinglegenome-hostassociated_libraries.tsv | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv index f9431421c..548d9d87c 100644 --- a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv +++ b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv @@ -3159,3 +3159,11 @@ Fiddaman2023 2023 10.1126/science.adg2238 OL1584 SRA PRJEB64489 ERS16164996 OL15 Fiddaman2023 2023 10.1126/science.adg2238 OL1584 SRA PRJEB64489 ERS16164996 OL1584ii double AmpliTaq Gold DNA none Illumina NovaSeq 6000 SINGLE Targeted-Capture 23678785 ERR11752806 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/006/ERR11752806/ERR11752806.fastq.gz 048c5746773f3c55c700d50f2e3dbb18 1664874891 Fiddaman2023 2023 10.1126/science.adg2238 OL1585 SRA PRJEB64489 ERS16164997 OL1585 double AmpliTaq Gold DNA none Illumina NovaSeq 6000 SINGLE Targeted-Capture 20374738 ERR11752797 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/097/ERR11752797/ERR11752797.fastq.gz f984b19b9778e16891f45ab5bc7394e4 584538336 Fiddaman2023 2023 10.1126/science.adg2238 OL1585 SRA PRJEB64489 ERS16164997 OL1585 double AmpliTaq Gold DNA none Illumina HiSeq 2500 SINGLE Targeted-Capture 2994421 ERR11752832 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR117/032/ERR11752832/ERR11752832.fastq.gz 05838e7aa914b34d6e43e0585467c2fc 109193304 +RodriguezVarela2024 2024 10.1126/sciadv.adp8625 ldo052 ENA PRJEB72246 ERS20844405 ldo052-b1e1l1p1 double AmpliTaq Gold DNA none Illumina NovaSeq 6000 SINGLE WGS 305483324 ERR13472628 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR134/028/ERR13472628/ERR13472628.fastq.gz f24e63f36222625b085df0bf6db03310 13435471604 +RodriguezVarela2024 2024 10.1126/sciadv.adp8625 ldo054 ENA PRJEB72246 ERS20844406 ldo054-b1e1l1p1 double AmpliTaq Gold DNA none Illumina NovaSeq 6000 SINGLE WGS 182031259 ERR13472629 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR134/029/ERR13472629/ERR13472629.fastq.gz b92ebd364384ad0d310c66b5b7163097 8279491119 +RodriguezVarela2024 2024 10.1126/sciadv.adp8625 ldo060 ENA PRJEB72246 ERS20844413 ldo060-b1e1l1p1 double AmpliTaq Gold DNA none Illumina NovaSeq 6000 SINGLE WGS 131534263 ERR13472637 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR134/037/ERR13472637/ERR13472637.fastq.gz 2aa39e4bda1fdc6583cd3d81359f7332 6217241214 +RodriguezVarela2024 2024 10.1126/sciadv.adp8625 ldo050 ENA PRJEB72246 ERS20844404 ldo050-b1e1l1p1 double AmpliTaq Gold DNA none Illumina NovaSeq 6000 SINGLE WGS 114553091 ERR13472627 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR134/027/ERR13472627/ERR13472627.fastq.gz 29b913c4540b46fcee71657f50bf915a 5562221281 +RodriguezVarela2024 2024 10.1126/sciadv.adp8625 ldo042 ENA PRJEB72246 ERS20844396 ldo042-b1e1l1p1 double AmpliTaq Gold DNA none Illumina NovaSeq 6000 SINGLE WGS 496384678 ERR13472616 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR134/016/ERR13472616/ERR13472616.fastq.gz c1129e5af16c93169a9f49f502a5dd55 27026125898 +RodriguezVarela2024 2024 10.1126/sciadv.adp8625 ldo042 ENA PRJEB72246 ERS20844396 ldo042-b1e2l1p1 double AmpliTaq Gold DNA none Illumina NovaSeq 6000 SINGLE WGS 32330711 ERR13472617 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR134/017/ERR13472617/ERR13472617.fastq.gz 957be09accf4b3c9c157f1235d56c1fa 1557579667 +RodriguezVarela2024 2024 10.1126/sciadv.adp8625 ldo049 ENA PRJEB72246 ERS20844403 ldo049-b1e1l1p1 double AmpliTaq Gold DNA none Illumina NovaSeq 6000 SINGLE WGS 354810947 ERR13472625 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR134/025/ERR13472625/ERR13472625.fastq.gz 5a9709f3d5ade306428d827982361c3b 16153185523 +RodriguezVarela2024 2024 10.1126/sciadv.adp8625 ldo049 ENA PRJEB72246 ERS20844403 ldo049r-b1e1l1p1 double AmpliTaq Gold DNA none Illumina NovaSeq 6000 SINGLE WGS 147249795 ERR13472626 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR134/026/ERR13472626/ERR13472626.fastq.gz 4de2f14b9addb8d393624b5c4b2f74bc 6674435548 From 347e6dda868e1f51f2b3032e19ad841aa89ca835 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Zo=C3=A9=20Pochon?= <78050804+ZoePochon@users.noreply.github.com> Date: Fri, 7 Feb 2025 14:00:44 +0100 Subject: [PATCH 4/4] Update CHANGELOG.md And add the change to singlegenome_species.json as well. --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0ed3be34f..53f77cab9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,10 +13,14 @@ and this project follows to [Calendar Versioning](https://calver.org/). #### Ancient Single Genome: Host Associated +- RodriguezVarela 2024 10.1126/sciadv.adp8625 (added by @ZoePochon) + #### Ancient Metagenome: Environmental ### Changed +- Added three new species names to singlegenome_species.json (added by @ZoePochon) + ### Removed ## v24.12: Old Town of Corfu