Merge branch 'main' into linkouts

Arachis/GENUS/pangenes/Arachis.pan3.BYQ9/README.Arachis.pan3.BYQ9.yml

@@ -0,0 +1,42 @@
+---
+identifier: Arachis.pan3.BYQ9
+
+provenance: "The files in this directory are a product of the staff of the LegumeInfo, PeanutBase, and SoyBase project teams. The method is described here: https://github.com/legumeinfo/pandagma"
+
+source: "https://data.legumeinfo.org"
+
+synopsis: "Pangene set for Arachis species, based on A. hypogaea, A. duranensis, and A. ipaensis. This pangene set includes four annotation sets from A. hypogaea and one each from A. duranensis and A. ipaensis."
+
+scientific_name: Arachis
+
+taxid: 3826
+
+annotations_main:
+  - arahy.BaileyII.gnm1.ann1
+  - arahy.Tifrunner.gnm1.ann2
+  - arahy.Tifrunner.gnm2.ann1
+  - arahy.Tifrunner.gnm2.ann2
+
+annotations_extra:
+  - aradu.V14167.gnm1.ann1
+  - araip.K30076.gnm1.ann1
+  - arast.V10309.gnm1.ann1
+
+description: "Pan-gene set for Arachis species, spanning 4 species and 7 annotation sets, calculated using the pandagma pipeline, version 2.0 (February, 2024)"
+
+original_file_creation_date: "2024-02-14"
+
+local_file_creation_date: "2024-02-14"
+
+dataset_release_date: "2024-02-14"
+
+contributors: The International Peanut Genome Initiative and authors of all constituent genomes and annotations
+
+data_curators: Steven Cannon, Andrew Farmer
+
+public_access_level: public
+
+license: Open
+
+keywords: Arachis, peanut, pan-gene, pangene, orthogroup
+

Arachis/duranensis/about_this_collection/description_Arachis_duranensis.yml

@@ -16,12 +16,6 @@ strains:
     origin: Argentina, via USDA National Plant Germplasm Repository
     description: "Arachis duranensis strain V14167 originates in a region east of the Andes, in the vicinity of northern Argentina and southern Bolivia. This accession is thought to be one of the diploid ancestors of cultivated peanut. Its genome has been sequenced as part of the Peanut Genomics Initiative, to help in the accurate assembly of the more important cultivated peanut, A. hypogaea. This accession is described in Bertioli et al., 2016 (doi:10.1038/ng.3517)"
     resources:
-      - name: Peanutbase Genome Browser (GBrowse)
-        URL: "https://legacy.peanutbase.org/gb2/gbrowse/Aradu1.0"
-        description: "GBrowse for V14167 assembly 1.0"
-      - name: Peanutbase Genome Browser (JBrowse)
-        URL: "https://legacy.peanutbase.org/genomes/jbrowse?data=Aradu1.0"
-        description: "JBrowse for V14167 assembly 1.0"
       - name: "Genome assembly at NCBI"
         URL: "http://www.ncbi.nlm.nih.gov/assembly/GCA_000817695.1/"
         description: "Genome assembly at NCBI, V14167"

Arachis/hypogaea/about_this_collection/description_Arachis_hypogaea.yml

@@ -36,15 +36,6 @@ strains:
     origin: Southeastern United States
     description: "Cultivar Tifrunner is a runner-type peanut bred in the United States and widely planted as a variety and widely used in breeding programs. The genome of this cultivar is described in Bertioli et al., 2019 (doi:10.1038/s41588-019-0405-z)."
     resources:
-      - name: Peanutbase Genome Browser (GBrowse)
-        URL: "https://legacy.peanutbase.org/gbrowse_peanut1.0"
-        description: "GBrowse for Tifrunner assembly 1.0"
-      - name: Peanutbase Genome Browser (JBrowse)
-        URL: "https://legacy.peanutbase.org/genomes/jbrowse?data=arahy.Tifrunner.gnm1"   
-        description: "JBrowse for Tifrunner assembly 1.0"
-      - name: PeanutBase Genome Browser (GBrowse)
-        URL: "https://legacy.peanutbase.org/gb2/gbrowse/arahy.Tifrunner.gnm2/"
-        description: "GBrowse for Tifrunner assembly 2.0"
       - name: NCBI Tifrunner assembly 2.0
         URL: "https://www.ncbi.nlm.nih.gov/nuccore/PIVG00000000"
         description: "Tifrunner gnm2.ann2 (assembly 2.0 annotation 2.0) at NCBI"

Arachis/ipaensis/about_this_collection/description_Arachis_ipaensis.yml

@@ -16,12 +16,6 @@ strains:
     origin: Southern Bolivia
     description: "Arachis ipaensis accession K30076 is the only accession collected from what is thought to be the origin of tetraploid peanut, Villa Montes Bolivia. It was likely carried there by early agriculturalists from a larger population several hundred kilometers to the north (Bertioli et al., 2016: doi:10.1038/ng.3517)"
     resources:
-      - name: Peanutbase Genome Browser (GBrowse)
-        URL: "https://legacy.peanutbase.org/gb2/gbrowse/Araip1.0"
-        description: "GBrowse for K30076 assembly 1.0"
-      - name: Peanutbase Genome Browser (JBrowse)
-        URL: "https://legacy.peanutbase.org/genomes/jbrowse?data=Araip1.0"
-        description: "JBrowse for K30076 assembly 1.0"
       - name: "Genome assembly at NCBI"
         URL: "http://www.ncbi.nlm.nih.gov/assembly/GCA_000816755.1/"
         description: "Genome assembly at NCBI, K30076"

Arachis/stenosperma/annotations/V10309.gnm1.ann1.CZRZ/BUSCO/arast.V10309.gnm1.ann1.CZRZ.busco.fabales_odb10.short_summary.json

@@ -0,0 +1,47 @@
+{
+    "parameters": {
+        "out_path": "/busco_wd",
+        "cpu": "16",
+        "force": "False",
+        "restart": "False",
+        "quiet": "False",
+        "download_path": "/erdos/adf/busco_downloads",
+        "datasets_version": "odb10",
+        "offline": "False",
+        "download_base_url": "https://busco-data.ezlab.org/v5/data/",
+        "auto-lineage": "False",
+        "auto-lineage-prok": "False",
+        "auto-lineage-euk": "False",
+        "update-data": "False",
+        "use_augustus": "False",
+        "batch_mode": "False",
+        "tar": "False",
+        "in": "/busco_wd/run_busco.bash.JhWvm4/arast.V10309.gnm1.ann1.CZRZ.protein_primary.faa",
+        "out": "BUSCO_proteins_fabales_odb10",
+        "mode": "proteins",
+        "lineage_dataset": "/erdos/adf/busco_downloads/lineages/fabales_odb10",
+        "main_out": "/busco_wd/BUSCO_proteins_fabales_odb10",
+        "lineage_results_dir": "run_fabales_odb10",
+        "domain": "eukaryota"
+    },
+    "lineage_dataset": {
+        "name": "fabales_odb10",
+        "creation_date": "2020-08-05",
+        "number_of_buscos": "5366",
+        "number_of_species": "10"
+    },
+    "versions": {
+        "hmmsearch": 3.1,
+        "busco": "5.4.3"
+    },
+    "results": {
+        "one_line_summary": "C:97.2%[S:92.0%,D:5.2%],F:0.2%,M:2.6%,n:5366",
+        "Complete": 97.2,
+        "Single copy": 92.0,
+        "Multi copy": 5.2,
+        "Fragmented": 0.2,
+        "Missing": 2.6,
+        "n_markers": 5366,
+        "domain": "eukaryota"
+    }
+}

Arachis/stenosperma/annotations/V10309.gnm1.ann1.CZRZ/CHECKSUM.V10309.gnm1.ann1.CZRZ.md5

@@ -0,0 +1,34 @@
+3f1a18896d5177db5fe45542ea95e258  ./MANIFEST.V10309.gnm1.ann1.CZRZ.correspondence.yml
+614df38a7cb60dc67f46a110be552eed  ./arast.V10309.gnm1.ann1.CZRZ.protein.faa.gz.gzi
+d8e6e51a1d21345c0cd09fae2f83216b  ./arast.V10309.gnm1.ann1.CZRZ.gene_models_noncoding.gff3.gz
+e1d17910856619103237a051c5ef1c63  ./arast.V10309.gnm1.ann1.CZRZ.gene_models_main.gff3.gz.tbi
+ca2619b180190a64447f8210e2d5eec6  ./arast.V10309.gnm1.ann1.CZRZ.legfed_v1_0.M65K.gfa.tsv.gz
+019172ff554aa12f41de5ae259c02e38  ./arast.V10309.gnm1.ann1.CZRZ.gene_models_main.bed.gz
+ec8680eb9ca6dfdb54f6add1cc7e1041  ./CHANGES.V10309.gnm1.ann1.CZRZ.txt
+18ab8a5e9e76c6cbb9627238879c77d6  ./arast.V10309.gnm1.ann1.CZRZ.mrna_primary.fna.gz.gzi
+e2a22e27ca2f90fd35972be47dd887e0  ./arast.V10309.gnm1.ann1.CZRZ.mrna.fna.gz.gzi
+7f128ca5e449152a6726d0d26a365b66  ./arast.V10309.gnm1.ann1.CZRZ.gene_models_exons.gff3.gz
+e2d0f1b8ac44771183d2192e529dad78  ./arast.V10309.gnm1.ann1.CZRZ.mrna_primary.fna.gz
+5d1928c4f5bf4245aae4d266531ba816  ./arast.V10309.gnm1.ann1.CZRZ.cds.fna.gz.fai
+b831cf6e0d31dd98b5445c62d49c10fe  ./arast.V10309.gnm1.ann1.CZRZ.cds_primary.fna.gz.gzi
+0bcd21094be2e521736a5f66d3727203  ./arast.V10309.gnm1.ann1.CZRZ.protein_primary.faa.gz
+7bc661e46f60e9308d5cd2663776e081  ./arast.V10309.gnm1.ann1.CZRZ.protein_primary.faa.gz.fai
+04ef98566b55ad667b058b1bfb3dc8df  ./arast.V10309.gnm1.ann1.CZRZ.featid_map.tsv.gz
+daed0de5d10057896f6b4f1ac5196e8b  ./arast.V10309.gnm1.ann1.CZRZ.iprscan.gff3.gz
+d0edbcc9dbd65df0dfc4a6f0f7b91d45  ./arast.V10309.gnm1.ann1.CZRZ.protein_primary.faa.gz.gzi
+14031d715fea66f1e566653240e66c96  ./arast.V10309.gnm1.ann1.CZRZ.mrna.fna.gz
+1b9fe9691705b63380ff110c8aedff36  ./arast.V10309.gnm1.ann1.CZRZ.cds_primary.fna.gz.fai
+9eb1a8a66ce49dffbf62d20395271da5  ./BUSCO/arast.V10309.gnm1.ann1.CZRZ.busco.fabales_odb10.full_table.tsv.gz
+8c144993f8edb2552eecf7d3b9a63acb  ./BUSCO/arast.V10309.gnm1.ann1.CZRZ.busco.fabales_odb10.short_summary.txt
+5987914f4a2958d9d07f39a607152e03  ./BUSCO/arast.V10309.gnm1.ann1.CZRZ.busco.fabales_odb10.short_summary.json
+6d706c9b8df610e5b9b93de84d864128  ./arast.V10309.gnm1.ann1.CZRZ.cds.fna.gz.gzi
+302486920ff3179e56516d1f8a68e9b5  ./arast.V10309.gnm1.ann1.CZRZ.cds_primary.fna.gz
+99e732d008bec0ab1ed5d278babecea0  ./arast.V10309.gnm1.ann1.CZRZ.protein.faa.gz
+9ec146a3ecd614dcb09c58d4acf5548f  ./arast.V10309.gnm1.ann1.CZRZ.gene_models_main.gff3.gz
+e24016df9c5d0d1b78a7d55f77115113  ./arast.V10309.gnm1.ann1.CZRZ.mrna_primary.fna.gz.fai
+2ac0bd000e3fd656d6ef6e1107337a52  ./arast.V10309.gnm1.ann1.CZRZ.mrna.fna.gz.fai
+b42d54c9910048ddb841ca2ff57eac91  ./MANIFEST.V10309.gnm1.ann1.CZRZ.descriptions.yml
+d037c86f41256501f7f40d94cb6a2d5e  ./arast.V10309.gnm1.ann1.CZRZ.protein.faa.gz.fai
+cef1c92ab0413ef9aacbadad1b2da421  ./arast.V10309.gnm1.ann1.CZRZ.cds.fna.gz
+cc9b81836241eb801e8856db6f09bb7b  ./arast.V10309.gnm1.ann1.CZRZ.gene_models_noncoding.gff3.gz.tbi
+e7e13718aea32fbff026133e7bb1bf33  ./README.V10309.gnm1.ann1.CZRZ.yml

Arachis/stenosperma/annotations/V10309.gnm1.ann1.CZRZ/README.V10309.gnm1.ann1.CZRZ.yml

@@ -0,0 +1,46 @@
+---
+identifier: V10309.gnm1.ann1.CZRZ
+
+provenance: "The files in this directory originated from GenBank, for RefSeq genome sequence GCF_014773155.1, submitted by the International Peanut Genome Initiative in 2018. The GenBank source is considered the primary repository and authoritative; files in this present directory are derived, and may have changes, as noted below. The files here are held as part of the LegumeInfo and Peanutbase projects, and are made available here for the purpose of reproducibility of analyses at these sites (e.g. gene family alignments and phylogenies, genome browsers, etc.) and for further use by researchers, as that research extends other analyses at the LegumeInfo and Peanutbase projects. If you are conducting research on large-scale data sets for this species, please consider retrieving the data from the primary repositories. If you use the data in the present directory, please respect any usage restrictions in the present and original repositories, and cite the data appropriately."
+
+source: "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_014773155.1"
+
+synopsis: "GenBank RefSeq annotation for Genome assembly 1 for Arachis stenosperma, genotype V10309"
+
+scientific_name: Arachis stenosperma
+
+taxid: 217475
+
+genotype:
+  - V10309
+
+chromosome_prefix: Chr
+
+supercontig_prefix: Scaffold
+
+description: "This annotation was produced by GenBank on the RefSeq assembly V10309 in 2023"
+
+genbank_accession: GCF_014773155.1
+
+original_file_creation_date: "2023-10-01"
+
+local_file_creation_date: "2024-01-17"
+
+dataset_release_date: "2024-01-22"
+
+publication_doi: 10.1038/s41588-019-0405-z
+
+publication_title: "The genome sequence of segmental allotetraploid peanut Arachis hypogaea"
+
+contributors: The International Peanut Genome Initiative; lead assembly group Jeremy Schmutz, Jerry Jenkins, Jane Grimwood; project leads David Bertioli; Soraya Bertioli; Brian Schleffler; Scott Jackson; Peggy Ozias-Akins
+
+citation: "Bertioli, D.J., Jenkins, J., Clevenger, J. et al. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nat Genet 51, 877-884 (2019). https://doi.org/10.1038/s41588-019-0405-z"
+
+data_curators: Steven Cannon, Andrew Farmer
+
+public_access_level: public
+
+license: open
+
+keywords: wild peanut, Arachis stenosperma
+

Arachis/stenosperma/genomes/V10309.gnm1.PFL2/BUSCO/arast.V10309.gnm1.PFL2.busco.fabales_odb10.short_summary.json

@@ -16,7 +16,7 @@
         "use_augustus": "False",
         "batch_mode": "False",
         "tar": "False",
-        "in": "/busco_wd/run_busco.bash.HhFEIb/arast.V10309.gnm1.PFL2.genome_main.fna",
+        "in": "/busco_wd/run_busco.bash.TUc4DD/arast.V10309.gnm1.PFL2.genome_main.fna",
         "out": "BUSCO_genome_fabales_odb10",
         "mode": "euk_genome_met",
         "lineage_dataset": "/erdos/adf/busco_downloads/lineages/fabales_odb10",

Arachis/stenosperma/genomes/V10309.gnm1.PFL2/CHECKSUM.V10309.gnm1.PFL2.md5

@@ -1,14 +1,12 @@
-c908fbab9e3ba8bd12ea4c15d81cf15f  ./BUSCO/arast.V10309.gnm1.PFL2.busco.fabales_odb10.short_summary.txt
-7f781e9bdc60c3f91ad6b50a4d77e8a8  ./BUSCO/arast.V10309.gnm1.PFL2.busco.fabales_odb10.short_summary.json
-fab12c1ce8e88fe52d35b2a19f553b9f  ./BUSCO/arast.V10309.gnm1.PFL2.busco.fabales_odb10.full_table.tsv.gz
-d41d8cd98f00b204e9800998ecf8427e  ./BUSCO/*.busco.fabales_odb10.full_table.tsv.gz
-faec240bbac90aa193a29ac1ea445fa5  ./MANIFEST.PFL2.correspondence.yml
-039116c908fc69fccfd9fb7e87dbf914  ./arast.V10309.gnm1.PFL2.genome_main.fna.gz.fai
-ec29d4bc0070da9437427107daad2ce8  ./CHANGES.V10309.gnm1.PFL2.txt
-73035054706eb276dcfe093afeeb7f88  ./MANIFEST.PFL2.descriptions.yml
-79e6bb587c84bf683645b6dc852af8b3  ./arast.V10309.gnm1.PFL2.agp_placed.txt.gz
-de9db7d3cde8f1bc4165d001bcdaae9d  ./arast.V10309.gnm1.PFL2.genome_main.fna.gz.gzi
-b1b1d846422d32f2bf7e06c7cd4d4663  ./usage_policy.txt
-6b55f7b9c5339a9d63dc7ae383775653  ./arast.V10309.gnm1.PFL2.agp_unplaced.txt.gz
-7c4ecbd0d8cd4cb34c2148b999059d99  ./arast.V10309.gnm1.PFL2.genome_main.fna.gz
-21de1a074eae6c2e77f6ed6d312e4fdf  ./README.V10309.gnm1.PFL2.yml
+b437e9a2e1a98b7ffcc6e5c19ed2a467  ./arast.V10309.gnm1.PFL2.genome_main.fna.gz.fai
+23600f3d3e963fca4db8171463a5511b  ./arast.V10309.gnm1.PFL2.genome_main.fna.gz
+23395511f3bea713fb4e99feffe7c7a1  ./arast.V10309.gnm1.PFL2.seqid_map.tsv.gz
+06a6c1322f3b6d318ec252ca06998774  ./arast.V10309.gnm1.PFL2.initial_seqid_map.tsv.gz
+c9b30ab32ad5a4d5b0d36264accf19c9  ./README.V10309.gnm1.PFL2.yml
+a0519ad7023d621523e1a4dbbfe69870  ./BUSCO/arast.V10309.gnm1.PFL2.busco.fabales_odb10.short_summary.json
+02058aeb14f69544672211741da0402f  ./BUSCO/arast.V10309.gnm1.PFL2.busco.fabales_odb10.short_summary.txt
+c7cffe7305a3c19b8b5787357ffb90d4  ./BUSCO/arast.V10309.gnm1.PFL2.busco.fabales_odb10.full_table.tsv.gz
+083bb2fc52e62d669290a8b8e291be4b  ./MANIFEST.V10309.gnm1.PFL2.descriptions.yml
+d13a0d5c902dff37ab7fbaeb9682e9fc  ./CHANGES.V10309.gnm1.PFL2.txt
+3dde83ffee922953772e2933f032e2e1  ./MANIFEST.V10309.gnm1.PFL2.correspondence.yml
+b294aff4939ad016dfeefec23f28154f  ./arast.V10309.gnm1.PFL2.genome_main.fna.gz.gzi

Arachis/stenosperma/genomes/V10309.gnm1.PFL2/README.V10309.gnm1.PFL2.yml

@@ -1,20 +1,16 @@
 ---
 identifier: V10309.gnm1.PFL2
 
-provenance: "The files in this directory originated from http://peanutbase.org. There is also a corresponding genome assembly at GenBank. Files in this directory are derived, and may have changes, as noted below. The files here are held as part of the LegumeInfo and PeanutBase projects, and are made available here for the purpose of reproducibility of analyses at these sites (e.g. gene family alignments and phylogenies, genome browsers, etc.) and for further use by researchers. If you use the data in the present directory, please 1) please cite the data appropriately - generally referring to the original publications for this data; and if you make use of any significant modifications in the files, then please also cite the respective database project(s) related to this directory."
+provenance: "The files in this directory originated from GenBank, for RefSeq genome sequence GCF_014773155.1, submitted by the International Peanut Genome Initiative in 2018. The GenBank source is considered the primary repository and authoritative; files in this present directory are derived, and may have changes, as noted below. The files here are held as part of the LegumeInfo and Peanutbase projects, and are made available here for the purpose of reproducibility of analyses at these sites (e.g. gene family alignments and phylogenies, genome browsers, etc.) and for further use by researchers, as that research extends other analyses at the LegumeInfo and Peanutbase projects. If you are conducting research on large-scale data sets for this species, please consider retrieving the data from the primary repositories. If you use the data in the present directory, please respect any usage restrictions in the present and original repositories, and cite the data appropriately."
 
-source: http://peanutbase.org
+source: "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_014773155.1"
 
-synopsis: Genome assembly 1 for Arachis stenosperma, accession V10309
+synopsis: "Genome assembly 1 for Arachis stenosperma, genotype V10309"
 
 scientific_name: Arachis stenosperma
 
 taxid: 217475
 
-bioproject: PRJNA610652
-
-scientific_name_abbrev: arast
-
 genotype:
   - V10309
 
@@ -24,22 +20,27 @@ supercontig_prefix: Scaffold
 
 description: "Genome assembly 1 for Arachis stenosperma, accession V10309, with sequenced generated using PacBio Sequel; Illumina HiSeq. Arachis stenosperma Krapov. & W.C. Greg. is a wild peanut relative native to central Brazil, in the past it was cultivated by native peoples of South America, and was carried to the Atlantic coast, where populations persist to the present day. It is a source of strong pest and disease resistance and has been used by peanut breeders and geneticists in interspecific hybrids. A. stenosperma is diploid species in the A-genome group of Arachis, which has similarity to the A genome of tetraploid cultivated peanut (A. hypogaea). This accession was sequenced with PacBio long reads, with contributions by USDA-ARS and researchers at Mars Inc. and the University of Georgia"
 
-genbank_accession: GCA_014773155.1
+genbank_accession: GCF_014773155.1
+
+original_file_creation_date: "2023-10-01"
 
-original_file_creation_date: "2020-10-02"
+local_file_creation_date: "2024-01-17"
 
-local_file_creation_date: "2020-05-20"
+dataset_release_date: "2024-01-22"
 
-publication_doi: 10.1016/B978-1-63067-038-2.00008-3
+publication_doi: 10.1038/s41588-019-0405-z
 
-dataset_release_date: "2022-12-01"
+publication_title: "The genome sequence of segmental allotetraploid peanut Arachis hypogaea"
 
-contributors: Clevenger,J., Cannon,S.B., Youngblood, C., Vaughn,J.N., Abernathy, B, Bertioli,D.J., Scheffler, B.
+contributors: The International Peanut Genome Initiative; lead assembly group Jeremy Schmutz, Jerry Jenkins, Jane Grimwood; project leads David Bertioli; Soraya Bertioli; Brian Schleffler; Scott Jackson; Peggy Ozias-Akins
 
-data_curators: Steven Cannon
+citation: "Bertioli, D.J., Jenkins, J., Clevenger, J. et al. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nat Genet 51, 877-884 (2019). https://doi.org/10.1038/s41588-019-0405-z"
 
-public_access_level: public, with usage restriction
+data_curators: Steven Cannon, Andrew Farmer
+
+public_access_level: public
 
 license: open
 
-keywords: Arachis stenosperma
+keywords: wild peanut, Arachis stenosperma
+

Cajanus/GENUS/about_this_collection/description_Cajanus.yml

@@ -15,5 +15,5 @@ resources:
     URL: "https://gcv.legumeinfo.org/gene;lis=cajca.C.cajan_19480?q=C.cajan_19480&sources=lis&algorithm=repeat&match=10&mismatch=-1&gap=-1&score=30&threshold=25&bmatched=20&bintermediate=10&bmask=10&linkage=average&cthreshold=20&neighbors=10&matched=4&intermediate=5&bregexp=&border=chromosome&regexp=&order=distance"
     description: "Browser for dynamically discovering and viewing genomic synteny across selected species."
   - name: Germplasm GIS  
-    URL: "https://legacy.legumeinfo.org/germplasm/map#?zoom=6&maxRecs=200&taxonQuery=Cajanus&traitScale=global&geocodedOnly=false&traitExcludeUnchar=false&limitToMapExtent=false&lat=35.87&lng=-109.47&mapHeight=188.25&baseMap=ESRI%20-%20NatGeo%20(default,%20reference%20map)&ne_lat=37.52715361723378&ne_lng=-93.97705078125001&sw_lat=34.17999758688084&sw_lng=-124.95849609375001&accessionIdsInclusive=false"
+    URL: "https://germplasm-map.legumeinfo.org/#?zoom=6&maxRecs=200&taxonQuery=Cajanus&traitScale=global&geocodedOnly=false&traitExcludeUnchar=false&limitToMapExtent=false&lat=35.87&lng=-109.47&mapHeight=188.25&baseMap=ESRI%20-%20NatGeo%20(default,%20reference%20map)&ne_lat=37.52715361723378&ne_lng=-93.97705078125001&sw_lat=34.17999758688084&sw_lng=-124.95849609375001&accessionIdsInclusive=false"
     description: "Geographic information system viewer, showing collection locations for Cajanus data held by the U.S. National Plant Germplasm System."