diff --git a/.github/workflows/check-database-urls.yml b/.github/workflows/check-database-urls.yml
index 17b59f6..ce03aea 100644
--- a/.github/workflows/check-database-urls.yml
+++ b/.github/workflows/check-database-urls.yml
@@ -7,7 +7,8 @@ on:
   workflow_dispatch:  # Allow manual triggering
   push:
     paths:
-      - 'funannotate2/downloads.json'  # Run when downloads.json is updated
+      - 'funannotate2/downloads.json'
+      - 'funannotate2/downloads_v2.json'
 
 jobs:
   check-urls:
diff --git a/CITATION.cff b/CITATION.cff
index 6fb3755..6aa362e 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -18,4 +18,4 @@ keywords:
   - consensus gene models
 license: BSD-2-Clause
 version: 26.6.9
-date-released: '2026-06-10'
+date-released: '2026-06-20'
diff --git a/funannotate2/config.py b/funannotate2/config.py
index 6587a09..66e9a2d 100755
--- a/funannotate2/config.py
+++ b/funannotate2/config.py
@@ -1036,6 +1036,12 @@
         "superkingdom": "Eukaryota",
         "kingdom": "Chromista",
     },
+    "amphibia": {
+        "superkingdom": "Eukaryota",
+        "kingdom": "Metazoa",
+        "phylum": "Chordata",
+        "class": "Amphibia",
+    },
     "apicomplexa": {
         "superkingdom": "Eukaryota",
         "kingdom": "Chromista",
@@ -1096,6 +1102,20 @@
         "class": "Mammalia",
         "order": "Artiodactyla",
     },
+    "cercopithecoidea": {
+        "superkingdom": "Eukaryota",
+        "kingdom": "Metazoa",
+        "phylum": "Chordata",
+        "class": "Mammalia",
+        "order": "Primates",
+    },
+    "cetacea": {
+        "superkingdom": "Eukaryota",
+        "kingdom": "Metazoa",
+        "phylum": "Chordata",
+        "class": "Mammalia",
+        "order": "Artiodactyla",
+    },
     "chaetothyriales": {
         "superkingdom": "Eukaryota",
         "kingdom": "Fungi",
diff --git a/funannotate2/downloads_v2.json b/funannotate2/downloads_v2.json
new file mode 100755
index 0000000..b52321d
--- /dev/null
+++ b/funannotate2/downloads_v2.json
@@ -0,0 +1,551 @@
+{
+  "downloads": {
+    "uniprot": "https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz",
+    "uniprot-release": "https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/reldate.txt",
+    "merops": "https://ftp.ebi.ac.uk/pub/databases/merops/current_release/meropsscan.lib",
+    "dbCAN": "https://pro.unl.edu/dbCAN2/download/Databases/V14/dbCAN-HMMdb-V14.txt",
+    "dbCAN-tsv": "https://pro.unl.edu/dbCAN2/download/Databases/V12/CAZyDB.08062022.fam-activities.txt",
+    "dbCAN-log": "https://pro.unl.edu/dbCAN2/download/Databases/V11/readme.txt",
+    "pfam": "https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz",
+    "pfam-tsv": "https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.clans.tsv.gz",
+    "pfam-log": "https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam.version.gz",
+    "repeats": "https://osf.io/vp87c/download?version=1",
+    "go": "https://purl.obolibrary.org/obo/go.obo",
+    "mibig": "https://dl.secondarymetabolites.org/mibig/mibig_prot_seqs_3.1.fasta",
+    "interpro": "https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/interpro.xml.gz",
+    "interpro-tsv": "https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list",
+    "gene2product": "https://raw.githubusercontent.com/nextgenusfs/gene2product/master/ncbi_cleaned_gene_products.txt",
+    "mito": "https://ftp.ncbi.nlm.nih.gov/refseq/release/mitochondrion/mitochondrion.1.1.genomic.fna.gz",
+    "mito-release": "https://ftp.ncbi.nlm.nih.gov/refseq/release/RELEASE_NUMBER"
+  },
+  "busco": {
+    "aconoidasida": [
+      "https://busco-data.ezlab.org/v6/data/lineages/aconoidasida_odb12.2.2026-05-13.tar.gz",
+      "aconoidasida_odb12.2"
+    ],
+    "actinopterygii": [
+      "https://busco-data.ezlab.org/v6/data/lineages/actinopterygii_odb12.2.2026-05-13.tar.gz",
+      "actinopterygii_odb12.2"
+    ],
+    "agaricales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/agaricales_odb12.2.2026-05-13.tar.gz",
+      "agaricales_odb12.2"
+    ],
+    "agaricomycetes": [
+      "https://busco-data.ezlab.org/v6/data/lineages/agaricomycetes_odb12.2.2026-05-13.tar.gz",
+      "agaricomycetes_odb12.2"
+    ],
+    "alveolata": [
+      "https://busco-data.ezlab.org/v6/data/lineages/alveolata_odb12.2.2026-05-13.tar.gz",
+      "alveolata_odb12.2"
+    ],
+    "apicomplexa": [
+      "https://busco-data.ezlab.org/v6/data/lineages/apicomplexa_odb12.2.2026-05-13.tar.gz",
+      "apicomplexa_odb12.2"
+    ],
+    "arachnida": [
+      "https://busco-data.ezlab.org/v6/data/lineages/arachnida_odb12.2.2026-05-13.tar.gz",
+      "arachnida_odb12.2"
+    ],
+    "arthropoda": [
+      "https://busco-data.ezlab.org/v6/data/lineages/arthropoda_odb12.2.2026-05-13.tar.gz",
+      "arthropoda_odb12.2"
+    ],
+    "ascomycota": [
+      "https://busco-data.ezlab.org/v6/data/lineages/ascomycota_odb12.2.2026-05-13.tar.gz",
+      "ascomycota_odb12.2"
+    ],
+    "aves": [
+      "https://busco-data.ezlab.org/v6/data/lineages/aves_odb12.2.2026-05-13.tar.gz",
+      "aves_odb12.2"
+    ],
+    "basidiomycota": [
+      "https://busco-data.ezlab.org/v6/data/lineages/basidiomycota_odb12.2.2026-05-13.tar.gz",
+      "basidiomycota_odb12.2"
+    ],
+    "boletales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/boletales_odb12.2.2026-05-13.tar.gz",
+      "boletales_odb12.2"
+    ],
+    "brassicales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/brassicales_odb12.2.2026-05-13.tar.gz",
+      "brassicales_odb12.2"
+    ],
+    "carnivora": [
+      "https://busco-data.ezlab.org/v6/data/lineages/carnivora_odb12.2.2026-05-13.tar.gz",
+      "carnivora_odb12.2"
+    ],
+    "cetartiodactyla": [
+      "https://busco-data.ezlab.org/v6/data/lineages/artiodactyla_odb12.2.2026-05-13.tar.gz",
+      "artiodactyla_odb12.2"
+    ],
+    "chaetothyriales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/chaetothyriales_odb12.2.2026-05-13.tar.gz",
+      "chaetothyriales_odb12.2"
+    ],
+    "chlorophyta": [
+      "https://busco-data.ezlab.org/v6/data/lineages/chlorophyta_odb12.2.2026-05-13.tar.gz",
+      "chlorophyta_odb12.2"
+    ],
+    "coccidia": [
+      "https://busco-data.ezlab.org/v6/data/lineages/coccidia_odb12.2.2026-05-13.tar.gz",
+      "coccidia_odb12.2"
+    ],
+    "cyprinodontiformes": [
+      "https://busco-data.ezlab.org/v6/data/lineages/cyprinodontiformes_odb12.2.2026-05-13.tar.gz",
+      "cyprinodontiformes_odb12.2"
+    ],
+    "diptera": [
+      "https://busco-data.ezlab.org/v6/data/lineages/diptera_odb12.2.2026-05-13.tar.gz",
+      "diptera_odb12.2"
+    ],
+    "dothideomycetes": [
+      "https://busco-data.ezlab.org/v6/data/lineages/dothideomycetes_odb12.2.2026-05-13.tar.gz",
+      "dothideomycetes_odb12.2"
+    ],
+    "embryophyta": [
+      "https://busco-data.ezlab.org/v6/data/lineages/embryophyta_odb12.2.2026-05-13.tar.gz",
+      "embryophyta_odb12.2"
+    ],
+    "endopterygota": [
+      "https://busco-data.ezlab.org/v6/data/lineages/endopterygota_odb12.2.2026-05-13.tar.gz",
+      "endopterygota_odb12.2"
+    ],
+    "euarchontoglires": [
+      "https://busco-data.ezlab.org/v6/data/lineages/euarchontoglires_odb12.2.2026-05-13.tar.gz",
+      "euarchontoglires_odb12.2"
+    ],
+    "eudicots": [
+      "https://busco-data.ezlab.org/v6/data/lineages/eudicotyledons_odb12.2.2026-05-13.tar.gz",
+      "eudicotyledons_odb12.2"
+    ],
+    "euglenozoa": [
+      "https://busco-data.ezlab.org/v6/data/lineages/euglenozoa_odb12.2.2026-05-13.tar.gz",
+      "euglenozoa_odb12.2"
+    ],
+    "eukaryota": [
+      "https://busco-data.ezlab.org/v6/data/lineages/eukaryota_odb12.2.2026-05-13.tar.gz",
+      "eukaryota_odb12.2"
+    ],
+    "eurotiales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/eurotiales_odb12.2.2026-05-13.tar.gz",
+      "eurotiales_odb12.2"
+    ],
+    "eurotiomycetes": [
+      "https://busco-data.ezlab.org/v6/data/lineages/eurotiomycetes_odb12.2.2026-05-13.tar.gz",
+      "eurotiomycetes_odb12.2"
+    ],
+    "eutheria": [
+      "https://busco-data.ezlab.org/v6/data/lineages/eutheria_odb12.2.2026-05-13.tar.gz",
+      "eutheria_odb12.2"
+    ],
+    "fabales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/fabales_odb12.2.2026-05-13.tar.gz",
+      "fabales_odb12.2"
+    ],
+    "fungi": [
+      "https://busco-data.ezlab.org/v6/data/lineages/fungi_odb12.2.2026-05-13.tar.gz",
+      "fungi_odb12.2"
+    ],
+    "glires": [
+      "https://busco-data.ezlab.org/v6/data/lineages/glires_odb12.2.2026-05-13.tar.gz",
+      "glires_odb12.2"
+    ],
+    "glomerellales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/glomerellales_odb12.2.2026-05-13.tar.gz",
+      "glomerellales_odb12.2"
+    ],
+    "helotiales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/helotiales_odb12.2.2026-05-13.tar.gz",
+      "helotiales_odb12.2"
+    ],
+    "hemiptera": [
+      "https://busco-data.ezlab.org/v6/data/lineages/hemiptera_odb12.2.2026-05-13.tar.gz",
+      "hemiptera_odb12.2"
+    ],
+    "hymenoptera": [
+      "https://busco-data.ezlab.org/v6/data/lineages/hymenoptera_odb12.2.2026-05-13.tar.gz",
+      "hymenoptera_odb12.2"
+    ],
+    "hypocreales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/hypocreales_odb12.2.2026-05-13.tar.gz",
+      "hypocreales_odb12.2"
+    ],
+    "insecta": [
+      "https://busco-data.ezlab.org/v6/data/lineages/insecta_odb12.2.2026-05-13.tar.gz",
+      "insecta_odb12.2"
+    ],
+    "laurasiatheria": [
+      "https://busco-data.ezlab.org/v6/data/lineages/laurasiatheria_odb12.2.2026-05-13.tar.gz",
+      "laurasiatheria_odb12.2"
+    ],
+    "leotiomycetes": [
+      "https://busco-data.ezlab.org/v6/data/lineages/leotiomycetes_odb12.2.2026-05-13.tar.gz",
+      "leotiomycetes_odb12.2"
+    ],
+    "lepidoptera": [
+      "https://busco-data.ezlab.org/v6/data/lineages/lepidoptera_odb12.2.2026-05-13.tar.gz",
+      "lepidoptera_odb12.2"
+    ],
+    "liliopsida": [
+      "https://busco-data.ezlab.org/v6/data/lineages/liliopsida_odb12.2.2026-05-13.tar.gz",
+      "liliopsida_odb12.2"
+    ],
+    "mammalia": [
+      "https://busco-data.ezlab.org/v6/data/lineages/mammalia_odb12.2.2026-05-13.tar.gz",
+      "mammalia_odb12.2"
+    ],
+    "metazoa": [
+      "https://busco-data.ezlab.org/v6/data/lineages/metazoa_odb12.2.2026-05-13.tar.gz",
+      "metazoa_odb12.2"
+    ],
+    "microsporidia": [
+      "https://busco-data.ezlab.org/v6/data/lineages/microsporidia_odb12.2.2026-05-13.tar.gz",
+      "microsporidia_odb12.2"
+    ],
+    "mollusca": [
+      "https://busco-data.ezlab.org/v6/data/lineages/mollusca_odb12.2.2026-05-13.tar.gz",
+      "mollusca_odb12.2"
+    ],
+    "mucorales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/mucorales_odb12.2.2026-05-13.tar.gz",
+      "mucorales_odb12.2"
+    ],
+    "mucoromycota": [
+      "https://busco-data.ezlab.org/v6/data/lineages/mucoromycota_odb12.2.2026-05-13.tar.gz",
+      "mucoromycota_odb12.2"
+    ],
+    "nematoda": [
+      "https://busco-data.ezlab.org/v6/data/lineages/nematoda_odb12.2.2026-05-13.tar.gz",
+      "nematoda_odb12.2"
+    ],
+    "onygenales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/onygenales_odb12.2.2026-05-13.tar.gz",
+      "onygenales_odb12.2"
+    ],
+    "passeriformes": [
+      "https://busco-data.ezlab.org/v6/data/lineages/passeriformes_odb12.2.2026-05-13.tar.gz",
+      "passeriformes_odb12.2"
+    ],
+    "plasmodium": [
+      "https://busco-data.ezlab.org/v6/data/lineages/plasmodium_odb12.2.2026-05-13.tar.gz",
+      "plasmodium_odb12.2"
+    ],
+    "pleosporales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/pleosporales_odb12.2.2026-05-13.tar.gz",
+      "pleosporales_odb12.2"
+    ],
+    "poales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/poales_odb12.2.2026-05-13.tar.gz",
+      "poales_odb12.2"
+    ],
+    "polyporales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/polyporales_odb12.2.2026-05-13.tar.gz",
+      "polyporales_odb12.2"
+    ],
+    "primates": [
+      "https://busco-data.ezlab.org/v6/data/lineages/primates_odb12.2.2026-05-13.tar.gz",
+      "primates_odb12.2"
+    ],
+    "saccharomycetes": [
+      "https://busco-data.ezlab.org/v6/data/lineages/saccharomycetes_odb12.2.2026-05-13.tar.gz",
+      "saccharomycetes_odb12.2"
+    ],
+    "sauropsida": [
+      "https://busco-data.ezlab.org/v6/data/lineages/sauropsida_odb12.2.2026-05-13.tar.gz",
+      "sauropsida_odb12.2"
+    ],
+    "solanales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/solanales_odb12.2.2026-05-13.tar.gz",
+      "solanales_odb12.2"
+    ],
+    "sordariomycetes": [
+      "https://busco-data.ezlab.org/v6/data/lineages/sordariomycetes_odb12.2.2026-05-13.tar.gz",
+      "sordariomycetes_odb12.2"
+    ],
+    "stramenopiles": [
+      "https://busco-data.ezlab.org/v6/data/lineages/stramenopiles_odb12.2.2026-05-13.tar.gz",
+      "stramenopiles_odb12.2"
+    ],
+    "tetrapoda": [
+      "https://busco-data.ezlab.org/v6/data/lineages/tetrapoda_odb12.2.2026-05-13.tar.gz",
+      "tetrapoda_odb12.2"
+    ],
+    "tremellomycetes": [
+      "https://busco-data.ezlab.org/v6/data/lineages/tremellomycetes_odb12.2.2026-05-13.tar.gz",
+      "tremellomycetes_odb12.2"
+    ],
+    "vertebrata": [
+      "https://busco-data.ezlab.org/v6/data/lineages/vertebrata_odb12.2.2026-05-13.tar.gz",
+      "vertebrata_odb12.2"
+    ],
+    "viridiplantae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/viridiplantae_odb12.2.2026-05-13.tar.gz",
+      "viridiplantae_odb12.2"
+    ],
+    "amoebozoa": [
+      "https://busco-data.ezlab.org/v6/data/lineages/amoebozoa_odb12.2.2026-05-13.tar.gz",
+      "amoebozoa_odb12.2"
+    ],
+    "bacillariophyta": [
+      "https://busco-data.ezlab.org/v6/data/lineages/bacillariophyta_odb12.2.2026-05-13.tar.gz",
+      "bacillariophyta_odb12.2"
+    ],
+    "chytridiomycota": [
+      "https://busco-data.ezlab.org/v6/data/lineages/chytridiomycota_odb12.2.2026-05-13.tar.gz",
+      "chytridiomycota_odb12.2"
+    ],
+    "ciliophora": [
+      "https://busco-data.ezlab.org/v6/data/lineages/ciliophora_odb12.2.2026-05-13.tar.gz",
+      "ciliophora_odb12.2"
+    ],
+    "cnidaria": [
+      "https://busco-data.ezlab.org/v6/data/lineages/cnidaria_odb12.2.2026-05-13.tar.gz",
+      "cnidaria_odb12.2"
+    ],
+    "crustacea": [
+      "https://busco-data.ezlab.org/v6/data/lineages/crustacea_odb12.2.2026-05-13.tar.gz",
+      "crustacea_odb12.2"
+    ],
+    "oomycota": [
+      "https://busco-data.ezlab.org/v6/data/lineages/oomycota_odb12.2.2026-05-13.tar.gz",
+      "oomycota_odb12.2"
+    ],
+    "rhodophyta": [
+      "https://busco-data.ezlab.org/v6/data/lineages/rhodophyta_odb12.2.2026-05-13.tar.gz",
+      "rhodophyta_odb12.2"
+    ],
+    "aspergillus": [
+      "https://busco-data.ezlab.org/v6/data/lineages/aspergillus_odb12.2.2026-05-13.tar.gz",
+      "aspergillus_odb12.2"
+    ],
+    "penicillium": [
+      "https://busco-data.ezlab.org/v6/data/lineages/penicillium_odb12.2.2026-05-13.tar.gz",
+      "penicillium_odb12.2"
+    ],
+    "cryptosporidium": [
+      "https://busco-data.ezlab.org/v6/data/lineages/cryptosporidium_odb12.2.2026-05-13.tar.gz",
+      "cryptosporidium_odb12.2"
+    ],
+    "trypanosoma": [
+      "https://busco-data.ezlab.org/v6/data/lineages/trypanosoma_odb12.2.2026-05-13.tar.gz",
+      "trypanosoma_odb12.2"
+    ],
+    "phytophthora": [
+      "https://busco-data.ezlab.org/v6/data/lineages/phytophthora_odb12.2.2026-05-13.tar.gz",
+      "phytophthora_odb12.2"
+    ],
+    "drosophila": [
+      "https://busco-data.ezlab.org/v6/data/lineages/drosophila_odb12.2.2026-05-13.tar.gz",
+      "drosophila_odb12.2"
+    ],
+    "drosophilidae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/drosophilidae_odb12.2.2026-05-13.tar.gz",
+      "drosophilidae_odb12.2"
+    ],
+    "anopheles": [
+      "https://busco-data.ezlab.org/v6/data/lineages/anopheles_odb12.2.2026-05-13.tar.gz",
+      "anopheles_odb12.2"
+    ],
+    "culicidae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/culicidae_odb12.2.2026-05-13.tar.gz",
+      "culicidae_odb12.2"
+    ],
+    "coleoptera": [
+      "https://busco-data.ezlab.org/v6/data/lineages/coleoptera_odb12.2.2026-05-13.tar.gz",
+      "coleoptera_odb12.2"
+    ],
+    "artiodactyla": [
+      "https://busco-data.ezlab.org/v6/data/lineages/artiodactyla_odb12.2.2026-05-13.tar.gz",
+      "artiodactyla_odb12.2"
+    ],
+    "rodentia": [
+      "https://busco-data.ezlab.org/v6/data/lineages/rodentia_odb12.2.2026-05-13.tar.gz",
+      "rodentia_odb12.2"
+    ],
+    "squamata": [
+      "https://busco-data.ezlab.org/v6/data/lineages/squamata_odb12.2.2026-05-13.tar.gz",
+      "squamata_odb12.2"
+    ],
+    "galloanserae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/galloanserae_odb12.2.2026-05-13.tar.gz",
+      "galloanserae_odb12.2"
+    ],
+    "anthozoa": [
+      "https://busco-data.ezlab.org/v6/data/lineages/anthozoa_odb12.2.2026-05-13.tar.gz",
+      "anthozoa_odb12.2"
+    ],
+    "chromadorea": [
+      "https://busco-data.ezlab.org/v6/data/lineages/chromadorea_odb12.2.2026-05-13.tar.gz",
+      "chromadorea_odb12.2"
+    ],
+    "acari": [
+      "https://busco-data.ezlab.org/v6/data/lineages/acari_odb12.2.2026-05-13.tar.gz",
+      "acari_odb12.2"
+    ],
+    "araneae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/araneae_odb12.2.2026-05-13.tar.gz",
+      "araneae_odb12.2"
+    ],
+    "hexapoda": [
+      "https://busco-data.ezlab.org/v6/data/lineages/hexapoda_odb12.2.2026-05-13.tar.gz",
+      "hexapoda_odb12.2"
+    ],
+    "lophotrochozoa": [
+      "https://busco-data.ezlab.org/v6/data/lineages/lophotrochozoa_odb12.2.2026-05-13.tar.gz",
+      "lophotrochozoa_odb12.2"
+    ],
+    "piroplasmida": [
+      "https://busco-data.ezlab.org/v6/data/lineages/piroplasmida_odb12.2.2026-05-13.tar.gz",
+      "piroplasmida_odb12.2"
+    ],
+    "leishmaniinae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/leishmaniinae_odb12.2.2026-05-13.tar.gz",
+      "leishmaniinae_odb12.2"
+    ],
+    "eudicotyledons": [
+      "https://busco-data.ezlab.org/v6/data/lineages/eudicotyledons_odb12.2.2026-05-13.tar.gz",
+      "eudicotyledons_odb12.2"
+    ],
+    "rosaceae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/rosaceae_odb12.2.2026-05-13.tar.gz",
+      "rosaceae_odb12.2"
+    ],
+    "rosales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/rosales_odb12.2.2026-05-13.tar.gz",
+      "rosales_odb12.2"
+    ],
+    "malpighiales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/malpighiales_odb12.2.2026-05-13.tar.gz",
+      "malpighiales_odb12.2"
+    ],
+    "lamiales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/lamiales_odb12.2.2026-05-13.tar.gz",
+      "lamiales_odb12.2"
+    ],
+    "chlorophyceae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/chlorophyceae_odb12.2.2026-05-13.tar.gz",
+      "chlorophyceae_odb12.2"
+    ],
+    "trebouxiophyceae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/trebouxiophyceae_odb12.2.2026-05-13.tar.gz",
+      "trebouxiophyceae_odb12.2"
+    ],
+    "saprolegniaceae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/saprolegniaceae_odb12.2.2026-05-13.tar.gz",
+      "saprolegniaceae_odb12.2"
+    ],
+    "debaryomycetaceae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/debaryomycetaceae_odb12.2.2026-05-13.tar.gz",
+      "debaryomycetaceae_odb12.2"
+    ],
+    "pichiaceae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/pichiaceae_odb12.2.2026-05-13.tar.gz",
+      "pichiaceae_odb12.2"
+    ],
+    "saccharomycetaceae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/saccharomycetaceae_odb12.2.2026-05-13.tar.gz",
+      "saccharomycetaceae_odb12.2"
+    ],
+    "nectriaceae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/nectriaceae_odb12.2.2026-05-13.tar.gz",
+      "nectriaceae_odb12.2"
+    ],
+    "clavicipitaceae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/clavicipitaceae_odb12.2.2026-05-13.tar.gz",
+      "clavicipitaceae_odb12.2"
+    ],
+    "cordycipitaceae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/cordycipitaceae_odb12.2.2026-05-13.tar.gz",
+      "cordycipitaceae_odb12.2"
+    ],
+    "ophiocordycipitaceae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/ophiocordycipitaceae_odb12.2.2026-05-13.tar.gz",
+      "ophiocordycipitaceae_odb12.2"
+    ],
+    "hypocreaceae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/hypocreaceae_odb12.2.2026-05-13.tar.gz",
+      "hypocreaceae_odb12.2"
+    ],
+    "mycosphaerellaceae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/mycosphaerellaceae_odb12.2.2026-05-13.tar.gz",
+      "mycosphaerellaceae_odb12.2"
+    ],
+    "pleosporaceae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/pleosporaceae_odb12.2.2026-05-13.tar.gz",
+      "pleosporaceae_odb12.2"
+    ],
+    "ajellomycetaceae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/ajellomycetaceae_odb12.2.2026-05-13.tar.gz",
+      "ajellomycetaceae_odb12.2"
+    ],
+    "pseudeurotiaceae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/pseudeurotiaceae_odb12.2.2026-05-13.tar.gz",
+      "pseudeurotiaceae_odb12.2"
+    ],
+    "polyporaceae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/polyporaceae_odb12.2.2026-05-13.tar.gz",
+      "polyporaceae_odb12.2"
+    ],
+    "sordariales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/sordariales_odb12.2.2026-05-13.tar.gz",
+      "sordariales_odb12.2"
+    ],
+    "xylariales": [
+      "https://busco-data.ezlab.org/v6/data/lineages/xylariales_odb12.2.2026-05-13.tar.gz",
+      "xylariales_odb12.2"
+    ],
+    "pucciniomycetes": [
+      "https://busco-data.ezlab.org/v6/data/lineages/pucciniomycetes_odb12.2.2026-05-13.tar.gz",
+      "pucciniomycetes_odb12.2"
+    ],
+    "ustilaginomycetes": [
+      "https://busco-data.ezlab.org/v6/data/lineages/ustilaginomycetes_odb12.2.2026-05-13.tar.gz",
+      "ustilaginomycetes_odb12.2"
+    ],
+    "microbotryomycetes": [
+      "https://busco-data.ezlab.org/v6/data/lineages/microbotryomycetes_odb12.2.2026-05-13.tar.gz",
+      "microbotryomycetes_odb12.2"
+    ],
+    "aculeata": [
+      "https://busco-data.ezlab.org/v6/data/lineages/aculeata_odb12.2.2026-05-13.tar.gz",
+      "aculeata_odb12.2"
+    ],
+    "apoidea": [
+      "https://busco-data.ezlab.org/v6/data/lineages/apoidea_odb12.2.2026-05-13.tar.gz",
+      "apoidea_odb12.2"
+    ],
+    "formicidae": [
+      "https://busco-data.ezlab.org/v6/data/lineages/formicidae_odb12.2.2026-05-13.tar.gz",
+      "formicidae_odb12.2"
+    ],
+    "papilionoidea": [
+      "https://busco-data.ezlab.org/v6/data/lineages/papilionoidea_odb12.2.2026-05-13.tar.gz",
+      "papilionoidea_odb12.2"
+    ],
+    "brachycera": [
+      "https://busco-data.ezlab.org/v6/data/lineages/brachycera_odb12.2.2026-05-13.tar.gz",
+      "brachycera_odb12.2"
+    ],
+    "nematocera": [
+      "https://busco-data.ezlab.org/v6/data/lineages/nematocera_odb12.2.2026-05-13.tar.gz",
+      "nematocera_odb12.2"
+    ],
+    "polyphaga": [
+      "https://busco-data.ezlab.org/v6/data/lineages/polyphaga_odb12.2.2026-05-13.tar.gz",
+      "polyphaga_odb12.2"
+    ],
+    "amphibia": [
+      "https://busco-data.ezlab.org/v6/data/lineages/amphibia_odb12.2.2026-05-13.tar.gz",
+      "amphibia_odb12.2"
+    ],
+    "cercopithecoidea": [
+      "https://busco-data.ezlab.org/v6/data/lineages/cercopithecoidea_odb12.2.2026-05-13.tar.gz",
+      "cercopithecoidea_odb12.2"
+    ],
+    "cetacea": [
+      "https://busco-data.ezlab.org/v6/data/lineages/cetacea_odb12.2.2026-05-13.tar.gz",
+      "cetacea_odb12.2"
+    ]
+  }
+}
\ No newline at end of file
diff --git a/funannotate2/install.py b/funannotate2/install.py
index c597bb5..06f8939 100644
--- a/funannotate2/install.py
+++ b/funannotate2/install.py
@@ -111,12 +111,12 @@ def install(args):
         logger.info("Retrieving download links from GitHub Repo")
         DBURL = json.loads(
             requests.get(
-                "https://raw.githubusercontent.com/nextgenusfs/funannotate2/master/funannotate2/downloads.json"
+                "https://raw.githubusercontent.com/nextgenusfs/funannotate2/master/funannotate2/downloads_v2.json"
             ).text
         )["downloads"]
     except:  # noqa: E722
         logger.error("Unable to download links from GitHub, using local copy from funannotate2")
-        DBURL = load_json(os.path.join(os.path.dirname(__file__), "downloads.json"))["downloads"]
+        DBURL = load_json(os.path.join(os.path.dirname(__file__), "downloads_v2.json"))["downloads"]
     logger.info(json.dumps(DBURL, indent=2))
 
     # let user know what you are doing
diff --git a/funannotate2/utilities.py b/funannotate2/utilities.py
index abbb781..4b15f0c 100755
--- a/funannotate2/utilities.py
+++ b/funannotate2/utilities.py
@@ -177,7 +177,7 @@ def ensure_busco_lineage(species, logger):
     - SystemExit(1): If the directory could not be made present after the
       download/extract attempt.
     """
-    downloads_json = os.path.join(os.path.dirname(__file__), "downloads.json")
+    downloads_json = os.path.join(os.path.dirname(__file__), "downloads_v2.json")
     odb_version = get_odb_version(downloads_json)
     busco_model_path = os.path.join(
         env["FUNANNOTATE2_DB"], f"{species}_{odb_version}"
diff --git a/pixi.lock b/pixi.lock
index 1d9bf91..4bb17ad 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -169,9 +169,8 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
       - pypi: https://files.pythonhosted.org/packages/2c/2f/51d27f44689aa1ee000bb145811570002d420c7dfa0b153a992c28e0e297/annorefine-2026.2.22-cp311-cp311-manylinux_2_28_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/15/12/7f9edf5a5a547ce0421e8f120c157b3602eabb12147ffea95eefbd55a94e/archspec-0.2.6-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/a7/ac/2d4a5fee4ef34c5631e936a29964a6cbce17bd63809156970100ae855393/buscolite-26.4.22-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/1e/6a/c4578014b6e73f307517fdecc9857140d403fe25a8473798931d003da6d2/buscolite-26.6.21-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/b1/89/2e3f29c41cb86273dcd8f3ec2df5b4e87ae0d554cbb268ae7c3092940cae/funannotate2_addons-26.3.7-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/ea/7e/c24801878ba6d7a1dff6d6928f5aeacd4eec1d6e0a463687594d07c8c18c/gapmm2-26.5.22-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/3d/cb/d0d829646b9ee685898d3c35712a43458af6f80f74e1bc632c1a4178af01/gfftk-26.5.22-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/31/f8/65d52c1383a1832761f80bad6206de6e9e675adb67aaa8673cc709fe84c2/helixerlite-25.5.27-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/7b/91/984aca2ec129e2757d1e4e3c81c3fcda9d0f85b74670a094cc443d9ee949/joblib-1.5.3-py3-none-any.whl
@@ -333,9 +332,8 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.7-hbf9d68e_6.conda
       - pypi: https://files.pythonhosted.org/packages/ad/82/7d12e63dfa9d2db71167c270a1fafa7292ce444fb0398afbcfaa57482c01/annorefine-2026.2.22-cp311-cp311-macosx_11_0_arm64.whl
       - pypi: https://files.pythonhosted.org/packages/15/12/7f9edf5a5a547ce0421e8f120c157b3602eabb12147ffea95eefbd55a94e/archspec-0.2.6-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/a7/ac/2d4a5fee4ef34c5631e936a29964a6cbce17bd63809156970100ae855393/buscolite-26.4.22-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/1e/6a/c4578014b6e73f307517fdecc9857140d403fe25a8473798931d003da6d2/buscolite-26.6.21-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/b1/89/2e3f29c41cb86273dcd8f3ec2df5b4e87ae0d554cbb268ae7c3092940cae/funannotate2_addons-26.3.7-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/ea/7e/c24801878ba6d7a1dff6d6928f5aeacd4eec1d6e0a463687594d07c8c18c/gapmm2-26.5.22-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/3d/cb/d0d829646b9ee685898d3c35712a43458af6f80f74e1bc632c1a4178af01/gfftk-26.5.22-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/51/02/79a58cfc45dd2fdc4747fbdb63304920faa095e456391e182972993ab075/helixerlite-25.5.27-cp311-cp311-macosx_11_0_arm64.whl
       - pypi: https://files.pythonhosted.org/packages/7b/91/984aca2ec129e2757d1e4e3c81c3fcda9d0f85b74670a094cc443d9ee949/joblib-1.5.3-py3-none-any.whl
@@ -810,10 +808,10 @@ packages:
   - pkg:pypi/brotli?source=hash-mapping
   size: 359588
   timestamp: 1764018467340
-- pypi: https://files.pythonhosted.org/packages/a7/ac/2d4a5fee4ef34c5631e936a29964a6cbce17bd63809156970100ae855393/buscolite-26.4.22-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/1e/6a/c4578014b6e73f307517fdecc9857140d403fe25a8473798931d003da6d2/buscolite-26.6.21-py3-none-any.whl
   name: buscolite
-  version: 26.4.22
-  sha256: c8c1cca1ea05ba5c28a71e349de7e1f8546f895ea209be9b5e80c8a4cb871707
+  version: 26.6.21
+  sha256: b878d94b05ef26d90e5dd62098599769361096d74019e6a3d744e4ebf1df5019
   requires_dist:
   - natsort
   - packaging
@@ -1101,13 +1099,13 @@ packages:
 - pypi: ./
   name: funannotate2
   version: 26.6.9
-  sha256: cfd6919273c0adc5b559e250385e7955f4941aa92c1f33d466664519cc774005
+  sha256: 5f4ab893b264f7f8fd3cfde73ae52cff0cfbab49f2bec1f8e3c78dcc6ff6ef33
   requires_dist:
   - natsort
   - numpy
   - mappy
   - gfftk>=26.5.22
-  - buscolite>=26.4.22
+  - buscolite>=26.6.21
   - gapmm2>=26.5.22
   - pyhmmer>=0.12.0
   - pyfastx>=2.0.0
@@ -1132,14 +1130,6 @@ packages:
   - pytest-cov>=4.0.0 ; extra == 'dev'
   - pytest>=7.0.0 ; extra == 'dev'
   requires_python: '>=3.7.0'
-- pypi: https://files.pythonhosted.org/packages/ea/7e/c24801878ba6d7a1dff6d6928f5aeacd4eec1d6e0a463687594d07c8c18c/gapmm2-26.5.22-py3-none-any.whl
-  name: gapmm2
-  version: 26.5.22
-  sha256: e2d60596c9b1a5a6c74caa853b99d0a5fcdcbf2a0a66b50cdafbcc395b975a6d
-  requires_dist:
-  - edlib
-  - mappy
-  requires_python: '>=3.10'
 - conda: https://conda.anaconda.org/bioconda/noarch/gapmm2-26.5.22-pyhdfd78af_0.conda
   sha256: d3d4745e45157befc6ed9d7263c53356937d70450de9f16e0072ac2a29634033
   md5: 93373ff3567d14a0819df231df0da7f7
@@ -1150,6 +1140,8 @@ packages:
   - python-edlib
   license: BSD-2-Clause
   license_family: BSD
+  purls:
+  - pkg:pypi/gapmm2?source=hash-mapping
   size: 24769
   timestamp: 1779521119590
 - conda: https://conda.anaconda.org/conda-forge/noarch/gast-0.7.0-pyhd8ed1ab_0.conda
diff --git a/pixi.toml b/pixi.toml
index 0d09f1d..d9a6941 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -67,7 +67,7 @@ funannotate2 = { path = ".", editable = false }
 helixerlite = "*"
 annorefine = ">=2026.2.9"
 # buscolite via pypi to avoid its bioconda recipe's augustus dependency
-buscolite = ">=26.4.22"
+buscolite = ">=26.6.21"
 # pytantan: built from the nextgenusfs/pytantan fork, which adds a
 # `PYTANTAN_DISABLE_SIMD` CMake option and a `PYTANTAN_SIMD` env-var override.
 # The PyPI wheels ship with AVX2 enabled and SIGILL under Rosetta 2 on Apple
diff --git a/pyproject.toml b/pyproject.toml
index 1c2565a..3f7de5d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,7 +16,7 @@ dependencies = [
     "numpy",
     "mappy",
     "gfftk>=26.5.22",
-    "buscolite>=26.4.22",
+    "buscolite>=26.6.21",
     "gapmm2>=26.5.22",
     "pyhmmer>=0.12.0",
     "pyfastx>=2.0.0",
@@ -49,6 +49,7 @@ funannotate2 = "funannotate2.__main__:main"
 include = [
   "funannotate2/*.py",
   "funannotate2/downloads.json",
+  "funannotate2/downloads_v2.json",
   "funannotate2/resources/*",
   "README.md",
   "LICENSE.md"
diff --git a/tests/README.md b/tests/README.md
index ee934b7..d9dc68a 100644
--- a/tests/README.md
+++ b/tests/README.md
@@ -11,10 +11,10 @@ This directory contains tests for the funannotate2 package.
 
 ### Special Tests
 
-- `unit/test_database_urls.py`: Tests that all database URLs in `funannotate2/downloads.json` are reachable. This test runs:
+- `unit/test_database_urls.py`: Tests that all database URLs in `funannotate2/downloads.json` and `funannotate2/downloads_v2.json` are reachable. This test runs:
   - On every push/PR (as part of the unit test suite)
   - Weekly (Monday at 2 AM UTC) via scheduled GitHub Actions workflow
-  - When `downloads.json` is modified
+  - When either JSON file is modified
 
   The test uses HEAD/GET requests with range headers to check URL availability without downloading large files.
 
diff --git a/tests/unit/test_database_urls.py b/tests/unit/test_database_urls.py
index e699b2d..8a56c11 100644
--- a/tests/unit/test_database_urls.py
+++ b/tests/unit/test_database_urls.py
@@ -12,13 +12,13 @@
 import requests
 
 
-@pytest.fixture(scope="module")
-def database_urls():
-    """Load database URLs from downloads.json."""
+@pytest.fixture(scope="module", params=["downloads.json", "downloads_v2.json"])
+def database_urls(request):
+    """Load database URLs from downloads.json or downloads_v2.json."""
     downloads_json = os.path.join(
         os.path.dirname(os.path.dirname(os.path.dirname(__file__))),
         "funannotate2",
-        "downloads.json",
+        request.param,
     )
     with open(downloads_json, "r") as f:
         data = json.load(f)