diff --git a/data_managers/data_manager_fetch_busco/data_manager/busco_fetcher.xml b/data_managers/data_manager_fetch_busco/data_manager/busco_fetcher.xml
index 272c76f807b..6a2624658de 100644
--- a/data_managers/data_manager_fetch_busco/data_manager/busco_fetcher.xml
+++ b/data_managers/data_manager_fetch_busco/data_manager/busco_fetcher.xml
@@ -1,22 +1,20 @@
-<tool id="busco_fetcher" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="23.1">
+<tool id="busco_fetcher" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="24.1">
     <description>dataset dowloader</description>
         <macros>
-        <token name="@TOOL_VERSION@">5.8.0</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@TOOL_VERSION@">6.0.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        busco --download_path '$out_file.extra_files_path' --download '$lineage' &&
-        ## remove unwanted lineage folders and placement files
-        ## https://gitlab.com/ezlab/busco/-/issues/784
-        if [ -d '$out_file.extra_files_path'/lineages ]; then
-            find '$out_file.extra_files_path'/lineages/ -mindepth 1 -maxdepth 1 ! -name '*_$datasets_version*' -exec rm -rf {} \;;
-        fi &&
-        if [ -d '$out_file.extra_files_path'/placement_files ]; then
-            find '$out_file.extra_files_path'/placement_files/ -mindepth 1 -maxdepth 1 ! -name '*_$datasets_version*' -delete;
-        fi &&
+        busco
+        --download_path '$out_file.extra_files_path'
+        #if $lineage == "virus"
+            --download virus &&
+        #else
+            --download all_'$lineage'$datasets_version &&
+        #end if
         ## unpack faa.gz files ready to use
         ## https://gitlab.com/ezlab/busco/-/issues/789
         if [ -d '$out_file.extra_files_path'/lineages ]; then
@@ -43,9 +41,9 @@
         </configfiles>
     <inputs>
         <param name="lineage" argument="--download" type="select" label="Select the lineage to be downloaded">
-            <option value="all">All</option>
-            <option value="prokaryota">Prokaryota</option>
-            <option value="eukaryota">Eukaryota</option>
+            <option value="">All</option>
+            <option value="prokaryota_">Prokaryota</option>
+            <option value="eukaryota_">Eukaryota</option>
             <option value="virus">Virus</option>
         </param>
         <param argument="--datasets_version" type="select" label="OrthoDB version" help="By March 2025 OrthoDB 12 datasets were only available for Prokaryota (https://busco-data2.ezlab.org/v5/data/)">
@@ -62,7 +60,7 @@
             <output name="out_file">
                 <assert_contents>
                     <has_text text="virus"/>
-                    <has_text text="5.8.0"/>
+                    <has_text text="@TOOL_VERSION@"/>
                 </assert_contents>
             </output>
         </test>
diff --git a/data_managers/data_manager_fetch_busco_options/data_manager/busco_options.xml b/data_managers/data_manager_fetch_busco_options/data_manager/busco_options.xml
index 8a9632065b2..72ae289bae4 100644
--- a/data_managers/data_manager_fetch_busco_options/data_manager/busco_options.xml
+++ b/data_managers/data_manager_fetch_busco_options/data_manager/busco_options.xml
@@ -1,7 +1,7 @@
-<tool id="busco_fetcher_options" name="Busco options" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="23.1">
+<tool id="busco_fetcher_options" name="Busco options" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="24.1">
     <description></description>
         <macros>
-        <token name="@TOOL_VERSION@">5.8.0</token>
+        <token name="@TOOL_VERSION@">6.0.0</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
diff --git a/data_managers/data_manager_fetch_busco_options/test-data/busco_database_options.loc b/data_managers/data_manager_fetch_busco_options/test-data/busco_database_options.loc
index 728d8fb65ef..d3c5223bc67 100644
--- a/data_managers/data_manager_fetch_busco_options/test-data/busco_database_options.loc
+++ b/data_managers/data_manager_fetch_busco_options/test-data/busco_database_options.loc
@@ -79,3 +79,30 @@ bclasvirinae_odb10	Bclasvirinae	test
 simplexvirus_odb10	Simplexvirus	test
 tequatrovirus_odb10	Tequatrovirus	test
 aviadenovirus_odb10	Aviadenovirus	test
+iridoviridae_odb10	Iridoviridae	test
+betabaculovirus_odb10	Betabaculovirus	test
+betaherpesvirinae_odb10	Betaherpesvirinae	test
+skunavirus_odb10	Skunavirus	test
+chordopoxvirinae_odb10	Chordopoxvirinae	test
+alphabaculovirus_odb10	Alphabaculovirus	test
+rudiviridae_odb10	Rudiviridae	test
+tevenvirinae_odb10	Tevenvirinae	test
+tunavirinae_odb10	Tunavirinae	test
+varicellovirus_odb10	Varicellovirus	test
+pahexavirus_odb10	Pahexavirus	test
+guernseyvirinae_odb10	Guernseyvirinae	test
+baculoviridae_odb10	Baculoviridae	test
+alphaherpesvirinae_odb10	Alphaherpesvirinae	test
+spounavirinae_odb10	Spounavirinae	test
+peduovirus_odb10	Peduovirus	test
+enquatrovirus_odb10	Enquatrovirus	test
+teseptimavirus_odb10	Teseptimavirus	test
+gammaherpesvirinae_odb10	Gammaherpesvirinae	test
+herpesviridae_odb10	Herpesviridae	test
+cheoctovirus_odb10	Cheoctovirus	test
+poxviridae_odb10	Poxviridae	test
+fromanvirus_odb10	Fromanvirus	test
+bclasvirinae_odb10	Bclasvirinae	test
+simplexvirus_odb10	Simplexvirus	test
+tequatrovirus_odb10	Tequatrovirus	test
+aviadenovirus_odb10	Aviadenovirus	test
diff --git a/tools/busco/busco.xml b/tools/busco/busco.xml
index 418d38195e9..0366bcd097f 100644
--- a/tools/busco/busco.xml
+++ b/tools/busco/busco.xml
@@ -1,4 +1,4 @@
-<tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+<tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
     <description>Assess genome assembly and annotation completeness</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/busco/macros.xml b/tools/busco/macros.xml
index 47e47718fc7..a23eb6c6f12 100644
--- a/tools/busco/macros.xml
+++ b/tools/busco/macros.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">5.8.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">6.0.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
 
     <xml name="citations">
         <citations>