Vaccinium Pangenome Project Graph

The pangenome graph data provided by the Vaccinium Pangenome Project is available to view via the UCSC Genome Browser through GDV.  Below are links to the regions of the pangenome graph either by aligned against predicted reconstruction of ancestral genome or by cultivar.  You can navigate to different chromosomes within region by typing coordinates into the navigation bar at the top of the Genome Browser.  The table below lists the pangenome region and the genomes that are present.  Genomes that are in GDV, have hyperlinks to more information.  A brief tutorial on how to use the browser can be found here.

 

You can also view the pangenome data in JBrowse2 in the following genomes:  W85-20 P0 | Draper | Stevens

 

Link to Graph Region Blueberry Genomes in Graph Cranberry Genomes in Graph
By Ancestral Genome*    
Anc00 Raven Black Veil, Cumberland, Budd's Blues, Early Richard, Stevens (vmacro)
Anc01 Raven Black Veil, Cumberland, Budd's Blues, Early Richard
Anc02 Duke, Draper, Liberty, W85-20 Early Richard
Anc03 W85-20, Pioneer Black Veil, Cumberland, Stevens (vmacro)
Anc04 Duke, Draper, Liberty, Brigitta Blue, Raven  
Anc05 Duke, W85-20, Bluecrop, Elliot Budd's Blues
Anc06 Raven Black Veil, Budd's Blues, Early Richard, Lemunyon
Anc07 Misty Black Veil, Budd's Blues, Early Richard, Lemunyon
Anc08 Duke, Draper, W85-20, Harding Stevens (vmacro)
Anc09 Duke, Draper, W85-20, Bluecrop, Raven  
Anc10 Bluecrop, Elliot, Rubel, Weymouth Cumberland
Anc11 Raven Budd's Blues, Early Black, Native Budd's Blues, Stanley US92
Anc12 Raven Budd's Blues, Early Black, Cranmoor Natives, Garwood Bell
Anc13 Duke, Liberty, Brigitta Blue, Chandler, Raven  
Anc14 Duke, Draper, Liberty, W85-20, Raven  
Anc15 W85-20, Rubel, Raven, Harding, Arcadia  
Anc16 W85-20, Raven, Harding, Misty, Pioneer  
Anc17 Raven Budd's Blues, Early Richard, Native Budd's Blues, Stanley US92
Anc18 Raven Budd's Blues, Early Black, Native Budd's Blues, Stanley US92
Anc19 Raven Early Black, Cranmoor Natives, Garwood Bell, Native Budd's Blues
Anc20 Duke, Draper, Liberty, Brigitta Blue, Raven  
Anc21 Rubel, Weymouth, Raven, Arcadia Black Veil
Anc22 Raven Early Black, Cranmoor Natives, Native Budd's Blues, Stanley US92
Anc23 Rubel, Raven, Harding, Arcadia Black Veil
Anc24 Raven, Harding, Misty, Arcadia Stevens (vmacro)
Anc25 Raven, Harding, Misty, Pioneer Stevens (vmacro)
Anc26 Chandler, Harding, Misty, Pioneer, Kee Krisp  
Anc27 Chandler, Misty, Pioneer, Kee Krisp, Windsor  
Anc28 Brigitta Blue, Pioneer, Kee Krisp, Windsor, Sharp Blue  
Anc29 Brigitta Blue, Kee Krisp, Windsor, Sharp Blue, Meadowlark  
Anc30 Liberty, Windsor, Sharp Blue, Meadowlark, Patrecia  
Anc31 Liberty, Sharp Blue, Meadowlark, Patrecia, Farthing  
Anc32 Draper, Meadowlark, Patrecia, Farthing, Southmoon  
Anc33 Duke, Farthing, Southmoon, Optimus, Southern Belle  
Anc34 W85-20, Optimus, Avon Blue, Legacy, Earlie Blue  
Anc35 Duke, Southmoon, Optimus, Southern Belle, Avon Blue  
Anc36 W85-20, Optimus, Southern Belle, Avon Blue, Legacy  
Anc37 W85-20, Optimus, Avon Blue, Legacy, Earlie Blue  
By Blueberry Cultivar    
Arcadia Elliot, Raven, Harding, Misty  
Avon Blue Elliot, Legacy, Earlie Blue, Stanley   
Bluecrop Duke, W85-20, Elliot, Arcadia  
Brigitta Blue Duke, Liberty, Chandler, Arcadia  
Chandler Duke, Liberty, Brigitta Blue, Arcadia  
Draper Duke, Liberty, Brigitta Blue, Arcadia  
Duke Draper, Liberty, Brigitta Blue, Arcadia  
Earlie Blue Elliot, Avon Blue, Legacy, Stanley   
Elliot Duke, W85-20, Bluecrop, Arcadia  
Farthing Elliot, Southmoon, Optimus, Southern Belle  
Harding Elliot, Misty, Pioneer, Kee Krisp  
Kee Krisp Elliot, Windsor, Sharp Blue, Meadowlark  
Legacy Elliot, Avon Blue, Earlie Blue, Stanley   
Liberty Duke, Brigitta Blue, Chandler, Arcadia  
Meadowlark Elliot, Patrecia, Farthing, Southmoon  
Misty Elliot, Pioneer, Kee Krisp, Windsor  
Optimus Elliot, Southern Belle, Avon Blue, Legacy  
Patrecia Elliot, Farthing, Southmoon, Optimus  
Pioneer Elliot, Kee Krisp, Windsor, Sharp Blue  
Raven Elliot, Harding, Misty, Pioneer  
Rubel Elliot, Weymouth, Raven, Arcadia  
Sharp Blue Elliot, Meadowlark, Patrecia, Farthing  
Southern Belle Elliot, Optimus, Avon Blue, Legacy  
Southmoon Elliot, Optimus, Southern Belle, Avon Blue  
Stanley (Stanley 73) Elliot, Avon Blue, Legacy, Earlie Blue  
W85-20 Duke, Draper, Liberty, Arcadia  
Weymouth Elliot, Rubel, Raven, Arcadia  
Windsor Elliot, Sharp Blue, Meadowlark, Patrecia  
By Cranberry Cultivar    
Black Veil Arcadia Cumberland, Budd's Blues, Early Richard
Budd's Blues Arcadia Early Richard, Lemunyon, Native Budd's Blues
Cranmoor Natives Arcadia Early Black, Garwood Bell, Native Budd's Blues
Cumberland Arcadia Black Veil, Budd's Blues, Early Richard
Early Black Arcadia Cranmoor Natives, Garwood Bell, Native Budd's Blues
Early Richard Arcadia Budd's Blues, Lemunyon, Native Budd's Blues
Garwood Bell Arcadia Early Black, Cranmoor Natives, Native Budd's Blues
Lemunyon Arcadia Budd's Blues, Early Richard, Native Budd's Blues
Native Budd's Blues Arcadia Early Black, Cranmoor Natives, Stanley US92
Stanley US92 Arcadia Early Black, Cranmoor Natives, Native Budd's Blues
Stevens (vmacro) Arcadia Black Veil, Cumberland, Budd's Blues

*predicted reconstruction of ancestral genome at a particular node. Below is the phylogeny

((((Black_veil_:0.00722459,Cumberland_:0.00722459)Anc06:0.00031299,((Budds_Blues_:0.00717794,(Early_Richard_:0.00647382,Lemunyon_:0.00647382)Anc17:0.000704122)Anc11:0.000353356,((Early_Black_:0.00697901,(Cranmoor_Natives_:0.00677004,Garwood_Bell_:0.00677004)Anc22:0.000208963)Anc18:0.000423688,(Native_BB_:0.00719122,Stanley_US92_:0.00719122)Anc19:0.000211472)Anc12:0.000128605)Anc07:6.28503e-06)Anc03:0.0168254,vmacro_:0.01)Anc01:1,((((Duke_:0.000476421,draper_:0.000476421)Anc13:0.000981894,(Liberty_:0.0013811,(Brigitta_Blue_:0.000242355,Chandler_:0.000242355)Anc20:0.00113875)Anc14:7.7212e-05)Anc08:0.00762685,w85_:0.01)Anc04:1,((Bluecrop_:0.00167809,Elliot_:0.00167809)Anc09:0.000600419,((Rubel_:0.00139428,Weymouth_:0.00139428)Anc15:0.000758517,((Raven_:0.00180891,(Harding_:0.00158382,(Misty_:0.00161393,(Pioneer_:0.00153843,(Kee_Krisp_:0.00128126,(Windsor_:0.0013457,(Sharp_Blue_:0.00126603,(Meadowlark_:0.00123773,(Patrecia_:0.00107333,(Farthing_:0.00100849,(Southmoon_:0.000925245,((Optimus_:0.000793152,Southern_Belle_:0.000793152)Anc34:4.60779e-05,(Avon_Blue_:0.00083445,(Legacy_:0.000723863,(Earlie_Blue_:0.000584437,Stanley_73_:0.000584437)Anc37:0.000139426)Anc36:0.000110586)Anc35:4.77984e-06)Anc33:8.60156e-05)Anc32:8.32421e-05)Anc31:6.48386e-05)Anc30:0.000164405)Anc29:2.82988e-05)Anc28:7.96728e-05)Anc27:1e-05)Anc26:0.000257173)Anc25:7.54995e-05)Anc24:1e-05)Anc23:0.000225094)Anc21:0.00034388,arcadia_:0.01)Anc16:1)Anc10:0.00012571)Anc05:0.00680666)Anc02:0.0152778)Anc00;