Historic genome assembly and annotation information



What are the main changes between RefGen_v2 and RefGen_v3?

What are the main changes between RefGen_v2 and RefGen_v3?

Changes to the assembly include:

  • v3 captured missing gene space in v2 using WGS reads (v2 improved initial BAC assembly using MTP)
  • X contigs were moved or flipped.

Changes to the v3 gene models include:
  • 251 improved gene models
  • Among the improved modes, the following Fgenesh models were improved and given GRMZM IDs:
    AC147602.5_FG004 -> GRMZM6G741210
    AC190882.3_FG003 -> GRMZM6G961377
    AC192244.3_FG001 -> GRMZM6G869379
    AC194389.3_FG001 -> GRMZM6G399977
    AC204604.3_FG008 -> GRMZM6G220418
    AC210529.3_FG004 -> GRMZM6G945840
    AC232289.2_FG005 -> GRMZM6G404540
    AC233893.1_FG001 -> GRMZM6G310687
    AC233910.1_FG005 -> GRMZM6G729818
    AC235534.1_FG001 -> GRMZM6G798998
  • 213 novel gene models
  • 10 gene models were merged into new models:
    GRMZM2G000964, GRMZM2G103315 -> GRMZM2G000964
    GRMZM2G045892, GRMZM2G452386 -> GRMZM2G045892
    GRMZM2G119720, GRMZM2G518717 -> GRMZM2G119720
    GRMZM2G142383, GRMZM2G020429 -> GRMZM2G142383
    GRMZM2G319465, GRMZM2G439578 -> GRMZM2G319465
    GRMZM2G338693, GRMZM2G117517 -> GRMZM2G338693
    GRMZM5G861997, GRMZM5G864178 -> GRMZM5G861997
    GRMZM5G872800, GRMZM2G143862 -> GRMZM5G872800
    GRMZM5G891969, GRMZM5G823855 -> GRMZM5G891969
  • The 39,656 FGS gene models in 5b are now 39,475 protein-coding gene models in 5b+ (loss is due to merging; non-protein-coding gene models indicated as low confidence, and transposable elements)