TxDb.Gmax.JGI.Gmv4 is a Bioconductor-compatible transcript annotation package for Glycine max generated from the official JGI/Phytozome GFF3 annotation based on the Glycine max Wm82.a4.v1 reference genome.
The package provides genomic coordinates and transcript models, including genes, transcripts, exons, coding sequences (CDS), and promoter regions. It is intended for downstream genomic analyses using Bioconductor packages such as GenomicFeatures, GenomicRanges, Signac, ArchR, and ChIPseeker.
The TxDb object is retrieved from AnnotationHub using its corresponding AnnotationHub record.
Install the package and its dependencies from Bioconductor with:
The TxDb object is available through AnnotationHub:
Check the class of the retrieved object:
## [1] "TxDb"
## attr(,"package")
## [1] "GenomicFeatures"Display the transcript database:
## TxDb object:
## # Db type: TxDb
## # Supporting package: GenomicFeatures
## # Data source: Joint Genome Institute (Phytozome)
## # Organism: Glycine max
## # Taxonomy ID: 3847
## # Genome: NA
## # Nb of transcripts: 86256
## # Db created by: txdbmaker package from Bioconductor
## # Creation time: 2026-08-08 12:23:25 +0500 (Sat, 08 Aug 2026)
## # txdbmaker version at creation time: 1.9.0
## # RSQLite version at creation time: 3.53.3
## # DBSCHEMAVERSION: 1.2A summary can also be obtained with:
## Length Class Mode
## 1 TxDb S4The chromosome and sequence information can be examined with
seqinfo():
## Seqinfo object with 282 sequences from an unspecified genome:
## seqnames seqnames seqlengths isCircular genome
## 1 Gm01 57932355 FALSE <NA>
## 2 Gm02 50400358 FALSE <NA>
## 3 Gm03 46951866 FALSE <NA>
## 4 Gm04 51203389 FALSE <NA>
## 5 Gm05 42274530 FALSE <NA>
## ... ... ... ... ...
## 278 Gm16_scaffold_1357 2431 FALSE <NA>
## 279 Gm10_scaffold_1369 1922 FALSE <NA>
## 280 Gm19_scaffold_1377 1571 FALSE <NA>
## 281 Gm13_scaffold_1386 1350 FALSE <NA>
## 282 Gm06_scaffold_1454 885 FALSE <NA>The available sequence levels can be obtained with:
## [1] "Gm01" "Gm02" "Gm03"
## [4] "Gm04" "Gm05" "Gm06"
## [7] "Gm07" "Gm08" "Gm09"
## [10] "Gm10" "Gm11" "Gm12"
## [13] "Gm13" "Gm14" "Gm15"
## [16] "Gm16" "Gm17" "Gm18"
## [19] "Gm19" "Gm20" "Gm13_scaffold_21"
## [22] "scaffold_22" "scaffold_24" "scaffold_25"
## [25] "scaffold_26" "Gm03_scaffold_27" "scaffold_28"
## [28] "scaffold_29" "scaffold_30" "scaffold_31"
## [31] "scaffold_32" "scaffold_33" "scaffold_34"
## [34] "scaffold_35" "scaffold_36" "scaffold_37"
## [37] "scaffold_39" "Gm13_scaffold_40" "scaffold_42"
## [40] "scaffold_43" "scaffold_44" "scaffold_46"
## [43] "scaffold_47" "scaffold_49" "scaffold_50"
## [46] "scaffold_51" "scaffold_52" "Gm18_scaffold_54"
## [49] "scaffold_55" "scaffold_56" "scaffold_57"
## [52] "scaffold_58" "Gm06_scaffold_59" "scaffold_60"
## [55] "scaffold_61" "scaffold_62" "scaffold_64"
## [58] "scaffold_65" "Gm07_scaffold_69" "Gm06_scaffold_70"
## [61] "scaffold_71" "scaffold_73" "scaffold_74"
## [64] "scaffold_76" "scaffold_78" "Gm05_scaffold_79"
## [67] "scaffold_80" "scaffold_82" "scaffold_83"
## [70] "Gm14_scaffold_84" "scaffold_85" "scaffold_86"
## [73] "scaffold_88" "scaffold_89" "scaffold_92"
## [76] "scaffold_93" "Gm19_scaffold_94" "scaffold_95"
## [79] "scaffold_96" "Gm06_scaffold_98" "scaffold_99"
## [82] "scaffold_101" "scaffold_102" "scaffold_103"
## [85] "scaffold_104" "scaffold_105" "scaffold_106"
## [88] "Gm10_scaffold_107" "scaffold_108" "scaffold_109"
## [91] "scaffold_110" "scaffold_111" "Gm15_scaffold_113"
## [94] "Gm10_scaffold_115" "Gm11_scaffold_116" "scaffold_117"
## [97] "scaffold_118" "Gm10_scaffold_119" "scaffold_120"
## [100] "scaffold_121" "Gm02_scaffold_122" "scaffold_123"
## [103] "scaffold_124" "scaffold_125" "scaffold_126"
## [106] "scaffold_127" "scaffold_128" "scaffold_129"
## [109] "scaffold_130" "scaffold_131" "scaffold_132"
## [112] "scaffold_134" "Gm03_scaffold_135" "scaffold_137"
## [115] "scaffold_138" "scaffold_140" "scaffold_141"
## [118] "Gm20_scaffold_142" "scaffold_143" "scaffold_145"
## [121] "scaffold_146" "scaffold_147" "scaffold_149"
## [124] "scaffold_151" "scaffold_152" "scaffold_155"
## [127] "scaffold_157" "scaffold_158" "scaffold_160"
## [130] "scaffold_162" "scaffold_163" "scaffold_164"
## [133] "Gm09_scaffold_165" "Gm01_scaffold_166" "scaffold_168"
## [136] "scaffold_174" "scaffold_175" "scaffold_178"
## [139] "scaffold_180" "Gm06_scaffold_183" "scaffold_184"
## [142] "scaffold_187" "Gm05_scaffold_188" "scaffold_189"
## [145] "scaffold_191" "scaffold_193" "scaffold_194"
## [148] "scaffold_195" "scaffold_196" "scaffold_198"
## [151] "scaffold_199" "scaffold_201" "scaffold_207"
## [154] "scaffold_209" "scaffold_210" "scaffold_211"
## [157] "Gm06_scaffold_214" "scaffold_216" "scaffold_217"
## [160] "scaffold_223" "scaffold_224" "scaffold_226"
## [163] "scaffold_229" "Gm11_scaffold_232" "scaffold_233"
## [166] "scaffold_234" "Gm03_scaffold_238" "scaffold_239"
## [169] "scaffold_240" "scaffold_241" "Gm03_scaffold_245"
## [172] "scaffold_246" "Gm19_scaffold_249" "scaffold_250"
## [175] "scaffold_252" "scaffold_253" "Gm16_scaffold_260"
## [178] "scaffold_261" "scaffold_264" "scaffold_269"
## [181] "scaffold_270" "scaffold_271" "scaffold_273"
## [184] "scaffold_277" "scaffold_282" "scaffold_288"
## [187] "scaffold_294" "scaffold_298" "Gm06_scaffold_301"
## [190] "scaffold_303" "scaffold_307" "scaffold_313"
## [193] "Gm12_scaffold_314" "scaffold_315" "scaffold_319"
## [196] "scaffold_324" "scaffold_327" "scaffold_328"
## [199] "scaffold_330" "scaffold_331" "scaffold_332"
## [202] "scaffold_336" "scaffold_337" "Gm15_scaffold_339"
## [205] "scaffold_340" "scaffold_344" "scaffold_352"
## [208] "Gm14_scaffold_354" "scaffold_355" "scaffold_367"
## [211] "scaffold_368" "scaffold_371" "scaffold_375"
## [214] "scaffold_377" "scaffold_383" "scaffold_387"
## [217] "scaffold_393" "scaffold_398" "scaffold_401"
## [220] "scaffold_405" "scaffold_408" "scaffold_411"
## [223] "scaffold_415" "scaffold_422" "scaffold_423"
## [226] "scaffold_426" "scaffold_431" "scaffold_436"
## [229] "scaffold_438" "scaffold_439" "scaffold_442"
## [232] "scaffold_449" "scaffold_452" "scaffold_456"
## [235] "scaffold_459" "scaffold_461" "scaffold_467"
## [238] "scaffold_475" "scaffold_478" "scaffold_483"
## [241] "scaffold_484" "scaffold_486" "scaffold_489"
## [244] "scaffold_492" "scaffold_496" "scaffold_498"
## [247] "scaffold_499" "scaffold_501" "scaffold_502"
## [250] "scaffold_506" "scaffold_508" "scaffold_511"
## [253] "scaffold_518" "scaffold_519" "Gm03_scaffold_521"
## [256] "scaffold_522" "scaffold_524" "scaffold_529"
## [259] "scaffold_535" "scaffold_540" "scaffold_542"
## [262] "scaffold_544" "scaffold_551" "scaffold_556"
## [265] "scaffold_560" "Gm18_scaffold_561" "scaffold_568"
## [268] "scaffold_570" "scaffold_576" "scaffold_578"
## [271] "scaffold_579" "Gm16_scaffold_661" "Gm14_scaffold_738"
## [274] "Gm19_scaffold_765" "Gm03_scaffold_926" "Gm08_scaffold_952"
## [277] "Gm10_scaffold_1052" "Gm16_scaffold_1357" "Gm10_scaffold_1369"
## [280] "Gm19_scaffold_1377" "Gm13_scaffold_1386" "Gm06_scaffold_1454"The Wm82.a4.v1 assembly contains 20 nuclear chromosomes, which contain the majority of the annotated genes.
Gene ranges can be retrieved with genes():
## GRanges object with 52872 ranges and 1 metadata column:
## seqnames ranges strand | gene_id
## <Rle> <IRanges> <Rle> | <character>
## Glyma.01G000100 Gm01 27344-28430 - | Glyma.01G000100
## Glyma.01G000137 Gm01 52485-52601 - | Glyma.01G000137
## Glyma.01G000174 Gm01 54356-55224 - | Glyma.01G000174
## Glyma.01G000211 Gm01 56132-64061 - | Glyma.01G000211
## Glyma.01G000248 Gm01 59057-60641 - | Glyma.01G000248
## ... ... ... ... . ...
## Glyma.U045402 scaffold_117 15414-16243 - | Glyma.U045402
## Glyma.U045502 scaffold_117 24320-25364 - | Glyma.U045502
## Glyma.U045602 scaffold_117 26126-26281 - | Glyma.U045602
## Glyma.U045702 scaffold_117 57476-58790 - | Glyma.U045702
## Glyma.U045802 scaffold_117 59809-61235 - | Glyma.U045802
## -------
## seqinfo: 282 sequences from an unspecified genomeTranscript ranges can be retrieved with
transcripts():
## GRanges object with 6 ranges and 2 metadata columns:
## seqnames ranges strand | tx_id tx_name
## <Rle> <IRanges> <Rle> | <integer> <character>
## [1] Gm01 120168-131881 + | 1 Glyma.01G000600.1
## [2] Gm01 120175-132004 + | 2 Glyma.01G000600.2
## [3] Gm01 147523-197485 + | 3 Glyma.01G000900.2
## [4] Gm01 200309-205971 + | 4 Glyma.01G001000.2
## [5] Gm01 209523-217546 + | 5 Glyma.01G001100.5
## [6] Gm01 209548-217799 + | 6 Glyma.01G001100.3
## -------
## seqinfo: 282 sequences from an unspecified genomeExon ranges can be retrieved with exons():
## GRanges object with 6 ranges and 1 metadata column:
## seqnames ranges strand | exon_id
## <Rle> <IRanges> <Rle> | <integer>
## [1] Gm01 120400-122559 + | 1
## [2] Gm01 120400-122559 + | 2
## [3] Gm01 129664-129914 + | 3
## [4] Gm01 131469-131499 + | 4
## [5] Gm01 131469-131639 + | 5
## [6] Gm01 147544-147624 + | 6
## -------
## seqinfo: 282 sequences from an unspecified genomeCoding sequence ranges can be retrieved with cds():
## GRanges object with 6 ranges and 1 metadata column:
## seqnames ranges strand | cds_id
## <Rle> <IRanges> <Rle> | <integer>
## [1] Gm01 120400-122559 + | 1
## [2] Gm01 120400-122559 + | 2
## [3] Gm01 129664-129914 + | 3
## [4] Gm01 131469-131499 + | 4
## [5] Gm01 131469-131639 + | 5
## [6] Gm01 147544-147624 + | 6
## -------
## seqinfo: 282 sequences from an unspecified genomePromoter regions can be generated using 2 kb upstream and 200 bp downstream of transcription start sites:
## Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE): GRanges object contains 34 out-of-bound ranges located on sequences Gm06,
## Gm08, Gm13, Gm13_scaffold_21, Gm07_scaffold_69, Gm05_scaffold_79,
## Gm14_scaffold_84, scaffold_120, scaffold_138, scaffold_164,
## Gm09_scaffold_165, scaffold_229, scaffold_273, scaffold_288, scaffold_328,
## Gm15_scaffold_339, scaffold_375, scaffold_551, Gm18_scaffold_561,
## Gm14_scaffold_738, and Gm10_scaffold_1052. Note that ranges located on a
## sequence whose length is unknown (NA) or on a circular sequence are not
## considered out-of-bound (use seqlengths() and isCircular() to get the lengths
## and circularity flags of the underlying sequences). You can use trim() to
## trim these ranges. See ?`trim,GenomicRanges-method` for more information.## GRanges object with 6 ranges and 2 metadata columns:
## seqnames ranges strand | tx_id tx_name
## <Rle> <IRanges> <Rle> | <integer> <character>
## Glyma.01G000600.1 Gm01 118168-120367 + | 1 Glyma.01G000600.1
## Glyma.01G000600.2 Gm01 118175-120374 + | 2 Glyma.01G000600.2
## Glyma.01G000900.2 Gm01 145523-147722 + | 3 Glyma.01G000900.2
## Glyma.01G001000.2 Gm01 198309-200508 + | 4 Glyma.01G001000.2
## Glyma.01G001100.5 Gm01 207523-209722 + | 5 Glyma.01G001100.5
## Glyma.01G001100.3 Gm01 207548-209747 + | 6 Glyma.01G001100.3
## -------
## seqinfo: 282 sequences from an unspecified genomeTranscripts can be grouped by gene using
transcriptsBy():
## GRangesList object of length 52872:
## $Glyma.01G000100
## GRanges object with 1 range and 2 metadata columns:
## seqnames ranges strand | tx_id tx_name
## <Rle> <IRanges> <Rle> | <integer> <character>
## [1] Gm01 27344-28430 - | 1759 Glyma.01G000100.1
## -------
## seqinfo: 282 sequences from an unspecified genome
##
## $Glyma.01G000137
## GRanges object with 1 range and 2 metadata columns:
## seqnames ranges strand | tx_id tx_name
## <Rle> <IRanges> <Rle> | <integer> <character>
## [1] Gm01 52485-52601 - | 1760 Glyma.01G000137.1
## -------
## seqinfo: 282 sequences from an unspecified genome
##
## $Glyma.01G000174
## GRanges object with 1 range and 2 metadata columns:
## seqnames ranges strand | tx_id tx_name
## <Rle> <IRanges> <Rle> | <integer> <character>
## [1] Gm01 54356-55224 - | 1761 Glyma.01G000174.1
## -------
## seqinfo: 282 sequences from an unspecified genome
##
## ...
## <52869 more elements>Exons can be grouped by transcript using exonsBy():
exons_by_transcript <- GenomicFeatures::exonsBy(
TxDb.Gmax.JGI.Gmv4,
by = "tx"
)
exons_by_transcript## GRangesList object of length 86256:
## $`1`
## GRanges object with 3 ranges and 3 metadata columns:
## seqnames ranges strand | exon_id exon_name
## <Rle> <IRanges> <Rle> | <integer> <character>
## [1] Gm01 120400-122559 + | 1 Glyma.01G000600.1.Wm..
## [2] Gm01 129664-129914 + | 3 Glyma.01G000600.1.Wm..
## [3] Gm01 131469-131499 + | 4 Glyma.01G000600.1.Wm..
## exon_rank
## <integer>
## [1] 1
## [2] 2
## [3] 3
## -------
## seqinfo: 282 sequences from an unspecified genome
##
## $`2`
## GRanges object with 2 ranges and 3 metadata columns:
## seqnames ranges strand | exon_id exon_name
## <Rle> <IRanges> <Rle> | <integer> <character>
## [1] Gm01 120400-122559 + | 2 Glyma.01G000600.2.Wm..
## [2] Gm01 131469-131639 + | 5 Glyma.01G000600.2.Wm..
## exon_rank
## <integer>
## [1] 1
## [2] 2
## -------
## seqinfo: 282 sequences from an unspecified genome
##
## ...
## <86254 more elements>## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] GenomicFeatures_1.65.0 AnnotationDbi_1.75.2
## [3] Biobase_2.73.2 GenomicRanges_1.65.4
## [5] Seqinfo_1.3.2 IRanges_2.47.5
## [7] S4Vectors_0.51.10 AnnotationHub_4.3.2
## [9] BiocFileCache_3.3.0 dbplyr_2.6.0
## [11] BiocGenerics_0.59.12 generics_0.1.4
## [13] TxDb.Gmax.JGI.Gmv4_0.99.1 BiocStyle_2.41.0
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.53.6 rjson_0.2.23 xfun_0.61
## [4] bslib_0.12.0 httr2_1.3.0 lattice_0.23-1
## [7] bitops_1.1-0 vctrs_0.7.3 tools_4.6.1
## [10] parallel_4.6.1 curl_8.0.0 tibble_3.3.1
## [13] RSQLite_3.53.3 blob_1.3.0 pkgconfig_2.0.3
## [16] BiocBaseUtils_1.15.1 Matrix_1.7-6 cigarillo_1.3.1
## [19] lifecycle_1.0.5 compiler_4.6.1 Rsamtools_2.29.0
## [22] Biostrings_2.81.9 codetools_0.2-20 htmltools_0.5.9
## [25] sys_3.4.3 buildtools_1.0.0 sass_0.4.10
## [28] RCurl_1.98-1.20 yaml_2.3.12 pillar_1.11.1
## [31] crayon_1.5.3 jquerylib_0.1.4 BiocParallel_1.47.0
## [34] cachem_1.1.0 tidyselect_1.2.1 digest_0.6.39
## [37] purrr_1.2.2 dplyr_1.2.1 restfulr_0.0.17
## [40] BiocVersion_3.24.0 maketools_1.3.2 grid_4.6.1
## [43] fastmap_1.2.0 cli_3.6.6 magrittr_2.0.5
## [46] XML_3.99-0.25 withr_3.0.3 filelock_1.0.3
## [49] rappdirs_0.3.4 bit64_4.8.6 rmarkdown_2.32
## [52] XVector_0.53.0 httr_1.4.9 bit_4.6.0
## [55] otel_0.2.0 png_0.1-9 memoise_2.0.1
## [58] evaluate_1.0.5 knitr_1.52 BiocIO_1.23.3
## [61] rtracklayer_1.73.0 rlang_1.3.0 glue_1.8.1
## [64] DBI_1.3.0 BiocManager_1.30.27 jsonlite_2.0.0
## [67] R6_2.6.1 GenomicAlignments_1.49.2