Installation

Install from Bioconductor

Once PlantTxDbHub is accepted into Bioconductor, install it with:

if (!require("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
BiocManager::install("PlantTxDbHub")

Install the development version from GitHub

While the package is under Bioconductor review, install the development version directly from GitHub:

if (!require("remotes", quietly = TRUE))
    install.packages("remotes")
remotes::install_github("kabilanbio/PlantTxDbHub")

Introduction

PlantTxDbHub provides ready‑to‑use TxDb (transcript database) annotations for plant genomes. The databases are stored as SQLite files and can be downloaded on demand using downloadPlantTxDbs(). The available species and their download URLs are maintained in a curated CSV file (inst/extdata/metadata.csv). This design allows the community to add new species without modifying any R code.

Finding available species

Use listPlantTxDbSpecies() to see the available species and their associated metadata (species name, genome build, source version, data provider, filename, and description):

listPlantTxDbSpecies()
#>            SpeciesID              Species     Genome SourceVersion
#> 1 Arabidopsis_TAIR10 Arabidopsis thaliana     TAIR10            62
#> 2  Glycine_Gmax_v2.1          Glycine max  Gmax_v2.1            62
#> 3      Oryza_IRGSP_1         Oryza sativa  IRGSP-1.0            62
#> 4 Glycine_Wm82.a4.v1          Glycine max Wm82.a4.v1            14
#>     DataProvider                         Filename
#> 1 Ensembl Plants TxDb.Athaliana.TAIR10.v62.sqlite
#> 2 Ensembl Plants         TxDb.Gmax.Wm82.a2.sqlite
#> 3 Ensembl Plants    TxDb.Osativa.IRGSP.v62.sqlite
#> 4      Phytozome         TxDb.Gmax.Wm82.a4.sqlite
#>                                            Description
#> 1    Ensembl Plants TAIR10 release 62 GTF-derived TxDb
#> 2 Ensembl Plants Wm82 v2.1 release 62 GTF-derived TxDb
#> 3 Ensembl Plants IRGSP-1.0 release 62 GTF-derived TxDb
#> 4                     Phytozome v14 GFF3- derived TxDb

Downloading the databases

downloadPlantTxDbs() reads the metadata CSV and downloads each SQLite file from its unique URL, caching it via BiocFileCache. By default it fetches all available databases; you can also request a subset by SpeciesID.

Download all databases:

downloadPlantTxDbs()

Download only specific species (as done in the setup chunk above):

# Only Arabidopsis
downloadPlantTxDbs(species = "Arabidopsis_TAIR10")

# Arabidopsis and rice together
downloadPlantTxDbs(species = c("Arabidopsis_TAIR10", "Oryza_IRGSP_1"))

Files are cached in a persistent user data directory via BiocFileCache, so subsequent calls are fast and corrupted files are re-downloaded automatically.

Loading a TxDb (Arabidopsis example)

Once downloaded, obtain the full path to a cached file with getTxDbPath(), then load it with GenomicFeatures::loadDb().

The remaining sections of this vignette require a successful download; they are skipped if the network was unavailable during vignette build.

ath_file <- getTxDbPath("Arabidopsis_TAIR10")
txdb_ath <- loadDb(ath_file)
txdb_ath
#> TxDb object:
#> # Db type: TxDb
#> # Supporting package: GenomicFeatures
#> # Data source: Ensembl Plants release 62 GTF
#> # Organism: Arabidopsis thaliana
#> # Taxonomy ID: 3702
#> # Source: Ensembl Plants
#> # Ensembl release: 62
#> # GTF file: Arabidopsis_thaliana.TAIR10.62.gtf.gz
#> # Genome assembly: TAIR10
#> # Creation date: 2026-06-09
#> # Created by: 
#> # Contact: Kabilan S <[email protected]>
#> # Genome: NA
#> # Nb of transcripts: 54013
#> # Db created by: txdbmaker package from Bioconductor
#> # Creation time: 2026-06-09 12:36:03 +0500 (Tue, 09 Jun 2026)
#> # txdbmaker version at creation time: 1.6.2
#> # RSQLite version at creation time: 3.52.0
#> # DBSCHEMAVERSION: 1.2

Available columns and keys

TxDb objects support the select() interface.

columns(txdb_ath)
#>  [1] "CDSCHROM"   "CDSEND"     "CDSID"      "CDSNAME"    "CDSPHASE"  
#>  [6] "CDSSTART"   "CDSSTRAND"  "EXONCHROM"  "EXONEND"    "EXONID"    
#> [11] "EXONNAME"   "EXONRANK"   "EXONSTART"  "EXONSTRAND" "GENEID"    
#> [16] "TXCHROM"    "TXEND"      "TXID"       "TXNAME"     "TXSTART"   
#> [21] "TXSTRAND"   "TXTYPE"
keytypes(txdb_ath)
#> [1] "CDSID"    "CDSNAME"  "EXONID"   "EXONNAME" "GENEID"   "TXID"     "TXNAME"

The column TXTYPE indicates the transcript biotype (e.g. protein_coding).

Retrieve all genes

genes() returns a GRanges with gene‑level information.

gene_gr <- genes(txdb_ath)
head(gene_gr)
#> GRanges object with 6 ranges and 1 metadata column:
#>             seqnames      ranges strand |     gene_id
#>                <Rle>   <IRanges>  <Rle> | <character>
#>   AT1G01010        1   3631-5899      + |   AT1G01010
#>   AT1G01020        1   6788-9130      - |   AT1G01020
#>   AT1G01030        1 11649-13714      - |   AT1G01030
#>   AT1G01040        1 23121-31227      + |   AT1G01040
#>   AT1G01046        1 28500-28706      + |   AT1G01046
#>   AT1G01050        1 31170-33171      - |   AT1G01050
#>   -------
#>   seqinfo: 7 sequences (2 circular) from an unspecified genome

Retrieve all transcripts

tx_gr <- transcripts(txdb_ath)
head(tx_gr)
#> GRanges object with 6 ranges and 2 metadata columns:
#>       seqnames      ranges strand |     tx_id     tx_name
#>          <Rle>   <IRanges>  <Rle> | <integer> <character>
#>   [1]        1   3631-5899      + |         1 AT1G01010.1
#>   [2]        1 11101-11372      + |         2 AT1G03987.1
#>   [3]        1 23121-31227      + |         3 AT1G01040.1
#>   [4]        1 23416-31120      + |         4 AT1G01040.2
#>   [5]        1 28500-28706      + |         5   at1g01046
#>   [6]        1 32727-33009      + |         6 AT1G03997.1
#>   -------
#>   seqinfo: 7 sequences (2 circular) from an unspecified genome

Retrieve all exons

ex_gr <- exons(txdb_ath, columns = "exon_id")
head(ex_gr)
#> GRanges object with 6 ranges and 1 metadata column:
#>       seqnames    ranges strand |   exon_id
#>          <Rle> <IRanges>  <Rle> | <integer>
#>   [1]        1 3631-3913      + |         1
#>   [2]        1 3996-4276      + |         2
#>   [3]        1 4486-4605      + |         3
#>   [4]        1 4706-5095      + |         4
#>   [5]        1 5174-5326      + |         5
#>   [6]        1 5439-5899      + |         6
#>   -------
#>   seqinfo: 7 sequences (2 circular) from an unspecified genome

Filter by gene ID

my_genes <- c("AT1G01010", "AT1G01020")
genes(txdb_ath, filter = list(gene_id = my_genes))
#> GRanges object with 2 ranges and 1 metadata column:
#>             seqnames    ranges strand |     gene_id
#>                <Rle> <IRanges>  <Rle> | <character>
#>   AT1G01010        1 3631-5899      + |   AT1G01010
#>   AT1G01020        1 6788-9130      - |   AT1G01020
#>   -------
#>   seqinfo: 7 sequences (2 circular) from an unspecified genome

Retrieving transcript types

tx_info <- select(txdb_ath,
  keys = keys(txdb_ath, "TXID"),
  columns = c("TXID", "TXTYPE"),
  keytype = "TXID"
)
#> 'select()' returned 1:1 mapping between keys and columns
table(tx_info$TXTYPE)
#> 
#> transcript 
#>      54013

Working with chromosome names

gene_gr_nuc <- keepSeqlevels(gene_gr,
  value = c("1", "2", "3", "4", "5"),
  pruning.mode = "coarse"
)
seqlevels(gene_gr_nuc) <- paste0("Chr", seqlevels(gene_gr_nuc))
seqlevels(gene_gr_nuc)
#> [1] "Chr1" "Chr2" "Chr3" "Chr4" "Chr5"

Soybean (Glycine max) example

Two soybean genome builds are available: Glycine_Gmax_v2.1 (Ensembl Plants) and Glycine_Wm82.a4.v1 (Phytozome). This example uses the Ensembl Plants build.

gmx_file <- getTxDbPath("Glycine_Gmax_v2.1")
txdb_gmx <- loadDb(gmx_file)
head(genes(txdb_gmx))
#> GRanges object with 6 ranges and 1 metadata column:
#>                   seqnames          ranges strand |         gene_id
#>                      <Rle>       <IRanges>  <Rle> |     <character>
#>   ENSRNA049760019       11 2675651-2675723      + | ENSRNA049760019
#>   ENSRNA049760020       11 2794530-2794602      + | ENSRNA049760020
#>   ENSRNA049760021       11 5126230-5126303      + | ENSRNA049760021
#>   ENSRNA049760022       11 8090262-8090334      + | ENSRNA049760022
#>   ENSRNA049760023       11 8422999-8423082      + | ENSRNA049760023
#>   ENSRNA049760024       11 9000534-9000605      + | ENSRNA049760024
#>   -------
#>   seqinfo: 22 sequences (2 circular) from an unspecified genome

Rice (Oryza sativa) example

osa_file <- getTxDbPath("Oryza_IRGSP_1")
txdb_osa <- loadDb(osa_file)
head(genes(txdb_osa))
#> GRanges object with 6 ranges and 1 metadata column:
#>                   seqnames            ranges strand |         gene_id
#>                      <Rle>         <IRanges>  <Rle> |     <character>
#>   ENSRNA049440515        1 33589412-33589483      - | ENSRNA049440515
#>   ENSRNA049440716        1 35264198-35264278      - | ENSRNA049440716
#>   ENSRNA049441102        1 37693591-37693662      - | ENSRNA049441102
#>   ENSRNA049441259        1 40086054-40086126      - | ENSRNA049441259
#>   ENSRNA049441339        1 40793762-40793842      - | ENSRNA049441339
#>   ENSRNA049441421        1 42318166-42318238      - | ENSRNA049441421
#>   -------
#>   seqinfo: 14 sequences (2 circular) from an unspecified genome

Contributing new species

We welcome the addition of TxDb databases for other plant species. To contribute:

Host the SQLite file on a permanent, publicly accessible URL (e.g., your own Zenodo record).
Fork the package repository and edit the file inst/extdata/metadata.csv.
Add a new row containing:
- SpeciesID – a unique identifier (e.g. Zea_mays_B73).
- Title – the exact filename of the SQLite file.
- Location_Prefix and RDataPath – the two parts of the download URL (they will be concatenated to form the full link).
- Other columns as appropriate (Description, Genome, Species, DataProvider, etc.). Follow the existing rows for guidance.
Submit a pull request with your changes. Once merged and a new version of the package is released, the new species will be instantly available to all users.

No R code changes are required – the package reads all necessary information directly from metadata.csv.

Data sources and licensing

TxDb resources in this package are derived from Ensembl Plants and Phytozome annotation data; see ?PlantTxDbHub for full licensing details and getTxDbProvenance() to query provenance per species.

Session information

sessionInfo()
#> 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] GenomeInfoDb_1.49.1    GenomicFeatures_1.65.0 AnnotationDbi_1.75.2  
#>  [4] Biobase_2.73.2         GenomicRanges_1.65.4   Seqinfo_1.3.2         
#>  [7] IRanges_2.47.5         S4Vectors_0.51.10      BiocGenerics_0.59.12  
#> [10] generics_0.1.4         PlantTxDbHub_0.99.6    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] vctrs_0.7.3              tools_4.6.1              bitops_1.1-0            
#> [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             dbplyr_2.6.0            
#> [19] cigarillo_1.3.1          lifecycle_1.0.5          compiler_4.6.1          
#> [22] Rsamtools_2.29.0         Biostrings_2.81.9        codetools_0.2-20        
#> [25] htmltools_0.5.9          sys_3.4.3                buildtools_1.0.0        
#> [28] sass_0.4.10              RCurl_1.98-1.20          yaml_2.3.12             
#> [31] pillar_1.11.1            crayon_1.5.3             jquerylib_0.1.4         
#> [34] BiocParallel_1.47.0      cachem_1.1.0             tidyselect_1.2.1        
#> [37] digest_0.6.39            purrr_1.2.2              dplyr_1.2.1             
#> [40] restfulr_0.0.17          maketools_1.3.2          grid_4.6.1              
#> [43] fastmap_1.2.0            cli_3.6.6                magrittr_2.0.5          
#> [46] XML_3.99-0.24            withr_3.0.3              UCSC.utils_1.9.0        
#> [49] filelock_1.0.3           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] BiocFileCache_3.3.0      rtracklayer_1.73.0       rlang_1.3.0             
#> [64] glue_1.8.1               DBI_1.3.0                BiocManager_1.30.27     
#> [67] jsonlite_2.0.0           R6_2.6.1                 GenomicAlignments_1.49.2

Local Analysis of Plant Genomes with PlantTxDbHub