Curated TALE annotations for ten published Xanthomonas oryzae genomes

The TALEs of ten complete, published genomes, named as the literature names them and annotated by hand. It is the reference this package's own discovery can be checked against: three of the ten genomes, MAI1, BAI3 and PXO86, are the ones tantale_genome() installs, so a tell_tales() run on them can be compared array by array with what is recorded here.

Usage

tale_annotations

Format

A tibble with 128 rows and 10 columns. One row is one TALE gene.

strain: The strain, e.g. "PXO99A". Ten of them.
label, tal_name: The TALE's name in the literature, capitalised ("Tal4a") and as written in the source publication ("tal4a"). strain and label together identify a row: a label repeats across strains, never within one. tal_name is missing where the source gives no name.
annotale_class: The AnnoTALE class the TALE belongs to ("TalAH"), from the catalogue of 2026-10-04. A class groups TALEs similar enough to be considered the same TALE across strains, and is how the literature refers to them. Missing for two rows, see Details.
replicon_id, genome_id: The RefSeq replicon and the GenBank assembly the TALE comes from, e.g. "NC_010717" and "GCA_000019585.2". Present for every row: this is what lets a reader fetch the sequence.
pubmed: PubMed identifier(s) of the publication(s) reporting the genome or the TALE, comma-separated where there is more than one.
truncTALE: TRUE for the nine truncTALEs, TALEs whose C-terminal region is naturally shortened so that they no longer activate transcription. See the truncTALE article for what this does to discovery and to frameshift correction.
rvd_seq: The repeat-variable diresidues in array order, dash-separated ("NI-HD-NG-..."), the format of tales_rvd_strings. tales_predict_targets takes them as a named BStringSet: Biostrings::BStringSet(setNames(rvd_seq, paste(strain, label))). A lowercase RVD ("ng", "n*") marks a repeat of non-standard length, the usual convention; 16 of the 128 arrays carry at least one, so do not upper-case this column before comparing it with anything.
unusual_feature: A note, for the nine arrays that carry one, on what makes the gene atypical: repeats of non-standard length, deletions, duplications, a premature stop.

Source

Compiled by Bao Tram Vi during the work that became this package, from the genome records and publications cited in each row; published here for the first time. annotale_class was taken from AnnoTALE's class catalogue as downloaded on 2026-10-04. The genome sequences themselves are the GenBank assemblies named in genome_id, at https://www.ncbi.nlm.nih.gov/datasets/genome/.

Details

The table is sparse where the sources are: tal_name is absent for 19 rows and pubmed for 19. The gaps are the state of the curation, not placeholders to be filled by a guess.

annotale_class is missing for one row: PXO99A's Tal7b, the five-repeat allele its own unusual_feature describes, too short to be catalogued.

The class is stored without the member index AnnoTALE appends to it ("TalAH", not "TalAH30"). That index numbers the members of a class as of the day it is read, and the catalogue grows: every one of the 73 indices recorded when this table was curated in 2021 had moved by 2026, while the class itself agreed in every case.

Identifiers that name an array within a single run are deliberately not included: the tell_tales array id and AnnoTALE's tempTALE name both depend on the run that produced them, so neither would survive a rerun. Matching a row to a fresh tell_tales result means matching on what the TALE is, its rvd_seq, rather than on what some run called it.

No column of DisTAL groups is included. The working file carried one, but how its values had been computed was not recorded, so they could not be vouched for. tales_compare_distal followed by tales_group_hclust computes such groups from rvd_seq.

Examples

# the TALEs of one strain
subset(tale_annotations, strain == "PXO86",
       select = c("label", "annotale_class", "truncTALE"))
#> # A tibble: 18 × 3
#>    label  annotale_class truncTALE
#>    <chr>  <chr>          <lgl>    
#>  1 AvrXa7 TalAC          FALSE    
#>  2 PthXo8 TalAP          FALSE    
#>  3 Tal1   TalAS          FALSE    
#>  4 Tal2a  TalAG          FALSE    
#>  5 Tal3   TalAI          TRUE     
#>  6 Tal4a  TalCA          FALSE    
#>  7 Tal4b  TalAN          FALSE    
#>  8 Tal5a  TalBA          FALSE    
#>  9 Tal5b  TalAA          FALSE    
#> 10 Tal5c  TalAR          FALSE    
#> 11 Tal6   TalAI          TRUE     
#> 12 Tal7a  TalAF          FALSE    
#> 13 Tal7c  TalBJ          FALSE    
#> 14 Tal8b  TalAQ          FALSE    
#> 15 Tal8c  TalAO          FALSE    
#> 16 Tal8d  TalAE          FALSE    
#> 17 Tal8e  TalAD          FALSE    
#> 18 aB4.5  TalAB          FALSE    

# the ten strains compared class by class; truncTALEs are marked "T"
grouped <- tale_annotations[!is.na(tale_annotations$annotale_class), ]
talomes_heatmap(grouped, group_col = "annotale_class",
                strain_col = "strain", rvd_col = "rvd_seq",
                trunc_tales_col = "truncTALE")


# the naturally truncated ones, across all ten genomes
table(tale_annotations$strain, tale_annotations$truncTALE)
#>          
#>           FALSE TRUE
#>   AXO1947     9    0
#>   BAI3        9    0
#>   MAI1        9    0
#>   MAI129      9    0
#>   MAI134      9    0
#>   MAI68       9    0
#>   PXO61      16    2
#>   PXO71      16    3
#>   PXO86      16    2
#>   PXO99A     17    2

# what makes the atypical arrays atypical
subset(tale_annotations, !is.na(unusual_feature),
       select = c("strain", "label", "unusual_feature"))
#> # A tibble: 9 × 3
#>   strain label  unusual_feature                                                 
#>   <chr>  <chr>  <chr>                                                           
#> 1 PXO61  Tal1b  Missing 2 first repeats compare to literature                   
#> 2 PXO86  AvrXa7 repeat 13 is of atypical length (encodes 40 aa)                 
#> 3 PXO86  Tal3   multiple deletions in the 5′ end, premature stop in the 3′ end …
#> 4 PXO86  Tal4b  an 11 codon duplication in the 3′ end                           
#> 5 PXO86  Tal5a  a five-codon deletion in 5′ end                                 
#> 6 PXO86  Tal5b  an 11-codon duplication in the 3′ end                           
#> 7 PXO86  Tal6   multiple deletions in the 5′ end, a 129 bp 3′ end and repeat 4 …
#> 8 PXO86  Tal8b  this gene is a nearly identical, functional allele of avrXa23 (…
#> 9 PXO99A Tal7b  An allele of tal7b or tal8b of PXO99A with a deletion in the ce…