B80 raw sequences underlying Genbank OQ798221-OQ798795 and associated B80 haplotype reference library

Data relevant for: Breakdown of self-incompatibility due to genetic interaction between a specific S-allele and an unlinked modifier. Nature Communications 2023.

These are sequence trace data with manual base calls for Genbank accessions OQ798221-OQ798795 and a reference library of B80 haplotypes. Sequences are of the S-locus linked gene B80 (aka PUB8,  U-box domain protein At4g21350), which can be used to genotype the S-locus owing to its close linkage (see linked papers). Haplotype identification is based on a B80 library originally developed by Barbara Mable (original library at https://doi.org/10.5061/dryad.832t8). The B80 refernce library we provide here is an update of the original library (we added H127, H128, H129 and H130).

Sequence names correspond to F1 progeny for which SC-index values (measure of self-compatibility) is available, and generally follow the following scheme.

For parents:

Pop-plant id-sequence barcode-haplotype information.

Example1: ed_KTT-11-67AF58 H75 H75 represents plant 11 from population KTT with sequence barcode 67AF58 identified as B80 haplotype H75-H75 (homozygous H75). 

Example2: ed_MAN-08-90IB55 represents plant 8 from population MAN with sequence barcode 90IB55. In this case the B80 haplotype information is not included in the filename. Note that these 

Example3: MAN-8-B80_H92 also represents plant 8 from population MAN. There is no sequence barcode, because this sequence was inferred from the parental and corresponding progeny sequences. These inferred sequences can be recognized as such by their names ending with B80_Hxxx (B80_H92 in this example).

For progeny:

Naming scheme 1: Round-maternal Pop-maternal plant id-paternal pop-paternal plant id-extraction id-sequence barcode-haplotype information.

Example:  R1_IND7-RON17_ex218_05DE08_H75_H50

Represents an F1 progeny from a cross between IND7 and RON17, with DNA extract ex218, sequence barcode 67AF58, identified B80 heterozygote with haplotypes H75 and H50

Potential file name addition may include CONTAM for cases where contamination was suspected (due to presence of non-parental haplotype), SELF where self-pollen-contamination was suspected (only maternal haplotype(s) found).

Naming scheme 2: Round-maternal Pop-maternal plant id-paternal pop-paternal plant id-numeric sequence id-indication of primer forward or reverse-haplotype information

Example: R2_TSS28-RON4-8-rev_H43_H50 

Represents an F1 progeny from a cross between TSS28 and RON, with numeric sequence id 8, identified B80 heterozygote with haplotypes H43 and H50