DOI: 10.5061/dryad.qz612jmv1
title: Data from: The structure and allelic diversity of the self-incompatibility locus (S-locus) in diploid potatoes inferred from genome sequences and transcriptome data from styles and pollen

description: Gametophytic Self-Incompatibility is a reproductive strategy to prevent
 inbreeding and promote outcrossing, and it is controlled by the
 self-incompatibility locus (S-locus). Studies to understand molecular and
 evolutionary aspects of the SI system in the Solanaceae have been
 conducted using several genera, including Petunia, Nicotiana, and Solanum.
 S-RNases are pistil determinants of gametophytic SI, and multiple S-RNase
 alleles have been identified in a few potato species. SLFs, the pollen
 determinants of SI, are linked to S-RNases on chromosome 1. The S-RNase
 and SLFs present on each chromatid determine an individual’s
 self-compatible (SC) or self-incompatible (SI) haplotypes. We used
 long-read genome sequencing and RNA sequencing from styles and pollen to
 assess the diversity and composition of elements within the S-locus. RNA
 for RNA-seq was collected from stylar tissue and germinated pollen. For
 three genotypes, PacBio Iso-Sequencing was used to confirm the presence of
 alternative transcripts for the S-RNase gene. The combined datasets
 enabled us to localize both the male (pollen) and female (stylar)
 components of the S-locus. Sequences of the identified S-RNases and SLFs
 were used to evaluate their phylogenies along with other Solanaceae
 sequences for the same genes obtained from databases. Our analysis showed
 that SLF sequences are expressed in pollen but not in styles, vary in
 number between individuals, and are distributed across a 9-17 Mb region
 flanking one S-RNase gene. Preferential associations within haplotigs of
 specific S-RNase types and SLF types were not observed. Extensive sequence
 diversity was observed for S-RNases and SLFs, and phylogenetic analysis
 indicates that diversification of both genes predates the divergence
 between tomatoes and potatoes.
description: # Data from: The structure and allelic diversity of the
 self-incompatibility locus (S-locus) in diploid potatoes inferred from
 genome sequences and transcriptome data from styles and pollen Dataset
 DOI: [10.5061/dryad.qz612jmv1](https://doi.org/10.5061/dryad.qz612jmv1) ##
 Description of the data and file structure #### Files and variables
 **File: Genomes.zip** **Description:** contains assembled phased genomes
 in fasta format and annotation files in gff format. Fasta files were
 generated from PacBio HiFi data and assembled using Hifiasm v. 0.19.9.
 Gene prediction was done using Augustus v.3.5.0. Each sub-folder inside
 the Genomes folder is dedicated to a specific genotype. The identity of
 each WiDiPo genotype is listed in the genotypes_list.txt file. **File:
 Style_RNAseq.zip** **Description:** contains assembled style
 transcriptomes in fasta format and classifications of transcripts based on
 functional annotations of T2-Ribonucleases (GO0033887) as DNA and protein
 sequences. Also, transcripts for the IPR025886 domain are included for
 each genotype. Illumina fastq data were used to assemble the
 transcriptomes using the Trinity Assembler V. 2.15.1. Transcriptome
 annotations were done using TRAPID 2.0. The identity of each WiDiPo
 genotype is listed in the genotypes_list.txt file. **File:
 Style_Isoseq.zip** **Description:** contains full-length and
 quasi-full-length style transcripts in fasta format and classifications of
 transcripts based on functional annotations of T2-Ribonucleases
 (GO0033887) as DNA and protein sequences. PacBio isosequencing data was
 used to assemble the transcriptomes using the Trinity Assembler V. 2.15.1.
 Transcriptome annotations were done using TRAPID 2.0. The identity of each
 WiDiPo genotype is listed in the genotypes_list.txt file. **File:
 Gene_Alignments_and_Phylogenies.zip** **Description:** Contains sequence
 alignments and phylogeny files of S-RNase and SLF genes. All sequence
 alignments for S-RNases and SLFs were done using MAFFT v7.490 (Katoh et
 al., 2002; Katoh and Standley, 2013), and maximum likelihood (ML)
 phylogenies were reconstructed with RAxML V.8 (Stamatakis et al., 2014)
 using a GTR Gamma nucleotide model with rapid bootstrapping and search for
 the best-scoring ML tree. Five hundred bootstrap replicates were
 calculated, and a consensus tree was created. There are three subfolders:
 1) S-RNases cDNAs, 2) S-RNase proteins 3) SLFs cDNAs. In each subfolder,
 the following types of files can be found: .fasta (alignment in fasta
 format); .nex (alignment in nexus format); .phy (alignment in phylip
 format); .newick (phylogenetic tree in newick format). The identity of
 each WiDiPo genotype is listed in the genotypes_list.txt file. **File:
 Pollen_RNAseq.zip** **Description:** contains assembled pollen
 transcriptome in fasta format and fasta files for transcripts functionally
 classified for F-box domain proteins. Illumina fastq data were used to
 assemble the transcriptomes using the Trinity Assembler V. 2.15.1.
 Transcriptome annotations were done using TRAPID 2.0. Each sub-folder
 inside the Pollen_RNAseq folder is dedicated to a specific genotype. The
 identity of each WiDiPo genotype is listed in the genotypes_list.txt file.
 **File: QC_Metrics_for_Transcriptomes.xlsx** **Description:** contains
 quality evaluation parameters for all the transcriptome datasets. **File:
 Data_Figure6.txt** **Description:** Contains data used to generate the
 relationships graph of haplotypes (Figure 6) **File: Genotypes_list.txt**
 **Description:** Contains the information for all genotypes from this
 dataset. **Code/software** Alignments and phylogenies can be visualized
 with Mega.  All fasta files with GFF annotations can be visualized with
 JBrowse or IGV.