DOI: 10.5061/dryad.qnk98sfpt
title: The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

description: Coffea arabica, an allotetraploid hybrid of C.
 eugenioides and C. canephora, is the source of
 approximately 60% of coffee products worldwide, and its cultivated
 accessions have undergone several population bottlenecks. We present
 chromosome-level assemblies of a di-haploid C.
 arabica accession and modern representatives of its diploid
 progenitors, C. eugenioides and C. canephora.
 The three species exhibit largely conserved genome structures between
 diploid parents and descendant subgenomes, with no obvious global
 subgenome dominance. We find evidence for a founding polyploidy event
 350,000-610,000 years ago, followed by several pre-domestication
 bottlenecks, resulting in narrow genetic variation. A split between wild
 accessions and cultivar progenitors occurred ∼30.5 kya, followed by a
 period of migration between the two populations. Analysis of modern
 varieties, including lines historically introgressed with C.
 canephora, highlights their breeding histories and loci that may
 contribute to pathogen resistance, laying the groundwork for future
 genomics-based breeding of C. arabica.
description: For syntenic alignments, the assemblies were aligned in CoGe
 platform (https://genomevolution.org/coge/) using default settings.  For the resequencing of 38 wild and cultivated <em>Coffea arabica</em>, two wild <em>C. eugenioides</em>, two cultivated and one wild <em>C. canephora </em>accessions, libraries were prepared using the KAPA HyperPrep Kits (Roche) following manufacturer's instructions, and paired-end (2 x 125) sequenced on a Illumina HiSeq2500 instrument to ~40x coverage. Additionally, Linnaean herbarium sample was sequenced to 46x coverage with Ion Torrent technology.  Following quality control with FastQC, Illumina short reads were trimmed using Trimmomatic v0.36 and mapped on the <em>C. arabica</em> reference assembly with BWA mem v0.7.16a-r1181. For the Linnaean sample, the reads were processed according to the protocols recommended for degraded DNA analysis in MapDamage v.2.0.8. GATK (v 3.8.0) pipeline was used for SNP calling. Duplicates were marked and removed using Picard v2.0.1 and genotype likelihoods were called into GVCF files using HaplotypeCaller (GATK). For the diploid progenitors, to allow interspecies comparisons, the mapping was done to each of the subgenomes separately, including chromosome zero, i.e., contigs not assembled into pseudomolecules, in both mappings. Joint calling was carried out using GenotypeGVCFs (GATK) and snpEff v4.3t was used to assess the impact of the SNPs. To remove regions with cross-species mappings, we removed the SNPs that were called as heterozygous when mapping the di-haploid ET39 sequencing data to the Arabica reference genome.
description: # The genome and population genomics of allopolyploid Coffea arabica
 reveal the diversification history of modern coffee cultivars
 The dataset contains two
 items: **(i)** syntenic alignments between *C. canephora*, *C.
 eugenioides* and *C. arabica* assemblies, and **(ii)** the variant calls
 used in the population analyses in the paper. ## Description of the data
 and file structure **i.** Syntenic alignments have been obtained in CoGe
 SynMap tool using default settings. In file names, the first two items
 give the CoGe IDs of the genomes being aligned: *C. canephora* - ID50947;
 *C. eugenioides* - ID51132; *C. arabica* subCC - ID65471; *C. arabica*
 subEE - ID65472; *C. arabica* - ID65463. The contents of the columns in
 syntenic alignments are described on row 3 of the files, and on row 1 in
 tandem duplicate files (which can be identified as having .*tandems.* in
 their names). **ii.** The variant calls are given in VCF formatted files.
 Each subgenome has its own file, Arabica_sgC.TIP.BB contains variant calls
 for subgenome CC of *C. arabica*, and Arabica_sgE.TIP.BB for subgenome EE,
 respectively. Variants have been filtered for SNPs that were called as
 heterozygous in di-haploid *C. arabica* accession Et39, but otherwise no
 quality filtering for the variants has been done in these files. See
 Supplementary Material, Section 6.2 for the specific filterings carried
 out in the publication. Mapping between the sequencing IDs and accession
 names is given in the provided Excel sheet (Accession_info.xlsx). Seq.ID
 (column B) shows the accession ID used in sequencing. accession_name
 (column C) gives the name of the accession/cultivar. Species_name (Column
 D) provides the species of the accession, three different Coffea species
 were analysed in this study. Variety (column E) gives information on the
 cultaivation status, Introgressed identifies *C. arabica* x *C. canephora*
 hybrids. Columns F-J provide the place of origin of the accession
 (district/location, country, as well as GPS coordinates). The cells are
 left empty if the exact value (GPS coordinate or altitude) is not known.
 Columns K-M provide genome information, ploidy level, estimated genome
 size and genome structure. Columns N-R give additional information, donor
 institute, collection location, additional notes on the accession as well
 as original reference. If exact collection location is not known the cell
 is left empty. In those cases the material has been obtained from line(s)
 maintained by the donor institute (column N). Cells in columns Q-R are
 left empty if there is no (known) original publication associated with the
 accession. Code/Software: For the syntenic alignments, CoGe platform was
 used. For the variant calls,. Linux operating system and GATK was used to
 obtain the VCF files, subsequent analysis was carried out using R, Plink,
 vcftools, smc++.