Genome assemblies, annotations, targets, and bait sequences from Gardner et al. 2016

A_camansi_v1.0_scaffolds.fasta -- Genome assembly v. 1.0 (Ray 2.3.1) A_camansi_v1.1_scaffolds.fasta -- Genome assembly v. 1.1 (L_RNA_Scaffolder) A_camansi_v1.1_genepredictions.gff -- Gene predictions in GFF format (Augustus) A_camansi_v1.1_genepredictions.fna -- Predicted coding sequences (Augustus) A_camansi_v1.1_genepredictions.faa.aa -- Predicted protein sequences (Augustus) A_camansi_v1.1_genepredictions_annotations.txt -- Gene annotations (Trinotate) artocarpus_333genes.fasta -- 333 phylogenetic marker sequences artocarpus_mbgenes.fasta -- 98 putativeMADS-box gene sequences artocarpus_volgenes.fasta -- 27 putative volatile gene sequences artocarpus_baits.fasta -- 120mer bait sequences (designed by MYcroarray

breadfruit assemblies

Assemblies for nine A. altilis, seven A. camansi, one A. mariannensis, and seven A. altilis × A. mariannensis hybrid samples. Raw reads were trimmed using Trimmomatic v0.30 to remove low quality bases, adapter sequences, and other sequencing artifacts. Poly-A and poly-T tails were removed with Trimest vEMBOSS:6.6.0.0. Trimmed paired and unpaired reads were assembled using Trinity vr2013-02-25 and only the longest isoform per component/subcomponent was retained

breadfruit vcf

Sequences were aligned to Artocarpus camansi draft genome with bwa v0.6.2 mem, called separately for triploids and diploids with GATK v3.2-2 HaplotypeCaller, and hard filtered according to GATK’s recommendations

XML file for SNAPP analysis

Random sample of one SNP per locus for Artocarpus camansi and Artocarpus altilis in XML format for use in SNAPP analysis

HybPiper assemblies for Johnson et al. (2016)

Output of HybPiper for 22 Artocarpus species and six outgroups, including Ficus and Morus. BWA was used to map the reads to the targets, including 333 genes used for phylogenetics (prefix "gene"), 98 MADS-Box genes (prefix "MB") and 27 genes functionally annotated as involved in volatile compounds (prefix "Vol"). After running the main HybPiper script (reads_first.py) we also ran "intronerate.py" to extract exon sequences, "paralog_investigator.py" to extract putative paralog sequences, "depth_calculator.py" to estimate depth of coverage in recovered exon sequence, and "cleanup.py" to remove redundant files from the SPAdes contig assembly. Data from: Johnson M., E.M. Gardner, J. Shaw, Y. Liu, R. Medina, B. Goffinet, N.J.C. Zerega, and N. Wickett. HybPiper: extracting phylogenetic datasets from high-throughput sequencing reads using targeted bait capture. Applications in Plant Science