DOI: 10.5061/dryad.3293r
title: Data from: Low-coverage, whole-genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery

description: Premise of the study: We used moderately low-coverage (17×) whole-genome
 sequencing of Artocarpus camansi (Moraceae) to develop genomic resources
 for Artocarpus and Moraceae. Methods and Results: A de novo assembly of
 Illumina short reads (251,378,536 pairs, 2 × 100 bp) accounted for 93% of
 the predicted genome size. Predicted coding regions were used in a
 three-way orthology search with published genomes of Morus notabilis and
 Cannabis sativa. Phylogenetic markers for Moraceae were developed from 333
 inferred single-copy exons. Ninety-eight putative MADS-box genes were
 identified. Analysis of all predicted coding regions resulted in
 preliminary annotation of 49,089 genes. An analysis of synonymous
 substitutions for pairs of orthologs (Ks analysis) in M. notabilis and A.
 camansi strongly suggested a lineage-specific whole-genome duplication in
 Artocarpus. Conclusions: This study substantially increases the genomic
 resources available for Artocarpus and Moraceae and demonstrates the value
 of low-coverage de novo assemblies for nonmodel organisms with moderately
 large genomes.
description: Genome assemblies,
 annotations, targets, and bait sequences from Gardner et al.
 2016A_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)Gardner_et_al_2016.tar.gzHybPiper 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 Sciencesartocarpus_hybseq_bwa.tar.gzAnalyses from Johnson et al. 2016README for HybPiper_artocarpus_analysis.tar.gz artocarpus_trimmed.exon.tar.gz Trimmed coding sequence (exon) alignments for 28 taxa for 333 genes. Sequences were aligned in MAFFT and trimmed using Trimal, discarding all columns with more than 80% missing data. supercontig_trimmed_fasta.tar.gz Trimmed supercontig sequence alignments (containing both exons and flanking "splash zone" intron sequence) for 28 taxa for 333 genes. Sequences were aligned in MAFFT and trimmed using Trimal, discarding all columns with more than 80% missing data. artocarpus_hybpiper_genelengths.txt Lengths of exon sequence (CDS) recovered for 458 loci for 28 taxa using the BWA method. File generated using "get_seq_lengths.py" in HybPiper, and used to generate the heatmap figure in the HybPiper manuscript (with "gene_recovery_heatmap.R") allbaitsuppercase.fna Nucleotide "target" file used with HybPiper. For 333 loci, there are two orthologous sequences per gene: one from the Artocarpus camansi draft genome, and one from the Morus notabalis genome. For the remaining genes, only an Artocarpus ortholog is present. artocarpus_bwa.supercontig.supermatrix.raxml.tre RAxML phylogeny generated from a concatenated supermatrix of supercontig sequences for 22 Artocarpus species and six outgroups, using the 333 "phylogenetic" loci. Tree generated from nucleotide data using the GTRCAT model, with one partition per gene. artocarpus_hybseq.exon.raxml.names.tre RAxML phylogeny generated from a concatenated supermatrix of exon sequences extracted by HybPiper for 22 Artocarpus species and six outgroups, using the 333 "phylogenetic" loci. Node labels indicate bootstrap support from 200 "fast bootstrap" replicates. Analyses 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 SciencesHybPiper_artocarpus_analysis.tar.gz