Next-generation sequencing has allowed for huge advances in developing genomic resources for non-model systems such as Artocarpus. We have assembled a draft genome sequence for A. camansi (breadnut), the wild progenitor of breadfruit, to support target-enrichment phylogenomics (HybSeq) and explore the evolution of genomes in Artocarpus.
Gardner, E.M., M.G. Johnson, D. Ragone, N.J. Wickett, and N.J.C. Zerega. 2016. Low-coverage, whole-genome sequencing ofArtocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery. Applications in Plant Sciences, 4(7), apps.1600017. http://doi.org/10.3732/apps.1600017
Johnson, M.G., E.M. Gardner, Y. Liu, R. Medina, B. Goffinet, A.J., N.J.C. Zerega, and N.J. Wickett. 2016. HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment.Applications in Plant Sciences,4(7), apps.1600016. http://doi.org/10.3732/apps.1600016
Supplemental data from E.M. Gardner, M.G. Johnson, D. Ragone, N.J. Wickets, and N.J.C. Zerega, in review. Low-coverage, whole-genome shotgun sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery:
- Genome assembly v. 1.0 (Ray 2.3.1)
- Genome assembly v. 1.1 (L_RNA_Scaffolder)
- Predicted coding sequences (Augustus)
- Predicted protein sequences (Augustus)
- Gene annotations (Trinotate)
- 333 phylogenetic marker sequences
- 98 putativeMADS-box gene sequences
- 27 putative volatile gene sequences
- 120mer bait sequences (designed by MYcroarray)
Supplemental data from M.G. Johnson, E.M. Gardner, B. Goffinet, Y. Liu, R. Medina, A.J. Shaw, N.J.C. Zerega, and N.J. Wickett, in review. HybPiper: extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment:
- HybPiper Reference bait file
- Recovered sequence lengths
- Gene alignments
- Maximum-likelihood tree