Data from: A transcriptome screen for positive selection in domesticated breadfruit and its wild relatives (Artocarpus spp.)
Laricchia, Kristen M., Northwestern University
Johnson, Matthew G., Northwestern University
Ragone, Diane, National Tropical Botanical Garden
Williams, Evelyn W., Department of Plant Science; Chicago Botanic Garden; Glencoe IL 60022 USA
Zerega, Nyree J.C., Northwestern University
Wickett, Norman J., Northwestern University
Zerega, Nyree J. C., Northwestern University
Published Mar 21, 2019 on Dryad.
Cite this dataset
Laricchia, Kristen M. et al. (2019). Data from: A transcriptome screen for positive selection in domesticated breadfruit and its wild relatives (Artocarpus spp.) [Dataset]. Dryad. https://doi.org/10.5061/dryad.r7q2s
PREMISE OF THE STUDY: Underutilized crops, such as breadfruit (Artocarpus altilis, Moraceae) have the potential to improve global food security. Humans have artificially selected many cultivars of breadfruit since its domestication began approximately 3,500 years ago. The goal of this research is to identify transcriptomic signals of positive selection and to develop genomic resources that may facilitate the development of improved breadfruit cultivars in the future.
METHODS: A reference transcriptome of breadfruit was assembled de novo and annotated. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that may have resulted from local adaptation or natural selection. Emphasis was placed on MADS-box genes, which are important because they often regulate fruiting timing and structures, and carotenoids biosynthesis genes, which can impact the nutritional quality of the fruit.
KEY RESULTS: Over 1,000 genes showed signals of positive selection, and these genes were enriched for localization to plastids. Nucleotide sites and individuals under positive selection were discovered in MADS-box genes and carotenoid biosynthesis genes, with several sites located in cofactor or DNA-binding domains. A McDonald-Kreitman test comparing wild to cultivated samples revealed selection in one of the carotenoid biosynthesis genes, abscisic acid 8'-hydroxylase 3.
CONCLUSIONS: This research highlights some of the many genes that may have been intentionally or unintentionally selected for during the human-mediated dispersal of breadfruit and stresses the importance of conserving a varied germplasm collection. It has revealed candidate genes for further study and produced new genomic resources for breadfruit.
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.
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.
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:18.104.22.168. Trimmed paired and unpaired reads were assembled using Trinity vr2013-02-25 and only the longest isoform per component/subcomponent was retained.