Abstract
Avocado (Persea americana Mill.), macadamia (Macadamia integrifolia L.) and mango (Mangifera indica L.) are important subtropical tree species grown for their edible fruits and nuts. Despite their commercial and nutritional importance, the genomic information for these species is largely lacking. Here we report the generation of avocado, macadamia and mango transcriptome assemblies from pooled leaf, stem, bud, root, floral and fruit/nut tissue. Using normalized cDNA libraries, we generated comprehensive RNA-Seq datasets from which we assembled 63420, 78871 and 82198 unigenes of avocado, macadamia and mango, respectively using a combination of de novo transcriptome assembly and redundancy reduction. These unigenes were functionally annotated using Basic Local Alignment Search Tool (BLAST) to query the Universal Protein Resource Knowledgebase (UniProtKB). A workflow encompassing RNA extraction, library preparation, transcriptome assembly, redundancy reduction, assembly validation and annotation is provided. This study provides avocado, macadamia and mango transcriptome and annotation data, which is valuable for gene discovery and gene expression profiling experiments as well as ongoing and future genome annotation and marker development applications.
Highlights
Background & SummaryFruits and nuts are an important source of vitamins and dietary fibre for consumers and a source of income for farmers
Avocado (Persea americana Mill.), macadamia (Macadamia integrifolia L.) and mango (Mangifera indica L.) are important commercial tree species grown in Australia and other tropical/sub-tropical regions
The assemblies generated in this study can be utilized as reference gene sets for a variety of tree genomics studies requiring transcriptome information of Persea americana, Macadamia integrifolia, Mangifera indica and related species
Summary
Fruits and nuts are an important source of vitamins and dietary fibre for consumers and a source of income for farmers. Mangoes are produced commercially in at least 87 countries on an estimated area 5 million hectares with an annual production of over 35 million tonnes[3] Despite their commercial and nutritional importance, these tree crops are yet to benefit from a substantial research effort required to generate significant public bioinformatic resources. Two studies published open-access transcriptome assemblies from several tissues of avocado and mango respectively[8,9,10] These assemblies were derived from RNA-Seq libraries that were not normalised and lack some essential yet lowly expressed genes and near-universal single-copy genes (Supplementary Fig. 1). The assemblies generated in this study can be utilized as reference gene sets for a variety of tree genomics studies requiring transcriptome information of Persea americana, Macadamia integrifolia, Mangifera indica and related species. Our transcriptome assemblies will assist in mRNA-based genome annotation[19] for ongoing whole genome sequencing projects of macadamia and mango[11,13]
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