ArticleScientific data2020
De novo transcriptome assembly and annotation for gene discovery in avocado, macadamia and mango.
Article in Scientific data, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 32 citations in OpenAlex.
- Stage-Specific Transcriptomic Insights into Seed Germination and Early Development inPlants (Basel, Switzerland) · 2025Article
- Advancing Enzyme-Based Detoxification Prediction with ToxZyme: An Ensemble Machine Learning Approach.Toxins · 2025Article
- The dark side of avocados: a review of anthracnose and stem-end rot in postharvest fruit.Frontiers in microbiology · 2025Review
- Integrated de novo transcriptome of Culex pipiens mosquito larvae as a resource for genetic control strategies.Scientific data · 2024Article
- Molecular Cues for Phenological Events in the Flowering Cycle in Avocado.Plants (Basel, Switzerland) · 2023Article
- Insights into the domestication of avocado and potential genetic contributors to heterodichogamy.G3 (Bethesda, Md.) · 2023Article
- Advances in sequencing and key character analysis of mango (Horticulture research · 2023Article
- A simple guide to de novo transcriptome assembly and annotation.Briefings in bioinformatics · 2022Review
- Article
- Chromosome-Scale Assembly and Annotation of the Macadamia Genome (G3 (Bethesda, Md.) · 2020Article
- De novo transcriptome assembly and annotation for gene discovery in avocado, macadamia and mango.Scientific data · 2020Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.