Abstract
Myrciaria dubia “camu-camu” is a native shrub of the Amazon that is commonly found in areas that are flooded for three to four months during the annual hydrological cycle. This plant species is exceptional for its capacity to biosynthesize and accumulate important quantities of a variety of health-promoting phytochemicals, especially vitamin C [1], yet few genomic resources are available [2]. Here we provide the dataset of a de novo assembly and functional annotation of the transcriptome from a pool of samples obtained from seeds during the germination process and seedlings during the initial growth (until one month after germination). Total RNA/mRNA was purified from different types of plant materials (i.e., imbibited seeds, germinated seeds, and seedlings of one, two, three, and four weeks old), pooled in equimolar ratio to generate the cDNA library and RNA paired-end sequencing was conducted on an Illumina HiSeq™2500 platform. The transcriptome was de novo assembled using Trinity v2.9.1 and SuperTranscripts v2.9.1. A total of 21,161 transcripts were assembled ranging in size from 500 to 10,001 bp with a N50 value of 1,485 bp. Completeness of the assembly dataset was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) software v2/v3. Finally, the assembled transcripts were functionally annotated using TransDecoder v3.0.1 and the web-based platforms Kyoto Encyclopedia of Genes and Genomes (KEGG) Automatic Annotation Server (KAAS), and FunctionAnnotator. The raw reads were deposited into NCBI and are accessible via BioProject accession number PRJNA615000 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA615000) and Sequence Read Archive (SRA) with accession number SRX7990430 (https://www.ncbi.nlm.nih.gov/sra/SRX7990430). Additionally, transcriptome shotgun assembly sequences and functional annotations are available via Discover Mendeley Data (https://data.mendeley.com/datasets/2csj3h29fr/1).
Original language | English |
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Article number | 105834 |
Journal | Data in Brief |
Volume | 31 |
DOIs | |
State | Published - Aug 2020 |
Externally published | Yes |
Bibliographical note
Funding Information:Authors received financial support from the Universidad Nacional de la Amazonia Peruana through the grant "Structural and Functional Analysis of the Genome of Myrciaria dubia "camu-camu" How Basis For Genetic Improvement" (Grant ID RR N° 0686–2015-UNAP). Additionally, we thank the Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú (UCP) and the Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History (Chicago, USA) for providing necessary infrastructure and equipment. Finally, we thank the Instituto Nacional de Innovación Agraria (INIA) for providing the authorization to collect the botanical samples in the germplasm collection of “camu-camu”.
Funding Information:
Authors received financial support from the Universidad Nacional de la Amazonia Peruana through the grant "Structural and Functional Analysis of the Genome of Myrciaria dubia "camu-camu" How Basis For Genetic Improvement" (Grant ID RR N° 0686–2015-UNAP ). Additionally, we thank the Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú (UCP) and the Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History (Chicago, USA) for providing necessary infrastructure and equipment. Finally, we thank the Instituto Nacional de Innovación Agraria (INIA) for providing the authorization to collect the botanical samples in the germplasm collection of “camu-camu”.
Publisher Copyright:
© 2020 The Author(s)
Keywords
- Gene expression
- Germination
- Metabolic pathways
- Molecular sequence annotation
- Plant development
- RNA-seq
- Seedlings