Dataset of de novo assembly and functional annotation of the transcriptome during germination and initial growth of seedlings of Myrciaria Dubia "camu-camu"

Juan C Castro; J Dylan Maddox; Hicler N Rodríguez; Carlos G Castro; Sixto A Imán-Correa; Marianela Cobos; Jae D Paredes; Jorge L Marapara; Janeth Braga; Pedro M Adrianzén

doi:10.1016/j.dib.2020.105834

Dataset of de novo assembly and functional annotation of the transcriptome during germination and initial growth of seedlings of Myrciaria Dubia "camu-camu"

Data Brief. 2020 Jun 11:31:105834. doi: 10.1016/j.dib.2020.105834. eCollection 2020 Aug.

Authors

Juan C Castro^{1

2}, J Dylan Maddox^{3

4

5}, Hicler N Rodríguez^{1

3}, Carlos G Castro^{1

3}, Sixto A Imán-Correa⁶, Marianela Cobos³, Jae D Paredes³, Jorge L Marapara^{1

2}, Janeth Braga^{1

2}, Pedro M Adrianzén^{1

2}

Affiliations

¹ Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Psje. Los Paujiles S/N, San Juan Bautista, Loreto, 16000, Perú.
² Departamento Académico de Ciencias Biomédicas y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional de la Amazonia Peruana (UNAP), Ciudad Universitaria - Zungarococha, San Juan Bautista, Loreto, 16000, Perú.
³ Laboratorio de Biotecnología y Bioenergética (LBB), Universidad Científica del Perú (UCP), Av. Abelardo Quiñones km. 2.5, San Juan Bautista, Loreto, 16000 Perú.
⁴ Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, United States.
⁵ Environmental Sciences, American Public University System, Charles Town, WV 25414, United States.
⁶ Estación Experimental Agraria San Roque, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Calle San Roque 236, San Juan Bautista, Loreto, 16000, Perú.

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).

Keywords: Gene expression; Germination; Metabolic pathways; Molecular sequence annotation; Plant development; RNA-seq; Seedlings.