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”

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

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

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
Article number	105834
Journal	Data in Brief
Volume	31
DOIs	https://doi.org/10.1016/j.dib.2020.105834
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

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10.1016/j.dib.2020.105834

Cite this

Castro, J. C., Maddox, J. D., Rodríguez, H. N., Castro, C. G., Imán-Correa, S. A., Cobos, M., Paredes, J. D., Marapara, J. L., Braga, J., & Adrianzén, P. M. (2020). Dataset of de novo assembly and functional annotation of the transcriptome during germination and initial growth of seedlings of Myrciaria Dubia “camu-camu”. Data in Brief, 31, Article 105834. https://doi.org/10.1016/j.dib.2020.105834

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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{\texttrademark}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",

author = "Castro, {Juan C.} and Maddox, {J. Dylan} and Rodr{\'i}guez, {Hicler N.} and Castro, {Carlos G.} and Im{\'a}n-Correa, {Sixto A.} and Marianela Cobos and Paredes, {Jae D.} and Marapara, {Jorge L.} and Janeth Braga and Adrianz{\'e}n, {Pedro M.}",

note = "Publisher Copyright: {\textcopyright} 2020 The Author(s)",

year = "2020",

month = aug,

doi = "10.1016/j.dib.2020.105834",

language = "Ingl{\'e}s",

volume = "31",

journal = "Data in Brief",

issn = "2352-3409",

publisher = "Elsevier BV",

}

Castro, JC, Maddox, JD, Rodríguez, HN, Castro, CG, Imán-Correa, SA, Cobos, M, Paredes, JD, Marapara, JL, Braga, J & Adrianzén, PM 2020, 'Dataset of de novo assembly and functional annotation of the transcriptome during germination and initial growth of seedlings of Myrciaria Dubia “camu-camu”', Data in Brief, vol. 31, 105834. https://doi.org/10.1016/j.dib.2020.105834

TY - JOUR

T1 - Dataset of de novo assembly and functional annotation of the transcriptome during germination and initial growth of seedlings of Myrciaria Dubia “camu-camu”

AU - Castro, Juan C.

AU - Maddox, J. Dylan

AU - Rodríguez, Hicler N.

AU - Castro, Carlos G.

AU - Imán-Correa, Sixto A.

AU - Cobos, Marianela

AU - Paredes, Jae D.

AU - Marapara, Jorge L.

AU - Braga, Janeth

AU - Adrianzén, Pedro M.

PY - 2020/8

Y1 - 2020/8

N2 - 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).

AB - 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).

KW - Gene expression

KW - Germination

KW - Metabolic pathways

KW - Molecular sequence annotation

KW - Plant development

KW - RNA-seq

KW - Seedlings

UR - http://www.scopus.com/inward/record.url?scp=85086599901&partnerID=8YFLogxK

U2 - 10.1016/j.dib.2020.105834

DO - 10.1016/j.dib.2020.105834

M3 - Artículo

AN - SCOPUS:85086599901

SN - 2352-3409

VL - 31

JO - Data in Brief

JF - Data in Brief

M1 - 105834

ER -

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

Abstract

Bibliographical note

Keywords

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