Dataset of de novo assembly and functional annotation of the transcriptome during germination and initial growth of seedlings of Myrciaria Dubia “camu-camu”
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-p...
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| Format: | info:eu-repo/semantics/article |
| Language: | Inglés |
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Elsevier
2020
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| Online Access: | https://repositorio.inia.gob.pe/handle/20.500.12955/1109 https://doi.org/10.1016/j.dib.2020.105834 |
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| author | Castro Gómez, Juan Carlos Maddox, J. Dylan Rodríguez, Hicler N. Castro, Carlos G. Imán Correa, Sixto Alfredo Cobos Ruiz, Marianela Paredes, Jae D. Marapara del Aguila, Jorge Luis Braga, Janeth Adrianzén Julca, Pedro Marcelino |
| author_browse | Adrianzén Julca, Pedro Marcelino Braga, Janeth Castro Gómez, Juan Carlos Castro, Carlos G. Cobos Ruiz, Marianela Imán Correa, Sixto Alfredo Maddox, J. Dylan Marapara del Aguila, Jorge Luis Paredes, Jae D. Rodríguez, Hicler N. |
| author_facet | Castro Gómez, Juan Carlos Maddox, J. Dylan Rodríguez, Hicler N. Castro, Carlos G. Imán Correa, Sixto Alfredo Cobos Ruiz, Marianela Paredes, Jae D. Marapara del Aguila, Jorge Luis Braga, Janeth Adrianzén Julca, Pedro Marcelino |
| author_sort | Castro Gómez, Juan Carlos |
| collection | Repositorio INIA |
| description | 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. |
| format | info:eu-repo/semantics/article |
| id | INIA1109 |
| institution | Institucional Nacional de Innovación Agraria |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Elsevier |
| publisherStr | Elsevier |
| record_format | dspace |
| spelling | INIA11092024-11-29T03:39:13Z Dataset of de novo assembly and functional annotation of the transcriptome during germination and initial growth of seedlings of Myrciaria Dubia “camu-camu” Castro Gómez, Juan Carlos Maddox, J. Dylan Rodríguez, Hicler N. Castro, Carlos G. Imán Correa, Sixto Alfredo Cobos Ruiz, Marianela Paredes, Jae D. Marapara del Aguila, Jorge Luis Braga, Janeth Adrianzén Julca, Pedro Marcelino Gene expression Germination Metabolic pathways Molecular sequence annotation Plant development RNA-seq Seedlings Tecnología de modificación genética 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. Specifications table. Value of the data. 1.- Data description. 2.- Experimental design, material, and methods. References. 2020-06-25T19:09:59Z 2020-06-25T19:09:59Z 2020-06-11 info:eu-repo/semantics/article Castro, J.; Maddox, J.; Rodríguez, H.; Castro, C.; Imán, S., Cobos, M.; Paredes, J.; Marapara, J.; Braga, J.; Adrianzén, P. (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, Volume 31, Agosto 2020,105834. Doi: 10.1016/j.dib.2020.105834 https://repositorio.inia.gob.pe/handle/20.500.12955/1109 Data in Brief https://doi.org/10.1016/j.dib.2020.105834 eng Data in Brief, Volume 31, Agosto 2020,105834 https://doi.org/10.1016/j.dib.2020.105834 info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/4.0/ application/pdf application/pdf Perú Elsevier Países bajos Instituto Nacional de Innovación Agraria Repositorio Institucional - INIA |
| spellingShingle | Gene expression Germination Metabolic pathways Molecular sequence annotation Plant development RNA-seq Seedlings Tecnología de modificación genética Castro Gómez, Juan Carlos Maddox, J. Dylan Rodríguez, Hicler N. Castro, Carlos G. Imán Correa, Sixto Alfredo Cobos Ruiz, Marianela Paredes, Jae D. Marapara del Aguila, Jorge Luis Braga, Janeth Adrianzén Julca, Pedro Marcelino Dataset of de novo assembly and functional annotation of the transcriptome during germination and initial growth of seedlings of Myrciaria Dubia “camu-camu” |
| title | Dataset of de novo assembly and functional annotation of the transcriptome during germination and initial growth of seedlings of Myrciaria Dubia “camu-camu” |
| title_full | Dataset of de novo assembly and functional annotation of the transcriptome during germination and initial growth of seedlings of Myrciaria Dubia “camu-camu” |
| title_fullStr | Dataset of de novo assembly and functional annotation of the transcriptome during germination and initial growth of seedlings of Myrciaria Dubia “camu-camu” |
| title_full_unstemmed | Dataset of de novo assembly and functional annotation of the transcriptome during germination and initial growth of seedlings of Myrciaria Dubia “camu-camu” |
| title_short | Dataset of de novo assembly and functional annotation of the transcriptome during germination and initial growth of seedlings of Myrciaria Dubia “camu-camu” |
| title_sort | dataset of de novo assembly and functional annotation of the transcriptome during germination and initial growth of seedlings of myrciaria dubia camu camu |
| topic | Gene expression Germination Metabolic pathways Molecular sequence annotation Plant development RNA-seq Seedlings Tecnología de modificación genética |
| url | https://repositorio.inia.gob.pe/handle/20.500.12955/1109 https://doi.org/10.1016/j.dib.2020.105834 |
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