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High-throughput sequencing analysis of Eugenia uniflora: insights into repetitive DNA, gene content and potential biotechnological applications

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Abstract

In this study, the Ion Torrent PGM platform was employed to conduct a whole-genome sequencing analysis of Eugenia uniflora L., aiming to generate new genomic information for this non-model species. The whole-genome set of assembled sequences (WGSAS) generated 2601 contigs, with a cumulative length of 3.15 Mbp. About 2.60% of the WGSAS was characterized by repetitive sequences, while 71.66% of the WGSAS was represented by predicted genes. A total of 147 metabolic pathways related to enzymes characterized in the E. uniflora WGSAS were detected. Proteins related to antifungal activity and to bacterium and fungi defense response as well as transcriptions factors related to abiotic stress responses were also identified. This sequencing provides important genomic resources for future breeding and selection regarding plants with higher production of such metabolites, as well as source of genes for genetic engineering of cultivated species, supporting a wide application of marker-assisted and genomic selection, towards the establishment of commercial orchards with improved cultivars of E. uniflora.

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Acknowledgements

We would like to thank CAPES for scholarship to D.S.S., CNPq/Brazil by financial support (Grant number 442995/2014-8) and Research Fellowship provided to V.M.S. (Process 302501/2017-7) and Universidade Federal do Pampa—UNIPAMPA (Edital PROPESQ/AGP/2016). We specially thank to MSc. Rafael Plá Matielo Lemos, Dr. Filipe de Carvalho Victoria and Dr. Victor Pyrlo by technical support in data analysis.

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Authors and Affiliations

  1. Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa, Rod. BR290, Campus Universitário, São Gabriel, RS, 97300-000, Brazil

    Valdir Marcos Stefenon & Luiz Fernando Würdig Roesch

  2. Universidade Federal Rural do Rio de Janeiro, Rod. BR 465, Km 07, s/n-Zona Rural, Seropédica-RJ, Rio de Janeiro, RJ, 23890-000, Brazil

    Deise Schröder Sarzi

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  1. Valdir Marcos Stefenon
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  2. Deise Schröder Sarzi
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  3. Luiz Fernando Würdig Roesch
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Correspondence to Valdir Marcos Stefenon.

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13205_2019_1729_MOESM1_ESM.tiff

Supplementary Figure 1: Number of BLAST hits of the E. uniflora sequences in relation to plant species sequences deposited in the GenBank/NCBI databank

13205_2019_1729_MOESM2_ESM.tiff

Supplementary Figure 2: Number of sequences of E. uniflora WGSAS matching each GO terms. Highlighted in red are GO terms with of putative biotechnological interest into the pharmaceutical and agronomical sectors

13205_2019_1729_MOESM3_ESM.tiff

Supplementary Figure 3: Summary of the E. uniflora WGSAS annotation. (A) Number of sequences with and without InterPro [IPS] matches and with gene ontology [GO] matches. (B) Number of sequences with GO matches and with IPS before and after merging results from the found GOs and the annotation project. (C) Number of enzyme families identified in the IPS search. (D) Distribution of GO terms designed for the DNA sequences

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Stefenon, V.M., Sarzi, D.S. & Roesch, L.F.W. High-throughput sequencing analysis of Eugenia uniflora: insights into repetitive DNA, gene content and potential biotechnological applications. 3 Biotech 9, 200 (2019). https://doi.org/10.1007/s13205-019-1729-1

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