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High-throughput sequencing of black pepper root transcriptome

Sheila MC Gordo1, Daniel G Pinheiro2, Edith CO Moreira1, Simone M Rodrigues3, Marli C Poltronieri3, Oriel F de Lemos3, Israel Tojal da Silva2, Rommel TJ Ramos4, Artur Silva4, Horacio Schneider1, Wilson A Silva2, Iracilda Sampaio1 and Sylvain Darnet4*

Author Affiliations

1 Genetics and Molecular Biology Laboratory, Coastal Studies Institute, Bragança Campus, Universidade Federal do Pará, Bragança, PA, 68.600-000, Brazil

2 Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Centro Regional de Hemoterapia de Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP 14051-140, Brazil

3 EMBRAPA Amazônia Oriental, Trav. Dr. Enéas Pinheiro s/nº, Caixa Postal 48, Belém, PA 66095-100, Brazil

4 Instituto de Ciências Biológicas, Universidade Federal do Pará, Campus Universitário do Guamá, Rua Augusto Corrêa, nº1, Belém, PA 66075-110, Brazil

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BMC Plant Biology 2012, 12:168  doi:10.1186/1471-2229-12-168

Published: 17 September 2012



Black pepper (Piper nigrum L.) is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host’s root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper.


The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant’s root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology.


This dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms.