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Logo of bmcpsBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Plant Biology
 
BMC Plant Biol. 2012; 12: 168.
Published online Sep 17, 2012. doi:  10.1186/1471-2229-12-168
PMCID: PMC3487918
High-throughput sequencing of black pepper root transcriptome
Sheila MC Gordo,1 Daniel G Pinheiro,2 Edith CO Moreira,1 Simone M Rodrigues,3 Marli C Poltronieri,3 Oriel F de Lemos,3 Israel Tojal da Silva,2 Rommel TJ Ramos,4 Artur Silva,4 Horacio Schneider,1 Wilson A Silva, Jr,2 Iracilda Sampaio,1 and Sylvain Darnetcorresponding author4
1Genetics and Molecular Biology Laboratory, Coastal Studies Institute, Bragança Campus, Universidade Federal do Pará, Bragança, PA, 68.600-000, Brazil
2Departamento 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
3EMBRAPA Amazônia Oriental, Trav. Dr. Enéas Pinheiro s/nº, Caixa Postal 48, Belém, PA 66095-100, Brazil
4Instituto de Ciências Biológicas, Universidade Federal do Pará, Campus Universitário do Guamá, Rua Augusto Corrêa, nº1, Belém, PA 66075-110, Brazil
corresponding authorCorresponding author.
Sheila MC Gordo: sheilamaysa/at/ufpa.br; Daniel G Pinheiro: dgpinheiro/at/usp.br; Edith CO Moreira: cibelle/at/ufpa.br; Simone M Rodrigues: simone.rodrigues/at/embrapa.br; Marli C Poltronieri: marli.poltronieri/at/embrapa.br; Oriel F de Lemos: oriel.lemos/at/embrapa.br; Israel Tojal da Silva: itojal/at/usp.br; Rommel TJ Ramos: rommelramos/at/ufpa.br; Artur Silva: asilva/at/ufpa.br; Horacio Schneider: horacio/at/ufpa.br; Wilson A Silva, Jr: wilsonjr/at/usp.br; Iracilda Sampaio: ira/at/ufpa.br; Sylvain Darnet: shd/at/laposte.net
Received January 26, 2012; Accepted August 29, 2012.
Abstract
Background
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.
Results
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.
Conclusions
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.
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