title: High-throughput sequencing of black pepper root transcriptome.
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.
authors.affiliation: Genetics and Molecular Biology Laboratory, Coastal Studies Institute, Bragança Campus, Universidade Federal do Pará, PA, Brazil.
authors.forename: Sheila M C
authors.initials: SM
authors.lastname: Gordo
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Pinheiro
authors.forename: Edith C O
authors.initials: EC
authors.lastname: Moreira
authors.forename: Simone M
authors.initials: SM
authors.lastname: Rodrigues
authors.forename: Marli C
authors.initials: MC
authors.lastname: Poltronieri
authors.forename: Oriel F
authors.initials: OF
authors.lastname: de Lemos
authors.forename: Israel Tojal
authors.initials: IT
authors.lastname: da Silva
authors.forename: Rommel T J
authors.initials: RT
authors.lastname: Ramos
authors.forename: Artur
authors.initials: A
authors.lastname: Silva
authors.forename: Horacio
authors.initials: H
authors.lastname: Schneider
authors.forename: Wilson A
authors.initials: WA
authors.lastname: Silva
authors.forename: Iracilda
authors.initials: I
authors.lastname: Sampaio
authors.forename: Sylvain
authors.initials: S
authors.lastname: Darnet
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D015723:Gene Library; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D029222:Piper nigrum / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics* / Q000378:metabolism; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D017386:Sequence Homology, Amino Acid; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D020543:Proteome; D018749:RNA, Plant