Journal of Applied Phycology

, Volume 24, Issue 4, pp 641–647 | Cite as

Analysis of expressed sequence tags from the agarophyte Gracilaria tenuistipitata (Rhodophyta)

  • Pi Nyvall Collén
  • Jonas Collén
  • Marcelo da Silva Reis
  • Marianne Pedersén
  • João C. Setubal
  • Alessandro M. Varani
  • Pio Colepicolo
  • Mariana C. Oliveira
Article

Abstract

A total of 3,631 expressed sequence tags (ESTs) were established from two size-selected cDNA libraries made from the tetrasporophytic phase of the agarophytic red alga Gracilaria tenuistipitata. The average sizes of the inserts in the two libraries were 1,600 bp and 600 bp, with an average length of the edited sequences of 850 bp. Clustering gave 2,387 assembled sequences with a redundancy of 53%. Of the ESTs, 65% had significant matches to sequences deposited in public databases, 11% to proteins without known function, and 35% were novel. The most represented ESTs were a Na/K-transporting ATPase, a hedgehog-like protein, a glycine dehydrogenase and an actin. Most of the identified genes were involved in primary metabolism and housekeeping. The largest functional group was thus genes involved in metabolism with 14% of the ESTs; other large functional categories included energy, transcription, and protein synthesis and destination. The codon usage was examined using a subset of the data, and the codon bias was found to be limited with all codon combinations used.

Keywords

Agarophyte Codon bias Expressed sequence tags Gracilaria tenuistipitata Rhodophyta 

Notes

Acknowledgment

This research was performed under a Swedish–Brazilian research cooperation founded by The Swedish Foundation for International Cooperation in Research (STINT). Support was also obtained from the State of São Paulo Research Foundation (FAPESP) and the Brazilian National Council for Scientific and Technological Development (CNPq). E.C. Oliveira collected the strain used in this work.

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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Pi Nyvall Collén
    • 1
    • 6
  • Jonas Collén
    • 2
  • Marcelo da Silva Reis
    • 3
  • Marianne Pedersén
    • 4
  • João C. Setubal
    • 5
  • Alessandro M. Varani
    • 1
  • Pio Colepicolo
    • 2
  • Mariana C. Oliveira
    • 1
  1. 1.Department of Botany, Institute of BiosciencesUniversity of São PauloSão PauloBrazil
  2. 2.Department of Biochemistry, Institute of ChemistryUniversity of São PauloSão PauloBrazil
  3. 3.Departement of mathematics and statisticsUniversity of São PauloSão PauloBrazil
  4. 4.Department of BotanyStockholm UniversityStockholmSweden
  5. 5.Virginia Bioinformatics InstituteVirginia Polytechnic Institute and State UniversityBlacksburgUSA
  6. 6.Université Pierre et Marie Curie, Paris VI, CNRS, Marine Plants and biomolecules, UMR 7139RoscoffFrance

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