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Structural features and transcript-editing analysis of sugarcane (Saccharum officinarum L.) chloroplast genome

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Abstract

The complete nucleotide sequence of the chloroplast genome of sugarcane (Saccharum officinarum) was determined. It consists of 141,182 base-pairs (bp), containing a pair of inverted repeat regions (IRA, IRB) of 22,794 bp each. The IRA and IRB sequences separate a small single copy region (12,546 bp) and a large single copy (83,048 bp) region. The gene content and relative arrangement of the 116 identified genes (82 peptide-encoding genes, four ribosomal RNA genes, 30 tRNA genes), with the 16 ycf genes, are highly similar to maize. Editing events, defined as C-to-U transitions in the mRNA sequences, were comparable with those observed in maize, rice and wheat. The conservation of gene organization and mRNA editing suggests a common ancestor for the sugarcane and maize plastomes. These data provide the basis for functional analysis of plastid genes and plastid metabolism within the Poaceae. The sugarcane chloroplast DNA sequence is available at GenBank under accession NC005878.

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Acknowledgements

The authors gratefully acknowledge Eugênio Cesar Ulian and William Lee Burnquist (Copersucar Technology Center, Piracicaba, São Paulo, Brazil) for supplying the sugarcane commercial hybrid SP 80-3280, Ralph Bock, Stephanie Ruf and Martin Hager for suggestions on sugarcane plastid DNA isolation, the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) for project grant 99/02860-8 and for fellowships granted to T.C.J. (99/02973-7) and D.M.C. (98/06206-8) and the Conselho Nacional de Pesquisa e Desenvolvimento (CNPq/PIBIC) for a fellowship granted to M.R.B. The authors declare that this work was carried out in compliance with the current laws governing genetic experimentation in Brazil.

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Author notes

  1. Tercilio Calsa Júnior

    Present address: CENA/Universidade de São Paulo, Av. Centenário 303, Piracicaba, 13400-961, São Paulo, Brazil

  2. Dirce Maria Carraro

    Present address: Instituto Ludwig de Pesquisa sobre Câncer, Rua Prof. Antonio Prudente 109, 4 andar, São Paulo, 01509.010, São Paulo, Brazil

  3. Matheus Romanos Benatti

    Present address: Horticulture Department, Purdue University, 625 Agriculture Mall Dr., West Lafayette, IN 49707-2010, USA

Authors and Affiliations

  1. ESALQ/Universidade de São Paulo, Av. Pádua Dias 11, Piracicaba, 13418-900, São Paulo, Brazil

    Tercilio Calsa Júnior, Dirce Maria Carraro, Matheus Romanos Benatti & Helaine Carrer

  2. Scylla Bioinformatics, Estrada Unicamp-Telebrás, km 0.97, Campinas, 13083-970, São Paulo, Brazil

    Alexandre Corrêa Barbosa

  3. Alellyx Applied Genomics, Rua James Clerk Maxwell 320, Techno Park, Rodoviaria Anhanguera, km 104, Campinas, 13067-850, São Paulo, Brazil

    João Paulo Kitajima

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  1. Tercilio Calsa Júnior
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Correspondence to Helaine Carrer.

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Communicated by A. Brennicke

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Calsa Júnior, T., Carraro, D.M., Benatti, M.R. et al. Structural features and transcript-editing analysis of sugarcane (Saccharum officinarum L.) chloroplast genome. Curr Genet 46, 366–373 (2004). https://doi.org/10.1007/s00294-004-0542-4

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