Codon Usage of Chloroplast Gene rbcL in Laurencia sensu lato (Rhodophyta) species

Authors

  • Ruben Cabrera Gabinete de Arqueología, Oficina del Historiador de la Ciudad, Habana Vieja, Cuba
  • Jhoana Díaz-Larrea Universidad Autónoma Metropolitana, Unidad Iztapalapa, CBS, Departamento de Hidrobiología, Cd de México, México
  • Arsenio J. Areces Instituto de Geografía Tropical, Ministerio de Ciencia, Tecnología y Medio Ambiente, Municipio Playa, Ciudad Habana, Cuba
  • Laura Nuñez García Universidad Autónoma Metropolitana, Unidad Iztapalapa, CBS, Departamento de Hidrobiología, Cd de México, México
  • J. Ricardo Cruz-Aviña Universidad Tecnológica de Calakmul Departamento de Recursos Naturales, Academia de investigación y Ciencia, Campeche, México
  • Gabriela Vázquez Silva Universidad Autónoma Metropolitana, Unidad Xochimilco, Departamento el Hombre y su Ambiente, Laboratorio de Limnobiología y Acuicultura, Cd de México, México

DOI:

https://doi.org/10.30564/jms.v3i4.3542

Abstract

Recent advances in molecular biology make it possible to sequence not only genes or genomes, but also to understand codon dynamics. For the organelle genes of these organisms, a small set of preferred codons are used for encoding proteins. For the first time, this paper treats the divergence of synonymous codon usage and its bias in the rbcL gene within the Laurencia complex of red algae. We observed that the synonymous codon preference biases in rbcL are large and differ among species. A clear distinction in codon usage between genera is evident: the genera Dasya and Delesseria use a set that fluctuated between 53 and 58 codons. Whereas, in the genera Ceramium, Chondrophycus, Chlamydomonas, Chlorella, Laurencia s.s, Osmundea, and Palisada codon usage indicates a higher restriction fluctuating between 40 to 51 codons. Laurencia complex genera and other representative algae showed a defined composition pattern, with lower percentage values of NNC/G (7-24.9%). Dasya and Delesseria showed a selective pattern tendency because of high percentage values of NNC/G (54-55%). The estimated codon bias parameters were tested to infer systematic relationships and match suitable codons with the NNC / G codon percentages. Cluster analysis based on Codon Usage supports phylogenetic relationships between Chondrophycus, Palisada, Laurencia, Osmundea, and Yuzurua species.

Keywords:

Codon; Laurencia sensu lato; Systematics; Rhodophyta; Marine algae

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