Structural, evolutionary and phylogenomic features of the plastid genome of Carya illinoinensis cv. Imperial

Authors

  • Jordana Caroline Nagel Federal University of the Pampa, Graduate Program in Biological Sciences, Campus São Gabriel, São Gabriel, RS, Brazil, Universidade Regional Integrada do Alto Uruguai e das Missões, Campus Santo Ângelo, Santo Ângelo, RS, Brazil
  • Lilian de Oliveira Machado Federal University of Santa Catarina, Graduate Program in Plant Genetic Resources, Florianópolis, SC, Brazil
  • Rafael Plá Matielo Lemos Federal University of the Pampa, Graduate Program in Biological Sciences, Campus São Gabriel, São Gabriel, RS, Brazil
  • Cristiane Barbosa D’Oliveira Matielo Federal University of the Pampa, Graduate Program in Biological Sciences, Campus São Gabriel, São Gabriel, RS, Brazil
  • Tales Poletto Federal University of Santa Maria, Graduate Program in Forest Engineering; Santa Maria, RS, Brazil
  • Igor Poletto Federal University of the Pampa, Graduate Program in Biological Sciences, Campus São Gabriel, São Gabriel, RS, Brazil
  • Valdir Marcos Stefenon Federal University of Santa Catarina, Graduate Program in Plant Genetic Resources, Florianópolis, SC, Brazil & Federal University of the Pampa, Graduate Program in Biological Sciences, Campus São Gabriel, São Gabriel, RS, Brazil

DOI:

https://doi.org/10.15287/afr.2019.1413

Keywords:

Pecan, chloroplast genome, phylogenomics, Juglandaceae

Abstract

The economically most important nut tree species in the world belong to family Juglandaceae, tribe Jungladeae. Evolutive investigations concerning species from this tribe are important for understanding the molecular basis driving the evolution and systematics of these species. In this study, we release the complete plastid genome of C. illinoinensis cv. Imperial. Using an IonTorrent NGS platform we generated 8.5´108 bp of raw sequences, enabling the assemblage of the complete plastid genome of this species. The plastid genome is 160,818 bp long, having a quadripartite structure with an LSC of 90,041 bp, an SSC of 18,791 bp and two IRs of 25,993 bp. A total of 78 protein-coding, 37 tRNA-coding, and 8 rRNA-coding regions were predicted. Bias in synonymous codon usage was detected in cultivar Imperial and three tRNA-coding regions were identified as hotspots of nucleotide divergence, with high estimations of dN/dS ratio. The high fraction of SSR loci prospected in non-coding regions may provide informative genetic markers, useful to a wide range of genetic researches. Despite the significant structural differences among plastid genomes, the phylogenetic relationships among species is supported by the whole plastid genome analysis,supporting the monophyly of subtribes Caryinae and Juglandinae within family Juglandaceae.

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Volume 63 , Issue 1

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2020-03-02

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Vol. 63 No. 1 (2020)

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