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The complete chloroplast genome of Secale strictum ssp. strictum provides insights into Triticeae evolution and breeding.

Lidia Skuza·Piotr Androsiuk·Romain Gastineau·Anna Kalinka·Łukasz Paukszto·Jan Paweł Jastrzębski
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Abstract

The complete chloroplast genome of Secale strictum ssp. strictum (Poaceae: Triticeae) was sequenced and analyzed to support its use in rye and wheat breeding. The genome is 137,063 bp long and includes a pair of inverted repeats (IRs; 21,580 bp each) that separate the small (SSC; 12,817 bp) and large (LSC; 81,086 bp) single-copy regions. It contains 113 genes: 74 protein-coding, 30 tRNA, four rRNA genes, and five conserved open reading frames. A total of 42 repeat sequences were identified, mainly in the LSC region, with direct repeats being most common. All mononucleotide SSRs consisted of A/T motifs. Seven highly variable regions were identified, offering potential as molecular markers for species identification and phylogenetic studies. Phylogenetic analysis based on 73 protein-coding genes confirmed the systematic placement of the species and showed that S. strictum ssp. strictum is closely related to S. cereale and other S. strictum accessions. This study presents the first complete plastome of S. strictum ssp. strictum, now available as a reference genome under GenBank accession number OL979486.

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Genome, ChloroplastPhylogenySecaleEvolution, MolecularPlant BreedingMicrosatellite RepeatsOpen Reading FramesTriticumSecale strictum ssp. strictumTriticeae evolutionChloroplast genomeComparative chloroplast genomicsCrop improvementPhylogenetic reconstructionJournal ArticleResearch Support, Non-U.S. Gov't

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Lidia Skuza, Piotr Androsiuk, Romain Gastineau, Anna Kalinka, Łukasz Paukszto, Jan Paweł Jastrzębski. 2025-12-01. The complete chloroplast genome of Secale strictum ssp. strictum provides insights into Triticeae evolution and breeding.. https://doi.org/10.1038/s41598-025-27062-1

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