Complete Chloroplast Genome Features and Phylogenetic Analysis of Linum usitatissimum L.

Background: The chloroplast genome provides rich genetic information for plant evolutionary studies. This study aimed to assemble, annotate, and analyze the complete chloroplast genome of flax cultivar ‘Longya 15’ (Linum usitatissimum L.) and clarify its phylogenetic relationships with other Linaceae species. Methods: We assembled and annotated the chloroplast genome of ‘Longya 15’ and retrieved chloroplast genomes of related species (e.g., Linum grandiflorum NC_058845.1, Linum lewisii NC_058799.1) from the NCBI database for phylogenetic analysis. Results: The chloroplast genome of ‘Longya 15’ was a 157,074-bp quadripartite structure with 37.42% GC content, encoding 128 genes (83 mRNAs, 37 tRNAs, 8 rRNAs) without pseudogenes. It showed codon bias for leucine (28 codons with RSCU > 1, ending in A/U), 260 dispersed repeats, and 240 SSRs. Ka/Ks analysis revealed purifying selection for most genes, while rps18 and ycf2 had positive selection. ycf1 was identified as the hypervariable region (pi = 0.25024). Phylogenetically, it clustered closest with Linum grandiflorum, followed by L. lewisii and L. perenne, and was related to Hypericum species. Conclusions: This is the first fine assembly and annotation of ‘Longya 15’ chloroplast genome, confirming no pseudogenes in flax chloroplast. It elucidates flax chloroplast genome conservation and evolutionary dynamics, enriches the database, and provides a foundation for Linaceae phylogenetics, germplasm development, and stress-resistant breeding.