Comparative plastome analyses and genomic resource development for five Neoporphyra haitanensis and two Neopyropia yezoensis cultivars based on genome skimming data.
Neoporphyra haitanensis and Neopyropia yezoensis are two economically important seaweeds in Asia, yet their germplasm identification is often hindered by high phenotypic plasticity and limited molecular resources. To address this, we utilized a genome skimming strategy on five No. haitanensis and two Ny. yezoensis cultivars to retrieve their plastome information (including whole plastome sequences, plastome-divergent hotspots, and plastome-derived SSRs) and to identify genome-wide polymorphic nuclear SSRs. The plastomes of No. haitanensis (201,110-201,310 bp) were markedly larger than those of Ny. yezoensis (191,974 bp), a difference largely driven by expansions in intergenic regions. Gene annotation identified 253 genes in No. haitanensis and 256 in Ny. yezoensis, with the latter uniquely containing two additional hypothetical ORFs (ORF33 and ORF35) and an extra rRNA gene (rrfB). Further comparative analysis revealed seven hypervariable regions (π > 0.1), five of which-apcE-tatC, psbW-trnR, psbX-accD, trnW-rpl11, and ycf32-rpl32-are intergenic spacers with strong potential as species-discriminatory barcodes. We also characterized 26-30 chloroplast-derived SSRs and identified notable interspecific variations in their repeat-type profiles. Importantly, we developed 230 and 505 high-quality polymorphic nuclear SSRs for No. haitanensis and Ny. yezoensis, respectively, predominantly trinucleotide repeats, offering a robust toolset for fine-scale genetic analyses. Phylogenetic reconstruction using 201 shared plastid protein-coding genes clearly separated the two species into distinct clades, supporting their independent evolutionary trajectories, and further revealed intraspecific genetic differentiation, particularly with the cultivar ZD-1 forming a distinct branch within No. haitanensis. This study provides comprehensive genomic resources-including complete plastomes, hypervariable regions, and polymorphic SSR markers-that will facilitate germplasm identification, phylogenetic studies, and molecular breeding in Porphyra sensu lato.