Assembly and comparison of organelle genomes for investigating the maternal inheritance in Peganum (Nitrariaceae)

Peganum are arid-adapted perennial diploid sandy plants distributed in Arid Central Asia (ACA). This genus features a variety of intermittent and hybrid entities (IHEs), making it an excellent model for studying hybrid speciation. Few organellar genomes have been published for Peganum, and the identification of the hybrid parental species in IHEs remains unresolved. Therefore, we conducted a systematic comparative organellar genome analysis and maternal inheritance study for Peganum.

Here, we assembled the plastomes and mitogenomes of Peganum using sequencing data from Illumina, HiFi, and Oxford Nanopore platforms. The assembled mitogenomes ranged in total length from 426,866 bp to 447,055 bp and were recovered as single circular DNA configurations supported by long-read sequencing data, containing 33–35 protein-coding genes (PCGs), 19 tRNAs, and 3 rRNAs. The plastomes ranged from 159,967 bp to 160,739 bp and contained 86 PCGs, 37 tRNAs, and 8 rRNAs. Genome collinearity analysis revealed more structural inconsistencies in the mitogenomes compared to the plastomes. The mitogenomes and plastomes contained 824 and 619 repeated sequences, respectively. Codon usage analysis revealed a preference for codons ending in A/T. The genes nad2, rpoC1, and atpF, associated with mitochondrial respiration and plastid gene expression and ATP synthesis, showed evidence of purifying selection, indicating strong functional constraints during Peganum evolution. DNA transfer analysis revealed significant genetic interactions between the two organellar genomes and between the organellar and nuclear genomes. Sequence similarity and phylogeny are broadly consistent with predominantly maternal origins of IHEs formed through hybridization, although more complex inheritance signals cannot be excluded.

We assembled and annotated the organellar genomes of Peganum and conducted a comparative analysis. Our findings contribute to the organellar genome database for Peganum and reveal both the stability and heterogeneity of organellar genomes. The results provide a representative case for investigating maternal inheritance in IHEs.