Giant mitogenomes in Rhynchospora are a result of nuclear gene and retrotransposon insertions in intergenic spaces.

Background and aims: The mitochondrial genomes of plants are large, with the majority ranging between 500 and 800 kb. However, the mitochondrial genomes of Cyperaceae (sedges) species were found to be much larger, exceeding 1 Mb in size. Here, we aimed to investigate the gigantism of the mitochondrial genomes of three Rhynchospora (beak-sedges) species and one related species of the sister family Juncaceae, the common rush (Juncus effusus).

Methods: Long PacBio HiFi reads were sequenced and assembled using Hifiasm software. The mitochondrial genomes were annotated using Geneious and Mitofy software. Transposable elements were annotated using DANTE and RepeatModeler pipelines, and gene prediction in intergenic regions was conducted using Augustus. The predicted genes were annotated using BLAST and gene ontology terms.

Key results: The mitogenome of R. breviuscula was 2,222,920 bp, that of R. pubera was 2,064,773 bp, that of R. tenuis was 1,678,054 bp, and that of the species of J. effusus was 553,985 bp. The results revealed giant intergenic spaces in all Rhynchospora, containing predicted nuclear genes and LTR retrotransposons. BLASTn revealed a high migration of DNA from the nucleus to the mitogenome.

Conclusions: Our findings show that the Rhynchospora mitogenome is the largest among the monocotyledons. These mitogenomes feature giant intergenic spaces, incorporation of chloroplast DNA and numerous rearrangements. Gigantism of the intergenic spaces is associated with the movement of nuclear DNA segments, suggesting a mechanism of DNA transfer from the nuclear genome to the mitochondrial genome.