The Complete Mitochondrial Genome of Ophioglossum vulgatum L. Is with Highly Repetitive Sequences: Intergenomic Fragment Transfer and Phylogenetic Analysis

Abstract

Many plant mitochondrial (mt) genomes have been sequenced but few in ferns. Ophioglossum vulgatum represents a typical species of fern genus Ophioglossum with medicinal and scientific value. However, its mt genome structure remains to be characterized. This study assembled and annotated the complete O. vulgatum mt genome and presented its structural characters and repeat sequences firstly. Its mt and chloroplast (cp) transfer sequences were explored, and the phylogenetic significance of both mt and cp genomes was also evaluated at the family level. Our results showed that the complete mt genome of O. vulgatum is a single circular genome of 369,673 bp in length, containing 5000 dispersed repetitive sequences. Phylogenetic trees reconstructed from cp and mt genomes displayed similar topologies, but also showed subtle differences at certain nodes. There exist 4818 bp common gene fragments between cp and mt genomes, of which more than 70% are located in tRNA intergenic regions (in mt). In conclusion, we assembled the complete mt genome of O. vulgatum, identified its remarkable structural characters, and provided new insights on ferns. The complementary results derived from mt and cp phylogeny highlighted that some higher taxonomic-level phylogenetic relationships among ferns remain to be resolved.

Organellar phylogenomics of Ophioglossaceae fern genera

“…Specifically, for either morffo1 or morffo2 , we didn’t find its presence in both organellar genomes in the same Ophioglossaceae collection. In other words, our study provided no supporting evidence for IGT of a MORFFO gene that could switch between organellar genomes in Ophioglossaceae, although such cases are likely true for other genic regions (e.g., plastid-derived DNA fragments in mitochondrial genomes; Guo et al., 2017 ; Hao et al., 2022b ). However, the mitogenome assemblies of most Ophioglossaceae genera are still incomplete, and thus mitochondrial MORFFO might be overlooked.…”

“…Apparently, these taxa have reduced mitogenomes, in which ccm genes and several introns are lost ( Figure 3 ; Table S5 ), and the total DNA amount is also decreased. Mitogenomes of Ophioglossum have been fully assembled that are revealed with a single chromosome of a smaller size of 0.37 Mbp ( Guo et al., 2017 ; Hao et al., 2022b ). By contrast, mitogenomes from other ferns, including Psilotum from the sister family, are typically with multiple chromosomes and total lengths ranging from 0.62 to 1.44 Mbp ( Guo et al., 2017 ; Feng and Wicke, 2022 ; Zumkeller et al., 2023 ).…”

Comparative analysis of mitochondrial genomes of Schisandra repanda and Kadsura japonica

“…Intergenomic gene transfer is the movement of DNA sequences between mitochondria, chloroplasts, and the nucleus, as opposed to DNA sequence movement by inheritance, and it is an important cause of mitogenome expansion and evolution ( Adams et al., 2001 ; Renner and Bellot, 2012 ; Hao et al., 2022 ). We compared the complete chloroplast sequence of S. chinensis (NC_034908.1) to the S. repanda and K. japonica mitogenomes and identified 16 (32–2,807 bp, 3.39%) and 37 (39–7,515 bp, 4.34%) fragments with high similarities to chloroplast genome, respectively ( Figure 3 ; Supplementary table 8 ).…”

Chloroplast gene expression level is negatively correlated with evolutionary rates and selective pressure while positively with codon usage bias in Ophioglossum vulgatum L

“…But whether the expression of cp genes is consistent or not with the E-R anticorrelation remains to be tested. O. vulgatum is a rare and ancient fern with high medicinal value [28][29][30]. The plant is 10-30 cm high with a huge number of chromosomes (2n = 240-1140), tending to live in shaded forests and wet meadows [30][31][32][33][34] (Fig.…”

“…O. vulgatum is a rare and ancient fern with high medicinal value [28][29][30]. The plant is 10-30 cm high with a huge number of chromosomes (2n = 240-1140), tending to live in shaded forests and wet meadows [30][31][32][33][34] (Fig. 1a).…”