Breaking the limits - multichromosomal structure of an early eudicot Pulsatilla patens mitogenome reveals extensive RNA-editing, longest repeats and chloroplast derived regions among sequenced land plant mitogenomes

Abstract

Background The mitogenomes of vascular plants are one of the most structurally diverse molecules. In the present study we characterize mitogenomes of a rare and endangered species Pulsatilla patens. We investigated the gene content and its RNA editing potential, repeats distribution and plastid derived sequences. Results The mitogenome structure of early divergent eudicot, endangered Pulsatilla patens does not support the master chromosome hypothesis, revealing the presence of three linear chromosomes of total length 986 613 bp. The molecules are shaped by the presence of extremely long, exceeding 87 kbp repeats and multiple chloroplast-derived regions including nearly complete inverted repeat. Since the plastid IR content of Ranunculales is very characteristic, the incorporation into mitogenome could be explained rather by intracellular transfer than mitochondrial HGT. The mitogenome contains almost a complete set of genes known from other vascular plants with exception of rps10 and sdh3, the latter being present but pseudogenized. Analysis of long ORFs enabled the identification of genes which are rarely present in plant mitogenomes, including RNA and DNA polymerases, albeit their presence even at species level is variable. Mitochondrial transcripts of P. patens were edited with a high frequency, which exceeded the level known in other analyzed angiosperms, despite the strict qualification criteria of counting the editing events and taking into analysis generally less frequently edited leaf transcriptome. The total number of edited sites was 902 and nad4 was identified as the most heavily edited gene with 65 C to U changes. Non-canonical, reverse U to C editing was not detected. Comparative analysis of mitochondrial genes of three Pulsatilla species revealed a level of variation comparable to chloroplast CDS dataset and much higher infrageneric differentiation than in other known angiosperm genera. The variation found in CDS of mitochondrial genes is comparable to values found among Pulsatilla plastomes. Despite the complicated mitogenome structure, 14 single copy regions of 329 kbp, not splitted by repeats or plastid-derived sequences (MTPT), revealed the potential for phylogenetic, phylogeographic and population genetics studies by revealing intra- and interspecific collinearity. Conclusions This study provides valuable new information about mitochondrial genome of early divergent eudicots, Pulsatilla patens, revealed multi-chromosomal structure and shed new light on mitogenomics of early eudicots.

Insights into the multi-chromosomal mitochondrial genome structure of the Xero- halophytic plant Haloxylon ammodendron (C.A.Mey.) Bunge ex Fenzl

“…However, the close relatives Suaeda glauca (NC_060419.1) [18] and Chenopodium quinoa (NC_041093.1) [17] present a single molecule in a fully circularized conformation based on long reads data-based assembly. The origin and maintenance of the multi-ring structure in plant mitogenome are areas of ongoing research [30][31][32][33][34][35]. It is believed that mechanisms such as recombination and rearrangement events, possibly mediated by repeated sequences [36][37][38], could play a role in generating and maintaining this phenomenon.…”

RNA Editing in Chloroplast: Advancements and Opportunities

“…The editing can create changes at all levels involving loop nucleotides and acceptor stems and might affect the dynamics of mRNA molecules [ 38 , 39 ]. The rRNA is the most abundant (about 80%) RNA inside the cell, but RNA editing seems to have less frequency than that of protein-coding transcripts, and only a few such sites have been reported in plants, such as in Selaginella moellendorffii [ 40 ] and Pulsatilla patens [ 41 ].…”

Super-Mitobarcoding in Plant Species Identification? It Can Work! The Case of Leafy Liverworts Belonging to the Genus Calypogeia

“…The number of genes may also be variable [ 9 , 10 , 30 ], but it is not the main cause of the large size of plant mitogenomes. The primary reason for this phenomenon is an expansion of their intergenic regions by accumulating sequences from nuclear and chloroplast regions and via horizontal transfer [ 27 , 31 , 32 ]. By all appearances, plant mitogenomes seem to be very plastic.…”