Assembly and Characterization of the Mitochondrial Genome of Fallopia aubertii (L. Henry) Holub.

BACKGROUND: Fallopia aubertii (L. Henry) Holub is a perennial semi-shrub with both ornamental and medicinal value. The mitochondrial genomes of plants contain valuable genetic traits that can be utilized for the exploitation of genetic resources. The parsing of F. aubertii mitochondrial genome can provide insight into the role of mitochondria in plant growth and development, metabolism regulation, evolution, and response to environmental stress. METHODS: In this study, we sequenced the mitochondrial genome of F. aubertii using the Illumina NovaSeq 6000 platform and Nanopore platform. We conducted a comprehensive analysis of the mitochondrial genome of F. aubertii, which involved examining various aspects such as gene composition, repetitive sequences, RNA editing sites, phylogeny, and organelle genome homology. To achieve this, we employed several bioinformatics methods including sequence alignment analysis, repetitive sequence analysis, phylogeny analysis, and more. RESULTS: The mitochondrial genome of F. aubertii has 64 genes, including 34 protein-coding genes (PCGs), three rRNAs, and 27 tRNAs. There were 77 short tandem repeat sequences detected in the mitochondrial genome, five tandem repeat sequences identified by Tandem Repeats Finder (TRF), and 50 scattered repeat sequences observed, including 22 forward repeat sequences and 28 palindrome repeat sequences. A total of 367 RNA coding sites were predicted in PCGs, with the highest number (33) found within ccmB. Ka/Ks values estimated for mitochondrial genes of F. aubertii and three closely related species representing Caryophyllales were less than 1 for most of the genes. The maximum likelihood evolutionary tree showed that F. aubertii and Nepenthes ×ventrata are most closely related. CONCLUSIONS: In this study, we obtained basic information on the mitochondrial genome of F. aubertii and this study investigated repeat sequences and homologous segments, predicted RNA editing sites, and utilized the Ka/Ks ratio to estimate the selection pressure on mitochondrial genes of F. aubertii. We also discussed the systematic evolutionary position of F. aubertii based on mitochondrial genome sequences. Our study revealed variations in the sequence and structure of mitochondrial genomes in Caryophyllales. These findings are of great significance for identifying and improving valuable plant traits and serve as a reference for future molecular studies of F. aubertii.

Polyploidy and introgression in invasive giant knotweed (Fallopia sachalinensis) during the colonization of remote volcanic islands.

Invasive giant knotweed (Fallopia sachalinensis) is native to northeastern Asia. In Korea, F. sachalinensis is confined to two volcanic islands, Ullung and Dok islands, where it occurs as dodecaploids (2n = 132). We investigated the molecular variation in 104 accessions from 94 populations of F. sachalinensis and its relatives throughout their native range to elucidate the origin of these island populations. All F. sachalinensis plants on Ullung and Dok islands were uniquely dodecaploid, whereas other populations were tetraploid (2n = 44). Among the 39 cpDNA haplotypes identified, the accessions from these islands shared two unique haplotypes, and were resolved as a well-supported monophyletic clade. However, this clade was sister to a clade comprising F. japonica accessions from southwestern Japan and separated from the clade comprising F. sachalinensis from other areas; this relationship is inconsistent with morphological evidence. The monophyly of the F. sachalinensis populations on Ullung and Dok islands suggests a single colonization event. The progenitor was likely from Japan, where it possibly captured F. japonica var. japonica cpDNA via introgression. The Ullung Island populations subsequently differentiated through polyploidization and mutations post-introduction. Our results also indicate that giant knotweed in Europe and North America likely originated from northern Japan and/or Sakhalin Island.

A Survey of Genetic Variation and Genome Evolution within the Invasive Fallopia Complex.

The knotweed taxa Fallopia japonica, F. sachalinensis and their interspecific hybrid F. × bohemica are some of the most aggressive invaders in Europe and North America and they are serious threats to native biodiversity. At the same time, they constitute a unique model system for the creation of hybrids and studies of the initiation of evolutionary processes. In the presented study, we focused on (i) examining genetic diversity in selected populations of three Fallopia taxa in the invaded (Poland) and native ranges (Japan), (ii) establishing genome size and ploidy levels and (iii) identifying ribosomal DNA (rDNA)-bearing chromosomes in all of the taxa from the invaded range. We found that the genetic diversity within particular taxa was generally low regardless of their geographical origin. A higher level of clonality was observed for the Polish populations compared to the Japanese populations. Our study suggests that the co-occurrence of F. sachalinensis together with the other two taxa in the same stand may be the source of the higher genetic variation within the F. × bohemica hybrid. Some shift towards the contribution of F. japonica alleles was also observed for selected F. × bohemica individuals, which indicates the possibility of producing more advanced generations of F. × bohemica hybrids. All of the F. sachalinensis individuals were hexaploid (2n = 6x = 66; 2C = 6.01 pg), while those of F. japonica were mostly octoploid (2n = 8x = 88; 2C = 8.87 pg) and all of the F. × bohemica plants except one were hexaploid (2n = 6x = 66; 2C = 6.46 pg). Within the chromosome complement of F. japonica, F. sachalinensis and F. × bohemica, the physical mapping of the rDNA loci provided markers for 16, 13 and 10 chromosomes, respectively. In F. × bohemica, a loss of some of rDNA loci was observed, which indicates the occurrence of genome changes in the hybrid.

Identification of B-type procyanidins in Fallopia spp. involved in biological denitrification inhibition.

Nitrogen (N) is considered as a main limiting factor in plant growth, and nitrogen losses through denitrification can be responsible for severe decreases in plant productivity. Recently, it was demonstrated that Fallopia spp. is responsible for biological denitrification inhibition (BDI) through the release of unknown secondary metabolites. Here, we investigate the secondary metabolites involved in the BDI of Fallopia spp. The antioxidant, protein precipitation capability of Fallopia spp. extracts was measured in relation to the aerobic respiration and denitrification of two bacteria (Gram positive and Gram negative). Proanthocyanidin concentrations were estimated. Proanthocyanidins in extracts were characterized by chromatographic analysis, purified and tested on the bacterial denitrification and aerobic respiration of two bacterial strains. The effect of commercial procyanidins on denitrification was tested on two different soil types. Denitrification and aerobic respiration inhibition were correlated with protein precipitation capacity and concentration of proanthocyanidins but not to antioxidant capacity. These proanthocyanidins were B-type procyanidins that inhibited denitrification more than the aerobic respiration of bacteria. In addition, procyanidins also inhibited soil microbial denitrification. We demonstrate that procyanidins are involved in the BDI of Fallopia spp. Our results pave the way to a better understanding of plant-microbe interactions and highlight future applications for a more sustainable agriculture.