Accumulation of Large Lineage-Specific Repeats Coincides with Sequence Acceleration and Structural Rearrangement in Plantago Plastomes.

Repeats can mediate rearrangements and recombination in plant mitochondrial genomes and plastid genomes. While repeat accumulations are linked to heightened evolutionary rates and complex structures in specific lineages, debates persist regarding the extent of their influence on sequence and structural evolution. In this study, 75 Plantago plastomes were analyzed to investigate the relationships between repeats, nucleotide substitution rates, and structural variations. Extensive repeat accumulations were associated with significant rearrangements and inversions in the large inverted repeats (IRs), suggesting that repeats contribute to rearrangement hotspots. Repeats caused infrequent recombination that potentially led to substoichiometric shifting, supported by long-read sequencing. Repeats were implicated in elevating evolutionary rates by facilitating localized hypermutation, likely through DNA damage and repair processes. This study also observed a decrease in nucleotide substitution rates for loci translocating into IRs, supporting the role of biased gene conversion in maintaining lower substitution rates. Combined with known parallel changes in mitogenomes, it is proposed that potential dysfunction in nuclear-encoded genes associated with DNA replication, recombination, and repair may drive the evolution of Plantago organellar genomes. These findings contribute to understanding how repeats impact organellar evolution and stability, particularly in rapidly evolving plant lineages.

Cytonuclear Interactions and Subgenome Dominance Shape the Evolution of Organelle-Targeted Genes in the Brassica Triangle of U.

The interaction and coevolution between nuclear and cytoplasmic genomes are one of the fundamental hallmarks of eukaryotic genome evolution and, 2 billion yr later, are still major contributors to the formation of new species. Although many studies have investigated the role of cytonuclear interactions following allopolyploidization, the relative magnitude of the effect of subgenome dominance versus cytonuclear interaction on genome evolution remains unclear. The Brassica triangle of U features 3 diploid species that together have formed 3 separate allotetraploid species on similar evolutionary timescales, providing an ideal system for understanding the contribution of the cytoplasmic donor to hybrid polyploid. Here, we investigated the evolutionary pattern of organelle-targeted genes in Brassica carinata (BBCC) and 2 varieties of Brassica juncea (AABB) at the whole-genome level, with particular focus on cytonuclear enzyme complexes. We found partial evidence that plastid-targeted genes experience selection to match plastid genomes, but no obvious corresponding signal in mitochondria-targeted genes from these 2 separately formed allopolyploids. Interestingly, selection acting on plastid genomes always reduced the retention rate of plastid-targeted genes encoded by the B subgenome, regardless of whether the Brassica nigra (BB) subgenome was contributed by the paternal or maternal progenitor. More broadly, this study illustrates the distinct selective pressures experienced by plastid- and mitochondria-targeted genes, despite a shared pattern of inheritance and natural history. Our study also highlights an important role for subgenome dominance in allopolyploid genome evolution, even in genes whose function depends on separately inherited molecules.

Characterization of the Key Aroma Compounds in Five Varieties of Mandarins by Gas Chromatography-Olfactometry, Odor Activity Values, Aroma Recombination, and Omission Analysis.

In this study, volatile compounds of five varieties of mandarin juices [Tankan, Miyagawa, Mashui (MS), Skiranui, and Ponkan (PG)] were investigated by gas chromatography-olfactometry (GC-O) and gas chromatography-mass spectrometry (GC-MS). A total of 47 volatile compounds were identified by GC-MS. Partial least-squares regression was used to process the mean scores from sensory evaluation by panelists of volatile compounds and samples. The sample PG was associated with "fruity", "floral", and "sweet" notes, while MS was correlated with "green" and "peely" notes. In addition, 36 aroma-active compounds, including esters, alcohols, aldehydes, ketones, and monoterpenes, were detected by GC-O. According to the quantitative results, 29 aroma compounds were important, which indicated that their odor activity values (OAVs) were ≥1. On the basis of the GC-O results and OAVs of these volatile compounds, 22 odor-active compounds were mixed to simulate successfully the overall aroma of PG mandarin juice. Furthermore, omission experiments confirmed that nonanal, hexanal, linalool, and (R)-(+)-limonene were the key odorants for the overall aroma of PG juice sample and that ß-ionone, decanal, γ-terpinene, and methyl butyrate were also important odor-active compounds.