Transposable elements in Rosaceae: insights into genome evolution, expression dynamics, and syntenic gene regulation.

Transposable elements (TEs) exert significant influence on plant genomic structure and gene expression. Here, we explored TE-related aspects across 14 Rosaceae genomes, investigating genomic distribution, transposition activity, expression patterns, and nearby differentially expressed genes (DEGs). Analyses unveiled distinct long terminal repeat retrotransposon (LTR-RT) evolutionary patterns, reflecting varied genome size changes among nine species over the past million years. In the past 2.5 million years, Rubus idaeus showed a transposition rate twice as fast as Fragaria vesca, while Pyrus bretschneideri displayed significantly faster transposition compared with Crataegus pinnatifida. Genes adjacent to recent TE insertions were linked to adversity resistance, while those near previous insertions were functionally enriched in morphogenesis, enzyme activity, and metabolic processes. Expression analysis revealed diverse responses of LTR-RTs to internal or external conditions. Furthermore, we identified 3695 pairs of syntenic DEGs proximal to TEs in Malus domestica cv. 'Gala' and M. domestica (GDDH13), suggesting TE insertions may contribute to varietal trait differences in these apple varieties. Our study across representative Rosaceae species underscores the pivotal role of TEs in plant genome evolution within this diverse family. It elucidates how these elements regulate syntenic DEGs on a genome-wide scale, offering insights into Rosaceae-specific genomic evolution.

A novel inversion method of 2D TD-NMR signals based on realizing unconstrained maximization of objective function.

The inversion of time-domain nuclear magnetic resonance (TD-NMR) signals is an ill-posed problem, which presents enormous challenges for the inversion algorithm. We propose a novel inversion method that converts conventional minimum objective function with non-negative constraints into an unconstrained maximization problem in the inversion of TD-NMR signals. Hence, the objective function becomes a differentiable concave function that can be solved more easily. The validity of the proposed method was verified by the uncertainty estimation of NMR inversion spectra with different signal-to-noise ratios (SNR). Through the inversion of simulated 2D D-T2 and T1-T2 signals under different SNR, the proposed method was proved to be less sensitive to noise than the conventional inversion method. We use the proposed method to study the migrations of oil and water in shales, the components change in shale could be identified and quantified according to the 2D T1-T2 inversion spectra. The proposed method was also used to analyze the hydration process of cement. The 2D T1-T2 inversion spectra could distinctly present the component of tiny volume with short relaxation time, and the migration regularity of capillary water, gel water, and bound water could also be found. In conclusion, the proposed method could be a reliable method to invert TD-NMR signals, especially the identification of the 2D NMR signals with a short relaxation time in low SNR.

Citrus mangshanensis Pollen Confers a Xenia Effect on Linalool Oxide Accumulation in Pummelo Fruit by Enhancing the Expression of a Cytochrome P450 78A7 Gene CitLO1.

The aroma quality of citrus fruit is determined by volatiles that are present at extremely low levels in the citrus fruit juice sacs; it can be greatly improved by increasing volatiles. In this study, we showed that the contents of cis- and trans-linalool oxides were significantly increased in the juice sacs of three pummelos artificially pollinated with the Citrus mangshanensis (MS) pollen. A novel cytochrome P450 78A7 gene (CitLO1) was significantly upregulated in the juice sacs of Huanong Red pummelo pollinated with MS pollen in comparison to that with open pollination. Compared to wild-type tobacco Bright-Yellow2 cells, transgenic cells overexpressing CitLO1 promoted a 3- to 4-fold more conversion of (-)-linalool to cis- and trans-linalool oxides. Overall, our results suggest that MS pollen has a xenia effect on pummelo fruit aroma quality, and CitLO1 is a linalool oxide synthase gene that played an important role in the xenia effect.