Chromosomal-scale genomes of two Rosa species provide insights into genome evolution and ascorbate accumulation.

Rosa roxburghii and Rosa sterilis, two species belonging to the Rosaceae family, are widespread in the southwest of China. These species have gained recognition for their remarkable abundance of ascorbate in their fresh fruits, making them an ideal vitamin C resource. In this study, we generated two high-quality chromosome-scale genome assemblies for R. roxburghii and R. sterilis, with genome sizes of 504 and 981.2 Mb, respectively. Notably, we present a haplotype-resolved, chromosome-scale assembly for diploid R. sterilis. Our results indicated that R. sterilis originated from the hybridization of R. roxburghii and R. longicuspis. Genome analysis revealed the absence of recent whole-genome duplications in both species and identified a series of duplicated genes that possibly contributing to the accumulation of flavonoids. We identified two genes in the ascorbate synthesis pathway, GGP and GalLDH, that show signs of positive selection, along with high expression levels of GDP-d-mannose 3', 5'-epimerase (GME) and GDP-l-galactose phosphorylase (GGP) during fruit development. Furthermore, through co-expression network analysis, we identified key hub genes (MYB5 and bZIP) that likely regulate genes in the ascorbate synthesis pathway, promoting ascorbate biosynthesis. Additionally, we observed the expansion of terpene synthase genes in these two species and tissue expression patterns, suggesting their involvement in terpenoid biosynthesis. Our research provides valuable insights into genome evolution and the molecular basis of the high concentration of ascorbate in these two Rosa species.

Genomic Characterization of the Mycoparasite Pestalotiopsis sp. Strain cr013 from Cronartium ribicola.

The Pestalotiopsis sp. strain cr013 is a mycoparasite of Cronartium ribicola, a potential biocontrol fungus for Armand pine (Pinus armandii) blister rust. A previous study showed that the strain cr013 has great potential to produce new compounds. However, there has been no report of the whole-genome sequence of the mycoparasite Pestalotiopsis sp. In this study, the BGISEQ-500 and Oxford Nanopore GridION X5 sequencing platforms were used to sequence the strain cr013 isolates and assemble the reads to obtain the complete genome. We first report the whole-genome information of the mycoparasite Pestalotiopsis sp. strain cr013 (GenBank accession number: JACFXT010000000, BioProject ID: PRJNA647543, BioSample ID: SAMN15589943), and the genomic components and gene functions related to the mycoparasitism process were analyzed. This study provides a theoretical basis for understanding the lifestyle strategy of the mycoparasite Pestalotiopsis sp. and reveals the mechanisms underlying secondary metabolite diversity in the strain cr013.

Identification of Reliable Reference Genes under Different Stresses and in Different Tissues of Toxicodendron succedaneum.

Toxicodendron succedaneum (L.) Kuntze (T. succedaneum) is an economic tree species that produces urushiol and urushi wax, and it is of great value in industry and medicine. However, the stability of reference genes (RGs) has not been systematically reported in T. succedaneum to date. In this study, the expression of 10 candidate RGs was analyzed by RT-qPCR in different tissues (roots, stems, leaves), stress treatments (high/low temperature, drought), and hormone stimulation (jasmonic acid, JA). Then, the stability ranking of 10 candidate genes was evaluated by ∆Ct analysis and three software programs: geNorm, NormFinder, and BestKeeper. Finally, RefFinder was used to comprehensively analyze the expression stability of 10 candidate genes. The comprehensive analysis showed that TsRG05/06, TsRG01/06, and TsRG03/ACT were stable under high/low-temperature stress, drought stress, and JA treatment, respectively. TsRG03 and ACT had stable expression in different tissues. While the TsRG03 and ACT were recommended as the suitable RGs for T. succedaneum in all samples. Meanwhile, UBQ was the least suitable as a reference gene for T. succedaneum. In addition, the results of geNorm showed that the combination of two stable RGs could make the results of gene expression more accurate. These results provide alternative RGs for the study of gene function, correction, and normalization of target gene expression and directed molecular breeding in T. succedaneum.

In situ infrared spectroscopy depth profilometer for organic thin films.

Organic films are widely used in organic optoelectronics due to their flexibility, low-cost fabrication, and ability to be processed over large areas. Typically, the composition of these thin films varies along the film depth direction. In this work, we present a home-developed in situ instrument comprised of a capacitive coupled plasma generator in combination with a Fourier transform infrared spectrometer, to measure the composition distribution along the film-normal direction. During the measurement, the film is sequentially etched by the soft plasma and the evolution of the infrared spectra of the film is in situ monitored by a spectrometer, from which the film-depth-dependent infrared spectra are extracted. The film-depth resolution of this analytical method has been improved to ∼1 nanometer. Thus, it is possible to calculate the composition that varies with depth by utilizing this analysis method. This equipment, which can be applied effectively to the characterization of thin films for both conjugated and unconjugated organic molecules by directly measuring their distinctive molecular vibration signatures, is simple and clear to set up in a large number of laboratories.

Spectroscopic depth profilometry of organic thin films upon inductively coupled plasma etching.

During the deposition and post-treatments of organic films, phase separation along the film-depth direction is a commonly observed phenomenon. Thus, film-depth profilometry of organic thin films and the corresponding scientific instruments are attracting extensive interest. Here, we propose spectroscopic film-depth profilometry of organic thin films upon inductively coupled plasma etching. Compared with capacitively coupled plasma, which usually generates inhomogeneous filamentous discharge, damaging films underneath the etched surface, inductively coupled plasma studied in this work refers to a so-called soft plasma source generated by a well-defined homogenous glow discharge. The absorption spectra of the etched films are monitored by using a spectrometer, from which the film-depth-dependent light absorption spectra are, thus, numerically obtained with a film-depth resolution better than 1 nm. This methodology is available not only for non-conjugated molecules but also for conjugated organic semiconductors, which are usually known as unstable materials for many ionic plasma sources. Organic films for solar cells and field-effect transistors are investigated as model materials to demonstrate the applications of this depth profilometry.

P3HT-Based Organic Solar Cells with a Photoresponse to 1000 nm Enabled by Narrow Band Gap Nonfullerene Acceptors with High HOMO Levels.

Three narrow band gap (NBG) acceptors, namely, TTDTC-0F, TTDTC-2F, and TTDTC-4F, were synthesized by introducing a strong electron-donating unit as the central core. The enhanced intramolecular charge transfer endows the three acceptors with high-lying highest occupied molecular orbitals (HOMOs) of ∼-5.20 eV and ultranarrow band gaps (∼1.25 eV). When blended with poly(3-hexylthiophene) (P3HT), all organic solar cells (OSCs) exhibited a broad photoresponse from 300 to ∼1000 nm. Among them, P3HT:TTDTC-4F-based devices achieved the highest efficiency of 7.81% with a prominent Jsc exceeding 22 mA·cm-2. This study demonstrates that the conjugated molecules with high HOMOs can also function as acceptor materials for P3HT-based OSCs, which opens a window to increase PCEs of P3HT-based OSCs in the future to the level of the devices based on the current state-of-the-art polymer donor materials.

Infrared spectroscopy depth profiling of organic thin films.

Organic thin films are widely used in organic electronics and coatings. Such films often feature film-depth dependent variations of composition and optoelectronic properties. State-of-the-art depth profiling methods such as mass spectroscopy and photoelectron spectroscopy rely on non-intrinsic species (vaporized ions, etching-induced surface defects), which are chemically and functionally different from the original materials. Here we introduce an easily-accessible and generally applicable depth profiling method: film-depth-dependent infrared (FDD-IR) spectroscopy profilometry based on directly measuring the intrinsic material after incremental surface-selective etching by a soft plasma, to study the material variations along the surface-normal direction. This depth profiling uses characteristic vibrational signatures of the involved compounds, and can be used for both conjugated and non-conjugated, neutral and ionic materials. A film-depth resolution of one nanometer is achieved. We demonstrate the application of this method for investigation of device-relevant thin films, including organic field-effect transistors and organic photovoltaic cells, as well as ionized dopant distributions in doped semiconductors.

Genomic Analysis of the Mycoparasite Pestalotiopsis sp. PG52.

Pestalotiopsis sp. is a mycoparasite of the plant pathogen Aecidium wenshanense. To further understand the mycoparasitism mechanism of Pestalotiopsis sp., we assembled and analyzed its genome. The genome of Pestalotiopsis sp. strain PG52 was assembled into 335 scaffolds and had a size of 58.01 Mb. A total of 20,023 predicted genes and proteins were annotated. This study compared PG52 with the mycoparasites Trichoderma harzianum, Trichoderma atroviride, and Trichoderma virens. This study reveals the entirely different mycoparasitism mechanism of Pestalotiopsis compared to Trichoderma and reveals this mycoparasite's strong ability to produce secondary metabolites.

Bark tissue transcriptome analyses of inverted Populus yunnanensis cuttings reveal the crucial role of plant hormones in response to inversion.

Inverted cuttings of Populus yunnanensis exhibit an interesting growth response to inversion. This response is characterized by enlargement of the stem above the shoot site, while the upright stem shows obvious outward growth below the shoot site. In this study, we examined transcriptome changes in bark tissue at four positions on upright and inverted cuttings of P. yunnanensis: position B, the upper portion of the stem; position C, the lower portion of the stem; position D, the bottom of new growth; and position E, the top of new growth. The results revealed major transcriptomic changes in the stem, especially at position B, but little alteration was observed in the bark tissue of the new shoot. The differentially expressed genes (DEGs) were mainly assigned to four pathways: plant hormone signal transduction, plant-pathogen interaction, mitogen-activated protein kinase (MAPK) signaling pathway-plant, and adenosine triphosphate-binding cassette (ABC) transporters. Most of these DEGs were involved in at least two pathways. The levels of many hormones, such as auxin (IAA), cytokinin (CTK), gibberellins (GAs), ethylene (ET), and brassinosteroids (BRs), underwent large changes in the inverted cuttings. A coexpression network showed that the top 20 hub unigenes at position B in the upright and inverted cutting groups were associated mainly with the BR and ET signaling pathways, respectively. Furthermore, brassinosteroid insensitive 1-associated receptor kinase 1 (BAK1) in the BR pathway and both ethylene response (ETR) and constitutive triple response 1 (CTR1) in the ET pathway were important hubs that interfaced with multiple pathways.

Draft genome of the kiwifruit Actinidia chinensis.

The kiwifruit (Actinidia chinensis) is an economically and nutritionally important fruit crop with remarkably high vitamin C content. Here we report the draft genome sequence of a heterozygous kiwifruit, assembled from ~140-fold next-generation sequencing data. The assembled genome has a total length of 616.1 Mb and contains 39,040 genes. Comparative genomic analysis reveals that the kiwifruit has undergone an ancient hexaploidization event (γ) shared by core eudicots and two more recent whole-genome duplication events. Both recent duplication events occurred after the divergence of kiwifruit from tomato and potato and have contributed to the neofunctionalization of genes involved in regulating important kiwifruit characteristics, such as fruit vitamin C, flavonoid and carotenoid metabolism. As the first sequenced species in the Ericales, the kiwifruit genome sequence provides a valuable resource not only for biological discovery and crop improvement but also for evolutionary and comparative genomics analysis, particularly in the asterid lineage.

Rice choline monooxygenase (OsCMO) protein functions in enhancing glycine betaine biosynthesis in transgenic tobacco but does not accumulate in rice (Oryza sativa L. ssp. japonica).

UNLABELLED: Glycine betaine (GB) is a compatible quaternary amine that enables plants to tolerate abiotic stresses, including salt, drought and cold. In plants, GB is synthesized through two-step of successive oxidations from choline, catalyzed by choline monooxygenase (CMO) and betaine aldehyde dehydrogenase (BADH), respectively. Rice is considered as a typical non-GB accumulating species, although the entire genome sequencing revealed rice contains orthologs of both CMO and BADH. Several studies unraveled that rice has a functional BADH gene, but whether rice CMO gene (OsCMO) is functional or a pseudogene remains to be elucidated. In the present study, we report the functional characterization of rice CMO gene. The OsCMO gene was isolated from rice cv. Nipponbare (Oryza sativa L. ssp. japonica) using RT-PCR. Northern blot demonstrated the transcription of OsCMO is enhanced by salt stress. Transgenic tobacco plants overexpressing OsCMO results in increased GB content and elevated tolerance to salt stress. Immunoblotting analysis demonstrates that a functional OsCMO protein with correct size was present in transgenic tobacco but rarely accumulated in wild-type rice plants. Surprisingly, a large amount of truncated proteins derived from OsCMO was induced in the rice seedlings in response to salt stresses. This suggests that it is the lack of a functional OsCMO protein that presumably results in non-GB accumulation in the tested rice plant. KEY MESSAGE: Expression and transgenic studies demonstrate OsCMO is transcriptionally induced in response to salt stress and functions in increasing glycinebetaine accumulation and enhancing tolerance to salt stress. Immunoblotting analysis suggests that no accumulation of glycinebetaine in the Japonica rice plant presumably results from lack of a functional OsCMO protein.

Mitochondrial aldehyde dehydrogenase-2 (ALDH2) Glu504Lys polymorphism contributes to the variation in efficacy of sublingual nitroglycerin.

Glyceryl trinitrate (GTN), also known as nitroglycerin, has been used to treat angina and heart failure for more than 130 years. Recently, it was shown that mitochondrial aldehyde dehydrogenase-2 (ALDH2) is responsible for formation of NO, the metabolite needed for GTN efficacy. In the present study, we show that the common G-to-A polymorphism in exon 12 of ALDH2--resulting in a Glu504Lys replacement that virtually eliminates ALDH2 activity in both heterozygotes and homozygotes--is associated with a lack of efficacy of sublingual GTN in Chinese subjects. We also show that the catalytic efficiency (Vmax/Km) of GTN metabolism of the Glu504 protein is approximately 10-fold higher than that of the Lys504 enzyme. We conclude that the presence of the Lys504 allele contributes in large part to the lack of an efficacious clinical response to nitroglycerin; we recommend that this genetic factor be considered when administering nitroglycerin to patients, especially Asians, 30-50% of whom possess the inactive ALDH2*2 mutant allele.

[Relationship between six single nucleotide polymorphisms of angiotensinogen gene and essential hypertension].

OBJECTIVE: To evaluate the relationship of six single nucleotide polymorphisms(SNPs) and their haplotypes of angiotensinogen(AGT) gene to essential hypertension(EH) in Chinese Han population. METHODS: The genotypes in 185 patients with EH and 185 healthy controls were determined by the method of ABI PRISM SNaPshot Multiplex Kit using six AGT gene polymorphisms at position -217(G/A), -152(G/A), -20(A/C) and -6(G/A) in the promoter region and T174M, M235T in exon 2. RESULTS: The distribution of AGT genotypes and alleles frequencies showed no significant difference between the group of EH and group of controls (P>0.05). However, haplotype analysis revealed that H4 haplotype frequency, which included -152A, -20C, -6A and 235T alleles, was significantly increased in the group of EH (P<0.05). CONCLUSION: G-152A, A-20C, G-6A and M235T polymorphisms of AGT gene might play an important role in the occurrence of EH in Chinese Han population.

Single nucleotide polymorphisms in promoter of angiotensin II type 1 receptor gene associated with essential hypertension and coronary heart disease in Chinese population.

AIM: To discover single nucleotide polymorphisms (SNPs) in the promoter region of angiotensin II type 1 receptor (AT1) gene and evaluate their associations with the occurrence of essential hypertension (EH) and coronary heart disease (CHD) in Chinese Han population. METHODS: SNPs detection was performed by PCR-sequencing. The genotype was determined by the same method in a total number of 473 unrelated patients including 160 EH cases, 128 CHD cases, and 185 EH combined with CHD cases as well as 160 healthy controls. RESULTS: Six SNPs were discovered in the promoter region of AT1 gene. -810A/T was almost in completely linkage disequilibrium with -713G/T, -214A/C, -213G/C, and -153A/G polymorphisms. No statistically association was found in our population between -810A/T polymorphism and EH, the association of -810A allele and CHD was of borderline significant (chi2=3.649, P=0.056). However, significant differences of genotype distributions were observed in the EH combined with CHD group (TT=126, TA=51, AA=8) compared with the EH patients (TT=127,TA=26, AA=7, chi2=6.410, P=0.041) and the healthy controls (TT=130, TA=24, AA=6, chi2=7.742, P=0.021). The EH combined with CHD patients had a significantly increased A allele frequency than the normal references (0.181 vs 0.106, chi2=7.690, P=0.006) and the EH subjects (0.181 vs 0.125, chi2=4.119, P=0.042). Hypertensive patients carrying TA genotype (OR=1.977, 95 % CI 1.160-3.354, P=0.011) or A allele (OR=1.548, 95 % CI 1.015-2.361, P=0.043) had an increased risk for CHD morbidity. CONCLUSION: we firstly report that -810A/T polymorphism in the promoter region of AT1 gene might be a genetic risk factor for the pathogenesis of CHD complicated with EH in Chinese Han population.

High glucose enhance expression of matrix metalloproteinase-2 in smooth muscle cells.

AIM: To investigate the effects of high glucose on expression of matrix metalloproteinase-2 (MMP-2) in rat aortic smooth muscle cells and the influence of matrix remodeling on atherogenesis in diabetic patients. METHODS: The smooth muscle cells were cultured from the thoracic aorta of Sprague-Dawley (SD) rat. MMP-2 mRNA was determined by reverse transcriptase-polymerase chain reaction (RT-PCR), MMP-2 protein was measured by Western blotting, and MMP-2 activity in conditioned medium was observed by zymography. RESULTS: In comparison with the control, there was no difference in the expression of MMP-2 when glucose concentration was 1 g/L, whereas MMP-2 activity in smooth muscle cells was significantly increased by the glucose 5 g/L (P<0.01). CONCLUSION: High glucose enhanced the expression and activity of MMP-2 in smooth muscle cells, which may provide an explanation for the phenomenon that diabetes patients are prone to have atherosclerotic lesions.

[Study on plasma coagulation factor VII (FVII) levels and polymorphisms of FVII gene in patients with coronary heart disease].

OBJECTIVE: To investigate the plasma levels of coagulation factor VII (FVII) and polymorphisms of FVII gene in patients with coronary heart disease (CHD), and evaluate the effect of plasma FVII levels and FVII gene polymorphisms on CHD. METHODS: Plasma FVIIa, FVII: Ag and FVIIc were measured and polymorphisms of FVII gene were analyzed in 149 control cases and 60 CHD cases, including 33 acute myocardial infarction (AMI) cases by a combination of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and agarose gel electrophoresis. RESULTS: FVIIa, FVIIc in AMI group were significantly higher than that in control group, but FVII: Ag wasn't. There were no significant difference in plasma FVIIa, FVII: Ag and FVIIc between CHD and control group. The IVS7 genotypic frequency in AMI group was significantly different from that in control group. There was no significant difference in genotypic frequencies and allelic frequencies in other polymphism sites. FVII: Ag was significantly higher in -402A homozygote than that in -402G homozygote. CONCLUSIONS: Increased FVII levels, especially FVIIa and FVIIc in plasma, may contribute to coronary artery thrombosis. There was significant difference in IVS7 genotype frequency between control and AMI groups, but the rest weren't significantly different. FVII: Ag was significantly higher in -402A homozygote than that in -402G homozygote. Polymorphism of -402 G/A may play an indirect role in AMI by regulating plasma FVII levels.