Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants.

The auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA) family of genes are central components of the auxin signaling pathway and play essential roles in plant growth and development. Their large-scale analysis and evolutionary trajectory of origin are currently not known. Here, we identified the corresponding ARF and Aux/IAA family members and performed a large-scale analysis by scanning 406 plant genomes. The results showed that the ARF and Aux/IAA gene families originated from charophytes. The ARF family sequences were more conserved than the Aux/IAA family sequences. Dispersed duplications were the common expansion mode of ARF and Aux/IAA families in bryophytes, ferns, and gymnosperms; however, whole-genome duplication was the common expansion mode of the ARF and Aux/IAA families in basal angiosperms, magnoliids, monocots, and dicots. Expression and regulatory network analyses revealed that the Arabidopsis thaliana ARF and Aux/IAA families responded to multiple hormone, biotic, and abiotic stresses. The APETALA2 and serum response factor-transcription factor gene families were commonly enriched in the upstream and downstream genes of the ARF and Aux/IAA gene families. Our study provides a comprehensive overview of the evolutionary trajectories, structural functions, expansion mechanisms, expression patterns, and regulatory networks of these two gene families.

Gut-Derived Exosomes Mediate the Microbiota Dysbiosis-Induced Spermatogenesis Impairment by Targeting Meioc in Mice.

Diseases like obesity and intestinal inflammation diseases are accompanied by dysbiosis of the gut microbiota (DSGM), which leads to various complications, including systemic metabolic disorders. DSGM reportedly impairs the fertility of male mice; however, the regulatory mechanism is unclear. Exosomes are molecular mediators of intercellular communication, but the regulation of spermatogenesis by non-reproductive tissue-originated exosomes remains unknown. The present study shows that DSGM altered the miRNA expression profile of mouse circulating exosomes and impaired spermatogenesis. Moreover, the single-cell sequencing results indicate that circulating exosomes from mice with DSGM impaired spermatogenesis, while circulating exosomes from wild mice improved spermatogenesis by promoting meiosis. Further study demonstrates that DSGM leads to abnormal upregulation of miR-211-5p in gut-derived circulating exosomes, which inhibited the expression of meiosis-specific with coiled-coil domain (Meioc) in the testes and impaired spermatogenesis by disturbing meiosis process. In summary, this study defines the important role of gut-derived exosomes in connecting the "gut-testis" axis.

The genome of Stephania japonica provides insights into the biosynthesis of cepharanthine.

Stephania japonica is an early-diverging eudicotyledon plant with high levels of cepharanthine, proven to be effective in curing coronavirus infections. Here, we report a high-quality S. japonica genome. The genome size is 688.52 Mb, and 97.37% sequences anchor to 11 chromosomes. The genome comprises 67.46% repetitive sequences and 21,036 genes. It is closely related to two Ranunculaceae species, which diverged from their common ancestor 55.90-71.02 million years ago (Mya) with a whole-genome duplication 85.59-96.75 Mya. We further reconstruct ancestral karyotype of Ranunculales. Several cepharanthine biosynthesis genes are identified and verified by western blot. Two genes (Sja03G0243 and Sja03G0241) exhibit catalytic activity as shown by liquid chromatography-mass spectrometry. Then, cepharanthine biosynthesis genes, transcription factors, and CYP450 family genes are used to construct a comprehensive network. Finally, we construct an early-diverging eudicotyledonous genome resources (EEGR) database. As the first genome of the Menispermaceae family to be released, this study provides rich resources for genomic studies.

YTHDF2 as a Mediator in BDNF-Induced Proliferation of Porcine Follicular Granulosa Cells.

In female mammals, the proliferation and apoptosis of granulosa cells (GCs) are critical in determining the fate of follicles and are influenced by various factors, including brain-derived neurotrophic factor (BDNF). Previous research has shown that BDNF primarily regulates GC proliferation through the PI3K/AKT, NF-kB, and CREB tumour pathways; however, the role of other molecular mechanisms in mediating BDNF-induced GC proliferation remains unclear. In this study, we investigated the involvement of the m6A reader YTH domain-containing family member 2 (YTHDF2) in BDNF-stimulated GC proliferation and its underlying mechanism. GCs were cultured in DMEM medium supplemented with varying BDNF concentrations (0, 10, 30, 75, and 150 ng/mL) for 24 h. The viability, number, and cell cycle of GCs were assessed using the CCK-8 assay, cell counting, and flow cytometry, respectively. Further exploration into YTHDF2's role in BDNF-stimulated GC proliferation was conducted using RT-qPCR, Western blotting, and sequencing. Our findings indicate that YTHDF2 mediates the effect of BDNF on GC proliferation. Additionally, this study suggests for the first time that BDNF promotes YTHDF2 expression by increasing the phosphorylation level of the ERK1/2 signalling pathway. This study offers a new perspective and foundation for further elucidating the mechanism by which BDNF regulates GC proliferation.

Follicular fluid exosomes inhibit expression of BTG2 and promote glucose uptake in granulosa cells by delivering miR-21-5p.

Glucose metabolism in granulosa cells (GCs) is essential for follicle development and oocyte maturation. Porcine follicular fluid exosomes promote the proliferation of porcine GCs and the synthesis of steroid hormones. However, their role in regulating glucose uptake in GCs is unclear. The objective of this study was to elucidate the effects of porcine follicular fluid exosomes on glucose uptake in porcine GCs and the intrinsic mechanisms involved. First, transcriptome sequencing revealed that glucose metabolism-related pathways were altered in GCs treated with follicular fluid exosomes. Next, in vitro culture experiments showed that glucose uptake was increased and the IRS1/AKT signaling pathway was activated in GCs after treatment with follicular fluid exosomes. Finally, miRNA sequencing of follicular fluid exosomes revealed that miR-21-5p was the most abundant miRNA. Subsequent investigations indicated that miR-21-5p promoted glucose uptake in GCs by targeting BTG2, which activated the IRS1/AKT signaling pathway. In conclusion, the findings of this study indicate that porcine follicular fluid exosomes promote glucose uptake in porcine GCs by delivering miR-21-5p, which inhibits the expression of BTG2, activating the IRS1/AKT signaling pathway.

lnc RNA LOC102163816 Promotes Proliferation of Porcine Follicular Granulosa Cells Via miR-455-3p/PTK2B/PI3K/AKT Pathway.

The proliferation and differentiation of granulosa cells (GCs) is a crucial process in follicular development. However, the molecular regulatory mechanism of follicular proliferation and differentiation of GCs needs further research. Studies have reported that follicular fluid exosomes are involved in regulation of proliferation of GCs, but the specific mechanism is unclear. This study demonstrated that LOC102163816 is upregulated in porcine GCs treated with follicular fluid exosomes. Further study defined LOC102163816 to be a novel long noncoding RNA that is highly homologous to human metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and enriched in porcine follicular fluid exosomes. We have speculated that LOC102163816 might have a cell-proliferative effect similar to that of MALAT1. We found that overexpression of LOC102163816 promoted transition from the G1 phase to the S phase of the cell cycle, thereby promoting proliferation of GCs. To explore the specific mechanism underlying this promotion of proliferation, miRNA sequencing was performed after overexpression of LOC102163816. Our results showed that LOC102163816 sponged miR-455-3p, promoting expression of protein tyrosine kinase 2 beta (PTK2B), thereby activating the PI3K/AKT signaling pathway to regulate proliferation of porcine follicular GCs. These findings provide useful insights into follicular development.

The high-quality sequencing of the Brassica rapa 'XiangQingCai' genome and exploration of genome evolution and genes related to volatile aroma.

'Vanilla' (XQC, brassica variety chinensis) is an important vegetable crop in the Brassica family, named for its strong volatile fragrance. In this study, we report the high-quality chromosome-level genome sequence of XQC. The assembled genome length was determined as 466.11 Mb, with an N50 scaffold of 46.20 Mb. A total of 59.50% repetitive sequences were detected in the XQC genome, including 47 570 genes. Among all examined Brassicaceae species, XQC had the closest relationship with B. rapa QGC ('QingGengCai') and B. rapa Pakchoi. Two whole-genome duplication (WGD) events and one recent whole-genome triplication (WGT) event occurred in the XQC genome in addition to an ancient WGT event. The recent WGT was observed to occur during 21.59-24.40 Mya (after evolution rate corrections). Our findings indicate that XQC experienced gene losses and chromosome rearrangements during the genome evolution of XQC. The results of the integrated genomic and transcriptomic analyses revealed critical genes involved in the terpenoid biosynthesis pathway and terpene synthase (TPS) family genes. In summary, we determined a chromosome-level genome of B. rapa XQC and identified the key candidate genes involved in volatile fragrance synthesis. This work can act as a basis for the comparative and functional genomic analysis and molecular breeding of B. rapa in the future.

Genome assembly of Polygala tenuifolia provides insights into its karyotype evolution and triterpenoid saponin biosynthesis.

Polygala tenuifolia is a perennial medicinal plant that has been widely used in traditional Chinese medicine for treating mental diseases. However, the lack of genomic resources limits the insight into its evolutionary and biological characterization. In the present work, we reported the P. tenuifolia genome, the first genome assembly of the Polygalaceae family. We sequenced and assembled this genome by a combination of Illumnina, PacBio HiFi, and Hi-C mapping. The assembly includes 19 pseudochromosomes covering ~92.68% of the assembled genome (~769.62 Mb). There are 36 463 protein-coding genes annotated in this genome. Detailed comparative genome analysis revealed that P. tenuifolia experienced two rounds of whole genome duplication that occurred ~39-44 and ~18-20 million years ago, respectively. Accordingly, we systematically reconstructed ancestral chromosomes of P. tenuifolia and inferred its chromosome evolution trajectories from the common ancestor of core eudicots to the present species. Based on the transcriptomics data, enzyme genes and transcription factors involved in the synthesis of triterpenoid saponin in P. tenuifolia were identified. Further analysis demonstrated that whole-genome duplications and tandem duplications play critical roles in the expansion of P450 and UGT gene families, which contributed to the synthesis of triterpenoid saponins. The genome and transcriptome data will not only provide valuable resources for comparative and functional genomic researches on Polygalaceae, but also shed light on the synthesis of triterpenoid saponin.

Metabolomic Profiling of Female Mink Serum during Early to Mid-Pregnancy to Reveal Metabolite Changes.

Mink embryos enter a period of diapause after the embryo develops into the blastocyst, and its reactivation is mainly caused by an increase in polyamine. The specific process of embryo diapause regulation and reactivation remains largely unexamined. This study aimed to identify changes in metabolites in the early pregnancy of mink by comparing and analyzing in serum metabolites up to twenty-nine days after mating. Blood samples were taken on the first day of mating, once a week until the fifth week. Metabolomic profiles of the serum samples taken during this period were analyzed by ultra-performance liquid chromatography/mass spectrometry. Multivariate statistical analyses identified differential metabolite expression at different time points in both positive and negative ion modes. The levels of dopamine, tyramine, L-phenylalanine, L-tyrosine, tyrosine, L-kynurenine, L-lysine, L-arginine, D-ornithine, and leucine changed significantly. These metabolites may be associated with the process of embryo diapause and subsequent reactivation.

Inter-regional environmental inequality under lasting pandemic exacerbated by residential response.

Pandemics greatly affect transportation, economic and household activities and their associated air pollutant emissions. In less affluent regions, household energy use is often the dominant pollution source and is sensitive to the affluence change caused by a persisting pandemic. Air quality studies on COVID-19 have shown declines in pollution levels over industrialized regions as an immediate response to pandemic-caused lockdown and weakened economy. Yet few have considered the response of residential emissions to altered household affluence and energy choice supplemented by social distancing. Here we quantify the potential effects of long-term pandemics on ambient fine particulate matter pollution (PM2.5) and resulting premature mortality worldwide, by comprehensively considering the changes in transportation, economic production and household energy use. We find that a persisting COVID-like pandemic would reduce the global gross domestic product by 10.9 % and premature mortality related to black carbon, primary organic aerosols and secondary inorganic aerosols by 9.5 %. The global mortality decline would reach 13.0 % had the response of residential emissions been excluded. Among the 13 aggregated regions worldwide, the least affluent regions exhibit the greatest fractional economic losses with no comparable magnitudes of mortality reduction. This is because their weakened affluence would cause switch to more polluting household energy types on top of longer stay-at-home time, largely offsetting the effect of reduced transportation and economic production. International financial, technological and vaccine aids could reduce such environmental inequality.

The Mechanisms of BDNF Promoting the Proliferation of Porcine Follicular Granulosa Cells: Role of miR-127 and Involvement of the MAPK-ERK1/2 Pathway.

As a member of the neurotrophic family, brain-derived neurotrophic factor (BDNF) provides a key link in the physiological process of mammalian ovarian follicle development, in addition to its functions in the nervous system. The emphasis of this study lay in the impact of BDNF on the proliferation of porcine follicular granulosa cells (GCs) in vitro. BDNF and tyrosine kinase B (TrkB, receptor of BDNF) were detected in porcine follicular GCs. Additionally, cell viability significantly increased during the culture of porcine GCs with BDNF (100 ng/mL) in vitro. However, BDNF knockdown in GCs decreased cell viability and S-phase cells proportion-and BDNF simultaneously regulated the expression of genes linked with cell proliferation (CCND1, p21 and Bcl2) and apoptosis (Bax). Then, the results of the receptor blocking experiment showed that BDNF promoted GC proliferation via TrkB. The high-throughput sequencing showed that BDNF also regulated the expression profiles of miRNAs in GCs. The differential expression profiles were obtained by miRNA sequencing after BDNF (100 ng/mL) treatment with GCs. The sequencing results showed that, after BDNF treatment, 72 significant differentially-expressed miRNAs were detected-5 of which were related to cell process and proliferation signaling pathways confirmed by RT-PCR. Furthermore, studies showed that BDNF promoted GCs' proliferation by increasing the expression of CCND1, downregulating miR-127 and activating the ERK1/2 signal pathway. Moreover, BDNF indirectly activated the ERK1/2 signal pathway by downregulating miR-127. In conclusion, BDNF promoted porcine GC proliferation by increasing CCND1 expression, downregulating miR-127 and stimulating the MAPK-ERK1/2 signaling cascade.

Corrigendum: Whole transcriptome profiling of the effects of cadmium on the liver of the Xiangxi yellow heifer.

[This corrects the article DOI: 10.3389/fvets.2022.846662.].

Spatiotemporal regulation of maternal mRNAs during vertebrate oocyte meiotic maturation.

Vertebrate oocytes face a particular challenge concerning the regulation of gene expression during meiotic maturation. Global transcription becomes quiescent in fully grown oocytes, remains halted throughout maturation and fertilization, and only resumes upon embryonic genome activation. Hence, the oocyte meiotic maturation process is largely regulated by protein synthesis from pre-existing maternal messenger RNAs (mRNAs) that are transcribed and stored during oocyte growth. Rapidly developing genome-wide techniques have greatly expanded our insights into the global translation changes and possible regulatory mechanisms during oocyte maturation. The storage, translation, and processing of maternal mRNAs are thought to be regulated by factors interacting with elements in the mRNA molecules. Additionally, posttranscriptional modifications of mRNAs, such as methylation and uridylation, have recently been demonstrated to play crucial roles in maternal mRNA destabilization. However, a comprehensive understanding of the machineries that regulate maternal mRNA fate during oocyte maturation is still lacking. In particular, how the transcripts of important cell cycle components are stabilized, recruited at the appropriate time for translation, and eliminated to modulate oocyte meiotic progression remains unclear. A better understanding of these mechanisms will provide invaluable insights for the preconditions of developmental competence acquisition, with important implications for the treatment of infertility. This review discusses how the storage, localization, translation, and processing of oocyte mRNAs are regulated, and how these contribute to oocyte maturation progression.

Follicular fluid exosomes inhibit BDNF expression and promote the secretion of chemokines in granulosa cells by delivering miR-10b-5p.

Ovulation is an inflammatory response. Before ovulation, follicle cells release chemokines to recruit immune cells and promote ovulation. The objective of this study was to investigate whether follicular fluid exosomes promote chemokine secretion by granulosa cells (GCs). Porcine follicular fluid exosomes and follicular GCs were isolated in vitro. GCs were treated with follicular fluid exosomes in vitro and the differential gene expression profiles of the exosome-treated and control groups were obtained by transcriptome sequencing. The results showed that, when compared to the controls, the expression of the chemokines CCL2 and CXCL8 was significantly increased, whereas the expression of brain-derived neurotrophic factor (BDNF) was significantly decreased. The miRNA expression profiles in follicular fluid exosomes were obtained by microRNA sequencing. The results showed that exosomes carried many microRNAs, and that miR-10b-5p carried by exosomes could promote the secretion of CCL2 and CXCL8 by targeting BDNF. In conclusion, the present study demonstrates that exosomes promote the secretion of CCL2 and CXCL8 by granulosa cells through the miR-10b-5p/BDNF axis to promote ovulation.

Follicular fluid exosomes regulate oxidative stress resistance, proliferation, and steroid synthesis in porcine theca cells.

Theca cells (TCs) are regulated by various factors during ovarian development. However, the role of follicular fluid exosomes in ovarian TCs has not yet been reported. In the present study, we explored the effects of follicular fluid exosomes on porcine ovarian TCs. TCs were treated with follicular fluid exosomes in vitro, and the differential gene expression profiles of TCs in the exosome and control groups were obtained via transcriptome sequencing. Differentially expressed genes were identified and found to be associated with antioxidative stress, proliferation, and steroid hormone synthesis of TCs. In addition, exosomes were found to increase antioxidative stress, proliferation, and steroid synthesis, as revealed by a higher mRNA and protein expression of GPX1, CCND1, PCNA, CYP11A1, and HSD3B1 and lower mRNA and protein expression of TNFR1 and BAX. In conclusion, we demonstrated that exosomes are essential components in regulating the physiological function of TCs.

The Impact of Assisted Hatching on Monozygotic Twinning is Related to Female Age and Insemination Method: A New Perspective.

Whether assisted hatching (AH) is associated with a higher incidence of monozygotic twinning (MZT) in women undergoing assisted reproductive technology remains controversial; the aim of the study was to demonstrate the relationship between AH and MZT. A total of 8900 clinical pregnancies were selected among embryo transfer cycles from January 2011 to October 2019. Women receiving day (D) 3 embryos were divided into groups A-C: group A (n = 1651) and group B (n = 1045) included women aged ≤37 or ≥38 years, respectively, with zona pellucida (ZP) thinning; group C (n = 3865) included women aged ≤37 years without AH. Women aged ≤37 years who underwent blastocyst transfer and/or blastocyst ZP breaching were included in group D (n = 2339). The incidence of MZT was compared among groups A, B and C, and between groups C and D. The incidence of MZT in group B (2.2%) was significantly higher than in group A (1.0%), especially following intracytoplasmic sperm injection (ICSI), while the incidence of MZT in group A (1.0%) was significantly lower than in group C (2.2%). The MZT rate with in vitro fertilization was higher in group D (2.8%) than in group C (2.2%), but the MZT rate following ICSI was not significantly different between the two groups. ZP thinning of D3 embryos may increase the risk of MZT in older women (≥38 years), but decrease it in younger women (≤37 years). ZP breaching may be useful to reduce the incidence of MZT in ICSI-generated blastocysts.

The effects of microbiota on reproductive health: A review.

Reproductive issues are becoming an increasing global problem. There is increasing interest in the relationship between microbiota and reproductive health. Stable microbiota communities exist in the gut, reproductive tract, uterus, testes, and semen. Various effects (e.g., epigenetic modifications, nervous system, metabolism) of dysbiosis in the microbiota can impair gamete quality; interfere with zygote formation, embryo implantation, and embryo development; and increase disease susceptibility, thus adversely impacting reproductive capacity and pregnancy. The maintenance of a healthy microbiota can protect the host from pathogens, increase reproductive potential, and reduce the rates of adverse pregnancy outcomes. In conclusion, this review discusses microbiota in the male and female reproductive systems of multiple animal species. It explores the effects and mechanisms of microbiota on reproduction, factors that influence microbiota composition, and applications of microbiota in reproductive disorder treatment and detection. The findings support novel approaches for managing reproductive diseases through microbiota improvement and monitoring. In addition, it will stimulate further systematic explorations of microbiota-mediated effects on reproduction.

Adipose mesenchymal stem cell-derived exosomal microRNAs ameliorate polycystic ovary syndrome by protecting against metabolic disturbances.

Polycystic ovary syndrome (PCOS) is the most common endocrine and metabolic disorder in women of childbearing age. Adipose mesenchymal stem cells (AMSCs) secrete cytokines involved in the regulation of metabolism and immunity. However, it remains unclear whether exosomes secreted by AMSCs (AMSC-EXOs) can rescue the polycystic phenotype and metabolic dysfunction in PCOS ovaries. Here, we show that AMSC-EXOs can protect against metabolic disturbances, ameliorate ovarian polycystic, and improve fertility in a rat model of PCOS. AMSC-EXOs inhibited the expression of B-cell translocation gene 2 by transferring miR-21-5p to the livers of rats with PCOS, thus activating the IRS1/AKT pathway and increasing hepatic metabolism. The role of AMSC-EXOs in transferring miRNAs to the liver to improve metabolic dysfunction in PCOS and reproduction by rescuing a non-coding RNA pathway was also discovered. This study provides a theoretical basis for the use of rat adipose stem cells and their secreted exosomes to treat PCOS.