The Spatio-Temporal Expression Profiles of Silkworm Pseudogenes Provide Valuable Insights into Their Biological Roles.

Background: Pseudogenes are sequences that have lost the ability to transcribe RNA molecules or encode truncated but possibly functional proteins. While they were once considered to be meaningless remnants of evolution, recent researches have shown that pseudogenes play important roles in various biological processes. However, the studies of pseudogenes in the silkworm, an important model organism, are limited and have focused on single or only a few specific genes. Objective: To fill these gaps, we present a systematic genome-wide studies of pseudogenes in the silkworm. Methods: We identified the pseudogenes in the silkworm using the silkworm genome assemblies, transcriptome, protein sequences from silkworm and its related species. Then we used transcriptome datasets from 832 RNA-seq analyses to construct spatio-temporal expression profiles for these pseudogenes. Additionally, we identified tissue-specifically expressed and differentially expressed pseudogenes to further understand their characteristics. Finally, the functional roles of pseudogenes as lncRNAs were systematically analyzed. Results: We identified a total of 4410 pseudogenes, which were grouped into 4 groups, including duplications (DUPs), unitary pseudogenes (Unitary), processed pseudogenes (retropseudogenes, RETs), and fragments (FRAGs). The most of pseudogenes in the domestic silkworm were generated before the divergence of wild and domestic silkworm, however, the domestication may also involve in the accumulation of pseudogenes. These pseudogenes were clearly divided into 2 cluster, a highly expressed and a lowly expressed, and the posterior silk gland was the tissue with the most tissue-specific pseudogenes (199), implying these pseudogenes may be involved in the development and function of silkgland. We identified 3299 lncRNAs in these pseudogenes, and the target genes of these lncRNAs in silkworm pseudogenes were enriched in the egg formation and olfactory function. Conclusions: This study replenishes the genome annotations for silkworm, provide valuable insights into the biological roles of pseudogenes. It will also contribute to our understanding of the complex gene regulatory networks in the silkworm and will potentially have implications for other organisms as well.

Network pharmacology and transcriptomics analysis reveal the mechanism of BushenHuoxue formula attenuates premature ovarian failure via modulation PI3K/AKT pathway.

This study aims to analyze the active components and mechanism of Bushen Huoxue (BSHX) formula on the autoimmune premature ovarian insufficiency (POI) by combining network pharmacology and Transcriptomics. The active components and targets of BSHXF were screened through Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). POI-related targets were identified through Therapeutic Targets Database (TTD), DisGeNET and drugbank database. The Veen diagram was performed to obtain the action targets. The active compound-target network and Protein-Protein Interaction (PPI) network were built by using STRING database and Cytoscape software. Key targets and active compounds were further identified by topological analysis. Molecular docking shows that Kaempferol, Isorhamnetin and Anhydroicaritin have strong binding to AKT. Finally, a zp3-induced autoimmune ovarian function deficiency mouse model was used to explore the potential mechanism of POI. The potential pathways of BSHXF for the treatment of POI were identified by Transcriptomic analysis. PI3K-AKT and NF-kb pathways were the common pathways between network pharmacology and transcriptomics. Our results revealed that BSHXF could reduce the FSH expression levels and raise the E2, and AMH levels in the serum. Western bloting demonstrates that BSHXF could upregulate the expression of p-PI3K and p-AKT.

Eclampsia as the First Manifestation of Primary Hyperparathyroidism: a Case Report.

BACKGROUND: This study aimed to explore the diagnosis and treatment strategies of eclampsia during pregnancy and postpartum acute pancreatitis caused by primary hyperparathyroidism. METHODS: This study reported a 26-year-old patient who had maternal eclampsia as her first symptom and was admitted to the hospital. The pregnancy was terminated by cesarean section immediately. Postpartum life-threatening complications, such as severe hypercalcemia and acute pancreatitis, occurred afterward. Following completion of the relevant examination, primary hyperparathyroidism was initially considered to be the cause. Symptomatic treatment is ongoing and will be improved, and the patient will be admitted again for parathyroidectomy. RESULTS: The patient gave birth to a premature neonate via cesarean section. The postpartum diagnosis was primary hyperparathyroidism, for which post-surgical pathology showed a parathyroid adenoma. CONCLUSIONS: The clinical manifestations of pregnancy with primary hyperparathyroidism are atypical but may cause serious maternal and fetal complications. Early diagnosis and appropriate treatment can prevent serious prenatal and postnatal complications and foster better pregnancy outcomes.

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes.

Evidence of whole-genome duplications (WGDs) and subsequent karyotype changes has been detected in most major lineages of living organisms on Earth. To clarify the complex resulting multi-layered patterns of gene collinearity in genome analyses, there is a need for convenient and accurate toolkits. To meet this need, we developed WGDI (Whole-Genome Duplication Integrated analysis), a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidization events and cross-species genome alignments. WGDI supports three main workflows (polyploid inference, hierarchical inference of genomic homology, and ancestral chromosome karyotyping) that can improve the detection of WGD and characterization of WGD-related events based on high-quality chromosome-level genomes. Significantly, it can extract complete synteny blocks and facilitate reconstruction of detailed karyotype evolution. This toolkit is freely available at GitHub (https://github.com/SunPengChuan/wgdi). As an example of its application, WGDI convincingly clarified karyotype evolution in Aquilegia coerulea and Vitis vinifera following WGDs and rejected the hypothesis that Aquilegia contributed as a parental lineage to the allopolyploid origin of core dicots.

The celery genome sequence reveals sequential paleo-polyploidizations, karyotype evolution and resistance gene reduction in apiales.

Celery (Apium graveolens L. 2n = 2x = 22), a member of the Apiaceae family, is among the most important and globally grown vegetables. Here, we report a high-quality genome sequence assembly, anchored to 11 chromosomes, with total length of 3.33 Gb and N50 scaffold length of 289.78 Mb. Most (92.91%) of the genome is composed of repetitive sequences, with 62.12% of 31 326 annotated genes confined to the terminal 20% of chromosomes. Simultaneous bursts of shared long-terminal repeats (LTRs) in different Apiaceae plants suggest inter-specific exchanges. Two ancestral polyploidizations were inferred, one shared by Apiales taxa and the other confined to Apiaceae. We reconstructed 8 Apiales proto-chromosomes, inferring their evolutionary trajectories from the eudicot common ancestor to extant plants. Transcriptome sequencing in three tissues (roots, leaves and petioles), and varieties with different-coloured petioles, revealed 4 and 2 key genes in pathways regulating anthocyanin and coumarin biosynthesis, respectively. A remarkable paucity of NBS disease-resistant genes in celery (62) and other Apiales was explained by extensive loss and limited production of these genes during the last ~10 million years, raising questions about their biotic defence mechanisms and motivating research into effects of chemicals, for example coumarins, that give off distinctive odours. Celery genome sequencing and annotation facilitates further research into important gene functions and breeding, and comparative genomic analyses in Apiales.

Tetrandrine attenuates hyperoxia-induced lung injury in newborn rats via NF-κB p65 and ERK1/2 pathway inhibition.

BACKGROUND: Bronchopulmonary dysplasia (BPD) is an important cause of respiratory illness in preterm newborns that results in significant morbidity and mortality. Hyperoxia is a critical factor in the pathogenesis of BPD, hyperoxia-induced lung injury model has similar pathological manifestations as human BPD. Tetrandrine (Tet) is known to suppress oxidative stress, apoptosis and inflammation. Thus it has been used to prevent organ injuries. However, the protective effect of Tet against hyperoxia-induced lung injury in newborn rats has not been reported. METHODS: A hyperoxia-induced lung injury model was established using newborn rats exposed to high O2 levels. The models were treated with various concentrations of Tet, and a lung function test was conducted. Then, the lung tissues and blood were collected to detect the effect of Tet on cell apoptosis, inflammatory response, and fibrosis. The effect of Tet on nuclear factor-kappa B (NF-κB) and extracellular signal-regulated kinase1/2 (ERK1/2) pathways was also determined. RESULTS: Lung function was decreased in hyperoxia-induced rats, and Tet could reverse this inhibiting effect. For oxidative stress, Tet caused an increase in the levels of antioxidant enzymes. The apoptosis rate and apoptosis-related proteins were decreased in hyperoxia-induced rats after Tet treatment. Additionally, Tet treatment could reduce inflammatory factor levels, while increasing CD4+IFN-γ+ T cell levels and decreasing CD4+IL-4+ T cell levels. Tet treatment was also able to inhibit the expression of fibrosis-related markers and NF-κB and ERK1/2 pathways. CONCLUSIONS: Tet demonstrated potent activity against hyperoxia-induced lung injury in newborn rats through NF-κB and ERK1/2 pathway inhibition.

Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution.

Angiosperms represent one of the most spectacular terrestrial radiations on the planet1, but their early diversification and phylogenetic relationships remain uncertain2-5. A key reason for this impasse is the paucity of complete genomes representing early-diverging angiosperms. Here, we present high-quality, chromosomal-level genome assemblies of two aquatic species-prickly waterlily (Euryale ferox; Nymphaeales) and the rigid hornwort (Ceratophyllum demersum; Ceratophyllales)-and expand the genomic representation for key sectors of the angiosperm tree of life. We identify multiple independent polyploidization events in each of the five major clades (that is, Nymphaeales, magnoliids, monocots, Ceratophyllales and eudicots). Furthermore, our phylogenomic analyses, which spanned multiple datasets and diverse methods, confirm that Amborella and Nymphaeales are successively sister to all other angiosperms. Furthermore, these genomes help to elucidate relationships among the major subclades within Mesangiospermae, which contain about 350,000 species. In particular, the species-poor lineage Ceratophyllales is supported as sister to eudicots, and monocots and magnoliids are placed as successively sister to Ceratophyllales and eudicots. Finally, our analyses indicate that incomplete lineage sorting may account for the incongruent phylogenetic placement of magnoliids between nuclear and plastid genomes.

Arsenic release and speciation during the oxidative dissolution of arsenopyrite by O2 in the absence and presence of EDTA.

The oxidative decomposition of arsenopyrite is an important source of As in surface environment. This study investigated the oxidative dissolution of arsenopyrite by O2 and aqueous arsenic transformation at different pHs, dissolved oxygen (DO) contents, and temperatures in the absence and presence of EDTA. The oxidative dissolution was greatly inhibited at neutral and alkaline pH in the absence of EDTA. However, in the presence of EDTA, the oxidative dissolution rate increased linearly from pH 4 to 7. The highest dissolution rate was 3-4 times higher than that at pH 4 and 1-2 orders of magnitude higher than that at pH 7 in the absence of EDTA. This is possibly due to the lack of Fe oxyhydroxides on the surface of arsenopyrite. In the pH range of 7-10, the oxidative dissolution rate decreased linearly, possibly due to the formation of goethite and/or hematite coating. The oxidation of released arsenite (AsIII) to arsenate (AsV) took place simultaneously during the oxidative dissolution of arsenopyrite in the presence of dissolved Fe without EDTA, while no obvious aqueous AsIII oxidation was observed in the presence of EDTA, indicating that aqueous Fe species play an important role in AsIII oxidation.

Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform.

Mainly due to their economic importance, genomes of 10 legumes, including soybean (Glycine max), wild peanut (Arachis duranensis and Arachis ipaensis), and barrel medic (Medicago truncatula), have been sequenced. However, a family-level comparative genomics analysis has been unavailable. With grape (Vitis vinifera) and selected legume genomes as outgroups, we managed to perform a hierarchical and event-related alignment of these genomes and deconvoluted layers of homologous regions produced by ancestral polyploidizations or speciations. Consequently, we illustrated genomic fractionation characterized by widespread gene losses after the polyploidizations. Notably, high similarity in gene retention between recently duplicated chromosomes in soybean supported the likely autopolyploidy nature of its tetraploid ancestor. Moreover, although most gene losses were nearly random, largely but not fully described by geometric distribution, we showed that polyploidization contributed divergently to the copy number variation of important gene families. Besides, we showed significantly divergent evolutionary levels among legumes and, by performing synonymous nucleotide substitutions at synonymous sites correction, redated major evolutionary events during their expansion. This effort laid a solid foundation for further genomics exploration in the legume research community and beyond. We describe only a tiny fraction of legume comparative genomics analysis that we performed; more information was stored in the newly constructed Legume Comparative Genomics Research Platform (www.legumegrp.org).