Rfam 11.0: 10 years of RNA families

Chromosome-level genome assembly of the western flower thrips Frankliniella occidentalis

The western flower thrips Frankliniella occidentalis (Thysanoptera: Thripidae) is a global invasive species that causes increasing damage by direct feeding on crops and transmission of plant viruses. Here, we assemble a previously published scaffold-level genome into a chromosomal level using Hi-C sequencing technology. The assembled genome has a size of 302.58 Mb, with a contig N50 of 1533 bp, scaffold N50 of 19.071 Mb, and BUSCO completeness of 97.8%. All contigs are anchored on 15 chromosomes. A total of 16,312 protein-coding genes are annotated in the genome with a BUSCO completeness of 95.2%. The genome contains 492 non-coding RNA, and 0.41% of interspersed repeats. In conclusion, this high-quality genome provides a convenient and high-quality resource for understanding the ecology, genetics, and evolution of thrips.

Identifying widespread and recurrent variants of genetic parts to improve annotation of engineered DNA sequences

Engineered plasmids have been workhorses of recombinant DNA technology for nearly half a century. Plasmids are used to clone DNA sequences encoding new genetic parts and to reprogram cells by combining these parts in new ways. Historically, many genetic parts on plasmids were copied and reused without routinely checking their DNA sequences. With the widespread use of high-throughput DNA sequencing technologies, we now know that plasmids often contain variants of common genetic parts that differ slightly from their canonical sequences. Because the exact provenance of a genetic part on a particular plasmid is usually unknown, it is difficult to determine whether these differences arose due to mutations during plasmid construction and propagation or due to intentional editing by researchers. In either case, it is important to understand how the sequence changes alter the properties of the genetic part. We analyzed the sequences of over 50,000 engineered plasmids using depositor metadata and a metric inspired by the natural language processing field. We detected 217 uncatalogued genetic part variants that were especially widespread or were likely the result of convergent evolution or engineering. Several of these uncatalogued variants are known mutants of plasmid origins of replication or antibiotic resistance genes that are missing from current annotation databases. However, most are uncharacterized, and 3/5 of the plasmids we analyzed contained at least one of the uncatalogued variants. Our results include a list of genetic parts to prioritize for refining engineered plasmid annotation pipelines, highlight widespread variants of parts that warrant further investigation to see whether they have altered characteristics, and suggest cases where unintentional evolution of plasmid parts may be affecting the reliability and reproducibility of science.

The HABD: Home of All Biological Databases Empowering Biological Research With Cutting-Edge Database Systems

The emergence of computer technologies and computing power has led to the development of several database systems that provide standardized access to vast quantities of data, making it possible to collect, search, index, evaluate, and extract useful knowledge across various fields. The Home of All Biological Databases (HABD) has been established as a continually expanding platform that aims to store, organize, and distribute biological data in a searchable manner, removing all dead and non-accessible data. The platform meticulously categorizes data into various categories, such as COVID-19 Pandemic Database (CO-19PDB), Database relevant to Human Research (DBHR), Cancer Research Database (CRDB), Latest Database of Protein Research (LDBPR), Fungi Databases Collection (FDBC), and many other databases that are categorized based on biological phenomena. It currently provides a total of 22 databases, including 6 published, 5 submitted, and the remaining in various stages of development. These databases encompass a range of areas, including phytochemical-specific and plastic biodegradation databases. HABD is equipped with search engine optimization (SEO) analyzer and Neil Patel tools, which ensure excellent SEO and high-speed value. With timely updates, HABD aims to facilitate the processing and visualization of data for scientists, providing a one-stop-shop for all biological databases. Computer platforms, such as PhP, html, CSS, Java script and Biopython, are used to build all the databases. © 2024 Wiley Periodicals LLC.

Unveiling novel Neocosmospora species from Thai mangroves as potent biocontrol agents against Colletotrichum species

AIMS

Neocosmospora species are saprobes, endophytes, and pathogens belonging to the family Nectriaceae. This study aims to investigate the taxonomy, biosynthetic potential, and application of three newly isolated Neocosmospora species from mangrove habitats in the southern part of Thailand using phylogeny, bioactivity screening, genome sequencing, and bioinformatics analysis.

METHODS AND RESULTS

Detailed descriptions, illustrations, and a multi-locus phylogenetic tree with large subunit ribosomal DNA (LSU), internal transcribed spacer (ITS), translation elongation factor 1-alpha (ef1-α), and RNA polymerase II second largest subunit (RPB2) regions showing the placement of three fungal strains, MFLUCC 17-0253, MFLUCC 17-0257, and MFLUCC 17-0259 clustered within the Neocosmospora clade with strong statistical support. Fungal crude extracts of the new species N. mangrovei MFLUCC 17-0253 exhibited strong antifungal activity to control Colletotrichum truncatum CG-0064, while N. ferruginea MFLUCC 17-0259 exhibited only moderate antifungal activity toward C. acutatum CC-0036. Thus, N. mangrovei MFLUCC 17-0253 was sequenced by Oxford nanopore technology. The bioinformatics analysis revealed that 49.17 Mb genome of this fungus harbors 41 potential biosynthetic gene clusters.

CONCLUSION

Two fungal isolates of Neocosmospora and a new species of N. mangrovei were reported in this study. These fungal strains showed activity against pathogenic fungi causing anthracnose in chili. In addition, full genome sequencing and bioinformatics analysis of N. mangrovei MFLUCC 17-0253 were obtained.

Isolation, characterisation and description of the roseoflavin producer Streptomyces berlinensis sp. nov

The Gram-positive bacteria Streptomyces davaonensis and Streptomyces cinnabarinus have been the only organisms known to produce roseoflavin, a riboflavin (vitamin B2) derived red antibiotic. Using a selective growth medium and a phenotypic screening, we were able to isolate a novel roseoflavin producer from a German soil sample. The isolation procedure was repeated twice, that is, the same strain could be isolated from the same location in Berlin 6 months and 12 months after its first isolation. Whole genome sequencing of the novel roseoflavin producer revealed an unusual chromosomal arrangement and the deposited genome sequence of the new isolate (G + C content of 71.47%) contains 897 genes per inverted terminal repeat, 6190 genes in the core and 107 genes located on an illegitimate terminal end. We identified the roseoflavin biosynthetic genes rosA, rosB and rosC and an unusually high number of riboflavin biosynthetic genes. Overexpression of rosA, rosB and rosC in Escherichia coli and enzyme assays confirmed their predicted functions in roseoflavin biosynthesis. A full taxonomic analysis revealed that the isolate represents a previously unknown Streptomyces species and we propose the name Streptomyces berlinensis sp. nov. for this roseoflavin producer.

A chromosome-level genome for the flower thrips Frankliniella intonsa

The flower thrips Frankliniella intonsa (Thysanoptera: Thripidae) is a common insect found in flowers of many plants. Sometimes, F. intonsa causes damage to crops through direct feeding and transmission of plant viruses. Here, we assembled a chromosomal level genome of F. intonsa using the Illumina, Oxford Nanopore (ONT), and Hi-C technologies. The assembled genome had a size of 209.09 Mb, with a contig N50 of 997 bp, scaffold N50 of 13.415 Mb, and BUSCO completeness of 92.5%. The assembled contigs were anchored on 15 chromosomes. A set of 14,109 protein-coding genes were annotated in the genome with a BUSCO completeness of 95.0%. The genome contained 491 non-coding RNA and 0.57% of interspersed repeats. This high-quality genome provides a valuable resource for understanding the ecology, genetics, and evolution of F. intonsa, as well as for controlling thrips pests.

Spitting in the wind?-The challenges of RNA sequencing for biomarker discovery from saliva

Forensic trace contextualization, i.e., assessing information beyond who deposited a biological stain, has become an issue of great and steadily growing importance in forensic genetic casework and research. The human transcriptome encodes a wide variety of information and thus has received increasing interest for the identification of biomarkers for different aspects of forensic trace contextualization over the past years. Massively parallel sequencing of reverse-transcribed RNA ("RNA sequencing") has emerged as the gold standard technology to characterize the transcriptome in its entirety and identify RNA markers showing significant expression differences not only between different forensically relevant body fluids but also within a single body fluid between forensically relevant conditions of interest. Here, we analyze the quality and composition of four RNA sequencing datasets (whole transcriptome as well as miRNA sequencing) from two different research projects (the RNAgE project and the TrACES project), aiming at identifying contextualizing forensic biomarker from the forensically relevant body fluid saliva. We describe and characterize challenges of RNA sequencing of saliva samples arising from the presence of oral bacteria, the heterogeneity of sample composition, and the confounding factor of degradation. Based on these observations, we formulate recommendations that might help to improve RNA biomarker discovery from the challenging but forensically relevant body fluid saliva.

When online citizen science meets teaching: Storyfication of a science discovery game to teach, learn, and contribute to genomic research

In the last decade, video games became a common vehicle for citizen science initiatives in life science, allowing participants to contribute to real scientific data analysis while learning about it. Since 2010, our scientific discovery game (SDG) Phylo enlists participants in comparative genomic data analysis. It is frequently used as a learning tool, but the activities were difficult to aggregate to build a coherent teaching activity. Here, we describe a strategy and series of recipes to facilitate the integration of SDGs in courses and implement this approach in Phylo. We developed new roles and functionalities enabling instructors to create assignments and monitor the progress of students. A story mode progressively introduces comparative genomics concepts, allowing users to learn and contribute to the analysis of real genomic sequences. Preliminary results from a user study suggest this framework may help to boost user motivation and clarify pedagogical objectives.

Investigating the impact of feed-induced, subacute ruminal acidosis on rumen epimural transcriptome and metatranscriptome in young calves at 8- and 17-week of age

Introduction

With the goal to maximize intake of high-fermentable diet needed to meet energy needs during weaning period, calves are at risk for ruminal acidosis. Using the calves from previously established model of feed-induced, ruminal acidosis in young calves, we aimed to investigate the changes in rumen epimural transcriptome and its microbial metatranscriptome at weaning (8-week) and post-weaning (17-week) in canulated (first occurred at 3 weeks of age) Holstein bull calves with feed-induced subacute ruminal acidosis.

Methods

Eight bull calves were randomly assigned to acidosis-inducing diet (Treated, n = 4; pelleted, 42.7% starch, 15.1% neutral detergent fiber [NDF], and 57.8% nonfiber carbohydrates), while texturized starter was fed as a control (Control, n = 4; 35.3% starch, 25.3% NDF, and 48.1% nonfiber carbohydrates) starting at 1 week through 17 weeks. Calves fed acidosis-inducing diet showed significantly less (p < 0.01) body weight over the course of the experiment, in addition to lower ruminal pH (p < 0.01) compared to the control group. Rumen epithelial (RE) tissues were collected at both 8 weeks (via biopsy) and 17 weeks (via euthanasia) and followed for whole transcriptome RNA sequencing analysis. Differentially expressed genes (DEGs) analysis was done using cufflinks2 (fold-change ≥2 and p < 0.05) between treated and control groups at 8-week of age, and between 8- and 17-week for the treated group.

Results

At 8-week of age, DEGs between treatment groups showed an enrichment of genes related to the response to lipopolysaccharide (LPS) (p < 0.005). The impact of prolonged, feed-induced acidosis was reflected by the decreased expression (p < 0.005) in genes involved in cell proliferation related pathways in the RE at 17-week of age in the treated group. Unique sets of discriminant microbial taxa were identified between 8-and 17-week calves in the treated group and the treatment groups at 8-week, indicating that active microbial community changes in the RE are an integral part of the ruminal acidosis development and progression.

Whole-Transcriptome Profiling and Functional Prediction of Long Non-Coding RNAs Associated with Cold Tolerance in Japonica Rice Varieties

Low-temperature chilling is a major abiotic stress leading to reduced rice yield and is a significant environmental threat to food security. Low-temperature chilling studies have focused on physiological changes or coding genes. However, the competitive endogenous RNA mechanism in rice at low temperatures has not been reported. Therefore, in this study, antioxidant physiological indices were combined with whole-transcriptome data through weighted correlation network analysis, which found that the gene modules had the highest correlation with the key antioxidant enzymes superoxide dismutase and peroxidase. The hub genes of the superoxide dismutase-related module included the UDP-glucosyltransferase family protein, sesquiterpene synthase and indole-3-glycerophosphatase gene. The hub genes of the peroxidase-related module included the WRKY transcription factor, abscisic acid signal transduction pathway-related gene plasma membrane hydrogen-ATPase and receptor-like kinase. Therefore, we selected the modular hub genes and significantly enriched the metabolic pathway genes to construct the key competitive endogenous RNA networks, resulting in three competitive endogenous RNA networks of seven long non-coding RNAs regulating three co-expressed messenger RNAs via four microRNAs. Finally, the negative regulatory function of the WRKY transcription factor OsWRKY61 was determined via subcellular localization and validation of the physiological indices in the mutant.

Genome Analysis for Cholesterol-Lowing Action and Bacteriocin Production of Lactiplantibacillus plantarum WLPL21 and ZDY04 from Traditional Chinese Fermented Foods

Lactiplantibacillus plantarum, a typical ecological species against pathogens, used due to its bacteriocin yield in fermented foods, was proven to have the capacity to lower cholesterol. In this study, using L. plantarum ATCC8014 as the control, L. plantarum WLPL21 and ZDY04 were probed with whole-genome sequencing to ascertain their potential ability to lower cholesterol and yield bacteriocins, as well as to further evaluate their survival capacity in vitro. Our results showed 386 transport-system genes in both L. plantarum WLPL21 and ZDY04. Correspondingly, the in vitro results showed that L. plantarum WLPL21 and ZDY04 could remove cholesterol at 49.23% and 41.97%, respectively, which is 1.89 and 1.61 times that of L. plantarum ATCC8014. The survival rates of L. plantarum WLPL21 and ZDY04 in 1% H2O2, pH 3.0, and 0.3% bile salt were higher than those of L. plantarum ATCC8014. Our results exhibited a complete gene cluster for bacteriocin production encoded by L. plantarum WLPL21 and ZDY04, including plnJKR, plnPQAB, plnEFI, plnSUVWY, and plnJK; and plnMN, plnPQA and plnEFI, respectively, compared with only plnEF in L. plantarum ATCC8014. The present study suggests that the combination of genomic analysis with in vitro evaluations might be useful for exploring the potential functions of probiotics.

Characteristics of Amorphophallus konjac as indicated by its genome

Amorphophallus konjac, belonging to the genus Amorphophallus of the Araceae family, is an economically important crop widely used in health products and biomaterials. In the present work, we performed the whole-genome assembly of A. konjac based on the NovaSeq platform sequence data. The final genome assembly was 4.58 Gb with a scaffold N50 of 3212 bp. The genome includes 39,421 protein-coding genes, and 71.75% of the assemblies were repetitive sequences. Comparative genomic analysis showed 1647 gene families have expanded and 2685 contracted in the A. konjac genome. Likewise, genome evolution analysis indicated that A. konjac underwent whole-genome duplication, possibly contributing to the expansion of certain gene families. Furthermore, we identified many candidate genes involved in the tuber formation and development, cellulose and lignification synthesis. The genome of A. konjac obtained in this work provides a valuable resource for the further study of the genetics, genomics, and breeding of this economically important crop, as well as for evolutionary studies of Araceae family.

Complete Genome Sequence and Pan-Genome Analysis of Shewanella oncorhynchi Z-P2, a Siderophore Putrebactin-Producing Bacterium

In this study, we reported the complete genome sequence of Shewanella oncorhynchi for the first time. S. oncorhynchi Z-P2 is a bacterium that produces the siderophore putrebactin. Its genome consists of a circular chromosome of 5,034,612 bp with a G + C content of 45.4%. A total of 4544 protein-coding genes, 109 tRNAs and 31 rRNAs were annotated by the RAST. Five non-ribosomal peptide synthetase (NRPS) and polyketide synthetase (PKS) gene clusters were identified by the antiSMASH analysis. The pan-genome analysis of Z-P2 and 10 Shewanella putrefaciens revealed 9228 pan-gene clusters and 2681 core gene clusters, with Z-P2 having 618 unique gene clusters. Additionally, the gene cluster involved in putrebactin biosynthesis in Z-P2 was annotated, and the mechanism of putrebactin biosynthesis was analyzed. The putrebactin produced by Z-P2 was detected using UPLC-MS analysis, with an [M + H]+ molecular ion at m/z 373.21. These findings provide valuable support for further research on the genetic engineering of putrebactin biosynthetic genes of Z-P2 and their potential applications.

Novel Insights into the circRNA-Modulated Developmental Mechanism of Western Honey Bee Larval Guts

Circular RNAs (circRNAs) are a class of novel non-coding RNAs (ncRNAs) that play essential roles in the development and growth of vertebrates through multiple manners. However, the mechanism by which circRNAs modulate the honey bee gut development is currently poorly understood. Utilizing the transcriptome data we obtained earlier, the highly expressed circRNAs in the Apis mellifera worker 4-, 5-, and 6-day-old larval guts were analyzed, which was followed by an in-depth investigation of the expression pattern of circRNAs during the process of larval guts development and the potential regulatory roles of differentially expressed circRNAs (DEcircRNAs). In total, 1728 expressed circRNAs were detected in the A. mellifera larval guts. Among the most highly expressed 10 circRNAs, seven (novel_circ_000069, novel_circ_000027, novel_circ_000438, etc.) were shared by the 4-, 5-, and 6-day-old larval guts. In addition, 21 (46) up-regulated and 22 (27) down-regulated circRNAs were, respectively, screened in the Am4 vs. Am5 (Am5 vs. Am6) comparison groups. Additionally, nine DEcircRNAs, such as novel_circ_000340, novel_circ_000758 and novel_circ_001116, were shared by these two comparison groups. These DEcircRNAs were predicted to be transcribed from 14 and 29 parental genes; these were respectively annotated to 15 and 22 GO terms such as biological regulation and catalytic activity as well as 16 and 21 KEGG pathways such as dorsoventral axis formation and apoptosis. Moreover, a complicated competing endogenous RNA (ceRNA) network was observed; novel_circ_000838 in the Am4 vs. Am5 comparison group potentially targeted ame-miR-6000a-3p, further targeting 518 mRNAs engaged in several developmental signaling pathways (e.g., TGF-beta, hedgehog, and wnt signaling pathway) and immune pathways (e.g., phagosome, lysosome, and MAPK signaling pathway). The results demonstrated that the novel_circ_000838-ame-miR-6000a-3p axis may plays a critical regulatory part in the larval gut development and immunity. Furthermore, back-splicing sites of six randomly selected DEcircRNAs were amplified and verified by PCR; an RT-qPCR assay of these six DEcircRNAs confirmed the reliability of the used high-throughput sequencing data. Our findings provide a novel insight into the honey bee gut development and pave a way for illustration of the circRNA-modulated developmental mechanisms underlying the A. mellifera worker larval guts.

Genome Sequencing-Based Mining and Characterization of a Novel Alginate Lyase from Vibrio alginolyticus S10 for Specific Production of Disaccharides

Alginate oligosaccharides prepared by alginate lyases attracted great attention because of their desirable biological activities. However, the hydrolysis products are always a mixture of oligosaccharides with different degrees of polymerization, which increases the production cost because of the following purification procedures. In this study, an alginate lyase, Alg4755, with high product specificity was identified, heterologously expressed, and characterized from Vibrio alginolyticus S10, which was isolated from the intestine of sea cucumber. Alg4755 belonged to the PL7 family with two catalytic domains, which was composed of 583 amino acids. Enzymatic characterization results show that the optimal reaction temperature and pH of Alg4755 were 35 °C and 8.0, respectively. Furthermore, Alg4755 was identified to have high thermal and pH stability. Moreover, the final hydrolysis products of sodium alginate catalyzed by Alg4755 were mainly alginate disaccharides with a small amount of alginate trisaccharides. The results demonstrate that alginate lyase Alg4755 could have a broad application prospect because of its high product specificity and desirable catalytic properties.

Liver microbial community and associated host transcriptome in calves with feed induced acidosis

Introduction

In the dairy industry, calves are typically fed diets rich in highly fermentable carbohydrates and low in fibrous feeds to maximize ruminal papillae and tissue development. Calves on such diets are vulnerable at developing ruminal acidosis. Prevalent in cattle, liver abscess (LA) is considered a sequela to ruminal acidosis. LAs can cause significant liver function condemnation and decreased growth and production. Currently, we know little about the liver microbiome in calves with feed-induced acidosis.

Methods

Using our established model of ruminal acidosis, where young calves were fed an acidosis-inducing (AC) or -blunting (control) diet starting at birth until 17-week of age, we investigated microbial community changes in the liver resultant from ruminal acidosis. Eight calves were randomly assigned to each diet, with four animals per treatment. Rumen epithelium and liver tissues were collected at 17 weeks of age right after euthanasia. Total RNAs were extracted and followed by whole transcriptome sequencing. Microbial RNA reads were enriched bioinformatically and used for microbial taxonomy classification using Kraken2.

Results

AC Calves showed significantly less weight gain over the course of the experiment, in addition to significantly lower ruminal pH, and rumen degradation comparison to the control group (p < 0.05). In the liver, a total of 29 genera showed a significant (p < 0.05) abundance change (> 2-fold) between the treatments at 17-week of age. Among these, Fibrobacter, Treponema, Lactobacillus, and Olsenella have been reported in abscessed liver in cattle. Concurrent abundance changes in 9 of the genera were observed in both the liver and rumen tissues collected at 17-week of age, indicating potential crosstalk between the liver and rumen epithelial microbial communities. Significant association was identified between host liver gene and its embedded microbial taxa. Aside from identifying previously reported microbial taxa in cattle abscessed liver, new repertoire of actively transcribed microbial taxa was identified in this study.

Discussion

By employing metatranscriptome sequencing, our study painted a picture of liver microbiome in young calves with or without feed induced acidosis. Our study suggested that liver microbiome may have a critical impact on host liver physiology. Novel findings of this study emphasize the need for further in-depth analysis to uncover the functional roles of liver resident microbiome in liver metabolic acidosis resultant from feed-related ruminal acidosis.

A multicenter prospective study of comprehensive metagenomic and transcriptomic signatures for predicting outcomes of patients with severe community-acquired pneumonia

BACKGROUND

Severe community-acquired pneumonia (SCAP) results in high mortality as well as massive economic burden worldwide, yet limited knowledge of the bio-signatures related to prognosis has hindered the improvement of clinical outcomes. Pathogen, microbes and host are three vital elements in inflammations and infections. This study aims to discover the specific and sensitive biomarkers to predict outcomes of SCAP patients.

METHODS

In this study, we applied a combined metagenomic and transcriptomic screening approach to clinical specimens gathered from 275 SCAP patients of a multicentre, prospective study.

FINDINGS

We found that 30-day mortality might be independent of pathogen category or microbial diversity, while significant difference in host gene expression pattern presented between 30-day mortality group and the survival group. Twelve outcome-related clinical characteristics were identified in our study. The underlying host response was evaluated and enrichment of genes related to cell activation, immune modulation, inflammatory and metabolism were identified. Notably, omics data, clinical features and parameters were integrated to develop a model with six signatures for predicting 30-day mortality, showing an AUC of 0.953 (95% CI: 0.92-0.98).

INTERPRETATION

In summary, our study linked clinical characteristics and underlying multi-omics bio-signatures to the differential outcomes of patients with SCAP. The establishment of a comprehensive predictive model will be helpful for future improvement of treatment strategies and prognosis with SCAP.

FUNDING

National Natural Science Foundation of China (No. 82161138018), Shanghai Municipal Key Clinical Specialty (shslczdzk02202), Shanghai Top-Priority Clinical Key Disciplines Construction Project (2017ZZ02014), Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases (20dz2261100).

Signal-noise metrics for RNA binding protein identification reveal broad spectrum protein-RNA interaction frequencies and dynamics

Recent efforts towards the comprehensive identification of RNA-bound proteomes have revealed a large, surprisingly diverse family of candidate RNA-binding proteins (RBPs). Quantitative metrics for characterization and validation of protein-RNA interactions and their dynamic interactions have, however, proven analytically challenging and prone to error. Here we report a method termed LEAP-RBP (Liquid-Emulsion-Assisted-Purification of RNA-Bound Protein) for the selective, quantitative recovery of UV-crosslinked RNA-protein complexes. By virtue of its high specificity and yield, LEAP-RBP distinguishes RNA-bound and RNA-free protein levels and reveals common sources of experimental noise in RNA-centric RBP enrichment methods. We introduce strategies for accurate RBP identification and signal-based metrics for quantifying protein-RNA complex enrichment, relative RNA occupancy, and method specificity. In this work, the utility of our approach is validated by comprehensive identification of RBPs whose association with mRNA is modulated in response to global mRNA translation state changes and through in-depth benchmark comparisons with current methodologies.

Genome-wide transcriptomics and microRNAomics analyses uncover multi-faceted mechanisms to cope with copper stress in ancient macrobenthos amphioxus

The mechanisms underlying the toxicity of environmental stress are unclear for marine macrobenthos. Copper/Cu has posed the most serious threats to amphioxus, an ancient and model benthic cephalochordate. Herein, a dynamic change in the physiological parameters (GR, SOD, ATP, and MDA) was detected with ROS accumulation in Branchiostoma belcheri exposed to 0.3 mg·L-1 Cu. Transcriptomes and microRNAomes of B. belcheri were generated to investigate the molecular mechanisms by which this amphioxus copes with Cu exposure. Time-specific genes identified at different time points after exposure were involved in the stimulus and immune response, detoxification and ionic homeostasis, aging and the nervous system, sequentially, with prolongation of exposure time, forming a dynamic process of molecular response to Cu stress. In total, 57 differentially expressed miRNAs were identified under Cu stress. Transcriptomics-miRNAomics analyses indicate that these miRNAs targeted genes associated with many key biological processes such as xenobiotics degradation, oxidative stress, and energy metabolism. The constructed miRNA-mRNA-pathway network uncovered a broad post-transcriptional regulatory mechanism in B. belcheri to cope with Cu stress. Overall, this integrated analyses show that enhanced defense response, accelerated ROS elimination, and repressed ATP production constitute a comprehensive strategy to cope with Cu toxicity in the ancient macrobenthos.

Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics

Metatranscriptomics refers to the analysis of the collective microbial transcriptome of a sample. Its increased utilization for the characterization of human-associated microbial communities has enabled the discovery of many disease-state related microbial activities. Here, we review the principles of metatranscriptomics-based analysis of human-associated microbial samples. We describe strengths and weaknesses of popular sample preparation, sequencing, and bioinformatics approaches and summarize strategies for their use. We then discuss how human-associated microbial communities have recently been examined and how their characterization may change. We conclude that metatranscriptomics insights into human microbiotas under health and disease have not only expanded our knowledge on human health, but also opened avenues for rational antimicrobial drug use and disease management.

RNA-NRD: a non-redundant RNA structural dataset for benchmarking and functional analysis

The significance of RNA functions and their role in evolution and disease control have remarkably increased the research scope in the field of RNA science. Though the availability of RNA structure data in PBD has been growing tremendously, maintaining their quality and integrity has become the greater challenge. Since the data available in PDB are results of different independent research, they might contain redundancy. As a result, there remains a possibility of data bias for both protein and RNA chains. Quite a few studies have been conducted to remove the redundancy of protein structures by introducing high-quality representatives. However, the amount of research done to remove the redundancy of RNA structures is still very low. To remove RNA chain redundancy in PDB, we have introduced RNA-NRD, a non-redundant dataset of RNA chains based on sequence and 3D structural similarity. We compared RNA-NRD with the existing non-redundant RNA structure dataset RS-RNA and showed that it has better-formed clusters of redundant RNA chains with lower average RMSD and higher average PSI, thus improving the overall quality of the dataset.

Intracellular metabolomics and microRNAomics unveil new insight into the regulatory network for potential biocontrol mechanism of stress-tolerant Tricho-fusants interacting with phytopathogen Sclerotium rolfsii Sacc

The present study employed microRNA (miRNA) sequencing and metabolome profiling of Trichoderma parental strains and fusants during normal growth and interaction with the phytopathogen Sclerotium rolfsii Sacc. In-vitro antagonism indicated that abiotic stress-tolerant Tricho-fusant FU21 was examined as a potent biocontroller with mycoparasitic action after 10 days. During interaction with the test pathogen, the most abundant uprising intracellular metabolite was recognized as l-proline, which corresponds to held-down l-alanine, associated with arginine and proline metabolism, biosynthesis of secondary metabolites, and nitrogen metabolism linked to predicted genes controlled by miRNAs viz., cel-miR-8210-3p, hsa-miR-3613-5p, and mml-miR-7174-3p. The miRNAs- mml-miR-320c and mmu-miR-6980-5p were found to be associated with phenylpropanoid biosynthesis, transcription factors, and signal transduction pathways, respectively, and were ascertained downregulated in potent FU21_IB compared with FU21_CB. The amino benzoate degradation and T cell receptor signaling pathways were regulated by miRNAs cel-miR-8210 and tca-miR-3824 as stress tolerance mechanisms of FU21. The intracellular metabolites l-proline, maleic acid, d-fructose, Myo-inositol, arabinitol, d-xylose, mannitol, and butane were significantly elevated as potential biocontrol and stress-tolerant constituents associated with miRNA regulatory pathways in potent FU21_IB. A network analysis between regulatory miRNA-predicted genes and intracellular metabolomics acknowledged possible biocontrol pathways/mechanisms in potent FU21_IB to restrain phytopathogen.

REFMAKER: make your own reference to target nuclear loci in low coverage genome skimming libraries. Phylogenomic application in Sapotaceae

Genome skimming approach is widely used in plant systematics to infer phylogenies mostly from organelle genomes. However, organelles represent only 10% of the produced libraries, and the low coverage associated with these libraries (< 3X) prevents the capture of nuclear sequences, which are not always available in non-model organisms or limited to the ribosomal regions. We developed REFMAKER, a user-friendly pipeline, to create specific sets of nuclear loci that can next be extracted directly from the genome skimming libraries. For this, a catalogue is built from the meta-assembly of each library contigs and cleaned by selecting the nuclear regions and removing duplicates from clustering steps. Libraries are next mapped onto this catalogue and consensus sequences are generated to produce a ready-to-use phylogenetic matrix following different filtering parameters aiming at removing putative errors and paralogous sequences. REFMAKER allowed us to infer a well resolved phylogeny in Capurodendron (Sapotaceae) on 67 nuclear loci from low-coverage libraries (<1X). The resulting phylogeny is concomitant with one previously inferred on 638 nuclear genes from target enrichment libraries. While it remains preliminary because of this low sequencing depth, REFMAKER therefore opens perspectives in phylogenomics by allowing nuclear phylogeny reconstructions with genome skimming datasets.

Uterus proliferative period ceRNA network of Yunshang black goat reveals candidate genes on different kidding number trait

Pregnancy loss that occurs in the uterus is an important and widespread problem in humans and farm animals and is also a key factor affecting the fecundity of livestock. Understanding the differences in the fecundity of goats may be helpful in guiding the breeding of goats with high fecundity. In this study, we performed RNA sequencing and bioinformatics analysis to study the uterus of Yunshang black goats with high and low fecundity in the proliferative period. We identified mRNAs, long non-coding RNAs (lncRNAs), and microRNAs (miRNAs) by analyzing the uterine transcriptomes. The target genes of the identified miRNAs and lncRNAs were predicted, and miRNA-mRNA interaction and competitive endogenous RNA (ceRNA) networks were constructed. By comparisons between low- and high-fecundity groups, we identified 1,674 differentially expressed mRNAs (914 were upregulated, and 760 were downregulated), 288 differentially expressed lncRNAs (149 were upregulated, and 139 were downregulated), and 17 differentially expressed miRNAs (4 were upregulated, and 13 were downregulated). In addition, 49 miRNA-mRNA pairs and 45 miRNA-lncRNA pairs were predicted in the interaction networks. We successfully constructed a ceRNA interaction network with 108 edges that contained 19 miRNAs, 11 mRNAs, and 73 lncRNAs. Five candidate genes (PLEKHA7, FAT2, FN1, SYK, and ITPR2) that were annotated as cell adhesion or calcium membrane channel protein were identified. Our results provide the overall expression profiles of mRNAs, lncRNAs, and miRNAs in the goat uterus during the proliferative period and are a valuable reference for studies into the mechanisms associated with the high fecundity, which may be helpful to guide goat to reduce pregnancy loss.

Plasma Extracellular Vesicle MicroRNA Analysis of Alzheimer's Disease Reveals Dysfunction of a Neural Correlation Network

Small extracellular vesicle (sEV) is an emerging source of potential biomarkers of Alzheimer's disease (AD), but the role of microRNAs (miRNAs) in sEV is not well understood. In this study, we conducted a comprehensive analysis of sEV-derived miRNAs in AD using small RNA sequencing and coexpression network analysis. We examined a total of 158 samples, including 48 from AD patients, 48 from patients with mild cognitive impairment (MCI), and 62 from healthy controls. We identified an miRNA network module (M1) that was strongly linked to neural function and showed the strongest association with AD diagnosis and cognitive impairment. The expression of miRNAs in the module was decreased in both AD and MCI patients compared to controls. Conservation analysis revealed that M1 was highly preserved in the healthy control group but dysfunctional in the AD and MCI groups, suggesting that changes in the expression of miRNAs in this module may be an early response to cognitive decline prior to the appearance of AD pathology. We further validated the expression levels of the hub miRNAs in M1 in an independent population. The functional enrichment analysis showed that 4 hub miRNAs might interact with a GDF11-centered network and play a critical role in the neuropathology of AD. In summary, our study provides new insights into the role of sEV-derived miRNAs in AD and suggests that M1 miRNAs may serve as potential biomarkers for the early diagnosis and monitoring of AD.

Genomic and transcriptomic analyses support a silk gland origin of spider venom glands

BACKGROUND

Spiders comprise a hyperdiverse lineage of predators with venom systems, yet the origin of functionally novel spider venom glands remains unclear. Previous studies have hypothesized that spider venom glands originated from salivary glands or evolved from silk-producing glands present in early chelicerates. However, there is insufficient molecular evidence to indicate similarity among them. Here, we provide comparative analyses of genome and transcriptome data from various lineages of spiders and other arthropods to advance our understanding of spider venom gland evolution.

RESULTS

We generated a chromosome-level genome assembly of a model spider species, the common house spider (Parasteatoda tepidariorum). Module preservation, GO semantic similarity, and differentially upregulated gene similarity analyses demonstrated a lower similarity in gene expressions between the venom glands and salivary glands compared to the silk glands, which questions the validity of the salivary gland origin hypothesis but unexpectedly prefers to support the ancestral silk gland origin hypothesis. The conserved core network in the venom and silk glands was mainly correlated with transcription regulation, protein modification, transport, and signal transduction pathways. At the genetic level, we found that many genes in the venom gland-specific transcription modules show positive selection and upregulated expressions, suggesting that genetic variation plays an important role in the evolution of venom glands.

CONCLUSIONS

This research implies the unique origin and evolutionary path of spider venom glands and provides a basis for understanding the diverse molecular characteristics of venom systems.

Identifying widespread and recurrent variants of genetic parts to improve annotation of engineered DNA sequences

Engineered plasmids have been workhorses of recombinant DNA technology for nearly half a century. Plasmids are used to clone DNA sequences encoding new genetic parts and to reprogram cells by combining these parts in new ways. Historically, many genetic parts on plasmids were copied and reused without routinely checking their DNA sequences. With the widespread use of high-throughput DNA sequencing technologies, we now know that plasmids often contain variants of common genetic parts that differ slightly from their canonical sequences. Because the exact provenance of a genetic part on a particular plasmid is usually unknown, it is difficult to determine whether these differences arose due to mutations during plasmid construction and propagation or due to intentional editing by researchers. In either case, it is important to understand how the sequence changes alter the properties of the genetic part. We analyzed the sequences of over 50,000 engineered plasmids using depositor metadata and a metric inspired by the natural language processing field. We detected 217 uncatalogued genetic part variants that were especially widespread or were likely the result of convergent evolution or engineering. Several of these uncatalogued variants are known mutants of plasmid origins of replication or antibiotic resistance genes that are missing from current annotation databases. However, most are uncharacterized, and 3/5 of the plasmids we analyzed contained at least one of the uncatalogued variants. Our results include a list of genetic parts to prioritize for refining engineered plasmid annotation pipelines, highlight widespread variants of parts that warrant further investigation to see whether they have altered characteristics, and suggest cases where unintentional evolution of plasmid parts may be affecting the reliability and reproducibility of science.

Mining Chromodoris quadricolor symbionts for biosynthesis of novel secondary metabolites

Many secondary metabolites with medicinal potential are produced by various animals, plants, and microorganisms. Because marine creatures have a greater proportion of unexplored biodiversity than their terrestrial counterparts, they have emerged as a key research focus for the discovery of natural product drugs. Several studies have revealed that bacteria isolated from Chromodoris quadricolor (C. quadricolor) have antibiotic and anticancer properties. In this study, meta-transcriptomics and meta-proteimic analysis were combined to identify biosynthetic gene clusters (BGCs) in the symbiotic bacteria of the C. quadricolor mantle. Symbiotic bacteria were separated from the host by differential pelleting, and then total RNA was extracted, purified, and sequenced. Meta-transcriptomic analysis was done using different natural product mining tools to identify biosynthetic transcript clusters (BTCs). Furthermore, proteins were extracted from the same cells and then analyzed by LC-MS. A meta-proteomic analysis was performed to find proteins that are translated from BCGs. Finally, only 227 proteins have been translated from 40,742 BTCs. The majority of these clusters were polyketide synthases (PKSs) with antibacterial activity. Ten novel potential metabolic clusters with the ability to produce antibiotics have been identified in Novosphingobium and Microbacteriaceae, including members of the ribosomal synthesized and post-translationally modified peptides (RiPPs), polyketide synthases, and others. We realized that using a meta-proteomic approach to identify BGCs that have already been translated makes it easier to concentrate on BGCs that are utilized by bacteria. The symbiotic bacteria associated with C. quadricolor could be a source of novel antibiotics.

Exploring conserved and novel MicroRNA-like small RNAs from stress tolerant Trichoderma fusants and parental strains during interaction with fungal phytopathogen Sclerotium rolfsii Sacc

The study investigated potential microRNA-like small RNAs (milRNAs) from multi-stress-tolerant Tricho-fusants and parental strains (P1- Trichoderma virens NBAIITvs12 and P2- Trichoderma koningii MTCC796) for antagonistic activity during interaction with phytopathogen Sclerotium rolfsii. The Trichoderma was cultured in-vitro, with and without antagonism, against the pathogen and total RNA was extracted followed by small RNA library construction and sequencing. The milRNAs were identified by mapping high-quality unique reads against a reference genome. The milRNAs were recognized higher in antagonist Trichoderma during interaction with test pathogen compared to normal growth. The novel milRNAs candidates were found to vary during interaction with the pathogen and normal growth. The gene ontology and functional analysis illustrated that a total of 5828 potential targeted genes were recognized for 93 milRNAs of potent Fu21_IB and 3053 genes for 62 milRNAs of least fusant Fu28_IL. Functional annotation of milRNA-predicted genes integrating KEGG pathways indicates new insights into regulatory mechanisms, by interfering with milRNAs, associated with signal transduction, amino sugar metabolism, benzoate degradation, amino acid metabolism, and steroid and alkaloid metabolism for potential biocontrol of stress-tolerant Tricho-fusant FU21 during interaction with S. rolfsii. The present investigation is the first report of conserved and novel milRNAs from Tricho-fusants and parental strains interacting with S. rolfsii.

Strategy for the Adaptation to Stressful Conditions of the Novel Isolated Conditional Piezophilic Strain Halomonas titanicae ANRCS81

Microorganisms have successfully predominated deep-sea ecosystems, while we know little about their adaptation strategy to multiple environmental stresses therein, including high hydrostatic pressure (HHP). Here, we focused on the genus Halomonas, one of the most widely distributed halophilic bacterial genera in marine ecosystems and isolated a piezophilic strain Halomonas titanicae ANRCS81 from Antarctic deep-sea sediment. The strain grew under a broad range of temperatures (2 to 45°C), pressures (0.1 to 55 MPa), salinities (NaCl, 0.5 to 17.5%, wt/vol), and chaotropic agent (Mg2+, 0 to 0.9 M) with either oxygen or nitrate as an electron acceptor. Genome annotation revealed that strain ANRCS81 expressed potential antioxidant genes/proteins and possessed versatile energy generation pathways. Based on the transcriptomic analysis, when the strain was incubated at 40 MPa, genes related to antioxidant defenses, anaerobic respiration, and fermentation were upregulated, indicating that HHP induced intracellular oxidative stress. Under HHP, superoxide dismutase (SOD) activity increased, glucose consumption increased with less CO2 generation, and nitrate/nitrite consumption increased with more ammonium generation. The cellular response to HHP represents the common adaptation developed by Halomonas to inhabit and drive geochemical cycling in deep-sea environments. IMPORTANCE Microbial growth and metabolic responses to environmental changes are core aspects of adaptation strategies developed during evolution. In particular, high hydrostatic pressure (HHP) is the most common but least examined environmental factor driving microbial adaptation in the deep sea. According to recent studies, microorganisms developed a common adaptation strategy to multiple stresses, including HHP, with antioxidant defenses and energy regulation as key components, but experimental data are lacking. Meanwhile, cellular SOD activity is elevated under HHP. The significance of this research lies in identifying the HHP adaptation strategy of a Halomonas strain at the genomic, transcriptomic, and metabolic activity levels, which will allow researchers to bridge environmental factors with the ecological function of marine microorganisms.

Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes

We investigated the capability of internal normal modes to reproduce RNA flexibility and predict observed RNA conformational changes and, notably, those induced by the formation of RNA-protein and RNA-ligand complexes. Here, we extended our iNMA approach developed for proteins to study RNA molecules using a simplified representation of the RNA structure and its potential energy. Three data sets were also created to investigate different aspects. Despite all the approximations, our study shows that iNMA is a suitable method to take into account RNA flexibility and describe its conformational changes opening the route to its applicability in any integrative approach where these properties are crucial.

Integrative Transcriptome, miRNAs, Degradome, and Phytohormone Analysis of Brassica rapa L. in Response to Plasmodiophora brassicae

Clubroot is an infectious root disease caused by Plasmodiophora brassicae in Brassica crops, which can cause immeasurable losses. We analyzed integrative transcriptome, small RNAs, degradome, and phytohormone comprehensively to explore the infection mechanism of P. brassicae. In this study, root samples of Brassica rapa resistant line material BrT24 (R-line) and susceptible line material Y510-9 (S-line) were collected at four different time points for cytological, transcriptome, miRNA, and degradome analyses. We found the critical period of disease resistance and infection were at 0-3 DAI (days after inoculation) and 9-20 DAI, respectively. Based on our finding, we further analyzed the data of 9 DAI vs. 20 DAI of S-line and predicted the key genes ARF8, NAC1, NAC4, TCP10, SPL14, REV, and AtHB, which were related to clubroot disease development and regulating disease resistance mechanisms. These genes are mainly related to auxin, cytokinin, jasmonic acid, and ethylene cycles. We proposed a regulatory model of plant hormones under the mRNA-miRNA regulation in the critical period of P. brassicae infection by using the present data of the integrative transcriptome, small RNAs, degradome, and phytohormone with our previously published results. Our integrative analysis provided new insights into the regulation relationship of miRNAs and plant hormones during the process of disease infection with P. brassicae.

Integrative analysis of microRNAs and mRNAs reveals the regulatory networks of triterpenoid saponin metabolism in Soapberry (Sapindus mukorossi Gaertn.)

Triterpenoid saponin are important secondary metabolites and bioactive constituents of soapberry (Sapindus mukorossi Gaertn.) and are widely used in medicine and toiletry products. However, little is known about the roles of miRNAs in the regulation of triterpenoid saponin biosynthesis in soapberry. In this study, a total of 3036 miRNAs were identified, of which 1372 miRNAs were differentially expressed at different stages of pericarp development. Important KEGG pathways, such as terpenoid backbone biosynthesis, sesquiterpenoid and triterpenoid biosynthesis, and basal transcription factors were highlighted, as well the roles of some key miRNAs, such as ath-miR5021, han-miR3630-3p, and ppe-miR858, which may play important roles in regulating triterpenoid saponin biosynthesis. In addition, 58 miRNAs might participate in saponin biosynthesis pathways by predicting the targets of those miRNAs to 53 saponin biosynthesis structural genes. And 75 miRNAs were identified to potentially play vital role in saponin accumulation by targeting transcript factor genes, bHLH, bZIP, ERF, MYB, and WRKY, respectively, which are candidate regulatory genes in the pathway of saponin biosynthesis. The results of weighted gene coexpression network analysis (WGCNA) suggested that two saponin-specific miRNA modules and 10 hub miRNAs may participate in saponin biosynthesis. Furthermore, multiple miRNA-mRNA regulatory networks potentially involved in saponin biosynthesis were generated, e.g., ath-miR5021-SmIDI2/SmGPS5/SmbAS1/SmCYP71D-3/SmUGT74G-2, han-miR3630-3p-SmCYP71A-14/SmbHLH54/SmMYB135/SmWRKY32, and ppe-miR858-SmMYB5/SmMYB32. qRT-PCR analysis validated the expression patterns of nine miRNAs and 12 corresponding target genes. This study represents the first comprehensive analysis of miRNAs in soapberry and lays the foundation for further understanding of miRNA-based regulation in triterpenoid saponin biosynthesis.

Characterisation and sequencing of the novel phage Abp95, which is effective against multi-genotypes of carbapenem-resistant Acinetobacter baumannii

Acinetobacter baumannii has become one of the most challenging conditional pathogens in health facilities. It causes various infectious diseases in humans, such as wound or urinary tract infections and pneumonia. Phage therapy has been used as an alternative strategy for antibiotic-resistant A. baumannii infections and has been approved by several governments. Previously, we have reported two potential phage therapy candidates, Abp1 and Abp9, both of which are narrow-host-range phages. In the present study, we screened and isolated 22 A. baumannii bacteriophages from hospital sewage water and determined that Abp95 has a wide host range (29%; 58/200). The biological and genomic characteristics and anti-infection potential of Abp95 were also investigated. Abp95 belongs to the Myoviridae family, with a G+C content of 37.85% and a genome size of 43,176 bp. Its genome encodes 77 putative genes, none of which are virulence, lysogeny, or antibiotic resistance genes. Abp95 was found to accelerate wound healing in a diabetic mouse wound infection model by clearing local infections of multidrug-resistant A. baumannii. In conclusion, the lytic phage Abp95, which has a wide host range, demonstrates potential as a candidate for phage therapy against multiple sequence types of carbapenem-resistant A. baumannii.

Cucumber STACHYOSE SYNTHASE is regulated by its cis-antisense RNA asCsSTS to balance source-sink carbon partitioning

Photosynthate partitioning between source and sink is a key determinant of crop yield. In contrast to sucrose-transporting plants, cucumber (Cucumis sativus) plants mainly transport stachyose and stachyose synthase (CsSTS) synthesizes stachyose in the vasculature for loading. Therefore, CsSTS is considered a key regulator of carbon partitioning. We found that CsSTS expression and CsSTS enzyme activity were upregulated in the vasculature and downregulated in mesophyll tissues at fruiting. In situ hybridization and tissue enrichment experiments revealed that a cis-natural antisense noncoding transcript of CsSTS, named asCsSTS, is mainly expressed in mesophyll tissues. In vitro overexpression (OE), RNA interference (RNAi), and dual luciferase reporter experiments indicated that CsSTSs are negatively regulated by asCsSTS. Fluorescence in situ hybridization revealed that asCsSTS transcript localized in leaf cytoplasm, indicating that the regulation of CsSTS by asCsSTS is a posttranscriptional process. Further investigation revealed that this regulation occurred by reducing CsSTS transcript stability through a DICER-like protein-mediated pathway. Chemically induced OE and RNAi of asCsSTS led to promotion or inhibition, respectively, of assimilate export from leaves and altered fruit growth rates. Our results suggest that the regulation of CsSTSs between the mesophyll and vasculature reduces sugar storage in mesophyll tissue and promotes assimilate export from the leaf when the plant carries fruit.

Genomic and metabolic features of Bacillus cereus, inhibiting the growth of Sclerotinia sclerotiorum by synthesizing secondary metabolites

We investigated the biocontrol mechanism of Bacillus cereus CF4-51 to find powerful microbes that effectively control Sclerotinia sclerotiorum. To assess its inhibitory effect on fungal growth, the plant pathogen (S. sclerotiorum) was co-cultured with Bacillus cereus. Scanning electron microscope (SEM) was used to study the morphology of S. sclerotiorum treated with CF4-51 biofumigant. The expression of sclerotium formation-related genes was analyzed by qRT-PCR. We performed whole genome sequencing of CF4-51 by PacBio Sequel platform. Lipopeptides were extracted from strain CF4-51 according to the method of hydrochloric acid precipitation and methanol dissolution. The volatiles CF4-51 were identified using gas chromatography-mass spectrometry (GC-MS). We found that the volatile organic compounds (VOCs) released by CF4-51 damaged the S. sclerotiorum hyphae and inhibited the formation of sclerotia. The qRT-PCR data revealed the down-regulated expression of the genes involved in sclerotial formation. Moreover, we analyzed the B. cereus CF4-51 genome and metabolites. The genome consisted of 5.35 Mb, with a GC content of 35.74%. An examination of the genome revealed the presence of several gene clusters for the biosynthesis of antibiotics, siderophores, and various other bioactive compounds, including those belonging to the NRPS-like, LAP, RIPP-like, NRPS, betalactone, CDPS, terpene, ladderane, ranthipeptide, and lanthipeptide (class II) categories. A gas chromatography-tandem mass spectrometry analysis identified 45 VOCs produced by strain CF4-51. Among these, technical grade formulations of five were chosen for further study: 2-Pentadecanone, 6,10,14-trimethyl-,1,2-Benzenedicarboxylic acid, bis(2-methylpropyl) ester, Dibutyl phthalate, Cyclododecane, Heptadecane. the five major constituents play important roles in the antifungal activity of the VOCs CF4-51 on the growth of S. sclerotiorum. The secondary metabolites produced by strain CF4-51are critical for the inhibition of S. sclerotiorum hyphal growth and sclerotial formation.

Deciphering the potential of a plant growth promoting endophyte Rhizobium sp. WYJ-E13, and functional annotation of the genes involved in the metabolic pathway

Plant growth-promoting rhizobacteria (PGPR) are well-acknowledged root endophytic bacteria used for plant growth promotion. However, which metabolites produced by PGPR could promote plant growth remains unclear. Additionally, which genes are responsible for plant growth-promoting traits is also not elucidated. Thus, as comprehensive understanding of the mechanism of endophyte in growth promotion is limited, this study aimed to determine the metabolites and genes involved in plant growth-promotion. We isolated an endophytic Rhizobium sp. WYJ-E13 strain from the roots of Curcuma wenyujin Y.H. Chen et C. Ling, a perennial herb and medicinal plant. The tissue culture experiment showed its plant growth-promoting ability. The bacterium colonization in the root was confirmed by scanning electron microscopy and paraffin sectioning. Furthermore, it was noted that the WYJ-E13 strain produced cytokinin, anthranilic acid, and L-phenylalanine by metabolome analysis. Whole-genome analysis of the strain showed that it consists of a circular chromosome of 4,350,227 bp with an overall GC content of 60.34%, of a 2,149,667 bp plasmid1 with 59.86% GC, and of a 406,180 bp plasmid2 with 58.05% GC. Genome annotation identified 4,349 putative protein-coding genes, 51 tRNAs, and 9 rRNAs. The CDSs number allocated to the Kyoto Encyclopedia of Genes and Genomes, Gene Ontology, and Clusters of Orthologous Genes databases were 2027, 3,175 and 3,849, respectively. Comparative genome analysis displayed that Rhizobium sp. WYJ-E13 possesses the collinear region among three species: Rhizobium acidisoli FH23, Rhizobium gallicum R602 and Rhizobium phaseoli R650. We recognized a total set of genes that are possibly related to plant growth promotion, including genes involved in nitrogen metabolism (nifU, gltA, gltB, gltD, glnA, glnD), hormone production (trp ABCDEFS), sulfur metabolism (cysD, cysE, cysK, cysN), phosphate metabolism (pstA, pstC, phoB, phoH, phoU), and root colonization. Collectively, these findings revealed the roles of WYJ-E13 strain in plant growth-promotion. To the best of our knowledge, this was the first study using whole-genome sequencing for Rhizobium sp. WYJ-E13 associated with C. wenyujin. WYJ-E13 strain has a high potential to be used as Curcuma biofertilizer for sustainable agriculture.

Chromosome-level genome assembly of the Muscovy duck provides insight into fatty liver susceptibility

The Muscovy duck (Cairina moschata) is an economically important poultry species, which is susceptible to fatty liver. Thus, the Muscovy duck may serve as an excellent candidate animal model of non-alcoholic fatty liver disease. However, the mechanisms underlying fatty liver development in this species are poorly understood. In this study, we report a chromosome-level genome assembly of the Muscovy duck, with a contig N50 of 11.8 Mb and scaffold N50 of 83.16 Mb. The susceptibility of Muscovy duck to fatty liver was mainly attributed to weak lipid catabolism capabilities (fatty acid β-oxidation and lipolysis). Furthermore, conserved noncoding elements (CNEs) showing accelerated evolution contributed to fatty liver formation by down-regulating the expression of genes involved in hepatic lipid catabolism. We propose that the susceptibility of Muscovy duck to fatty liver is an evolutionary by-product. In conclusion, this study revealed the potential mechanisms underlying the susceptibility of Muscovy duck to fatty liver.

Trichoderma atroviride hyphal regeneration and conidiation depend on cell-signaling processes regulated by a microRNA-like RNA

The ability to respond to injury is essential for the survival of an organism and involves analogous mechanisms in animals and plants. Such mechanisms integrate coordinated genetic and metabolic reprogramming events requiring regulation by small RNAs for adequate healing of the wounded area. We have previously reported that the response to injury of the filamentous fungus Trichoderma atroviride involves molecular mechanisms closely resembling those of plants and animals that lead to the formation of new hyphae (regeneration) and the development of asexual reproduction structures (conidiophores). However, the involvement of microRNAs in this process has not been investigated in fungi. In this work, we explore the participation of microRNA-like RNAs (milRNAs) molecules by sequencing messenger and small RNAs during the injury response of the WT strain and RNAi mutants. We found that Dcr2 appears to play an important role in hyphal regeneration and is required to produce the majority of sRNAs in T. atroviride. We also determined that the three main milRNAs produced via Dcr2 are induced during the damage-triggered developmental process. Importantly, elimination of a single milRNA phenocopied the main defects observed in the dcr2 mutant. Our results demonstrate the essential role of milRNAs in hyphal regeneration and asexual development by post-transcriptionally regulating cellular signalling processes involving phosphorylation events. These observations allow us to conclude that fungi, like plants and animals, in response to damage activate fine-tuning regulatory mechanisms.

Identification and characterization of miRNAs and PHAS loci related to the early development of the embryo and endosperm in Fragaria × ananassa

BACKGROUND

The strawberry fleshy fruit is actually enlarged receptacle tissue, and the successful development of the embryo and endosperm is essential for receptacle fruit set. MicroRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs) play indispensable regulatory roles in plant growth and development. However, miRNAs and phasiRNAs participating in the regulation of strawberry embryo and endosperm development have yet to be explored.

RESULTS

Here, we performed genome-wide identification of miRNA and phasiRNA-producing loci (PHAS) in strawberry seeds with a focus on those involved in the development of the early embryo and endosperm. We found that embryos and endosperm have different levels of small RNAs. After bioinformatics analysis, the results showed that a total of 404 miRNAs (352 known and 52 novel) and 156 PHAS genes (81 21-nt and 75 24-nt genes) could be found in strawberry seed-related tissues, of which four and nine conserved miRNA families displayed conserved expression in the endosperm and embryo, respectively. Based on refined putative annotation of PHAS loci, some auxin signal-related genes, such as CM3, TAR2, AFB2, ASA1, NAC and TAS3, were found, which demonstrates that IAA biosynthesis is important for endosperm and embryo development during early fruit growth. Additionally, some auxin signal-related conserved (miR390-TAS3) and novel (miR156-ASA1) trigger-PHAS pairs were identified.

CONCLUSIONS

Taken together, these results expand our understanding of sRNAs in strawberry embryo and endosperm development and provide a genomic resource for early-stage fruit development.

Fermentation of NaHCO3-treated corn germ meal by Bacillus velezensis CL-4 promotes lignocellulose degradation and nutrient utilization

Sodium bicarbonate pretreatment and solid-state fermentation (SSF) were used to maximize the nutritional value of corn germ meal (CGM) by inoculating it with Bacillus velezensis CL-4 (isolated from chicken cecal contents and capable of degrading lignocellulose). Based on genome sequencing, B. velezensis CL-4 has a 4,063,558 bp ring chromosome and 46.27% GC content. Furthermore, genes associated with degradation of lignocellulose degradation were detected. Pretreatment of CGM (PCGM) with sodium bicarbonate (optimized to 0.06 g/mL) neutralized low pH. Fermented and pretreated CGM (FPCGM) contained more crude protein (CP), soluble protein of trichloroacetic acid (TCA-SP), and total amino acids (aa) than CGM and PCGM. Degradation rates of cellulose and hemicellulose were reduced by 21.33 and 71.35%, respectively, after 48 h fermentation. Based on electron microscopy, FPCGM destroys the surface structure and adds small debris of the CGM substrate, due to lignocellulose breakdown. Furthermore, 2-oxoadipic acid and dimethyl sulfone were the most important metabolites during pretreatment. Concentrations of adenosine, cytidine, guanosine, S-methyl-5'-thioadenosine, and adenine decreased significantly after 48 h fermentation, whereas concentrations of probiotics, enzymes, and fatty acids (including palmitic, 16-hydroxypalmitic, and linoleic acids) were significantly improved after fermentation. In conclusion, the novel pretreatment of CGM provided a proof of concept for using B. velezensis CL-4 to degrade lignocellulose components, improve nutritional characteristics of CGM, and expand CGM lignocellulosic biological feed production. KEY POINTS: • Sodium bicarbonate (baking soda) can be used as an economical and green additive to pretreat corn germ meal; • Fermentation with B. velezensis degrades the cellulose and hemicellulose component of corn germ meal and improves its feed quality; • As a novel qualified presumption of safety (QPS) strain, B. velezensis should have broad potential applications in food and feed industries.

Genomic insights into genetic diploidization in the homosporous fern Adiantum nelumboides

Whole genome duplication has been recognized as a major process in speciation of land plants, especially in ferns. Whereas genome downsizing contributes greatly to the post-genome shock responses of polyploid flowering plants, diploidization of polyploid ferns diverges by maintaining most of the duplicated DNA and is thus expected to be dominated by genic processes. As a consequence, fern genomes provide excellent opportunities to study ecological speciation enforced by expansion of protein families via polyploidy. To test the key predictions of this hypothesis, we reported the de novo genome sequence of Adiantum nelumboides, a tetraploid homosporous fern. The obtained draft genome had a size of 6.27 Gb assembled into 11,767 scaffolds with the contig N50 of 1.37 Mb. Repetitive DNA sequences contributed with about 81.7%, a remarkably high proportion of the genome. With 69,568 the number of predicted protein-coding genes exceeded those reported in most other land plant genomes. Intragenomic synteny analyses recovered 443 blocks with the average block size of 1.29 Mb and the average gene content of 16 genes. The results are consistent with the hypothesis of high ancestral chromosome number, lack of substantial genome downsizing, and dominance of genic diploidization. As expected in the calciphilous plants, a notable number of detected genes were involved in calcium uptake and transport. In summary, the genome sequence of a tetraploid homosporous fern not only provides access to a genomic resource of a derived fern, but also supports the hypothesis of maintenance of high chromosome numbers and duplicated DNA in young polyploid ferns.

Comparative Genomics and Physiology of Akkermansia muciniphila Isolates from Human Intestine Reveal Specialized Mucosal Adaptation

Akkermansia muciniphila is a champion of mucin degradation in the human gastrointestinal tract. Here, we report the isolation of six novel strains from healthy human donors and their genomic, proteomic and physiological characterization in comparison to the type-strains A. muciniphila MucT and A. glycaniphila PytT. Complete genome sequencing revealed that, despite their large genomic similarity (>97.6%), the novel isolates clustered into two distinct subspecies of A. muciniphila: Amuc1, which includes the type-strain MucT, and AmucU, a cluster of unassigned strains that have not yet been well characterized. CRISPR analysis showed all strains to be unique and confirmed that single healthy subjects can carry more than one A. muciniphila strain. Mucin degradation pathways were strongly conserved amongst all isolates, illustrating the exemplary niche adaptation of A. muciniphila to the mucin interface. This was confirmed by analysis of the predicted glycoside hydrolase profiles and supported by comparing the proteomes of A. muciniphila strain H2, belonging to the AmucU cluster, to MucT and A. glycaniphila PytT (including 610 and 727 proteins, respectively). While some intrinsic resistance was observed among the A. muciniphila straind, none of these seem to pose strain-specific risks in terms of their antibiotic resistance patterns nor a significant risk for the horizontal transfer of antibiotic resistance determinants, opening the way to apply the type-strain MucT or these new A. muciniphila strains as next generation beneficial microbes.

DNA methylation in transposable elements buffers the connection between three-dimensional chromatin organization and gene transcription upon rice genome duplication

INTRODUCTION

Polyploidy is a major force in plant evolution and the domestication of cultivated crops.

OBJECTIVES

The study aimed to explore the relationship and underlying mechanism between three-dimensional (3D) chromatin organization and gene transcription upon rice genome duplication.

METHODS

The 3D chromatin structures between diploid (2C) and autotetraploid (4C) rice were compared using high-throughput chromosome conformation capture (Hi-C) analysis. The study combined genetics, transcriptomics, whole-genome bisulfite sequencing (WGBS-seq) and 3D genomics approaches to uncover the mechanism for DNA methylation in modulating gene transcription through 3D chromatin architectures upon rice genome duplication.

RESULTS

We found that 4C rice presents weakened intra-chromosomal interactions compared to its 2C progenitor in some chromosomes. In addition, we found that changes of 3D chromatin organizations including chromatin compartments, topologically associating domains (TADs), and loops, are uncorrelated with gene transcription. Moreover, DNA methylations in the regulatory sequences of genes in compartment A/B switched regions and TAD boundaries are unrelated to their expression. Importantly, although there was no significant difference in the methylation levels in transposable elements (TEs) in differentially expressed gene (DEG) and non-DEG promoters between 2C and 4C rice, we found that the hypermethylated TEs across genes in compartment A/B switched regions and TAD boundaries may suppress the expression of these genes.

CONCLUSION

The study proposed that the rice genome doubling might modulate TE methylation to buffer the effects of chromatin architecture on gene transcription in compartment A/B switched regions and TAD boundaries, resulting in the disconnection between 3D chromatin structure alteration and gene transcription upon rice genome duplication.

Identification of photoperiod-induced specific miRNAs in the adrenal glands of Sunite sheep (Ovis aries)

In seasonal estrus, it is well known that melatonin-regulated biorhythm plays a key role. Some studies indicate that the adrenal gland plays an important role in reproduction in mammals, but the molecular mechanism is not clear. This study used an artificially controlled light photoperiod model, combined with RNA-seq technology and bioinformatics analysis, to analyze the messenger RNA (mRNA) and microRNA (miRNA) of ewe (Sunite) adrenal glands under different photoperiod treatments. After identification, the key candidate genes GRHL2, CENPF, FGF16 and SLC25A30 that photoperiod affects reproduction were confirmed. The miRNAs (oar-miR-544-3p, oar-miR-411b-5p, oar-miR-376e-3p, oar-miR-376d, oar-miR-376b-3p, oar-miR-376a-3p) were specifically expressed in the adrenal gland. The candidate mRNA-miRNA pairs (e.g., SLC25A30 coagulated by novel miRNA554, novel miRNA555 and novel miRNA559) may affect seasonal estrus. In summary, we constructed relation network of the mRNAs and miRNAs of sheep adrenal glands using RNA sequencing and bioinformatics analysis, thereby, providing a valuable genetic variation resource for sheep genome research, which will contribute to the study of complex traits in sheep.

Storing and structuring big data in histological research (vertebrates) using a relational database in SQL

Database systems store data (big data) for various areas dealing with finance (banking, insurance) and are also an essential part of corporate firms. In the field of biology, however, not much attention has been paid to database systems, with the exception of genetics (RNA, DNA) and human protein. Therefore data storage and subsequent implementation is insufficient for this field. The current situation in the field of data use for the assessment of biological relationships and trends is conditioned by constantly changing requirements, while data stored in simple databases used in the field of biology cannot respond operatively to these changes. In the recent period, developments in technology in the field of histology caused an increase in biological information stored in databases with which database technology did not deal. We proposed a new database for histology with designed data types (data format) in database program Microsoft SQL Server Management Studio. In order that the information to support identification of biological trends and regularities is relevant, the data must be provided in real time and in the required format at the strategic, tactical and operational levels. We set the data type according to the needs of our database, we used numeric (smallint,numbers, float), text string (nvarchar, varchar) and date. To select, insert, modify and delete data, we used Structured Query Language (SQL), which is currently the most widely used language in relational databases. Our results represent a new database for information about histology, focusing on histological structures in systems of animals. The structure and relational relations of the histology database will help in analysis of big data, the objective of which was to find relations between histological structures in species and the diversity of habitats in which species live. In addition to big data, the successful estimation of biological relationships and trends also requires the rapid accuracy of scientists who derive key information from the data. A properly functioning database for meta-analyses, data warehousing, and data mining includes, in addition to technological aspects, planning, design, implementation, management, and implementation.

Isolation and Genome Sequence of a Novel Phosphate-Solubilizing Rhizobacterium Bacillus altitudinis GQYP101 and Its Effects on Rhizosphere Microbial Community Structure and Functional Traits of Corn Seedling

Bacillus altitudinis is a widely distributed soil bacterium that has various functional activities, including remediation of contaminated soil, degradation of herbicides, and enhancement of plant growth. B. altitudinis GQYP101 was isolated from the rhizosphere soil of Lycium barbarum L. and demonstrated potential as a plant growth-promoting bacterium. In this work, strain GQYP101 could solubilize phosphorus, and increased the stem diameter, maximum leaf area, and fresh weight of corn in a pot experiment. Nitrogen and phosphorus contents of corn seedlings (aerial part) increased by 100% and 47.9%, respectively, after application of strain GQYP101. Concurrently, nitrogen and phosphorus contents of corn root also increased, by 55.40% and 20.3%, respectively. Furthermore, rhizosphere soil nutrients were altered and the content of available phosphorus increased by 73.2% after application of strain GQYP101. The mechanism by which strain GQYP101 improved plant growth was further investigated by whole genome sequence analysis. Strain GQYP101 comprises a circular chromosome and a linear plasmid. Some key genes of strain GQYP101 were identified that were related to phosphate solubilization, alkaline phosphatase, chemotaxis, and motility. The findings of this study may provide a theoretical basis for strain GQYP101 to enhance crop yield as microbial fertilizer.

The structural and functional divergence of a neglected three-finger toxin subfamily in lethal elapids

Bungarus multicinctus is a widely distributed and medically important elapid snake that produces lethal neurotoxic venom. To study and enhance existing antivenom, we explore the complete repertoire of its toxin genes based on de novo chromosome-level assembly and multi-tissue transcriptome data. Comparative genomic analyses suggest that the three-finger toxin family (3FTX) may evolve through the neofunctionalization of flanking LY6E. A long-neglected 3FTX subfamily (i.e., MKA-3FTX) is also investigated. Only one MKA-3FTX gene, which evolves a different protein conformation, is under positive selection and actively transcribed in the venom gland, functioning as a major toxin effector together with MKT-3FTX subfamily homologs. Furthermore, this lethal snake may acquire self-resistance to its β-bungarotoxin via amino acid replacements on fast-evolving KCNA2. This study provides valuable resources for further evolutionary and structure-function studies of snake toxins, which are fundamental for the development of effective antivenoms and drug candidates.