Simple cDNA normalization using kamchatka crab duplex-specific nuclease

Multiplexed discrimination of SARS-CoV-2 variants via duplex-specific nuclease combined MALDI-TOF MS

The frequent mutations in SARS-CoV-2 significantly increase the virus's pathogenicity and transmissibility while also diminishing the effectiveness of vaccines. Consequently, assays capable of rapidly and simultaneously identifying multiple SARS-CoV-2 variants are essential for large-scale applications that aim to monitor the evolution of the virus. In this work, we propose a method combining duplex-specific nuclease (DSN)-assisted cyclic amplification with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) detection, enabling the simultaneous identification of multiple SARS-CoV-2 variants at high-throughput. Due to the high specificity of DSN, single-base mutations can be resolved by the method. With ultra-sensitive detection by MALDI-TOF MS, a limit of detection of 100 pM viral RNA fragment was demonstrated. The assay was used for simultaneous identification and typing of SARS-CoV-2 Alpha, Beta, and Delta variants. The whole assay can be accomplished within 3 h, and the amplification is performed under constant temperature, making the technique simple in operation and efficient. It is also feasible to extend the technique to the detection of many other variants of the virus. We expect that the method can add value to the rapid screening of viral variants and can play an important role in pandemic control.

Detection of low-frequency mutations in clinical samples by increasing mutation abundance via the excision of wild-type sequences

The efficiency of DNA-enrichment techniques is often insufficient to detect mutations that occur at low frequencies. Here we report a DNA-excision method for the detection of low-frequency mutations in genomic DNA and in circulating cell-free DNA at single-nucleotide resolution. The method is based on a competitive DNA-binding-and-digestion mechanism, effected by deoxyribonuclease I (DNase) guided by single-stranded phosphorothioated DNA (sgDNase), for the removal of wild-type DNA strands. The sgDNase can be designed against any wild-type DNA sequences, allowing for the uniform enrichment of all the mutations within the target-binding region of single-stranded phosphorothioated DNA at mild-temperature conditions. Pretreatment with sgDNase enriches all mutant strands with initial frequencies down to 0.01% and leads to high discrimination factors for all types of single-nucleotide mismatch in multiple sequence contexts, as we show for the identification of low-abundance mutations in samples of blood or tissue from patients with cancer. The method can be coupled with next-generation sequencing, droplet digital polymerase chain reaction, Sanger sequencing, fluorescent-probe-based assays and other mutation-detection methods.

Early zygotic gene product Dunk interacts with anillin to regulate Myosin II during Drosophila cleavage

Drosophila melanogaster cellularization is a special form of cleavage that converts syncytial embryos into cellular blastoderms by partitioning the peripherally localized nuclei into individual cells. An early event in cellularization is the recruitment of nonmuscle myosin II ("myosin") to the leading edge of cleavage furrows, where myosin forms an interconnected basal array before reorganizing into individual cytokinetic rings. The initial recruitment and organization of basal myosin are regulated by a cellularization-specific gene, dunk, but the underlying mechanism is unclear. Through a genome-wide yeast two-hybrid screen, we identified anillin (Scraps in Drosophila), a conserved scaffolding protein in cytokinesis, as the primary binding partner of Dunk. Dunk colocalizes with anillin and regulates its cortical localization during the formation of cleavage furrows, while the localization of Dunk is independent of anillin. Furthermore, Dunk genetically interacts with anillin to regulate the basal myosin array during cellularization. Similar to Dunk, anillin colocalizes with myosin since the very early stage of cellularization and is required for myosin retention at the basal array, before the well-documented function of anillin in regulating cytokinetic ring assembly. Based on these results, we propose that Dunk regulates myosin recruitment and spatial organization during early cellularization by interacting with and regulating anillin.

Exonuclease-based aptasensors: Promising for food safety and diagnostic aims

As of today's requirement, developing cost-effective smart sensing tools with ultrahigh sensitivity for food safety insurance is of special importance. For this purpose, aptamer-based biosensors (aptasensors) powered by the superiorities of the recycling signal amplification strategies have been expanded especially. Target recycling supported by enzymes is an appealing approach for implementing signal amplification. As the supreme biocatalyst enzymes, exonucleases can inaugurate signal improvement by involving a single target in a process would result in appreciable repeating cycles of the cleavage of the phosphodiester bonds between the building blocks of the nucleic acid strands, and also, their terminals. Although there are diverse substances for catalyzing amplification strategies, including nanoparticles, carbon-based nanocomposites, and quantum dots (QDs), exonucleases are of superiority over them by simplifying the amplification process with no need for the complicated pre-treatment processes. The outstanding selectivity and great sensitivity of the aptasensors tuned by amplification potency of exonucleases nominate them as the promising sensing tools for label-free, ease-of-use, cost-effective, and real-time diagnosis of diverse targets. Here, we summarize the achievements and perspectives in the scientific branch of aptasensor design for the qualitative monitoring of diverse targets by cooperation of exonucleases with the conspicuous potential for the signal amplification. Finally, some results are expressed to provide a comprehensive viewpoint for developing novel nuclease-based aptasensors in the future.

CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes

High-throughput genotyping enables the large-scale analysis of genetic diversity in population genomics and genome-wide association studies that combine the genotypic and phenotypic characterization of large collections of accessions. Sequencing-based approaches for genotyping are progressively replacing traditional genotyping methods because of the lower ascertainment bias. However, genome-wide genotyping based on sequencing becomes expensive in species with large genomes and a high proportion of repetitive DNA. Here we describe the use of CRISPR-Cas9 technology to deplete repetitive elements in the 3.76-Gb genome of lentil (Lens culinaris), 84% consisting of repeats, thus concentrating the sequencing data on coding and regulatory regions (single-copy regions). We designed a custom set of 566,766 gRNAs targeting 2.9 Gbp of repeats and excluding repetitive regions overlapping annotated genes and putative regulatory elements based on ATAC-seq data. The novel depletion method removed ∼40% of reads mapping to repeats, increasing those mapping to single-copy regions by ∼2.6-fold. When analyzing 25 million fragments, this repeat-to-single-copy shift in the sequencing data increased the number of genotyped bases of ∼10-fold compared to nondepleted libraries. In the same condition, we were also able to identify ∼12-fold more genetic variants in the single-copy regions and increased the genotyping accuracy by rescuing thousands of heterozygous variants that otherwise would be missed because of low coverage. The method performed similarly regardless of the multiplexing level, type of library or genotypes, including different cultivars and a closely related species (L. orientalis). Our results showed that CRISPR-Cas9-driven repeat depletion focuses sequencing data on single-copy regions, thus improving high-density and genome-wide genotyping in large and repetitive genomes.

Thermostable enzyme research advances: a bibliometric analysis

Thermostable enzymes are enzymes that can withstand elevated temperatures as high as 50 °C without altering their structure or distinctive features. The potential of thermostable enzymes to increase the conversion rate at high temperature has been identified as a key factor in enhancing the efficiency of industrial operations. Performing procedures at higher temperatures with thermostable enzymes minimises the risk of microbial contamination, which is one of the most significant benefits. In addition, it helps reduce substrate viscosity, improve transfer speeds, and increase solubility during reaction operations. Thermostable enzymes offer enormous industrial potential as biocatalysts, especially cellulase and xylanase, which have garnered considerable amount of interest for biodegradation and biofuel applications. As the usage of enzymes becomes more common, a range of performance-enhancing applications are being explored. This article offers a bibliometric evaluation of thermostable enzymes. Scopus databases were searched for scientific articles. The findings indicated that thermostable enzymes are widely employed in biodegradation as well as in biofuel and biomass production. Japan, the United States, China, and India, as along with the institutions affiliated with these nations, stand out as the academically most productive in the field of thermostable enzymes. This study's analysis exposed a vast number of published papers that demonstrate the industrial potential of thermostable enzymes. These results highlight the significance of thermostable enzyme research for a variety of applications.

Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition

The catalytic function of lysyl hydroxylase-2 (LH2), a member of the Fe(II)/αKG-dependent oxygenase superfamily, is to catalyze the hydroxylation of lysine to hydroxylysine in collagen, resulting in stable hydroxylysine aldehyde-derived collagen cross-links (HLCCs). Reports show that high amounts of LH2 lead to the accumulation of HLCCs, causing fibrosis and specific types of cancer metastasis. Some members of the Fe(II)/αKG-dependent family have also been reported to have intramolecular O2 tunnels, which aid in transporting one of the required cosubstrates into the active site. While LH2 can be a promising target to combat these diseases, efficacious inhibitors are still lacking. We have used computational simulations to investigate a series of 44 small molecules as lead compounds for LH2 inhibition. Tunneling analyses indicate the existence of several intramolecular tunnels. The lengths of the calculated O2-transporting tunnels in holoenzymes are relatively longer than those in the apoenzyme, suggesting that the ligands may affect the enzyme's structure and possibly block (at least partially) the tunnels. The sequence alignment analysis between LH enzymes from different organisms shows that all of the amino acid residues with the highest occurrence rate in the oxygen tunnels are conserved. Our results suggest that the enolate form of diketone compounds establishes stronger interactions with the Fe(II) in the active site. Branching the enolate compounds with functional groups such as phenyl and pyridinyl enhances the interaction with various residues around the active site. Our results provide information about possible leads for further LH2 inhibition design and development.

Construction of an experimental study and addition of adapter sequences using HiDi DNA polymerase for improving DNA normalization methods relevant to novel gene discovery

Microorganisms in the environment can be distinguished into dominant and rare microbial species based on their genes. It is difficult to obtain genetic information derived from rare microbial species (rare genes) because of the differences in relative abundance. DNA normalization is an approach that is used to obtain genetic information derived from rare microbial species from an environmental sample. This method involves the addition of adapter sequences for the amplification, denaturation, and reassociation of the DNA fragments and single-stranded DNA (ssDNA)/double-stranded DNA (dsDNA) separation. In this method, the amount of a high-copy-number of DNA fragments and a low-copy-number of DNA fragments can be equalized. Improvements in this technique are expected to provide novel genetic information or genes in rare microbial species. However, few model experimental systems have been reported to validate the DNA normalization techniques. This study is aimed to improve the DNA normalization technique used to obtain genetic information of rare genes from rare microbial species. An experimental study was constructed with two antibiotic resistance genes, whose copy numbers differed up to a million-fold. Both genes were mixed and the mixture of DNA fragments, of high- and low-copy-number, containing these genes was normalized by separating ssDNA/dsDNA fragments using hydroxyapatite. Normalized DNA fragments were introduced into Escherichia coli and DNA normalization was evaluated by counting colonies. Moreover, we improved the method to amplify a low-copy-number of DNA fragments by the addition of adapter sequences to DNA fragments using HiDi DNA polymerase to increase the efficiency of DNA normalization. This normalization method was achieved with a 100,000-fold difference. These methods allowed for quantitative evaluation of the DNA normalization efficiency. The experimental data and methods obtained in this study are expected to improve the DNA normalization efficiency to obtain novel genetic information or genes.

Dual signal magnification for ultrasensitive biosensing based on well-regulated SERS of AuNTs@AuHg and DSN-assisted amplification

AuNTs@AuHg alloy with well-regulated SERS properties was proposed, which displayed wonderful SERS intensity and effective salt resistance. Using miRNA-21 as a model analyte and combining with DSN-assisted amplification, a dual signal amplification strategy for ultrasensitive miRNA biosensing with a low detection limit (0.53 fM) and satisfactory selectivity was designed.

Pore-Forming Cardiotoxin VVA2 (Volvatoxin A2) Variant I82E/L86K Is an Atypical Duplex-Specific Nuclease

VVA2 (volvatoxin A chain 2) is a cardiotoxic protein purified from Volvariella volvacea. Its biological activities include hemolysis, writhing reaction, neurotoxicity, and ventricular systolic arresting activity. The cytotoxicity of VVA2 was mainly considered due to its pore-forming activity. Here we report a novel biological activity of its variants VVA2 I82E/K86K as a duplex-specific nuclease. Recombinant VVA2 variant I82E/L86K (Re-VVA2 I82E/L86K), deprived of the oligomerization property, shows increased nuclease activity compared to VVA2. Re-VVA2 I82E/L86K converts supercoiled DNA (Replicative form I, RF I) into nicked form (RF II) and linear form (RF III) in the presence of Mg²⁺ or Mn²⁺. Besides plasmid DNA, it also exhibits nuclease activity on E. coli genomic DNA rather than ssDNA or RNA. Re-VVA2 I82E/L86K preferentially cleaves dG-dC-rich dsDNA regions and shows the best performance at pH 6–9 and 55 °C. Our structure–function study has revealed amino acid E111 may take an active part in nuclease activity through interacting with metal ions. Based on the sequences of its cleavage sites, a “double-hit” mechanism was thereby proposed. Given that Re-VVA2 I82E/L86K did not exhibit the conserved nuclease structure and sequence, it is considered an atypical duplex-specific nuclease.

Molecular biology applications of the red king crab duplex-specific nuclease

Duplex-specific nuclease (DSN) from hepatopancreas of the craboid Paralithodes camtschaticus (red king crab) has a unique combination of properties. Along with thermal stability and a high optimal temperature of catalysis, this enzyme exhibits high substrate selectivity, cleaving only DNA in duplexes (DNA-DNA or DNA-RNA). Accordingly, it digests neither single strands (nor single-stranded regions) of DNA, nor RNA strands with any secondary structure. Such properties make it possible to create unique protocols based on DSN, which is also an important object of fundamental research in the field of nuclease evolution. The review considers diverse applications of the red king crab DSN in modern methods of molecular biology.

Identification of Olfactory Genes in Monochamus saltuarius and Effects of Bursaphelenchus xylophilus Infestation on Their Expression

The pine wood nematode (PWN) Bursaphelenchus xylophilus has caused disastrous losses of pine forests in many countries, and the success of PWN depends strongly on interactions with its insect vectors. Monochamus saltuarius is a newly recorded vector in Northeast China. Feeding (i.e., immature) and egg-laying (i.e., mature) Monochamus spp. target different host plants, and olfactory cues play important roles regarding host choice. Whether infestation with PWN affects olfactory mechanisms in M. saltuarius related to feeding and oviposition is of interest as this may affect the spread of nematodes to new healthy hosts. However, little is known about molecular mechanisms of the olfactory system of M. saltuarius. We identified chemosensory-related genes in adult M. saltuarius and examined the influence of B. xylophilus on the respective expression patterns. Fifty-three odorant-binding proteins (OBPs), 15 chemosensory proteins, 15 olfactory receptors (ORs), 10 gustatory receptors, 22 ionotropic receptors (IRs), and two sensory neuron membrane proteins were identified, and sex bias among non-infested beetles was mainly found with respect to expression of OBPs. Interestingly, OBPs and ORs were markedly down-regulated in male M. saltuarius infested with B. xylophilus, which may reduce olfactory sensitivity of male M. saltuarius and affect the spreading of B. xylophilus to new hosts. Our results will help understand the interactions between B. xylophilus and M. saltuarius, which may lead to the identification of new control targets in the olfactory system of M. saltuarius.

Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit

While transcriptome- and proteome-wide technologies to assess processes in protein biogenesis are now widely available, we still lack global approaches to assay post-ribosomal biogenesis events, in particular those occurring in the eukaryotic secretory system. We here develop a method, SECRiFY, to simultaneously assess the secretability of >10⁵ protein fragments by two yeast species, S. cerevisiae and P. pastoris, using custom fragment libraries, surface display and a sequencing-based readout. Screening human proteome fragments with a median size of 50-100 amino acids, we generate datasets that enable datamining into protein features underlying secretability, revealing a striking role for intrinsic disorder and chain flexibility. The SECRiFY methodology generates sufficient amounts of annotated data for advanced machine learning methods to deduce secretability patterns. The finding that secretability is indeed a learnable feature of protein sequences provides a solid base for application-focused studies.

Genome-Wide Transcriptome Profiling, Characterization, and Functional Identification of NAC Transcription Factors in Sorghum under Salt Stress

Salinity stress has become a significant concern to global food security. Revealing the mechanisms that enable plants to survive under salinity has immense significance. Sorghum has increasingly attracted researchers interested in understanding the survival and adaptation strategies to high salinity. However, systematic analysis of the DEGs (differentially expressed genes) and their relative expression has not been reported in sorghum under salt stress. The de novo transcriptomic analysis of sorghum under different salinity levels from 60 to 120 mM NaCl was generated using Illumina HiSeq. Approximately 323.49 million high-quality reads, with an average contig length of 1145 bp, were assembled de novo. On average, 62% of unigenes were functionally annotated to known proteins. These DEGs were mainly involved in several important metabolic processes, such as carbohydrate and lipid metabolism, cell wall biogenesis, photosynthesis, and hormone signaling. SSG 59-3 alleviated the adverse effects of salinity by suppressing oxidative stress (H₂O₂) and stimulating enzymatic and non-enzymatic antioxidant activities (SOD, APX, CAT, APX, POX, GR, GSH, ASC, proline, and GB), as well as protecting cell membrane integrity (MDA and electrolyte leakage). Significant up-regulation of transcripts encoding the NAC, MYB, and WRYK families, NHX transporters, the aquaporin protein family, photosynthetic genes, antioxidants, and compatible osmolyte proteins were observed. The tolerant line (SSG 59-3) engaged highly efficient machinery in response to elevated salinity, especially during the transport and influx of K⁺ ions, signal transduction, and osmotic homeostasis. Our data provide insights into the evolution of the NAC TFs gene family and further support the hypothesis that these genes are essential for plant responses to salinity. The findings may provide a molecular foundation for further exploring the potential functions of NAC TFs in developing salt-resistant sorghum lines.

RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics

RNA sequencing techniques have enabled the systematic elucidation of gene expression (RNA-Seq), transcription start sites (differential RNA-Seq), transcript 3′ ends (Term-Seq), and post-transcriptional processes (ribosome profiling). The main challenge of transcriptomic studies is to remove ribosomal RNAs (rRNAs), which comprise more than 90% of the total RNA in a cell. Here, we report a low-cost and robust bacterial rRNA depletion method, RiboRid, based on the enzymatic degradation of rRNA by thermostable RNase H. This method implemented experimental considerations to minimize nonspecific degradation of mRNA and is capable of depleting pre-rRNAs that often comprise a large portion of RNA, even after rRNA depletion. We demonstrated the highly efficient removal of rRNA up to a removal efficiency of 99.99% for various transcriptome studies, including RNA-Seq, Term-Seq, and ribosome profiling, with a cost of approximately $10 per sample. This method is expected to be a robust method for large-scale high-throughput bacterial transcriptomic studies.

Removal of ribosomal RNAs, a major constituent (over 90%) of cellular RNA is a critical experimental step for transcriptomic studies that deal with messenger RNAs. In this manuscript, we describe a robust method to subtract ribosomal RNA from various RNA samples. The method is based on the enzymatic degradation of target RNA by short complementary DNA and RNA:DNA duplex specific nuclease. The method comprises carefully designed experimental procedures to minimize experimental bias and unwanted removal of messenger RNAs. We validate the method on various types of transcriptomic studies for seven diverse bacterial species. This method successfully removed ribosomal RNA with over 99% of efficiency and it was comparable to commercial systems even for degraded RNA samples at a fraction of a cost.

Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost

New approaches to characterizing microbiomes via high-throughput sequencing provide impressive gains in efficiency and cost reduction compared to approaches that were standard just a few years ago. However, the speed of method development has been such that staying abreast of the latest technological advances is challenging. Moreover, shifting laboratory protocols to include new methods can be expensive and time consuming. To facilitate adoption of new techniques, we provide a guide and review of recent advances that are relevant for single-locus sequence-based study of microbiomes—from extraction to library preparation—including a primer regarding the use of liquid-handling automation in small-scale academic settings. Additionally, we describe several amendments to published techniques to improve throughput, track contamination, and reduce cost. Notably, we suggest adding synthetic DNA molecules to each sample during nucleic acid extraction, thus providing a method of documenting incidences of cross-contamination. We also describe a dual-indexing scheme for Illumina sequencers that allows multiplexing of many thousands of samples with minimal PhiX input. Collectively, the techniques that we describe demonstrate that laboratory technology need not impose strict limitations on the scale of molecular microbial ecology studies.

IMPORTANCE New methods to characterize microbiomes reduce technology-imposed limitations to study design, but many new approaches have not been widely adopted. Here, we present techniques to increase throughput and reduce contamination alongside a thorough review of current best practices.

Recent advances in engineering of microbial cell factories for intelligent pH regulation and tolerance

pH regulation is a serious concern in the industrial fermentation process as pH adjustment heavily utilizes acid/base and pollutes the environment. Under pH-stress conditions, microbial growth and production of valuable target products may be severely affected. Furthermore, some strains generating acidic or alkaline products require self pH regulation and increased tolerance against pH-stress. For pH control, synthetic biology has provided advanced engineering approaches to construct robust and more intelligent microbial strains, exhibiting tolerance to pH-stress to cope with limitations of pH regulation. This study reviewed the current progress of advanced strain evolution strategies to engineer pH-stress tolerant strains via synthetic biology. In addition, a large number of pH-responsive elements, including promoters, riboswitches, and some proteins have been investigated and applied for construction of pH-responsive genetic circuits and intelligent pH-responsive microbial strains.

High-throughput 5'P sequencing enables the study of degradation-associated ribosome stalls

RNA degradation is critical for gene expression and mRNA quality control. mRNA degradation is connected to the translation process up to the degree that 5'-3' mRNA degradation follows the last translating ribosome. Here, we present an improved high-throughput 5'P degradome RNA-sequencing method (HT-5Pseq). HT-5Pseq is easy, scalable, and uses affordable duplex-specific nuclease-based rRNA depletion. We investigate in vivo ribosome stalls focusing on translation termination. By comparing ribosome stalls identified by ribosome profiling, disome-seq and HT-5Pseq, we find that degradation-associated ribosome stalls are often enriched in Arg preceding the stop codon. On the contrary, mRNAs depleted for those stalls use more frequently a TAA stop codon preceded by hydrophobic amino acids. Finally, we show that termination stalls found by HT-5Pseq, and not by other approaches, are associated with decreased mRNA stability. Our work suggests that ribosome stalls associated with mRNA decay can be easily captured by investigating the 5'P degradome.

Identification of host factors binding to dengue and Zika virus subgenomic RNA by efficient yeast three-hybrid screens of the human ORFeome

Flaviviruses such as the dengue (DENV) and the Zika virus (ZIKV) are important human pathogens causing around 100 million symptomatic infections each year. During infection, small subgenomic flavivirus RNAs (sfRNAs) are formed inside the infected host cell as a result of incomplete degradation of the viral RNA genome by cellular exoribonuclease XRN1. Although the full extent of sfRNA functions is to be revealed, these non-coding RNAs are key virulence factors and their detrimental effects on multiple cellular processes seem to consistently involve molecular interactions with RNA-binding proteins (RBPs). Discovery of such sfRNA-binding host-factors has followed established biochemical pull-down approaches skewed towards highly abundant proteins hampering proteome-wide coverage. Yeast three-hybrid (Y3H) systems represent an attractive alternative approach. To facilitate proteome-wide screens for RBP, we revisited and improved existing RNA-Y3H methodology by (1) implementing full-length ORF libraries in combination with (2) efficient yeast mating to increase screening depth and sensitivity, and (3) stringent negative controls to eliminate over-representation of non-specific RNA-binders. These improvements were validated employing the well-characterized interaction between DDX6 (DEAD-box helicase 6) and sfRNA of DENV as paradigm. Our advanced Y3H system was used to screen for human proteins binding to DENV and ZIKV sfRNA, resulting in a list of 69 putative sfRNA-binders, including several previously reported as well as numerous novel RBP host factors. Our methodology requiring no sophisticated infrastructure or analytic pipeline may be employed for the discovery of meaningful RNA-protein interactions at large scale in other fields.

A de novo Full-Length mRNA Transcriptome Generated From Hybrid-Corrected PacBio Long-Reads Improves the Transcript Annotation and Identifies Thousands of Novel Splice Variants in Atlantic Salmon

Atlantic salmon (Salmo salar) is a major species produced in world aquaculture and an important vertebrate model organism for studying the process of rediploidization following whole genome duplication events (Ss4R, 80 mya). The current Salmo salar transcriptome is largely generated from genome sequence based in silico predictions supported by ESTs and short-read sequencing data. However, recent progress in long-read sequencing technologies now allows for full-length transcript sequencing from single RNA-molecules. This study provides a de novo full-length mRNA transcriptome from liver, head-kidney and gill materials. A pipeline was developed based on Iso-seq sequencing of long-reads on the PacBio platform (HQ reads) followed by error-correction of the HQ reads by short-reads from the Illumina platform. The pipeline successfully processed more than 1.5 million long-reads and more than 900 million short-reads into error-corrected HQ reads. A surprisingly high percentage (32%) represented expressed interspersed repeats, while the remaining were processed into 71 461 full-length mRNAs from 23 071 loci. Each transcript was supported by several single-molecule long-read sequences and at least three short-reads, assuring a high sequence accuracy. On average, each gene was represented by three isoforms. Comparisons to the current Atlantic salmon transcripts in the RefSeq database showed that the long-read transcriptome validated 25% of all known transcripts, while the remaining full-length transcripts were novel isoforms, but few were transcripts from novel genes. A comparison to the current genome assembly indicates that the long-read transcriptome may aid in improving transcript annotation as well as provide long-read linkage information useful for improving the genome assembly. More than 80% of transcripts were assigned GO terms and thousands of transcripts were from genes or splice-variants expressed in an organ-specific manner demonstrating that hybrid error-corrected long-read transcriptomes may be applied to study genes and splice-variants expressed in certain organs or conditions (e.g., challenge materials). In conclusion, this is the single largest contribution of full-length mRNAs in Atlantic salmon. The results will be of great value to salmon genomics research, and the pipeline outlined may be applied to generate additional de novo transcriptomes in Atlantic Salmon or applied for similar projects in other species.

de novo transcriptomic profiling of differentially expressed genes in grass halophyte Urochondra setulosa under high salinity

Soil salinity is one of the major limiting factors for crop productivity across the world. Halophytes have recently been a source of attraction for exploring the survival and tolerance mechanisms at extreme saline conditions. Urochondra setulosa is one of the obligate grass halophyte that can survive in up to 1000 mM NaCl. The de novo transcriptome of Urochondra leaves at different salt concentrations of 300-500 mM NaCl was generated on Illumina HiSeq. Approximately 352.78 million high quality reads with an average contig length of 1259 bp were assembled de novo. A total of 120,231 unigenes were identified. On an average, 65% unigenes were functionally annotated to known proteins. Approximately 35% unigenes were specific to Urochondra. Differential expression revealed significant enrichment (P < 0.05) of transcription factors, transporters and metabolites suggesting the transcriptional regulation of ion homeostasis and signalling at high salt concentrations in this grass. Also, about 143 unigenes were biologically related to salt stress responsive genes. Randomly selected genes of important pathways were validated for functional characterization. This study provides useful information to understand the gene regulation at extremely saline levels. The study offers the first comprehensive evaluation of Urochondra setulosa leaf transcriptome. Examining non-model organisms that can survive in harsh environment can provide novel insights into the stress coping mechanisms which can be useful to develop improved agricultural crops.

SARS-CoV-2 RNA Detection with Duplex-Specific Nuclease Signal Amplification

The emergence of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a zoonotic pathogen, has led to the outbreak of coronavirus disease 2019 (COVID-19) pandemic and brought serious threats to public health worldwide. The gold standard method for SARS-CoV-2 detection requires both reverse transcription (RT) of the virus RNA to cDNA and then polymerase chain reaction (PCR) for the cDNA amplification, which involves multiple enzymes, multiple reactions and a complicated assay optimization process. Here, we developed a duplex-specific nuclease (DSN)-based signal amplification method for SARS-CoV-2 detection directly from the virus RNA utilizing two specific DNA probes. These specific DNA probes can hybridize to the target RNA at different locations in the nucleocapsid protein gene (N gene) of SARS-CoV-2 to form a DNA/RNA heteroduplex. DSN cleaves the DNA probe to release fluorescence, while leaving the RNA strand intact to be bound to another available probe molecule for further cleavage and fluorescent signal amplification. The optimized DSN amount, incubation temperature and incubation time were investigated in this work. Proof-of-principle SARS-CoV-2 detection was demonstrated with a detection sensitivity of 500 pM virus RNA. This simple, rapid, and direct RNA detection method is expected to provide a complementary method for the detection of viruses mutated at the PCR primer-binding regions for a more precise detection.

Optimized design of antisense oligomers for targeted rRNA depletion

RNA sequencing (RNA-seq) is extensively used to quantify gene expression transcriptome-wide. Although often paired with polyadenylate (poly(A)) selection to enrich for messenger RNA (mRNA), many applications require alternate approaches to counteract the high proportion of ribosomal RNA (rRNA) in total RNA. Recently, digestion using RNaseH and antisense DNA oligomers tiling target rRNAs has emerged as an alternative to commercial rRNA depletion kits. Here, we present a streamlined, more economical RNaseH-mediated rRNA depletion with substantially lower up-front costs, using shorter antisense oligos only sparsely tiled along the target RNA in a 5-min digestion reaction. We introduce a novel Web tool, Oligo-ASST, that simplifies oligo design to target regions with optimal thermodynamic properties, and additionally can generate compact, common oligo pools that simultaneously target divergent RNAs, e.g. across different species. We demonstrate the efficacy of these strategies by generating rRNA-depletion oligos for Xenopus laevis and for zebrafish, which expresses two distinct versions of rRNAs during embryogenesis. The resulting RNA-seq libraries reduce rRNA to <5% of aligned reads, on par with poly(A) selection, and also reveal expression of many non-adenylated RNA species. Oligo-ASST is freely available at https://mtleelab.pitt.edu/oligo to design antisense oligos for any taxon or to target any abundant RNA for depletion.

The Characteristics of Chemosensory and Opsin Genes in Newly Emerged and Sexually Mature Agrilus planipennis, an Important Quarantine Forest Beetle

The emerald ash borer (EAB), Agrilus planipennis, is a highly destructive quarantine pest. The olfactory and visual systems of A. planipennis play different but critical roles at newly emerged and sexually mature stages; however, the molecular basis underlying these differences remain unclear. Consequently, based on deep transcriptome sequencing, we evaluated the expression levels of chemosensory-related proteins and opsins at the two developmental stages of A. planipennis. We found 15 new chemosensory-related genes in our transcriptome assembly compared with the previous genome assembly, including 6 that code for odorant-binding proteins (OBPs) and 9 for chemosensory proteins (CSPs). The expression of several chemosensory-related genes (OBP7, OBP10, CSP1, and CSP12) differed markedly between newly emerged and sexually mature A. planipennis. We also found that the expression of UV opsin 2 and LW opsin 1 was higher in sexually mature male A. planipennis, which may be associated with their strong visual mate detection ability. This study forms the basis for further investigation of the chemosensory and visual system of A. planipennis, and these differentially expressed genes between newly emerged and sexually mature stages may serve as targets for the management of this destructive forest pest after sexual maturity.

Prospects of Red King Crab Hepatopancreas Processing: Fundamental and Applied Biochemistry

Since the early 1980s, a large number of studies on enzymes from the red king crab hepatopancreas were conducted. They have been relevant both from a fundamental point of view in terms of studying the enzymes of marine organisms and in terms of rational natural resource management aimed to obtain new valuable products from the processing of crab fishing waste. Most of these works were performed by Russian scientists due to the area and amount of waste of red king crab processing in Russia (or the Soviet Union). However, the close phylogenetic kinship and the similar ecological niches of commercial crab species and the production scale of the catch provide the bases for the successful transfer of experience in the processing of the red king crab hepatopancreas to other commercial crab species caught worldwide. This review describes the value of recycled commercial crab species, discusses processing problems, and suggests possible solutions for these issues. The main emphasis is made on hepatopancreatic enzymes as the most salubrious products of red king crab waste processing.

Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing

Despite longstanding appreciation of gene expression heterogeneity in isogenic bacterial populations, affordable and scalable technologies for studying single bacterial cells have been limited. Although single-cell RNA sequencing (scRNA-seq) has revolutionized studies of transcriptional heterogeneity in diverse eukaryotic systems1-13, the application of scRNA-seq to prokaryotes has been hindered by their extremely low mRNA abundance14-16, lack of mRNA polyadenylation and thick cell walls17. Here, we present prokaryotic expression profiling by tagging RNA in situ and sequencing (PETRI-seq)-a low-cost, high-throughput prokaryotic scRNA-seq pipeline that overcomes these technical obstacles. PETRI-seq uses in situ combinatorial indexing11,12,18 to barcode transcripts from tens of thousands of cells in a single experiment. PETRI-seq captures single-cell transcriptomes of Gram-negative and Gram-positive bacteria with high purity and low bias, with median capture rates of more than 200 mRNAs per cell for exponentially growing Escherichia coli. These characteristics enable robust discrimination of cell states corresponding to different phases of growth. When applied to wild-type Staphylococcus aureus, PETRI-seq revealed a rare subpopulation of cells undergoing prophage induction. We anticipate that PETRI-seq will have broad utility in defining single-cell states and their dynamics in complex microbial communities.

Does hunger lead to hybridization in a genus of sexually cannibalistic insects (Orthoptera: Prophalangopsidae)?

Allochronic isolation can be a strong mechanism for reproductive isolation and speciation. However, imperfect allochrony and the expression of phenological plasticity can erode temporal barriers to gene flow and result in hybridization between divergent lineages. Here, we combine behavioural ecology and genomics to investigate this scenario in two closely related species of grigs in the genus Cyphoderris. These species exhibit a unique mating system whereby females feed on the fleshy hind wings of the male during copulation, and copulation with conspecific males is more likely in food-restricted females than in well-fed females. In western Canada, Cyphoderris buckelli and Cyphoderris monstrosa are sympatric but largely allochronically separated, with C. buckelli breeding earlier. However, their breeding seasons can overlap, leading to potential for older C. buckelli females to mate with young C. monstrosa males to obtain resources via sexual cannibalism. We used behavioural assays to test whether female feeding status affects the propensity for interspecific mating between C. buckelli females and C. monstrosa males. We then tested for hybridization and gene exchange in wild populations of both species, using morphology, mitochondrial DNA and genome-wide nuclear markers. We found that interspecific courtship and mating can occur, but the relationship between food restriction and increased propensity for hybridization was not significant. Although we observed intraspecific population genetic structure in both species, we found no signatures of hybridization in the morphological or genetic datasets, which suggests that postmating reproductive barriers might be preventing successful hybridization in the wild.

Construction of prokaryotic strand-specific primary-transcripts saturated RNASeq library by controlled heat magnesium-dependent mRNA degradation

The main limiting factors for RNA-Seq analysis are quality and quantity of the isolated mRNA. In prokaryotes, the proportion of messenger RNA to total RNA is rather low. Therefore, the main strategy of library preparation for sequencing is mRNA enrichment. Ribosomal and transfer RNAs, both monophosphorylated at the 5'-ends, are the major fractions of total RNA, while the bulk of primary transcripts is triphosphorylated at the 5'-teminus. Due to its low molecular weight, transfer RNA could be easily removed by a quick precipitation in LiCl solution. Ribosomal RNA may be degraded enzymatically by 5'-end terminal exonuclease XRN-1. These steps allow enriching samples in mRNA during the first stages of RNA-Seq library preparation. The desired level of fragmentation of enriched mRNA necessary for the 2^nd generation sequencing can be controlled by the duration of incubation at elevated temperatures in the presence of Mg²⁺-ions. Here, we describe a simple protocol for construction of the primary prokaryotic mRNA-saturated library without long depletion procedures.

Phylogenomic test of mitochondrial clues to archaic ancestors in a group of hybridizing swallowtail butterflies

Genomics has revolutionized our understanding of hybridization and introgression, but most of the early evidence for these processes came from studies of mitochondrial introgression. To expand these evolutionary insights from mitochondrial patterns, we evaluate phylogenetic discordance across the nuclear genomes of a hybridizing system, the Papilio machaon group of swallowtail butterflies. This species group contains three hybrid lineages (P. brevicauda, P. joanae, and P. m. kahli) that are geographically disjunct across North America and have complete fixation of a mitochondrial lineage that is otherwise primarily found in P. m. hudsonianus, a boreal subspecies of the Holarctic P. machaon. Genome-wide nuclear markers place the three hybrid lineages as a monophyletic group that is sister to P. polyxenes/P. zelicaon rather than P. machaon, although ancient hybridization between a subspecies of P. machaon and the ancestor of these three lineages is also shown by their greater nuclear affinity to P. m. hudsonianus than to other subspecies of P. machaon. Individuals from contemporary hybrid swarms in Alberta, where mitochondrial DNA fixation has not occurred, were more intermediate between their respective parent species, demonstrating diversity in mito-nuclear discordance following hybrid interactions. Our new phylogenetic findings for the P. machaon species group also include: subspecific paraphyly within P. machaon itself across its Holarctic distribution; paraphyly of P. zelicaon relative to P. polyxenes; and more divergent placement of a Mediterranean species, P. hospiton. These results provide the first comprehensive genomic evaluation of relationships within this species group and provide insight into the evolutionary dynamics of hybridization and mitochondrial introgression.

Improving the diversity of captured full-length isoforms using a normalized single-molecule RNA-sequencing method

Human genes form a large variety of isoforms after transcription, encoding distinct transcripts to exert different functions. Single-molecule RNA sequencing facilitates accurate identification of the isoforms by extending nucleotide read length significantly. However, the gene or isoform diversity is lowly represented by the mRNA molecules captured by single-molecule RNA sequencing. Here, we show that a cDNA normalization procedure before the library preparation for PacBio RS II sequencing captures 3.2–6.0 fold more full-length high-quality isoform species for different human samples, as compared to the non-normalized capture procedure. Many lowly expressed, functionally important isoforms can be detected. In addition, normalized PacBio RNA sequencing also resolves more allele-specific haplotype transcripts. Finally, we apply the cDNA normalization based long-read RNA sequencing method to profile the transcriptome of human gastric signet-ring cell carcinomas, identify new cancer-specific transcriptome signatures, and thus, bring out the utility of the improved protocols in gene expression studies.

Hu et al. combine cDNA normalization before library preparation with a software tool to increase the capture of RNA isoform species in single-molecule RNA sequencing. They demonstrate that this approach can detect previously unknown transcripts in gastric signet-ring cell carcinomas that are not present in non-malignant tissue.

Advances in RNAi-Assisted Strain Engineering in Saccharomyces cerevisiae

Saccharomyces cerevisiae is a widely used eukaryotic model and microbial cell factory. RNA interference (RNAi) is a conserved regulatory mechanism among eukaryotes but absent from S. cerevisiae. Recent reconstitution of RNAi machinery in S. cerevisiae enables the use of this powerful tool for strain engineering. Here we first discuss the introduction of heterologous RNAi pathways in S. cerevisiae, and the design of various expression cassettes of RNAi precursor reagents for tunable, dynamic, and genome-wide regulation. We then summarize notable examples of RNAi-assisted functional genomics and metabolic engineering studies in S. cerevisiae. We conclude with the future challenges and opportunities of RNAi-based approaches, as well as the potential of other regulatory RNAs in advancing yeast engineering.

Ancestral Reconstruction of Karyotypes Reveals an Exceptional Rate of Nonrandom Chromosomal Evolution in Sunflower

Mapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here, we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package syntR. The syntR algorithm performs as well as previous ad hoc methods while being systematic, repeatable, and applicable to mapping chromosomal rearrangements in any group of species. In addition, we present a systematic survey of chromosomal rearrangements in the annual sunflowers, which is a group known for extreme karyotypic diversity. We build high-density genetic maps for two subspecies of the prairie sunflower, Helianthus petiolaris ssp. petiolaris and H. petiolaris ssp. fallax Using syntR, we identify blocks of synteny between these two subspecies and previously published high-density genetic maps. We reconstruct ancestral karyotypes for annual sunflowers using those synteny blocks and conservatively estimate that there have been 7.9 chromosomal rearrangements per million years, a high rate of chromosomal evolution. Although the rate of inversion is even higher than the rate of translocation in this group, we further find that every extant karyotype is distinguished by between one and three translocations involving only 8 of the 17 chromosomes. This nonrandom exchange suggests that specific chromosomes are prone to translocation and may thus contribute disproportionately to widespread hybrid sterility in sunflowers. These data deepen our understanding of chromosome evolution and confirm that Helianthus has an exceptional rate of chromosomal rearrangement that may facilitate similarly rapid diversification.

Continent-wide population genomic structure and phylogeography of North America's most destructive conifer defoliator, the spruce budworm (Choristoneura fumiferana)

The spruce budworm, Choristoneura fumiferana, is presumed to be panmictic across vast regions of North America. We examined the extent of panmixia by genotyping 3,650 single nucleotide polymorphism (SNP) loci in 1975 individuals from 128 collections across the continent. We found three spatially structured subpopulations: Western (Alaska, Yukon), Central (southeastern Yukon to the Manitoba-Ontario border), and Eastern (Manitoba-Ontario border to the Atlantic). Additionally, the most diagnostic genetic differentiation between the Central and Eastern subpopulations was chromosomally restricted to a single block of SNPs that may constitute an island of differentiation within the species. Geographic differentiation in the spruce budworm parallels that of its principal larval host, white spruce (Picea glauca), providing evidence that spruce budworm and spruce trees survived in the Beringian refugium through the Last Glacial Maximum and that at least two isolated spruce budworm populations diverged with spruce/fir south of the ice sheets. Gene flow in the spruce budworm may also be affected by mountains in western North America, habitat isolation in West Virginia, regional adaptations, factors related to dispersal, and proximity of other species in the spruce budworm species complex. The central and eastern geographic regions contain individuals that assign to Eastern and Central subpopulations, respectively, indicating that these barriers are not complete. Our discovery of previously undetected geographic and genomic structure in the spruce budworm suggests that further population modelling of this ecologically important insect should consider regional differentiation, potentially co-adapted blocks of genes, and gene flow between subpopulations.

Proteomic and Transcriptomic Changes in Hibernating Grizzly Bears Reveal Metabolic and Signaling Pathways that Protect against Muscle Atrophy

Muscle atrophy is a physiological response to disuse and malnutrition, but hibernating bears are largely resistant to this phenomenon. Unlike other mammals, they efficiently reabsorb amino acids from urine, periodically activate muscle contraction, and their adipocytes differentially responds to insulin. The contribution of myocytes to the reduced atrophy remains largely unknown. Here we show how metabolism and atrophy signaling are regulated in skeletal muscle of hibernating grizzly bear. Metabolic modeling of proteomic changes suggests an autonomous increase of non-essential amino acids (NEAA) in muscle and treatment of differentiated myoblasts with NEAA is sufficient to induce hypertrophy. Our comparison of gene expression in hibernation versus muscle atrophy identified several genes differentially regulated during hibernation, including Pdk4 and Serpinf1. Their trophic effects extend to myoblasts from non-hibernating species (including C. elegans), as documented by a knockdown approach. Together, these changes reflect evolutionary favored adaptations that, once translated to the clinics, could help improve atrophy treatment.

Temporal variation in spatial genetic structure during population outbreaks: Distinguishing among different potential drivers of spatial synchrony

Spatial synchrony is a common characteristic of spatio-temporal population dynamics across many taxa. While it is known that both dispersal and spatially autocorrelated environmental variation (i.e., the Moran effect) can synchronize populations, the relative contributions of each, and how they interact, are generally unknown. Distinguishing these mechanisms and their effects on synchrony can help us to better understand spatial population dynamics, design conservation and management strategies, and predict climate change impacts. Population genetic data can be used to tease apart these two processes as the spatio-temporal genetic patterns they create are expected to be different. A challenge, however, is that genetic data are often collected at a single point in time, which may introduce context-specific bias. Spatio-temporal sampling strategies can be used to reduce bias and to improve our characterization of the drivers of spatial synchrony. Using spatio-temporal analyses of genotypic data, our objective was to identify the relative support for these two mechanisms to the spatial synchrony in population dynamics of the irruptive forest insect pest, the spruce budworm (Choristoneura fumiferana), in Quebec (Canada). AMOVA, cluster analysis, isolation by distance, and sPCA were used to characterize spatio-temporal genomic variation using 1,370 SBW larvae sampled over four years (2012-2015) and genotyped at 3,562 SNP loci. We found evidence of overall weak spatial genetic structure that decreased from 2012 to 2015 and a genetic diversity homogenization among the sites. We also found genetic evidence of a long-distance dispersal event over >140 km. These results indicate that dispersal is the key mechanism involved in driving population synchrony of the outbreak. Early intervention management strategies that aim to control source populations have the potential to be effective through limiting dispersal. However, the timing of such interventions relative to outbreak progression is likely to influence their probability of success.

Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus

Gene annotation is a critical resource in genomics research. Many computational approaches have been developed to assemble transcriptomes based on high-throughput short-read sequencing, however, only with limited accuracy. Here, we combine next-generation and third-generation sequencing to reconstruct a full-length transcriptome in the rat hippocampus, which is further validated using independent 5´ and 3´-end profiling approaches. In total, we detect 28,268 full-length transcripts (FLTs), covering 6,380 RefSeq genes and 849 unannotated loci. Based on these FLTs, we discover co-occurring alternative RNA processing events. Integrating with polysome profiling and ribosome footprinting data, we predict isoform-specific translational status and reconstruct an open reading frame (ORF)-eome. Notably, a high proportion of the predicted ORFs are validated by mass spectrometry-based proteomics. Moreover, we identify isoforms with subcellular localization pattern in neurons. Collectively, our data advance our knowledge of RNA and protein isoform diversity in the rat brain and provide a rich resource for functional studies.

It is challenging to characterize diverse transcript isoforms by short-read sequencing. Here the authors report full-length transcriptomes in rat hippocampus by hybrid-sequencing, predict isoform-specific translational status, and reconstruct open reading frames validated by mass spectrometry.

A streamlined and predominantly diploid genome in the tiny marine green alga Chloropicon primus

Tiny marine green algae issued from two deep branches of the Chlorophyta, the Mamiellophyceae and Chloropicophyceae, dominate different regions of the oceans and play key roles in planktonic communities. Considering that the Mamiellophyceae is the sole lineage of prasinophyte algae that has been intensively investigated, the extent to which these two algal groups differ in their metabolic capacities and cellular processes is currently unknown. To address this gap of knowledge, we investigate here the nuclear genome sequence of a member of the Chloropicophyceae, Chloropicon primus. Among the main biological insights that emerge from this 17.4 Mb genome, we find an unexpected diploid structure for most chromosomes and a propionate detoxification pathway in green algae. Our results support the notion that separate events of genome minimization, which entailed differential losses of genes/pathways, have occurred in the Chloropicophyceae and Mamiellophyceae, suggesting different strategies of adaptation to oceanic environments.

The Impact of cDNA Normalization on Long-Read Sequencing of a Complex Transcriptome

Normalization of cDNA is widely used to improve the coverage of rare transcripts in analysis of transcriptomes employing next-generation sequencing. Recently, long-read technology has been emerging as a powerful tool for sequencing and construction of transcriptomes, especially for complex genomes containing highly similar transcripts and transcript-spliced isoforms. Here, we analyzed the transcriptome of sugarcane, a highly polyploidy plant genome, by PacBio isoform sequencing (Iso-Seq) of two different cDNA library preparations, with and without a normalization step. The results demonstrated that, while the two libraries included many of the same transcripts, many longer transcripts were removed, and many new generally shorter transcripts were detected by normalization. For the same input cDNA and data yield, the normalized library recovered more total transcript isoforms and number of predicted gene families and orthologous groups, resulting in a higher representation for the sugarcane transcriptome, compared to the non-normalized library. The non-normalized library, on the other hand, included a wider transcript length range with more longer transcripts above ∼1.25 kb and more transcript isoforms per gene family and gene ontology terms per transcript. A large proportion of the unique transcripts comprising ∼52% of the normalized library were expressed at a lower level than the unique transcripts from the non-normalized library, across three tissue types tested including leaf, stalk, and root. About 83% of the total 5,348 predicted long noncoding transcripts was derived from the normalized library, of which ∼80% was derived from the lowly expressed fraction. Functional annotation of the unique transcripts suggested that each library enriched different functional transcript fractions. This demonstrated the complementation of the two approaches in obtaining a complete transcriptome of a complex genome at the sequencing depth used in this study.

Genetic Diversity and Phylogenetic Relationships of Annual and Perennial Glycine Species

We have estimated the average genetic diversity of two Glycine annual and six perennial species based upon 76 orthologous gene sets and performed phylogenetic analysis, divergence analysis and tests for departure from neutrality of the eight species using 52 orthologous gene sets. In addition, 367 orthologous gene sets were used to estimate the relationships of 11 G. canescens accessions. Among the perennials, G. canescens showed the highest nucleotide diversity. The other perennials, except for G. tomentella, had higher nucleotide diversity than the two annuals. Phylogenetic analysis of the Glycine showed a similar genome grouping with the previous report except for G. cyrtoloba and G. stenophita which formed a sister clade in the study. Divergence analysis supported the phylogenetic relationships that G. falcata was the most divergent from G. max, followed by G. cyrtoloba, G. syndetika, G. tomentella D3, G. stenophita and G. canescens. Most genic sequences were homogeneous in the levels of polymorphism and divergence between G. max and other Glycine species based on the HKA test, thus, Glycine perennials may have experienced a very similar evolution as inferred by trans-specific mutation analysis. The greater genetic diversity of most perennial Glycine species and their origins from the warmer and drier climates of Australia suggests the perennials maybe a potential source of heat and drought resistance that will be of value in the face of climate change.

Electrochemical-based biosensors for microRNA detection: Nanotechnology comes into view

Nanotechnology plays an undeniable significant role in medical sciences, particularly in the field of biomedicine. Development of several diagnostic procedures in medicine has been possible through the beneficial application of nano-materials, among which electrochemical nano-biosensors can be mentioned. They can be employed to quantify various clinical biomarkers in detection, evaluation, and follow up stages of the illnesses. MicroRNAs, a group of regulatory short RNA fragments, added a new dimension to the management and diagnosis of several diseases. Mature miRNAs are single-stranded RNA molecules approximately 22 nucleotides in length, which regulate a vast range of biological functions from cellular proliferation and death to cancer development and progression. Recently, diagnostic value of miRNAs in various diseases has been demonstrated. There are many traditional methods for detection of miRNAs including northern blotting, quantitative real time PCR (qRT-PCR), microarray technology, nanotechnology-based approaches, and molecular biology tools including miRNA biosensors. In comparison with other techniques, electrochemical nucleic acid biosensor methods exhibit many interesting features, and could play an important role in the future nucleic acid analysis. This review paper provides an overview of some different types of nanotechnology-based biosensors for detection of miRNAs.

Dicyemida and Orthonectida: Two Stories of Body Plan Simplification

Two enigmatic groups of morphologically simple parasites of invertebrates, the Dicyemida (syn. Rhombozoa) and the Orthonectida, since the 19th century have been usually considered as two classes of the phylum Mesozoa. Early molecular evidence suggested their relationship within the Spiralia (=Lophotrochozoa), however, high rates of dicyemid and orthonectid sequence evolution led to contradicting phylogeny reconstructions. Genomic data for orthonectids revealed that they are highly simplified spiralians and possess a reduced set of genes involved in metazoan development and body patterning. Acquiring genomic data for dicyemids, however, remains a challenge due to complex genome rearrangements including chromatin diminution and generation of extrachromosomal circular DNAs, which are reported to occur during the development of somatic cells. We performed genomic sequencing of one species of Dicyema, and obtained transcriptomic data for two Dicyema spp. Homeodomain (homeobox) transcription factors, G-protein-coupled receptors, and many other protein families have undergone a massive reduction in dicyemids compared to other animals. There is also apparent reduction of the bilaterian gene complements encoding components of the neuromuscular systems. We constructed and analyzed a large dataset of predicted orthologous proteins from three species of Dicyema and a set of spiralian animals including the newly sequenced genome of the orthonectid Intoshia linei. Bayesian analyses recovered the orthonectid lineage within the Annelida. In contrast, dicyemids form a separate clade with weak affinity to the Rouphozoa (Platyhelminthes plus Gastrotricha) or (Entoprocta plus Cycliophora) suggesting that the historically proposed Mesozoa is a polyphyletic taxon. Thus, dramatic simplification of body plans in dicyemids and orthonectids, as well as their intricate life cycles that combine metagenesis and heterogony, evolved independently in these two lineages.

Molecular evolution and functional characterisation of insulin related peptides in molluscs: Contributions of Crassostrea gigas genomic and transcriptomic-wide screening

Insulin Related Peptides (IRPs) belong to the insulin superfamily and possess a typical structure with two chains, B and A, linked by disulphide bonds. As the sequence conservation is usually low between members, IRPs are classified according to the number and position of their disulphide bonds. In molluscan species, the first IRPs identified, named Molluscan Insulin-related Peptides (MIPs), exhibit four disulphide bonds. The genomic and transcriptomic data screening in the Pacific oyster Crassostrea gigas (Mollusc, Bivalvia) allowed us to identify six IRP sequences belonging to three structural groups. Cg-MIP1 to 4 have the typical structure of MIPs with four disulphide bonds. Cg-ILP has three disulphide bonds like vertebrate Insulin-Like Peptides (ILPs). The last one, Cg-MILP7 has a significant homology with Drosophila ILP7 (DILP7) associated with two additional cysteines allowing the formation of a fourth disulphide bond. The phylogenetic analysis points out that ILPs may be the most ancestral form. Moreover, it appears that ILP7 orthologs are probably anterior to lophotrochozoa and ecdysozoa segregation. In order to investigate the diversity of physiological functions of the oyster IRPs, we combine in silico expression data, qPCR measurements and in situ hybridization. The Cg-ilp transcript, mainly detected in the digestive gland and in the gonadal area, is potentially involved in the control of digestion and gametogenesis. The expression of Cg-mip4 is mainly associated with the larval development. The Cg-mip transcript shared by the Cg-MIP1, 2 and 3, is mainly expressed in visceral ganglia but its expression was also observed in the gonads of mature males. This pattern suggested the key roles of IRPs in the control of sexual reproduction in molluscan species.

Molecular mechanisms of fission in echinoderms: Transcriptome analysis

Echinoderms are capable of asexual reproduction by fission. An individual divides into parts due to changes in the strength of connective tissue of the body wall. The structure of connective tissue and the mechanisms of variations in its strength in echinoderms remain poorly studied. An analysis of transcriptomes of individuals during the process of fission provides a new opportunity to understand the mechanisms of connective tissue mutability. In the holothurian Cladolabes schmeltzii, we have found a rather complex organization of connective tissue. Transcripts of genes encoding a wide range of structural proteins of extracellular matrix, as well as various proteases and their inhibitors, have been discovered. All these molecules may constitute a part of the mechanism of connective tissue mutability. According to our data, the extracellular matrix of echinoderms is substantially distinguished from that of vertebrates by the lack of elastin, fibronectins, and tenascins. In case of fission, a large number of genes of transcription factors and components of different signaling pathways are expressed. Products of these genes are probably involved in regulation of asexual reproduction, connective tissue mutability, and preparation of tissues for subsequent regeneration. It has been shown that holothurian tensilins are a special group of tissue inhibitors of metalloproteinases, which has formed within the class Holothuroidea and is absent from other echinoderms. Our data can serve a basis for the further study of the mechanisms of extracellular matrix mutability, as well as the mechanisms responsible for asexual reproduction in echinoderms.

Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction

All sequencing experiments and most functional genomics screens rely on the generation of libraries to comprehensively capture pools of targeted sequences. In the past decade especially, driven by the progress in the field of massively parallel sequencing, numerous studies have comprehensively assessed the impact of particular manipulations on library complexity and quality, and characterized the activities and specificities of several key enzymes used in library construction. Fortunately, careful protocol design and reagent choice can substantially mitigate many of these biases, and enable reliable representation of sequences in libraries. This review aims to guide the reader through the vast expanse of literature on the subject to promote informed library generation, independent of the application.