Evolutionary Connection Research Articles

Identification of nuclear pore complexes (NPCs) and revealed outer-ring component BnHOS1 related to cold tolerance in B. napus

Nuclear pore complexes (NPCs) consist of ~30 different nucleoporins (Nups), are the unique channels that govern development, hormonal response, and roles in both biotic and abiotic responses, as well as the transport and information exchange of biomacromolecules between nucleoplasms. Here, we report the comprehensive identification of 77 BnNups throughout the zhongshuang11 (ZS11) genome, which were classified into 29 distinct categories based on their evolutionary connections. We compared and contrasted different BnNups by analyzing at their gene structures, protein domains, putative three-dimensional (3D) models and expression patterns. Additional examples of genome-wide duplication events and cross-species synteny are provided to demonstrate the proliferation and evolutionary conservation of BnNups. When BnHOS1 was modified using CRISPR/Cas9 technology, the resulting L10 and L28 lines exhibited substantial freezing resistance. This not only demonstrated the negative regulatory impact of BnHOS1 on cold stress, but also offered a promising candidate gene for cold tolerance breeding and augmented the available B. napus material. These findings not only help us learn more about the composition and function of BnNPCs in B. napus, but they also provide light on how NPCs in other eukaryotic organism functions.

Characterizing non-thermal equilibrium contact binaries

ABSTRACT Formation and evolution of marginal contact binaries with larger temperature difference between their two components remain inexplicable to date. To get a better understanding of the nature of such population we investigate on an individual, NSVS 7358116, by analysing observational data obtained from ground-based and space-based telescopes. It is found that NSVS 7358116 is a marginal contact totally eclipsing binary with a small fill-out factor by 3 per cent but large temperature difference by 2000 K or t-ratio by 0.3. This suggests that its two components are in poor thermal contact. By collecting all available targets in literature, we compiled a table of 80 non-thermal equilibrium contact binaries (nTCBs) including 39 STRONG t-ratio samples and 41 WEAK t-ratio samples. We performed statistical distribution analysis on physical parameters which reveals that STRONG t-ratio samples will evolve to WEAK t-ratio samples through heat and mass transfer along with angular momentum loss, meanwhile thickening their common envelop. This current investigation is acted as only an appetizer, because more exploration on nTCBs and its evolutionary connection with related populations will follow.

Rapid growth preceded gigantism in sauropodomorph evolution

Sauropod dinosaurs include the largest land animals to have walked the earth, mostly weighing 10-70 tons (e.g., Sander etal.1 and Carballido etal.2). Osteohistology suggests that derived physiological traits evolved near the origin of sauropod gigantism, including both rapid and uninterrupted growth from juvenile to adult with little developmental plasticity.1,3,4 This differs from the slower, seasonally interrupted growth of their direct ancestors, as evident in most non-sauropodan sauropodomorphs, which also show developmental plasticity in some groups. Accelerated but seasonally interrupted growth is present in Lessemsauridae, the sister clade to Sauropoda, which also attained giant adult body sizes (>10 tons).5 These observations suggest a correlation between giant size and accelerated growth. However, testing this evolutionary connection has been limited by the incomplete understanding of the growth patterns in some of the closest non-giant relatives of sauropods. We present the osteohistology of two such taxa, Aardonyx celestae and Sefapanosaurus zatronensis. Both exhibit highly vascularized woven-parallel complexes, with fibrolamellar complexes during early to mid-ontogeny, containing regular growth marks. These observations provide strong evidence for rapid but seasonally interrupted growth with limited developmental plasticity (indicated by the regular spacing of growth marks). Combined with our review of early branching sauropodomorph osteohistology, these results show that highly accelerated growth rates originated among smaller, non-sauropodan sauropodomorphs weighing 1 to 2 tons but preceded the origins of giant size (>10 tons). Therefore, the capacity for rapid bone tissue formation, a derived aspect of rapid growth seen in sauropods, did not evolve specifically to enable giant body sizes but may have been a prerequisite for them.

Parkinson’s disease, dopaminergic drugs and the plant world

A large proportion of drugs used for the treatment of neurological disorders relate to naturally occurring compounds, many of which are plant alkaloids. This is particularly true of Parkinson’s disease (PD). The pharmacopoeia of PD has strong botanical origins, while major discoveries about the neurochemistry of the basal ganglia came from the study of phytochemicals. This article narrates the development of pharmacotherapy for PD in terms of historically important plant-derived substances—tropane and hamala alkaloids, reserpine, levodopa, apomorphine, and ergoline dopamine receptor agonists. Alkaloids are nitrogen-containing secondary metabolic products that tend to be biologically active. They appear to be involved in plants’ adaptation to herbivorous animals, though their exact purpose and the ways in which they work are uncertain. A sizable group of alkaloids influence animal dopaminergic systems, highlighting a key biological relationship. While animals must acquire the energy that plants harness, plants need to engage with the animal attribute that they lack—movement—in order to maximize their reproductive fitness. Neuroactive flowering plant compounds have been interacting with vertebrate and invertebrate motor systems for 100 million years. A deep evolutionary connection helps to explain why the pharmacological treatment of PD is imprinted with the power of these mysterious botanical chemicals.

Galactic Chemical Evolution of Exoplanet Hosting Stars: Are High-mass Planetary Systems Young?

The imprints of stellar nucleosynthesis and chemical evolution of the galaxy can be seen in different stellar populations, with older generation stars showing higher α-element abundances and the later generations becoming enriched with iron-peak elements. The evolutionary connections and chemical characteristics of circumstellar disks, stars, and their planetary companions can be inferred by studying the interdependence of planetary and host star properties. Numerous studies in the past have confirmed that high-mass giant planets are commonly found around metal-rich stars, while the stellar hosts of low-mass planets have a wide range of metallicity. In this work, we analyzed the detailed chemical abundances for a sample of >900 exoplanet hosting stars drawn from different radial velocity and transit surveys. We correlate the stellar abundance trends for α- and iron-peak elements with the planets’ mass. We find the planet mass–abundance correlation to be primarily negative for α-elements and marginally positive or zero for the iron-peak elements, indicating that stars hosting giant planets are relatively younger. This is further validated by the age of the host stars obtained from isochrone fitting. The later enrichment of protoplanetary material with iron and iron-peak elements is also consistent with the formation of the giant planets via the core accretion process. A higher metal fraction in the protoplanetary disk is conducive to rapid core growth, thus providing a plausible route for the formation of giant planets. This study, therefore, indicates that the observed trends in stellar abundances and planet mass are most likely a natural consequence of Galactic chemical evolution.

Genome-Wide Classification and Evolutionary Analysis Reveal Diverged Patterns of Chalcone Isomerase in Plants

Flavonoids as a class of important secondary metabolites are widely present in land plants, and chalcone isomerase (CHI) is the key rate-limiting enzyme that participates in catalyzing the stereospecific isomerization of chalcones to yield their corresponding flavanones. However, the phylogenetic dynamics and functional divergence of CHI family genes during the evolutionary path of green plants remains poorly understood. Here, a total of 122 CHI genes were identified by performing a genome-wide survey of 15 representative green plants from the most ancestral basal plant chlorophyte algae to higher angiosperm plants. Phylogenetic, orthologous groups (OG) classification, and genome structure analysis showed that the CHI family genes have evolved into four distinct types (types I–IV) containing eight OGs after gene duplication, and further studies indicated type III CHIs consist of three subfamilies (FAP1, FAP2, and FAP3). The phylogeny showed FAP3 CHIs as an ancestral out-group positioned on the outer layers of the main branch, followed by type IV CHIs, which are placed in an evolutionary intermediate between FAP3 CHIs and bona fide CHIs (including type I and type II). The results imply a potential intrinsic evolutionary connection between CHIs existing in the green plants. The amino acid substitutions occurring in several residues have potentially affected the functional divergence between CHI proteins. This is supported by the analysis of transcriptional divergence and cis-acting element analysis. Evolutionary dynamics analyses revealed that the differences in the total number of CHI family genes in each plant are primarily attributed to the lineage-specific expansion by natural selective forces. The current studies provide a deeper understanding of the phylogenetic relationships and functional diversification of CHI family genes in green plants, which will guide further investigation on molecular characteristics and biological functions of CHIs.

Predicting Cancerous Genes through an In-Silico Approach

Abstract: In Sequence alignment, the chains of DNA, RNA, or protein are aligned and compared to recognize homogeneous portions which could be the result of functional, organizational, or evolutionary connections between the chains. This process gives similar sequences as its result. Similar sequences often have the same biological function. This knowledge can be used to draw further conclusions that we can ascertain the function of a query DNA sequence by comparing it with a target sequence performing a known function. In this article, we use this idea to develop an Advanced Java-based web application where the user interface allows the user to enter an unknown DNA sequence. Using pattern-matching algorithms, the application can calculate how similar the sequence is with genes stored in a database. Based on the result, a trained medical practitioner will be able to determine whether the unknown gene can be cancerous

Archaeal bundling pili of Pyrobaculum calidifontis reveal similarities between archaeal and bacterial biofilms

While biofilms formed by bacteria have received great attention due to their importance in pathogenesis, much less research has been focused on the biofilms formed by archaea. It has been known that extracellular filaments in archaea, such as type IV pili, hami, and cannulae, play a part in the formation of archaeal biofilms. We have used cryo-electron microscopy to determine the atomic structure of a previously uncharacterized class of archaeal surface filaments from hyperthermophilic Pyrobaculum calidifontis. These filaments, which we call archaeal bundling pili (ABP), assemble into highly ordered bipolar bundles. The bipolar nature of these bundles most likely arises from the association of filaments from at least two different cells. The component protein, AbpA, shows homology, both at the sequence and structural level, to the bacterial protein TasA, a major component of the extracellular matrix in bacterial biofilms, contributing to biofilm stability. We show that AbpA forms very stable filaments in a manner similar to the donor-strand exchange of bacterial TasA fibers and chaperone-usher pathway pili where a β-strand from one subunit is incorporated into a β-sheet of the next subunit. Our results reveal likely mechanistic similarities and evolutionary connection between bacterial and archaeal biofilms, and suggest that there could be many other archaeal surface filaments that are as yet uncharacterized.

Metastasis model of tumor deposit in colorectal cancer based on phylogenetic tree.

e15549 Background: Colorectal cancer(CRC) is often accompanied by tumor deposit(TD) metastasis, and TD status was only adressed in N1c staging in the TNM staging for CRC. However, TD states are very complex and diverse, including quantity, morphology, and biological behavior. The correlation between TD and clinical prognosis is far more complicated and needs to be discussed in more dimensions. At present, there are no reports of TD research from the genetic perspective. In this study, the phylogenetic tree approach was used to explore the metastasis pattern of TD, which might lay a foundation for better understanding its clinical significance. Methods: Poly-G was used to sequence multiple sections (n = 427) of normal tissue, primary tumor, TD, positive lymph node, and distant metastasis from 25 patients. Then, using the poly-G genotype to calculated the genetic distance between tumor and normal tissue and built the phylogenetic tree. We use root diversity score (RDS) index to reflect the intratumor heterogeneity of TDs. The evolutionary connection and clone origin between TD and paired samples was evaluated using a phylogenetic tree and RDS index. Results: A total of 427 samples from 25 patients were included, including 171 primary tumor (40.0%), 94 positive lymph nodes (22.0%), 110 tumor deposits (25.8%), 28 liver metastases (6.6%), 4 lung metastases (0.9%), and 20 peritoneal metastases (4.7%). There were 43 (39.1%) TDs with envelope and 67 (60.9%) TDs with irregular morphology, according to pathological morphology. A phylogenetic tree based on migration patterns and clonal origins was used to highlight the differences between envelope-TDs and irregular-TDs. The genetic distance between envelope-TDs and positive lymph nodes appeared to be less, and they were more likely to derive from the same source, but the genetic distance between irregular-TDs and positive lymph nodes was larger (P < 0.05). Envelope-TDs had a sequential metastatic model that was consistent with positive lymph nodes. Unlike envelope-TDs, irregular-TDs tend to show more complex biological characteristics, such as nerve and vascular invasion, resulting in a more convoluted evolutionary relationship in the phylogenetic tree. Conclusions: Our findings provide genetic evidence for TD metastatic model, which has to be supported in future studies to ameliorate CRC TNM staging.

Flavonoid Profiles and Antioxidant Potential of Monochoria angustifolia (G. X. Wang) Boonkerd & Tungmunnithum, a New Species from the Genus Monochoria C. Presl.

Plants of the genus Monochoria have long been utilized in food, cosmetics, and traditional herbal treatments. Thailand has the highest species diversity of this genus and a new member, Monochoria angustifolia (G. X. Wang) Boonkerd & Tungmunnithum has been recently described. This plant is called “Siam Violet Pearl” as a common name or “Khimuk Si Muang Haeng Siam” as its vernacular name with the same meaning in the Thai language. Despite their importance, little research on Monochoria species has been conducted. This study, thus, provides the results to fill in this gap by: (i) determining flavonoid phytochemical profiles of 25 natural populations of M. angustifolia covering the whole floristic regions in Thailand, and (ii) determining antioxidant activity using various antioxidant assays to investigate probable mechanisms. The results revealed that M. angustifolia presents a higher flavonoid content than the outgroup, M. hastata. Our results also revealed that flavonoids might be used to investigate Monochoria evolutionary connections and for botanical authentication. The various antioxidant assays revealed that M. angustifolia extracts preferentially act through a hydrogen atom transfer antioxidant mechanism. Pearson correlation analysis indicated significant correlations, emphasizing that the antioxidant capacity is most probably due to the complex action of several phytochemicals rather than that of a single molecule. Together, these results showed that this new species provide an attractive alternative starting material with phytochemical variety and antioxidant potential for the phytopharmaceutical industry.

Radial velocity variability and the evolution of hot subdwarf stars

Hot subdwarf stars represent a late and peculiar stage in the evolution of low-mass stars, since they are likely formed by close binary interactions. In this work, we perform a radial velocity (RV) variability study of a sample of 646 hot subdwarfs with multi-epoch radial velocities based on spectra from Sloan Digital Sky Survey (SDSS) and Large Sky Area Multi-Object Fibre Spectroscopic Telescope (LAMOST). The atmospheric parameters and RVs were taken from the literature. For stars with archival spectra but without literature values, we determined the parameters by fitting model atmospheres. In addition, we redetermined the atmospheric parameters and RVs for all the He-enriched sdO/Bs. This broad sample allowed us to study RV-variability as a function of the location in the Teff − log g- and Teff − log n(He)/n(H) diagrams in a statistically significant way. We used the fraction of RV-variable stars and the distribution of the maximum RV variations ΔRVmax as diagnostics. Both indicators turned out to be quite inhomogeneous across the studied parameter ranges. A striking feature is the completely dissimilar behaviour of He-poor and He-rich hot subdwarfs. While the former have a high fraction of close binaries, almost no significant RV variations could be detected for the latter. This has led us to the conclusion that there is likely no evolutionary connection between these subtypes. On the other hand, intermediate He-rich- and extreme He-rich sdOB/Os are more likely to be related. Furthermore, we conclude that the vast majority of this population is formed via one or several binary merger channels. Hot subdwarfs with temperatures cooler than ∼24 000 K tend to show fewer and smaller RV-variations. These objects might constitute a new subpopulation of binaries with longer periods and late-type or compact companions. The RV-variability properties of the extreme horizontal branch (EHB) and corresponding post-EHB populations of the He-poor hot subdwarfs match and confirm the predicted evolutionary connection between them. Stars found below the canonical EHB at somewhat higher surface gravities show large RV variations and a high RV variability fraction. These properties are consistent with most of them being low-mass EHB stars or progenitors of low-mass helium white dwarfs in close binaries.

The first complete mitochondrial genomes for Serranus papilionaceus and Serranus scriba, and their phylogenetic position within Serranidae.

Butterfly-winged comber, Serranus papilionaceus Valenciennes, 1832, was recently resurrected and so it is no longer considered as a junior synonym of the Painted comber, Serranus scriba (Linneus, 1758). This calls for a more comprehensive phylogenetic assessment using mitochondria DNA genomes to better understand the relationship and delineate these two species. Next-generation Sequencing was applied to sequence the genome of these two Serranus species. The data generated was then used to construct the mitochondrial genome of these two species. This produced the first complete mitochondrial genomes for the genus Serranus here represented by Serranus papilionaceus and Serranus scriba. These two mitochondrial genomes are 16,514bp and 16,512bp respectively, and both contained the typical 37 genes found in vertebrates (13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs), together with the OL and the control region. These mitochondrial genomes provide a new insight into the phylogenetic and evolutionary connections between the various subfamilies within Serranidae, while providing new molecular data that can be applied to discriminate between the studied species.

Evolution, characterization, and expression profile of Egl-9 family hypoxia-inducible factor (egln) in rainbow trout (Oncorhynchus mykiss) under hypoxia stress

Egl-9 family hypoxia-inducible factor (egln), an oxygen-sensing enzyme family, has been thoroughly characterized in mammals and certain fishes, but there is few research on its involvement in reproductive development and hypoxic stress in rainbow trout. In this study, we investigated the gene structure, physicochemical properties, and evolutionary connection of the egln gene family. The expression profile of egln gene family and their regulatory mechanism were explored using bioinformatics analysis and hypoxia treatment experiments. Five egln genes were discovered in the rainbow trout genome in this investigation (egln1, egln2a, egln2b, egln3a, and egln3b). Domain prediction revealed that all egln proteins have p4hc conserved domains, and phylogenetic analysis revealed that rainbow trout egln2 and egln3 were closely related to Atlantic salmon. The results of real-time quantitative PCR (RT-qPCR) showed that egln genes were generally expressed in all detected tissues, and higher in the ovary, testis, and brain in normoxia. Under hypoxia, the expression level of eglns was significantly down-regulated in most tissues except the liver. Our research contributes to future research on the functional properties of egln genes, as well as the evolution of teleosts and the impact of hypoxia on biological immunity.

Back to the roots, Part 1—early life cycle data of Rhopaliophora (Scyphozoa, Cubozoa and Staurozoa)

The phylogeny of the Rhopaliophora (Scyphozoa, Cubozoa and Staurozoa) has been discussed and modified extensively up to the present day. Attempting to finally solve this question, the morphology and development of the different early life history stages stages of 17 scyphozoan, 2 staurozoan and 8 cubozoan species were investigated. Due to the magnitude of the study, the findings will be published in two parts. This first part will focus on the comparison of early life cycle stages, the second part (to be published in the following issue of Plankton & Benthos Research) will focus on the evolutionary connection and systematics. The present part of the study focused on the morphology of different types of sessile stages (polyps), the processes of strobilation and metamorphosis, and the resulting products (residues and ephyrae/young medusa) and their further development. The different morphological characters in the polyps helped to categorize them into types. By using the strobilation rates and information on the way morphological characters changed during the process of strobilation/metamorphosis, the strobilae were able to be separately categorized.

Identification and molecular analysis of the annexin genes in Cyamopsis tetragonoloba L

Annexins are a family of multigene proteins involved in plant development and stress responses. In the current study, the guar transcriptome database yielded a total of five annexin unigenes (named AnnCt1-AnnCt5). The predicted molecular weight of detected AnnCts was estimated to be between 35.22 and 37.03 kDa, with theoretical pIs ranging from 5.97 to 9.15. AnnCts have four annexin repeats that contain endonexin domains with Ca2+-binding sites with 24.44 to 71.74% of amino acid similarity among each other. The coding sequences (CDS) of two of the five guar annexins (AnnCt1 and AnnCt5) were completely cloned and were similar to the ones retrieved. AnnCts were divided into four groups based on their phylogenetic study, indicating evolutionary connections with higher plant annexins and a close relationship with Glycine max. Predominant expression of AnnCt1 followed by AnnCt2 and AnnCt5 were observed more in green organs such mature leaves, shoots, and developing seeds (30DAF) indicated their significant roles. AnnCts genes have respond to drought, salt, cold, and abscisic acid (ABA) treatments showing possible roles in ABA-dependent or independent stress signaling pathways. In-silico analysis of soybean annexin (evolutionary close to guar annexin) predicted interactions with proteins that are possibly involve in organogenesis, transportation, and transcription regulation. The purified rAnnCt1 protein has shown DPPH (2,2-diphenyl-1-picryl-hydrazyl-hydrate) radical scavenging activity in-vitro. Our findings show that AnnCts are often guar annexins, that may play critical roles in different guar organs as well as contribute to stress tolerance and, its purified rAnnCt1 protein has antioxidant activity.

Of vascular defense, hemostasis, cancer, and platelet biology: an evolutionary perspective.

We have established considerable expertise in studying the role of platelets in cancer biology. From this expertise, we were keen to recognize the numerous venous-, arterial-, microvascular-, and macrovascular thrombotic events and immunologic disorders are caused by severe, acute-respiratory-syndrome coronavirus 2 (SARS-CoV-2) infections. With this offering, we explore the evolutionary connections that place platelets at the center of hemostasis, immunity, and adaptive phylogeny. Coevolutionary changes have also occurred in vertebrate viruses and their vertebrate hosts that reflect their respective evolutionary interactions. As mammals adapted from aquatic to terrestrial life and the heavy blood loss associated with placentalization-based live birth, platelets evolved phylogenetically from thrombocytes toward higher megakaryocyte-blebbing-based production rates and the lack of nuclei. With no nuclei and robust RNA synthesis, this adaptation may have influenced viral replication to become less efficient after virus particles are engulfed. Human platelets express numerous receptors that bind viral particles, which developed from archetypal origins to initiate aggregation and exocytic-release of thrombo-, immuno-, angiogenic-, growth-, and repair-stimulatory granule contents. Whether by direct, evolutionary, selective pressure, or not, these responses may help to contain virus spread, attract immune cells for eradication, and stimulate angiogenesis, growth, and wound repair after viral damage. Because mammalian and marsupial platelets became smaller and more plate-like their biophysical properties improved in function, which facilitated distribution near vessel walls in fluid-shear fields. This adaptation increased the probability that platelets could then interact with and engulf shedding virus particles. Platelets also generate circulating microvesicles that increase membrane surface-area encounters and mark viral targets. In order to match virus-production rates, billions of platelets are generated and turned over per day to continually provide active defenses and adaptation to suppress the spectrum of evolving threats like SARS-CoV-2.

From Pebbles and Planetesimals to Planets and Dust: The Protoplanetary Disk–Debris Disk Connection

Abstract The similar orbital distances and detection rates of debris disks and the prominent rings observed in protoplanetary disks suggest a potential connection between these structures. We explore this connection with new calculations that follow the evolution of rings of pebbles and planetesimals as they grow into planets and generate dusty debris. Depending on the initial solid mass and planetesimal formation efficiency, the calculations predict diverse outcomes for the resulting planet masses and accompanying debris signature. When compared with debris disk incidence rates as a function of luminosity and time, the model results indicate that the known population of bright cold debris disks can be explained by rings of solids with the (high) initial masses inferred for protoplanetary disk rings and modest planetesimal formation efficiencies that are consistent with current theories of planetesimal formation. These results support the possibility that large protoplanetary disk rings evolve into the known cold debris disks. The inferred strong evolutionary connection between protoplanetary disks with large rings and mature stars with cold debris disks implies that the remaining majority population of low-mass stars with compact protoplanetary disks leaves behind only modest masses of residual solids at large radii and evolves primarily into mature stars without detectable debris beyond 30 au. The approach outlined here illustrates how combining observations with detailed evolutionary models of solids strongly constrains the global evolution of disk solids and underlying physical parameters such as the efficiency of planetesimal formation and the possible existence of invisible reservoirs of solids in protoplanetary disks.

Rab1b-GBF1-ARF1 Secretory Pathway Axis Is Required for Birnavirus Replication.

Birnaviruses are members of the Birnaviridae family, responsible for major economic losses to poultry and aquaculture. The family is composed of nonenveloped viruses with a segmented double-stranded RNA (dsRNA) genome. Infectious bursal disease virus (IBDV), the prototypic family member, is the etiological agent of Gumboro disease, a highly contagious immunosuppressive disease in the poultry industry worldwide. We previously demonstrated that IBDV hijacks the endocytic pathway for establishing the viral replication complexes on endosomes associated with the Golgi complex (GC). Here, we report that IBDV reorganizes the GC to localize the endosome-associated replication complexes without affecting its secretory functionality. By analyzing crucial proteins involved in the secretory pathway, we showed the essential requirement of Rab1b for viral replication. Rab1b comprises a key regulator of GC transport and we demonstrate that transfecting the negative mutant Rab1b N121I or knocking down Rab1b expression by RNA interference significantly reduces the yield of infectious viral progeny. Furthermore, we showed that the Rab1b downstream effector Golgi-specific BFA resistance factor 1 (GBF1), which activates the small GTPase ADP ribosylation factor 1 (ARF1), is required for IBDV replication, since inhibiting its activity by treatment with brefeldin A (BFA) or golgicide A (GCA) significantly reduces the yield of infectious viral progeny. Finally, we show that ARF1 dominant negative mutant T31N overexpression hampered IBDV infection. Taken together, these results demonstrate that IBDV requires the function of the Rab1b-GBF1-ARF1 axis to promote its replication, making a substantial contribution to the field of birnavirus-host cell interactions. IMPORTANCE Birnaviruses are unconventional members of the dsRNA viruses, with the lack of a transcriptionally active core being the main differential feature. This structural trait, among others that resemble those of the plus single-stranded (+ssRNA) viruses features, suggests that birnaviruses might follow a different replication program from that conducted by prototypical dsRNA members and the hypothesis that birnaviruses could be evolutionary links between +ssRNA and dsRNA viruses has been argued. Here, we present original data showing that IBDV-induced GC reorganization and the cross talk between IBDV and the Rab1b-GBF1-ARF1 mediate the intracellular trafficking pathway. The replication of several +ssRNA viruses depends on the cellular protein GBF1, but its role in the replication process is not clear. Thus, our findings make a substantial contribution to the field of birnavirus-host cell interactions and provide further evidence supporting the proposed evolutionary connection role of birnaviruses, an aspect which we consider especially relevant for researchers working in the virology field.

Identification of Raf-Like Kinases B Subfamily Genes in Gossypium Species Revealed GhRAF42 Enhanced Salt Tolerance in Cotton.

Salinity is a critical abiotic factor that significantly reduces agricultural production. Cotton is an important fiber crop and a pioneer on saline soil, hence genetic architecture that underpins salt tolerance should be thoroughly investigated. The Raf-like kinase B-subfamily (RAF) genes were discovered to regulate the salt stress response in cotton plants. However, understanding the RAFs in cotton, such as Enhanced Disease Resistance 1 and Constitutive Triple Response 1 kinase, remains a mystery. This study obtained 29, 28, 56, and 54 RAF genes from G. arboreum, G. raimondii, G. hirsutum, and G. barbadense, respectively. The RAF gene family described allopolyploidy and hybridization events in allotetraploid cotton evolutionary connections. Ka/Ks analysis advocates that cotton evolution was subjected to an intense purifying selection of the RAF gene family. Interestingly, integrated analysis of synteny and gene collinearity suggested dispersed and segmental duplication events involved in the extension of RAFs in cotton. Transcriptome studies, functional validation, and virus-induced gene silencing on salt treatments revealed that GhRAF42 is engaged in salt tolerance in upland cotton. This research might lead to a better understanding of the role of RAFs in plants and the identification of suitable candidate salt-tolerant genes for cotton breeding.

Sequence specific integration by the family 1 casposase from CandidatusNitrosopumilus koreensis AR1

Casposase, a homolog of Cas1 integrase, is encoded by a superfamily of mobile genetic elements known as casposons. While family 2 casposase has been well documented in both function and structure, little is known about the other three casposase families. Here, we studied the family 1 casposase lacking the helix-turn-helix (HTH) domain from Candidatus Nitrosopumilus koreensis AR1 (Ca. N. koreensis). The determinants for integration by Ca. N. koreensis casposase were extensively investigated, and it was found that a 13-bp target site duplication (TSD) sequence, a minimal 3-bp leader and three different nucleotides of the TSD sequences are indispensable for target specific integration. Significantly, the casposase can site-specifically integrate a broad range of terminal inverted repeat (TIR)-derived oligonucleotides ranging from 7-nt to ∼4000-bp, and various oligonucleotides lacking the 5′-TTCTA-3′ motif at the 3′ end of TIR sequence can be integrated efficiently. Furthermore, similar to some Cas1 homologs, the casposase utilizes a 5′-ATAA-3′ motif in the TSD as a molecular ruler to dictate nucleophilic attack at 9-bp downstream of the end of the ruler during the spacer-side integration. By characterizing the family 1 Ca. N. koreensis casposase, we have extended our understanding on mechanistic similarities and evolutionary connections between casposons and the adaptation elements of CRISPR-Cas immunity.