Synthesis, secretion, and perception of abscisic acid regulates stress responses in \u3ci\u3eChlorella sorokiniana\u3c/i\u3e

Abscisic acid (ABA) is a phytohormone that has been extensively characterized in higher plants for its roles in seed and bud dormancy, leaf abscission, and stress responses. Genomic studies have identified orthologs for ABA-related genes throughout the Viridiplantae, including in unicellular algae; however, the role of ABA in algal physiology has not been characterized, and the existence of such a role has been a matter of dispute. In this study, we demonstrate that ABA is involved in regulating algal stress responses. Chlorella sorokiniana strain UTEX 1230 contains genes orthologous to those of higher plants which are essential for ABA biosynthesis, sensing, and degradation. RNAseq-based transcriptomic studies reveal that treatment with ABA induces dramatic changes in gene expression profiles, including the induction of a subset of genes involved in DNA replication and repair, a phenomenon which has been demonstrated in higher plants. Pretreatment of C. sorokiniana cultures with ABA exerts a protective effect on cell viability in response to ultraviolet radiation. Additionally, C. sorokiniana produces and secretes biologically relevant amounts of both ABA and the oxylipin 12-oxo-phytodienoic acid (OPDA) into the growth medium in response to abiotic stressors. Taken together, these phenomena suggest that ABA signaling evolved as an intercellular stress response signaling molecule in eukaryotic microalgae prior to the evolution of multicellularity and colonization of land

Role of whole grains versus fruits and vegetables in reducing subclinical inflammation and promoting gastrointestinal health in individuals affected by overweight and obesity: a randomized controlled trial

Background: Whole grains (WG) and fruits and vegetables (FV) have been shown to reduce the risk of metabolic disease, possibly via modulation of the gut microbiota. The purpose of this study was to determine the impact of increasing intake of either WG or FV on inflammatory markers and gut microbiota composition. Methods: A randomized parallel arm feeding trial was completed on forty-nine subjects with overweight or obesity and low intakes of FV and WG. Individuals were randomized into three groups (3 servings/d provided): WG, FV, and a control (refined grains). Stool and blood samples were collected at the beginning of the study and after 6 weeks. Inflammatory markers [tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), lipopolysaccharide binding protein (LBP), and high sensitivity C-reactive protein (hs-CRP)] were measured. Stool sample analysis included short/branched chain fatty acids (S/BCFA) and microbiota composition. Results: There was a significant decrease in LBP for participants on the WG (− 0.2 μg/mL, p = 0.02) and FV (− 0.2 μg/mL, p = 0.005) diets, with no change in those on the control diet (0.1 μg/mL, p = 0.08). The FV diet induced a significant change in IL-6 (− 1.5 pg/mL, p = 0.006), but no significant change was observed for the other treatments (control, − 0.009 pg/mL, p = 0.99; WG, − 0.29, p = 0.68). The WG diet resulted in a significant decrease in TNF-α (− 3.7 pg/mL; p \u3c 0.001), whereas no significant effects were found for those on the other diets (control, − 0.6 pg/mL, p =0.6; FV, − 1.4 pg/mL, p = 0.2). The treatments induced individualized changes in microbiota composition such that treatment group differences were not identified, except for a significant increase in α-diversity in the FV group. The proportions of Clostridiales (Firmicutes phylum) at baseline were correlated with the magnitude of change in LBP during the study Conclusions: These data demonstrate that WG and FV intake can have positive effects on metabolic health; however, different markers of inflammation were reduced on each diet suggesting that the anti-inflammatory effects were facilitated via different mechanisms. The anti-inflammatory effects were not related to changes in gut microbiota composition during the intervention, but were correlated with microbiota composition at baseline

Patterns of Gene Expression in Western Corn Rootworm (\u3ci\u3eDiabrotica virgifera virgifera\u3c/i\u3e) Neonates, Challenged with Cry34Ab1, Cry35Ab1 and Cry34/35Ab1, Based on Next-Generation Sequencing

With Next Generation Sequencing technologies, high-throughput RNA sequencing (RNAseq) was conducted to examine gene expression in neonates of Diabrotica virgifera virgifera (LeConte) (Western Corn Rootworm, WCR) challenged with individual proteins of the binary Bacillus thuringiensis insecticidal proteins, Cry34Ab1 and Cry35Ab1, and the combination of Cry34/Cry35Ab1, which together are active against rootworm larvae. Integrated results of three different statistical comparisons identified 114 and 1300 differentially expressed transcripts (DETs) in the Cry34Ab1 and Cry34/35Ab1 treatment, respectively, as compared to the control. No DETs were identified in the Cry35Ab1 treatment. Putative Bt binding receptors previously identified in other insect species were not identified in DETs in this study. The majority of DETs (75% with Cry34Ab1 and 68.3% with Cry34/35Ab1 treatments) had no significant hits in the NCBI nr database. In addition, 92 DETs were shared between Cry34Ab1 and Cry34/35Ab1 treatments. Further analysis revealed that the most abundant DETs in both Cry34Ab1 and Cry34/35Ab1 treatments were associated with binding and catalytic activity. Results from this study confirmed the nature of these binary toxins against WCR larvae and provide a fundamental profile of expression pattern of genes in response to challenge of the Cry34/35Ab1 toxin, which may provide insight into potential resistance mechanisms

Evolutionary History of Chemosensory-Related Gene Families across the Arthropoda

Chemosensory-related gene (CRG) families have been studied extensively in insects, but their evolutionary history across the Arthropoda had remained relatively unexplored. Here, we address current hypotheses and prior conclusions on CRG family evolution using a more comprehensive data set. In particular, odorant receptors were hypothesized to have proliferated during terrestrial colonization by insects (hexapods), but their association with other pancrustacean clades and with independent terrestrial colonizations in other arthropod subphyla have been unclear. We also examine hypotheses on which arthropod CRG family is most ancient. Thus, we reconstructed phylogenies of CRGs, including those from new arthropod genomes and transcriptomes, and mapped CRG gains and losses across arthropod lineages. Our analysis was strengthened by including crustaceans, especially copepods, which reside outside the hexapod/branchiopod clade within the subphylum Pancrustacea. We generated the first high-resolution genome sequence of the copepod Eurytemora affinis and annotated its CRGs. We found odorant receptors and odorant binding proteins present only in hexapods (insects) and absent from all other arthropod lineages, indicating that they are not universal adaptations to land. Gustatory receptors likely represent the oldest chemosensory receptors among CRGs, dating back to the Placozoa. We also clarified and confirmed the evolutionary history of antennal ionotropic receptors across the Arthropoda. All antennal ionotropic receptors in E. affinis were expressed more highly in males than in females, suggestive of an association with male mate-recognition behavior. This study is the most comprehensive comparative analysis to date of CRG family evolution across the largest and most speciose metazoan phylum Arthropoda

THE ORIGIN AND MOLECULAR EVOLUTION OF TWO MULTIGENE FAMILIES: G-PROTEIN COUPLED RECEPTORS AND GLYCOSIDE HYDROLASE FAMILIES

Multigene family is a group of genes that arose from a common ancestor by gene duplication. Gene duplications are a major driving force of new function acquisition. Multigene family thus has a fundamental role in adaptation. To elucidate their molecular evolutionary mechanisms, I chose two multigene families: chemosensory receptors and glycoside hydrolases. I have identified complete repertoires of trace amine-associated receptors (TAARs), a member of chemosensory receptors, from 38 metazoan genomes. An ancestral-type TAAR emerged before the divergence between gnathostomes (jawed vertebrates) and sea lamprey (jawless fish). Primary amine detecting TAARs (TAAR1-4) are found to be older and have evolved under strong functional constraints. In contrast, tertiary amine detectors (TAAR5-9) emerged later, experienced higher rates of gene duplications, and experienced positive selection that could have affected ligand-binding activities and specificities. Expansions of tertiary amine detectors must have played important roles in terrestrial adaptations of therian mammals. During the primate evolution, TAAR gene losses are found to be a major trend. Relaxed selective constraints found in primate lineages of TAARs support dispensability of these primate genes. Reduced predator exposures owing to the start of arboreal life by ancestoral primates may attribute to this change. For another type of multigene family, glycoside hydrolase (GH) genes were identified in the western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae). Three GH family genes (GH45, GH48, and GH28) were found only in two coleopteran superfamilies (Chrysomeloidea and Curculionoidea) among insects (except for hemipteran GH28s), indicating their origin from horizontal gene transfer (HGT). Several independent HGTs in fungi and other insects were also detected. Two multigene families in this study are characterized with frequent gene duplications and losses, the birth-and-death process. A high rate of HGTs found in the GH family gene evolution must have accelerated functional evolution. In conclusion, this study showed that birth-and-death process, positive selection, and HGTs, all play a critical role in driving the evolution of multigene families and allow organismal adaptation to novel environmental niches. Advisor: Etsuko Moriyam

Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies

Abstract Background Copepods play a critical role in marine ecosystems but have been poorly investigated in phylogenetic studies. Morphological evidence supports the monophyly of copepods, whereas interordinal relationships continue to be debated. In particular, the phylogenetic position of the order Harpacticoida is still ambiguous and inconsistent among studies. Until now, a small number of molecular studies have been done using only a limited number or even partial genes and thus there is so far no consensus at the order-level. Results This study attempted to resolve phylogenetic relationships among and within four major copepod orders including Harpacticoida and the phylogenetic position of Copepoda among five other crustacean groups (Anostraca, Cladocera, Sessilia, Amphipoda, and Decapoda) using 24 nuclear protein-coding genes. Phylogenomics has confirmed the monophyly of Copepoda and Podoplea. However, this study reveals surprising differences with the majority of the copepod phylogenies and unexpected similarities with postembryonic characters and earlier proposed morphological phylogenies; More precisely, Cyclopoida is more closely related to Siphonostomatoida than to Harpacticoida which is likely the most basally-branching group of Podoplea. Divergence time estimation suggests that the origin of Harpacticoida can be traced back to the Devonian, corresponding well with recently discovered fossil evidence. Copepoda has a close affinity to the clade of Malacostraca and Thecostraca but not to Branchiopoda. This result supports the hypothesis of the newly proposed clades, Communostraca, Multicrustacea, and Allotriocarida but further challenges the validity of Hexanauplia and Vericrustacea. Conclusions The first phylogenomic study of Copepoda provides new insights into taxonomic relationships and represents a valuable resource that improves our understanding of copepod evolution and their wide range of ecological adaptations

An Evolutionary Expressed Sequence Tag Analysis of \u3ci\u3eDrosophila\u3c/i\u3e Spermatheca Genes

This study investigates genes enriched for expression in the spermatheca, the long-term sperm storage organ (SSO) of female Drosophila. SSO genes are likely to play an important role in processes of sexual selection such as sperm competition and cryptic female choice. Although there is keen interest in the mechanisms of sexual selection at the molecular level, very little is known about the female genes that are involved. In the present study, a high proportion of genes enriched for expression in the spermatheca are evolving rapidly. Most of the rapidly evolving genes are proteases and genes of unknown function that could play a specialized role in the spermatheca. A high percentage of the rapidly evolving genes have secretion signals and thus could encode proteins that directly interact with ejaculate proteins and coevolve with them. In addition to identifying rapidly evolving genes, the present study documents categories of genes that could play a role in spermatheca function such as storing, maintaining, and utilizing sperm. In general, candidate genes discovered in this study could play a key role in sperm competition, cryptic female choice of sperm, and sexually antagonistic coevolution, and ultimately speciation

Molecular Evolution and Functional Divergence of Trace Amine–Associated Receptors

Trace amine-associated receptors (TAARs) are a member of the G-protein-coupled receptor superfamily and are known to be expressed in olfactory sensory neurons. A limited number of molecular evolutionary studies have been done for TAARs so far. To elucidate how lineage-specific evolution contributed to their functional divergence, we examined 30 metazoan genomes. In total, 493 TAAR gene candidates (including 84 pseudogenes) were identified from 26 vertebrate genomes. TAARs were not identified from non-vertebrate genomes. An ancestral-type TAAR-like gene appeared to have emerged in lamprey.We found four therian-specific TAAR subfamilies (one eutherian-specific and three metatherian- specific) in addition to previously known nine subfamilies. Many species-specific TAAR gene duplications and losses contributed to a large variation of TAAR gene numbers among mammals, ranging from 0 in dolphin to 26 in flying fox. TAARs are classified into two groups based on binding preferences for primary or tertiary amines as well as their sequence similarities. Primary amine-detecting TAARs (TAAR1-4) have emerged earlier, generally have single-copy orthologs (very few duplication or loss), and have evolved under strong functional constraints. In contrast, tertiary amine-detecting TAARs (TAAR5-9) have emerged more recently and the majority of them experienced higher rates of gene duplications. Protein members that belong to the tertiary amine-detecting TAAR group also showed the patterns of positive selection especially in the area surrounding the ligand-binding pocket, which could have affected ligand-binding activities and specificities. Expansions of the tertiary amine-detecting TAAR gene family may have played important roles in terrestrial adaptations of therian mammals. Molecular evolution of the TAAR gene family appears to be governed by a complex, species-specific, interplay between environmental and evolutionary factors

Comparative Evaluation of Genome Assemblers from Long-Read Sequencing for Plants and Crops

The availability of recent state-of-the-art long-read sequencing technologies has significantly increased the ease and speed of producing high-quality plant genome assemblies. A wide variety of genome-related software tools are now available and they are typically benchmarked using microbial or model eukaryotic genomes such as Arabidopsis and rice. However, many plant species have much larger and more complex genomes than these, and the choice of tools, parameters, and/or strategies that can be used is not always obvious. Thus, we have compared the metrics of assemblies generated by various pipelines to discuss how assembly quality can be affected by two different assembly strategies. First, we focused on optimizing read preprocessing and assembler variables using eight different de novo assemblers on five different Pacific Biosciences long-read datasets of diploid and tetraploid species. Then, we examined a single scaffolding tool (quickmerge) that has been employed for the postprocessing step. We then merged the outputs from multiple assemblies to produce a higher quality consensus assembly. Then, we benchmarked the assemblies for completeness and accuracy (assembly metrics and BUSCO), computer memory, and CPU times. Two lightweight assemblers, Miniasm/Minimap/Racon and WTDBG, were deemed good for novice users because they involved smaller required learning curves and light computational resources. However, two heavyweight tools, CANU and Flye, should be the first choice when the goal is to achieve accurate and complete assemblies. Our results will provide valuable guidance in future plant genome projects and beyond. </p