Expressed Sequence Tags Research Articles

Analysis Polyadenylation Signal Usage in Sus scrofa.

Simple SummaryRNA polyadenylation is an important step of eukaryotic gene expression and the progress depends on a highly conserved AAUAAA hexamer motif, known as the polyadenylation signal (PAS). We identified polyadenylation signals in Sus scrofa, the PAS motif similar with other mammalians. APA (alternative polyadenylation) analysis show that most gene was affect by the alternative polyadenlation in Sus scrofa. The PAS data presented in this manuscript will be useful for Sus scrofa research by facilitating the improved annotation of the Sus scrofa genome and post-transcriptionally regulation mode.RNA polyadenylation is an important step in the messenger RNA (mRNA) maturation process, and the first step is recognizing the polyadenylation signal (PAS). The PAS type and distribution is a key determinant of post-transcriptional mRNA modification and gene expression. However, little is known about PAS usage and alternative polyadenylation (APA) regulation in livestock species. Recently, sequencing technology has enabled the generation of a large amount of sequencing data revealing variation in poly(A) signals and APA regulation in Sus scrofa. We identified 62,491 polyadenylation signals in Sus scrofa using expressed sequence tag (EST) sequences combined with RNA-seq analysis. The composition and usage frequency of polyadenylation signal in Sus scrofa is similar with that of human and mouse. The most highly conserved polyadenylation signals are AAUAAA and AUUAAA, used for over 63.35% of genes. In addition, we also analyzed the U/GU-rich downstream sequence (DSE) element, located downstream of the cleavage site. Our results indicate that APA regulation was widely occurred in Sus scrofa, as in other organisms. Our result was useful for the accurate annotation of RNA 3′ ends in Sus scrofa and the analysis of polyadenylation signal usage in Sus scrofa would give the new insights into the mechanisms of transcriptional regulation.

Development of expressed sequence tag simple sequence repeat (EST-SSR) markers and genetic resource analysis of tea oil plants (Camellia spp.)

Development of expressed sequence tag simple sequence repeat (EST-SSR) markers and genetic resource analysis of tea oil plants (Camellia spp.)

Sea Anemones Responding to Sex Hormones, Oxybenzone, and Benzyl Butyl Phthalate: Transcriptional Profiling and in Silico Modelling Provide Clues to Decipher Endocrine Disruption in Cnidarians.

Endocrine disruption is suspected in cnidarians, but questions remain how occurs. Steroid sex hormones are detected in corals and sea anemones even though these animals do not have estrogen receptors and their repertoire of steroidogenic enzymes appears to be incomplete. Pathways associated with sex hormone biosynthesis and sterol signaling are an understudied area in cnidarian biology. The objective of this study was to identify a suite of genes that can be linked to exposure of endocrine disruptors. Exaiptasia diaphana were exposed to nominal 20ppb concentrations of estradiol (E2), testosterone (T), cholesterol, oxybenzone (BP-3), or benzyl butyl phthalate (BBP) for 4 h. Eleven genes of interest (GOIs) were chosen from a previously generated EST library. The GOIs are 17β-hydroxysteroid dehydrogenases type 14 (17β HSD14) and type 12 (17β HSD12), Niemann-Pick C type 2 (NPC2), Equistatin (EI), Complement component C3 (C3), Cathepsin L (CTSL), Patched domain-containing protein 3 (PTCH3), Smoothened (SMO), Desert Hedgehog (DHH), Zinc finger protein GLI2 (GLI2), and Vitellogenin (VTG). These GOIs were selected because of functional associations with steroid hormone biosynthesis; cholesterol binding/transport; immunity; phagocytosis; or Hedgehog signaling. Quantitative Real-Time PCR quantified expression of GOIs. In silico modelling utilized protein structures from Protein Data Bank as well as creating protein structures with SWISS-MODEL. Results show transcription of steroidogenic enzymes, and cholesterol binding/transport proteins have similar transcription profiles for E2, T, and cholesterol treatments, but different profiles when BP-3 or BBP is present. C3 expression can differentiate between exposures to BP-3 versus BBP as well as exposure to cholesterol versus sex hormones. In silico modelling revealed all ligands (E2, T, cholesterol, BBP, and BP-3) have favorable binding affinities with 17β HSD14, 17β HSD12, NPC2, SMO, and PTCH proteins. VTG expression was down-regulated in the sterol treatments but up-regulated in BP-3 and BBP treatments. In summary, these eleven GOIs collectively generate unique transcriptional profiles capable of discriminating between the five chemical exposures used in this investigation. This suite of GOIs are candidate biomarkers for detecting transcriptional changes in steroidogenesis, gametogenesis, sterol transport, and Hedgehog signaling. Detection of disruptions in these pathways offers new insight into endocrine disruption in cnidarians.

Development and identification of an elite wheat-Hordeum californicum T6HcS/6BL translocation line ND646 containing several desirable traits.

Hordeum californicum (H. californicum, 2n=2X=14, HcHc), one of the wild relatives of wheat (Triticum aestivum L.), harbors many desirable genes and is a potential genetic resource for wheat improvement. In this study, an elite line ND646 was selected from a BC4F5 population, which was developed using 60Co-γ irradiated wheat-H. californicum disomic addition line WJ28-1 (DA6Hc) as the donor parent and Ningchun 4 as the recurrent parent. ND646 was identified as a novel wheat-H. californicum 6HcS/6BL translocation line using genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH), and H. californicum-specific expressed sequence tag (EST) markers. Further evaluation revealed that ND646 had excellent performance in several traits, such as a higher sedimentation value (SV), higher water absorption rate (WAR), and higher hardness index (HI). More importantly, it had more kernels per spike (KPS), a higher grain yields (GY), and good resistance to powdery mildew, leaf rust, and 2,4-D butylate (2,4-D). Its excellent phenotypic performance laid the foundation for further investigation of its genetic architecture and makes ND646 a useful germplasm resource for wheat breeding.

Combined physiological responses and differential expression of drought-responsive genes preliminarily explain the drought resistance mechanism of Lotus corniculatus.

Lotus corniculatus L. is a perennial high-quality legume forage species but is vulnerable to drought, and water deficit reduces productivity. To understand the drought response mechanism of L. corniculatus , we investigated physiological responses under drought stress and constructed suppression subtractive hybridisation (SSH) cDNA libraries to isolate drought-inducible genes and quantitatively study the expression levels of candidate drought- responsive genes. Genes encoding calmodulin-like protein, mitogen-activated protein kinase, indole-3-acetic acid-induced protein, ser/thr-protein phosphatase homolog-related proteins, and β -galactosidase-related protein with hydrolysis activity were isolated and considered the main factors that explained the resistance of L. corniculatus to drought. Approximately 632 expressed sequence tags (ESTs) were identified and confirmed in the constructed SSH library. The Gene Ontology (GO) analysis revealed that these genes were involved mainly in transcription processes, protein synthesis, material metabolism, catalytic reactions, sugar metabolism, and photosynthesis. The interaction between the functions of these drought-related genes and the physiological responses preliminarily explains the drought resistance mechanisms of L. corniculatus .

Bioinformatic Deconstruction of Differentially Expressed Sequence Tags in Hepatocellular Carcinoma Based on Artificial Neural Network.

Traditional medical imaging methods for diagnosing hepatocellular carcinoma can only provide information for differential diagnosis in terms of morphology and blood supply of the lesion, and the determination of the nature of the lesion still relies on tissue biopsy. Although ultrasound or CT-guided biopsy has become an effective method for the diagnosis of liver cancer in recent years, the puncture has the possibility of tumor irritation, liver tumor rupture, or needle tract metastasis. In this paper, the use of bioinformatics method is to gradually screen potentially high-risk genes associated with HCC recurrence on a genome-wide scale would help to discover the key target molecules. The ANN method was used to establish a gene prediction model that can predict the recurrence and survival of HCC, so as to construct a tool to identify patients at risk of HCC recurrence. It provided a certain therapeutic basis for future clinical work, thereby improving the prognosis of patients with HCC. Using the “survfit” function of the “survival” package in the R language, the log-rank test (the log-rank test was a common method for comparing two survival curves) was performed on all genes with posthoc recurrence of hepatocellular carcinoma as the outcome event. Then, the BLAST tool (Basic Local Alignment Search Tool) was used to search the similarity of each hepatocellular carcinoma database to find out the genes with similar sequences to each hepatocellular carcinoma, so as to determine the function of each differentially expressed sequence tag. This paper found that the AUC of the ANN model was greater than that of the discriminant analysis model (P < 0.05). This paper promoted the development of new therapeutic measures for hepatocellular carcinoma and provided important theoretical guidance for human beings to fight cancer.

Expressed sequence tag simple sequence repeats (EST-SSRs) mining and marker development from Leucaena leucocephala root transcriptome

Leucaena leucocephala is a nitrogen-fixing legume and a fast-growing species used for various purposes, including food, medicine, and most recently, energy-source wood. Compared to other commonly planted legumes, this species has a high-stress tolerance, and only one recorded insect infestation. The transcriptome analysis revealed genes involved in the production of stress tolerance compounds in the root. In this study, we attempted to extract simple sequence repeats (SSRs) from the transcriptome data of L. leucocephala root to establish molecular markers. The SSRs mined from L. leucocephala transcriptome deposited in NCBI with accession number GDRZ00000000. We used Krait v.1.3.3 to extract the SSRs and developed the primers. The SSRs cover 0.3% of the total transcriptome sequence, with 21.321 perfect SSRs found and relative density 2908.63 (bp/Mb). The most abundant type of SSRs was found in mononucleotide (39.85%), followed by dinucleotide (33.49%) and trinucleotide (24.75). However, for tetra, penta, and hexanucleotide, the percentage was lower than 2%. The number of primers generated was 8137 primers, with 3969 dinucleotides, 3947 trinucleotides, 150 tetranucleotides, 21 pentanucleotides, and 50 hexanucleotide SSR primers. This finding may help to accelerate stress-tolerant legume improvement in the future.

Von Willebrand factor D and EGF domains regulate ameloblast differentiation and enamel formation.

Cell- and tissue-specific extracellular matrix (ECM) composition plays an important role in organ development, including teeth, by regulating cell behaviors, such as cell proliferation and differentiation. Here, we demonstrate for the first time that von Willebrand factor D and epidermal growth factor (EGF) domains (Vwde), a previously uncharacterized ECM protein, is specifically expressed in teeth and regulates cell proliferation and differentiation in inner enamel epithelial cells (IEEs) and enamel formation. We identified the Vwde as a novel ECM protein through bioinformatics using the NCBI expressed sequence tag database for mice. Vwde complementary DNA encodes 1773 amino acids containing a signal peptide, a von Willebrand factor type D domain, and tandem calcium-binding EGF-like domains. Real-time polymerasechain reaction demonstrated that Vwde is highly expressed in tooth tissue but not in other tissues including the brain, lung, heart, liver, kidney, and bone. In situ hybridization revealed that the IEEs expressed Vwde messenger RNA in developing teeth. Immunostaining showed that VWDE was localized at the proximal and the distal ends of the pericellular regions of the IEEs. Vwde was induced during the differentiation of mouse dental epithelium-derived M3H1 cells. Vwde-transfected M3H1 cells secreted VWDE protein into the culture medium and inhibited cell proliferation, whereas ameloblastic differentiation was promoted. Furthermore, Vwde increased the phosphorylation of extracellular signal-regulated kinase 1/2 and protein kinase B and strongly induced the expression of the intercellular junction protein, N-cadherin (Ncad). Interestingly, the suppression of endogenous Vwde inhibited the expression of Ncad. Finally, we created Vwde-knockout mice using the CRISPR-Cas9 system. Vwde-null mice showed low mineral density, rough surface, and cracks in the enamel, indicating the enamel hypoplasia phenotype. Our findings suggest that Vwde assembling the matrix underneath the IEEs is essential for Ncad expression and enamel formation.

Molecular cytogenetics for a wheat\u2013Aegilops geniculata 3Mg alien addition line with resistance to stripe rust and powdery mildew

BackgroundAegilops geniculata Roth is closely related to common wheat (Triticum aestivum L.) and is a valuable genetic resource for improvement of wheat.ResultsIn this study, the W19513 line was derived from the BC1F10 progeny of a cross between wheat ‘Chinese Spring’ and Ae. geniculata SY159. Cytological examination showed that W19513 contained 44 chromosomes. Twenty-two bivalents were formed at the first meiotic metaphase I in the pollen mother cellsand the chromosomes were evenly distributed to opposite poles at meiotic anaphase I. Genomic in situ hybridization demonstrated that W19513 carried a pair of alien chromosomes from the M genome. Fluorescence in situ hybridization confirmed detection of variation in chromosomes 4A and 6B. Functional molecular marker analysis using expressed sequence tag–sequence-tagged site and PCR-based landmark unique gene primers revealed that the alien gene belonged to the third homologous group. The marker analysis confirmed that the alien chromosome pair was 3Mg. In addition, to further explore the molecular marker specificity of chromosome 3Mg, based on the specific locus amplified fragment sequencing technique, molecular markers specific for W19513 were developed with efficiencies of up to 47.66%. The W19513 line was inoculated with the physiological race E09 of powdery mildew (Blumeria graminis f. sp. tritici) at the seedling stage and showed moderate resistance. Field inoculation with a mixture of the races CYR31, CYR32, CYR33, and CYR34 of the stripe rust fungus (Puccinia striiformis f. sp. triticii) revealed that the line W19513 showed strong resistance.ConclusionsThis study provides a foundation for use of the line W19513 in future genetic research and wheat improvement.

Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.).

Ginger (Zingiber officinale Rosc.) is an economically important and valuable spice crop around the world. It is used as food, spice, condiment, and medicine. A considerable extent of genetic diversity in ginger occurs in the Western Ghats and North-Eastern India. However, genetic diversity studies at the molecular level in ginger is limited due to limited availability of genetic and genomic information. In the present study, for the first time, we have identified and validated expressed sequence tag (EST)-simple sequence repeat (SSR) markers from ginger. We obtained 16,790 EST-SSR loci from 78987 unigenes, and 4597 SSR loci in the predicted 76929 coding sequences from RNA-Seq assembled contigs of ginger through Illumina paired-end sequencing. Gene ontology results indicate that the unigenes with SSR loci participate in various biological processes such as metabolism, growth, and development in ginger. One hundred and twenty-five primer pairs were designed from unigenes and coding sequences. These primers were tested for PCR optimization, characterization, and amplification and identified 12 novel EST-SSR markers. Twelve flanking polymorphic EST-SSR primers were validated using 48 ginger genotypes representing North-Eastern India and different eco-geographical adaptations by PCR amplification and allele sizing through capillary electrophoresis. Twelve EST-SSR primers generated a total of 111 alleles with an average of 9.25 alleles per locus and allele sizes ranging between 115-189bp. This study implies that the SSR markers designed from transcriptome sequences provides ample EST-SSR resources, which are helpful for genetic diversity analysis of Zingiberaceae species and molecular verification of ginger genotypes.

Identification of protease serine S1 family member 53 as a mitochondrial protein in murine islet beta cells

ABSTRACT The aim of this study was to identify genes that are specifically expressed in pancreatic islet β-cells (hereafter referred to as β-cells). Large-scale complementary DNA-sequencing analysis was performed for 3,429 expressed sequence tags derived from murine MIN6 β-cells, through homology comparisons using the GenBank database. Three individual ESTs were found to code for protease serine S1 family member 53 (Prss53). Prss53 mRNA is processed into both a short and long form, which encode 482 and 552 amino acids, respectively. Transient overexpression of myc-tagged Prss53 in COS-7 cells showed that Prss53 was strongly associated with the luminal surfaces of organellar membranes and that it underwent signal peptide cleavage and N-glycosylation. Immunoelectron microscopy and western blotting revealed that Prss53 localized to mitochondria in MIN6 cells. Short hairpin RNA-mediated Prss53 knockdown resulted in Ppargc1a downregulation and Ucp2 and Glut2 upregulation. JC-1 staining revealed that the mitochondria were depolarized in Prss53-knockdown MIN6 cells; however, no change was observed in glucose-stimulated insulin secretion. Our results suggest that mitochondrial Prss53 expression plays an important role in maintaining the health of β-cells.

Identification and characterization of eight metallothionein genes involved in heavy metal tolerance from the ectomycorrhizal fungus Laccaria bicolor.

Metallothioneins (MTs) are small, cysteine-rich, heavy metal-binding proteins involved in metal homeostasis and detoxification. The increasing numbers of available genomic sequences of ectomycorrhizal (ECM) fungi enable deeper insights into the characteristics of MT genes in these fungi that form the most important symbiosis with the host trees in forest ecosystems. The aim of this study was to establish a comprehensive, genome-wide inventory of MT genes from the ECM fungus Laccaria bicolor. Eight MT genes in L. bicolor were cloned, and the expression patterns of their transcripts at various developmental stages based on expressed sequence tag (EST) counts were analyzed. The expression levels of four MTs were significantly increased during symbiosis stages. Quantitative real-time PCR (qRT-PCR) analysis revealed that transcripts of LbMT1 were dominant in free-living mycelia and strongly induced by excessive copper (Cu), cadmium (Cd), and hydrogen peroxide (H2O2). To determine whether these eight MTs functioned as metal chelators, we expressed them in the Cu- and Cd-sensitive yeast mutants, cup1∆ and yap1∆, respectively. All LbMT proteins provided similar levels of Cu(II) or Cd(II) tolerance, but did not affect by H2O2. Our findings provide novel data on the evolution and diversification of fungal MT gene duplicates, a valuable resource for understanding the vast array of biological processes in which these proteins are involved.

Exon and intron sharing in opposite direction-an undocumented phenomenon in human genome-between Pou5f1 and Tcf19 genes

BackgroundOverlapping genes share same genomic regions in parallel (sense) or anti-parallel (anti-sense) orientations. These gene pairs seem to occur in all domains of life and are best known from viruses. However, the advantage and biological significance of overlapping genes is still unclear. Expressed sequence tags (ESTs) analysis enabled us to uncover an overlapping gene pair in the human genome.ResultsBy using in silico analysis of previous experimental documentations, we reveal a new form of overlapping genes in the human genome, in which two genes found on opposite strands (Pou5f1 and Tcf19), share two exons and one intron enclosed, at the same positions, between OCT4B3 and TCF19-D splice variants.ConclusionsThis new form of overlapping gene expands our previous perception of splicing events and may shed more light on the complexity of gene regulation in higher organisms. Additional such genes might be detected by ESTs analysis also of other organisms.

Discovery of SNPs in important legumes through comparative genome analysis and conversion of SNPs into PCR-based markers

Compared to cereal crops several legumes are less characterized at the genomic level and rightly referred as orphan crops. Transfer of knowledge between model and crop legumes allows development of orthologous pan-taxon genomic tools to benefit research on resource poor taxa. Here, we developed 278 intron flanking gene-specific markers by BLAST aligning pigeonpea (Cajanus cajan (L.) Millsp.) expressed sequence tags (ESTs) with complete genome sequence of barrel medic (Medicago truncatula). A random 192 PCR primer pairs representing loci across the haploid genome (n = 8) of barrel medic were tested on a few important members of legume family. The single copy amplification rates of 31.8% (peanut, Arachis hypogaea) to 77.6% (barrel medic) signifies the success of cross taxon primers and suggested their potential use in comparative legume genomics. Genetic diversity was assessed in 48 pigeonpea genotypes using 143 intron flanking markers which revealed 71 polymorphic markers with PIC values ranging from 0.04 to 0.45 with an average of 0.23 per marker. The PCR products of different varieties of pigeonpea, cowpea and chickpea were sequenced and aligned to find putative SNPs. Integration of these newly developed markers into genetic maps in resource poor legumes will not only aid in the map saturation but also in designing successful marker-assisted selection programmes.

The Landscapes of Full-Length Transcripts and Splice Isoforms as Well as Transposons Exonization in the Lepidopteran Model System, Bombyx mori.

The domesticated silkworm, Bombyx mori, is an important model system for the order Lepidoptera. Currently, based on third-generation sequencing, the chromosome-level genome of Bombyx mori has been released. However, its transcripts were mainly assembled by using short reads of second-generation sequencing and expressed sequence tags which cannot explain the transcript profile accurately. Here, we used PacBio Iso-Seq technology to investigate the transcripts from 45 developmental stages of Bombyx mori. We obtained 25,970 non-redundant high-quality consensus isoforms capturing ∼60% of previous reported RNAs, 15,431 (∼47%) novel transcripts, and identified 7,253 long non-coding RNA (lncRNA) with a large proportion of novel lncRNA (∼56%). In addition, we found that transposable elements (TEs) exonization account for 11,671 (∼45%) transcripts including 5,980 protein-coding transcripts (∼32%) and 5,691 lncRNAs (∼79%). Overall, our results expand the silkworm transcripts and have general implications to understand the interaction between TEs and their host genes. These transcripts resource will promote functional studies of genes and lncRNAs as well as TEs in the silkworm.

Genetic diversity, genetic structure, and demographic history of Cinnamomum chago, a plant species with extremely small populations in China

As a species with restricted and fragmented distribution in Yunnan Province, Cinnamomum chago possesses high economic and phylogenetic values. Although this species has been categorized as an endangered plant in the IUCN Red List and has extremely small populations in China, the genetic information of C. chago has been rarely studied. In the present study, we used 4 pairs of DNA markers and 11 pairs of expressed sequence tag–simple sequence repeat markers to conduct a systematic and comprehensive assessment about the genetic diversity, genetic structure, and demographic history of 5 C. chago populations. A low genetic diversity but a significant genetic differentiation were detected (Na=2.509, Np=3.8, Ra=2.423, AE=1.635, HO=0.177, He=0.340). The five populations presented obvious inbreeding phenomenon given the high value of inbreeding coefficient (Fis=0.462) and low value of outcrossing rate (t = 0.365). Although the genetic distance and geographic distance were not correlated, geographical structures were detected in C. chago. Extremely low historical and contemporary gene flow was detected between pairwise populations of C. chago. Additionally, the remnant populations of C. chago experienced a recent historical bottleneck, but the neutrality tests and mismatch distribution analysis revealed that this species did not underwent a recent population expansion. In consideration of the above consequence, we advocate in situ conservation of natural habitats and remaining individuals of C. chago, as well as artificial breeding. This study not only provides important insights into the genetic characteristic but also emphasizes the relevance of the conservation of C. chago and other extremely endangered plants.

OrchidBase 4.0: a database for orchid genomics and molecular biology

BackgroundThe Orchid family is the largest families of the monocotyledons and an economically important ornamental plant worldwide. Given the pivotal role of this plant to humans, botanical researchers and breeding communities should have access to valuable genomic and transcriptomic information of this plant. Previously, we established OrchidBase, which contains expressed sequence tags (ESTs) from different tissues and developmental stages of Phalaenopsis as well as biotic and abiotic stress-treated Phalaenopsis. The database includes floral transcriptomic sequences from 10 orchid species across all the five subfamilies of Orchidaceae.DescriptionRecently, the whole-genome sequences of Apostasia shenzhenica, Dendrobium catenatum, and Phalaenopsis equestris were de novo assembled and analyzed. These datasets were used to develop OrchidBase 4.0, including genomic and transcriptomic data for these three orchid species. OrchidBase 4.0 offers information for gene annotation, gene expression with fragments per kilobase of transcript per millions mapped reads (FPKM), KEGG pathways and BLAST search. In addition, assembled genome sequences and location of genes and miRNAs could be visualized by the genome browser. The online resources in OrchidBase 4.0 can be accessed by browsing or using BLAST. Users can also download the assembled scaffold sequences and the predicted gene and protein sequences of these three orchid species.ConclusionsOrchidBase 4.0 is the first database that contain the whole-genome sequences and annotations of multiple orchid species. OrchidBase 4.0 is available at http://orchidbase.itps.ncku.edu.tw/

English

It is very important to establish an optimal seed priming process in order to increase the vitality of the seeds and promote the metabolism for the germination of the seeds. The optimum concentrations and species of priming agents to improve seed germination of both medicinal plants were also estimated. To improve the germination rate of Perilla frutescens(Korean perilla) seeds, various seed priming agents were used to analyze seed germination rates in the Saeyeopsil, Okdong and 141 collection Korean perilla cultivars. The agents used for seed priming were CaCl2, Ca(NO3)2, NaCl, K3PO4, polyethylene glycol, and gibberellic acid (GA3). When 0.1 mMGA3was used for seed priming, germination rates of Okdong, and the 141 collection showed a greater than 70% increase compared to the controls. Nine genes were selected for expression analysis by searching for genes related to seed germination and plant development in the EST(Expressed Sequence Tag) database of the Korean perilla cDNA library. GA3priming treatment for 1 d induced higher transcriptional levels of genes related to germination and plant developmentthan controls treated with water only. These genes were identified as protochlorophyllide reductase-like, magnesium-chelatase subunit ChlI, heme-binding protein 2-like, glyceraldehyde 3-phosphate dehydrogenase A, Chlorophyll a-b binding protein 6, B2 protein, 2-Cys peroxiredoxin BAS1, and 21 kDa protein. From these results, we suggest that when priming Korean perilla seeds with GA3, a large number of genes involved in plant development at early stages of seed germination play a role in improving the seed germination rate. Also, these induced genes are ideal candidate biomarkers for seed priming of Korean perilla. Specially, protochlorophyllide reductase-like is thought to be a potential gene for future molecular marker.© 2021 Friends Science Publishers

Utilizing a Biology-Driven Approach to Map the Exposome in Health and Disease: An Essential Investment to Drive the Next Generation of Environmental Discovery.

Background:Recent developments in technologies have offered opportunities to measure the exposome with unprecedented accuracy and scale. However, because most investigations have targeted only a few exposures at a time, it is hypothesized that the majority of the environmental determinants of chronic diseases remain unknown.Objectives:We describe a functional exposome concept and explain how it can leverage existing bioassays and high-resolution mass spectrometry for exploratory study. We discuss how such an approach can address well-known barriers to interpret exposures and present a vision of next-generation exposomics.Discussion:The exposome is vast. Instead of trying to capture all exposures, we can reduce the complexity by measuring the functional exposome—the totality of the biologically active exposures relevant to disease development—through coupling biochemical receptor-binding assays with affinity purification–mass spectrometry. We claim the idea of capturing exposures with functional biomolecules opens new opportunities to solve critical problems in exposomics, including low-dose detection, unknown annotations, and complex mixtures of exposures. Although novel, biology-based measurement can make use of the existing data processing and bioinformatics pipelines. The functional exposome concept also complements conventional targeted and untargeted approaches for understanding exposure-disease relationships.Conclusions:Although measurement technology has advanced, critical technological, analytical, and inferential barriers impede the detection of many environmental exposures relevant to chronic-disease etiology. Through biology-driven exposomics, it is possible to simultaneously scale up discovery of these causal environmental factors. https://doi.org/10.1289/EHP8327

High macro-collinearity between Crassostrea angulata and C. gigas genomes was revealed by comparative genetic mapping with transferable EST-SNP markers

Comparative genomics has become an important strategy for transferring genetic information from a well-characterized model species to one that is less described and can facilitate in functional gene mining and genomic evolution. Crassostrea angulata and Crassostrea gigas are closed related species that they can hybridize to produce fertile offspring, and C. gigas has accumulated a considerable number of genetic and genomic resources while C. angulata lags far behind. In the current study, 684 single nucleotide polymorphism (SNP) markers developed from C. gigas expressed sequence tags (ESTs) were used for transferability test in C. angulata, and 635 loci were successfully amplified. Then a genetic linkage map of C. angulata was for the first time constructed using these transferable SNP markers. A total of 988 transferable SNP markers were used for polymorphism screening in a mapping family, and 273 loci were distributed on the genetic map which was composed of 10 linkage groups and estimated 1040.29 cM in total length. The average spacing between markers was 3.96 cM. By comparing the shared EST-SNP marker locations on homologous linkage groups, comparative mapping analysis between the C. angulata genetic map and an integrated map of C. gigas revealed putative macro-collinearity in the two oyster genomes with little difference in markers order. These transferable SNP markers could be applied in genetic diversity and population structure studies, and the genetic map would be useful for quantitative trait loci mapping and genetic improvement through marker-assisted selection for C. angulata.