Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato)

The corm of Hypoxis hemerocallidea, commonly known as the African potato, is used in traditional medicine to treat several medical conditions such as urinary infections, benign prostate hyperplasia, inflammatory conditions and testicular tumours. The metabolites contributing to the medicinal properties of H. hemerocallidea have been identified in several studies and, more recently, the active terpenoids of the plant were profiled. However, the biosynthetic pathways and the enzymes involved in the production of the terpene metabolites in H. hemerocallidea have not been characterised at a transcriptomic or proteomic level. In this study, total RNA extracted from the corm, leaf and flower tissues of H. hemerocallidea was sequenced on the Illumina HiSeq 2500 platform. A total of 143,549 transcripts were assembled de novo using Trinity and 107,131 transcripts were functionally annotated using the nr, GO, COG, KEGG and SWISS-PROT databases. Additionally, the proteome of the three tissues were sequenced using LC-MS/MS, revealing aspects of secondary metabolism and serving as data validation for the transcriptome. Functional annotation led to the identification of numerous terpene synthases such as nerolidol synthase, germacrene D synthase, and cycloartenol synthase amongst others. Annotations also revealed a transcript encoding the terpene synthase phytoalexin momilactone A synthase. Differential expression analysis using edgeR identified 946 transcripts differentially expressed between the three tissues and revealed that the leaf upregulates linalool synthase compared to the corm and the flower tissues. The transcriptome as well as the proteome of Hypoxis hemerocallidea presented here provide a foundation for future research.

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Functional characterisation of the transcriptome from leaf tissue of the fluoroacetate-producing plant, Dichapetalum cymosum, in response to mechanical wounding

Scientific Reports ◽

10.1038/s41598-020-77598-7 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Selisha A. Sooklal ◽

Phelelani T. Mpangase ◽

Mihai-Silviu Tomescu ◽

Shaun Aron ◽

Scott Hazelhurst ◽

...

Keyword(s):

Differential Expression Analysis ◽

Leaf Tissue ◽

Wound Response ◽

Future Research ◽

Mechanical Wounding ◽

Illumina Hiseq ◽

Functional Characterisation ◽

Wound Responses ◽

Illumina Hiseq Platform ◽

And Function

AbstractDichapetalum cymosum produces the toxic fluorinated metabolite, fluoroacetate, presumably as a defence mechanism. Given the rarity of fluorinated metabolites in nature, the biosynthetic origin and function of fluoroacetate have been of particular interest. However, the mechanism for fluorination in D. cymosum was never elucidated. More importantly, there is a severe lack in knowledge on a genetic level for fluorometabolite-producing plants, impeding research on the subject. Here, we report on the first transcriptome for D. cymosum and investigate the wound response for insights into fluorometabolite production. Mechanical wounding studies were performed and libraries of the unwounded (control) and wounded (30 and 60 min post wounding) plant were sequenced using the Illumina HiSeq platform. A combined reference assembly generated 77,845 transcripts. Using the SwissProt, TrEMBL, GO, eggNOG, KEGG, Pfam, EC and PlantTFDB databases, a 69% annotation rate was achieved. Differential expression analysis revealed the regulation of 364 genes in response to wounding. The wound responses in D. cymosum included key mechanisms relating to signalling cascades, phytohormone regulation, transcription factors and defence-related secondary metabolites. However, the role of fluoroacetate in inducible wound responses remains unclear. Bacterial fluorinases were searched against the D. cymosum transcriptome but transcripts with homology were not detected suggesting the presence of a potentially different fluorinating enzyme in plants. Nevertheless, the transcriptome produced in this study significantly increases genetic resources available for D. cymosum and will assist with future research into fluorometabolite-producing plants.

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Freshwater mussels (Unionidae) brought into captivity exhibit up-regulation of genes involved in stress and energy metabolism

Scientific Reports ◽

10.1038/s41598-021-81856-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ieva Roznere ◽

Brandon T. Sinn ◽

Marymegan Daly ◽

G. Thomas Watters

Keyword(s):

Immune Response ◽

Energy Metabolism ◽

De Novo ◽

Differential Expression Analysis ◽

Freshwater Mussel ◽

Gill Tissue ◽

The United States ◽

Illumina Hiseq ◽

Functional Annotations ◽

Shock Proteins

AbstractApproximately two thirds of freshwater mussel species in the United States and Canada are imperiled, and populations are declining rapidly. Translocation and captive management are commonly used to mitigate losses of freshwater mussel biodiversity, but these conservation tools may result in decreased growth and increased mortality. This study uses RNA-Seq to determine how translocation into captivity affects gene expression in Amblema plicata. Mussels were collected from the Muskingum River in Ohio, USA and brought into a captive holding facility. RNA was extracted from gill tissue 11 months post translocation from mussels in captivity and the Muskingum River on the same day. RNA was sequenced on an Illumina HiSeq 2500, and differential expression analysis was performed on de novo assembled transcripts. More than 1200 transcripts were up-regulated in captive mussels, and 246 were assigned functional annotations. Many up-regulated transcripts were involved in energy metabolism and the stress response, such as heat shock proteins and antioxidants. More than 500 transcripts were down-regulated in captive mussels, and 41 were assigned functional annotations. We observed an over-representation of down-regulated transcripts associated with immune response. Our work suggests that A. plicata experienced moderate levels of stress and altered energy metabolism and immune response for at least 11 months post translocation into captivity.

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A novel terpene synthase produces an anti-aphrodisiac pheromone in the butterfly Heliconius melpomene

10.1101/779678 ◽

2019 ◽

Cited By ~ 6

Author(s):

Kathy Darragh ◽

Anna Orteu ◽

Kelsey J. R. P. Byers ◽

Daiane Szczerbowski ◽

Ian A. Warren ◽

...

Keyword(s):

De Novo ◽

Floral Scent ◽

Ips Pini ◽

Evolutionary Origin ◽

Insect Species ◽

Terpene Synthase ◽

Terpene Synthases ◽

Common Component ◽

Heliconius Melpomene ◽

Aphrodisiac Pheromone

AbstractTerpenes, a group of structurally diverse compounds, are the biggest class of secondary metabolites. While the biosynthesis of terpenes by enzymes known as terpene synthases (TPSs) has been described in plants and microorganisms, few TPSs have been identified in insects, despite the presence of terpenes in multiple insect species. Indeed, in many insect species, it remains unclear whether terpenes are sequestered from plants or biosynthesised de novo. No homologs of plant TPSs have been found in insect genomes, though insect TPSs with an independent evolutionary origin have been found in Hemiptera and Coleoptera. In the butterfly Heliconius melpomene, the monoterpene (E)-β-ocimene acts as an anti-aphrodisiac pheromone, where it is transferred during mating from males to females to avoid re-mating by deterring males. To date only one insect monoterpene synthase has been described, in Ips pini (Coleoptera), and is a multifunctional TPS and isoprenyl diphosphate synthase (IDS). Here, we combine linkage mapping and expression studies to identify candidate genes involved in the biosynthesis of (E)-β-ocimene. We confirm that H. melpomene has two enzymes that exhibit TPS activity, and one of these, HMEL037106g1 is able to synthesise (E)-β-ocimene in vitro. Unlike the enzyme in Ips pini, these enzymes only exhibit residual IDS activity, suggesting they are more specialised TPSs, akin to those found in plants. Phylogenetic analysis shows that these enzymes are unrelated to previously described plant and insect TPSs. The distinct evolutionary origin of TPSs in Lepidoptera suggests that they have evolved multiple times in insects.Significance statementTerpenes are a diverse class of natural compounds, used by both plants and animals for a variety of functions, including chemical communication. In insects it is often unclear whether they are synthesised de novo or sequestered from plants. Some plants and insects have converged to use the same compounds. For instance, (E)-β-ocimene is a common component of floral scent and is also used by the butterfly Heliconius melpomene as an anti-aphrodisiac pheromone. We describe two novel terpene synthases, one of which synthesises (E)-β-ocimene in H. melpomene, unrelated not only to plant enzymes but also other recently identified insect terpene synthases. This provides the first evidence that the ability to synthesise terpenes has arisen multiple times independently within the insects.

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De novo Sequencing and Analysis of Salvia hispanica Tissue-Specific Transcriptome and Identification of Genes Involved in Terpenoid Biosynthesis

Plants ◽

10.3390/plants9030405 ◽

2020 ◽

Vol 9 (3) ◽

pp. 405

Author(s):

James Wimberley ◽

Joseph Cahill ◽

Hagop S. Atamian

Keyword(s):

Fatty Acid ◽

De Novo ◽

Fatty Acid Content ◽

Differential Expression Analysis ◽

Food Supplement ◽

Healthy Food ◽

Terpene Synthase ◽

Illumina Platform ◽

Salvia Hispanica ◽

Polyunsaturated Fatty Acid Content

Salvia hispanica (commonly known as chia) is gaining popularity worldwide as a healthy food supplement due to its low saturated fatty acid and high polyunsaturated fatty acid content, in addition to being rich in protein, fiber, and antioxidants. Chia leaves contain plethora of secondary metabolites with medicinal properties. In this study, we sequenced chia leaf and root transcriptomes using the Illumina platform. The short reads were assembled into contigs using the Trinity software and annotated against the Uniprot database. The reads were de novo assembled into 103,367 contigs, which represented 92.8% transcriptome completeness and a diverse set of Gene Ontology terms. Differential expression analysis identified 6151 and 8116 contigs significantly upregulated in the leaf and root tissues, respectively. In addition, we identified 30 contigs belonging to the Terpene synthase (TPS) family and demonstrated their evolutionary relationships to tomato TPS family members. Finally, we characterized the expression of S. hispanica TPS members in leaves subjected to abiotic stresses and hormone treatments. Abscisic acid had the most pronounced effect on the expression of the TPS genes tested in this study. Our work provides valuable community resources for future studies aimed at improving and utilizing the beneficial constituents of this emerging healthy food source.

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Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea)

Scientific Reports ◽

10.1038/s41598-021-94545-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Tongqing Zhang ◽

Jiawen Yin ◽

Shengkai Tang ◽

Daming Li ◽

Xiankun Gu ◽

...

Keyword(s):

De Novo ◽

Corbicula Fluminea ◽

Gene Families ◽

Ruditapes Philippinarum ◽

Genomic Sequences ◽

Future Research ◽

Asian Clam ◽

Sequencing Technologies ◽

East And Southeast Asia ◽

Clam Corbicula

AbstractThe Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve, which is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is rich in protein, amino acids, and microelements. The genome of C. fluminea has not yet been characterized; therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The phylogenetic tree showed that C. fluminea diverged from Ruditapes philippinarum, ~ 228.89 million years ago (Mya), and the genomes of C. fluminea and R. philippinarum shared 244 syntenic blocks. Additionally, we identified 2 MITF members and 99 NLRP members in C. fluminea genome. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research.

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Cohort profile of Acutelines: a large data/biobank of acute and emergency medicine

BMJ Open ◽

10.1136/bmjopen-2020-047349 ◽

2021 ◽

Vol 11 (7) ◽

pp. e047349

Author(s):

Ewoud ter Avest ◽

Barbara C van Munster ◽

Raymond J van Wijk ◽

Sanne Tent ◽

Sanne Ter Horst ◽

...

Keyword(s):

Acute Care ◽

De Novo ◽

Medical Center ◽

Large Data ◽

Future Research ◽

Imaging Data ◽

Novel Studies ◽

Long Term Follow Up ◽

Registration Number

PurposeResearch in acute care faces many challenges, including enrolment challenges, legal limitations in data sharing, limited funding and lack of singular ownership of the domain of acute care. To overcome these challenges, the Center of Acute Care of the University Medical Center Groningen in the Netherlands, has established a de novo data, image and biobank named ‘Acutelines’.ParticipantsClinical data, imaging data and biomaterials (ie, blood, urine, faeces, hair) are collected from patients presenting to the emergency department (ED) with a broad range of acute disease presentations. A deferred consent procedure (by proxy) is in place to allow collecting data and biomaterials prior to obtaining written consent. The digital infrastructure used ensures automated capturing of all bed-side monitoring data (ie, vital parameters, electrophysiological waveforms) and securely importing data from other sources, such as the electronic health records of the hospital, ambulance and general practitioner, municipal registration and pharmacy. Data are collected from all included participants during the first 72 hours of their hospitalisation, while follow-up data are collected at 3 months, 1 year, 2 years and 5 years after their ED visit.Findings to dateEnrolment of the first participant occurred on 1 September 2020. During the first month, 653 participants were screened for eligibility, of which 180 were approached as potential participants. In total, 151 (84%) provided consent for participation of which 89 participants fulfilled criteria for collection of biomaterials.Future plansThe main aim of Acutelines is to facilitate research in acute medicine by providing the framework for novel studies and issuing data, images and biomaterials for future research. The protocol will be extended by connecting with central registries to obtain long-term follow-up data, for which we already request permission from the participant.Trial registration numberNCT04615065.

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Health system wide “big data” analysis of rheumatologic conditions and scleritis

BMC Ophthalmology ◽

10.1186/s12886-020-01769-3 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Meghan K. Berkenstock ◽

Andrew R. Carey

Keyword(s):

Relative Risk ◽

Health System ◽

Systemic Disease ◽

Autoimmune Disorder ◽

Future Research ◽

Inflammatory Conditions ◽

Autoimmune Conditions ◽

Icd 10 ◽

Autoimmune Condition ◽

Referral Bias

Abstract Background The development of scleritis in the setting of autoimmune conditions has been well documented. Prior series have assessed the relationship between systemic autoimmune disorders and scleritis only in patients referred for rheumatologic or ocular inflammation. This can lead to a referral bias. We reviewed all charts within the electronic medical record (EMR) of a health system for patients with systemic autoimmune and scleritis diagnoses to determine the prevalence of both and which disorders had the highest relative risk of developing scleritis. Methods The EMR was searched for scleritis and systemic inflammatory diagnoses in the past medical history and diagnosis tabs, and for associated disease specific laboratory values. The intersection of scleritis and systemic inflammatory conditions was assessed through searching both SNOMED Clinical Terminology and ICD-10 codes for diagnoses. The prevalence of each autoimmune disorder, scleritis prevalence, the percentage of patients with an autoimmune condition having scleritis, the percentage of patients with scleritis having an autoimmune condition; the relative risk (RR) of scleritis patients having a specific autoimmune disorder were calculated. Results A total of 5.9 million charts were searched with autoimmune conditions identified in 148,993 patients. The most common autoimmune conditions overall were HLA-B27-associated diseases (n = 26,680; prevalence 0.45%); rheumatoid arthritis (RA)(N = 19,923; prevalence 0.34%). Conversely, 2702 patients were identified with scleritis (prevalence 0.05%), of which 31.4% had an associated autoimmune condition. Patients with RA represented the highest percentage of patients with an autoimmune condition having scleritis. Granulomatosis with polyangiitis (GPA) represented the highest the percentage of patients with scleritis having an autoimmune condition. Sjogrens was the third most common condition associated with scleritis- making up 4.5% of cases. An association with juvenile idiopathic arthritis (JIA) was seen in 0.3% of patients. Conclusions While this is the largest retrospective review examining the association between autoimmune disease and scleritis, the findings are similar to prior studies with nearly a third of scleritis patients having an underlying autoimmune diagnosis. Limitations of the study included accurate chart coding; having laboratory results within the searchable EMR. Future research is needed to delineate associations of systemic disease with the anatomic location of scleritis using EMR.

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Abstract P625: Non-coding Rna Regulation Of Gene Expression In Angiotensin Ii-induced Vascular Damage

Hypertension ◽

10.1161/hyp.66.suppl_1.p625 ◽

2015 ◽

Vol 66 (suppl_1) ◽

Author(s):

Kugeng Huo ◽

Tlili Barhoumi ◽

Júlio C Fraulob-Aquino ◽

Chantal Richer ◽

Mathieu Lajoie ◽

...

Keyword(s):

Gene Expression ◽

Differential Expression Analysis ◽

Regulation Of Gene Expression ◽

Vascular Damage ◽

Mesenteric Arteries ◽

Functional Enrichment ◽

Molecular Networks ◽

Mirna Cluster ◽

Ang Ii ◽

Illumina Hiseq

Introduction: Non-coding RNAs (ncRNAs), including long ncRNAs (lncRNAs) and microRNAs (miRs), account for ~98% of the transcribed RNAs. They have been shown to play a role in cardiovascular disease. Vascular damage is an early manifestation and a cause of end-organ damage in hypertension. However, it is unknown whether ncRNAs are involved in the development of vascular injury in hypertension. We hypothesize that ncRNA regulation participates in mechanisms of vascular remodeling and plays an important role in the pathophysiology of hypertension. Methods and Results: Ten-week old male C57BL/6 mice were infused or not with angiotensin (Ang) II for 14 days. Systolic blood pressure (BP) determined by telemetry was increased by Ang II infusion compared to control (146±8 vs 113±5 mmHg, P<0.001). Total RNA was extracted from mesenteric arteries for total and small RNA deep sequencing using Illumina HiSeq-2500. Sequences were aligned to the mm10 genome with STAR, annotated and counted using HTSeq-count or miRDeep2. Differential expression analysis was done in R. Differentially expressed (DE) mRNAs (550 up & 266 down), lncRNAs (7 up & 42 down), miRs (23 up & 12 down) were identified in the Ang II-treated group (1.5 fold change, q<0.05). Targetscan was used to predict interactions between DE miRs and the inversely correlated DE mRNAs or DE lncRNAs. MEME Suite was used to predict DE transcription factor binding sites in the promoter region of genes encoding DE mRNAs, lncRNAs and miRs. Cytoscape was used to construct molecular networks integrating the above interactions and the gene expression profile and to perform functional enrichment analysis, which revealed enrichment of extracellular matrix and developmental processes in DE miR-targeting DE mRNAs (q<1E-20). Ten DE miRNAs whose expression levels correlated (P<0.05) with BP were identified, 9 of which are located in a single miRNA cluster that is conserved in humans. Conclusions: We have identified a conserved miRNA cluster that may play a pivotal role in the regulation of vascular damage in hypertension. A sub-network of genes that participates in the interaction between the miRNA cluster and other BP-correlated RNAs was selected for future investigation to identify therapeutic targets.

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De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes

BMC Genomics ◽

10.1186/s12864-019-6157-4 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 3

Author(s):

Inés González-Castellano ◽

Chiara Manfrin ◽

Alberto Pallavicini ◽

Andrés Martínez-Lage

Keyword(s):

Transcriptome Analysis ◽

De Novo ◽

Expression Patterns ◽

Gonadal Development ◽

Differentially Expressed ◽

Rna Seq ◽

Illumina Hiseq ◽

Specific Expression ◽

Development Processes ◽

The Common

Abstract Background The common littoral shrimp Palaemon serratus is an economically important decapod resource in some European communities. Aquaculture practices prevent the genetic deterioration of wild stocks caused by overfishing and at the same time enhance the production. The biotechnological manipulation of sex-related genes has the proved potential to improve the aquaculture production but the scarcity of genomic data about P. serratus hinders these applications. RNA-Seq analysis has been performed on ovary and testis samples to generate a reference gonadal transcriptome. Differential expression analyses were conducted between three ovary and three testis samples sequenced by Illumina HiSeq 4000 PE100 to reveal sex-related genes with sex-biased or sex-specific expression patterns. Results A total of 224.5 and 281.1 million paired-end reads were produced from ovary and testis samples, respectively. De novo assembly of ovary and testis trimmed reads yielded a transcriptome with 39,186 transcripts. The 29.57% of the transcriptome retrieved at least one annotation and 11,087 differentially expressed genes (DEGs) were detected between ovary and testis replicates. Six thousand two hundred seven genes were up-regulated in ovaries meanwhile 4880 genes were up-regulated in testes. Candidate genes to be involved in sexual development and gonadal development processes were retrieved from the transcriptome. These sex-related genes were discussed taking into account whether they were up-regulated in ovary, up-regulated in testis or not differentially expressed between gonads and in the framework of previous findings in other crustacean species. Conclusions This is the first transcriptome analysis of P. serratus gonads using RNA-Seq technology. Interesting findings about sex-related genes from an evolutionary perspective (such as Dmrt1) and for putative future aquaculture applications (Iag or vitellogenesis genes) are reported here. We provide a valuable dataset that will facilitate further research into the reproductive biology of this shrimp.

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De novo transcriptome and tissue specific expression analysis of genes associated with biosynthesis of secondary metabolites in Operculina turpethum (L.)

Scientific Reports ◽

10.1038/s41598-021-01906-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Bhagyashree Biswal ◽

Biswajit Jena ◽

Alok Kumar Giri ◽

Laxmikanta Acharya

Keyword(s):

Secondary Metabolite ◽

De Novo ◽

Differentially Expressed Gene ◽

Homology Search ◽

Biosynthesis Pathway ◽

Terpenoid Biosynthesis ◽

De Novo Transcriptome ◽

Illumina Hiseq ◽

Secondary Metabolite Biosynthesis ◽

Root Tissues

AbstractThis study reported the first-ever de novo transcriptome analysis of Operculina turpethum, a high valued endangered medicinal plant, using the Illumina HiSeq 2500 platform. The de novo assembly generated a total of 64,259 unigenes and 20,870 CDS (coding sequence) with a mean length of 449 bp and 571 bp respectively. Further, 20,218 and 16,458 unigenes showed significant similarity with identified proteins of NR (non-redundant) and UniProt database respectively. The homology search carried out against publicly available database found the best match with Ipomoea nil sequences (82.6%). The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis identified 6538 unigenes functionally assigned to 378 modules with phenylpropanoid biosynthesis pathway as the most enriched among the secondary metabolite biosynthesis pathway followed by terpenoid biosynthesis. A total of 17,444 DEGs were identified among which majority of the DEGs (Differentially Expressed Gene) involved in secondary metabolite biosynthesis were found to be significantly upregulated in stem as compared to root tissues. The qRT-PCR validation of 9 unigenes involved in phenylpropanoid and terpenoid biosynthesis also showed a similar expression pattern. This finding suggests that stem tissues, rather than root tissues, could be used to prevent uprooting of O. turpethum in the wild, paving the way for the plant's effective conservation. Moreover, the study formed a valuable repository of genetic information which will provide a baseline for further molecular research.

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