Full-Length Transcriptome Sequencing Provides Insights into Flavonoid Biosynthesis in Fritillaria hupehensis

One of the most commonly utilized medicinal plants in China is Fritillaria hupehensis (Hsiao et K.C. Hsia). However, due to a lack of genomic resources, little is known about the biosynthesis of relevant compounds, particularly the flavonoid biosynthesis pathway. A PacBio RS II sequencing generated a total of 342,044 reads from the bulb, leaf, root, and stem, of which 316,438 were full-length (FL) non-redundant reads with an average length of 1365 bp and a N50 of 1888 bp. There were also 38,607 long non-coding RNAs and 7914 simple sequence repeats detected. To improve our understanding of processes implicated in regulating secondary metabolite biosynthesis in F. hupehensis tissues, we evaluated potential metabolic pathways. Overall, this study provides a repertoire of FL transcripts in F. hupehensis for the first time, and it will be a valuable resource for marker-assisted breeding and research into bioactive compounds for medicinal and pharmacological applications.

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Full-Length Transcriptome of Thalassiosira weissflogii as a Reference Resource and Mining of Chitin-Related Genes

Marine Drugs ◽

10.3390/md19070392 ◽

2021 ◽

Vol 19 (7) ◽

pp. 392

Author(s):

Haomiao Cheng ◽

Chris Bowler ◽

Xiaohui Xing ◽

Vincent Bulone ◽

Zhanru Shao ◽

...

Keyword(s):

Cell Wall ◽

Full Length ◽

Biosynthetic Pathways ◽

Glycosidic Linkage ◽

Thalassiosira Weissflogii ◽

Ecological Value ◽

Pacbio Sequencing ◽

Non Coding Rnas ◽

Chitin And Chitosan ◽

Simple Sequence

β-Chitin produced by diatoms is expected to have significant economic and ecological value due to its structure, which consists of parallel chains of chitin, its properties and the high abundance of diatoms. Nevertheless, few studies have functionally characterised chitin-related genes in diatoms owing to the lack of omics-based information. In this study, we first compared the chitin content of three representative Thalassiosira species. Cell wall glycosidic linkage analysis and chitin/chitosan staining assays showed that Thalassiosira weissflogii was an appropriate candidate chitin producer. A full-length (FL) transcriptome of T. weissflogii was obtained via PacBio sequencing. In total, the FL transcriptome comprised 23,362 annotated unigenes, 710 long non-coding RNAs (lncRNAs), 363 transcription factors (TFs), 3113 alternative splicing (AS) events and 3295 simple sequence repeats (SSRs). More specifically, 234 genes related to chitin metabolism were identified and the complete biosynthetic pathways of chitin and chitosan were explored. The information presented here will facilitate T. weissflogii molecular research and the exploitation of β-chitin-derived high-value enzymes and products.

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Transcriptomic Analysis of Marine Gastropod Hemifusus tuba Provides Novel Insights into Conotoxin Genes

Marine Drugs ◽

10.3390/md17080466 ◽

2019 ◽

Vol 17 (8) ◽

pp. 466 ◽

Cited By ~ 2

Author(s):

Ronghua Li ◽

Michaël Bekaert ◽

Luning Wu ◽

Changkao Mu ◽

Weiwei Song ◽

...

Keyword(s):

High Throughput Sequencing ◽

De Novo ◽

Average Length ◽

Bioactive Molecules ◽

Asian Countries ◽

Marine Gastropod ◽

Sequencing Technologies ◽

First Time ◽

Aquaculture Development ◽

Simple Sequence

The marine gastropod Hemifusus tuba is served as a luxury food in Asian countries and used in traditional Chinese medicine to treat lumbago and deafness. The lack of genomic data on H. tuba is a barrier to aquaculture development and functional characteristics of potential bioactive molecules are poorly understood. In the present study, we used high-throughput sequencing technologies to generate the first transcriptomic database of H. tuba. A total of 41 unique conopeptides were retrieved from 44 unigenes, containing 6-cysteine frameworks belonging to four superfamilies. Duplication of mature regions and alternative splicing were also found in some of the conopeptides, and the de novo assembly identified a total of 76,306 transcripts with an average length of 824.6 nt, of which including 75,620 (99.1%) were annotated. In addition, simple sequence repeats (SSRs) detection identified 14,000 unigenes containing 20,735 SSRs, among which, 23 polymorphic SSRs were screened. Thirteen of these markers could be amplified in Hemifusus ternatanus and seven in Rapana venosa. This study provides reports of conopeptide genes in Buccinidae for the first time as well as genomic resources for further drug development, gene discovery and population resource studies of this species.

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Simple sequence repeat (SSR) markers linked to E1, E3, E4, and E7 maturity genes in soybean

Genome ◽

10.1139/g03-079 ◽

2003 ◽

Vol 46 (6) ◽

pp. 1024-1036 ◽

Cited By ~ 63

Author(s):

Stephen J Molnar ◽

Satish Rai ◽

Martin Charette ◽

Elroy R Cober

Keyword(s):

Molecular Markers ◽

Reproductive Period ◽

Soybean Genome ◽

Isogenic Line ◽

Near Isogenic Lines ◽

Marker Assisted Breeding ◽

Trait Locus ◽

First Time ◽

Map Location ◽

Simple Sequence

Soybean near isogenic lines (NILs), contrasting for maturity and photoperiod sensitivity loci, were genotyped with approximately 430 mapped simple sequence repeats (SSRs), also known as microsatellite markers. By analysis of allele distributions across the NILs, it was possible to confirm the map location of the Dt1 indeterminate growth locus, to refine the SSR mapping of the T tawny pubescence locus, to map E1 and E3 maturity loci with molecular markers, and to map the E4 and E7 maturity loci for the first time. Molecular markers flanking these loci are now available for marker-assisted breeding for these traits. Analysis of map locations identified a putative homologous relationship among four chromosomal regions; one in the middle of linkage group (LG) C2 carrying E1 and E7, one on LG I carrying E4, one at the top of LG C2, at which there is a reproductive period quantitative trait locus (QTL), and the fourth on LG B1. Other evidence suggests that homology also exists between the E1 + E7 region on LG C2 and a region on LG L linked to a pod maturity QTL. Homology relationships predict possible locations in the soybean genome of additional maturity loci, as well as which maturity loci may share a common evolutionary origin and similar mechanism(s) of action.Key words: soybean, maturity, photoperiod, microsatellite marker, near isogenic line.

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Reconstruction and functional annotation of Ascosphaera apis full-length transcriptome via PacBio single-molecule long-read sequencing

10.1101/770040 ◽

2019 ◽

Author(s):

Dafu Chen ◽

Yu Du ◽

Xiaoxue Fan ◽

Zhiwei Zhu ◽

Haibin Jiang ◽

...

Keyword(s):

Single Molecule ◽

Average Length ◽

Full Length ◽

Ascosphaera Apis ◽

Protein Coding ◽

Entomogenous Fungi ◽

Consensus Sequences ◽

Long Read ◽

Non Coding Rnas ◽

Lower Expression

AbstractAscosphaera apis is a widespread fungal pathogen of honeybee larvae that results in chalkbrood disease, leading to heavy losses for the beekeeping industry in China and many other countries. This work was aimed at generating a full-length transcriptome of A. apis using PacBio single-molecule real-time (SMRT) sequencing. Here, more than 23.97 Gb of clean reads was generated from long-read sequencing of A. apis mecylia, including 464,043 circular consensus sequences (CCS) and 394,142 full-length non-chimeric (FLNC) reads. In total, we identified 174,095 high-confidence transcripts covering 5141 known genes with an average length of 2728 bp. We also discovered 2405 genic loci and 11,623 isoforms that have not been annotated yet within the current reference genome. Additionally, 16,049, 10,682, 4520 and 7253 of the discovered transcripts have annotations in the Non-redundant protein (Nr), Clusters of Eukaryotic Orthologous Groups (KOG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Moreover, 1205 long non-coding RNAs (lncRNAs) were identified, which have less exons, shorter exon and intron lengths, shorter transcript lengths, lower GC percent, lower expression levels, and fewer alternative splicing (AS) evens, compared with protein-coding transcripts. A total of 253 members from 17 transcription factor (TF) families were identified from our transcript datasets. Finally, the expression of A. apis isoforms was validated using a molecular approach. Overall, this is the first report of a full-length transcriptome of entomogenous fungi including A. apis. Our data offer a comprehensive set of reference transcripts and hence contributes to improving the genome annotation and transcriptomic study of A. apis.

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The mechanism of full activation of tumor suppressor PTEN at the phosphatidylinositol-enriched membrane

10.1101/2021.01.06.425565 ◽

2021 ◽

Author(s):

Hyunbum Jang ◽

Iris Nira Smith ◽

Charis Eng ◽

Ruth Nussinov

Keyword(s):

Drug Discovery ◽

Cell Growth ◽

Tumor Suppressor ◽

Full Length ◽

Detailed Mechanism ◽

Explicit Solvent ◽

Signaling Lipids ◽

Cell Growth And Proliferation ◽

First Time ◽

Full Activation

AbstractTumor suppressor PTEN dephosphorylates signaling lipid PIP3 produced by PI3Ks. Abundant PIP3 promotes cell growth and proliferation. PTEN is the second most highly mutated protein in cancer and is drugless. The detailed mechanism at the membrane of this pivotal phosphatase is unknown hindering understanding and drug discovery. Here for the first time, exploiting explicit solvent simulations, we tracked full-length PTEN trafficking from the cytosol to the membrane, its interaction with membranes composed of zwitterionic phosphatidylcholine and anionic phosphatidylserine and phosphatidylinositol, including signaling lipids PIP2 and PIP3, and moving away from the zwitterionic and getting absorbed onto the anionic membrane that harbors the PIP3. PIP3 then allosterically unfolds the N-terminal PIP2 binding domain, translocating it to the membrane where its polybasic motif interacts with PIP2, localizing on microdomains enriched in signaling lipids, as PI3K does. Finally, we determined PTEN catalytic action at the membrane, all in line with available experimental observations.

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Transcriptome analysis of two contrasting genotypes of pearl millet to gain insight into heat stress responses

10.21203/rs.3.rs-23605/v1 ◽

2020 ◽

Author(s):

Albert Maibam ◽

Sunil Nigombam ◽

Harinder Vishwakarma ◽

Showkat Ahmad Lone ◽

Kishor Gaikwad ◽

...

Keyword(s):

Heat Stress ◽

Pearl Millet ◽

Stress Responses ◽

Simple Sequence Repeats ◽

Pennisetum Glaucum ◽

Average Length ◽

Gc Content ◽

Functional Markers ◽

Sequencing Data ◽

Simple Sequence

Abstract Background Pennisetum glaucum (L.) R. Br. is mainly grown in arid and semi-arid regions. Being naturally tolerant to various adverse condtitions, it is a good biological resource for deciphering the molecular basis of abiotic stresses such as heat stress in plants but limited studies have been carried out till date to this effect. Here, we performed RNA-sequencing from the leaf of two contrasting genotypes of pearl millet (841-B and PPMI-69) subjected to heat stress (42 °C for 6 h). Results Over 274 million high quality reads with an average length of 150 nt were generated. Assembly was carried out using trinity, obtaining 47,310 unigenes having an average length of 1254 nucleotides, N50 length of 1853 nucleotides and GC content of 53.11%. Blastx resulted in annotation of 35,628 unigenes and functional classification showed 15,950 unigenes designated to 51 Gene Ontology terms, 13,786 unigenes allocated to 23 Clusters of Orthologous Groups and 4,255 unigenes distributed into 132 functional KEGG pathways. 12,976 simple sequence repeats were identified from 10,294 unigenes for the development of functional markers. A total of 3,05,759 SNPs were observed in the transcriptome data. Out of 2,301 differentially expressed genes, 10 potential candidates genes were selected based on log2 fold change and adjusted p-value parameters for their differential gene expression by qRT-PCR. Conclusions The dynamic expression changes in two genotypes of P. glaucum reflect transcriptome regulation of signaling pathways in heat stress response. In order to develop genetic markers, 12,976 simple sequence repeats (SSRs) were identified. The sequencing data generated in this study shall serve as an important resource for further research in the area of crop biotechnology.

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PacBio Single-Molecule Long-Read Sequencing Reveals Genes Tolerating Manganese Stress in Schima superba Saplings

Frontiers in Genetics ◽

10.3389/fgene.2021.635043 ◽

2021 ◽

Vol 12 ◽

Author(s):

Fiza Liaquat ◽

Muhammad Farooq Hussain Munis ◽

Samiah Arif ◽

Urooj Haroon ◽

Jianxin Shi ◽

...

Keyword(s):

Single Molecule ◽

Gene Annotation ◽

Treated Group ◽

Full Length ◽

Open Reading Frames ◽

Interacting Protein ◽

Schima Superba ◽

Long Read ◽

First Time ◽

Potential Tool

Schima superba (Theaceae) is a subtropical evergreen tree and is used widely for forest firebreaks and gardening. It is a plant that tolerates salt and typically accumulates elevated amounts of manganese in the leaves. With large ecological amplitude, this tree species grows quickly. Due to its substantial biomass, it has a great potential for soil remediation. To evaluate the thorough framework of the mRNA, we employed PacBio sequencing technology for the first time to generate S. Superba transcriptome. In this analysis, overall, 511,759 full length non-chimeric reads were acquired, and 163,834 high-quality full-length reads were obtained. Overall, 93,362 open reading frames were obtained, of which 78,255 were complete. In gene annotation analyses, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Genes (COG), Gene Ontology (GO), and Non-Redundant (Nr) databases were allocated 91,082, 71,839, 38,914, and 38,376 transcripts, respectively. To identify long non-coding RNAs (lncRNAs), we utilized four computational methods associated with protein families (Pfam), Cooperative Data Classification (CPC), Coding Assessing Potential Tool (CPAT), and Coding Non-Coding Index (CNCI) databases and observed 8,551, 9,174, 20,720, and 18,669 lncRNAs, respectively. Moreover, nine genes were randomly selected for the expression analysis, which showed the highest expression of Gene 6 (Na_Ca_ex gene), and CAX (CAX-interacting protein 4) was higher in manganese (Mn)-treated group. This work provided significant number of full-length transcripts and refined the annotation of the reference genome, which will ease advanced genetic analyses of S. superba.

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Discovery and evaluation of a novel step in the flavonoid biosynthesis pathway regulated by F3H gene using a yeast expression system

10.1101/753210 ◽

2019 ◽

Cited By ~ 1

Author(s):

Rahmatullah Jan ◽

Sajjad Asaf ◽

Sanjita Paudel ◽

Sangkyu Lee ◽

Kyung-Min Kim

Keyword(s):

Western Blotting ◽

Rice Plant ◽

Expression System ◽

Plant Secondary Metabolites ◽

Flavonoid Biosynthesis ◽

Yeast Expression ◽

List Type ◽

Biosynthesis Pathway ◽

Yeast Expression System ◽

Flavonoid Biosynthesis Pathway

AbstractKaempferol and quercetin are the essential plant secondary metabolites that confer huge biological functions in the plant defense system. These metabolites are produced in low quantities in plants, therefore engineering microbial factory is a favorable strategy for the production of these metabolites. In this study, biosynthetic pathways for kaempferol and quercetin were constructed in Saccharomyces cerevisiae using naringenin as a substrate. The results elucidated a novel step for the first time in kaempferol and quercetin biosynthesis directly from naringenin catalyzed by flavonol 3-hydroxylase (F3H). F3H gene from rice was cloned into pRS42K yeast episomal plasmid (YEP) vector using BamH1 and Xho1 restriction enzymes. We analyzed our target gene activity in engineered and in empty strains. The results were confirmed through TLC followed by Western blotting, nuclear magnetic resonance (NMR), and LC-MS. TLC showed positive results on comparing both compounds extracted from the engineered strain with the standard reference. Western blotting confirmed lack of Oryza sativa flavonol 3-hydroxylase (OsF3H) activity in empty strains while high OsF3H expression in engineered strains. NMR spectroscopy confirmed only quercetin, while LCMS-MS results revealed that F3H is responsible for naringenin conversion to both kaempferol and quercetin. These results concluded that rice F3H catalyzes naringenin metabolism via hydroxylation and synthesizes kaempferol and quercetin.HighlightsCurrent study is a discovery of a novel step in flavonoid biosynthesis pathway of rice plant.In this study F3H gene from rice plant was functionally expressed in yeast expression system.Results confirmed that, F3H gene is responsible for the canalization of naringenin and converted into kaempferol and quercetin.The results were confirmed through, western blotting, TLC, HPLC and NMR analysis.

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Pollen morphology of the Balkan-Carpathian endemic Campanula lingulata Waldst. & Kit. (Campanulaceae)

Zbornik Matice srpske za prirodne nauke ◽

10.2298/zmspn1630075m ◽

2016 ◽

pp. 75-82

Author(s):

Marina Macukanovic-Jocic ◽

Snezana Jaric

Keyword(s):

Electron Microscopy ◽

Scanning Electron Microscopy ◽

Light Microscopy ◽

Endemic Species ◽

Pollen Morphology ◽

Average Length ◽

Pollen Grains ◽

Polar Axis ◽

First Time ◽

Scanning Electron

Palynomorphological characteristics of Campanula lingulata, the Balkan-Carpathian endemic species growing in Serbia, have been investigated using light microscopy and scanning electron microscopy for the first time, in order to provide some information helpful for a better understanding of the taxonomic position of this species within the genus, as well as to contribute to the pollen atlas of Serbian apiflora. The pollen grains are radially symmetrical, isopolar, 3-zonoporate and medium-sized monads oblate-sphaeroidal in shape. Mean of the polar axis (P) is 27.6?1.9 ?m, while the average length of the equatorial axis (E) is 28.8?1.6 ?m. The apertures are operculate. The sculpturing pattern of the exine is microre?ticulate-microechinatae. The exine surface is covered with evenly distributed supratectal spinules of variable length and sparse granules. The longest supratectal spinules are 0.64?0.05 ?m in length and the smallest sculptural elements are less than 0.2 ?m high. The microechinae density per sample area of 5 ?m x 5 ?m averages 17.4?2.4.

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Colour genes (R and Rc) for grain and coleoptile upregulate flavonoid biosynthesis genes in wheat

Genome ◽

10.1139/g05-026 ◽

2005 ◽

Vol 48 (4) ◽

pp. 747-754 ◽

Cited By ~ 60

Author(s):

Eiko Himi ◽

Ahmed Nisar ◽

Kazuhiko Noda

Keyword(s):

Flavonoid Biosynthesis ◽

R Gene ◽

Homoeologous Group ◽

Wheat Grain ◽

Polyphenol Compounds ◽

Grain Color ◽

Group 3 ◽

Significant Expression ◽

Wheat Lines ◽

Flavonoid Biosynthesis Pathway

Pigmentation of wheat grain and coleoptile is controlled by the R gene on chromosomes of the homoeologous group 3 and the Rc gene on chromosomes of the homoeologous group 7, respectively. Each of these genes is inherited monogenically. The pigment of grain has been suggested to be a derivative of catechin-tannin and that of coleoptile to be anthocyanin. These polyphenol compounds are known to be synthesized through the flavonoid biosynthesis pathway. We isolated 4 partial nucleotide sequences of the early flavonoid biosynthesis genes (CHS, CHI, F3H, and DFR) in wheat. The expression of these genes was examined in the developing grain of red-grained and white-grained wheat lines. CHS, CHI, F3H, and DFR were highly upregulated in the grain coat tissue of the red-grained lines, whereas there was no significant expression in the white-grained lines. These results indicate that the R gene is involved in the activation of the early flavonoid biosynthesis genes. As for coleoptile pigmentation, all 4 genes were expressed in the red coleoptile; however, DFR was not activated in the white coleoptile. The Rc gene appears to be involved in DFR expression. The possibility that wheat R and Rc genes might be transcription factors is discussed.Key words: flavonoid biosynthesis genes, R gene for grain color, Rc gene for coleoptile color, wheat.

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