Comparative transcriptome analysis of high-growth and wild-type strains of Pyropia yezoensis

Pyropia yezoensis (Ueda) M.S.Hwang et H.G.Choi is a popular edible macro-alga that is found mostly in intertidal zones. It is one of the most economically important seaweed species and has been cultivated extensively in the cold waters of East Asia. Various reports have been published on the isolation and characterization of improved strains of Pyropia. However, there are few studies focusing on the molecular basis underlying these mutant strains. In this study, we performed a comparative analysis of whole transcriptomes of wild-type (PyWT) and high-growth (Py500G) strains of P. yezoensis using next generation RNA sequencing (RNA-seq). After sequencing, a total of 167,110,896 paired-end reads with a length of 151 nucleotides, were obtained. De novo transcriptome assembly and redundancy removal generated 19,441 transcripts. The assembly was annotated in NCBI nr, Swiss-Prot, Pfam, KEGG, GO and KOG databases. To unravel the differences in Py500G and PyWT, we mapped Py500G and PyWT reads to the assembly and calculated the expression levels. In total, there were 454 transcripts that were differentially expressed. Among the differentially expressed transcripts, candidate genes were identified with well-known growth and development functions. This study not only identifies candidate genes responsible for the high-growth phenotype of Py500G, but it also provides more comprehensive genomic data for future research on P. yezoensis.

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RNA-Seq and differential gene expression analysis in Temora stylifera copepod females with contrasting non-feeding nauplii survival rates: an environmental transcriptomics study

BMC Genomics ◽

10.1186/s12864-020-07112-w ◽

2020 ◽

Vol 21 (1) ◽

Cited By ~ 2

Author(s):

Ennio Russo ◽

Chiara Lauritano ◽

Giuliana d’Ippolito ◽

Angelo Fontana ◽

Diana Sarno ◽

...

Keyword(s):

Differential Expression ◽

De Novo ◽

Transcriptome Assembly ◽

Survival Rates ◽

Natural Populations ◽

Zooplankton Community ◽

Differentially Expressed ◽

Diatom Cell ◽

Functional Interpretation ◽

Protein Ubiquitination

Abstract Background Copepods are fundamental components of pelagic food webs, but reports on how molecular responses link to reproductive success in natural populations are still scarce. We present a de novo transcriptome assembly and differential expression (DE) analysis in Temora stylifera females collected in the Gulf of Naples, Mediterranean Sea, where this copepod dominates the zooplankton community. High-Throughput RNA-Sequencing and DE analysis were performed from adult females collected on consecutive weeks (May 23rd and 30th 2017), because opposite naupliar survival rates were observed. We aimed at detecting key genes that may have influenced copepod reproductive potential in natural populations and whose expression was potentially affected by phytoplankton-derived oxylipins, lipoxygenase-derived products strongly impacting copepod naupliar survival. Results On the two sampling dates, temperature, salinity, pH and oxygen remained stable, while variations in phytoplankton cell concentration, oxylipin concentration and oxylipin-per-diatom-cell production were observed. T. stylifera naupliar survival was 25% on May 23rd and 93% on May 30th. De novo assembly generated 268,665 transcripts (isoforms) and 120,749 unique ‘Trinity predicted genes’ (unigenes), of which 50% were functionally annotated. Out of the 331 transcript isoforms differentially expressed between the two sampling dates, 119 sequences were functionally annotated (58 up- and 61 down-regulated). Among predicted genes (unigenes), 144 sequences were differentially expressed and 31 (6 up-regulated and 25 down-regulated) were functionally annotated. Most of the significantly down-regulated unigenes and isoforms were A5 Putative Odorant Binding Protein (Obp). Other differentially expressed sequences (isoforms and unigenes) related to developmental metabolic processes, protein ubiquitination, response to stress, oxidation-reduction reactions and hydrolase activities. DE analysis was validated through Real Time-quantitative PCR of 9 unigenes and 3 isoforms. Conclusions Differential expression of sequences involved in signal detection and transduction, cell differentiation and development offered a functional interpretation to the maternally-mediated low naupliar survival rates observed in samples collected on May 23rd. Down-regulation of A5 Obp along with higher quantities of oxylipins-per-litre and oxylipins-per-diatom-cell observed on May 23rd could suggest oxylipin-mediated impairment of naupliar survival in natural populations of T. stylifera. Our results may help identify biomarker genes explaining variations in copepod reproductive responses at a molecular level.

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Transcriptome Analysis of Young Ovaries Reveals Candidate Genes Involved in Gamete Formation in Lantana camara

Plants ◽

10.3390/plants8080263 ◽

2019 ◽

Vol 8 (8) ◽

pp. 263 ◽

Cited By ~ 1

Author(s):

Ze Peng ◽

Krishna Bhattarai ◽

Saroj Parajuli ◽

Zhe Cao ◽

Zhanao Deng

Keyword(s):

Candidate Genes ◽

De Novo ◽

Transcriptome Assembly ◽

Gene Families ◽

Unreduced Gametes ◽

Lantana Camara ◽

Unreduced Gamete ◽

Genomic Resources ◽

Gamete Formation ◽

Gamete Production

Lantana (Lantana camara L., Verbenaceae) is an important ornamental crop, yet can be a highly invasive species. The formation of unreduced female gametes (UFGs) is a major factor contributing to its invasiveness and has severely hindered the development of sterile cultivars. To enrich the genomic resources and gain insight into the genetic mechanisms of UFG formation in lantana, we investigated the transcriptomes of young ovaries of two lantana genotypes, GDGHOP-36 (GGO), producing 100% UFGs, and a cultivar Landmark White Lantana (LWL), not producing UFGs. The de novo transcriptome assembly resulted in a total of 90,641 unique transcript sequences with an N50 of 1692 bp, among which, 29,383 sequences contained full-length coding sequences (CDS). There were 214 transcripts associated with the biological processes of gamete production and 10 gene families orthologous to genes known to control unreduced gamete production in Arabidopsis. We identified 925 transcription factor (TF)-encoding sequences, 91 nucleotide-binding site (NBS)-containing genes, and gene families related to drought/salt tolerance and allelopathy. These genomic resources and candidate genes involved in gamete formation will be valuable for developing new tools to control the invasiveness in L. camara, protect native lantana species, and understand the formation of unreduced gametes in plants.

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Using de novo transcriptome assembly and analysis to study RNAi in Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae)

Scientific Reports ◽

10.1038/s41598-019-49997-y ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 6

Author(s):

Satnam Singh ◽

Mridula Gupta ◽

Suneet Pandher ◽

Gurmeet Kaur ◽

Neha Goel ◽

...

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Instar Nymph ◽

Future Research ◽

Rnai Machinery ◽

Phenacoccus Solenopsis ◽

Atpase Subunit ◽

Molecular Sequence ◽

Rnai Efficiency ◽

Average Size

Abstract Phenacoccus solenopsis is one of the major polyphagous crop pests in India. Inadequate genomic or transcriptomic resources have limited the molecular studies in this insect despite its huge economic importance. The existing molecular sequence resources of this insect were supplemented through RNA sequencing, de novo transcriptome assembly and analysis, which generated 12, 925 CDS from 23,643 contigs with an average size of 1077.5 bp per CDS and 85.1% positive BLAST hits with NCBI Non redundant (nr) database. Twenty three genes involved in RNAi machinery identified through BLASTx search against NCBI nr database suggested the existence of robust RNAi in mealybug. RNAi in P. solenopsis was demonstrated through knockdown of IAP (Inhibitor of Apoptosis), AQP (Aquaporin), CAL (Calcitonin), VATPase (V-type proton ATPase subunit F 1), bursicon, chitin synthase, SNF7 and α-amylase by injecting sequence specific dsRNA of respective genes in adult female. Additionally, feeding RNAi has been demonstrated in 2nd instar nymph through dsRNA uptake in plant. The knockdown of core RNAi machinery genes such as Dicer, Argonaute and Staufen significantly hampered RNAi efficiency in this insect. However, downregulation of dsRNases improved RNAi efficiency. Sequential studies for understanding RNAi in P. solenopsis using transcriptome sequences have also been reported. The present study provides a base for future research on developing RNAi as strategy for management of this pest.

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Identification of cordycepin biosynthesis-related genes through de novo transcriptome assembly and analysis in Cordyceps cicadae

Royal Society Open Science ◽

10.1098/rsos.181247 ◽

2018 ◽

Vol 5 (12) ◽

pp. 181247 ◽

Cited By ~ 3

Author(s):

Tengfei Liu ◽

Ziyao Liu ◽

Xueyan Yao ◽

Ying Huang ◽

Qingsong Qu ◽

...

Keyword(s):

Fruiting Body ◽

De Novo ◽

Transcriptome Assembly ◽

Quantitative Polymerase Chain Reaction ◽

Nucleotide Metabolism ◽

Differentially Expressed ◽

Parasitic Fungus ◽

Active Constituent ◽

Illumina Hiseq ◽

Cordyceps Cicadae

Cordyceps cicadae (Chanhua) is a parasitic fungus that grows on Cicada flammata larvae and is used to relieve exhaustion and treat numerous diseases, in part through its active constituent, cordycepin. We used de novo Illumina HiSeq 4000 sequencing to obtain transcriptomes of C. cicadae mycelium, fruiting body, and sclerotium, and identify differentially expressed genes. In the mycelium versus sclerotium libraries, 1576 upregulated and 2300 downregulated genes were identified. In the mycelium versus fruiting body and fruiting body versus sclerotium body libraries, 1604 and 1474 upregulated and 1365 and 1320 downregulated genes, respectively, were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses identified 19 genes differentially expressed in mycelium versus fruiting body as related to the purine pathway, along with 28 and 16 genes differentially expressed in the mycelium versus sclerotium and fruiting body versus sclerotium groups, respectively. Gene expression of six key enzymes was validated by quantitative polymerase chain reaction. Specifically, 5′-nucleotidase (c62060g1) and adenosine deaminase (c35629g1) in purine nucleotide metabolism, which are involved in cordycepin biosynthesis, were significantly upregulated in the sclerotium group. These findings improved our understanding of genes involved in the biosynthesis of cordycepin and other characteristic secondary metabolites in C. cicadae .

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De novo transcriptome assembly and quantification reveal differentially expressed genes between soft-seed and hard-seed pomegranate (Punica granatum L.)

PLoS ONE ◽

10.1371/journal.pone.0178809 ◽

2017 ◽

Vol 12 (6) ◽

pp. e0178809 ◽

Cited By ~ 15

Author(s):

Hui Xue ◽

Shangyin Cao ◽

Haoxian Li ◽

Jie Zhang ◽

Juan Niu ◽

...

Keyword(s):

Differentially Expressed Genes ◽

De Novo ◽

Transcriptome Assembly ◽

Punica Granatum ◽

Differentially Expressed ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome ◽

Hard Seed ◽

Punica Granatum L

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Transcriptional profiling of Impatiens walleriana genes through different stages of downy mildew infection reveals novel genes involved in disease susceptibility

10.1101/622480 ◽

2019 ◽

Author(s):

Stephanie Suarez ◽

Zunaira Afzal Naveed ◽

Gul Shad Ali

Keyword(s):

Downy Mildew ◽

Disease Susceptibility ◽

De Novo ◽

Transcriptome Assembly ◽

Transcriptional Profiling ◽

Differential Expression Analysis ◽

Plant Stress ◽

Differentially Expressed ◽

Mildew Resistance ◽

Impatiens Walleriana

AbstractImpatiens downy mildew is a highly destructive disease of Impatiens walleriana, and economically important bedding ornamental crop. This disease is caused by a recently emerged pathogen Plasmopara obducens. Since both the host and pathogen are relatively less studied, there are only a few genomic resources available for both I. walleriana and P. obducens. In this study, we have analyzed transcriptional changes in I. walleriana in response to P. obducens infection during different stages of disease development. Our main goal was to identify candidate genes that may be involved in I. walleriana susceptibility to P. obducens. Since the genome of I. walleriana is not available publicly, we constructed and optimized a de novo transcriptome assembly consisting of 73,022 transcripts. Differential expression analysis based on this optimized de novo transcriptome assembly revealed 3,000 to 4,500 differentially expressed transcripts (DETs) at 0 hr, 12 hr, 48 hr, 120 hr, and 240 hr time points after infection. Functional annotation of these DETs revealed that numerous plant stress responsive genes are activated and deactivated throughout the infection cycle. Genes in the calcium signaling pathways, receptor-like kinases (RLKs) including 10 disease resistance associated RLK transcripts, powdery mildew resistance genes (MLO), and many other plant stress related genes were predominantly differentially expressed in I. walleriana in response to P. obducens. Analyses reported here provides molecular insights into the disease susceptibility mechanism of the Impatiens downy mildew, and lays out a strong foundation for future studies aimed at improving downy mildew resistance in I. walleriana.

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De novo transcriptome assembly and functional annotation for Y-organs of the blue crab (Callinectes sapidus), and analysis of differentially expressed genes during pre-molt

General and Comparative Endocrinology ◽

10.1016/j.ygcen.2020.113567 ◽

2020 ◽

Vol 298 ◽

pp. 113567

Author(s):

Megan E. Roegner ◽

R. Douglas Watson

Keyword(s):

Differentially Expressed Genes ◽

Blue Crab ◽

Functional Annotation ◽

De Novo ◽

Callinectes Sapidus ◽

Transcriptome Assembly ◽

Differentially Expressed ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome

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Integrative Transcriptome and Proteome Analysis Identifies Major Molecular Regulation Pathways Involved in Ramie (Boehmeria nivea (L.) Gaudich) under Nitrogen and Water Co-Limitation

Plants ◽

10.3390/plants9101267 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1267

Author(s):

Jikang Chen ◽

Gang Gao ◽

Ping Chen ◽

Kunmei Chen ◽

Xiaofei Wang ◽

...

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Proteome Analysis ◽

Differentially Expressed ◽

Poor Correlation ◽

Factors Affecting ◽

Protein Levels ◽

Boehmeria Nivea ◽

N Efficiency ◽

New Information

Water and N are the most important factors affecting ramie (Boehmeria nivea (L.) Gaudich) growth. In this study, de novo transcriptome assembly and Tandem Mass Tags (TMT) based quantitative proteome analysis of ramie under nitrogen and water co-limitation conditions were performed, and exposed to treatments, including drought and N-deficit (WdNd), proper water but N-deficit (WNd), proper N but drought (WdN), and proper N and water (CK), respectively. A total of 64,848 unigenes (41.92% of total unigenes) were annotated in at least one database, including NCBI non-redundant protein sequences (Nr), Swiss-Prot, Protein family (Pfam), Gene Ontology (GO) and KEGG Orthology (KO), and 4268 protein groups were identified. Most significant changes in transcript levels happened under water-limited conditions, but most significant changes in protein level happened under water-limited conditions only with proper N. Poor correlation between differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) was observed in ramie responding to the treatments. DEG/DEP regulation patterns related to major metabolic processes responding to water and N deficiency were analyzed, including photosynthesis, ethylene responding, glycolysis, and nitrogen metabolism. Moreover, 41 DEGs and 61 DEPs involved in regulating adaptation of ramie under water and N stresses were provided in the study, including DEGs/DEPs related to UDP—glucuronosyhransferase (UGT), ATP synthase, and carbonate dehydratase. The strong dependency of N-response of ramie on water conditions at the gene and protein levels was highlighted. Advices for simultaneously improving water and N efficiency in ramie were also provided, especially in breeding N efficient varieties with drought resistance. This study provided extensive new information on the transcriptome, proteome, their correlation, and diversification in ramie responding to water and N co-limitation.

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Physiological Characterization and Transcriptome Analysis of Camellia oleifera Abel. during Leaf Senescence

Forests ◽

10.3390/f11080812 ◽

2020 ◽

Vol 11 (8) ◽

pp. 812

Author(s):

Shiwen Yang ◽

Kehao Liang ◽

Aibin Wang ◽

Ming Zhang ◽

Jiangming Qiu ◽

...

Keyword(s):

Molecular Mechanism ◽

Leaf Senescence ◽

Transcriptome Analysis ◽

Unsaturated Fatty Acids ◽

De Novo ◽

Transcriptome Assembly ◽

Economic Value ◽

Differentially Expressed ◽

Pcr Analysis ◽

Rna Seq

Camellia (C.) oleifera Abel. is an evergreen small arbor with high economic value for producing edible oil that is well known for its high level of unsaturated fatty acids. The yield formation of tea oil extracted from fruit originates from the leaves, so leaf senescence, the final stage of leaf development, is an important agronomic trait affecting the production and quality of tea oil. However, the physiological characteristics and molecular mechanism underlying leaf senescence of C. oleifera are poorly understood. In this study, we performed physiological observation and de novo transcriptome assembly for annual leaves and biennial leaves of C. oleifera. The physiological assays showed that the content of chlorophyll (Chl), soluble protein, and antioxidant enzymes including superoxide dismutase, peroxide dismutase, and catalase in senescing leaves decreased significantly, while the proline and malondialdehyde concentration increased. By analyzing RNA-Seq data, we identified 4645 significantly differentially expressed unigenes (DEGs) in biennial leaves with most associated with flavonoid and phenylpropanoid biosynthesis and phenylalanine metabolism pathways. Among these DEGs, 77 senescence-associated genes (SAGs) including NOL, ATAF1, MDAR, and SAG12 were classified to be related to Chl degradation, plant hormone, and oxidation pathways. The further analysis of the 77 SAGs based on the Spearman correlation algorithm showed that there was a significant expression correlation between these SAGs, suggesting the potential connections between SAGs in jointly regulating leaf senescence. A total of 162 differentially expressed transcription factors (TFs) identified during leaf senescence were mostly distributed in MYB (myeloblastosis), ERF (Ethylene-responsive factor), WRKY, and NAC (NAM, ATAF1/2 and CUCU2) families. In addition, qRT-PCR analysis of 19 putative SAGs were in accordance with the RNA-Seq data, further confirming the reliability and accuracy of the RNA-Seq. Collectively, we provide the first report of the transcriptome analysis of C. oleifera leaves of two kinds of age and a basis for understanding the molecular mechanism of leaf senescence.

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