Investigating Resistance to Emamectin Benzoate in the Tomato Borer Tuta Absoluta

Abstract The tomato borer Tuta absoluta is a major pest of tomato mainly controlled by chemical insecticides. However, development of resistance to specific chemical classes has made control of the pest extremely difficult. Emamectin benzoate belongs to the avermectin mode of action and to date, low or no resistance levels against this insecticide have been documented. Recently, reduced efficacy of emamectin benzoate was documented, in a field population from Crete (9-fold resistant ratio (RR)). Subsequent laboratory selections with emamectin benzoate for eight sequential generations, resulted in an increase of the RR to 60-fold, the highest resistance level reported to the particular insecticide. Hereby, we are presenting the characterization of emamectin benzoate resistance in T. absoluta. Sequencing of the GluCl and GABA receptor (rdl) genes, the molecular targets of emamectin benzoate, indicted absence of non-synonymous SNPs. The use of known enzyme inhibitors (PBO, DEF and DEM) revealed that P450s partially synergized emamectin benzoate resistance, suggesting potential implication of metabolic resistance. RNA-seq approach was used to identify differentially expressed genes, from emamectin benzoate resistant and susceptible T. absoluta populations. Twelve libraries were sequenced using the Illumina platform, which generated 81 Gbp, thus substantially increasing the number of publicly available genomic resources for this species. The de novo transcriptome assembly consisted of 549,601 contigs, grouped in 233,453 unigenes. Differential expression analysis and qPCR validation revealed over-expression of one unigene similar to cytochrome P450 (Clan 4) potentially implicated in emamectin benzoate resistance, supporting further the involvement of P450s in the observed resistance phenotype.

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De novo assembly of the Brown trout (Salmo trutta m. fario) brain and muscle transcriptome: transcript annotation, tissue differential expression profile and SNP discovery

BMC Research Notes ◽

10.1186/s13104-020-05351-4 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

J. Fibla ◽

N. Oromi ◽

M. Pascual-Pons ◽

J. L. Royo ◽

A. Palau ◽

...

Keyword(s):

Differential Expression ◽

Brown Trout ◽

Salmo Trutta ◽

De Novo ◽

Transcriptome Assembly ◽

Differential Expression Analysis ◽

Cdna Libraries ◽

Significant Differential Expression ◽

Reference Transcriptome ◽

Salmonid Species

Abstract Objectives The Brown trout is a salmonid species with a high commercial value in Europe. Life history and spawning behaviour include resident (Salmo trutta m. fario) and migratory (Salmo trutta m. trutta) ecotypes. The main objective is to apply RNA-seq technology in order to obtain a reference transcriptome of two key tissues, brain and muscle, of the riverine trout Salmo trutta m. fario. Having a reference transcriptome of the resident form will complement genomic resources of salmonid species. Data description We generate two cDNA libraries from pooled RNA samples, isolated from muscle and brain tissues of adult individuals of Salmo trutta m. fario, which were sequenced by Illumina technology. Raw reads were subjected to de-novo transcriptome assembly using Trinity, and coding regions were predicted by TransDecoder. A final set of 35,049 non-redundant ORF unigenes were annotated. Tissue differential expression analysis was evaluated by Cuffdiff. A False Discovery Rate (FDR) ≤ 0.01 was considered for significant differential expression, allowing to identify key differentially expressed unigenes. Finally, we have identified SNP variants that will be useful tools for population genomic studies.

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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 of Senna occidentalis Sheds Light on the Anthraquinone Biosynthesis Pathway

Frontiers in Plant Science ◽

10.3389/fpls.2021.773553 ◽

2022 ◽

Vol 12 ◽

Author(s):

Sang-Ho Kang ◽

Woo-Haeng Lee ◽

Joon-Soo Sim ◽

Niha Thaku ◽

Saemin Chang ◽

...

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Differential Expression Analysis ◽

Biosynthesis Pathway ◽

Rna Seq ◽

Pharmacological Activities ◽

Secondary Metabolite Biosynthesis ◽

Long Read ◽

Gene Expression Levels

Senna occidentalis is an annual leguminous herb that is rich in anthraquinones, which have various pharmacological activities. However, little is known about the genetics of S. occidentalis, particularly its anthraquinone biosynthesis pathway. To broaden our understanding of the key genes and regulatory mechanisms involved in the anthraquinone biosynthesis pathway, we used short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) to perform a spatial and temporal transcriptomic analysis of S. occidentalis. This generated 121,592 RNA-Seq unigenes and 38,440 Iso-Seq unigenes. Comprehensive functional annotation and classification of these datasets using public databases identified unigene sequences related to major secondary metabolite biosynthesis pathways and critical transcription factor families (bHLH, WRKY, MYB, and bZIP). A tissue-specific differential expression analysis of S. occidentalis and measurement of the amount of anthraquinones revealed that anthraquinone accumulation was related to the gene expression levels in the different tissues. In addition, the amounts and types of anthraquinones produced differ between S. occidentalis and S. tora. In conclusion, these results provide a broader understanding of the anthraquinone metabolic pathway in S. occidentalis.

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Investigating mechanisms associated with emamectin benzoate resistance in the tomato borer Tuta absoluta

Journal of Pest Science ◽

10.1007/s10340-021-01448-2 ◽

2021 ◽

Author(s):

Marianna Stavrakaki ◽

Aris Ilias ◽

Panagiotis Ioannidis ◽

John Vontas ◽

Emmanouil Roditakis

Keyword(s):

Tuta Absoluta ◽

Emamectin Benzoate ◽

Tomato Borer

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De novo transcriptome assembly and analysis to identify potential gene targets for RNAi-mediated control of the tomato leafminer (Tuta absoluta)

BMC Genomics ◽

10.1186/s12864-015-1841-5 ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 16

Author(s):

Roberto de A. Camargo ◽

Roberto H. Herai ◽

Luana N. Santos ◽

Flavia M M Bento ◽

Joni E. Lima ◽

...

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Tuta Absoluta ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome ◽

Tomato Leafminer

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Assembly-free rapid differential gene expression analysis in non-model organisms using DNA-protein alignment

10.1101/2021.04.23.441097 ◽

2021 ◽

Author(s):

Anish M.S. Shrestha ◽

Joyce Emlyn B. Guiao ◽

Kyle Christian R. Santiago

Keyword(s):

Gene Expression ◽

Differential Expression ◽

Expression Analysis ◽

De Novo ◽

Transcriptome Assembly ◽

Differential Expression Analysis ◽

Homology Search ◽

Model Organisms ◽

Rna Seq ◽

Protein Database

AbstractRNA-seq is being increasingly adopted for gene expression studies in a panoply of non-model organisms, with applications spanning the fields of agriculture, aquaculture, ecology, and environment. Conventional differential expression analysis for organisms without reference sequences requires performing computationally expensive and error-prone de-novo transcriptome assembly, followed by homology search against a high-confidence protein database for functional annotation. We propose a shortcut, where we obtain counts for differential expression analysis by directly aligning RNA-seq reads to the protein database. Through experiments on simulated and real data, we show drastic reductions in run-time and memory usage, with no loss in accuracy. A Snakemake implementation of our workflow is available at:https://bitbucket.org/project_samar/samar

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Tissue-specific de novo transcriptome analysis in kiwifruit [Actinidia deliciosa (A Chev) Liang et Ferguson]

10.21203/rs.2.17801/v1 ◽

2019 ◽

Author(s):

JUAN SALAZAR ◽

Cristian Vergara ◽

Claudia Jorquera ◽

Patricio Zapata ◽

Pedro Martínez Gómez ◽

...

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Differential Expression Analysis ◽

Actinidia Deliciosa ◽

Fleshy Fruit ◽

De Novo Transcriptome ◽

Flower Bud ◽

Protein Database ◽

Tissue Specific ◽

Conserved Genes

Abstract Background Kiwifruit [Actinidia deliciosa (A Chev) Liang et Ferguson] is a sub-tropical vine from the Actinidiaceae family native from China. This specie has an allohexaploid genome (from a diploid and autotetraploid parents) contained in 174 chromosomes producing a climacteric and fleshy fruit called kiwifruit. Currently there's no too much genomic and transcriptomic information about this species. In this low molecular knowledge context, the main goal of this work is to construct a tissue-specific de novo transcriptome assembly generating a differential expression analysis among these specific tissues to obtain new useful database for a better knowledge of vegetative, floral and fruit growth in different phenological states of Actinidia deliciosa cv. ‘Hayward’. Results In the present study we have analyzed different whole transcriptomes from shoot, leaf, flower bud, flower and fruit at 4 development stages (7,50,120 and 160 days after flowering; DAF) in kiwifruit by using RNA-seq. We sequenced twenty-four libraries, obtaining 604,735,364 reads which were assembled using Trinity software. The first version of Actinidia deliciosa de novo transcriptome contained 142,025 contigs (x̅=1,044bp, N50=1,133bp). CEGMA and BUSCO were used for assembly quality assessment, obtaining close to 90.0% (35.1% partial) and over 85.0% (18.3% partial) of the ultra-conserved genes for eukaryote and plants, respectively. Annotation was performed with BLASTx against TAIR10 protein database and we found an annotation proportion of 35.6% (50,508), leaving 64.4% (91,517) of the contigs assembly without annotation. Conclusions These results represent a reference transcriptome for allohexaploid kiwifruit generating a database of Actinidia deliciosa genes related to leaf, flower and fruit development. Thus, the present study provides a high valuable information, identifying over 20,000 exclusive genes including all tissue comparisons, which are associated with the proteins involved in different biological processes and molecular functions. Transcriptome assembly and refining as well as the assembly metric assessment, has implied an enough quality to be a putative database of this specie and high number of ultra-conserved proteins were found. With respect to transcriptome close to 65% of contigs did not match with any protein. Therefore, future functional annotation will be required in order to obtain a better knowledge of the tissue-specific development.

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De novo transcriptome sequencing, assembly and characterization of Heliopsis longipes roots vs. leaves to discover putative genes involved in specialized metabolites biosynthesis

Plant Omics ◽

10.21475/poj.14.01.21.p3067 ◽

2021 ◽

pp. 11-22

Author(s):

Génesis V. Buitimea-Cantúa ◽

Jorge Molina-Torres

Keyword(s):

Leucine Zipper ◽

De Novo ◽

Transcriptome Assembly ◽

Differential Expression Analysis ◽

Carotenoid Biosynthesis ◽

P Value ◽

De Novo Transcriptome ◽

Basic Leucine Zipper ◽

Specialized Metabolites ◽

Helix Loop Helix

Heliopsis longipes is a valuable source of specialized metabolites (or secondary metabolites) with medicinal properties mainly in roots. However, little is known about genes involved in the biosynthesis of these metabolites, primarily due to the lack of genome or transcriptome resources. In this work, the genes of the biosynthetic pathway of the specialized metabolism from H. longipes roots and leaves through de novo RNA sequencing (RNA-Seq) using the platform of Illumina paired-end sequencing were studied. After de novo transcriptome assembly using the software Newbler, a total of 172,342 non-redundant transcripts with an N50 value of 816 bp was obtained. Further functional classification and annotation with Gene Ontology (GO), BLAST2GO, Kyoto Encyclopedia of Genes and Genome (KEGG), and KEGG automatic annotation server (KAAS), revealed that active genes in tissues are predominately involved in the metabolic process and biosynthesis of specialized metabolite pathways. Differential expression analysis of roots vs. leaves using Cuffdiff software (p-value ≤0.05 and log-fold change ratio (log2) ≥1) revealed that differentially expressed genes (DEGs) were in an organ-specific manner, such as in leaf, DEGs were significantly enriched in photosynthesis, while in roots, were a higher enriched function of plant hormone signal transduction. A total of 63 transcripts DEGs were related to 9 specialized metabolites pathways, in roots the most abundant was the phenylpropanoid biosynthesis, and in leaves was the carotenoids biosynthesis. Several regulatory genes including the basic-helix-loop-helix and basic leucine zipper domain, transcriptions factor families involved in the regulation of phenylpropanoids and carotenoid biosynthesis, respectively, were discovered. This study established a global transcriptome dataset for H. longipes. Data shall be useful to study the functional genomics or genetic engineering of this specie. These results will promote the understanding of the genetic mechanism involved in the biosynthesis of specialized metabolites in H. longipes

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De Novo Transcriptome Sequencing in Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) and Development of Tissue-Specific Transcriptomic Resources

Agronomy ◽

10.3390/agronomy11050919 ◽

2021 ◽

Vol 11 (5) ◽

pp. 919

Author(s):

Juan Alfonso Salazar ◽

Cristian Vergara-Pulgar ◽

Claudia Jorquera ◽

Patricio Zapata ◽

David Ruiz ◽

...

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Small Body ◽

Differential Expression Analysis ◽

Fleshy Fruit ◽

Actinidia Chinensis ◽

De Novo Transcriptome ◽

Flower Bud ◽

Protein Database ◽

Tissue Specific

Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) is a sub-tropical vine species from the Actinidiaceae family native to China. This species has an allohexaploid genome (from diploid and autotetraploid parents), contained in 174 chromosomes producing a climacteric and fleshy fruit called kiwifruit. Currently, only a small body of transcriptomic and proteomic data are available for A. chinensis var. deliciosa. In this low molecular knowledge context, the main goal of this study is to construct a tissue-specific de novo transcriptome assembly, generating differential expression analysis among these specific tissues, to obtain new useful transcriptomic information for a better knowledge of vegetative, floral and fruit growth in this species. In this study, we have analyzed different whole transcriptomes from shoot, leaf, flower bud, flower and fruit at four development stages (7, 50, 120 and 160 days after flowering; DAF) in kiwifruit obtained through RNA-seq sequencing. The first version of the developed A. chinensis var. deliciosa de novo transcriptome contained 142,025 contigs (x¯ = 1044 bp, N50 = 1133 bp). Annotation was performed with BLASTX against the TAIR10 protein database, and we found an annotation proportion of 35.6% (50,508), leaving 64.4% (91,517) of the contigs without annotation. These results represent a reference transcriptome for allohexaploid kiwifruit generating a database of A. chinensis var. deliciosa genes related to leaf, flower and fruit development. These results provided highly valuable information identifying over 20,000 exclusive genes including all tissue comparisons, which were associated with the proteins involved in different biological processes and molecular functions.

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De Novo Sporophyte Transcriptome Assembly and Functional Annotation in the Endangered Fern Species Vandenboschia speciosa (Willd.) G. Kunkel

Genes ◽

10.3390/genes12071017 ◽

2021 ◽

Vol 12 (7) ◽

pp. 1017

Author(s):

Mohammed Bakkali ◽

Rubén Martín-Blázquez ◽

Mercedes Ruiz-Estévez ◽

Manuel A. Garrido-Ramos

Keyword(s):

Functional Annotation ◽

Vascular Plants ◽

De Novo ◽

Transcriptome Assembly ◽

Systematic Position ◽

Important Data ◽

Ecological Requirements ◽

Physiological Adaptations ◽

Fern Species ◽

Go Terms

We sequenced the sporophyte transcriptome of Killarney fern (Vandenboschia speciosa (Willd.) G. Kunkel). In addition to being a rare endangered Macaronesian-European endemism, this species has a huge genome (10.52 Gb) as well as particular biological features and extreme ecological requirements. These characteristics, together with the systematic position of ferns among vascular plants, make it of high interest for evolutionary, conservation and functional genomics studies. The transcriptome was constructed de novo and contained 36,430 transcripts, of which 17,706 had valid BLAST hits. A total of 19,539 transcripts showed at least one of the 7362 GO terms assigned to the transcriptome, whereas 6547 transcripts showed at least one of the 1359 KEGG assigned terms. A prospective analysis of functional annotation results provided relevant insights on genes involved in important functions such as growth and development as well as physiological adaptations. In this context, a catalogue of genes involved in the genetic control of plant development, during the vegetative to reproductive transition, in stress response as well as genes coding for transcription factors is given. Altogether, this study provides a first step towards understanding the gene expression of a significant fern species and the in silico functional and comparative analyses reported here provide important data and insights for further comparative evolutionary studies in ferns and land plants in general.

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