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

Plant Omics ◽  
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

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

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.

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

Agronomy ◽  
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.

scholarly journals The brain transcriptome of the wolf spider, Schizocosa ocreata

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Daniel Stribling ◽  
Peter L. Chang ◽  
Justin E. Dalton ◽  
Christopher A. Conow ◽  
Malcolm Rosenthal ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Model Organisms ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Wolf Spiders ◽  
Schizocosa Ocreata ◽  
Genomic Studies ◽  
The Brain

Abstract Objectives Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression. Data description To examine sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA was isolated from brain tissue of male and female subadult and mature wolf spiders (Schizocosa ocreata). The raw data consist of sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly and differential expression analyses. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from publicly-available databases.

scholarly journals Sub-Chronic Effects of Slight PAH- and PCB-Contaminated Mesocosms in Paracentrotus lividus Lmk: A Multi-Endpoint Approach and De Novo Transcriptomic

2021 ◽  
Vol 22 (13) ◽  
pp. 6674
Author(s):  
Luisa Albarano ◽  
Valerio Zupo ◽  
Davide Caramiello ◽  
Maria Toscanesi ◽  
Marco Trifuoggi ◽  
...  
Keyword(s):  
De Novo ◽  
Sea Urchins ◽  
Transcriptome Assembly ◽  
Paracentrotus Lividus ◽  
Marine Biota ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Limit Values ◽  
The Impact ◽  
Endpoint Approach

Sediment pollution is a major issue in coastal areas, potentially endangering human health and the marine environments. We investigated the short-term sublethal effects of sediments contaminated with polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) on the sea urchin Paracentrotus lividus for two months. Spiking occurred at concentrations below threshold limit values permitted by the law (TLVPAHs = 900 µg/L, TLVPCBs = 8 µg/L, Legislative Italian Decree 173/2016). A multi-endpoint approach was adopted, considering both adults (mortality, bioaccumulation and gonadal index) and embryos (embryotoxicity, genotoxicity and de novo transcriptome assembly). The slight concentrations of PAHs and PCBs added to the mesocosms were observed to readily compartmentalize in adults, resulting below the detection limits just one week after their addition. Reconstructed sediment and seawater, as negative controls, did not affect sea urchins. PAH- and PCB-spiked mesocosms were observed to impair P. lividus at various endpoints, including bioaccumulation and embryo development (mainly PAHs) and genotoxicity (PAHs and PCBs). In particular, genotoxicity tests revealed that PAHs and PCBs affected the development of P. lividus embryos deriving from exposed adults. Negative effects were also detected by generating a de novo transcriptome assembly and its annotation, as well as by real-time qPCR performed to identify genes differentially expressed in adults exposed to the two contaminants. The effects on sea urchins (both adults and embryos) at background concentrations of PAHs and PCBs below TLV suggest a need for further investigations on the impact of slight concentrations of such contaminants on marine biota.

scholarly journals De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum

PLoS ONE ◽  
2014 ◽  
Vol 9 (5) ◽  
pp. e96855 ◽  
Author(s):  
Samuel E. Fox ◽  
Matthew Geniza ◽  
Mamatha Hanumappa ◽  
Sushma Naithani ◽  
Chris Sullivan ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Triticum Monococcum ◽  
Diploid Wheat ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome

scholarly journals Sequencing and De Novo Transcriptome Assembly ofBrachypodium sylvaticum(Poaceae)

2013 ◽  
Vol 1 (3) ◽  
pp. 1200011 ◽  
Author(s):  
Samuel E. Fox ◽  
Justin Preece ◽  
Jeffrey A. Kimbrel ◽  
Gina L. Marchini ◽  
Abigail Sage ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome
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