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GTax: improving de novo transcriptome assembly by removing foreign RNA contamination
The cost and complexity of generating a complete reference genome means that many organisms lack an annotated reference. An alternative is to use a...
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transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
BackgroundRNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but...
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A multi-tissue de novo transcriptome assembly and relative gene expression of the vulnerable freshwater salmonid Thymallus ligericus
Freshwater ecosystems are among the most endangered ecosystems worldwide. While numerous taxa are on the verge of extinction as a result of global...
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Transcriptome Data Analysis Using a De Novo Assembly Approach
Characterization and profiling of the gene expression data or, more formally, called transcriptome are crucial steps in revealing the involvement of...
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Inference of Ancient Polyploidy Using Transcriptome Data
Polyploidizations, or whole-genome duplications (WGDs), in plants have increased biological complexity, facilitated evolutionary innovation, and...
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Transcriptome sequencing of the endangered land snail Karaftohelix adamsi from the Island Ulleung: De novo assembly, annotation, valuation of fitness genes and SSR markers
BackgroundThe Bradybaenidae snail Karaftohelix adamsi is endemic to Korea, with the species tracked from Island Ulleung in North Gyeongsang Province...
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De novo transcriptome assembly of the oak processionary moth Thaumetopoea processionea
ObjectivesThe oak processionary moth (OPM) ( Thaumetopoea processionea ) is a species of moth (order: Lepidoptera ) native to parts of central Europe....
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A consensus-based ensemble approach to improve transcriptome assembly
BackgroundSystems-level analyses, such as differential gene expression analysis, co-expression analysis, and metabolic pathway reconstruction, depend...
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The de novo transcriptome assembly of Agave angustifolia Haw, mining for carbohydrates and cellulose synthesis genes profiling, and molecular markers development
Although Agave angustifolia Haw is one of the most cultural and industrial promising species in Mexico, no extensive genomic resources were...
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De novo assembly-based transcriptome analysis of resistant and susceptible potato varieties to Phytophthora infestans
An effective tool for discovering differentially expressed genes (DEGs) related to late blight (LB) resistance is the transcriptome sequencing of...
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De novo transcriptome assembly for the basal angiosperm Illicium anisatum provides insights into the biosynthesis of shikimate and neurotoxin anisatin
Illicium anisatum , an ancient angiosperm belonging to the ANITA grade, contains abundant plant metabolites with antimicrobial activity, including...
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De novo transcriptome assembly reveals characteristics of flower sex determination of Excoecaria agallocha
Key messageMADS-box genes family may play important roles in the flower sex determination in Excoecaria agallocha . A total of 73 MADS-box genes were...
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RNA-Seq Data Analysis Pipeline for Plants: Transcriptome Assembly, Alignment, and Differential Expression Analysis
In this chapter, we describe methods for analyzing RNA-Seq data, presented as a flow along a pipeline beginning with raw data from a sequencer and...
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De novo transcriptome assembly and global analysis of differential gene expression of aphid tolerant wild mustard Rorippa indica (L.) Hiern infested by mustard aphid Lipaphis Erysimi (L.) Kaltenbach
Rapeseed-mustard, the oleiferous Brassica species are important oilseed crops cultivated all over the globe. Mustard aphid Lipaphis erysimi (L.)...
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De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms – a brief guide
Many questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the...
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De novo assembly and functional annotation of the nervous system transcriptome in the Caribbean spiny lobster Panulirus argus
The spiny lobster Panulirus argus is an ecologically relevant species in shallow water coral reefs and the target of the most lucrative fishery in...
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De novo assembly of a fruit transcriptome set identifies AmMYB10 as a key regulator of anthocyanin biosynthesis in Aronia melanocarpa
Aronia is a group of deciduous fruiting shrubs, of the Rosaceae family, native to eastern North America. Interest in Aronia has increased because of...
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Aging-related aneuploidy is associated with mitochondrial imbalance and failure of spindle assembly
Despite aging is closely linked to increased aneuploidy in the oocytes, the mechanism of how aging affects aneuploidy remains largely elusive. Here,...
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Elucidating the ecophysiology of soybean pod-sucking stinkbug Riptortus pedestris (Hemiptera: Alydidae) based on de novo genome assembly and transcriptome analysis
Food security is important for the ever-growing global population. Soybean, Glycine max (L.) Merr., is cultivated worldwide providing a key source of...
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De novo transcriptome assembly and variable salinity induced differential biochemical and transcript responses in Kappaphycus alvarezii, a red carrageenophyte
Kappaphycus alvarezii is an important kappa-carrageenan producer. Fluctuating environmental conditions, especially seawater salinity, significantly...
