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Mapping and differential expression analysis from short-read RNA-Seq data in model organisms

China (No. 31571310). COMPLIANCE WITH ETHICS GUIDELINES The authors Qiong-Yi Zhao, Jacob Gratten, Restuadi Restuadi and Xuan Li declare that they have no conflict of interest. This article does not

De novo assembly of transcriptome from next-generation sequencing data

(Nos. 31571310 and 31271409). COMPLIANCE WITH ETHICS GUIDELINES The authors Xuan Li, Yimeng Kong, Qiong-Yi Zhao, Yuan-Yuan Li and Pei Hao declare they have no conflict of interests. This article does

Global transcriptome and gene regulation network for secondary metabolite biosynthesis of tea plant (Camellia sinensis)

Background Major secondary metabolites, including flavonoids, caffeine, and theanine, are important components of tea products and are closely related to the taste, flavor, and health benefits of tea. Secondary metabolite biosynthesis in Camellia sinensis is differentially regulated in different tissues during growth and development. Until now, little was known about the expression ...

Transcriptomic analyses reveal the adaptive features and biological differences of guts from two invasive whitefly species

Background The gut of phloem feeding insects is critical for nutrition uptake and xenobiotics degradation. However, partly due to its tiny size, genomic information for the gut of phloem feeding insects is limited. Results In this study, the gut transcriptomes of two species of invasive whiteflies in the Bemisia tabaci complex, Middle East Asia Minor 1 (MEAM1) and Mediterranean ...

The characteristics and expression profiles of the mitochondrial genome for the Mediterranean species of the Bemisia tabaci complex

Background The whiteflies under the name Bemisia tabaci (Gennadius) (Aleyrodidae: Hemiptera) are species complex of at least 31 cryptic species some of which are globally invasive agricultural pests. Previously, the mitochondrial genome (mitogenome) of the indigenous New World B. tabaci species was sequenced and major differences of gene order from the postulated whitefly ancestral ...

A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data

Recent advances in next-generation sequencing technology allow high-throughput cDNA sequencing (RNA-Seq) to be widely applied in transcriptomic studies, in particular for detecting differentially expressed genes between groups. Many software packages have been developed for the identification of differentially expressed genes (DEGs) between treatment groups based on RNA-Seq data. ...

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

Background With the fast advances in nextgen sequencing technology, high-throughput RNA sequencing has emerged as a powerful and cost-effective way for transcriptome study. De novo assembly of transcripts provides an important solution to transcriptome analysis for organisms with no reference genome. However, there lacked understanding on how the different variables affected ...

Analysis of a native whitefly transcriptome and its sequence divergence with two invasive whitefly species

Background Genomic divergence between invasive and native species may provide insight into the molecular basis underlying specific characteristics that drive the invasion and displacement of closely related species. In this study, we sequenced the transcriptome of an indigenous species, Asia II 3, of the Bemisia tabaci complex and compared its genetic divergence with the ...

Global transcriptome profiles of Camellia sinensis during cold acclimation

Background Tea is the most popular non-alcoholic health beverage in the world. The tea plant (Camellia sinensis (L.) O. Kuntze) needs to undergo a cold acclimation process to enhance its freezing tolerance in winter. Changes that occur at the molecular level in response to low temperatures are poorly understood in tea plants. To elucidate the molecular mechanisms of cold ...