The Iso-Seq technology, based on PacBio sequencing, enables the generation of high-quality, full-length transcripts, providing insights into transcriptome complexity. In this study, total RNA from promastigotes of four species ( and ) was sequenced using Single Molecule, Real-Time (SMRT) Sequencing (PacBio) methodology. The Iso-seq transcripts were categorized as either complete or truncated according to the presence or absence of the Spliced-Leader (SL) sequence at their 5'-end, respectively. Moreover, only transcripts having a poly-A at their 3'-end were considered. Supplied datasets represent valuable information that may help to uncover novel transcripts and alternative splicing events in a parasite that regulates its gene expression at the post-transcriptional level. A better knowledge of gene expression regulation in will open avenues for the development of new drugs to treat leishmaniasis, a devastating disease that has worldwide distribution. Additionally, the bioinformatics pipeline followed here may guide the analysis of Iso-Seq data derived from related trypanosomatids like (Chagas disease agent) and (sleeping disease). © 2023 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
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http://dx.doi.org/10.1016/j.dib.2023.109838 | DOI Listing |
Genes (Basel)
November 2024
Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark.
: Transcriptome assembly and functional annotation are essential in understanding gene expression and biological function. Nevertheless, many existing pipelines lack the flexibility to integrate both short- and long-read sequencing data or fail to provide a complete, customizable workflow for transcriptome analysis, particularly for non-model organisms. : We present TrAnnoScope, a transcriptome analysis pipeline designed to process Illumina short-read and PacBio long-read data.
View Article and Find Full Text PDFDrought is one of the main environmental factors affecting plant survival and growth. Atraphaxis bracteata is a common desert plant mainly utilized in afforestation and desertification control. This study analyzed the morphological, physiological and molecular regulatory characteristics of different organs of A.
View Article and Find Full Text PDFPoult Sci
December 2024
College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, PR China.; The Shennong Laboratory, Zhengzhou 450002, PR China.. Electronic address:
Chickens are vital economic poultry and serve as exemplary models for avian research. The incomplete reference genome of chickens and the limited availability of full-length cDNA impede the identification of alternatively spliced transcripts, thereby delaying many fundamental chicken studies. We utilized PacBio Iso-seq technology on various chicken tissues, obtaining 170,162 full-length transcripts through comprehensive transcriptome sequencing and annotation.
View Article and Find Full Text PDFSci Data
December 2024
School of Pharmaceutical Sciences, Xiamen University, 4221 Xiangannan road, Xiamen, 361104, China.
Pyrosomes represent a group of marine holozooplankton. They do not exist as individual entities but as intricate colonies comprising numerous zooids, well-known for their bioluminescent properties. Pyrosomes inhabit most oceanic waters spanning tropical to temperate regions.
View Article and Find Full Text PDFAnimals (Basel)
November 2024
Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
The Chinese sturgeon () is an ancient, complex autooctoploid fish species that is currently facing conservation challenges throughout its distribution. To comprehensively characterize the expression profiles of genes and their associated biological functions across different tissues, we performed a transcriptome-scale gene expression analysis, focusing on housekeeping genes (HKGs), tissue-specific genes (TSGs), and co-expressed gene modules in various tissues. We collected eleven tissues to establish a transcriptomic repository, including data from Pacific Biosciences isoform sequencing (PacBio Iso-seq) and RNA sequencing (RNA-seq), and then obtained 25,434 full-length transcripts, with lengths from 307 to 9515 bp and an N50 of 3195 bp.
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