Recent Publications Demonstrate Rapid Adoption of SMRT Sequencing for Plant and Animal Transcriptome Analysis
Monday, May 22, 2017
Genome annotation using short-read technology (RNA-seq) is challenging because individual reads are too short to span entire gene transcripts, which can be multiple kilobases long. As a result, scientists must stitch together many short reads using error-prone assembly processes. Alternative splicing, in which the same gene expresses functionally different transcripts, is particularly difficult to detect with short reads because segments of those transcripts are often conflated during assembly. SMRT Sequencing produces significantly longer reads, achieving mean lengths of 10-18 kb, allowing scientists to generate full-length transcripts or isoforms without introducing errors from assembly algorithms. For transcriptome analysis, this is known as the Iso-Seq™ method because it produces full-length isoform sequences.
“Scientists are embracing the Iso-Seq method to produce
a more complete genetic view of everything from important crops, such as wheat and barley, to livestock, including chickens,” said
“In our analysis of gene activity in chickens, SMRT Sequencing allowed us to overcome challenges that had limited our view of genes in this bird for years,” said
Recent Iso-Seq publications include:
Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human, BMC Genomics
David Burtand his team studied embryonic and brain tissue from chickens, finding 70% more genes than were previously known to exist in this animal.
Matthew Clark, this project analyzed gene content in Chinese
Spring bread wheat. PacBio data revealed more than 6,600 genes missed by other technologies, and corrected more than 8,100 gene models that were inaccurate in previous annotations.
Nils Steinand collaborators used SMRT Sequencing and other tools to characterize the transcriptome of barley. Their analysis revealed about 40,000 high-confidence genes.
Senior author Young
Changand team reported a detailed analysis of gene content in abalone, finding that transcriptome patterns differed substantially between males and females. More than 500 genes in females and nearly 400 genes in males had multiple isoforms, i.e., evidence of alternative splicing.
Single-cell mRNA isoform diversity in the mouse brain, BMC Genomics
Scientists Kasper Karlsson and Sten Linnarsson report unexpected alternative splicing diversity in mouse brain tissue, with many cells expressing unique isoforms.
For more information, please visit https://www.pacb.com/research-focus/plant-animal-sciences/.
About Pacific Biosciences
in reference genomes, characterize alternatively spliced isoforms in important gene families, and find novel genes; targeted sequencing to more comprehensively characterize genetic variations; and real-time kinetic information for epigenome characterization. Pacific Biosciences’ technology provides high accuracy, ultra-long reads, uniform coverage, and the ability to simultaneously detect epigenetic changes. PacBio® sequencing systems, including consumables and software, provide a simple, fast, end-to-end workflow for SMRT Sequencing. More information is available at www.pacb.com.
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