Pacific Biosciences of California Inc (PACB)

[Paulieme]

Thursday, April 24, 2014--SMRT Sequencing of Chicken Heart Transcripts Yields New Genes and Isoforms
The Gallus gallus (common chicken) genome was initially published in 2004, but the latest RefSeq and Ensembl annotations remain incomplete. The chicken is an important model organism, especially for research on embryogenesis and heart development. In a new paper published in PLOS One, researchers representing the Cardiovascular Development Consortium of the Bench to Bassinet Program and Pacific Biosciences describe work to improve the chicken genome annotation using SMRT® DNA Sequencing.


In “Long-Read Sequencing of Chicken Transcripts and Identification of New Transcript Isoforms,” the consortium describes how they used SMRT sequencing to generate full-length cDNA reads from embryonic chicken hearts, combined these with short-read sequences from five different adult chicken tissues, and identified more than 9,000 novel transcript isoforms, as well as more than 500 genes not currently included in the Ensembl annotations.


“All of the important work being done now to uncover the regulatory mechanisms that control when and how genes are active rely heavily on a foundation built with solid genome assemblies and annotations,” the authors note.


Database searches yielded homologs for three of the new gene regions, FOXE3, RASA1, and FAM179B, but the remaining genes remain uncharacterized, including 121 gene regions that exhibited tissue-specific expression and might play key roles in chicken biology.


The authors suggest that beyond the results benefiting the community of researchers interested in the chicken genome, the methodology employed in this study will help other researchers improve efforts to annotate the genomes of other model organisms.

http://blog.pacificbiosciences.com/2014/04/smrt-sequencing-of-chicken-heart.html