April 24, 2014  |  General

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

“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.

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