Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts.
Transcript annotation in plant databases is incomplete and often inaccurate, leading to misinterpretation. As more and more RNA-seq data are generated, plant scientists need to be aware of potential pitfalls and understand the nature and impact of specific alternative splicing transcripts on protein production. A primary area of concern and the topic of this article is the (mis)annotation of open reading frames and premature termination codons. The basic message is that to adequately address expression and functions of transcript isoforms, it is necessary to be able to predict their fate in terms of whether protein isoforms are generated or specific transcripts are unproductive or degraded.
Plant Sciences Division, School of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom j.w.s.brown@dundee.ac.uk.
John W S
http://orcid.org/0000-0003-2979-779X
JW
Brown
Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom.
Craig G
http://orcid.org/0000-0002-1723-1492
CG
Simpson
Max F. Perutz Laboratories, Medical University of Vienna, 1030 Vienna, Austria Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Medical University of Vienna, 1030 Vienna, Austria.
Yamile
http://orcid.org/0000-0003-1686-5992
Y
Marquez
Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom.
Geoffrey M
http://orcid.org/0000-0001-6874-870X
GM
Gadd
Max F. Perutz Laboratories, Medical University of Vienna, 1030 Vienna, Austria.
Andrea
http://orcid.org/0000-0002-8851-406X
A
Barta
Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria.
Maria
http://orcid.org/0000-0003-4702-7625
M
Kalyna
D017398:Alternative Splicing; D008957:Models, Genetic; D016366:Open Reading Frames / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics*; D010944:Plants / Q000235:genetics*; D014176:Protein Biosynthesis / Q000235:genetics*; D020033:Protein Isoforms / Q000235:genetics; D020871:RNA Stability; D012333:RNA, Messenger / Q000235:genetics
D010940:Plant Proteins; D020033:Protein Isoforms; D012333:RNA, Messenger