Computational Molecular Biology 2017, Vol.7, No.1, 1-11
1
Research Article Open Access
Comprehensive Cataloging and Analysis of Alternative Splicing in Maize
Min X.J.
Department of Biological Sciences, Center for Applied Chemical Biology, Youngstown State University, Youngstown, OH 44555, USA
Corresponding author Email
Computational Molecular Biology, 2017, Vol.7, No.1 doi
Received: 20 July, 2017
Accepted: 01 Sep., 2017
Published:,04 Sep., 2017
Copyright © 2017
Min, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use,
distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article
:
Min X.J., 2017, Comprehensive cataloging and analysis of alternative splicing in maize,
Computational Molecular Biology, 7(1): 1-11 (doi:
Abstract
Gene expression is a key step in developmental regulation and responses in changing environments in plants. Alternative
splicing (AS) is a process generating multiple RNA isoforms from a single gene pre-mRNA transcript that increases the diversity of
functional proteins and RNAs. Identification and analysis of alternatively splicing events are critical for crop improvement and
understanding regulatory mechanisms. In maize large numbers of transcripts generated by RNA-seq technology are available, we
incorporated these data with data assembled with ESTs and mRNAs to comprehensively catalog all genes having pre-mRNAs
undergoing AS. A total of 192 624 AS events were detected and classified, including 103 566 (53.8%) basic events and 89 058
(46.2%) complex events which were formed by combination of various types of basic events. Intron retention was the dominant type
of basic AS event, accounting for 24.1%. These AS events were identified from 91 128 transcripts which were generated from 26 669
genomic loci, of which consisted of 20 860 gene models. It was estimated that 55.3% maize genes may be subjected to AS. The
transcripts mapping information can be used to improve the predicted gene models in maize. The data can be accessed at Plant
Alternative Splicing Database
/).
Keywords
Alternative splicing; Cereal crops; Gene expression; Maize; mRNA
Introduction
Maize (
Zea mays
subsp.
mays
) is an important food, feed and biofuel crop. It is also an important model organism
for fundamental research in genetics, genomics and plant physiology. Its genome consisting of 10 chromosomes
and having a size of ~2.3 gigabases has been completed sequenced, with 32 475 protein coding gene models
predicted (Schnable et al., 2009; Andorf et al., 2016). Gene expression in plants is a highly regulated process
during plant growth and development as well as in response to changing environment s. Alternative splicing (AS)
is a process generating more than one transcript from one pre-mRNA in gene transcription (Reddy et al., 2013).
There are four basic types of AS, including exon skipping (ES), alternative donor site (AltD), alternative acceptor
(AltA) site, and intron retention (IR). Various complex types can be formed by combination of basic events
(Sablok et al., 2011). In addition to the above mentioned AS types, alternative transcripts may arise as a
consequence of the alternative transcription initiation, alternative transcription termination, and alternative
polyadenylation (Roberts et al., 2002). An AS transcript isoform may or may not encode a distinct functional
protein. However, when harboring a premature termination codon in an AS isoform, the encoded protein may be
nonfunctional. The nonfunctional isoforms are degraded by a process known as nonsense-mediated decay (NMD)
(Lewis et al., 2003).
AS plays a major role in expanding the transcriptome and proteome diversity in plants, with 60 % of multi-exon
genes undergoing alternative splicing in
Arabidopsis thaliana
(Carvalho et al., 2013; Yu et al., 2016).
Genome-wide identification and physiological implications of AS have been reported in plant species including
A.
thaliana
(Filichkin et al., 2010; Zhang et al., 2010; Marquez et al., 2012; Syed et al., 2012),
Oryza sativa
(Wang
and Brendel, 2006),
Nelumbo nucifera
(sacred lotus) (VanBuren et al., 2013),
Vitis vinifera
(Vitulo et al., 2014),
Brachypodium distachyon
(Sablok et al., 2011; Walters et al., 2013),
Zea mays
(maize), and
Sorghum bicolor
(sorghum) (Thatcher et al., 2014; Min et al., 2015). Approximately 60 - 75% of AS events occur within the protein
coding regions of mRNAs, resulting changes in binding properties, intracellular localization, protein stability,
