Computational Molecular Biology, 2018, Vol.8, No.1, 1-13
1
Research Article
Open Access
A Survey of Alternative Splicing in Allotetraploid Cotton (
Gossypium hirsutum
L.)
Xiangjia Min
Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA
Corresponding author email:
Computational Molecular Biology, 2018, Vol.8, No.1 doi:
Received: 10 Apr., 2018
Accepted: 23 May, 2018
Published: 27 Jul., 2018
Copyright © 2018
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., 2018, A survey of alternative splicing in allotetraploid cotton (
Gossypium hirsutum
L.), Computational Molecular Biology, 8(1): 1-13 (doi:
)
Abstract
Allotetraploid cotton (
Gossypium hirsutum
L.), accounting for more than 90% of cultivated cotton worldwide, provides
textile fibers and seeds. Alternative splicing (AS) is a post-transcriptional process that generates more than one RNA isoforms from a
single pre-mRNA transcript, increasing the diversity of functional proteins and RNAs. We surveyed the alternatively spliced genes in
cotton using expressed sequence tag (EST) and mRNA sequences available in the public databases. A total of 56,080 AS events,
including 41,150 (73.4%) basic events and 14,930 (26.6%) complex events were identified, which were generated from
approximately 23,930 genes. Intron retention was the most frequent event, accounting for 34.8%, followed by alternative acceptor
site events (18.8%) and alternative donor site events (11.8%), and exon skipping being the least frequent event (8.0%). Complex
types, which are formed by more than one basic event, are accounted for 26.6%. The estimated AS rates of genes generating AS
isoforms was 27.1% in cotton. Gene Ontology and protein family analysis showed that the products of alternatively spliced genes
were involved in many biological processes with diverse molecular functions. The transcripts to cotton genome mapping information
can be used to improve the predicted gene models in cotton. The annotation information of AS isoforms of these genes provides a
basis for future investigation on the functions of these AS genes in cotton biology. The data can be accessed at Plant Alternative
Splicing Database (
/).
Keywords
Alternative splicing; Cotton; Gene expression;
Gossypium hirsutum
; mRNA; Plant
Background
The most widely cultivated upland cotton (
Gossypium hirsutum
L.) is an allotetraploid species (AtAtDtDt),
consisting of both A sub-genomes and D sub-genomes (Lubbers and Chee, 2009; Li et al., 2015; Zhang et al.,
2015).
G. hirsutum
accounts for more than 90% of commercial cotton production worldwide and is the main
sources of renewable textile fibers and seeds (Wendel and Grover, 2015). The genomes of the two extant
progenitor relatives,
G. arboreum
(AA) and
G. rainondii
(DD), and
G. hirsutum
have been sequenced (Wang et
al., 2012; Li et al., 2014a; Li et al., 2015; Zhang et al., 2015). Sequencing these genomes provides insights on the
genome evolution, gene contents, regulatory elements, genomic signatures of selection and domestication in these
species. The genome sequences of
G. hirsutum
(acc. TM-1) have been reported independently by two teams with
66,434 and 76,943 genes annotated from the assembled genomes, respectively (Li et al., 2015; Zhang et al., 2015).
Plant gene expression is a tightly controlled process in regulating growth and development as well as in response
to changing environments. In addition to alternative transcription initiation site and polyadenylation site that
generate different transcript isoforms, alternative splicing (AS) is a common process in plants that generates two
or more transcript isoforms from one pre-mRNA sequence (Reddy et al., 2013). Thus, the diversities of mRNAs
and proteins in the organism are significantly increased by AS. There are already well documented experimental
data showing AS plays critical roles in many biological processes in plants such as photosynthesis, defense
responses, flowering timing, grain quality, and responses to stresses (Reddy et al., 2013; Staiger 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 found in transcript isoforms by combination
of basic events (Sablok et al., 2011). AS isoforms may encode a distinct functional protein or become
