Computational Molecular Biology 2017, Vol.7, No.1, 1-11
8
the other not having a Pfam hit or the pairs had different Pfam categories. Thus, about 19.6% of AS event
generated isoforms may have their protein functionalities changed. In pineapple AS analysis it was estimated
24.9% of AS events resulting encoded protein functional changes (Wai et al., 2014). These Pfam loss or changes
are most likely caused by the translation frame changes. The biological significance of the change in protein
family functional domains in these genes certainly warrants further investigation.
2.5 Conserved alternatively spliced genes
Genes generating AS with biological roles might be conserved during evolution. Previously we have reported
conserved AS genes among maize, rice (both
japonica
and
indica
), sorghum, and
B. distachyon
(Min et al., 2015).
A total of 8 734 AS genes were identified in
japonica
rice and within them 3 246 were conserved AS genes
between rice and maize (Min et al., 2015). As in the current work the number of identified AS genes in maize
were increased from 10 687 to 20 860, we re-analyzed the conserved AS gene pairs between these two cereal
plants. The conserved AS genes were indeed increased to 4 766 (Figure 1). However, we expect more AS genes in
rice as well as more AS genes conserved among cereal or grass plants will be identified if we incorporate more
available transcript data generated from RNA-seq experiments in rice and in other plants, as previous transcripts
data were assembled using EST and mRNA sequences only (Min et al., 2015).
Figure 1 Conserved genes undergoing alternative splicing in maize and rice plants.
3 Conclusion
In this work, we incorporated all available transcripts data including ESTs, mRNAs, and transcripts generated
using RNA-seq technology for comprehensively cataloging AS in maize. A total of 192 624 AS events were
detected and classified. These AS events were identified from 91 128 transcripts which were generated from
26 669 genomic loci. Of which 20 680 predicted gene models were identified generating mRNAs having AS. Thus
about 55.3% maize genes may undergo AS. Based on our work in AS identification in cereal plants as well AS
research in other plants by other researchers (Min et al., 2015; Thatcher et al., 2016; Reddy et al., 2013), we
believe that AS is common in plant intron-containing genes, thus needs to be considered closely in all research
work related to plant gene expression experiments. Systematically identification and cataloging these AS genes in
important crop plants and making the AS gene data available to the community would facilitate the crop plant
community to better understand the gene regulation in plant growth and development as well as their coping
strategies in stress environments.
Acknowledgements
The work was supported by the Youngstown State University Research Professorship award to XJM.
