Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops

Abstract

BackgroundProtein functional diversity at the post-transcriptional level is regulated through spliceosome mediated pre-mRNA alternative splicing (AS) events and that has been widely demonstrated to be a key player in regulating the functional diversity in plants. Identification and analysis of AS genes in cereal crop plants are critical for crop improvement and understanding regulatory mechanisms.ResultsWe carried out the comparative analyses of the functional landscapes of the AS using the consensus assembly of expressed sequence tags and available mRNA sequences in four cereal plants. We identified a total of 8,734 in Oryza sativa subspecies (ssp) japonica, 2,657 in O. sativa ssp indica, 3,971 in Sorghum bicolor, and 10,687 in Zea mays AS genes. Among the identified AS events, intron retention remains to be the dominant type accounting for 23.5 % in S. bicolor, and up to 55.8 % in O. sativa ssp indica. We identified a total of 887 AS genes that were conserved among Z. mays, S. bicolor, and O. sativa ssp japonica; and 248 AS genes were found to be conserved among all four studied species or ssp. Furthermore, we identified 53 AS genes conserved with Brachypodium distachyon. Gene Ontology classification of AS genes revealed functional assignment of these genes in many biological processes with diverse molecular functions.ConclusionsAS is common in cereal plants. The AS genes identified in four cereal crops in this work provide the foundation for further studying the roles of AS in regulation of cereal plant growth and development. The data can be accessed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/).Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1914-5) contains supplementary material, which is available to authorized users.

Comprehensive Cataloging and Analysis of Alternative Splicing in Maize

“…AS events identified in this study along with the integrated genomic tracks of predicted gene models, as well as data reported previously, are (Table 1). Compared with our previous assembled maize transcripts (Min et al, 2015), the number of PUTs was increased by ~26%, and the length was also significantly increased from 466 bp to 815 bp. All the assembled PUTs were structurally and functionally annotated including putative open reading frame (ORF) prediction, coding region full -length prediction, a putative function and Pfam prediction.…”

“…In our previous report, we have identified conserved AS genes among rice, maize, sorghum and Brachypodium (Min et al, 2015). In the current work, only maize and rice (ssp japonica) conserved AS genes were identified.…”

“…The data sources consisted of a total of pre-assembled 778 172 transcripts obtained from four sources: (1) 488 243 putative unique transcripts (PUTs) assembled with over 2 million of expressed sequence tags and mRNA sequences which were collected from NCBI dbEST and nucleotide database (as of Oct 2013) (Min et al, 2015); (2) 181 779 transcripts assembled from over 200 RNA-seq libraries (Thatcher et al, 2014); (3) 48 432 novel transcript isoforms identified from 147 RNA-seq libraries generated in different developmental stages with and without drought stresses (Thatcher et al, 2016), these sequences were extracted using the version 2 maize genome based on the mapping information provided in the Sup. Table 1 (Thatcher et al, 2015); and (4) recently deposited 59 263 mRNA sequences and 465 ESTs (from Oct 2013 to Dec 2015) with their polyA/T ends trimmed using trimmest tool in the EMBOSS package (Rice et al, 2000).…”

“…Previous reports on the identification and prevalence of the alternative splicing events in rice (Campbell et al, 2006;Wang and Brendel, 2006), sorghum (Panahi et al, 2014), and maize (Thatcher et al, 2014) have shown the functional diversity changes through EST/RNA-seq approaches. Recently we also reported our efforts in identification of AS genes in rice (both japonica and indica), maize, and sorgum (Min et al, 2015). We compared the AS event landscape and the AS gene functional diversity in cereal plants and also comparatively analyzed these AS genes with AS genes identified from B. distachyon to reveal conserved patterns of the AS across the grass species.…”

“…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, enzymatic, and signaling activities (Stamm et al, 2005).…”