Analysis of Alternative Splicing Landscape in Pineapple (Ananas comosus)
- 4.1k Downloads
Pineapple (Ananas comosus L. Merrill) is an important tropical and subtropical fruit crop and possesses crassulacean acid metabolism (CAM) photosynthesis. Recent release of its genome sequences makes it possible to identify genes transcribed with alternatively spliced isoforms in this plant. Mapping the assembled transcripts generated by next-generation sequencing technology and existing expressed sequence tags as well as mRNA sequences to the published pineapple genome, we identified and analyzed alternative splicing (AS) events. We identified a total of 10,348 AS events involving 13,449 assembled putative unique transcripts, which were mapped to 5146 pineapple gene models that equivalent to 29.7 % of total expressed gene models. Consistent with previous findings in other plant species, intron retention (61.9 %) remains to be the dominant type among the identified AS events. Comparative genomic analysis of genes which generated pre-mRNAs having AS revealed a total of 481 genes conserved among Oryza sativa (ssp japonica), Sorghum bicolor, Zea mays, and pineapple, with 51 of them were also conserved with Brachypodium distachyon. Gene Ontology classification revealed that the products of these genes which generate AS isoforms are involved in many biological processes with diverse molecular functions. We annotated all assembled transcripts and also associated them with predicted gene models. The annotated information of these data provides a resource for further characterizing these genes and their biological roles. The data can be accessed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/).
KeywordsAlternative splicing Expressed sequence tags mRNA Pineapple
Expressed sequence tags
Putative unique transcript
Fragments Per Kilobase of exon model per Million mapped reads
Reversed position specific BLAST.
The work was supported by the University of Illinois at Urbana-Champaign to RM and Youngstown State University to XJM.
- Bartholomew DP (2013) History and perspectives on the role of ethylene in pineapple flowering. In: XII international symposium on plant Bioregulators in fruit production. Acta Hortic 1042:269–284Google Scholar
- Bartholomew DP, Malézieux EP (1994) Pineapple. In: Schaffer B, Andersen PC (eds) Handbook of environmental physiology of fruit crops, vol 2. CRC Press, Boca Raton, pp. 243–291Google Scholar
- Bartholomew DP, Paull RE, Rohrbach KG (eds) (2002) The pineapple: botany, production, and uses. CABI, WallingfordGoogle Scholar
- Barz M, Delivand MK (2011) Agricultural residues as promising biofuels for biomass power generation in Thailand. J Sustainable Energy Environment Special Issue 2011:21–27Google Scholar
- Lum G, Meinken J, Orr J, Frazier S, Min XJ (2014) PlantSecKB: the plant secretome and subcellular proteome knowledgebase. Comput Molec Biol 4:1–17Google Scholar
- Sablok G, Harikrishna JA, Min XJ (2013) Next generation sequencing for better understanding alternative splicing: way ahead for model and non-model plants. Transcriptomics 1:e103Google Scholar
- Surles T, Foley M, Turn S, Staackmann M (2009) A scenario for accelerated use of renewable resources for transportation fuels in Hawai ‘i. University of Hawaii, Hawaii Natural Energy Institute, School of Ocean and Earth Science and Technology, pp. 1–38Google Scholar
- VanBuren R, Walters B, Ming R, Min XJ (2013) Analysis of expressed sequence tags and alternative splicing genes in sacred lotus (Nelumbo Nucifera Gaertn.). Plant Omics J 6:311–317Google Scholar
- Wang RH, Hsu YM, Bartholomew DP, Maruthasalam S, Lin CH (2007) Delaying natural flowering in pineapple through foliar application of aviglycine, an inhibitor of ethylene biosynthesis. HortSci 42:1188–1191Google Scholar