Tropical Plant Biology

, Volume 9, Issue 3, pp 150–160 | Cite as

Analysis of Alternative Splicing Landscape in Pineapple (Ananas comosus)

  • Ching Man Wai
  • Brian Powell
  • Ray Ming
  • Xiang Jia Min
Article

Abstract

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/).

Keywords

Alternative splicing Expressed sequence tags mRNA Pineapple 

Abbreviations

AS

Alternative splicing

ESTs

Expressed sequence tags

GO

Gene ontology

PUT

Putative unique transcript

FPKM

Fragments Per Kilobase of exon model per Million mapped reads

rpsBLAST

Reversed position specific BLAST.

Supplementary material

12042_2016_9168_MOESM1_ESM.xlsx (579 kb)
Supplementary Table 1Alternative splicing events in pineapple (XLSX 578 kb)
12042_2016_9168_MOESM2_ESM.xlsx (194 kb)
Supplementary Table 2Protein family (Pfam) distribution of proteins encoded by genes undergoing alternative splicing and genes not undergoing alternative splicing in pineapple (XLSX 193 kb)
12042_2016_9168_MOESM3_ESM.xlsx (78 kb)
Supplementary Table 3Protein domain changes in different isoforms of alternatively spliced genes (XLSX 77 kb)
12042_2016_9168_MOESM4_ESM.xlsx (20 kb)
Supplementary Table 4Alternative splicing isoforms encoded proteins having different subcellular locations (XLSX 20 kb)
12042_2016_9168_MOESM5_ESM.xlsx (143 kb)
Supplementary Table 5Differentially expressed genes in pineapple (XLSX 142 kb)
12042_2016_9168_MOESM6_ESM.xlsx (119 kb)
Supplementary Table 6Lists of differentially expressed genes (DEG), genes having transcripts alternatively spliced (AS), and genes with both DEG and AS (XLSX 119 kb)

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Ching Man Wai
    • 1
  • Brian Powell
    • 2
  • Ray Ming
    • 1
  • Xiang Jia Min
    • 3
  1. 1.Department of Plant BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  2. 2.Department of Computer Science and Information SystemsYoungstown State UniversityYoungstownUSA
  3. 3.Center for Applied Chemical Biology, Department of Biological SciencesYoungstown State UniversityYoungstownUSA

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