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Analysis of Alternative Splicing Landscape in Pineapple (Ananas comosus)

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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/).

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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.

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Acknowledgments

The work was supported by the University of Illinois at Urbana-Champaign to RM and Youngstown State University to XJM.

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Correspondence to Xiang Jia Min.

Additional information

Communicated by: Paulo Arruda

Electronic supplementary material

Supplementary Table 1

Alternative splicing events in pineapple (XLSX 578 kb)

Supplementary Table 2

Protein family (Pfam) distribution of proteins encoded by genes undergoing alternative splicing and genes not undergoing alternative splicing in pineapple (XLSX 193 kb)

Supplementary Table 3

Protein domain changes in different isoforms of alternatively spliced genes (XLSX 77 kb)

Supplementary Table 4

Alternative splicing isoforms encoded proteins having different subcellular locations (XLSX 20 kb)

Supplementary Table 5

Differentially expressed genes in pineapple (XLSX 142 kb)

Supplementary Table 6

Lists 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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Wai, C.M., Powell, B., Ming, R. et al. Analysis of Alternative Splicing Landscape in Pineapple (Ananas comosus). Tropical Plant Biol. 9, 150–160 (2016). https://doi.org/10.1007/s12042-016-9168-1

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  • DOI: https://doi.org/10.1007/s12042-016-9168-1

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