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Genome-Wide Identification and Analysis of Genes Encoding Proteolytic Enzymes in Pineapple

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Pineapple, Ananas comosus, is an economically important fruit crop. Recently its genome was completely sequenced and a total of 27,024 protein coding genes were predicted. Using a set of well evaluated bioinformatics tools we have predicted the protein subcellular locations and comparatively analyzed the protein conserved domains of the predicted proteomes in pineapple, Oryza sativa (rice), Sorghum bicolor (sorghum), and Brachypodium distachyson. Our analysis revealed that ~24–26 % of proteins were located in nucleus, 17–21 % in cytosol, 9–11 % in chloroplast, and 8–11 % proteins were secreted in these monocot plants. The secretomes in the four species were analyzed comparatively and a large number of secreted glycosyl hydrolases were identified. As pineapple proteolytic enzymes, knowns as bromelains, have been used for medical treatments, we focused on genome-wide identification and analysis of pineapple genes encoding proteases. A total of 512 pineapple genes encoding putative proteolytic enzymes were identified, with 152 secreted, 74 localized in cytosol, 67 in nucleus, 60 in chloroplast, 18 in mitochondria, and the remaining in other subcellular locations. The top large protease families in pineapple were papain family cysteine protease (62 genes), peptidase S8 family (56 genes), aspartyl protease family (38 genes), and serine carboxypeptidase (33 genes). Gene expression analysis revealed that among 512 protease genes 432 were expressed in various tissues and 72 genes were differentially expressed. The highly expressed protease genes were identified including 7 papain family cysteine proteases. The protease genes with the predicted protein subcellular locations will facilitate the efforts for examining their biological roles in pineapple growth and development and for expressing the recombinant proteases for medical use. The information of protein subcellular location of all plant species can be accessed at the PlantSecKB website (

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basic local alignment search tool.


endoplasmic reticulum.


Gene ontology.


Fragments Per Kilobase exon per Million reads mapped.


reversed position specific BLAST.


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

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Correspondence to Xiang Jia Min.

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Communicated by: Paulo Arruda

Electronic Supplementary Material

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Supplementary Table 1

Gene Ontology classification of proteomes in four monocot plants (XLSX 17 kb)

Supplementary Table 2

Protein family and conserved domain distribution in different plants (XLSX 404 kb)

Supplementary Table 3

Summary of conserved protein domain families in the secretomes of different plants (XLSX 87 kb)

Supplementary Table 4

Protease family including secreted protein family distribution in different plants (XLSX 23 kb)

Supplementary Table 5

Putative proteolytic enzymes with their subcellular locations (XLSX 29 kb)

Supplementary Table 6

Differentially expressed genes in ripening fruits of pineapple (XLSX 62 kb)

Supplementary Table 7

Gene expression of pineapple protease coding genes (XLSX 29 kb)

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Wai, C.M., Powell, B., Ming, R. et al. Genome-Wide Identification and Analysis of Genes Encoding Proteolytic Enzymes in Pineapple. Tropical Plant Biol. 9, 161–175 (2016).

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