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Secretome Prediction and Analysis in Sacred Lotus (Nelumbo nucifera Gaertn.)

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Abstract

Sacred lotus, Nelumbo nucifera (Gaertn.), is a basal eudicot with agricultural and medicinal importance. The secretome and proteins in some other subcellular locations including endoplasmic reticulum (ER), mitochondrion, chloroplast, and membrane of sacred lotus were predicted using a set of computational tools. The distribution of proteins in each subcellular location in sacred lotus was compared with proteins in five other plant species. Plant proteomes contained approximately 6–9 % of secreted proteins, 13–15 % membrane proteins, 12–20 % mitochondrial or chloroplast proteins, respectively. Plant secreted proteins consist of a large number of hydrolases and peroxidases which may contribute to cell wall formation, rhizome development and seed germination regulation. The information of secretome and other protein subcellular locations in sacred lotus and other species can be accessed at the PlantSecKB website (http://proteomics.ysu.edu/secretomes/plant.php).

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Abbreviations

BLAST:

Basic local alignment search tool

ER:

Endoplasmic reticulum

GO:

Gene ontology

GPI:

Glycosylphosphatidylinositol

RPKM:

Reads 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 the Ohio Plant Biotechnology Consortium and Youngstown State University (YSU) Research Council to XJM.

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Correspondence to Xiang Jia Min.

Additional information

Communicated by Paulo Arruda

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

Supplementary Table 1

Subcellular location prediction of Lotus proteome (XLS 3523 kb)

Supplementary Table 2

Pfam analysis of secretomes in three species (XLS 92 kb)

Supplementary Table 3

RNA-seq expression levels of identified highly genes coding for secreted proteins (XLS 51 kb)

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Lum, G., VanBuren, R., Ming, R. et al. Secretome Prediction and Analysis in Sacred Lotus (Nelumbo nucifera Gaertn.). Tropical Plant Biol. 6, 131–137 (2013). https://doi.org/10.1007/s12042-013-9121-5

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  • DOI: https://doi.org/10.1007/s12042-013-9121-5

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