EST-based in silico identification and in vitro test of antimicrobial peptides in Brassica napus

BMC Genomics
Tao KeShengyi Liu

Abstract

Brassica napus is the third leading source of vegetable oil in the world after soybean and oil palm. The accumulation of gene sequences, especially expressed sequence tags (ESTs) from plant cDNA libraries, has provided a rich resource for genes discovery including potential antimicrobial peptides (AMPs). In this study, we used ESTs including those generated from B. napus cDNA libraries of seeds, pathogen-challenged leaves and deposited in the public databases, as a model, to perform in silico identification and consequently in vitro confirmation of putative AMP activities through a highly efficient system of recombinant AMP prokaryotic expression. In total, 35,788 were generated from cDNA libraries of pathogen-challenged leaves and 187,272 ESTs from seeds of B. napus, and the 644,998 ESTs of B. napus were downloaded from the EST database of PlantGDB. They formed 201,200 unigenes. First, all the known AMPs from the AMP databank (APD2 database) were individually queried against all the unigenes using the BLASTX program. A total of 972 unigenes that matched the 27 known AMP sequences in APD2 database were extracted and annotated using Blast2GO program. Among these unigenes, 237 unigenes from B. napus pathogen-challenged leaves had...Continue Reading

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Citations

Apr 26, 2018·Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology·P UmadeviM Anandaraj
Feb 18, 2021·Journal of Food Biochemistry·Xiaojie DuanFusheng Chen
Mar 6, 2021·Journal of Agricultural and Food Chemistry·Li-Na DingXiao-Li Tan

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Methods Mentioned

BETA
PCR
transgenic
454 sequencing
protein assay

Software Mentioned

CAP3
BLAST
blast2go
BLASTP
BLASTX
getORF
JalView
Quantity One
ClustalW
MEGA5

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