Application of in-house virtual protein database performed in genomic-proteomic combined research on heavy-metal stressed onion roots

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Application of in-house virtual protein database performed in genomic-proteomic combined research on heavy-metal stressed onion roots. / Ning, Chanjuan; Qin, Rong; Chen, Da; Björn, Lars Olof; Li, Shaoshan.

In: Biotechnology Letters, Vol. 38, No. 8, 2016, p. 1293-1300.

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TY - JOUR

T1 - Application of in-house virtual protein database performed in genomic-proteomic combined research on heavy-metal stressed onion roots

AU - Ning, Chanjuan

AU - Qin, Rong

AU - Chen, Da

AU - Björn, Lars Olof

AU - Li, Shaoshan

PY - 2016

Y1 - 2016

N2 - Objectives To establish an in-house virtual protein database that can be employed in proteomic research on non-model plants. Results A total of 87,430 unigenes were obtained through transcriptome sequencing from onion roots. Of these, 24,305 unigenes were annotated and their nucleotide sequences of coding regions were translated into amino acid sequences. The corresponding 24,305 amino acid sequences were considered as an in-house virtual protein database. Thirty-two protein spots with significant differential abundance were selected. Their MS data were submitted to a restriction enzyme map which was converted from the in-house virtual protein database. A total of 27 proteins were finally matched.Conclusions The in-house protein database is afeasible and innovative strategy for proteomicresearch on non-model plants.

AB - Objectives To establish an in-house virtual protein database that can be employed in proteomic research on non-model plants. Results A total of 87,430 unigenes were obtained through transcriptome sequencing from onion roots. Of these, 24,305 unigenes were annotated and their nucleotide sequences of coding regions were translated into amino acid sequences. The corresponding 24,305 amino acid sequences were considered as an in-house virtual protein database. Thirty-two protein spots with significant differential abundance were selected. Their MS data were submitted to a restriction enzyme map which was converted from the in-house virtual protein database. A total of 27 proteins were finally matched.Conclusions The in-house protein database is afeasible and innovative strategy for proteomicresearch on non-model plants.

KW - In-house database

KW - Non-model plants

KW - Proteomic research

KW - Restriction enzyme map

KW - Unigenes

U2 - 10.1007/s10529-016-2114-3

DO - 10.1007/s10529-016-2114-3

M3 - Article

VL - 38

SP - 1293

EP - 1300

JO - Biotechnology Letters

T2 - Biotechnology Letters

JF - Biotechnology Letters

SN - 1573-6776

IS - 8

ER -