Identification of Lipoxygenase Genes across Plant Species

Sequences of Arabidopsis LOX proteins were obtained from the Arabidopsis Information Resource (TAIR, http://www.Arabidopsis.org/, release 10.0). Sequences of Cucumis sativus, Glycine max, Hordeum vulgare, Lens culinaris, Lycopersicon esculentum, Nicotiana attenuata, Nicotiana tabacum, Oryza sativa, Pisum sativum, Phaseolus vulgaris, Solanum tuberosum, Zea mays, Vitis vinifera, Actindia deliciosa, and Triticum aestivum were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/). Sequences of Populus were downloaded from Phytozome (http://www.phytozome.net/). Local Blast searching was performed using Arabidopsis LOX proteins as queries for the identification of LOX genes from poplar. For the misannotated genes, manual reannotation was performed using the online web server Pfam (http://pfam.sanger.ac.uk/)[26 (link)]. All of the sequences were further manually analyzed to confirm the presence of LOX domain and PLAT/LH2 (polycystin-1, lipoxygenase, α-toxin domain or the lipoxygenase homology) domain using the InterProScan program (http://www.ebi.ac.uk/Tools/InterProScan/) [27 (link)].

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Chen Z., Chen X., Yan H., Li W., Li Y., Cai R, & Xiang Y. (2015). The Lipoxygenase Gene Family in Poplar: Identification, Classification, and Expression in Response to MeJA Treatment. PLoS ONE, 10(4), e0125526.

Publication 2015

Arabidopsis Arabidopsis proteins Cucumis sativus Genes Glycine max Hordeum vulgare Lens culinaris Lipoxygenase Lycopersicon esculentum Nicotiana Nicotiana tabacum Oryza sativa Phaseolus vulgaris Pisum sativum Plat Polycystin 1 Poplar Solanum tuberosum Triticum aestivum Vitis Zea mays α toxin

Corresponding Organization : Anhui Agricultural University

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Variable analysis

independent variables

Sequences of Arabidopsis LOX proteins
Sequences of Cucumis sativus, Glycine max, Hordeum vulgare, Lens culinaris, Lycopersicon esculentum, Nicotiana attenuata, Nicotiana tabacum, Oryza sativa, Pisum sativum, Phaseolus vulgaris, Solanum tuberosum, Zea mays, Vitis vinifera, Actindia deliciosa, and Triticum aestivum
Sequences of Populus

dependent variables

Identification of LOX genes from poplar

control variables

Arabidopsis LOX proteins used as queries for the identification of LOX genes from poplar
Manual reannotation of misannotated genes using the Pfam web server
Manual analysis to confirm the presence of LOX domain and PLAT/LH2 domain using the InterProScan program

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