title: Genome-wide identification, classification, and analysis of NADP-ME family members from 12 crucifer species.
abstract: NADP-dependent malic enzymes (NADP-MEs) play essential roles in both normal development and stress responses in plants. Here, genome-wide analysis was performed to identify 65 putative NADP-ME genes from 12 crucifer species. These NADP-ME genes were grouped into five categories of syntenic orthologous genes and were divided into three clades of a phylogenic tree. Promoter motif analysis showed that NADP-ME1 genes in Group IV were more conserved with each other than the other NADP-ME genes in Groups I and II. A nucleotide motif involved in ABA responses, desiccation and seed development was found in the promoters of most NADP-ME1 genes. Generally, the NADP-ME genes of Brassica rapa, B. oleracea and B. napus had less introns than their corresponding Arabidopsis orthologs. In these three Brassica species, the NADP-ME genes derived from the least fractionated subgenome have lost less introns than those from the medium fractionated and most fractionated subgenomes. BrNADP-ME1 showed the highest expression in petals and mature embryos. Two paralogous NADP-ME2 genes (BrNADP-ME2a and BrNADP-ME2b) shared similar expression profiles and differential expression levels. BrNADP-ME3 showed down-regulation during embryogenesis and reached its lowest expression in early cotyledonary embryos. BrNADP-ME4 was expressed widely in multiple organs and showed high expression during the whole embryogenesis process. Different NADP-ME genes of B. rapa showed differential gene expression profiles in young leaves after ABA treatment or cold stress. Our genome-wide identification and characterization of NADP-ME genes extend our understanding of the evolution or function of this family in Brassicaceae.
authors.affiliation: Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Tao
authors.affiliation: Zhejiang University of Media and Communications, Hangzhou, 310018, China.
authors.forename: Weiling
authors.initials: W
authors.lastname: Guo
authors.affiliation: Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
authors.forename: Biyuan
authors.initials: B
authors.lastname: Li
authors.affiliation: Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
authors.forename: Wuhong
authors.initials: W
authors.lastname: Wang
authors.affiliation: Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
authors.forename: Zhichen
authors.initials: Z
authors.lastname: Yue
authors.affiliation: Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
authors.forename: Juanli
authors.initials: J
authors.lastname: Lei
authors.affiliation: Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
authors.forename: Yanting
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China. zhongxm@mail.zaas.ac.cn.
authors.forename: Xinmin
authors.initials: X
authors.lastname: Zhong
mesh_terms: D019607:Brassicaceae / Q000145:classification / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development; D019143:Evolution, Molecular; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D005810:Multigene Family; D009249:NADP / Q000378:metabolism*; D009928:Organ Specificity; D010802:Phylogeny; D018515:Plant Leaves / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics*; D011401:Promoter Regions, Genetic
chemical_list: D010940:Plant Proteins; D009249:NADP
keywords: Brassicaceae; Gene expression; Gene structure; NADP-ME; Promoter
references.citation: Mol Genet Genomics. 2014 Jun;289(3):361-72
references.pmid: 24488150
references.citation: Mol Genet Genomics. 2014 Dec;289(6):1131-45
references.pmid: 24972664
references.citation: Front Plant Sci. 2012 Aug 30;3:198
references.pmid: 22969786
references.citation: Protein Sci. 1999 May;8(5):978-84
references.pmid: 10338008
references.citation: Nat Genet. 2011 Aug 28;43(10):1035-9
references.pmid: 21873998
references.citation: Science. 2014 Aug 22;345(6199):950-3
references.pmid: 25146293
references.citation: Mol Biol Evol. 2007 Jan;24(1):171-81
references.pmid: 17065597
references.citation: Plant J. 2009 Sep;59(5):723-37
references.pmid: 19453445
references.citation: C R Biol. 2009 Jul;332(7):591-602
references.pmid: 19523599
references.citation: Plant J. 2003 Apr;34(2):137-48
references.pmid: 12694590
references.citation: Plant Cell Physiol. 2002 Jan;43(1):136-40
references.pmid: 11828032
references.citation: Plant Physiol. 2011 Apr;155(4):2081-95
references.pmid: 21289102
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: FEBS Lett. 2001 Feb 9;490(1-2):1-6
references.pmid: 11172800
references.citation: Nature. 1996 Nov 28;384(6607):346-9
references.pmid: 8934517
references.citation: Gene. 2000 Feb 8;243(1-2):85-92
references.pmid: 10675616
references.citation: Genome Biol. 2009;10(6):R68
references.pmid: 19549309
references.citation: FEBS J. 2009 Oct;276(19):5665-77
references.pmid: 19725876
references.citation: Plant Cell. 2013 May;25(5):1541-54
references.pmid: 23653472
references.citation: Plant Mol Biol. 2008 Jun;67(3):231-42
references.pmid: 18288573
references.citation: Plant Mol Biol. 2008 Nov;68(4-5):355-67
references.pmid: 18622731
references.citation: Mol Biol Rep. 2013 Feb;40(2):1385-96
references.pmid: 23096088
references.citation: J Exp Bot. 2002 Apr;53(369):699-705
references.pmid: 11886890
references.citation: Biosci Biotechnol Biochem. 2004 Sep;68(9):1865-74
references.pmid: 15388961
references.citation: New Phytol. 2012 Jul;195(1):189-202
references.pmid: 22497207
references.citation: Plant Mol Biol. 2001 Mar;45(4):409-20
references.pmid: 11352460
references.citation: Plant Mol Biol. 2014 Nov;86(4-5):425-42
references.pmid: 25214014
references.citation: Arch Biochem Biophys. 2004 Sep 15;429(2):134-44
references.pmid: 15313216
references.citation: Genome Biol Evol. 2009 Jul 20;1:221-30
references.pmid: 20333192
references.citation: J Exp Bot. 2011 May;62(9):3061-9
references.pmid: 21459769
references.citation: Plant Mol Biol. 2007 May;64(1-2):49-58
references.pmid: 17245561
references.citation: Nat Commun. 2014 Apr 23;5:3706
references.pmid: 24759634
references.citation: Phytochemistry. 1992 Jun;31(6):1845-57
references.pmid: 1368216
references.citation: BMC Plant Biol. 2010 Oct 27;10:233
references.pmid: 20977772
references.citation: Plant J. 2007 Apr;50(2):347-63
references.pmid: 17376166
references.citation: Plant Physiol. 2005 Sep;139(1):39-51
references.pmid: 16113210
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W369-73
references.pmid: 16845028
references.citation: Genetics. 2012 Apr;190(4):1563-74
references.pmid: 22308264
references.citation: Nat Genet. 2005 May;37(5):501-6
references.pmid: 15806101
references.citation: Nat Commun. 2014 May 23;5:3930
references.pmid: 24852848