title: Genome-wide characterization of phenylalanine ammonia-lyase gene family in watermelon (Citrullus lanatus).
abstract: Phenylalanine ammonia-lyase (PAL), the first enzyme in the phenylpropanoid pathway, plays a critical role in plant growth, development, and adaptation. PAL enzymes are encoded by a gene family in plants. Here, we report a genome-wide search for PAL genes in watermelon. A total of 12 PAL genes, designated ClPAL1-12, are identified . Nine are arranged in tandem in two duplication blocks located on chromosomes 4 and 7, and the other three ClPAL genes are distributed as single copies on chromosomes 2, 3, and 8. Both the cDNA and protein sequences of ClPALs share an overall high identity with each other. A phylogenetic analysis places 11 of the ClPALs into a separate cucurbit subclade, whereas ClPAL2, which belongs to neither monocots nor dicots, may serve as an ancestral PAL in plants. In the cucurbit subclade, seven ClPALs form homologous pairs with their counterparts from cucumber. Expression profiling reveals that 11 of the ClPAL genes are expressed and show preferential expression in the stems and male and female flowers. Six of the 12 ClPALs are moderately or strongly expressed in the fruits, particularly in the pulp, suggesting the potential roles of PAL in the development of fruit color and flavor. A promoter motif analysis of the ClPAL genes implies redundant but distinctive cis-regulatory structures for stress responsiveness. Finally, duplication events during the evolution and expansion of the ClPAL gene family are discussed, and the relationships between the ClPAL genes and their cucumber orthologs are estimated.
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China.
authors.forename: Chun-Juan
authors.initials: CJ
authors.lastname: Dong
authors.forename: Qing-Mao
authors.initials: QM
authors.lastname: Shang
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D020134:Catalytic Domain; D029773:Citrullus / Q000201:enzymology / Q000235:genetics*; D019143:Evolution, Molecular; D005091:Exons; D005638:Fruit / Q000201:enzymology / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D007438:Introns; D008969:Molecular Sequence Data; D005810:Multigene Family; D010650:Phenylalanine Ammonia-Lyase / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid
chemical_list: D010940:Plant Proteins; D010650:Phenylalanine Ammonia-Lyase
references.citation: Nucleic Acids Res. 2002 Aug 1;30(15):e77
references.pmid: 12140339
references.citation: BMC Plant Biol. 2007 Mar 30;7:17
references.pmid: 17397551
references.citation: Plant Physiol. 2001 Sep;127(1):230-9
references.pmid: 11553751
references.citation: Plant Mol Biol. 1992 Jul;19(4):665-75
references.pmid: 1627779
references.citation: Plant Physiol. 2010 Oct;154(2):506-11
references.pmid: 20921174
references.citation: Plant Physiol Biochem. 2008 Mar;46(3):356-70
references.pmid: 18272377
references.citation: J Exp Bot. 2009;60(1):169-85
references.pmid: 19073962
references.citation: EMBO J. 1996 Oct 15;15(20):5690-700
references.pmid: 8896462
references.citation: Plant Cell. 2004 Oct;16(10):2749-71
references.pmid: 15377757
references.citation: Nucleic Acids Res. 1997 Dec 15;25(24):4876-82
references.pmid: 9396791
references.citation: Plant Physiol. 2011 Oct;157(2):790-803
references.pmid: 21825105
references.citation: PLoS One. 2007 Apr 18;2(4):e383
references.pmid: 17440619
references.citation: FEBS Lett. 1999 Aug 20;457(1):47-52
references.pmid: 10486561
references.citation: Plant Cell. 2004 Dec;16(12):3426-36
references.pmid: 15548745
references.citation: Development. 2003 Feb;130(4):635-43
references.pmid: 12505995
references.citation: Plant Mol Biol. 1996 Feb;30(4):711-22
references.pmid: 8624404
references.citation: J Mol Biol. 1993 Oct 20;233(4):580-96
references.pmid: 8411166
references.citation: Curr Opin Plant Biol. 2012 Apr;15(2):122-30
references.pmid: 22280839
references.citation: Proc Biol Sci. 2001 Nov 7;268(1482):2211-20
references.pmid: 11674868
references.citation: Planta. 2012 Oct;236(4):1093-105
references.pmid: 22572777
references.citation: Plant Cell. 2003 Jul;15(7):1591-604
references.pmid: 12837949
references.citation: Plant Physiol. 2003 Nov;133(3):1051-71
references.pmid: 14612585
references.citation: Plant Mol Biol. 2006 Jan;60(1):51-68
references.pmid: 16463099
references.citation: BMC Genomics. 2011 Sep 28;12:471
references.pmid: 21955985
references.citation: Plant Mol Biol. 1999 Mar;39(4):695-708
references.pmid: 10350084
references.citation: Plant Physiol. 2005 Aug;138(4):2075-86
references.pmid: 16040666
references.citation: BMC Plant Biol. 2004 Jun 01;4:10
references.pmid: 15171794
references.citation: Biochem J. 2009 Nov 11;424(2):233-42
references.pmid: 19725811
references.citation: Trends Plant Sci. 2000 May;5(5):199-206
references.pmid: 10785665
references.citation: Plant Cell. 2004 Sep;16(9):2481-98
references.pmid: 15319476
references.citation: Plant Physiol. 2010 Aug;153(4):1526-38
references.pmid: 20566705
references.citation: Plant J. 2003 Aug;35(4):429-41
references.pmid: 12904206
references.citation: Nat Genet. 2013 Jan;45(1):51-8
references.pmid: 23179023
references.citation: J Biol Chem. 2004 Feb 27;279(9):8102-10
references.pmid: 14660650
references.citation: Plant Mol Biol. 1989 Apr;12(4):367-83
references.pmid: 24272898
references.citation: J Biol Chem. 2002 Mar 29;277(13):11582-90
references.pmid: 11782472
references.citation: Nat Genet. 2009 Dec;41(12):1275-81
references.pmid: 19881527
references.citation: Annu Rev Microbiol. 2004;58:119-42
references.pmid: 15487932
references.citation: Plant J. 2001 Jun;26(5):487-94
references.pmid: 11439135
references.citation: Plant Cell. 2002 Apr;14(4):795-803
references.pmid: 11971135
references.citation: J Biol Chem. 2008 Nov 28;283(48):33591-601
references.pmid: 18838378
references.citation: Plant J. 1993 Apr;3(4):563-71
references.pmid: 8220463
references.citation: Mol Cell Biol. 1986 Feb;6(2):559-65
references.pmid: 3023855
references.citation: Mol Plant. 2010 Jan;3(1):2-20
references.pmid: 20035037
references.citation: Arabidopsis Book. 2011;9:e0152
references.pmid: 22303276
references.citation: Proc Natl Acad Sci U S A. 1988 Oct;85(19):7089-93
references.pmid: 2902624
references.citation: Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1187-92
references.pmid: 22232673
references.citation: Science. 1996 Mar 22;271(5256):1690-2
references.pmid: 8596928
references.citation: J Plant Physiol. 2008 Sep 29;165(14):1491-9
references.pmid: 18242769
references.citation: J Plant Physiol. 2012 Jan 1;169(1):78-85
references.pmid: 21940067
references.citation: PLoS One. 2012;7(1):e29453
references.pmid: 22247776
references.citation: Plant Physiol. 1997 Mar;113(3):755-63
references.pmid: 9085571
references.citation: Plant Cell. 1997 Oct;9(10):1859-68
references.pmid: 9368419
references.citation: Plant J. 2000 Sep;23(5):663-76
references.pmid: 10972892
references.citation: Plant Mol Biol. 1994 Oct;26(1):473-9
references.pmid: 7948894
references.citation: Plant Physiol. 2002 Oct;130(2):796-807
references.pmid: 12376645