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U Johanson (2001)
The complete set of genes encoding major intrinsic proteins in arabidopsis provides a framework for a new nomenclature for major intrinsic proteins in plantsPlant Physiol, 126
L Yang, BS Gaut (2011)
Factors that contribute to variation in evolutionary rate among Arabidopsis genesMol Biol Evolution, 28
Z-L Yang, H-J Liu, X-R Wang, Q-Y Zeng (2013)
Molecular evolution and expression divergence of the Populus polygalacturonase supergene family shed light on the evolution of increasingly complex organs in plantsNew Phytol, 197
O Markovic, S Janecek (2001)
Pectin degrading glycoside hydrolases of family 28: sequence-structural features, specificities and evolutionProtein Eng, 14
SY Rhee, CR Somerville (1998)
Tetrad pollen formation in quartet mutants of Arabidopsis thaliana is associated with persistence of pectic polysaccharides of the pollen mother cell wallPlant J, 15
KA Hadfield, JKC Rose, DS Yaver, RM Berka, AB Bennett (1998)
Polygalacturonase gene expression in ripe melon fruit supports a role for polygalacturonase in ripening-associated pectin disassemblyPlant Physiol, 117
T Ariizumi, M Amagai, D Shibata, K Hatakeyama, M Watanabe, K Toriyama (2002)
Comparative study of promoter activity of three anther-specific genes encoding lipid transfer protein, xyloglucan endotransglucosylase/hydrolase and polygalacturonase in transgenic Arabidopsis thalianaPlant Cell Rep, 21
MB Eisen, PT Spellman, PO Brown, D Botstein (1998)
Cluster analysis and display of genome-wide expression patternsProc Natl Acad Sci USA, 95
KC Park, SJ Kwon, PH Kim, T Bureau, NS Kim (2008)
Gene structure dynamics and divergence of the polygalacturonase gene family of plants and fungusGenome, 51
Y Wang, X Wang, H Tang, X Tan, SP Ficklin, FA Feltus, AH Paterson (2011)
Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiospermsPLoS ONE, 6
L Son (2009)
The BURP domain protein AtUSPL1 of Arabidopsis thaliana is destined to the protein storage vacuoles and overexpression of the cognate gene distorts seed developmentPlant Mol Biol, 71
J Kim, SE Patterson (2006)
Expression divergence and functional redundancy of polygalacturonases in floral organ abscissionPlant Signal Behav, 1
SB Hong, R Sexton, ML Tucker (2000)
Analysis of gene promoters for two tomato polygalacturonases expressed in abscission zones and the stigmaPlant Physiol, 123
DV Savatin, S Ferrari, F Sicilia, G Lorenzo (2011)
Oligogalacturonide-auxin antagonism does not require posttranscriptional gene silencing or stabilization of auxin response repressors in ArabidopsisPlant Physiol, 157
J Wu (2012)
Genome-wide analysis of Aux/IAA gene family in Solanaceae species using tomato as a modelMol Genet Genomics, 287
MA Banuelos, B Garciadeblas, B Cubero, A Rodriguez-Navarro (2002)
Inventory and functional characterization of the HAK potassium transporters of ricePlant Physiol, 130
CI Castillo-Davis, DL Hartl, G Achaz (2004)
cis-Regulatory and protein evolution in orthologous and duplicate genesGenome Res, 14
A Zhang, Q Chen, L Huang, L Qiu, J Cao (2011)
Cloning and expression of an anther-abundant polygalacturonase gene BcMF17 from Brassica campestris ssp chinensisPlant Mol Biol Rep, 29
R Dominguez-Perles, P Mena, C Garcia-Viguera, DA Moreno (2014)
Brassica foods as a dietary source of vitamin C: a reviewCrit Rev Food Sci Nutr, 54
SY Rhee, E Osborne, PD Poindexter, CR Somerville (2003)
Microspore separation in the quartet 3 mutants of Arabidopsis is impaired by a defect in a developmentally regulated polygalacturonase required for pollen mother cell wall degradationPlant Physiol, 133
HM Fei, VK Sawhney (2001)
Ultrastructural characterization of male sterile33 (ms33) mutant in Arabidopsis affected in pollen desiccation and maturationCan J Bot, 79
JP Fabi, SG Broetto, SLGL Silva, S Zhong, FM Lajolo, JRO Nascimento (2014)
Analysis of papaya cell wall-related genes during fruit ripening indicates a central role of polygalacturonases during pulp softeningPLoS ONE, 9
H Tang, JE Bowers, X Wang, R Ming, M Alam, AH Paterson (2008)
Perspective—synteny and collinearity in plant genomesScience, 320
V Sundaresan (1995)
Patterns of gene-action in plant development revealed by enhancer trap and gene trap transposable elementsGenes Dev, 9
A Zhang, L Qiu, L Huang, X Yu, G Lu, J Cao (2012)
Isolation and characterization of an anther-specific polygalacturonase gene, BcMF16, in Brassica campestris ssp. chinensisPlant Mol Biol Rep, 30
DR Smyth, JL Bowman, EM Meyerowitz (1990)
Early flower development in ArabidopsisPlant Cell, 2
M Freeling, BC Thomas (2006)
Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexityGenome Res, 16
M Karimi, D Inze, A Depicker (2002)
GATEWAY((TM)) vectors for Agrobacterium-mediated plant transformationTrends Plant Sci, 7
LA Yang, S Takuno, ER Waters, BS Gaut (2011)
Lowly expressed genes in Arabidopsis thaliana bear the signature of possible pseudogenization by promoter degradationMol Biol Evol, 28
HP Hong, JL Gerster, RSS Datla, D Albani, G Scoles, W Keller, LS Robert (1997)
The promoter of a Brassica napus polygalacturonase gene directs pollen expression of beta-glucuronidase in transgenic Brassica plantsPlant Cell Rep, 16
H Innan, F Kondrashov (2010)
The evolution of gene duplications: classifying and distinguishing between modelsNat Rev Genet, 11
JKC Rose, J Braam, SC Fry, K Nishitani (2002)
The XTH family of enzymes involved in xyloglucan endotransglucosylation and endohydrolysis: current perspectives and a new unifying nomenclaturePlant Cell Physiol, 43
M Bekaert, PP Edger, JC Pires, GC Conant (2011)
Two-phase resolution of polyploidy in the arabidopsis metabolic network gives rise to relative and absolute dosage constraintsPlant Cell, 23
F Cheng, T Mandakova, J Wu, Q Xie, MA Lysak, X Wang (2013)
Deciphering the diploid ancestral genome of the mesohexaploid brassica rapaPlant Cell, 25
X Wang (2011)
The genome of the mesopolyploid crop species Brassica rapaNat Genet, 43
M Krzywinski (2009)
Circos: an information aesthetic for comparative genomicsGenome Res, 19
J Kim, S-H Shiu, S Thoma, W-H Li, SE Patterson (2006)
Patterns of expansion and expression divergence in the plant polygalacturonase gene familyGenome Biol, 7
ZH Yang (2007)
PAML 4: phylogenetic analysis by maximum likelihoodMol Biol Evol, 24
PP Edger, JC Pires (2009)
Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genesChromosom Res, 17
S Freilich, T Massingham, S Bhattacharyya, H Ponsting, PA Lyons, TC Freeman, JM Thornton (2005)
Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteinsGenome Biol, 6
I Arabidopsis Genome (2000)
Analysis of the genome sequence of the flowering plant Arabidopsis thalianaNature, 408
D Farre, N Bellora, L Mularoni, X Messeguer, MM Alba (2007)
Housekeeping genes tend to show reduced upstream sequence conservationGenome Biol, 8
K-C Park, S-J Kwon, N-S Kim (2010)
Intron loss mediated structural dynamics and functional differentiation of the polygalacturonase gene family in land plantsGenes Genomics, 32
GA Wray, MW Hahn, E Abouheif, JP Balhoff, M Pizer, MV Rockman, LA Romano (2003)
The evolution of transcriptional regulation in eukaryotesMol Biol Evolution, 20
L Huang, Y Ye, Y Zhang, A Zhang, T Liu, J Cao (2009)
BcMF9, a novel polygalacturonase gene, is required for both Brassica campestris intine and exine formationAnn Bot, 104
J Jiang, L Yao, Y Miao, J Cao (2013)
Genome-wide characterization of the pectate lyase-like (PLL) genes in Brassica rapaMol Genet Genomics, 288
F Senechal, C Wattier, C Rusterucci, J Pelloux (2014)
Homogalacturonan-modifying enzymes: structure, expression, and roles in plantsJ Exp Bot, 65
CD Town (2006)
Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidyPlant Cell, 18
ZH Gonzalez-Carranza, KA Elliott, JA Roberts (2007)
Expression of polygalacturonases and evidence to support their role during cell separation processes in Arabidopsis thalianaJ of Exp Bot, 58
Q Zhang, L Huang, T Liu, X Yu, J Cao (2008)
Functional analysis of a pollen-expressed polygalacturonase gene BcMF6 in Chinese cabbage (Brassica campestris L. ssp chinensis Makino)Plant Cell Rep, 27
P Lou, J Wu, F Cheng, LG Cressman, X Wang, CR McClung (2012)
Preferential retention of circadian clock genes during diploidization following whole genome triplication in Brassica rapaPlant Cell, 24
CS Chin, JH Chuang, H Li (2005)
Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequenceGenome Res, 15
T Czechowski, M Stitt, T Altmann, MK Udvardi, WR Scheible (2005)
Genome-wide identification and testing of superior reference genes for transcript normalization in ArabidopsisPlant Physiol, 139
YW Yang, KN Lai, PY Tai, WH Li (1999)
Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineagesJ Mol Evol, 48
M Ogawa, P Kay, S Wilson, SM Swain (2009)
ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE1 (ADPG1), ADPG2, and QUARTET2 are polygalacturonases required for cell separation during reproductive development in ArabidopsisPlant Cell, 21
MM Alba, J Castresana (2005)
Inverse relationship between evolutionary rate and age of mammalian genesMol Biol Evol, 22
F Cheng, J Wu, L Fang, X Wang (2012)
Syntenic gene analysis between Brassica rapa and other Brassicaceae speciesFront Plant Sci, 3
L Berke, GF Sanchez-Perez, B Snel (2012)
Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in ArabidopsisGenome Biol, 13
NC Carpita, DM Gibeaut (1993)
Structural models of primary-cell walls in flowering plants—consistency of molecular-structure with the physical-properties of the walls during growthPlant J, 3
M Torki, P Mandaron, R Mache, D Falconet (2000)
Characterization of a ubiquitous expressed gene family encoding polygalacturonase in Arabidopsis thalianaGene, 242
Y Yu, Y Liang, M Lv, J Wu, G Lu, J Cao (2014)
Genome-wide identification and characterization of polygalacturonase genes in Cucumis sativus and Citrullus lanatusPlant Physiol Biochem, 74
C Xiao, C Somerville, CT Anderson (2014)
POLYGALACTURONASE INVOLVED IN EXPANSION1 functions in cell elongation and flower development in ArabidopsisPlant Cell, 26
KH Caffall, D Mohnen (2009)
The structure, function, and biosynthesis of plant cell wall pectic polysaccharidesCarbohydr Res, 344
F Cheng (2012)
Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapaPLoS ONE, 7
L Huang, J Cao, A Zhang, Y Ye, Y Zhang, T Liu (2009)
The polygalacturonase gene BcMF2 from Brassica campestris is associated with intine developmentJ Exp Bot, 60
P Wu (2014)
Loss/retention and evolution of NBS-encoding genes upon whole genome triplication of Brassica rapaGene, 540
Polygalacturonases (PGs) participate in pectin disassembly of cell wall and belong to one of the largest hydrolase families in plants. In this study, we identified 99 PG genes in Brassica rapa. Comprehensive analysis of phylogeny, gene structures, physico-chemical properties and coding sequence evolution demonstrated that plant PGs should be classified into seven divergent clades and each clade’s members had specific sequence and structure characteristics, and/or were under specific selection pressures. Genomic distribution and retention rate analysis implied duplication events and biased retention contributed to PG family’s expansion. Promoter divergence analysis using “shared motif method” revealed a significant correlation between regulatory and coding sequence evolution of PGs, and proved Clades A and E were of ancient origin. Quantitative real-time PCR analysis showed that expression patterns of PGs displayed group specificities in B. rapa. Particularly, nearly half of PG family members, especially those of Clades C, D and F, closely relates to reproductive development. Most duplicates showed similar expression profiles, suggesting dosage constraints accounted for preservation after duplication. Promoter-GUS assay further indicated PGs’ extensive roles and possible redundancy during reproductive development. This work can provide a scientific classification of plant PGs, dissect the internal relationships between their evolution and expressions, and promote functional researches.
Plant Molecular Biology – Springer Journals
Published: Oct 27, 2015
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