title: A comparative analysis of the evolution, expression, and cis-regulatory element of polygalacturonase genes in grasses and dicots.
abstract: Cell walls are a distinguishing characteristic of plants essential to their survival. The pectin content of primary cell walls in grasses and dicots is distinctly different. Polygalacturonases (PGs) can degrade pectins and participate in multiple developmental processes of plants. This study comprehensively compared the evolution, expression, and cis-regulatory element of PGs in grasses and dicots. A total of 577 PGs identified from five grasses and five dicots fell into seven clades. Evolutionary analysis demonstrated the distinct differences between grasses and dicots in patterns of gene duplication and loss, and evolutionary rates. Grasses generally contained much fewer clade C and F members than dicots. We found that this disparity was the result of less duplication and more gene losses in grasses. More duplications occurred in clades D and E, and expression analysis showed that most of clade E members were expressed ubiquitously at a high overall level and clade D members were closely related to male reproduction in both grasses and dicots, suggesting their biological functions were highly conserved across species. In addition to the general role in reproductive development, PGs of clades C and F specifically played roles in root development in dicots, shedding light on organ differentiation between the two groups of plants. A regulatory element analysis of clade C and F members implied that possible functions of PGs in specific biological responses contributed to their expansion and preservation. This work can improve the knowledge of PGs in plants generally and in grasses specifically and is beneficial to functional studies.
authors.affiliation: Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.|Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Liang
authors.affiliation: Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.|Department of Horticulture, College of Agriculture and Food Science, Zhejiang A & F University, Lin'an, 311300, China.
authors.forename: Youjian
authors.initials: Y
authors.lastname: Yu
authors.affiliation: Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.|Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China.
authors.forename: Jinlong
authors.initials: J
authors.lastname: Cui
authors.affiliation: Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.|Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China.
authors.forename: Meiling
authors.initials: M
authors.lastname: Lyu
authors.affiliation: Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.|Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China.
authors.forename: Liai
authors.initials: L
authors.lastname: Xu
authors.affiliation: Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China. jshcao@zju.edu.cn.|Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China. jshcao@zju.edu.cn.
authors.forename: Jiashu
authors.initials: J
authors.lastname: Cao
mesh_terms: D002473:Cell Wall / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D019684:Magnoliopsida / Q000235:genetics; D010368:Pectins / Q000235:genetics / Q000378:metabolism*; D010802:Phylogeny; D018517:Plant Roots / Q000235:genetics / Q000254:growth & development; D006109:Poaceae / Q000145:classification / Q000235:genetics*; D011096:Polygalacturonase / Q000096:biosynthesis / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics
chemical_list: D010368:Pectins; D011096:Polygalacturonase
keywords: Dicots; Expression patterns; Grasses; Molecular evolution; Polygalacturonases; Regulatory elements