title: Genome-wide characterization of the Pectate Lyase-like (PLL) genes in Brassica rapa.
abstract: Pectate lyases (PL) depolymerize demethylated pectin (pectate, EC 4.2.2.2) by catalyzing the eliminative cleavage of α-1,4-glycosidic linked galacturonan. Pectate Lyase-like (PLL) genes are one of the largest and most complex families in plants. However, studies on the phylogeny, gene structure, and expression of PLL genes are limited. To understand the potential functions of PLL genes in plants, we characterized their intron-exon structure, phylogenetic relationships, and protein structures, and measured their expression patterns in various tissues, specifically the reproductive tissues in Brassica rapa. Sequence alignments revealed two characteristic motifs in PLL genes. The chromosome location analysis indicated that 18 of the 46 PLL genes were located in the least fractionated sub-genome (LF) of B. rapa, while 16 were located in the medium fractionated sub-genome (MF1) and 12 in the more fractionated sub-genome (MF2). Quantitative RT-PCR analysis showed that BrPLL genes were expressed in various tissues, with most of them being expressed in flowers. Detailed qRT-PCR analysis identified 11 pollen specific PLL genes and several other genes with unique spatial expression patterns. In addition, some duplicated genes showed similar expression patterns. The phylogenetic analysis identified three PLL gene subfamilies in plants, among which subfamily II might have evolved from gene neofunctionalization or subfunctionalization. Therefore, this study opens the possibility for exploring the roles of PLL genes during plant development.
authors.affiliation: Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China, jingjingjiang@zju.edu.cn.
authors.forename: Jingjing
authors.initials: J
authors.lastname: Jiang
authors.forename: Lina
authors.initials: L
authors.lastname: Yao
authors.forename: Ying
authors.initials: Y
authors.lastname: Miao
authors.forename: Jiashu
authors.initials: J
authors.lastname: Cao
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D029741:Brassica rapa / Q000235:genetics*; D002874:Chromosome Mapping; D030561:Databases, Nucleic Acid; D005091:Exons; D035264:Flowers / Q000235:genetics; D020440:Gene Duplication; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D040342:Genetic Structures; D018745:Genome, Plant / Q000235:genetics*; D007438:Introns; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D011133:Polysaccharide-Lyases / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant; D011133:Polysaccharide-Lyases; C023911:pectate lyase