title: Genome-Wide Identification and Evolution Analysis of Trehalose-6-Phosphate Synthase Gene Family inNelumbo nucifera.
abstract: Trehalose-6-phosphate synthase (TPS) plays a key role in plant carbohydrate metabolism and the perception of carbohydrate availability. In the present work, the publicly availableNelumbo nucifera(lotus) genome sequence database was analyzed which led to identification of nine lotusTPSgenes (NnTPS). It was found that at least two introns are included in the coding sequences ofNnTPSgenes. When the motif compositions were analyzed we found thatNnTPSgenerally shared the similar motifs, implying that they have similar functions. ThedN/dSratios were always less than 1 for different domains and regions outside domains, suggesting purifying selection on the lotusTPSgene family. The regions outside TPS domain evolved relatively faster than NnTPS domains. A phylogenetic tree was constructed using all predicted coding sequences of lotusTPSgenes, together with those fromArabidopsis, poplar, soybean, and rice. The result indicated that thoseTPSgenes could be clearly divided into two main subfamilies (I-II), where each subfamily could be further divided into 2 (I) and 5 (II) subgroups. Analyses of divergence and adaptive evolution show that purifying selection may have been the main force driving evolution of plantTPSgenes. Some of the critical sites that contributed to divergence may have been under positive selection. Transcriptome data analysis revealed that mostNnTPSgenes were predominantly expressed in sink tissues. Expression pattern ofNnTPSgenes under copper and submergence stress indicated that NNU_014679 and NNU_022788 might play important roles in lotus energy metabolism and participate in stress response. Our results can facilitate further functional studies ofTPSgenes in lotus.
authors.affiliation: College of Horticulture, Nanjing Agricultural University Nanjing, China.
authors.forename: Qijiang
authors.initials: Q
authors.lastname: Jin
authors.affiliation: College of Horticulture, Nanjing Agricultural University Nanjing, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Hu
authors.affiliation: Leisure Agricultural Section, Institute of Agricultural Science of Taihu Lake District Suzhou, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Li
authors.affiliation: College of Horticulture, Nanjing Agricultural University Nanjing, China.
authors.forename: Bei
authors.initials: B
authors.lastname: Wang
authors.affiliation: College of Horticulture, Nanjing Agricultural University Nanjing, China.
authors.forename: Yanjie
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Leisure Agricultural Section, Institute of Agricultural Science of Taihu Lake District Suzhou, China.
authors.forename: Hongwei
authors.initials: H
authors.lastname: Jiang
authors.affiliation: Horticulture Section, School of Integrative Plant Science, Cornell University Ithaca, NY, USA.
authors.forename: Neil
authors.initials: N
authors.lastname: Mattson
authors.affiliation: College of Horticulture, Nanjing Agricultural University Nanjing, China.
authors.forename: Yingchun
authors.initials: Y
authors.lastname: Xu
keywords: Nelumbo nucifera; expression pattern; molecular evolution; protein properties; trehalose-6-phosphate synthase