Genome-Wide Identification and Evolution Analysis of Trehalose-6-Phosphate Synthase Gene Family in Nelumbo 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 available Nelumbo nucifera (lotus) genome sequence database was analyzed which led to identification of nine lotus TPS genes (NnTPS). It was found that at least two introns are included in the coding sequences of NnTPS genes. When the motif compositions were analyzed we found that NnTPS generally shared the similar motifs, implying that they have similar functions. The dN/dS ratios were always less than 1 for different domains and regions outside domains, suggesting purifying selection on the lotus TPS gene family. The regions outside TPS domain evolved relatively faster than NnTPS domains. A phylogenetic tree was constructed using all predicted coding sequences of lotus TPS genes, together with those from Arabidopsis, poplar, soybean, and rice. The result indicated that those TPS genes 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 plant TPS genes. Some of the critical sites that contributed to divergence may have been under positive selection. Transcriptome data analysis revealed that most NnTPS genes were predominantly expressed in sink tissues. Expression pattern of NnTPS genes 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 of TPS genes in lotus.

Characteristics and Expression Analyses of Trehalose-6-Phosphate Synthase Family in Prunus mume Reveal Genes Involved in Trehalose Biosynthesis and Drought Response

“…TPS, known as the crucial catalytic enzyme in trehalose accumulation, plays a vital role in abiotic stress tolerance and plant development. The genome-wide identification and characterization of TPS family genes have been conducted in Arabidopsis [ 14 ], rice [ 15 ], poplar [ 13 ], potato [ 62 ], lotus [ 63 ], apple [ 64 ], cotton [ 65 ], and Moringa oleifera [ 44 ]. There have been no systematic studies focused on the biological functions of the TPS family in P. mume .…”

“…This is consistent with studies in sunflower and soybean, which have reported that positive selection forces could drive the divergence of gene function in the same clades by accelerating the retention of favorable amino acid mutations [ 67 , 68 ]. Evolutionary analyses in soybean [ 68 ], potato [ 62 ], lotus [ 63 ], poplar, and salix [ 69 ] have revealed that amino acid substitutions can result in genetic functional divergence [ 53 , 70 ]. Therefore, the genetic functional divergence of the TPS family was analyzed by DIVERGE to identify the crucial amino acid substitutions.…”

Genome-wide analyses of the bHLH gene family reveals structural and functional characteristics in the aquatic plantNelumbo nucifera

“…qRT-PCR was conducted using the LightCycler ® /LightCycler ® 96 System Real Time PCR (Roche, Basel, Switzerland) with SYBR Premix Ex Taq II (TaKaRa, Kusatsu, Japan). The actin gene (GeneBank: ) was used as an internal control for normalization of the expression levels of candidate NnbHLHs among different samples, following previous studies (Cheng et al, 2013; Diao et al, 2014; Jin et al, 2016), and expression levels were calculated using the delta–delta CT method (Livak & Schmittgen, 2001).…”

Invertebrate Trehalose-6-Phosphate Synthase Gene: Genetic Architecture, Biochemistry, Physiological Function, and Potential Applications

“…TPS plays a key role in the perception of carbohydrate availability and carbohydrate metabolism (Jin et al, 2016 ) in insects, other invertebrates, as well as in plants (Gao et al, 2014 ). TPS is considered a cytoplasmic protein with two functionally distinct catalytic domains (Elbein et al, 2003 ; Matsuda et al, 2015 ).…”