Genome-wide Identification and analysis of the stress-resistance function of the TPS (Trehalose-6-Phosphate Synthase) gene family in cotton

Mu, Mingchun; Lu, Xuke; Wang, Junjuan; Wang, Delong; Yin, Zujun; Wang, Shuai; Fan, Weili; Ye, Wuwei

doi:10.1186/s12863-016-0360-y

Cited by 51 publications

(52 citation statements)

References 36 publications

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“…Twenty two PUB genes, including 18 genes from GhPUB8A to GhPUB51D in subgroup I and 4 genes from GhPUB32A to GhPUB38D in subgroup V, showed significant expression differences under different abiotic stresses, suggesting that they evolved toward specific functions in the long history. This perspective was consistent with previous documents [38,39].…”

Section: Discussionsupporting

confidence: 93%

Genome-wide identification and expression analysis of PUB genes in cotton

Shu²,

Wang

et al. 2020

BMC Genomics

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Background: The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stresses, but few reports about PUBs in cotton were available. Therefore research on PUBs is of great importance and a necessity when studying the mechanisms of stress-tolerance in cotton. Results: In this study, we identified 93, 96, 185 and 208 PUBs from four sequenced cotton species G. raimondii (D 5), G. arboreum (A 2), G. hirsutum (AD 1) and G. barbadense (AD2), respectively. Prediction analysis of subcellular localization showed that the PUBs in cotton were widely localized in cells, but primarily in the nucleus. The PUBs in cotton were classified into six subfamilies (A-F) on the basis of phylogenetic analysis, which was testified by the analysis of conserved motifs and exon-intron structures. Chromosomal localization analysis showed that cotton PUBs were unevenly anchored on all chromosomes, varying from 1 to 14 per chromosome. Through multiple sequence alignment analysis, 3 tandem duplications and 28 segmental duplications in cotton genome D 5 , 2 tandem duplications and 25 segmental duplications in A 2 , and 143 homologous gene pairs in A 2 and D 5 were found; however no tandem duplications in A 2 or D 5 were found. Additionally, 105, 14 and 17 homologous gene pairs were found in the intrasubgenome of At and Dt, At sub-genome and Dt sub-genome of G. hirsutum, respectively. Functional analysis of GhPUB85A and GhPUB45D showed that these genes positively responded to abiotic stresses, but the expression patterns were different. In addition, although the expression levels of these two homologous genes were similar, their contributions were different when responding to stresses, specifically showing different responses to abiotic stresses and functional differences between the two subgenomes of G. hirsutum. Conclusions: This study reported the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs were highly conserved throughout the evolutionary history of cotton. All PUB genes were involved in the response to abiotic stresses (including salt, drought, hot and cold) to varying degrees.

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Section: Discussionsupporting

confidence: 93%

Genome-wide identification and expression analysis of PUB genes in cotton

Shu²,

Wang

et al. 2020

BMC Genomics

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show abstract

“…Twenty two PUB genes, including 18 genes from GhPUB8A to GhPUB51D in subgroup I and 4 genes from GhPUB32A to GhPUB38D in subgroup V, showed an significant expression difference under different abiotic stresses, suggesting that they evolved toward specific functions in the long history. This perspective was consistent with previous documents [38,39].…”

Section: Discussionsupporting

confidence: 94%

Genome-wide identification and expression analysis of PUB genes in cotton

Shu¹,

Wang

Wang³

et al. 2020

Preprint

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Background: The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stress, but few reports about PUBs in cotton were available. Therefore research on PUBs is of great importance and is a necessity when studying the mechanism of stress tolerance in cotton. Results: In this study, we identified 93, 96, 185 and 208 PUBs from four sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. barbadense (AD2), respectively. Prediction analysis of subcellular localization showed that the PUBs in cotton were widely distributed in cells, but primarily in the nucleus. The PUBs in cotton were divided into six subfamilies (A-F) on the basis of phylogenetic analysis, and the intron/exon structure was comparatively conserved within each subfamily. Location analysis showed that cotton PUBs were unevenly anchored on all chromosomes, varying from 1 to 14 per chromosome. Through multiple sequence alignment, 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs shared in A2 and D5 were found; however no tandem duplication region in A2 or D5 was found. Additionally, 105, 14 and 17 homologous gene pairs were found in the intra-subgenome of At and Dt, the At subgenome and the Dt subgenome of allotetraploid cotton, respectively. Functional analysis of GhPUB85A and GhPUB45D showed that these genes positively responded to abiotic stresses, but the expression patterns were different. In addition, although the expression levels of these two homologous genes were similar, their contributions were different when responding to stresses, specifically showing different responses to abiotic stresses and functional differences between the two subgenomes of G. hirsutum. Conclusion: This study reports the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs were highly conserved throughout the evolutionary history of cotton. All PUB genes were involved in response to abiotic stresses (including those genes induced by salt, drought, hot and cold) to varying degrees.

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“…Then, T6P is dephosphorylated as catalyzed by trehalose-6-phosphate phosphatase (TPP) to produce the disaccharide trehalose. TPS expression levels in cotton increased under drought stress (Mu et al, 2016 ). When maize was under salt and temperature stress, TPS genes were upregulated (Jiang et al, 2010 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Evolution Analysis of Trehalose-6-Phosphate Synthase Gene Family in Nelumbo nucifera

Jin

Li³

et al. 2016

Front. Plant Sci.

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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.

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Genome-wide Identification and analysis of the stress-resistance function of the TPS (Trehalose-6-Phosphate Synthase) gene family in cotton

Cited by 51 publications

References 36 publications

Genome-wide identification and expression analysis of PUB genes in cotton

Genome-wide identification and expression analysis of PUB genes in cotton

Genome-wide identification and expression analysis of PUB genes in cotton

Genome-Wide Identification and Evolution Analysis of Trehalose-6-Phosphate Synthase Gene Family in Nelumbo nucifera

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