Genome-wide analysis of the Solanum tuberosum (potato) trehalose-6-phosphate synthase (TPS) gene family: evolution and differential expression during development and stress.
Genome-wide analysis of the Solanum tuberosum (potato) trehalose-6-phosphate synthase (TPS) gene family: evolution and differential expression during development and stress.
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马铃薯海藻糖 6-磷酸合酶 (TPS) 基因家族的全基因组分析：发育和胁迫过程中的进化和差异表达
DOI：
10.1186/s12864-017-4298-x
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发表时间：
2017-12-01
期刊：
影响因子：
4.4
通讯作者：
Jin Q
中科院分区：
文献类型：
--
作者：
Xu Y;Wang Y;Mattson N;Yang L;Jin Q
背景：海藻糖-6-磷酸合成酶(TPS)在植物的脱水耐性和对环境刺激的反应中具有重要作用。目前，对马铃薯TPS基因家族的功能分类、分子进化、表达模式等方面的研究还很欠缺。通过搜索最新的马铃薯基因组序列，共鉴定出8个可能的马铃薯TPS基因(StTP)。8个STTP的氨基酸同源性为59.91%~89.54%。对dN/dS比率的分析表明，TPP(海藻糖-6-磷酸磷酸酶)结构域的区域进化速度快于TPS结构域。虽然8个StTPS基因的序列具有很高的相似性(2571-2796bp)，但它们的基因长度却有很高的差异(3189-8406bp)。在不同的TPS基因中发现了许多可能与植物激素、非生物胁迫和发育有关的调控元件。根据马铃薯和其他4种茄科植物的TPS基因构建的系统发育树，TPS基因可分为6个不同的类群。分析表明，净化选择很可能在该家族的进化过程中发挥了重要作用。在系统发育树的特定分支中检测到的氨基酸变化表明，放松的限制可能是导致群体之间功能差异的原因之一。此外，通过对转录组数据的分析和qRT-PCR的分析，发现StTPS具有组织和处理特异性的表达模式。结论：本研究为马铃薯TPS基因家族的全基因组鉴定提供了参考，并为进一步研究这一重要基因家族在发育和胁迫反应中的功能奠定了基础。
Background:Trehalose-6-phosphate synthase (TPS) serves important functions in plant desiccation tolerance and response to environmental stimuli. At present, a comprehensive analysis, i.e. functional classification, molecular evolution, and expression patterns of this gene family are still lacking in Solanum tuberosum (potato).Results:In this study, a comprehensive analysis of the TPS gene family was conducted in potato. A total of eight putative potato TPS genes (StTPSs) were identified by searching the latest potato genome sequence. The amino acid identity among eight StTPSs varied from 59.91 to 89.54%. Analysis of dN/dSratios suggested that regions in the TPP (trehalose-6-phosphate phosphatase) domains evolved faster than the TPS domains. Although the sequence of the eight StTPSs showed high similarity (2571-2796 bp), their gene length is highly differentiated (3189-8406 bp). Many of the regulatory elements possibly related to phytohormones, abiotic stress and development were identified in different TPS genes. Based on the phylogenetic tree constructed using TPS genes of potato, and four other Solanaceae plants, TPS genes could be categorized into 6 distinct groups. Analysis revealed that purifying selection most likely played a major role during the evolution of this family. Amino acid changes detected in specific branches of the phylogenetic tree suggests relaxed constraints might have contributed to functional divergence among groups. Moreover, StTPSs were found to exhibit tissue and treatment specific expression patterns upon analysis of transcriptome data, and performing qRT-PCR.Conclusions:This study provides a reference for genome-wide identification of the potato TPS gene family and sets a framework for further functional studies of this important gene family in development and stress response.
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DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
影响因子：
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影响因子：
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作者：
Li, Wei;Cui, Xiao;Liang, Wanqi
通讯作者：
Liang, Wanqi
影响因子：
4.8
作者：
Gibson, RP;Tarling, CA;Davies, GJ
通讯作者：
Davies, GJ
DOI：
10.1098/rstb.2012.0003
发表时间：
2012-09-19
影响因子：
6.3
作者：
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