The pattern of Phosphate transporter 1 genes evolutionary divergence in Glycine maxL.

Fan, Chengming; Wang, Xu; Hu, Ruibo; Wang, Yahui; Xiao, Chaowen; Jiang, Ying; Zhang, Xiaomei; Zheng, Changying; Fu, Yong-Fu

doi:10.1186/1471-2229-13-48

Cited by 81 publications

(45 citation statements)

References 90 publications

(142 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Interestingly, within some other plant species, such as in soybean, there exists specialized Pht1 member(s) that is (are) mainly expressed in sink tissues, such as in flowers, implying possible functions of these genes in Pi import from source to sink [13,71]. However, in our present study, we did not observe any member in the tomato Pht1 family that is dominantly expressed in the flower or fruit tissue.…”

Section: Discussioncontrasting

confidence: 72%

Genome-wide investigation and expression analysis suggest diverse roles and genetic redundancy of Pht1 family genes in response to Pi deficiency in tomato

et al. 2014

View full text Add to dashboard Cite

BackgroundPhosphorus (P) deficiency is one of the major nutrient stresses limiting plant growth. The uptake of P by plants is well considered to be mediated by a number of high-affinity phosphate (Pi) transporters belonging to the Pht1 family. Although the Pht1 genes have been extensively identified in several plant species, there is a lack of systematic analysis of the Pht1 gene family in any solanaceous species thus far.ResultsHere, we report the genome-wide analysis, phylogenetic evolution and expression patterns of the Pht1 genes in tomato (Solanum lycopersicum). A total of eight putative Pht1 genes (LePT1 to 8), distributed on three chromosomes (3, 6 and 9), were identified through extensive searches of the released tomato genome sequence database. Chromosomal organization and phylogenetic tree analysis suggested that the six Pht1 paralogues, LePT1/3, LePT2/6 and LePT4/5, which were assigned into three pairs with very close physical distance, were produced from recent tandem duplication events that occurred after Solanaceae splitting with other dicot families. Expression analysis of these Pht1 members revealed that except LePT8, of which the transcript was undetectable in all tissues, the other seven paralogues showed differential but partial-overlapping expression patterns. LePT1 and LePT7 were ubiquitously expressed in all tissues examined, and their transcripts were induced abundantly in response to Pi starvation; LePT2 and LePT6, the two paralogues harboring identical coding sequence, were predominantly expressed in Pi-deficient roots; LePT3, LePT4 and LePT5 were strongly activated in the roots colonized by arbuscular mycorrhizal fungi under low-P, but not high-P condition. Histochemical analysis revealed that a 1250-bp LePT3 promoter fragment and a 471-bp LePT5 promoter fragment containing the two elements, MYCS and P1BS, were sufficient to direct the GUS reporter expression in mycorrhizal roots and were limited to distinct cells harboring AM fungal structures. Additionally, the four paralogues, LePT1, LePT2, LePT6 and LePT7, were very significantly down-regulated in the mycorrhizal roots under low Pi supply condition.ConclusionsThe results obtained from this study provide new insights into the evolutionary expansion, functional divergence and genetic redundancy of the Pht1 genes in response to Pi deficiency and mycorrhizal symbiosis in tomato.

show abstract

Section: Discussioncontrasting

confidence: 72%

Genome-wide investigation and expression analysis suggest diverse roles and genetic redundancy of Pht1 family genes in response to Pi deficiency in tomato

et al. 2014

View full text Add to dashboard Cite

show abstract

“…Thus, the differential expression together with the low Ka/Ks supports a possible subfunctionalization of these genes. Previous studies have shown that the prevalence of variable expression in soybean after polyploidization has revealed that several paralogous genes undergo subfunctionalization (Fan et al 2013;Roulin et al 2013). Accordingly, our results reinforce the theory of the retention of duplicate genes through subfunctionalization, which may constitute a transitional step to neofunctionalization (Roulin et al 2013).…”

Section: Synteny Analysis Demonstrates High Conservation Between the supporting

confidence: 89%

“…The Ka/Ks ratio generates insights into the processes that drive the changes at the molecular level. A Ka/Ks ratio >1 shows that neofunctionalization through positive selection acted during the sequence divergence, and a Ka/Ks ratio <1 suggests that subfunctionalization through negative selection operated during the divergence (Fan et al 2013;Zhang et al 2002).…”

Section: Synteny Analysis Demonstrates High Conservation Between the mentioning

confidence: 99%

The phylogeny and evolutionary history of the Lesion Simulating Disease (LSD) gene family in Viridiplantae

et al. 2015

View full text Add to dashboard Cite

The Lesion Simulating Disease (LSD) genes encode a family of zinc finger proteins that play a role in programmed cell death (PCD) and other biological processes, such as plant growth and photosynthesis. In the present study, we report the reconstruction of the evolutionary history of the LSD gene family in Viridiplantae. Phylogenetic analysis revealed that the monocot and eudicot genes were distributed along the phylogeny, indicating that the expansion of the family occurred prior to the diversification between these clades. Sequences encoding proteins that present one, two, or three LSD domains formed separate groups. The secondary structure of these different LSD proteins presented a similar composition, with the β-sheets being their main component. The evolution by gene duplication was identified only to the genes that contain three LSD domains, which generated proteins with equal structure. Moreover, genes encoding proteins with one or two LSD domains evolved as single-copy genes and did not result from loss or gain in LSD domains. These results were corroborated by synteny analysis among regions containing paralogous/orthologous genes in Glycine max and Populus trichocarpa. The Ka/Ks ratio between paralogous/orthologous genes revealed that a subfunctionalization process possibly could be occurring with the LSD genes, explaining the involvement of LSD members in different biological processes, in addition to the negative regulation of PCD. This study presents important novelty in the evolutionary history of the LSD family and provides a basis for future research on individual LSD genes and their involvement in important pathway networks in plants.

show abstract

“…Thus, understanding how plants acquire and utilize P i , and how low P i -tolerant plants thrive in harsh growing conditions, is critical to improving agricultural systems. In soybean, studies have characterized the expression pattern and role of genes important in model species P i homeostasis (Liao et al 2003;Qin et al 2012;Fan et al 2013;Song et al 2013;Li et al 2014;Yao et al 2014;Zhang et al 2014. Classical QTL studies have identified P i efficiency QTL in soybean (Liang et al 2010;Zhang et al 2009Zhang et al , 2014Zhang et al , 2017, one of which included RNA-seq analysis of two recombinant inbred lines (RILs) with contrasting tolerance to P i deficiency stress (-P i ).…”

Section: Introductionmentioning

confidence: 99%

Dynamic gene expression changes in response to micronutrient, macronutrient, and multiple stress exposures in soybean

O’Rourke

McCabe

Graham

2019

Funct Integr Genomics

View full text Add to dashboard Cite

Preserving crop yield is critical for US soybean production and the global economy. Crop species have been selected for increased yield for thousands of years with individual lines selected for improved performance in unique environments, constraints not experienced by model species such as Arabidopsis. This selection likely resulted in novel stress adaptations, unique to crop species. Given that iron deficiency is a perennial problem in the soybean growing regions of the USA and phosphate deficiency looms as a limitation to global agricultural production, nutrient stress studies in crop species are critically important. In this study, we directly compared whole-genome expression responses of leaves and roots to iron (Fe) and phosphate (P i) deficiency, representing a micronutrient and macronutrient, respectively. Conducting experiments side by side, we observed soybean responds to both nutrient deficiencies within 24 h. While soybean responds largely to-Fe deficiency, it responds strongly to P i resupply. Though the timing of the responses was different, both nutrient stress signals used the same molecular pathways. Our study is the first to demonstrate the speed and diversity of the soybean stress response to multiple nutrient deficiencies. We also designed the study to examine gene expression changes in response to multiple stress events. We identified 865 and 3375 genes that either altered their direction of expression after a second stress exposure or were only differentially expressed after a second stress event. Understanding the molecular underpinnings of these responses in crop species could have major implications for improving stress tolerance and preserving yield.

show abstract

The pattern of Phosphate transporter 1 genes evolutionary divergence in Glycine maxL.

Cited by 81 publications

References 90 publications

Genome-wide investigation and expression analysis suggest diverse roles and genetic redundancy of Pht1 family genes in response to Pi deficiency in tomato

Genome-wide investigation and expression analysis suggest diverse roles and genetic redundancy of Pht1 family genes in response to Pi deficiency in tomato

The phylogeny and evolutionary history of the Lesion Simulating Disease (LSD) gene family in Viridiplantae

Dynamic gene expression changes in response to micronutrient, macronutrient, and multiple stress exposures in soybean

Contact Info

Product

Resources

About