Genome-wide identification and analysis of late embryogenesis abundant (LEA) genes in Prunus mume

Du, Dongliang; Zhang, Qixiang; Cheng, Tangren; Pan, Huitang; Yang, Weiru; Sun, Lidan

doi:10.1007/s11033-012-2250-3

Cited by 92 publications

(90 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Interestingly, the sole gene induced by exogenous ABA treatment was SCL28 (Table 1; see also Figure 2), which harbors only a single coupling element in its upstream region (Figure 6B; Table 1). In line with this, six late embryogenesis abundant ( LEA ) genes in Prunus mume were found to be induced by ABA, but all six corresponding promoters lacked ABREs, highlighting the likelihood that there are other, yet unidentified, ABA-responsive elements important in regulating gene expression in the presence of ABA [90]. The upregulation of SR34 , SCL30a , SCL28 , RS40 , SR45 and SR45a in the aba2-1 mutant (Table 1; see also Figure 3) is also suggestive of other cis elements and/or transcription factors mediating their ABA responsiveness.…”

Section: Resultsmentioning

confidence: 83%

Abscisic Acid (ABA) Regulation of Arabidopsis SR Protein Gene Expression

Cruz

Carvalho

Richardson

et al. 2014

IJMS

View full text Add to dashboard Cite

Serine/arginine-rich (SR) proteins are major modulators of alternative splicing, a key generator of proteomic diversity and flexible means of regulating gene expression likely to be crucial in plant environmental responses. Indeed, mounting evidence implicates splicing factors in signal transduction of the abscisic acid (ABA) phytohormone, which plays pivotal roles in the response to various abiotic stresses. Using real-time RT-qPCR, we analyzed total steady-state transcript levels of the 18 SR and two SR-like genes from Arabidopsis thaliana in seedlings treated with ABA and in genetic backgrounds with altered expression of the ABA-biosynthesis ABA2 and the ABA-signaling ABI1 and ABI4 genes. We also searched for ABA-responsive cis elements in the upstream regions of the 20 genes. We found that members of the plant-specific SC35-Like (SCL) Arabidopsis SR protein subfamily are distinctively responsive to exogenous ABA, while the expression of seven SR and SR-related genes is affected by alterations in key components of the ABA pathway. Finally, despite pervasiveness of established ABA-responsive promoter elements in Arabidopsis SR and SR-like genes, their expression is likely governed by additional, yet unidentified cis-acting elements. Overall, this study pinpoints SR34, SR34b, SCL30a, SCL28, SCL33, RS40, SR45 and SR45a as promising candidates for involvement in ABA-mediated stress responses.

show abstract

Section: Resultsmentioning

confidence: 83%

Abscisic Acid (ABA) Regulation of Arabidopsis SR Protein Gene Expression

Cruz

Carvalho

Richardson

et al. 2014

IJMS

View full text Add to dashboard Cite

show abstract

“…Subsequently, each of the PPRs were positioned on the nine foxtail millet chromosome pseudo molecules based on their ascending order of physical position (bp) according to BLASTN searching against the Phytozome database adopting default settings. The analytical tools available at the Plant Genome Duplication Database were used to identify segmentally duplicated PPR gene in foxtail millet [63], and detailed methods according to the previous description [64, 65]. Segmental duplications were drew using Circos 0.67 (http://circos.ca) [66].…”

Section: Methodsmentioning

confidence: 99%

Genome-wide investigation and expression analyses of the pentatricopeptide repeat protein gene family in foxtail millet

Liu

et al. 2016

BMC Genomics

View full text Add to dashboard Cite

BackgroundPentatricopeptide repeat (PPR) proteins are encoded by a large gene family of approximately 450 members in Arabidopsis and 477 in rice, which characterized by tandem repetitions of a degenerate 35 amino acid characteristic sequence motifs. A large majority of the PPR genes in the higher plants are localized in organelles. Their functions remain as yet largely unknown. The majority of characterized PPR proteins have been found to function in modulating the expression plastid and mitochondrial genes in plants.ResultsHere, a genome-wide identification and comparison of the PPR genes from 5 organisms was performed, including the moss Physcomitrella patens, the lycophyte Selaginella moellendorffii, the eudicot Arabidopsis, and the monocots rice and foxtail millet. It appears that the expansion of this gene family prior to the divergence of the euphyllophytes and the lycophytes in land plants. The duplication and divergence rates of the foxtail millet PPR genes (SiPPRs) showed that the expansion period of this gene family around 400 Mya, and indicated that genome segmental duplication was very likely the primary mechanism underlying the expansion of the PPR gene family in vascular plants. An analysis of a complete set of SiPPR genes/proteins that included classification, chromosomal location, orthologous relationships, duplication analysis, and auxiliary motifs is presented. Expression analysis of the SiPPR genes under stress conditions revealed that the expression of 24 SiPPR genes was responsive to abiotic stress. Subcellular localization analysis of 11 PPR proteins indicated that 5 proteins were localized to chloroplasts, that 4 were localized to mitochondria, and that 2 were localized to the cytoplasm.ConclusionsOur results contribute to a more comprehensive understanding the roles of PPR proteins and will be useful in the prioritization of particular PPR proteins for subsequent functional validation studies in foxtail millet.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3184-2) contains supplementary material, which is available to authorized users.

show abstract

“…Multiple genes of one family were characterized as tandem genes when they were located within the same or a neighboring region (within 100 kb). Segmental duplications were determined using the method of Du et al (2013), Xu et al (2014), and Lu et al (2015). Firstly, BLASTP was used to identify potential anchors (E b 1 e−5 , top 5 matches); subsequently, the homologous regions were determined using software MCscan.…”

Section: Chromosomal Localization and Duplication Of Citrus Omt Genesmentioning

confidence: 99%

Systematic analysis of O -methyltransferase gene family and identification of potential members involved in the formation of O -methylated flavonoids in Citrus

Liu

Luo

et al. 2016

Gene

View full text Add to dashboard Cite

Genome-wide identification and analysis of late embryogenesis abundant (LEA) genes in Prunus mume

Cited by 92 publications

References 54 publications

Abscisic Acid (ABA) Regulation of Arabidopsis SR Protein Gene Expression

Abscisic Acid (ABA) Regulation of Arabidopsis SR Protein Gene Expression

Genome-wide investigation and expression analyses of the pentatricopeptide repeat protein gene family in foxtail millet

Systematic analysis of O -methyltransferase gene family and identification of potential members involved in the formation of O -methylated flavonoids in Citrus

Contact Info

Product

Resources

About