Skip to main page content
U.S. flag

An official website of the United States government

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Nov 15;19(1):819.
doi: 10.1186/s12864-018-5204-x.

MicroRNAs and their targets in cucumber shoot apices in response to temperature and photoperiod

Xiaohui Zhang  1 , Yunsong Lai  1   2 , Wei Zhang  1 , Jalil Ahmad  1 , Yang Qiu  1 , Xiaoxue Zhang  1 , Mengmeng Duan  1 , Tongjin Liu  1 , Jiangping Song  1 , Haiping Wang  1 , Xixiang Li  3
Affiliations

MicroRNAs and their targets in cucumber shoot apices in response to temperature and photoperiod

Xiaohui Zhang et al. BMC Genomics. .

Abstract

Background: The cucumber is one of the most important vegetables worldwide and is used as a research model for study of phloem transport, sex determination and temperature-photoperiod physiology. The shoot apex is the most important plant tissue in which the cell fate and organ meristems have been determined. In this study, a series of whole-genome small RNA, degradome and transcriptome analyses were performed on cucumber shoot apical tissues treated with high vs. low temperature and long vs. short photoperiod.

Results: A total of 164 known miRNAs derived from 68 families and 203 novel miRNAs from 182 families were identified. Their 4611 targets were predicted using psRobot and TargetFinder, amongst which 349 were validated by degradome sequencing. Fourteen targets of six miRNAs were differentially expressed between the treatments. A total of eight known and 16 novel miRNAs were affected by temperature and photoperiod. Functional annotations revealed that "Plant hormone signal transduction" pathway was significantly over-represented in the miRNA targets. The miR156/157/SBP-Boxes and novel-mir153/ethylene-responsive transcription factor/senescence-related protein/aminotransferase/acyl-CoA thioesterase are the two most credible miRNA/targets combinations modulating the plant's responsive processes to the temperature-photoperiod changes. Moreover, the newly evolved, cucumber-specific novel miRNA (novel-mir153) was found to target 2087 mRNAs by prediction and has 232 targets proven by degradome analysis, accounting for 45.26-58.88% of the total miRNA targets in this plant. This is the largest sum of genes targeted by a single miRNA to the best of our knowledge.

Conclusions: These results contribute to a better understanding of the miRNAs mediating plant adaptation to combinations of temperature and photoperiod and sheds light on the recent evolution of new miRNAs in cucumber.

Keywords: Cucumber; Photoperiod; Shoot apex; Temperature; miRNAs.

PubMed Disclaimer

Conflict of interest statement

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Differentially expressed miRNAs. HS, high temperature, short day; LS, low temperature, short day; HL, high temperature, long day; LL, low temperature, long day. The red shading indicate up-regulated expression; the green shadows indicate down-regulated expression; and the light green shadows indicate down-regulated expression with p-value slightly exceeding the 1E-3 level
Fig. 2
Fig. 2
Degradome proven targets of known miRNAs. a Cleavage site plots of two typical targets. b Pairing of the known miRNAs with the mRNA target sites. The red arrows indicate the cut sites, the differential bases within a group are marked in blue
Fig. 3
Fig. 3
Pairing of the novel miRNAs (except novel-mir153) with the mRNA target sites. The red arrows indicate the cut sites, the differential bases within a group are marked in blue
Fig. 4
Fig. 4
Pairing of the novel-mir153 with its mRNA target sites. The red arrows indicate the cut sites, the differential bases within a group are marked in blue
Fig. 5
Fig. 5
GO annotation of targets of miRNAs
Fig. 6
Fig. 6
Heat maps of differentially expressed targets and their miRNAs
Fig. 7
Fig. 7
Negative correlation pattern of miRNAs and targets
Fig. 8
Fig. 8
Evolution of novel-mir153 in cucumber. a alignment of novel-mir153 harbouring sequences of three cucumber genotypes and the homologous sequences in melon, watermelons and pumpkins. Grey shading shows the exons, the multicolour shading shows the intron, the green shading shows the conserved sequences, and the yellow shading shows the novel-mir153 hairpin sequences. The blue shading shows the watermelon retained sequences. b secondary structures of the novel-mir153 hairpin and its homologs in watermelon, melon and Gy14 cucumber. The yellow shading shows the mature RNA and its homologs. c alignment of novel-mir153 and its targets
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Schultz TF, Kay SA. Circadian clocks in daily and seasonal control of development. Science. 2003;301:326–328. doi: 10.1126/science.1085935. - DOI - PubMed
    1. Lagercrantz U. At the end of the day: a common molecular mechanism for photoperiod responses in plants? J Exp Bot. 2009;60:2501–2515. doi: 10.1093/jxb/erp139. - DOI - PubMed
    1. Kahlen K, Chen TW. Predicting plant performance under simultaneously changing environmental conditions-the interplay between temperature, light, and internode growth. Front Plant Sci. 2015;6:1130. doi: 10.3389/fpls.2015.01130. - DOI - PMC - PubMed
    1. Bian ZH, Yang QC, Liu WK. Effects of light quality on the accumulation of phytochemicals in vegetables produced in controlled environments: a review. J Sci Food Agr. 2015;95:869–877. doi: 10.1002/jsfa.6789. - DOI - PubMed
    1. Miao M, Yang X, Han X, Wang K. Sugar signalling is involved in the sex expression response of monoecious cucumber to low temperature. J Exp Bot. 2011;62:797–804. doi: 10.1093/jxb/erq315. - DOI - PubMed