SRNAome and degradome sequencing analysis reveals specific regulation of sRNA in response to chilling injury in tomato fruit.

Abstract:

:Plant genomes encode diverse small RNA classes that function in distinct gene-silencing pathways. To elucidate the intricate regulation of microRNAs (miRNAs) and endogenous small-interfering RNAs (siRNAs) in response to chilling injury in tomato fruit, the deep sequencing and bioinformatic methods were combined to decipher the small RNAs landscape in the control and chilling-injured groups. Except for the known miRNAs and ta-siRNAs, 85 novel miRNAs and 5 ta-siRNAs members belonging to 3 TAS families (TAS5, TAS9 and TAS10) were identified, 34 putative phased small RNAs and 740 cis/trans-natural antisense small-interfering RNAs (nat-siRNAs) were also found in our results which enriched the tomato small RNAs repository. A large number of genes targeted by those miRNAs and siRNAs were predicted to be involved in the chilling injury responsive process and five of them were verified via degradome sequencing. Based on the above results, a regulatory model that comprehensively reveals the relationships between the small RNAs and their targets was set up. This work provides a foundation for further study of the regulation of miRNAs and siRNAs in the plant in response to chilling injury.

journal_name

Physiol Plant

journal_title

Physiologia plantarum

authors

Zuo J,Wang Q,Han C,Ju Z,Cao D,Zhu B,Luo Y,Gao L

doi

10.1111/ppl.12509

subject

Has Abstract

pub_date

2017-06-01 00:00:00

pages

142-154

issue

2

eissn

0031-9317

issn

1399-3054

journal_volume

160

pub_type

杂志文章
  • Ultrastructural observation of mesophyll cells and temporal expression profiles of the genes involved in transitory starch metabolism in flag leaves of wheat after anthesis.

    abstract::Transitory starch in cereal plant leaves is synthesized during the day and remobilized at night to provide a carbon source for growth and grain filling, but its mechanistic basis is still poorly understood. The objective of this study is to explore the regulatory mechanism for starch biosynthesis and degradation in pl...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/ppl.12233

    authors: Kang G,Peng X,Wang L,Yang Y,Shao R,Xie Y,Ma D,Wang C,Guo T,Zhu Y

    更新日期:2015-01-01 00:00:00

  • A transnational and holistic breeding approach is needed for sustainable wheat production in the Baltic Sea region.

    abstract::The Baltic Sea is one of the largest brackish water bodies in the world. Eutrophication is a major concern in the Baltic Sea due to the leakage of nutrients to the sea with agriculture being the primary source. Wheat (Triticum aestivum L.) is the most widely grown crop in the countries surrounding the Baltic Sea and t...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章,评审

    doi:10.1111/ppl.12726

    authors: Chawade A,Armoniené R,Berg G,Brazauskas G,Frostgård G,Geleta M,Gorash A,Henriksson T,Himanen K,Ingver A,Johansson E,Jørgensen LN,Koppel M,Koppel R,Makela P,Ortiz R,Podyma W,Roitsch T,Ronis A,Svensson JT,Vallenback

    更新日期:2018-12-01 00:00:00

  • Temporal analysis of poplar woody root response to bending stress.

    abstract::Temperate perennial woody plants use different environmental signals to coordinate their growth and development in relation to seasonal changes. Preliminary evidences suggest that, even during dormancy, plants maintain effective metabolic activities and molecular mechanisms ensuring them an eventual recording of mecha...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/ppl.12072

    authors: Trupiano D,Rocco M,Renzone G,Scaloni A,Rossi M,Viscosi V,Chiatante D,Scippa GS

    更新日期:2014-02-01 00:00:00

  • Molecular characterization of rice arsenic-induced RING finger E3 ligase 2 (OsAIR2) and its heterogeneous overexpression in Arabidopsis thaliana.

    abstract::Arsenic (As) accumulation adversely affects the growth and productivity of plants and poses a serious threat to human health and food security. In this study, we identified one As-responsive Really Interesting New Gene (RING) E3 ubiquitin ligase gene from rice root tissues during As stress. We named it Oryza sativa As...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/ppl.12607

    authors: Hwang SG,Chapagain S,Han AR,Park YC,Park HM,Kim YH,Jang CS

    更新日期:2017-11-01 00:00:00

  • Influx and efflux of K(+) in sunflower roots after transfer between solutions with different K(+) concentrations.

    abstract::It was investigated whether K(+) efflux, like K(+) influx, is affected when roots are transferred between solutions with different K(+) concentrations. Sunflower plants (Hehanthus annuus L. cv. Uniflorus) were grown on complete nutrient solutions with 0.1, 1.0, 10 or 25 mM K(+) . This produced plants with K(+) concent...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/j.1399-3054.1990.tb00045.x

    authors: Pettersson S,Kasimir-Klemedtsson A

    更新日期:1990-08-01 00:00:00

  • A Prunus persica genome-wide RNA-seq approach uncovers major differences in the transcriptome among chilling injury sensitive and non-sensitive varieties.

    abstract::Chilling injury represents a major constrain for crops productivity. Prunus persica, one of the most relevant rosacea crops, have early season varieties that are resistant to chilling injury, in contrast to late season varieties, which display chilling symptoms such as mealiness (dry, sandy fruit mesocarp) after prolo...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/ppl.12831

    authors: Nilo-Poyanco R,Vizoso P,Sanhueza D,Balic I,Meneses C,Orellana A,Campos-Vargas R

    更新日期:2019-07-01 00:00:00

  • Ecophysiological responses of Abies fabri seedlings to drought stress and nitrogen supply.

    abstract::Abies fabri (Mast.) Craib. (A. fabri) is an endemic and dominant species in typical subalpine dark coniferous forests distributed in mountainous regions of Western Sichuan, China. We investigated the ecophysiological responses of A. fabri seedlings to short-term experimental drought, nitrogen supply and their interact...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/j.1399-3054.2010.01370.x

    authors: Guo J,Yang Y,Wang G,Yang L,Sun X

    更新日期:2010-08-01 00:00:00

  • Regulation of nitrate reduction in Arabidopsis WT and hxk1 mutant under C and N metabolites.

    abstract::As in plants sugar sensing and signal transduction involve pathways dependent or independent on hexokinase 1 (HXK1) as a glucose sensor, research was conducted to determine which pathway is responsible for regulation of the nitrate reduction. An Arabidopsis mutant with T-DNA insertion in the AtHXK1 gene and defects in...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/ppl.12045

    authors: Reda M

    更新日期:2013-10-01 00:00:00

  • Cloning and functional characterization of a GNA-like lectin from Chinese Narcissus (Narcissus tazetta var. Chinensis Roem).

    abstract::A full-length cDNA encoding Narcissus tazetta lectin (NTL) was isolated from Chinese narcissus (N. tazetta var. Chinensis Roem). The open reading frame (ORF) was 519 bp long and encoded 172 amino acids with a theoretical isoelectric point of 5.27 and a calculated molecular mass of 18.6 kDa. Conserved domain analysis i...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/j.1399-3054.2011.01449.x

    authors: Gao ZM,Zheng B,Wang WY,Li Q,Yuan QP

    更新日期:2011-06-01 00:00:00

  • Investigations into the possible regulation of negative gravitropic curvature in intact Avena sativa plants and in isolated stem segments by ethylene and gibberellins.

    abstract::Using Avena sativa L. cv. Victory oat seedlings and excised p-1 stem segments (including the p-1 and p-2 internodes) the effect of exogenously supplied ethylene and the removal of ethylene on internodal extension and gravitropic bending was assessed. Similarly, the ability of the excised system to respond to gravisti...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/j.1399-3054.1985.tb02389.x

    authors: Kaufman P,Pharis RP,Reid DM,Beall FD

    更新日期:1985-01-01 00:00:00

  • Effect of arbuscular mycorrhizal inoculation on water status and photosynthesis of Populus cathayana males and females under water stress.

    abstract::Drought is one of the most serious environmental limitations for poplar growth. Although the ways in which plants deal with water stress and the effects of arbuscular mycorrhizal (AM) formation have been well documented, little is known about how the male and female plants of Populus cathayana respond to drought and A...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/ppl.12336

    authors: Li Z,Wu N,Liu T,Chen H,Tang M

    更新日期:2015-10-01 00:00:00

  • Antimicrobial solid media for screening non-sterile Arabidopsis thaliana seeds.

    abstract::Stable genetic transformation of plants is a low-efficiency process, and identification of positive transformants usually relies on screening for expression of a co-transformed marker gene. Often this involves germinating seeds on solid media containing a selection reagent. Germination on solid media requires surface ...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/ppl.13079

    authors: Behrendorff JBYH,Borràs-Gas G,Pribil M

    更新日期:2020-08-01 00:00:00

  • What causes the differences in cavitation resistance of two shrubs? Wood anatomical explanations and reliability testing of vulnerability curves.

    abstract::Relationships between xylem anatomical traits and cavitation resistance have always been a major content of plant hydraulics. To know how plants cope with drought, it is extremely important to acquire detailed knowledge about xylem anatomical traits and assess the cavitation resistance accurately. This study aims to i...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/ppl.13059

    authors: Zhao H,Jiang Z,Ma J,Cai J

    更新日期:2020-06-01 00:00:00

  • Enzymatic characterization of peroxisomal and cytosolic betaine aldehyde dehydrogenases in barley.

    abstract::Betaine aldehyde dehydrogenase (BADH; EC 1.2.1.8) is an important enzyme that catalyzes the last step in the synthesis of glycine betaine, a compatible solute accumulated by many plants under various abiotic stresses. In barley (Hordeum vulgare L.), we reported previously the existence of two BADH genes (BBD1 and BBD2...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/j.1399-3054.2008.01122.x

    authors: Fujiwara T,Hori K,Ozaki K,Yokota Y,Mitsuya S,Ichiyanagi T,Hattori T,Takabe T

    更新日期:2008-09-01 00:00:00

  • Effect of nitrogen on root release of phytosiderophores and root uptake of Fe(III)-phytosiderophore in Fe-deficient wheat plants.

    abstract::Root release of phytosiderophores (PSs) is an important step in iron (Fe) acquisition of grasses, and this adaptive reaction of plants is affected by various plant and environmental factors. The objectives of this study were to study the effects of varied nitrogen (N) supply on (1) root and leaf concentrations of meth...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/j.1399-3054.2011.01460.x

    authors: Aciksoz SB,Ozturk L,Gokmen OO,Römheld V,Cakmak I

    更新日期:2011-07-01 00:00:00

  • SRNAome parsing yields insights into tomato fruit ripening control.

    abstract::Small RNAs have emerged as critical regulators in the expression and function of eukaryotic genomes at the post-transcriptional level. To elucidate the functions of microRNA (miRNAs) and endogenous small-interfering RNAs (siRNAs) in tomato fruit ripening process, the deep sequencing and bioinformatics methods were com...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/ppl.12055

    authors: Zuo J,Fu D,Zhu Y,Qu G,Tian H,Zhai B,Ju Z,Gao C,Wang Y,Luo Y,Zhu B

    更新日期:2013-12-01 00:00:00

  • The Effect of Deleterious Concentrations of Copper on the Photosynthesis of Chlorella pyrenoidosa.

    abstract::If a single salt solution of CuSO(4) is used, Cu penetrates immediately iuto the plasma of Chlorella cells, reducing the rates of photosynthesis at both high and low illumination. If CuSO(4) is added to ordinary Österlind culture-medium (pH 8) it takes some hours before any influence of deleterious concentrations of C...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/j.1399-3054.1969.tb09100.x

    authors: Nielsen ES,Kamp-Nielsen L,Wium-Andersen S

    更新日期:1969-01-01 00:00:00

  • Effects of Pb-EDTA and EDTA on oxidative stress reactions and mineral uptake in Phaseolus vulgaris.

    abstract::Sequestration of Pb by synthetic chelates has been reported to increase bioavailability, uptake, and translocation of this metal in plants. In this work the potential phytotoxic effects of Pb-EDTA were investigated in Phaseolus vulgaris L. cv. Limburgse vroege plants grown on hydroponics. Addition of 50 microM Pb-EDTA...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1034/j.1399-3054.2002.1150307.x

    authors: Geebelen W,Vangronsveld J,Adriano DC,Van Poucke LC,Clijsters H

    更新日期:2002-07-01 00:00:00

  • The microtubule cytoskeleton does not integrate auxin transport and gravitropism in maize roots.

    abstract::The Cholodny-Went hypothesis of gravitropism suggests that the graviresponse is controlled by the distribution of auxin. However, the mechanism of auxin transport during the graviresponse of roots is still unresolved. To determine whether the microtubule (MT) cytoskeleton is participating in auxin transport, the cytos...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1034/j.1399-3054.1999.105418.x

    authors: Hasenstein KH,Blancaflor EB,Lee JS

    更新日期:1999-04-01 00:00:00

  • Identification and characterization of soluble and insoluble myrosinase isoenzymes in different organs of Sinapis alba.

    abstract::Extraction of Sinapis alba seeds under native conditions solubilized 3 myrosinase isoforms, pool I, II and III, which could be separated by ion exchange chromatography. Sequencing of numerous peptides of the I and III isoforms showed that they belonged to the Myrosinase A (MA) family of myrosinases and that they were ...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1034/j.1399-3054.2001.1110313.x

    authors: Eriksson S,Ek B,Xue J,Rask L,Meijer J

    更新日期:2001-03-01 00:00:00

  • MtMAPKK4 is an essential gene for growth and reproduction of Medicago truncatula.

    abstract::Mitogen-activated protein kinase (MAPK) cascades are universal signaling modules in eukaryotes, including yeasts, animals and plants. They are involved in responses to various biotic and abiotic stresses, hormones, cell division and developmental processes. A MAPK cascade is composed of three functionally tiered prote...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/ppl.12533

    authors: Chen T,Zhou B,Duan L,Zhu H,Zhang Z

    更新日期:2017-04-01 00:00:00

  • Different proportions of cadmium occur as Cd-binding phytochelatin complexes in plants.

    abstract::The aim was to determine cadmium (Cd) speciation in various plants, between buffer-soluble and acid-soluble Cd, and also within the buffer-soluble Cd. A better understanding of Cd speciation shows the relative importance of different biological mechanisms for Cd sequestration. Roots of Pistia stratiodes, Eichhornia cr...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/j.1399-3054.2007.00960.x

    authors: Marentes E,Rauser WE

    更新日期:2007-10-01 00:00:00

  • Ability of leaf mesophyll to retain potassium correlates with salinity tolerance in wheat and barley.

    abstract::This work investigated the importance of the ability of leaf mesophyll cells to control K(+) flux across the plasma membrane as a trait conferring tissue tolerance mechanism in plants grown under saline conditions. Four wheat (Triticum aestivum and Triticum turgidum) and four barley (Hordeum vulgare) genotypes contras...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/ppl.12056

    authors: Wu H,Shabala L,Barry K,Zhou M,Shabala S

    更新日期:2013-12-01 00:00:00

  • What physiological acclimation supports increased growth at high CO2 conditions?

    abstract::Chlamydomonas acidophila Negoro is a green algal species abundant in acidic waters (pH 2-3.5), in which inorganic carbon is present only as CO(2). Previous studies have shown that aeration with CO(2) increased its maximum growth rate, suggesting CO(2) limitation under natural conditions. To unravel the underlying phys...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/j.1399-3054.2008.01062.x

    authors: Spijkerman E

    更新日期:2008-05-01 00:00:00

  • Involvement of the chloroplast plastoquinone pool in the Mehler reaction.

    abstract::Light-dependent oxygen reduction in the photosynthetic electron transfer chain, i.e. the Mehler reaction, has been studied using isolated pea thylakoids. The role of the plastoquinone pool in the Mehler reaction was investigated in the presence of dinitrophenyl ether of 2-iodo-4-nitrothymol (DNP-INT), the inhibitor of...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/ppl.12560

    authors: Vetoshkina DV,Ivanov BN,Khorobrykh SA,Proskuryakov II,Borisova-Mubarakshina MM

    更新日期:2017-09-01 00:00:00

  • "Adaptation" and chromosome variability in excised roots of cereals.

    abstract::Heteroploidy, often coinciding with phenotypic or metabolic changes, was found in cereal root cultures. In some cases the changes were apparent after only 4 passages and affected the roots of bread wheat as well as those containing all or some of the wheat and rye genomes. It is unsafe to assume that cultured organise...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/j.1399-3054.1969.tb09120.x

    authors: Beuzenberg EJ,Ferguson JD,Pearson BE

    更新日期:1969-01-01 00:00:00

  • Leaf senescence in a non-yellowing cultivar of chrysanthemum (Dendranthema grandiflora).

    abstract::Chlorophyll (Chl) and total soluble protein decreased and proteolytic activity increased over a 12-day period during dark-induced senescence in detached leaves of Tara, a yellowing cultivar (Y) of Dendranthema grandiflora. In Boaldi, a non-yellowing cultivar (NY), Chl and soluble protein remained near initial levels a...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1034/j.1399-3054.2001.1110415.x

    authors: Reyes-Arribas T,Barrett JE,Huber DJ,Nell TA,Clark DG

    更新日期:2001-04-01 00:00:00

  • The presence of cutan limits the interpretation of cuticular chemistry and structure: Ficus elastica leaf as an example.

    abstract::Plant cuticles have been traditionally classified on the basis of their ultrastructure, with certain chemical composition assumptions. However, the nature of the plant cuticle may be misinterpreted in the prevailing model, which was established more than 150 years ago. Using the adaxial leaf cuticle of Ficus elastica,...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/ppl.12414

    authors: Guzmán-Delgado P,Graça J,Cabral V,Gil L,Fernández V

    更新日期:2016-06-01 00:00:00

  • Importance of the cytochrome pathway of mitochondrial electron transport over the alternative pathway during the Kok effect in leaf discs of pea (Pisum sativum).

    abstract::The Kok effect refers to the progressive light-induced inhibition of dark respiration at low light intensities, which saturates around the light compensation point. This appears as a sudden break around the light compensation point in the plot of photosynthesis versus light intensity. The magnitude of the break can be...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1034/j.1399-3054.2001.1130318.x

    authors: Padmavathi L,Raghavendra AS

    更新日期:2001-11-01 00:00:00

  • Cloning and characterization of a novel Nicotiana tabacum ABC transporter involved in shoot branching.

    abstract::The ATP-binding cassette (ABC) superfamily is a large protein family with diverse physiological functions in all kingdoms of life. One distinguished subfamily, the pleiotropic drug resistance (PDR) transporters, has only been identified in plants and fungi. Here, we identified a Nicotiana tabacum PDR gene, NtPDR6, whi...

    journal_title:Physiologia plantarum

    pub_type: 杂志文章

    doi:10.1111/ppl.12267

    authors: Xie X,Wang G,Yang L,Cheng T,Gao J,Wu Y,Xia Q

    更新日期:2015-02-01 00:00:00