De novo transcriptome assembly and identification of salt-responsive genes in sugar beet M14. (August 2018)

• Record Type: Journal Article
• Authors: Lv, Xiaoyan; Jin, Ying; Wang, Yuguang
• Is Part Of: Computational biology and chemistry. Volume 75(2018)
• Page Start: 1
• Page End: 10
• Publication Date: 2018-08
• Subjects: 1, 3-PGA 1, 3-phosphoglycerate -- 3-PGA 3-phosphoglycerate -- ACC aminocyclopropane-1-carboxylate -- ACP acyl carrier protein -- Accase acetyl-coenzyme A carboxylase carboxyl transferase -- ADP adenosine diphosphate -- AdoHcyase adenosylhomocysteinase -- AdoMet S-adenosylmethionine -- AOX alternative oxidase -- APX ascorbate peroxidase -- ATP adenosine triphosphate -- BADH betaine aldehyde dehydrogenase -- BAH betaine aldehyde -- bHLH basic/helix_loop_helix -- BP binding protein -- CAB chlorophyll a/b-binding protein -- CAT catalase -- CaX calcium exchanger protein -- CaH sodium/calcium exchanger protein -- CES cellulose synthase -- CMO choline monooxygenase -- CoA coenzyme A -- Cytb6f cytochromeb6f -- CNGC cyclic nucleotide-gated ion channel -- DHA dehydroascorbate -- DHAP dihydroxyacetone phosphate -- DHAR dehydroascorbate reductase -- E4P erythrose-4-phosphate -- EF elongation factor -- EIF eukaryotic initiation factor -- F-6-P fructose-6-phosphate -- FabB 3-ketoacyl-ACP synthase -- FabH 3-oxoacyl-ACP synthase -- FabG 3-oxoacyl-acyl-carrier- protein reductase -- FAD flavin adenine dinucleotide -- FBPase d-fructose 1, 6-bisphosphatase -- Fd ferredoxin -- FNR ferredoxin−NADP reductase -- FTP guanosine triphosphate -- G glucose -- G-1-P glucose-1-phosphate -- GADPH glyceraldehyde-3- phosphate dehydrogenase -- GAP glycerate 3-phosphate -- GB glycine betaine -- GOX glycolate oxidase -- GPAT glucose-1-phosphate adenylytransferase -- GPX glutathione peroxidase -- GR glutathione reductase -- GSH reduced glutathione -- GSSG oxidized glutathione -- GST glutathione S-transferase -- HMT homocysteine S-methyltransferase -- HSP heat shock protein -- HXK hexokinase -- IDH isocitrate dehydrogenase -- KOC outward-rectifying potassium channel -- LHC light-harvesting complex -- LPD dihydrolipoyl dehydrogenase -- MDA monodehydroascorbate -- MDHAR monodehydroascorbate reductase -- Met methionine -- MIP major intrinsic protein -- NAC nascent polypeptide-associated complex -- NAD nicotinamide adenine dinucleotide -- NADP nicotinamide adenine dinucleotide phosphate -- NBP nucleic acid binding protein -- NDGPD NADP-dependent glyceraldehydes-3-phosphate dehydrogenase -- NCKX sodium/potassium/calcium exchanger -- NHX Na+/H+ exchanger -- OEC oxygen evolving complex -- OEE oxygen evolving enhancer protein -- PDC pyruvate decarboxylase -- PDI protein disulfide isomerase -- PDHE1 pyruvate dehydrogenase E1 -- PFP pyrophosphate–fructose 6-phosphate 1-phosphotransferase -- PG polygalacturonase -- PGA 3-phosphoglycerate -- PGK phosphoglycerate kinase -- Pi inorganic phosphate -- PIP plasma membrane intrinsic protein -- PPA-AT prephenate aminotransferase -- PPIase peptidyl-prolyl cis-trans isomerase -- PPR pentatricopeptide repeat-containing protein -- PRK phosphoribulokinase -- PrxR peroxiredoxin -- PS I photosystem I -- PS II photosystem II -- Q quinine -- QH2 reduced quinone -- R5P ribose-5-phosphate -- RCA ribulose-1, 5-bisphosphate carboxylase/oxygenase activase -- RRF ribosome-recycling factor -- RPI ribulose-5-phosphate isomerase -- Ru5P ribulose-5-phosphate -- RuBisCO ribulose-1, 5-bisphosphate carboxylase/oxygenase -- RuBP ribulose-1, 5-bisphosphate -- S7P sedoheptulose-7-phosphate -- SAMDC S-adenosylmethionine decarboxylase proenzyme -- SBP sedoheptulose-1, 7-bisphosphate -- SBPase sedoheptulose-1, 7-bisphosphatase -- SCoAL succinic acid synthetase -- SF splicing factor -- SOS1 salt overly sensitive 1B -- SOD superoxide dismutase -- SPDSY spermidine synthase -- TCTP translationally controlled tumor protein -- TEF translation elongation factor -- TF transcription factor -- TIF translation initiation factor -- TIP tonoplast intrinsic protein -- TK transketolase -- TL thylakoid lumen -- TPI triose-phosphate isomerase -- Trx thioredoxin -- UDP uridine diphosphate -- UDPG uridine diphosphate glucose -- UDPGDH UDP-glucose 6-dehydrogenase -- VHA vacuolar H+-ATP synthase subunit B -- Xyl xylanase -- Xu5P xylulose-5-phosphate; Sugar beet M14 line -- Salt stress -- Transcriptome assembly -- Transcriptomics -- Transcription factor -- ROS scavenging system; Chemistry -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; Biochemistry -- Data processing; Biology -- Data processing; Molecular biology -- Data processing; Periodicals; Electronic journals; 542.85
• DOI: 10.1016/j.compbiolchem.2018.04.014
• Languages: English
• ISSNs: 1476-9271

Abstract

Graphical abstract: Highlights: A reference transcriptome dataset of sugar beet M14 was generated using RNAseq technology. Differentially expressed genes in the sugar beet M14 leaves and roots under salt stress were analyzed. QRT-PCR approach was used to validate changes in transcript levels of sugar beet M14 under salt. Abstract: Sugar beet ( Beta vulgaris ) is an important crop of sugar production in the world. Previous studies reported that sugar beet monosomic addition line M14 obtained from the intercross between Beta vulgaris L. (cultivated species) and B. corolliflora Zoss (wild species) exhibited tolerance to salt (up to 0.5 M NaCl) stress. To estimate a broad spectrum of genes involved in the M14 salt tolerance will help elucidate the molecular mechanisms underlying salt stress. Comparative transcriptomics was performed to monitor genes differentially expressed in the leaf and root samples of the sugar beet M14 seedlings treated with 0, 200 and 400 mM NaCl, respectively. Digital gene expression revealed that 3856 unigenes in leaves and 7157 unigenes in roots were differentially expressed under salt stress. Enrichment analysis of the differentially expressed genes based on GO and KEGG databases showed that in both leaves and roots genes related to regulation of redox balance, signal transduction, and protein phosphorylation were differentially expressed. Comparison of gene expression in the leaf and root samples treated with 200 and 400 mM NaCl revealed different mechanisms for coping with salt stress. In addition, the expression levels of nine unigenes in the reactive oxygen species (ROS) scavenging system exhibited significant differences in the leaves and roots. Our transcriptomics results have provided new insights into the salt-stress responses in the leaves and roots of sugar beet.