Wallis JG, Watts JL, Browse J. Polyunsaturated fatty acid synthesis: what will they think of next? Trends Biochem Sci. 2002;27(9):467–73.
Article
CAS
PubMed
Google Scholar
Li M-J, Wang X-J, Su L, Bi Y-P, Wan S-B. Characterization of five putative acyl carrier protein (ACP) isoforms from developing seeds of Arachis hypogaea L. Plant Mol Biol Report. 2010;28(3):365–72.
Article
CAS
Google Scholar
Sperling P, Ternes P, Zank T, Heinz E. The evolution of desaturases. Prostaglandins Leukot Essent Fat Acids. 2003;68(2):73–95.
Article
CAS
Google Scholar
Luo T, Deng WY, Zeng J, Zhang FL. Cloning and characterization of a stearoyl–acyl carrier protein desaturase gene from Cinnamomum longepaniculatum. Plant Mol Biol Report. 2009;27(1):13.
Article
CAS
Google Scholar
Singh SC, Sinha RP, Hader D-P. Role of lipids and fatty acids in stress tolerance in cyanobacteria. Acta Protozool. 2002;41(4):297–308.
CAS
Google Scholar
Ohlrogge J, Browse J. Lipid biosynthesis. Plant Cell. 1995;7(7):957.
CAS
PubMed
PubMed Central
Google Scholar
Díaz ML, Cuppari S, Soresi D, Carrera A. In Silico analysis of fatty acid Desaturase genes and proteins in grasses. Appl Biochem Biotechnol. 2018;184(2):484–99.
Article
PubMed
CAS
Google Scholar
Sharma A, Chauhan RS. In silico identification and comparative genomics of candidate genes involved in biosynthesis and accumulation of seed oil in plants. Comp Func Genom. 2012;2012:914843.
Article
CAS
Google Scholar
Mikkilineni V, Rocheford T. Sequence variation and genomic organization of fatty acid desaturase-2 (fad2) and fatty acid desaturase-6 (fad6) cDNAs in maize. Theor Appl Genet. 2003;106(7):1326–32.
Article
CAS
PubMed
Google Scholar
Celik Altunoglu Y, Unel NM, Baloglu MC, Ulu F, Can TH, Cetinkaya R. Comparative identification and evolutionary relationship of fatty acid desaturase (FAD) genes in some oil crops: the sunflower model for evaluation of gene expression pattern under drought stress. Biotechnol Biotechnol Equip. 2018;32(4):846–57.
Article
CAS
Google Scholar
Matteucci M, D'angeli S, Errico S, Lamanna R, Perrotta G, Altamura M. Cold affects the transcription of fatty acid desaturases and oil quality in the fruit of Olea europaea L. genotypes with different cold hardiness. J Exp Bot. 2011;62(10):3403–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu L, Zeng W, Li J, Liu H, Yan G, Si P, et al. Characteristics of membrane-bound fatty acid desaturase (FAD) genes in Brassica napus L. and their expressions under different cadmium and salinity stresses. Environ Exp Bot. 2019;162:144–56.
Article
CAS
Google Scholar
Xue Y, Zhang X, Wang R, Chen B, Jiang J, Win AN, et al. Cloning and expression of Perilla frutescens FAD2 gene and polymorphism analysis among cultivars. Acta Physiol Plant. 2017;39(3):84.
Article
CAS
Google Scholar
Dar AA, Choudhury AR, Kancharla PK, Arumugam N. The FAD2 gene in plants: occurrence, regulation, and role. Front Plant Sci. 2017;8:1789.
Article
PubMed
PubMed Central
Google Scholar
Feng J, Dong Y, Liu W, He Q, Daud M, Chen J, et al. Genome-wide identification of membrane-bound fatty acid desaturase genes in Gossypium hirsutum and their expressions during abiotic stress. Sci Rep. 2017;7:45711.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu W, Li W, He Q, Daud MK, Chen J, Zhu S. Characterization of 19 genes encoding membrane-bound fatty acid desaturases and their expression profiles in Gossypium raimondii under low temperature. PLoS One. 2015;10(4):e0123281.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhao X, Wei J, He L, Zhang Y, Zhao Y, Xu X, et al. Identification of fatty acid Desaturases in maize and their differential responses to low and high temperature. Genes. 2019;10(6):445.
Article
CAS
PubMed Central
Google Scholar
Byfield G, Xue H, Upchurch R. Two genes from soybean encoding soluble Δ9 stearoyl-ACP desaturases. Crop Sci. 2006;46(2):840–6.
Article
CAS
Google Scholar
Wang H, Cao F, Zhang W, Wang G, Yu W. Cloning and expression of Stearoyl-ACP Desaturase and two Oleate Desaturases genes from Ginkgo biloba L. Plant Mol Biol Report. 2013;31(3):633–48.
Article
CAS
Google Scholar
Hernández ML, Mancha M, Martínez-Rivas JM. Molecular cloning and characterization of genes encoding two microsomal oleate desaturases (FAD2) from olive. Phytochemistry. 2005;66(12):1417–26.
Article
PubMed
CAS
Google Scholar
Zhang J, Liu H, Sun J, Li B, Zhu Q, Chen S, et al. Arabidopsis fatty acid desaturase FAD2 is required for salt tolerance during seed germination and early seedling growth. PLoS One. 2012;7(1):e30355.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang J-T, Zhu J-Q, Zhu Q, Liu H, Gao X-S, Zhang H-X. Fatty acid desaturase-6 (Fad6) is required for salt tolerance in Arabidopsis thaliana. Biochem Biophys Res Commun. 2009;390(3):469–74.
Article
CAS
PubMed
Google Scholar
Zhang M, Barg R, Yin M, Gueta-Dahan Y, Leikin-Frenkel A, Salts Y, et al. Modulated fatty acid desaturation via overexpression of two distinct ω-3 desaturases differentially alters tolerance to various abiotic stresses in transgenic tobacco cells and plants. Plant J. 2005;44(3):361–71.
Article
CAS
PubMed
Google Scholar
Ghafoor K, Özcan MM, AL-Juhaımı F, Babıker EE, Sarker ZI, IAM A, et al. Nutritional composition, extraction, and utilization of wheat germ oil: a review. Eur J Lipid Sci Technol. 2017;119(7):1600160.
Article
CAS
Google Scholar
Kong W, Gong Z, Zhong H, Zhang Y, Zhao G, Gautam M, et al. Expansion and evolutionary patterns of glycosyltransferase family 8 in Gramineae crop genomes and their expression under salt and cold stresses in Oryza sativa ssp. japonica. Biomolecules. 2019;9(5):188.
Article
CAS
PubMed Central
Google Scholar
Zhang W, Wang S, Yu F, Tang J, Yu L, Wang H, et al. Genome-wide identification and expression profiling of sugar transporter protein (STP) family genes in cabbage (Brassica oleracea var. capitata L.) reveals their involvement in clubroot disease responses. Genes. 2019;10(1):71.
Article
PubMed Central
CAS
Google Scholar
Sharp PA. Speculations on RNA splicing. Cell. 1981;23(3):643–6.
Article
CAS
PubMed
Google Scholar
Miao X, Zhang L, Hu X, Nan S, Chen X, Fu H. Cloning and functional analysis of the FAD2 gene family from desert shrub Artemisia sphaerocephala. BMC Plant Biol. 2019;19(1):481.
Article
PubMed
PubMed Central
CAS
Google Scholar
Chodok P, Eiamsa-ard P, Cove DJ, Quatrano RS, Kaewsuwan S. Identification and functional characterization of two Δ 12-fatty acid desaturases associated with essential linoleic acid biosynthesis in Physcomitrella patens. J Ind Microbiol Biotechnol. 2013;40(8):901–13.
Article
CAS
PubMed
Google Scholar
Rajwade AV, Joshi RS, Kadoo NY, Gupta VS. Sequence characterization and in silico structure prediction of fatty acid desaturases in linseed varieties with differential fatty acid composition. J Sci Food Agric. 2016;96(15):4896–906.
Article
CAS
PubMed
Google Scholar
Shanklin J, Whittle E, Fox BG. Eight histidine residues are catalytically essential in a membrane-associated iron enzyme, stearoyl-CoA desaturase, and are conserved in alkane hydroxylase and xylene monooxygenase. Biochemistry. 1994;33(43):12787–94.
Article
CAS
PubMed
Google Scholar
Broadwater JA, Whittle E, Shanklin J. Desaturation and hydroxylation residues 148 and 324 of arabidopsis fad2, in addition to substrate chain length, exert a major influence in partitioning of catalytic specificity. J Biol Chem. 2002;277(18):15613–20.
Article
CAS
PubMed
Google Scholar
Xue Y, Chen B, Wang R, Win AN, Li J, Chai Y. Genome-wide survey and characterization of fatty acid desaturase gene family in Brassica napus and its parental species. Appl Biochem Biotechnol. 2018;184(2):582–98.
Article
CAS
PubMed
Google Scholar
Chi X, Yang Q, Lu Y, Wang J, Zhang Q, Pan L, et al. Genome-wide analysis of fatty acid desaturases in soybean (Glycine max). Plant Mol Biol Report. 2011;29(4):769–83.
Article
CAS
Google Scholar
Zhang Z, Wei X, Liu W, Min X, Jin X, Ndayambaza B, et al. Genome-wide identification and expression analysis of the fatty acid desaturase genes in Medicago truncatula. Biochem Biophys Res Commun. 2018;499(2):361–7.
Article
CAS
PubMed
Google Scholar
Johnson DA, Thomas MA. The monosaccharide transporter gene family in Arabidopsis and rice: a history of duplications, adaptive evolution, and functional divergence. Mol Biol Evol. 2007;24(11):2412–23.
Article
CAS
PubMed
Google Scholar
Ma J, Yang Y, Luo W, Yang C, Ding P, Liu Y, et al. Genome-wide identification and analysis of the MADS-box gene family in bread wheat (Triticum aestivum L.). PLoS One. 2017;12:7.
Google Scholar
Cao J, Shi F. Evolution of the RALF gene family in plants: gene duplication and selection patterns. Evol Bioinforma. 2012;8:S9652.
Article
CAS
Google Scholar
Cannon SB, Mitra A, Baumgarten A, Young ND, May G. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol. 2004;4(1):10.
Article
PubMed
PubMed Central
Google Scholar
Xu G, Guo C, Shan H, Kong H. Divergence of duplicate genes in exon–intron structure. Proc Natl Acad Sci. 2012;109(4):1187–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hanada K, Zou C, Lehti-Shiu MD, Shinozaki K, Shiu S-H. Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol. 2008;148(2):993–1003.
Article
CAS
PubMed
PubMed Central
Google Scholar
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, et al. The Sorghum bicolor genome and the diversification of grasses. Nature. 2009;457(7229):551.
Article
CAS
PubMed
Google Scholar
Dong C-J, Cao N, Zhang Z-G, Shang Q-M. Characterization of the fatty acid desaturase genes in cucumber: structure, phylogeny, and expression patterns. PLoS One. 2016;11(3):e0149917.
Article
PubMed
PubMed Central
CAS
Google Scholar
PMG N, Kang I-S, Moon B-Y, Lee C-H. Effects of low temperature stress on rice (Oryzasativa L.) plastid ω-3 desaturase gene, OsFAD8 and its functional analysis using T-DNA mutants. Plant Cell Tissue Organ Cult (PCTOC). 2009;98(1):87–96.
Article
CAS
Google Scholar
Dyer JM, Mullen RT. Immunocytological localization of two plant fatty acid desaturases in the endoplasmic reticulum. FEBS Lett. 2001;494(1–2):44–7.
Article
CAS
PubMed
Google Scholar
Huang W, Xian Z, Kang X, Tang N, Li Z. Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato. BMC Plant Biol. 2015;15(1):209.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lindemose S, O'Shea C, Jensen M, Skriver K. Structure, function and networks of transcription factors involved in abiotic stress responses. Int J Mol Sci. 2013;14(3):5842–78.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dong C-J, Shang Q-M. Genome-wide characterization of phenylalanine ammonia-lyase gene family in watermelon (Citrullus lanatus). Planta. 2013;238(1):35–49.
Article
CAS
PubMed
Google Scholar
Cao J, Li M, Chen J, Liu P, Li Z. Effects of MeJA on Arabidopsis metabolome under endogenous JA deficiency. Sci Rep. 2016;6:37674.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu Z, Zhang M, Kong L, Lv Y, Zou M, Lu G, et al. Genome-wide identification, phylogeny, duplication, and expression analyses of two-component system genes in Chinese cabbage (Brassica rapa ssp. pekinensis). DNA Res. 2014;21(4):379–96.
Article
PubMed
PubMed Central
CAS
Google Scholar
Upchurch RG. Fatty acid unsaturation, mobilization, and regulation in the response of plants to stress. Biotechnol Lett. 2008;30(6):967–77.
Article
CAS
PubMed
Google Scholar
Haasl RJ, Payseur BA. Microsatellites as targets of natural selection. Mol Biol Evol. 2012;30(2):285–98.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li Y-C, Korol AB, Fahima T, Nevo E. Microsatellites within genes: structure, function, and evolution. Mol Biol Evol. 2004;21(6):991–1007.
Article
CAS
PubMed
Google Scholar
Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan H. Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Gen Genomics. 2003;270(4):315–23.
Article
CAS
Google Scholar
Kumar A, Batra R, Gahlaut V, Gautam T, Kumar S, Sharma M, et al. Genome-wide identification and characterization of gene family for RWP-RK transcription factors in wheat (Triticum aestivum L.). PLoS One. 2018;13:12.
Google Scholar
Qin Z, Wang Y, Wang Q, Li A, Hou F, Zhang L. Evolution analysis of simple sequence repeats in plant genome. PLoS One. 2015;10:12.
Google Scholar
Wang Z, Qiao Y, Zhang J, Shi W, Zhang J. Genome wide identification of microRNAs involved in fatty acid and lipid metabolism of Brassica napus by small RNA and degradome sequencing. Gene. 2017;619:61–70.
Article
CAS
PubMed
Google Scholar
Agharbaoui Z, Leclercq M, Remita MA, Badawi MA, Lord E, Houde M, et al. An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress. BMC Genomics. 2015;16(1):339.
Article
PubMed
PubMed Central
CAS
Google Scholar
Fileccia V, Bertolini E, Ruisi P, Giambalvo D, Frenda AS, Cannarozzi G, et al. Identification and characterization of durum wheat microRNAs in leaf and root tissues. Func Integr Genom. 2017;17(5):583–98.
Article
CAS
Google Scholar
Liu H, Able AJ, Able JA. Water-deficit stress-responsive microRNAs and their targets in four durum wheat genotypes. Func Integr Genom. 2017;17(2–3):237–51.
Article
CAS
Google Scholar
Zhao Y-Y, Guo C-J, Li X-J, Duan W-W, Ma C-Y, Chan H-M, et al. Characterization and expression pattern analysis of microRNAs in wheat under drought stress. Biol Plant. 2015;59(1):37–46.
Article
CAS
Google Scholar
Phillips JR, Dalmay T, Bartels D. The role of small RNAs in abiotic stress. FEBS Lett. 2007;581(19):3592–7.
Article
CAS
PubMed
Google Scholar
Liu S, Wang N, Zhang P, Cong B, Lin X, Wang S, et al. Next-generation sequencing-based transcriptome profiling analysis of Pohlia nutans reveals insight into the stress-relevant genes in Antarctic moss. Extremophiles. 2013;17(3):391–403.
Article
CAS
PubMed
Google Scholar
Wang J-W, Wang L-J, Mao Y-B, Cai W-J, Xue H-W, Chen X-Y. Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis. Plant Cell. 2005;17(8):2204–16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ma X, Xin Z, Wang Z, Yang Q, Guo S, Guo X, et al. Identification and comparative analysis of differentially expressed miRNAs in leaves of two wheat (Triticum aestivum L.) genotypes during dehydration stress. BMC Plant Biol. 2015;15(1):21.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kantar M, Unver T, Budak H. Regulation of barley miRNAs upon dehydration stress correlated with target gene expression. Func Integr Genom. 2010;10(4):493–507.
Article
CAS
Google Scholar
Sun L, Sun G, Shi C, Sun D. Transcriptome analysis reveals new microRNAs-mediated pathway involved in anther development in male sterile wheat. BMC Genomics. 2018;19(1):333.
Article
PubMed
PubMed Central
CAS
Google Scholar
Luo Y, Guo Z, Li L. Evolutionary conservation of microRNA regulatory programs in plant flower development. Dev Biol. 2013;380(2):133–44.
Article
CAS
PubMed
Google Scholar
Nakashima K, Takasaki H, Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K. NAC transcription factors in plant abiotic stress responses. Biochim et Biophys Acta (BBA)-Gene Regul Mech. 2012;1819(2):97–103.
Article
CAS
Google Scholar
Ma C, Burd S, Lers A. mi R 408 is involved in abiotic stress responses in a rabidopsis. Plant J. 2015;84(1):169–87.
Article
CAS
PubMed
Google Scholar
Hajyzadeh M, Turktas M, Khawar KM, Unver T. miR408 overexpression causes increased drought tolerance in chickpea. Gene. 2015;555(2):186–93.
Article
CAS
PubMed
Google Scholar
Bai Q, Wang X, Chen X, Shi G, Liu Z, Guo C, et al. Wheat miRNA TaemiR408 acts as an essential mediator in plant tolerance to pi deprivation and salt stress via modulating stress-associated physiological processes. Front Plant Sci. 2018;9:499.
Article
PubMed
PubMed Central
Google Scholar
Liu Z, Wang X, Chen X, Shi G, Bai Q, Xiao K. TaMIR1139: a wheat miRNA responsive to pi-starvation, acts a critical mediator in modulating plant tolerance to pi deprivation. Plant Cell Rep. 2018;37(9):1293–309.
Article
CAS
PubMed
Google Scholar
Han R, Jian C, Lv J, Yan Y, Chi Q, Li Z, et al. Identification and characterization of microRNAs in the flag leaf and developing seed of wheat (Triticum aestivum L.). BMC Genomics. 2014;15(1):289.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li T, Ma L, Geng Y, Hao C, Chen X, Zhang X. Small RNA and degradome sequencing reveal complex roles of miRNAs and their targets in developing wheat grains. PLoS One. 2015;10:10.
Google Scholar
Akdogan G, Tufekci ED, Uranbey S, Unver T. miRNA-based drought regulation in wheat. Func Integr Genom. 2016;16(3):221–33.
Article
CAS
Google Scholar
Li M, Liang Z, He S, Zeng Y, Jing Y, Fang W, et al. Genome-wide identification of leaf abscission associated microRNAs in sugarcane (Saccharum officinarum L.). BMC Genomics. 2017;18(1):754.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ravichandran S, Ragupathy R, Edwards T, Domaratzki M, Cloutier S. MicroRNA-guided regulation of heat stress response in wheat. BMC Genomics. 2019;20(1):488.
Article
PubMed
PubMed Central
CAS
Google Scholar
Guo G, Liu X, Sun F, Cao J, Huo N, Wuda B, et al. Wheat miR9678 affects seed germination by generating phased siRNAs and modulating abscisic acid/gibberellin signaling. Plant Cell. 2018;30(4):796–814.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nishiuchi T, Hamada T, Kodama H, Iba K. Wounding changes the spatial expression pattern of the arabidopsis plastid omega-3 fatty acid desaturase gene (FAD7) through different signal transduction pathways. Plant Cell. 1997;9(10):1701–12.
CAS
PubMed
PubMed Central
Google Scholar
Soria-García Á, Rubio MC, Lagunas B, López-Gomollón S. Luján MdlÁ, Díaz-Guerra R, et al. tissue distribution and specific contribution of Arabidopsis FAD7 and FAD8 plastid Desaturases to the JA-and ABA-mediated cold stress or defense responses. Plant Cell Physiol. 2019;60(5):1025–40.
Article
CAS
Google Scholar
Im YJ, Han O, Chung GC, Cho BH. Antisense expression of an Arabidopsis omega-3 fatty acid desaturase gene reduces salt/drought tolerance in transgenic tobacco plants. Mol Cell. 2002;13(2):264–71.
CAS
Google Scholar
Hernández ML, Padilla MN, Sicardo MD, Mancha M, Martínez-Rivas JM. Effect of different environmental stresses on the expression of oleate desaturase genes and fatty acid composition in olive fruit. Phytochemistry. 2011;72(2–3):178–87.
Article
PubMed
CAS
Google Scholar
Chen M, Markham JE, Cahoon EB. Sphingolipid Δ8 unsaturation is important for glucosylceramide biosynthesis and low-temperature performance in Arabidopsis. Plant J. 2012;69(5):769–81.
Article
CAS
PubMed
Google Scholar
Iba K. Acclimative response to temperature stress in higher plants: approaches of gene engineering for temperature tolerance. Annu Rev Plant Biol. 2002;53(1):225–45.
Article
CAS
PubMed
Google Scholar
Román Á, Andreu V, Hernández ML, Lagunas B, Picorel R, Martínez-Rivas JM, et al. Contribution of the different omega-3 fatty acid desaturase genes to the cold response in soybean. J Exp Bot. 2012;63(13):4973–82.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wang J, Ming F, Pittman J, Han Y, Hu J, Guo B, et al. Characterization of a rice (Oryza sativa L.) gene encoding a temperature-dependent chloroplast ω-3 fatty acid desaturase. Biochem Biophys Res Commun. 2006;340(4):1209–16.
Article
CAS
PubMed
Google Scholar
Wang HS, Yu C, Tang XF, Wang LY, Dong XC, Meng QW. Antisense-mediated depletion of tomato endoplasmic reticulum omega-3 fatty acid desaturase enhances thermal tolerance. J Integr Plant Biol. 2010;52(6):568–77.
Article
CAS
PubMed
Google Scholar
Yurchenko OP, Park S, Ilut DC, Inmon JJ, Millhollon JC, Liechty Z, et al. Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium. BMC Plant Biol. 2014;14(1):312.
Article
PubMed
PubMed Central
CAS
Google Scholar
He X, Zhang J. Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics. 2005;169(2):1157–64.
Article
PubMed
PubMed Central
Google Scholar
Teshima KM, Innan H. Neofunctionalization of duplicated genes under the pressure of gene conversion. Genetics. 2008;178(3):1385–98.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, et al. The Pfam protein families database. Nucleic Acids Res. 2004;32(suppl_1):D138–D41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011;39(suppl_2):W29–37.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bolser D, Staines DM, Pritchard E, Kersey P. Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomics data. Plant Bioinform. 2016;1:115–40.
Article
CAS
Google Scholar
Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, De Castro E, et al. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res. 2012;1:gks400.
Google Scholar
Almagro Armenteros JJ, Sønderby CK, Sønderby SK, Nielsen H, OJB W. DeepLoc: prediction of protein subcellular localization using deep learning. Bioinformatics. 2017;33(21):3387–95.
Article
PubMed
CAS
Google Scholar
Yu CS, Chen YC, Lu CH, Hwang JKJPS. Function, bioinformatics. Prediction of protein subcellular localization. Proteins. 2006;64(3):643–51.
Article
CAS
PubMed
Google Scholar
Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;1:msw054.
Google Scholar
Felsenstein JJE. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39(4):783–91.
Article
PubMed
Google Scholar
Chen C, Chen H, He Y, Xia R. TBtools, a toolkit for biologists integrating various biological data handling tools with a user-friendly interface. BioRxiv. 2018;1:289660.
Google Scholar
Wei K, Pan S, Li Y. Functional characterization of maize C 2 H 2 zinc-finger gene family. Plant Mol Biol Report. 2016;34(4):761–76.
Article
CAS
Google Scholar
Wu C, Ding X, Ding Z, Tie W, Yan Y, Wang Y, et al. The class III peroxidase (POD) gene family in cassava: identification, phylogeny, duplication, and expression. Int J Mol Sci. 2019;20(11):2730.
Article
CAS
PubMed Central
Google Scholar
Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009;25(11):1451–2.
Article
CAS
PubMed
Google Scholar
Malviya N, Jaiswal P, Yadav DJP. Plants mbo. Genome-wide characterization of nuclear factor Y (NF-Y) gene family of sorghum [Sorghum bicolor (L.) Moench]: a bioinformatics approach. Physiol Mol Biol Plants. 2016;22(1):33–49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hu B, Jin J, Guo A-Y, Zhang H, Luo J, Gao G. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 2014;1:btu817.
Google Scholar
Bailey TL, Williams N, Misleh C, Li WW. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 2006;34(suppl 2):W369–W73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2013;1:gkt1223.
Google Scholar
Letunic I, Doerks T, Bork P. SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res. 2012;40(D1):D302–D5.
Article
CAS
PubMed
Google Scholar
Howe KL, Contreras-Moreira B, De Silva N, Maslen G, Akanni W, Allen J, et al. Ensembl genomes 2020—enabling non-vertebrate genomic research. Nucleic Acids Res. 2019;48(D1):D689–D95.
Article
PubMed Central
CAS
Google Scholar
Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, et al. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002;30(1):325–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
You FM, Huo N, Gu YQ, Luo M-c, Ma Y, Hane D, et al. BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC bioinformatics. 2008;9(1):253.
Article
PubMed
PubMed Central
CAS
Google Scholar
Borrill P, Ramirez-Gonzalez R, Uauy C. expVIP: a customizable RNA-seq data analysis and visualization platform. Plant Physiol. 2016;170(4):2172–86.
Article
CAS
PubMed
PubMed Central
Google Scholar
ZhangY RAK. I- TASSER: Aunifiedplatform forautomated proteinstructureandfunction prediction. NatureProtocols. 2010;5(4):725.
Google Scholar
Xu D, Zhang Y. Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophys J. 2011;101(10):2525–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Laskowski RA, Chistyakov VV, Thornton JM. PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res. 2005;33(suppl_1):D266–D8.
CAS
PubMed
Google Scholar
Lovell SC, Davis IW, Arendall WB III, De Bakker PI, Word JM, Prisant MG, et al. Structure validation by Cα geometry: ϕ, ψ and Cβ deviation. Proteins. 2003;50(3):437–50.
Article
CAS
PubMed
Google Scholar
Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, et al. PubChem 2019 update: improved access to chemical data. Nucleic Acids Res. 2019;47(D1):D1102–D9.
Article
PubMed
Google Scholar
Wu Q, Peng Z, Zhang Y, Yang J. COACH-D: improved protein–ligand binding sites prediction with refined ligand-binding poses through molecular docking. Nucleic Acids Res. 2018;46(W1):W438–W42.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang J, Roy A, Zhang Y. Protein–ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics. 2013;29(20):2588–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Roy A, Yang J, Zhang Y. COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res. 2012;40(W1):W471–W7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brylinski M, Skolnick J. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci. 2008;105(1):129–34.
Article
CAS
PubMed
Google Scholar
Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput Biol. 2009;5:12.
Article
CAS
Google Scholar
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, et al. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem. 2009;30(16):2785–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, et al. UCSF chimera—a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605–12.
Article
CAS
PubMed
Google Scholar