Gutterman Y. Seed germination in desert plants. Springer-Verlag Berlin Heidelberg; 1993.
Gutterman Y. Survival strategies of annual desert plants. Springer-Verlag Berlin Heidelberg; 2002.
Wang L, Huang Z, Baskin CC, Baskin JM, Dong M. Germination of dimorphic seeds of the desert annual halophyte Suaeda aralocaspica (Chenopodiaceae), a C4 plant without Kranz anatomy. Ann Bot. 2008;102:757–69.
Article
PubMed
PubMed Central
Google Scholar
Baskin JM, Baskin CC. A classification system for seed dormancy. Seed Sci Res. 2004;14:1–16.
Google Scholar
Hilhorst HW. A critical update on seed dormancy. I. Primary dormancy. Seed Sci Res. 1995;5:61–73.
Article
CAS
Google Scholar
Bewley JD. Seed germination and dormancy. Plant Cell. 1997;9:1055.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li B, Foley ME. Genetic and molecular control of seed dormancy. Trends Plant Sci. 1997;2:384–9.
Article
Google Scholar
Venable DL. The evolutionary ecology of seed heteromorphism. Am Nat. 1985:577–95.
Khan MA, Gul B. High salt tolerance in germinating dimorphic seeds of Arthrocnemum Indicum. Int J Plant Sci. 1998:826–32.
Wei Y, Dong M, Huang Z-Y. seed polymorphism, dormancy and germination of Salsola Affinis (Chenopodiaceae), a dominant desert annual inhabiting the Junggar Basin of Xinjiang, China. Aust J Bot. 2007;55:464–70.
Article
Google Scholar
Nakabayashi K, Okamoto M, Koshiba T, Kamiya Y, Nambara E. Genome-wide profiling of stored mRNA in Arabidopsis Thaliana seed germination: epigenetic and genetic regulation of transcription in seed. Plant J. 2005;41:697–709.
Article
CAS
PubMed
Google Scholar
Preston J, Tatematsu K, Kanno Y, Hobo T, Kimura M, Jikumaru Y, Yano R, Kamiya Y, Nambara E. Temporal expression patterns of hormone metabolism genes during imbibition of Arabidopsis Thaliana seeds: a comparative study on dormant and non-dormant accessions. Plant Cell Physiol. 2009;50:1786–800.
Article
CAS
PubMed
Google Scholar
Narsai R, Law SR, Carrie C, Xu L, Whelan J. In-depth temporal transcriptome profiling reveals a crucial developmental switch with roles for RNA processing and organelle metabolism that are essential for germination in Arabidopsis. Plant Physiol. 2011;157:1342–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Endo A, Tatematsu K, Hanada K, Duermeyer L, Okamoto M, Yonekura-Sakakibara K, Saito K, Toyoda T, Kawakami N, Kamiya Y. Tissue-specific transcriptome analysis reveals cell wall metabolism, flavonol biosynthesis and defense responses are activated in the endosperm of germinating Arabidopsis Thaliana seeds. Plant Cell Physiol. 2012;53:16–27.
Article
CAS
PubMed
Google Scholar
Penfield S, Li Y, Gilday AD, Graham S, Graham IA. Arabidopsis ABA INSENSITIVE4 regulates lipid mobilization in the embryo and reveals repression of seed germination by the endosperm. Plant Cell. 2006;18:1887–99.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu S, Li W, Wu Y, Chen C, Lei J. De novo transcriptome assembly in chili pepper (Capsicum Frutescens) to identify genes involved in the biosynthesis of capsaicinoids. PLoS One. 2013. doi:10.1371/journal.pone.0048156.
Wu T, Luo S, Wang R, Zhong Y, Xu X. Lin ye, he X, sun B, Huang H: the first Illumina-based de novo transcriptome sequencing and analysis of pumpkin (Cucurbita Moschata Duch.) and SSR marker development. Mol Breed. 2014;34:1437–47.
Article
CAS
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9:357–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28:3150–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21:3674–6.
Article
CAS
PubMed
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.
Article
CAS
PubMed
Google Scholar
Yuan K, Rashotte AM, Wysocka-Diller JW. ABA and GA signaling pathways interact and regulate seed germination and seedling development under salt stress. Acta Physiol Plant. 2011;33:261–71.
Article
CAS
Google Scholar
Weitbrecht K, Müller K, Leubner-Metzger G. First off the mark: early seed germination. J Exp Bot. 2011;62:3289–309.
Article
CAS
PubMed
Google Scholar
Rajjou L, Duval M, Gallardo K, Catusse J, Bally J, Job C, Job D. Seed germination and vigor. Annu Rev Plant Biol. 2012;63:507–33.
Article
CAS
PubMed
Google Scholar
Penfield S, Hall A. A role for multiple circadian clock genes in the response to signals that break seed dormancy in Arabidopsis. Plant Cell. 2009;21:1722–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Covington MF, Maloof JN, Straume M, Kay SA, Harmer SL. Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol. 2008;9:1.
Article
Google Scholar
Michael TP, Breton G, Hazen SP, Priest H, Mockler TC, Kay SA, Chory J. A morning-specific phytohormone gene expression program underlying rhythmic plant growth. PLoS Biol. 2008. doi:10.1371/journal.pbio.0060225.
Henderson IR, Zhang X, Lu C, Johnson L, Meyers BC, Green PJ, Jacobsen SE. Dissecting Arabidopsis Thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet. 2006;38:721–5.
Article
CAS
PubMed
Google Scholar
Zhang B, Pan X, Cox S, Cobb G, Anderson T. Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci. 2006;63:246–54.
Article
CAS
PubMed
Google Scholar
Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31:3406–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bonnet E, He Y, Billiau K, Van de Peer Y. TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics. 2010;26:1566–8.
Article
CAS
PubMed
Google Scholar
Feng J, Wang J, Fan P, Jia W, Nie L, Jiang P, Chen X, Lv S, Wan L, Chang S. High-throughput deep sequencing reveals that microRNAs play important roles in salt tolerance of euhalophyte Salicornia Europaea. BMC Plant Biol. 2015;15:1.
Article
Google Scholar
Ronemus M, Vaughn MW, Martienssen RA. MicroRNA-targeted and small interfering RNA–mediated mRNA degradation is regulated by Argonaute, Dicer, and RNA-dependent RNA polymerase in Arabidopsis. Plant Cell. 2006;18:1559–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wan L-C, Zhang H, Lu S, Zhang L, Qiu Z, Zhao Y, Zeng Q-Y, Lin J. Transcriptome-wide identification and characterization of miRNAs from Pinus Densata. BMC Genomics. 2012;13:132.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rolletschek H, Radchuk R, Klukas C, Schreiber F, Wobus U, Borisjuk L. Evidence of a key role for photosynthetic oxygen release in oil storage in developing soybean seeds. New Phytol. 2005;167:777–86.
Article
CAS
PubMed
Google Scholar
Rolletschek H, Weber H, Borisjuk L. Energy status and its control on embryogenesis of legumes. Embryo photosynthesis contributes to oxygen supply and is coupled to biosynthetic fluxes. Plant Physiol. 2003;132:1196–206.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ruuska SA, Schwender J, Ohlrogge JB. The capacity of green oilseeds to utilize photosynthesis to drive biosynthetic processes. Plant Physiol. 2004;136:2700–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brown DE, Rashotte AM, Murphy AS, Normanly J, Tague BW, Peer WA, Taiz L, Muday GK. Flavonoids act as negative regulators of auxin transport in vivo in Arabidopsis. Plant Physiol. 2001;126:524–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Buer CS, Djordjevic MA. Architectural phenotypes in the transparent testa mutants of Arabidopsis Thaliana. J Exp Bot. 2009;60:751–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Buer CS, Muday GK. The transparent testa4 mutation prevents flavonoid synthesis and alters auxin transport and the response of Arabidopsis roots to gravity and light. Plant Cell. 2004;16:1191–205.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lewis DR, Ramirez MV, Miller ND, Vallabhaneni P, Ray WK, Helm RF, Winkel BS, Muday GK. Auxin and ethylene induce flavonol accumulation through distinct transcriptional networks. Plant Physiol. 2011;156:144–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Peer WA, Bandyopadhyay A, Blakeslee JJ, Makam SN, Chen RJ, Masson PH, Murphy AS. Variation in expression and protein localization of the PIN family of auxin efflux facilitator proteins in flavonoid mutants with altered auxin transport in Arabidopsis Thaliana. Plant Cell. 2004;16:1898–911.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sabatini S, Beis D, Wolkenfelt H, Murfett J, Guilfoyle T, Malamy J, Benfey P, Leyser O, Bechtold N, Weisbeek P. An auxin-dependent distal organizer of pattern and polarity in the Arabidopsis root. Cell. 1999;99:463–72.
Article
CAS
PubMed
Google Scholar
Dubrovsky JG, Sauer M, Napsucialy-Mendivil S, Ivanchenko MG, Friml J, Shishkova S, Celenza J, Benková E. Auxin acts as a local morphogenetic trigger to specify lateral root founder cells. Proc Natl Acad Sci. 2008;105:8790–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Friml J, Benková E, Blilou I, Wisniewska J, Hamann T, Ljung K, Woody S, Sandberg G, Scheres B, Jürgens G. AtPIN4 mediates sink-driven auxin gradients and root patterning in Arabidopsis. Cell. 2002;108:661–73.
Article
CAS
PubMed
Google Scholar
Pelletier MK, Shirley BW. Analysis of flavanone 3-hydroxylase in Arabidopsis seedlings (coordinate regulation with chalcone synthase and chalcone isomerase). Plant Physiol. 1996;111:339–45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cain CC, Saslowsky DE, Walker RA, Shirley BW. Expression of chalcone synthase and chalcone isomerase proteins in Arabidopsis seedlings. Plant Mol Biol. 1997;35:377–81.
Article
CAS
PubMed
Google Scholar
Dharmasiri N, Dharmasiri S, Estelle M. The F-box protein TIR1 is an auxin receptor. Nature. 2005;435:441–5.
Article
CAS
PubMed
Google Scholar
Dharmasiri N, Dharmasiri S, Weijers D, Lechner E, Yamada M, Hobbie L, Ehrismann JS, Jürgens G, Estelle M. Plant development is regulated by a family of auxin receptor F box proteins. Dev Cell. 2005;9:109–19.
Article
CAS
PubMed
Google Scholar
Kepinski S, Leyser O. The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature. 2005;435:446–51.
Article
CAS
PubMed
Google Scholar
Kepinski S, Leyser O. The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature. 2005;435:446.
Article
CAS
PubMed
Google Scholar
Lee YP, Giorgi FM, Lohse M, Kvederaviciute K, Klages S, Usadel B, Meskiene I, Reinhardt R, Hincha DK. Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella Salsuginea (Eutrema Salsugineum). BMC Genomics. 2013;14:793.
Article
CAS
PubMed
PubMed Central
Google Scholar
Diray-Arce J, Clement M, Gul B, Khan MA, Nielsen BL. Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda Fruticosa provides insights into salt tolerance. BMC Genomics. 2015;16:353.
Article
PubMed
PubMed Central
Google Scholar
Boudsocq M, Barbier-Brygoo H, Laurière C. Identification of nine sucrose nonfermenting 1-related protein kinases 2 activated by hyperosmotic and saline stresses in Arabidopsis Thaliana. J Biol Chem. 2004;279:41758–66.
Article
CAS
PubMed
Google Scholar
Yoshida R, Hobo T, Ichimura K, Mizoguchi T, Takahashi F, Aronso J, Ecker JR, Shinozaki K. ABA-activated SnRK2 protein kinase is required for dehydration stress signaling in Arabidopsis. Plant Cell Physiol. 2002;43:1473–83.
Article
CAS
PubMed
Google Scholar
Piskurewicz U, Jikumaru Y, Kinoshita N, Nambara E, Kamiya Y, Lopez-Molina L. The gibberellic acid signaling repressor RGL2 inhibits Arabidopsis seed germination by stimulating abscisic acid synthesis and ABI5 activity. Plant Cell. 2008;20:2729–45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tyler L, Thomas SG, Hu J, Dill A, Alonso JM, Ecker JR, Sun T-P. DELLA proteins and gibberellin-regulated seed germination and floral development in Arabidopsis. Plant Physiol. 2004;135:1008–19.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kurihara Y, Watanabe Y. Arabidopsis Micro-RNA biogenesis through Dicer-like 1 protein functions. Proc Natl Acad Sci U S A. 2004;101:12753–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xie Z, Kasschau KD, Carrington JC. Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr Biol. 2003;13:784–9.
Article
CAS
PubMed
Google Scholar
Das SS, Karmakar P, Nandi AK, Sanan-Mishra N. Small RNA mediated regulation of seed germination. Front Plant Sci. 2015. doi:10.3389/fpls.2015.00828.
Martin RC, Liu P-P, Goloviznina NA, Nonogaki H. microRNA, seeds, and Darwin?: diverse function of miRNA in seed biology and plant responses to stress. J Exp Bot. 2010;61:2229–34.
Article
CAS
PubMed
Google Scholar
Martin RC, Asahina M, Liu P-P, Kristof JR, Coppersmith JL, Pluskota WE, Bassel GW, Goloviznina NA, Nguyen TT, Martínez-Andújar C. The regulation of post-germinative transition from the cotyledon-to vegetative-leaf stages by microRNA-targeted SQUAMOSA PROMOTER-BINDING PROTEIN LIKE13 in Arabidopsis. Seed Sci Res. 2010;20:89.
Article
CAS
Google Scholar
Martin RC, Asahina M, Liu P-P, Kristof JR, Coppersmith JL, Pluskota WE, Bassel GW, Goloviznina NA, Nguyen TT, Martínez-Andújar C. The microRNA156 and microRNA172 gene regulation cascades at post-germinative stages in Arabidopsis. Seed Sci Res. 2010;20:79–87.
Article
CAS
Google Scholar
Li D, Wang L, Liu X, Cui D, Chen T, Zhang H, Jiang C, Xu C, Li P, Li S. Deep sequencing of maize small RNAs reveals a diverse set of microRNA in dry and imbibed seeds. PLoS One. 2013;8:e55107.
Article
CAS
PubMed
PubMed Central
Google Scholar
Reyes JL, Chua NH. ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J. 2007;49:592–606.
Stanga JP, Smith SM, Briggs WR, Nelson DC. SUPPRESSOR OF MORE AXILLARY GROWTH2 1 controls seed germination and seedling development in Arabidopsis. Plant Physiol. 2013;163:318–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ma Z, Hu X, Cai W, Huang W, Zhou X, Luo Q, Yang H, Wang J, Huang J. Arabidopsis miR171-targeted scarecrow-like proteins bind to GT cis-elements and mediate gibberellin-regulated chlorophyll biosynthesis under light conditions. PLoS Genet. 2014. doi:10.1371/journal.pgen.1004519.
Gao M-J, Li X, Huang J, Gropp GM, Gjetvaj B, Lindsay DL, Wei S, Coutu C, Chen Z, Wan X-C. SCARECROW-LIKE15 interacts with HISTONE DEACETYLASE19 and is essential for repressing the seed maturation programme. Nat Commun. 2015. doi:10.1038/ncomms8243.
Zhao B, Liang R, Ge L, Li W, Xiao H, Lin H, Ruan K, Jin Y. Identification of drought-induced microRNAs in rice. Biochem Biophys Res Commun. 2007;354:585–90.
Article
CAS
PubMed
Google Scholar
Zhao B, Ge L, Liang R, Li W, Ruan K, Lin H, Jin Y. Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor. BMC Mol Biol. 2009;10:29.
Article
PubMed
PubMed Central
Google Scholar
Zhang Q, Zhao C, Li M, Sun W, Liu Y, Xia H, Sun M, Li A, Li C, Zhao S. Genome-wide identification of Thellungiella Salsuginea microRNAs with putative roles in the salt stress response. BMC Plant Biol. 2013;13:180.
Article
PubMed
PubMed Central
Google Scholar
Sorin C, Declerck M, Christ A, Blein T, Ma L, Lelandais-Brière C, Njo MF, Beeckman T, Crespi M, Hartmann C. A miR169 isoform regulates specific NF-YA targets and root architecture in Arabidopsis. New Phytol. 2014;202:1197–211.
Article
CAS
PubMed
Google Scholar
Ni Z, Hu Z, Jiang Q, Zhang H. GmNFYA3, a target gene of miR169, is a positive regulator of plant tolerance to drought stress. Plant Mol Biol. 2013;82:113–29.
Article
CAS
PubMed
Google Scholar
Hundertmark M, Hincha DK. LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis Thaliana. BMC Genomics. 2008;9:118.
Article
PubMed
PubMed Central
Google Scholar
Nishimura N, Yoshida T, Kitahata N, Asami T, Shinozaki K, Hirayama T. ABA-hypersensitive Germination1 encodes a protein phosphatase 2C, an essential component of abscisic acid signaling in Arabidopsis seed. Plant J. 2007;50:935–49.
Article
CAS
PubMed
Google Scholar
Bhaskara GB, Nguyen TT, Verslues PE. Unique drought resistance functions of the highly ABA-induced clade a protein phosphatase 2Cs. Plant Physiol. 2012;160:379–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Karali D, Oxley D, Runions J, Ktistakis N, Farmaki T. The Arabidopsis Thaliana immunophilin ROF1 directly interacts with PI (3) P and PI (3, 5) P 2 and affects germination under osmotic stress. PLoS One. 2012. doi:10.1371/journal.pone.0048241.
Jia X, Wang W-X, Ren L, Chen Q-J, Mendu V, Willcut B, Dinkins R, Tang X, Tang G. Differential and dynamic regulation of miR398 in response to ABA and salt stress in Populustremula and Arabidopsisthaliana. Plant Mol Biol. 2009;71:51–9.
Article
CAS
PubMed
Google Scholar
Sunkar R, Kapoor A, Zhu J-K. Posttranscriptional induction of two cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell. 2006;18:2051–65.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou ZS, Huang SQ, Yang ZM. Bioinformatic identification and expression analysis of new microRNAs from Medicago Truncatula. Biochem Biophys Res Commun. 2008;374:538–42.
Article
CAS
PubMed
Google Scholar
Yamasaki H, Abdel-Ghany SE, Cohu CM, Kobayashi Y, Shikanai T, Pilon M. Regulation of copper homeostasis by micro-RNA in Arabidopsis. J Biol Chem. 2007;282:16369–78.
Article
CAS
PubMed
Google Scholar
Abdel-Ghany SE, Pilon M. MicroRNA-mediated systemic down-regulation of copper protein expression in response to low copper availability in Arabidopsis. J Biol Chem. 2008;283:15932–45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marschner H. Mineral nutrition of higher plants. London: Academic Press; 1995.
Google Scholar
Senadheera P, Maathuis FJ. Differentially regulated kinases and phosphatases in roots may contribute to inter-cultivar difference in rice salinity tolerance. Plant Signal Behav. 2009;4:1163–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Verica JA, Chae L, Tong H, Ingmire P, He Z-H. Tissue-specific and developmentally regulated expression of a cluster of tandemly arrayed cell wall-associated kinase-like kinase genes in Arabidopsis. Plant Physiol. 2003;133:1732–46.
Article
CAS
PubMed
PubMed Central
Google Scholar
Khan S, Stone JM. Arabidopsis thalianaGH3. 9 influences primary root growth. Planta. 2007;226:21–34.
Article
CAS
PubMed
Google Scholar
Wenig U, Meyer S, Stadler R, Fischer S, Werner D, Lauter A, Melzer M, Hoth S, Weingartner M, Sauer N. Identification of MAIN, a factor involved in genome stability in the meristems of Arabidopsis Thaliana. Plant J. 2013;75:469–83.
Article
CAS
PubMed
Google Scholar
Prigge MJ, Otsuga D, Alonso JM, Ecker JR, Drews GN, Clark SE. Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development. Plant Cell. 2005;17:61–76.
Article
CAS
PubMed
PubMed Central
Google Scholar
Williams L, Grigg SP, Xie M, Christensen S, Fletcher JC. Regulation of Arabidopsis shoot apical meristem and lateral organ formation by microRNA miR166g and its AtHD-ZIP target genes. Development. 2005;132:3657–68.
Article
CAS
PubMed
Google Scholar
Singh A, Singh S, Panigrahi KC, Reski R, Sarkar AK. Balanced activity of microRNA166/165 and its target transcripts from the class III homeodomain-leucine zipper family regulates root growth in Arabidopsisthaliana. Plant Cell Rep. 2014;33:945–53.
Article
CAS
PubMed
Google Scholar
Gordon A, Hannon G: Fastx-toolkit. FASTQ/A short-reads preprocessing tools (unpublished) http://hannonlab cshl edu/fastx_toolkit 2010,5.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Article
CAS
PubMed
Google Scholar
Iseli C, Jongeneel CV, Bucher P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. In: ISMB; 1999. p. 138–48.
Google Scholar
Dohm JC, Minoche AE, Holtgräwe D, Capella-Gutiérrez S, Zakrzewski F, Tafer H, Rupp O, Sörensen TR, Stracke R, Reinhardt R. The genome of the recently domesticated crop plant sugar beet (Beta Vulgaris). Nature. 2014;505:546–9.
Article
CAS
PubMed
Google Scholar
Ma T, Wang J, Zhou G, Yue Z, Hu Q, Chen Y, Liu B, Qiu Q, Wang Z, Zhang J. Genomic insights into salt adaptation in a desert poplar. Nat Commun. 2013. doi:10.1038/ncomms3797.
Kent WJ. BLAT—the BLAST-like alignment tool. Genome Res. 2002;12:656–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A: Rfam 11.0: 10 years of RNA families. Nucleic acids research 2012:gks1005.
Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014;42:D68–73.
Article
CAS
PubMed
Google Scholar
Yang X, Li L. miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants. Bioinformatics. 2011;27:2614–5.
Article
CAS
PubMed
Google Scholar
Wan L-C, Zhang H, Lu S, Zhang L, Qiu Z, Zhao Y, Zeng Q-Y, Lin J. Transcriptome-wide identification and characterization of miRNAs from Pinus Densata. BMC Genomics. 2012;13:1.
Article
Google Scholar
Fisher RA. On the interpretation of χ 2 from contingency tables, and the calculation of P. J R Stat Soc. 1922;85:87–94.
Article
Google Scholar
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCT method methods. 2001;25:402–8.
Wang L, Wang H, Yin L, Tian C. Suaeda aralocaspica raw sequence reads. In: BioProject. National Center for Biotechnology Information. 2016. http://www.ncbi.nlm.nih.gov/bioproject/325861.