The first transcriptome sequencing and analysis of the endangered plant species Picea neoveitchii Mast. and potential EST-SSR markers development

References

• Cai J, Yang XP, Jiang ZM. Researches on the state key conservation plant species in zhouzhi national-level nature reserve. J Northwest Forest Univ. 2014;17:63–66.
   Google Scholar
• Zhang DS, Yongshik K, Maunder M, et al. The conservation status and conservation strategy of Picea neoveitchii. Chin J Popul Resource Environ. 2006;4:58–64.
   Google Scholar
• Chen WQ, Song ZJ, Xu HH. A new antifungal and cytotoxic C-methylated flavone glycoside from Picea neoveitchii. Bioorg Med Chem Lett. 2012;22:5819–5822.
   PubMed Web of Science ®Google Scholar
• Song Z, Chen W, Du X, et al. Chemical constituents of Picea neoveitchii. Phytochemistry. 2011;72:490–494.
   PubMed Web of Science ®Google Scholar
• Li L, Zhang H, Liu Z, et al. Comparative transcriptome sequencing and de novo analysis of Vaccinium corymbosum during fruit and color development. BMC Plant Biol. 2016;16:223–232.
   PubMed Web of Science ®Google Scholar
• Ma T, Wang J, Zhou G, et al. Genomic insights into salt adaptation in a desert poplar. Nat Commun. 2013;4:2797–2806.
   PubMed Web of Science ®Google Scholar
• Qi X, Li MW, Xie M, et al. Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun. 2014;5:1–11.
   Web of Science ®Google Scholar
• Xiao L, Yang G, Zhang L, et al. The resurrection genome of Boea hygrometrica: A blueprint for survival of dehydration. Proc Natl Acad Sci USA. 2015;112:5833–5837.
   PubMed Web of Science ®Google Scholar
• Dai X, Hu Q, Cai Q, et al. The willow genome and divergent evolution from poplar after the common genome duplication. Cell Res. 2014;24:1274–1277.
   PubMed Web of Science ®Google Scholar
• He N, Zhang C, Qi X, et al. Draft genome sequence of the mulberry tree Morus notabilis. Nat Commun. 2013;4:1–9.
   Web of Science ®Google Scholar
• Liu MJ, Zhao J, Cai QL, et al. The complex jujube genome provides insights into fruit tree biology. Nat Commun. 2014;5:1–12.
   Web of Science ®Google Scholar
• Myburg AA, Grattapaglia D, Tuskan GA, et al. The genome of Eucalyptus grandis. Nature. 2014;510:356–362.
   PubMed Web of Science ®Google Scholar
• Tuskan GA, Difazio S, Jansson S, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006;313:1596–1604.
   PubMed Web of Science ®Google Scholar
• Velasco R, Zharkikh A, Affourtit J, et al. The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet. 2010;42:833–839.
   PubMed Web of Science ®Google Scholar
• Verde I, Abbott AG, Scalabrin S, et al. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet. 2013;45:487–494.
   PubMed Web of Science ®Google Scholar
• Birol I, Raymond A, Jackman SD, et al. Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics. 2013;29:1492–1497.
   PubMed Web of Science ®Google Scholar
• Nystedt B, Street NR, Wetterbom A, et al. The Norway spruce genome sequence and conifer genome evolution. Nature. 2013;497:579–584.
   PubMed Web of Science ®Google Scholar
• Zimin A, Stevens KA, Crepeau MW, et al. Sequencing and assembly of the 22-gb loblolly pine genome. Genetics. 2014;196:875–890.
   PubMed Web of Science ®Google Scholar
• Kuzmin DA, Feranchuk SI, Sharov VV, et al. Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb. ). BMC Bioinformatics. 2019;20:36–52.
   PubMed Web of Science ®Google Scholar
• Zimin AV, Stevens KA, Crepeau MW, et al. An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing. Gigascience. 2017;6:1–4.
   Web of Science ®Google Scholar
• Guan R, Zhao Y, Zhang H, et al. Draft genome of the living fossil Ginkgo biloba. Gigascience. 2016;5:49–63.
   PubMed Web of Science ®Google Scholar
• Englehardt J. Sources, industrial derivatives, and commercial applications of cellulose. Carbohydr Eur. 1995;12:5–14.
   Google Scholar
• Kieber JJ, Polko J. The regulation of cellulose biosynthesis in plants. Plant Cell. 2019;31:282–296.
   PubMed Web of Science ®Google Scholar
• Moura JC, Bonine CA, de Oliveira Fernandes Viana J, et al. Abiotic and biotic stresses and changes in the lignin content and composition in plants. J Integr Plant Biol. 2010;52:360–376.
   PubMed Web of Science ®Google Scholar
• Ohtani M, Demura T. The quest for transcriptional hubs of lignin biosynthesis: beyond the NAC-MYB-gene regulatory network model. Curr Opin Biotechnol. 2019;56:82–87.
   PubMed Web of Science ®Google Scholar
• Grabherr MG, Haas BJ, Yassour M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644–652.
   PubMed Web of Science ®Google Scholar
• Mortazavi A, Williams BA, McCue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Meth. 2008;5:621–628.
   PubMed Web of Science ®Google Scholar
• Conesa A, Götz S. Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genom. 2008;2008:1–12.
   Google Scholar
• Djerbi S, Lindskog M, Arvestad L, et al. The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes. Planta. 2005;221:739–746.
   PubMed Web of Science ®Google Scholar
• Guerriero G, Fugelstad J, Bulone V. What do we really know about cellulose biosynthesis in higher plants? J Integr Plant Biol. 2010;52:161–175.
   PubMed Web of Science ®Google Scholar
• Feng G, Burleigh JG, Braun EL, et al. MYB gene family in plants. Genome Biol Evol. 2017;9:1013–1029.
   PubMed Web of Science ®Google Scholar
• Cui MH, Yoo KS, Hyoung S, et al. An Arabidopsis R2R3-MYB transcription factor, AtMYB20, negatively regulates type 2C serine/threonine protein phosphatases to enhance salt tolerance. FEBS Lett. 2013;587:1773–1778.
   PubMed Web of Science ®Google Scholar
• Dai X, Wang Y, Yang A, et al. OsMYB2P-1, an R2R3 MYB transcription factor, is involved in the regulation of phosphate-starvation responses and root architecture in rice. Plant Physiol. 2012;159:169–183.
   PubMed Web of Science ®Google Scholar
• Seo PJ, Lee SB, Suh MC, et al. The MYB96 transcription factor regulates cuticular wax biosynthesis under drought conditions in Arabidopsis. Plant Cell. 2011;23:1138–1152.
   PubMed Web of Science ®Google Scholar
• Shin D, Moon SJ, Han S, et al. Expression of StMYB1R-1, a novel potato single MYB-like domain transcription factor, increases drought tolerance. Plant Physiol. 2011;155:421–432.
   PubMed Web of Science ®Google Scholar
• De Clercq I, Vermeirssen V, Van Aken O, et al. The membrane-bound NAC transcription factor ANAC013 functions in mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis. Plant Cell. 2013;25:3472–3290.
   PubMed Web of Science ®Google Scholar
• Ishihama N, Yamada R, Yoshioka M, et al. Phosphorylation of the Nicotiana benthamiana WRKY8 transcription factor by MAPK functions in the defense response. Plant Cell. 2011;23:1153–1170.
   PubMed Web of Science ®Google Scholar
• Jiang Y, Duan Y, Yin J, et al. Genome-wide identification and characterization of the Populus WRKY transcription factor family and analysis of their expression in response to biotic and abiotic stresses. J Exp Botany. 2014;65:6629–6644.
   PubMed Web of Science ®Google Scholar
• Jiang Y, Liang G, Yu D. Activated expression of WRKY57 confers drought tolerance in Arabidopsis. Mol Plant. 2012;5:1375–1388.
   PubMed Web of Science ®Google Scholar
• Lee S, Seo PJ, Lee HJ, et al. A NAC transcription factor NTL4 promotes reactive oxygen species production during drought-induced leaf senescence in Arabidopsis. Plant J. 2012;70:831–844.
   PubMed Web of Science ®Google Scholar
• Xu ZY, Kim SY, Hyeon do Y, et al. The Arabidopsis NAC transcription factor ANAC096 cooperates with bZIP-type transcription factors in dehydration and osmotic stress responses. Plant Cell. 2013;25:4708–4724.
   PubMed Web of Science ®Google Scholar
• Chen MK, Hsu WH, Lee PF, et al. The MADS box gene, FOREVER YOUNG FLOWER, acts as a repressor controlling floral organ senescence and abscission in Arabidopsis. Plant J. 2011;68:168–185.
   PubMed Web of Science ®Google Scholar
• Deng W, Ying H, Helliwell CA, et al. FLOWERING LOCUS C (FLC) regulates development pathways throughout the life cycle of Arabidopsis. Proc Natl Acad Sci USA. 2011;108:6680–6685.
   PubMed Web of Science ®Google Scholar
• Garay-Arroyo A, Ortiz-Moreno E, de la Paz Sanchez M, et al. The MADS transcription factor XAL2/AGL14 modulates auxin transport during Arabidopsis root development by regulating PIN expression. EMBO J. 2013;32:2884–2895.
   PubMed Web of Science ®Google Scholar
• Sang X, Li Y, Luo Z, et al. CHIMERIC FLORAL ORGANS1, encoding a monocot-specific MADS box protein, regulates floral organ identity in rice. Plant Physiol. 2012;160:788–807.
   PubMed Web of Science ®Google Scholar
• Smaczniak C, Immink RG, Angenent GC, et al. Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies. Development. 2012;139:3081–3098.
   PubMed Web of Science ®Google Scholar
• Albert VA, Barbazuk WB, dePamphilis CW, et al. The Amborella genome and the evolution of flowering plants. Science. 2013;342:1467–1477.
   Web of Science ®Google Scholar
• Uddenberg D, Reimegard J, Clapham D, et al. Early cone setting in Picea abies acrocona is associated with increased transcriptional activity of a MADS box transcription factor. Plant Physiol. 2013;161:813–823.
   PubMed Web of Science ®Google Scholar
• Wegrzyn JL, Lee JM, Tearse BR, et al. TreeGenes: A forest tree genome database. Int J Plant Genom. 2008;2008:1–7.
   Google Scholar
• Pireyre M, Burow M. Regulation of MYB and bHLH transcription factors: a glance at the protein level. Mol Plant. 2015;8:378–388.
   PubMed Web of Science ®Google Scholar
• Nemesiogorriz M, Blair PB, Dalman K, et al. Identification of Norway spruce MYB-bHLH-WDR transcription factor complex members linked to regulation of the flavonoid pathway. Front Plant Sci. 2017; [cited 2019 May 02]8:305.
   PubMed Web of Science ®Google Scholar
• Zhang H, Forde BG. An Arabidopsis MADS box gene that controls nutrient-induced changes in root architecture. Science. 1998;279:407–409.
   PubMed Web of Science ®Google Scholar
• Agarwal M, Hao Y, Kapoor A, et al. A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance. J Biol Chem. 2006;281:37636–37645.
   PubMed Web of Science ®Google Scholar