Abbasi Kejani A., Hosseini Tafreshi S. A., Khayyam Nekouei S. M. and Mofid M. R. 2010 Efficient isolation of high-quality nucleic acids from different tissues of Taxus baccata L. Mol. Biol. Rep. 37, 797–800.
Article CAS PubMed Google Scholar
Brouwer B., Ziolkowsk A., Bagard M., Keech O. and Gardeström P. 2012 The impact of light intensity on shade-induced leaf senescence. Plant, Cell Environ. 35, 1084–1098.
Cantalapiedra C. P., Hernández-Plaza A., Letunic I., Bork P. and Huerta-Cepas J. 2021 eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825–5829.
Article CAS PubMed PubMed Central Google Scholar
Chen L., Hänninen H., Rossi S., Smith N. G., Pau S., Liu Z. et al. 2020 Leaf senescence exhibits stronger climatic responses during warm than during cold autumns. Nat. Clim. Change 10, 777–780.
Estiarte M. and Peñuelas J. 2015 Alteration of the phenology of leaf senescence and fall in winter deciduous species by climate change: effects on nutrient proficiency. Global Change Biol. 21, 1005–1017.
Fu L., Niu B., Zhu Z., Wu S. and Li W. 2012 CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152.
Article CAS PubMed PubMed Central Google Scholar
Grabherr M. G., Haas B. J., Yassour M., Levin J. Z., Thompson D. A., Amit I. et al. 2011 Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652.
Article CAS PubMed PubMed Central Google Scholar
Guo Y., Ren G., Zhang K., Li Z., Miao Y. and Guo H. 2021 Leaf senescence: progression, regulation, and application. Mol. Horticulture 1, 1–25.
He Y. and Gan S. 2002 A gene encoding an acyl hydrolase is involved in leaf senescence in Arabidopsis. Plant Cell 14, 805–815.
Article CAS PubMed PubMed Central Google Scholar
Keskitalo J., Bergquist G., Gardestrom P. and Jansson S. 2005 A cellular timetable of autumn senescence. Plant Physiol. 139, 1635–1648.
Article CAS PubMed PubMed Central Google Scholar
Krueger F., James F., Ewels P., Afyounian E., Weinstein M., Schuster-Boeckler B. et al. 2023 FelixKrueger/TrimGalore: v0. 6.10-add default decompression path. Zenodo.
Kucukural A., Yukselen O., Ozata D. M., Moore M. J. and Garber M. 2019 DEBrowser: interactive differential expression analysis and visualization tool for count data. BMC Genomics 20, 1–12.
Kusaba M., Ito H., Morita R., Iida S., Sato Y., Fujimoto M. et al. 2007 Rice NON-YELLOW COLORING1 is involved in light-harvesting complex II and grana degradation during leaf senescence. Plant Cell 19, 1362–1375.
Article CAS PubMed PubMed Central Google Scholar
Langmead B. and Salzberg S. L. 2012 Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359.
Article CAS PubMed PubMed Central Google Scholar
Li B. and Dewey C. N. 2011 RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 1–16.
Li W., Wang L., He Z., Lu Z., Cui J., Xu N. et al. 2020 Physiological and transcriptomic changes during autumn coloration and senescence in Ginkgo biloba leaves. Hort. Plant J. 6, 396–408.
Liao Y., Wang J., Jaehnig E. J., Shi Z. and Zhang B. 2019 WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs. Nucleic Acids Res. 47, W199–W205.
Article CAS PubMed PubMed Central Google Scholar
Lim P. O., Kim H. J. and Gil Nam H. 2007 Leaf senescence. Annu. Rev. Plant Biol. 58, 115–136.
Article CAS PubMed Google Scholar
Liu X., Li X., Yang H., Yang R. and Zhang D. 2023 Genome-wide characterization and expression profiling of ABA biosynthesis genes in a desert moss Syntrichia caninervis. Plants 12, 1114.
Article CAS PubMed PubMed Central Google Scholar
Love M., Anders S. and Huber W. 2014 Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550.
Article PubMed PubMed Central Google Scholar
Majeed A., Singh A., Sharma R. K., Jaitak V. and Bhardwaj P. 2020 Comprehensive temporal reprogramming ensures dynamicity of transcriptomic profile for adaptive response in Taxus contorta. Mol. Genet. Genom. 295, 1401–1414.
Mishra Y., Johansson Jänkänpää. H., Kiss A. Z., Funk C., Schröder W. P. and Jansson S. 2012 Arabidopsis plants grown in the field and climate chambers significantly differ in leaf morphology and photosystem components. BMC Plant Biol. 12, 1–18.
Morita R., Sato Y., Masuda Y., Nishimura M. and Kusaba M. 2009 Defect in non-yellow coloring 3, an α/β hydrolase-fold family protein, causes a stay-green phenotype during leaf senescence in rice. Plant J. 59, 940–952.
Article CAS PubMed Google Scholar
Moschen S., Bengoa Luoni S., Di Rienzo J. A., Caro M. D. P., Tohge T., Watanabe M. et al. 2016 Integrating transcriptomic and metabolomic analysis to understand natural leaf senescence in sunflower. Plant Biotechnol. J. 14, 719–734.
Article CAS PubMed Google Scholar
Nagano A. J., Kawagoe T., Sugisaka J., Honjo M. N., Iwayama K. and Kudoh H. 2019 Annual transcriptome dynamics in natural environments reveals plant seasonal adaptation. Nat. Plants 5, 74–83.
Nawaz M., Sun J., Shabbir S., Khattak W. A., Ren G., Nie X. et al. 2023 A review of plants strategies to resist biotic and abiotic environmental stressors. Sci. Total Environ. 165832.
Oda-Yamamizo C., Mitsuda N., Sakamoto S., Ogawa D., Ohme-Takagi M. and Ohmiya A. 2016 The NAC transcription factor ANAC046 is a positive regulator of chlorophyll degradation and senescence in Arabidopsis leaves. Sci. Rep. 6, 23609.
Article CAS PubMed PubMed Central Google Scholar
Okamoto M., Kuwahara A., Seo M., Kushiro T., Asami T., Hirai N. et al. 2006 CYP707A1 and CYP707A2, which encode abscisic acid 8′-hydroxylases, are indispensable for proper control of seed dormancy and germination in Arabidopsis. Plant Physiol. 141, 97–107.
Article CAS PubMed PubMed Central Google Scholar
Rao X., Huang X., Zhou Z. and Lin X. 2013 An improvement of the 2ˆ (–delta delta CT) method for quantitative real-time polymerase chain reaction data analysis. Biostat. Bioinform. Biomath. 3, 71.
Ren G., Zhou Q., Wu S., Zhang Y., Zhang L., Huang J. et al. 2010 Reverse genetic identification of CRN1 and its distinctive role in chlorophyll degradation in Arabidopsis. J. Integr. Plant Biol. 52, 496–504.
Article CAS PubMed Google Scholar
Schwacke R., Ponce-Soto G. Y., Krause K., Bolger A. M., Arsova B., Hallab A. et al. 2019 MapMan4: a refined protein classification and annotation framework applicable to multi-omics data analysis. Mol. Plant 12, 879–892.
Article CAS PubMed Google Scholar
Simão F. A., Waterhouse R. M., Ioannidis P., Kriventseva E. V. and Zdobnov E. M. 2015 BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212.
Singh A., Majeed A., Sharma V., Gadri H. S., Chowdhary M. A. and Bhardwaj P. 2023 Transcriptome analysis revealed behavior complexity of senescence responses in Himalayan tree species Ulmus wallichiana. Plant Mol. Biol. Rep. 41, 600–610.
Tian F., Yang D.-C., Meng Y.-Q., Jin J. and Gao G. 2020 PlantRegMap: charting functional regulatory maps in plants. Nucleic Acids Res. 48, D1104–D1113.
Untergasser A., Nijveen H., Rao X., Bisseling T., Geurts R. and Leunissen J. A. 2007 Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res. 35, W71–W74.
Comments (0)