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Bioinformatics for Saffron-Omics and Crop Improvement

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The Saffron Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

Bioinformatics is the bedrock of modern studies using omics-based approaches like genomics, transcriptomics, proteomics, metabalomics, ionomics, etc. The complex web of molecular and genetic interactions that connect individual components of an organelle or a cell with the overall scheme of organismal behaviour cannot be elucidated without bioinformatics. There are hundreds of bioinformatics tools available to the researchers for conducting the studies involving the processing of high-throughput data. In this chapter, we highlight some of the major bioinformatics tools that are popularly used by plant biologists, and some of which have been used in saffron research for the analysis of complex data generated by modern omics-technologies. There is a huge scope for such molecular studies in saffron owing to its peculiar nature and importance as a spice, and medicinal plant. Bioinformatics is therefore indispensible for understanding the biology of saffron.

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References

  • Ahmed SA, Husaini AM (2021) Investigating binding potential of carotenoid pathway bioactive molecules for ACE2 receptor of SARS-CoV-2: possibility of a saffron based remedy for novel coronavirus! J Hortic Postharvest Res 69–78

    Google Scholar 

  • Ahrazem O, Argandoña J, Fiore A, Aguado C, Luján R, Rubio-Moraga Á, Marro M, Araujo-Andrade C, Loza-Alvarez P, Diretto G (2018) Transcriptome analysis in tissue sectors with contrasting crocins accumulation provides novel insights into apocarotenoid biosynthesis and regulation during chromoplast biogenesis. Sci Rep 8:1–17

    Article  CAS  Google Scholar 

  • Ahrazem O, López AJ, Argandoña J, Castillo R, Rubio-Moraga Á, Gómez-Gómez L (2020) Differential interaction of or proteins with the PSY enzymes in saffron. Sci Rep 10:1–11

    Article  Google Scholar 

  • Alva V, Nam S-Z, Söding J, Lupas AN (2016) The MPI bioinformatics toolkit as an integrative platform for advanced protein sequence and structure analysis. Nucl Acids Res 44:W410–W415

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Anabat MM, Riahi H, Sheidai M, Koohdar F (2020) Population genetic study and barcoding in Iran saffron (Crocus sativus L.). Ind Crops Prod 143:111915

    Google Scholar 

  • Beier S, Thiel T, Münch T, Scholz U, Mascher M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33:2583–2585

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2007) GenBank. Nucl Acids Res 35:D21–D25

    Article  CAS  PubMed  Google Scholar 

  • Bhattacharjee B, Vijayasarathy S, Karunakar P, Chatterjee J (2012) Comparative reverse screening approach to identify potential anti-neoplastic targets of saffron functional components and binding mode. Asian Pac J Cancer Prev 13:5605–5611

    Article  PubMed  Google Scholar 

  • Bolser DM, Staines DM, Perry E, Kersey PJ (2017) Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomic data. In: Plant genomics databases. Springer

    Google Scholar 

  • Busconi M, Colli L, Sánchez RA, Santaella M, Pascual MD-L-M, Santana O, Roldan M, Fernandez J-A (2015) AFLP and MS-AFLP analysis of the variation within saffron crocus (Crocus sativus L.) germplasm. PLoS One 10:e0123434

    Google Scholar 

  • Cappelli C (1994) Occurrence of Fusarium oxysporum f.sp. gladioli on saffron in Italy. Phytopathol Mediterr 33:93–94

    Google Scholar 

  • Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X (2016) A survey of best practices for RNA-seq data analysis. Genome Biol 17:1–19

    Google Scholar 

  • Consortium U (2019) UniProt: a worldwide hub of protein knowledge. Nucl Acids Res 47:D506–D515

    Google Scholar 

  • D’Agostino N, Pizzichini D, Chiusano ML, Giuliano G (2007) An EST database from saffron stigmas. BMC Plant Biol 7:1–8

    Article  Google Scholar 

  • da Silva SR, Perrone GC, Dinis JM, de Almeida RM (2014) Reproducibility enhancement and differential expression of non predefined functional gene sets in human genome. BMC Genom 15:1–18

    Article  Google Scholar 

  • Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucl Acids Res 39:W155–W159

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dai X, Sinharoy S, Udvardi M, Zhao PX (2013) PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool. BMC Bioinform 14:1–6

    Article  CAS  Google Scholar 

  • Dai X, Wang G, Yang DS, Tang Y, Broun P, Marks MD, Sumner LW, Dixon RA, Zhao PX (2010) TrichOME: a comparative omics database for plant trichomes. Plant Physiol 152:44–54

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM (2021) Twelve years of SAMtools and BCFtools. GigaScience 10:giab008

    Google Scholar 

  • Demurtas OC, Frusciante S, Ferrante P, Diretto G, Azad NH, Pietrella M, Aprea G, Taddei AR, Romano E, Mi J (2018) Candidate enzymes for saffron crocin biosynthesis are localized in multiple cellular compartments. Plant Physiol 177:990–1006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dong Q, Schlueter SD, Brendel V (2004) PlantGDB, plant genome database and analysis tools. Nucl Acids Res 32:D354–D359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson MD, Lawrence CJ, Lushbough C, Brendel V (2007) PlantGDB: a resource for comparative plant genomics. Nucl Acids Res 36:D959–D965

    Article  PubMed  PubMed Central  Google Scholar 

  • Eddy SR (2011) Accelerated profile HMM searches. PLoS Comput Biol 7:e1002195

    Google Scholar 

  • Fernández J-A (2004) Biology, biotechnology and biomedicine of saffron. Recent research developments in plant science, vol 2, pp 127–159

    Google Scholar 

  • Fraser C (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408

    Google Scholar 

  • Freedman A (2016) Best practices for de novo transcriptome assembly with trinity

    Google Scholar 

  • Frusciante S, Diretto G, Bruno M, Ferrante P, Pietrella M, Prado-Cabrero A, Rubio-Moraga A, Beyer P, Gomez-Gomez L, Al-Babili S (2014) Novel carotenoid cleavage dioxygenase catalyzes the first dedicated step in saffron crocin biosynthesis. Proc Natl Acad Sci 111:12246–12251

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gabler F, Nam SZ, Till S, Mirdita M, Steinegger M, Söding J, Lupas AN, Alva V (2020) Protein sequence analysis using the MPI bioinformatics toolkit. Curr Protoc Bioinform 72:e108

    Article  CAS  Google Scholar 

  • Ganai SA, Husaini AM (2021) Investigating binding potential of carotenoid pathway bioactive molecules for ACE2 receptor of SARS-CoV-2: possibility of a saffron based remedy for novel coronavirus! J Hortic Postharvest Res

    Google Scholar 

  • García-Alcalde F, García-López F, Dopazo J, Conesa A (2011) Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data. Bioinformatics 27:137–139

    Article  PubMed  Google Scholar 

  • Gómez-Gómez L, Rubio-Moraga Á, Ahrazem O (2010) Understanding carotenoid metabolism in saffron stigmas: unraveling aroma and colour formation. Funct Plant Sci Biotechnol 4:56–63

    Google Scholar 

  • Gonçalves JP, Madeira SC, Oliveira AL (2009) BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data. BMC Res Notes 2:1–11

    Article  Google Scholar 

  • Guan H, Kiss-Toth E (2008) Advanced technologies for studies on protein interactomes. Protein–Protein Interact 1–24

    Google Scholar 

  • Guo A-Y, Chen X, Gao G, Zhang H, Zhu Q-H, Liu X-C, Zhong Y-F, Gu X, He K, Luo J (2007) PlantTFDB: a comprehensive plant transcription factor database. Nucl Acids Res 36:D966–D969

    Article  PubMed  PubMed Central  Google Scholar 

  • Haas BJ, Papanicolaou A (2019) TransDecoder 5.5.0

    Google Scholar 

  • Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M (2013) De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512

    Article  CAS  PubMed  Google Scholar 

  • Hu J, Liu Y, Tang X, Rao H, Ren C, Chen J, Wu Q, Jiang Y, Geng F, Pei J (2020) Transcriptome profiling of the flowering transition in saffron (Crocus sativus L.). Sci Rep 10:1–14

    CAS  Google Scholar 

  • Husaini AM (2014) Challenges of climate change: omics-based biology of saffron plants and organic agricultural biotechnology for sustainable saffron production. GM Crops Food 5:97–105

    Google Scholar 

  • Husaini AM, Ashraf N (2010) Understanding saffron biology using bioinformatics tools. Saffron Funct Plant Sci Biotechnol 4:31–37

    Google Scholar 

  • Husaini AM, Wani AB (2020) Prospects of organic saffron kitchen gardens as a source of phytochemicals for boosting immunity in common households of semi-arid regions: a case study of trans-Himalayan Kashmir valley. J Pharmacog Phytochem 9:237–243

    Article  Google Scholar 

  • Husaini AM, Wani SA, Sofi P, Rather AG, Parray GA, Shikari AB, Mir JI (2009) Bioinformatics for saffron (Crocus sativus L.) improvement. Commun Biometry Crop Sci 4

    Google Scholar 

  • Husaini AM, Morimoto K, Chandrasekar B, Kelly S, Kaschani F, Palmero D, Jiang J, Kaiser M, Ahrazem O, Overkleeft HS (2018) Multiplex fluorescent, activity-based protein profiling identifies active α-glycosidases and other hydrolases in plants. Plant Physiol 177:24–37

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Husaini AM, Jan KN, Wani GA (2021) Saffron: a potential drug-supplement for severe acute respiratory syndrome coronavirus (COVID) management. Heliyon e07068

    Google Scholar 

  • Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11:1–11

    Article  Google Scholar 

  • Jhala M, Joshi C, Purohit T, Patel N, Sarvaiya J (2011) Role of bioinformatics in biotechnology. Information Technology Centre, GAU, Anand. Terdapat di http://openmed.nic.in/1383/01/Role_of_Bioinformatics_in_Biotechnology.pdf. 5 Feb 2011

  • Kahlem P, Newfeld SJ (2009) Informatics approaches to understanding TGFβ pathway regulation. Development 136:3729–3740

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucl Acids Res 32:D277–D280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M (2016) KEGG as a reference resource for gene and protein annotation. Nucl Acids Res 44:D457–D462

    Article  CAS  PubMed  Google Scholar 

  • Kaul S, Koo HL, Jenkins J, Rizzo M, Rooney T, Tallon LJ, Feldblyum T, Nierman W, Benito M-I, Lin X (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Article  CAS  Google Scholar 

  • Krogh A, Brown M, Mian IS, Sjölander K, Haussler D (1994) Hidden Markov models in computational biology: applications to protein modeling. J Mol Biol 235:1501–1531

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Langmead B (2010) Aligning short sequencing reads with Bowtie. Curr Protoc Bioinform 32(unit 11.7):1–14

    Google Scholar 

  • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:1–10

    Article  Google Scholar 

  • Larsen B, Orabi J, Pedersen C, Ørgaard M (2015) Large intraspecific genetic variation within the saffron-crocus group (crocus L., series crocus; Iridaceae). Plant Syst Evol 301:425–437

    Google Scholar 

  • Letunic I, Khedkar S, Bork P (2021) SMART: recent updates, new developments and status in 2020. Nucl Acids Res 49:D458–D460

    Article  CAS  PubMed  Google Scholar 

  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079

    Article  PubMed  PubMed Central  Google Scholar 

  • Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:1–21

    Article  Google Scholar 

  • Mahmodi P, Moeini A, Khayam Nekoie SM, Mardi M, Hosseini Salekdeh G (2014) Analysis of saffron stigma (Crocus sativus L.) transcriptome using SOAPdenovo and trinity assembly software. Crop Biotechnol 4:35–46

    Google Scholar 

  • McCarthy DJ, Chen Y, Smyth GK (2012) Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucl Acids Res 40:4288–4297

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meirmans PG, van Tienderen PH (2004) GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Mol Ecol Notes 4:792–794

    Article  Google Scholar 

  • Miotto YE, Da Costa CT, De Oliveira BH, Guzman F, Margis R, De Almeida RMC, Offringa R, Dos Santos Maraschin F (2019) Identification of root transcriptional responses to shoot illumination in Arabidopsis thaliana. Plant Mol Biol 101:487–498

    Google Scholar 

  • Monroe JD, Gough CM, Chandler LE, Loch CM, Ferrante JE, Wright PW (1999) Structure, properties, and tissue localization of apoplastic α-glucosidase in crucifers. Plant Physiol 119:385–398

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Morais DA, Almeida RM, Dalmolin RJ (2019) Transcriptogramer: an R/bioconductor package for transcriptional analysis based on protein–protein interaction. Bioinformatics 35:2875–2876

    Article  CAS  PubMed  Google Scholar 

  • Morimoto K, van der Hoorn RA (2016) The increasing impact of activity-based protein profiling in plant science. Plant Cell Physiol 57:446–461

    Article  CAS  PubMed  Google Scholar 

  • Nithya G, Sakthisekaran D (2015) In silico docking studies on the anti-cancer effect of thymoquinone on interaction with phosphatase and tensin homolog located on chromosome 10q23: a regulator of PI3K/AKT pathway. Asian J Pharm Clin Res 8:192–195

    CAS  Google Scholar 

  • Pandita D (2021) Saffron (Crocus sativus L.): phytochemistry, therapeutic significance and omics-based biology. In: Medicinal and aromatic plants. Elsevier

    Google Scholar 

  • Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Article  Google Scholar 

  • Pérez-Rodríguez P, Riano-Pachon DM, Corrêa LGG, Rensing SA, Kersten B, Mueller-Roeber B (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucl Acids Res 38:D822–D827

    Article  PubMed  Google Scholar 

  • Premkumar K, Ramesh A (2010) Anticancer, antimutagenic and antioxidant potential of saffron: an overview of current awareness and future perspectives. Funct Plant Sci Technol 4:91–97

    Google Scholar 

  • Rao J, Lv W, Yang J (2017) Proteomic analysis of saffron (Crocus sativus L.) grown under conditions of cadmium toxicity. Biosci J 33

    Google Scholar 

  • Riaño-Pachón DM, Ruzicic S, Dreyer I, Mueller-Roeber B (2007) PlnTFDB: an integrative plant transcription factor database. BMC Bioinform 8:1–10

    Article  Google Scholar 

  • Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140

    Article  CAS  PubMed  Google Scholar 

  • Rozas J, Ferrer-Mata A, Sánchez-Delbarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A (2017) DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol 34:3299–3302

    Article  CAS  PubMed  Google Scholar 

  • Rybarczyk-Filho JL, Castro MA, Dalmolin RJ, Moreira JC, Brunnet LG, de Almeida RM (2011) Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case. Nucl Acids Res 39:3005–3016

    Article  CAS  PubMed  Google Scholar 

  • Saffari B, Mohabatkar H, Mohsenzadeh S (2008) T and B-cell epitopes prediction of Iranian saffron (Crocus sativus) profilin by bioinformatics tools. Protein Pept Lett 15:280–285

    Article  CAS  PubMed  Google Scholar 

  • Sahihi M (2016) In-silico study on the interaction of saffron ligands and beta-lactoglobulin by molecular dynamics and molecular docking approach. J Macromol Sci Part B 55:73–84

    Google Scholar 

  • Sahoo A, Jena S, Sahoo S, Nayak S, Kar B (2016) Resequencing of Curcuma longa L. cv. kedaram through transcriptome profiling reveals various novel transcripts. Genom Data 9:160

    Google Scholar 

  • Saier Jr MH, Tran CV, Barabote RD (2006) TCDB: the transporter classification database for membrane transport protein analyses and information. Nucl Acids Res 34:D181–D186

    Google Scholar 

  • Sasaki T (2005) The map-based sequence of the rice genome. Nature 436:793–800

    Google Scholar 

  • Schlueter SD, Wilkerson MD, Dong Q, Brendel V (2006) xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features. Genome Biol 7:1–11

    Article  Google Scholar 

  • Schultz J, Milpetz F, Bork P, Ponting CP (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci 95:5857–5864

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Senizza B, Rocchetti G, Ghisoni S, Busconi M, Pascual MDLM, Fernandez JA, Lucini L, Trevisan M (2019) Identification of phenolic markers for saffron authenticity and origin: an untargeted metabolomics approach. Food Res Int 126:108584

    Article  CAS  PubMed  Google Scholar 

  • Serim S, Haedke U, Verhelst SH (2012) Activity-based probes for the study of proteases: recent advances and developments. ChemMedChem 7:1146–1159

    Article  CAS  PubMed  Google Scholar 

  • Singh V, Singh A, Chand R, Kushwaha C (2011) Role of bioinformatics in agriculture and sustainable development. Int J Bioinform Res 3:221–226

    Article  Google Scholar 

  • Smit A, Hubley R, Green P (2013) RepeatMasker. Institute for Systems Biology, Seattle, USA. https://www.repeatmasker.org

  • Tan H, Chen X, Liang N, Chen R, Chen J, Hu C, Li Q, Li Q, Pei W, Xiao W (2019) Transcriptome analysis reveals novel enzymes for apo-carotenoid biosynthesis in saffron and allows construction of a pathway for crocetin synthesis in yeast. J Exp Bot 70:4819–4834

    Article  CAS  PubMed  Google Scholar 

  • Tang S, Lomsadze A, Borodovsky M (2015) Identification of protein coding regions in RNA transcripts. Nucl Acids Res 43:e78–e78

    Article  PubMed  PubMed Central  Google Scholar 

  • Tokimatsu T, Sakurai N, Suzuki H, Ohta H, Nishitani K, Koyama T, Umezawa T, Misawa N, Saito K, Shibata D (2005) KaPPA-view. A web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps. Plant Physiol 138:1289–1300

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tokimatsu T, Sakurai N, Suzuki H, Shibata D (2006) KappA-view: a tool for integrating transcriptomic and metabolomic data on plant metabolic pathway maps. In: Plant metabolomics. Springer

    Google Scholar 

  • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and cufflinks. Nat Protoc 7:562

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tsaftaris AS, Pasentsis K, Iliopoulos I, Polidoros AN (2004) Isolation of three homologous AP1-like MADS-box genes in crocus (Crocus sativus L.) and characterization of their expression. Plant Sci 166:1235–1243

    Article  CAS  Google Scholar 

  • Tyanova S, Temu T, Cox J (2016a) The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc 11:2301–2319

    Article  CAS  PubMed  Google Scholar 

  • Tyanova S, Temu T, Sinitcyn P, Carlson A, Hein MY, Geiger T, Mann M, Cox J (2016b) The Perseus computational platform for comprehensive analysis of (prote) omics data. Nat Methods 13:731–740

    Article  CAS  PubMed  Google Scholar 

  • Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JA (2007) Primer3Plus, an enhanced web interface to Primer3. Nucl Acids Res 35:W71–W74

    Article  PubMed  PubMed Central  Google Scholar 

  • Wafai AH, Bukhari S, Mokhdomi TA, Amin A, Wani Z, Hussaini A, Mir JI, Qadri RA (2015) Comparative expression analysis of senescence gene CsNAP and B-class floral development gene CsAP3 during different stages of flower development in saffron (Crocus sativus L.). Physiol Mol Biol Plants 21:459–463

    Google Scholar 

  • Wafai AH, Husaini AM, Qadri RA (2019) Temporal expression of floral proteins interacting with CArG1 region of CsAP3 gene in Crocus sativus L. Gene Rep 16:100446

    Article  Google Scholar 

  • Wang Y, You FM, Lazo GR, Luo M-C, Thilmony R, Gordon S, Kianian SF, Gu YQ (2013) PIECE: a database for plant gene structure comparison and evolution. Nucl Acids Res 41:D1159–D1166

    Article  CAS  PubMed  Google Scholar 

  • Wetie AGN, Woods AG, Darie CC (2014) Mass spectrometric analysis of post-translational modifications (PTMs) and protein–protein interactions (PPIs). Advance Mass Spectrom Biomed Res 205–235

    Google Scholar 

  • Willems LI, Overkleeft HS, van Kasteren SI (2014) Current developments in activity-based protein profiling. Bioconjug Chem 25:1181–1191

    Article  CAS  PubMed  Google Scholar 

  • Xiao J-Z, Ohshima A, Kamakura T, Ishiyama T, Yamaguchi I (1994) Extracellular glycoprotein(s) associated with cellular differentiation in Magnaporthe grisea. Mol Plant Microbe Interact 7:639–644

    Google Scholar 

  • Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L (2006) WEGO: a web tool for plotting GO annotations. Nucl Acids Res 34:W293–W297

    Google Scholar 

  • Yue J, Wang R, Ma X, Liu J, Lu X, Thakar SB, An N, Liu J, Xia E, Liu Y (2020) Full-length transcriptome sequencing provides insights into the evolution of apocarotenoid biosynthesis in Crocus sativus. Comput Struct Biotechnol J 18:774–783

    Google Scholar 

  • Zarini HN, Jafari H, Ramandi HD, Bolandi AR, Karimishahri MR (2019) A comparative assessment of DNA fingerprinting assays of ISSR and RAPD markers for molecular diversity of saffron and other Crocus spp. in Iran. Nucleus 62:39–50

    Google Scholar 

  • Zeraatkar M, Khalili K, Foorginejad A (2015) Studying and generation of saffron flower’s 3D solid model. Proc Technol 19:62–69

    Google Scholar 

  • Zimmermann L, Stephens A, Nam S-Z, Rau D, Kübler J, Lozajic M, Gabler F, Söding J, Lupas AN, Alva V (2018) A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J Mol Biol 430:2237–2243

    Google Scholar 

  • Zinati Z, Shamloo-Dashtpagerdi R, Behpouri A (2016) In silico identification of miRNAs and their target genes and analysis of gene co-expression network in saffron (Crocus sativus L.) stigma. Mol Biol Res Commun 5:233

    Google Scholar 

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Acknowledgements

AMH is grateful to National Mission on Himalayan Studies, Ministry of Environment, Forest and Climate Change, Government of India for funding saffron research in the form of a research grant.

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Authors and Affiliations

  1. Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar Campus, Srinagar, Jammu and Kashmir, 190025, India

    Syed Anam Ul Haq & Amjad M. Husaini

  2. Department of Horticultural Science, Faculty of Engineering and Agricultural Science, University of Tehran, Tehran, Iran

    Seyed Alireza Salami

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  1. Syed Anam Ul Haq
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  2. Seyed Alireza Salami
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  3. Amjad M. Husaini
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Correspondence to Amjad M. Husaini .

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Editors and Affiliations

  1. School of Biotechnology, University of Jammu, Jammu, India

    Jyoti Vakhlu

  2. School of Biotechnology, University of Jammu, Jammu, India

    Sheetal Ambardar

  3. Department of Horticultural Sciences, University of Tehran, Keraj, Iran

    Seyed Alireza Salami

  4. ICAR- Nat.Inst.for Plant Biotechnology, Raja Ramanna Fellow, DAE, Govt. of India, New Delhi, India

    Chittaranjan Kole

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Haq, S.A.U., Salami, S.A., Husaini, A.M. (2022). Bioinformatics for Saffron-Omics and Crop Improvement. In: Vakhlu, J., Ambardar, S., Salami, S.A., Kole, C. (eds) The Saffron Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-031-10000-0_4

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