Skip to main content
SpringerLink
Log in

Genome Annotation and Gene Families in Sesame

  • Chapter
  • First Online:
The Sesame Genome

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

Abstract

In genomes, genes are the most important components because of the function in controlling various biological traits and regulating the complex biological processes in plants. Reliable chromosome-scaled genome assembly supplies the abundant and precise genome information for gene and gene family research in sesame. In this chapter, we deliberate on the main techniques used for genome annotation and gene prediction in sesame (var. Yuzhi 11). Distribution of all genes and gene families in sesame genome is described. Meanwhile, the main research achievements in some key gene families related to key biological processes, such as fatty acid biosynthesis and metabolism and responses to environmental conditions in sesame, are discussed in the section.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Aggarwal G, Ramaswamy R (2002) Ab initio gene identification: prokaryote genome annotation with GeneScan and GLIMMER. J Biosci 27(1):7–14

    Article  CAS  PubMed  Google Scholar 

  • Allen JE, Salzberg SL (2005) JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinformatics 21:3596–3603

    Article  CAS  PubMed  Google Scholar 

  • Altschul SF, Madden TL, Alejandro S, Zhang J, Zhang Z et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  • Ashburner M, Ball CA, Blake JA, Botstein BH et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Benson D, Karsch-Mizrachi I, Lipman D, Ostell J, Wheeler D (2005) GenBank. Nucleic Acids Res 1 (33 (Database issue)):D34–38

    Google Scholar 

  • Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Birney E, Clamp M, Durbin R (2004) Gene wise and genomewise. Genome Res 14(5):988–995

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brandi LC, Ian K, Sofia MC, Genis P, Eric R et al (2008) MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res 18(1):188–196

    Article  Google Scholar 

  • Chowdhury S, Basu A, Kundu S (2017) Overexpression of a new osmotin-like protein gene (SindOLP) confers tolerance against biotic and abiotic stresses in sesame. Front Plant Sci 8:410

    Article  PubMed  PubMed Central  Google Scholar 

  • Cunningham F, Amode MR, Barrell D, Beal K, Billis K et al (2015) Ensembl 2015. Nucleic Acids Res 43(D1):D662–D669

    Article  CAS  PubMed  Google Scholar 

  • Curwen V, Eyras E, Andrews TD, Clarke L, Mongin E et al (2004) The Ensembl automatic gene annotation system. Genome Res 14:942–950

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cao D, Wang M, Ge1 Y, Gong S (2019) Draft genome of the big-headed turtle Platysternon megacephalum. Sci Data 6(1):60

    Google Scholar 

  • Dossa K, Diouf D, Cissé N (2016) Genome-wide investigation of Hsf genes in sesame reveals their segmental duplication expansion and their active role in drought stress response. Front Plant Sci 7:1522

    Article  PubMed  PubMed Central  Google Scholar 

  • Dossa K, Wei X, Li D, Fonceka D, Zhang Y et al (2016) Insight into the ap2/erf transcription factor superfamily in sesame and expression profiling of DREB subfamily under drought stress. BMC Plant Biol 16(1):171

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL et al (2015) Rfam: updates to the RNA families database. Nucleic Acids Res 37(Database issue):D136–40

    Google Scholar 

  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA 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 

  • Grundmann N, Demester L, Makalowski W (2009) TEclass—a tool for automated classification of unknown eukaryotic transposable elements. Bioinformatics 25(10):1329–1330

    Article  PubMed  CAS  Google Scholar 

  • Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE et al (2008) Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble apliced alignments. Genome Biol 9(1):R7

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr et al (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 31:5654–5666

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hüttenhofer A, Schattner P, Polacek N (2005) Non-coding RNAs: hope or hype? Trends Genet 21(5):289–297

    Article  PubMed  CAS  Google Scholar 

  • Joshi AB (1961) Sesamum. Indian Central Oilseed Committee Hyderabad, India, p 109

    Google Scholar 

  • Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32(Database issue):D277-D80

    Google Scholar 

  • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R et al (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kitts P (2002) Genome assembly and annotation process. In: McEntyre J, Ostel (eds) The NCBI handbook, National Center for Biotechnology Information, Chap. 13

    Google Scholar 

  • Kitts PA, Church DM, Françoise TN, Jinna C, Vichet H et al (2016) Assembly: a resource for assembled genomes at NCBI. Nucleic Acids Res D1:D73–D80

    Article  CAS  Google Scholar 

  • Korf I (2004) Gene finding in novel genomes. BMC Bioinformatics 5(1):59

    Article  PubMed  PubMed Central  Google Scholar 

  • Korf I, Yandell M, Bedell J (2003) BLAST: an essential guide to the basic local alignment search tool, vol 339. O’Reilly & Associates

    Google Scholar 

  • Kristensen DM, Kannan L, Coleman MK, Wolf YI, Sorokin A et al (2010) A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinformatics 26(12):1481–1487

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li D, Liu P, Yu J, Wang L, Dossa K et al (2017) Genome-wide analysis of WRKY gene family in the sesame genome and identification of the WRKY genes involved in responses to abiotic stresses. BMC Plant Biol 17(1):152

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Li L, Stoeckert CJ Jr, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13(9):2178–2189

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu J, Tu L, Xu R, Zheng Y (1993) The relationship between the waterlogging resistance and the genotypes and the vigor of root system in sesame (Sesamum indicum L.). Acta Agri Bor-Sin 8(3):82–86

    Google Scholar 

  • Lowe TM, Eddy SR (1997) tRNAScan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964

    Google Scholar 

  • Lowe TM, Eddy SR (1999) A Computational screen for methylation guide snoRNAs in yeast. Science 283(5405):1168–1171

    Article  CAS  PubMed  Google Scholar 

  • Maja TG, Nansheng C (2009) Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinform 25, Chap. 4, Unit 4.10. https://doi.org/10.1002/0471250953.bi0410s25.

  • Majoros WH, Pertea M, Salzberg SL (2004) TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20(16):2878–2879

    Article  CAS  PubMed  Google Scholar 

  • Miao H, Li C, Duan Y, Wei L, Ju M et al (2019) Identification of a Sidwf1 gene controlling short internode length trait in the sesame dwarf mutant dw607. Theor Appl Genet 133(1):73–86

    Article  PubMed  CAS  Google Scholar 

  • Mmadi MA, Dossa K, Wang L, Zhou R, Wang Y et al (2017) Functional characterization of the versatile MYB gene family uncovered their important roles in plant development and responses to drought and waterlogging in sesame. Genes 8(12):362

    Article  PubMed Central  CAS  Google Scholar 

  • Nimmakayala P, Perumal R, Mulpuri S, Reddy UK (2011) Sesamum. In: Kole C (ed) Wild crop relatives: genomic and breeding resources. Volume oilseeds. Springer, Berlin Heidelberg, pp 261–273

    Google Scholar 

  • Pearson H (2006) Genetics: what is a gene? Nature 441(7092):398–401

    Article  CAS  PubMed  Google Scholar 

  • Parra G, Bradnam K, Korf I (2007) CEGMA. Bioinformatics 23:9

    Google Scholar 

  • Qiu C, Zhang H, Chang S, Wei L, Miao H (2014) Laboratory detecting method for pathogenicity of Fusarium oxysporum Schl. f. sp. sesami isolates. Acta Phytopathol Sin 44(1):26–35

    Google Scholar 

  • Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P et al (2000) Artemis: sequence visualization and annotation. Bioinformatics 16:944–945

    Article  CAS  PubMed  Google Scholar 

  • Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH (2009) JBrowse: a next generation genome browser. Genome Res 19:1630–1638

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stanke M, Keller O, Gunduz I, Hayes A, Waack S et al (2006) AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res 34:W435–W239

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stanke M, Waack S (2003) Gene prediction with a hidden Markov model and a new intron submodel. Bioinform Suppl 2:ii215–225

    Google Scholar 

  • Stanke M, Schoffmann O, Morgenstern B, Waack S (2006) Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinform 7:62

    Article  CAS  Google Scholar 

  • Uzo JO (1985) A search for drought resistance in the wild relatives of the cultivated sesame (Sesamum indicum). In: Ashri A (ed) Sesame and safflower: status and potential. FAO Plant production and protection paper 66, Rome, Italy, pp 163–165

    Google Scholar 

  • Vanin EF (1985) Processed pseudogenes: characteristics and evolution. Ann Rev Genet 19:253–272

    Article  CAS  PubMed  Google Scholar 

  • Wang L, Xia Q, Zhang Y, Zhu X, Zhu X et al (2016) Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map. BMC Genom 17:31

    Article  CAS  Google Scholar 

  • Wang L, Yu S, Tong C, Zhao Y, Liu Y et al (2014) Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis. Genome Biol 15(2):R39

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Zhang Y, Zhou R, Dossa K, Yu J et al (2018) Identification and characterization of the bZIP transcription factor family and its expression in response to abiotic stresses in sesame. PLoS ONE 13(7):e0200850

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Waterhouse RM, Seppey M, Simo FA, Manni M, Zdobnov EM (2017) Busco applications from quality assessments to gene prediction and phylogenomics. Mol Biol Evol 35(3):543–548

    Article  PubMed Central  CAS  Google Scholar 

  • Wei M, Liu A, Zhang Y, Zhou Y, Li D et al (2019) Genome-wide characterization and expression analysis of the HD-Zip gene family in response to drought and salinity stresses in sesame. BMC Genom 20(1):74

    Article  Google Scholar 

  • Wei X, Gong H, Yu J, Liu P, Wang L et al (2017) SesameFG: an integrated database for the functional genomics of sesame. Sci Rep 7(1):1–10

    CAS  Google Scholar 

  • Wei X, Wang L, Yu J, Zhang Y, Li D, Zhang X (2015) Genome-wide identification and analysis of the MADS-box gene family in sesame. Gene 569(1):66–76

    Article  CAS  PubMed  Google Scholar 

  • Yandell M, Ence D (2012) A beginner’s guide to eukaryotic genome annotation. Nat Rev Genet 13(5):329–342

    Article  CAS  PubMed  Google Scholar 

  • You J, Wang Y, Zhang Y, Dossa K, Li D et al (2018) Genome-wide identification and expression analyses of genes involved in raffinose accumulation in sesame. Sci Rep 8(1):1–11

    Article  Google Scholar 

  • Yu J, Golicz AA, Lu K, Dossa K, Zhang Y et al (2019) Insight into the evolution and functional characteristics of the pan-genome assembly from sesame landraces and modern cultivars. Plant Biotechnol J 17(5):881–892

    Article  CAS  PubMed  Google Scholar 

  • Zhang H, Miao H, Wang L, Qu L, Liu H et al (2013) Genome sequencing of the important oilseed crop Sesamum indicum L. Genome Biol 14(1):401

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang H, Miao H, Ju M (2019) Potential for adaptation to climate change through genomic breeding in sesame. In: Kole C (ed) Genomic designing of climate-smart oilseed crops. Springer, Cham, Switzerland, pp 374–376

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, P. R. China

    Hongmei Miao, Chun Li & Haiyang Zhang

  2. TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China

    Yamin Sun & Lei Wang

Authors
  1. Hongmei Miao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yamin Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Chun Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lei Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Haiyang Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Haiyang Zhang .

Editor information

Editors and Affiliations

  1. Henan Academy of Agricultural Sciences, Henan Sesame Research Center, Zhengzhou, China

    Hongmei Miao

  2. Henan Academy of Agricultural Sciences, Henan Sesame Research Center, Zhengzhou, China

    Haiyang Zhang

  3. ICAR-National Institute for Plant Biotechnology, New Delhi, India

    Chittaranjan Kole

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Miao, H., Sun, Y., Li, C., Wang, L., Zhang, H. (2021). Genome Annotation and Gene Families in Sesame. In: Miao, H., Zhang, H., Kole, C. (eds) The Sesame Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-98098-0_15

Download citation

Publish with us

Policies and ethics

Search

Navigation