Advertisement

Sequencing Ancestor Diploid Genomes for Enhanced Genome Understanding and Peanut Improvement

  • Spurthi N. Nayak
  • Manish K. Pandey
  • Scott A. Jackson
  • Xuanqiang Liang
  • Rajeev K. VarshneyEmail author
Chapter
Part of the Compendium of Plant Genomes book series (CPG)

Abstract

Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ~2.7 Gb. To understand the genome of the cultivated peanut, it is prerequisite to know the genome organization of its diploid progenitors, A-genome—Arachis duranensis and B-genome—A. ipaensis. Two genome sequencing projects conducted sequencing and analysis of the genomes of diploid ancestors: (1) International Peanut Genome Initiative (IPGI) reported the sequencing of both A- and B-genomes; while (2) Diploid Progenitor Peanut Arachis Genome Sequencing Consortium (DPPAGSC) reported the sequencing of A-genome. IPGI study showed that these genomes are similar to cultivated peanut’s A- and B-subgenomes and used them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut’s subgenomes thus providing evidence about direct descendant of the B subgenome in cultivated peanut. The DPPAGSC study, on the other hand, provided new insights into geocarpy, oil biosynthesis, and allergens in addition to providing information about evolution and polyploidization. These genome sequencing efforts have improved the understanding about the complex peanut genome and genome architecture which will play a very important role in peanut applied genomics and breeding.

Keywords

Genome sequencing Genome assembly Annotation Genes Arachis hypogaea A duranensis A ipaensis 

References

  1. Bertioli DJ, Cannon SB, Froenicke L, Huang G, Farmer AD, Cannon EK, Liu X, Gao D, Clevenger J, Dash S, Ren L et al (2016) The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat Genet 48(4):438–446CrossRefPubMedGoogle Scholar
  2. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W (2011) Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27(4):578–579CrossRefPubMedGoogle Scholar
  3. Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J, Achawanantakun R, Jiao D, Lawrence CJ, Ware D et al (2014) MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol 164(2):513–524CrossRefPubMedGoogle Scholar
  4. Cermeno MC, Orellana J, Santos JL, Lacadena JR (1984) Nucleolar activity and competition (amphiplasty) in the genus Aegilops. Heredity 53(3):603–611CrossRefGoogle Scholar
  5. Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M et al (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345(6199):950–953CrossRefPubMedGoogle Scholar
  6. Chen X, Li H, Pandey MK, Yang Q, Wang X, Garg V, Li H, Chi X, Doddamani D, Hong Y, Upadhyaya H et al (2016) Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens. Proc Natl Acad Sci 113(24):6785–6790CrossRefPubMedPubMedCentralGoogle Scholar
  7. Dhillon SS, Rake AV (1980) Miksche JP. Reassociation kinetics and cytophotometric characterization of peanut (Arachis hypogaea L.) DNA. Plant Physiol 65(6):1121–1127CrossRefPubMedPubMedCentralGoogle Scholar
  8. Fávero AP, Simpson CE, Valls JF, Vello NA (2006) Study of the evolution of cultivated peanut through crossability studies. Crop Sci 46(4):1546–1552CrossRefGoogle Scholar
  9. Fernández A, Krapovickas A (1994) Cromosomas Y Evolucion En” Arachis (Leguminosae)”. Bonplandia 187–220 Google Scholar
  10. Foncéka D, Hodo-Abalo T, Rivallan R, Faye I, Sall MN, Ndoye O, Fávero AP, Bertioli DJ, Glaszmann JC, Courtois B, Rami JF (2009) Genetic mapping of wild introgressions into cultivated peanut: a way toward enlarging the genetic basis of a recent allotetraploid. BMC Plant Biol 9(1):103CrossRefPubMedPubMedCentralGoogle Scholar
  11. Gautami B, Foncéka D, Pandey MK, Moretzsohn MC, Sujay V, Qin H, Hong Y, Faye I, Chen X, BhanuPrakash A, Shah TM et al (2012) An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.). PLoS One 7(7):e41213CrossRefPubMedPubMedCentralGoogle Scholar
  12. Huang S, Chen Z, Huang G, Yu T, Yang P, Li J, Fu Y, Yuan S, Chen S, Xu A (2012) HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies. Genome Res 22(8):1581–1588CrossRefPubMedPubMedCentralGoogle Scholar
  13. Jackson SA (2016) Rice: The first crop genome. Rice. doi: 10.1186/s12284-016-0087-4 PubMedPubMedCentralGoogle Scholar
  14. Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, Appels R, Pfeifer M, Tao Y, Zhang X, Jing R et al (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496(7443):91–95CrossRefPubMedGoogle Scholar
  15. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S et al (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20(2):265–272CrossRefPubMedPubMedCentralGoogle Scholar
  16. Lin R, Ding L, Casola C, Ripoll DR, Feschotte C, Wang H (2007) Transposase-derived transcription factors regulate light signaling in Arabidopsis. Science 318(5854):1302–1305CrossRefPubMedPubMedCentralGoogle Scholar
  17. Ling HQ, Zhao S, Liu D, Wang J, Sun H, Zhang C, Fan H, Li D, Dong L, Tao Y, Gao C et al (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496(7443):87–90CrossRefPubMedGoogle Scholar
  18. Liu B, Yuan J, Yiu SM, Li Z, Xie Y, Chen Y, Shi Y, Zhang H, Li Y, Lam TW, Luo R (2012) COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly. Bioinformatics 28(22):2870–2874CrossRefPubMedGoogle Scholar
  19. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience. 1(1):1CrossRefGoogle Scholar
  20. Marcussen T, Sandve SR, Heier L, Spannagl M, Pfeifer M International wheat genome sequencing consortium, et al. (2014) Ancient hybridizations among the ancestral genomes of bread wheat. Science 345Google Scholar
  21. McCoy RC, Taylor RW, Blauwkamp TA, Kelley JL, Kertesz M, Pushkarev D, Petrov DA, Fiston-Lavier AS (2014) Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements. PLoS One 9(9):e106689CrossRefPubMedPubMedCentralGoogle Scholar
  22. Medzihradszky M, Bindics J, Adam E, Viczian A, Klement E, Lorrain S, Gyula P, Merai Z, Fankhauser C, Medzihradszky KF, Kunkel T,  Schafer E, Nagy F (2013) Phosphorylation of phytochrome B inhibits light-induced signaling via accelerated dark reversion in Arabidopsis. The Plant Cell 25(2):535–544Google Scholar
  23. Michael TP, Jackson S (2013) The first 50 plant genomes. The Plant Genome, 6(2)Google Scholar
  24. Moretzsohn MC, Leoi L, Proite K, Guimaraes PM, Leal-Bertioli SC, Gimenes MA, Martins WS, Valls JF, Grattapaglia D, Bertioli DJ (2005) A microsatellite-based, gene-rich linkage map for the AA genome of Arachis (Fabaceae). Theor Appl Genet 111(6):1060–1071CrossRefPubMedGoogle Scholar
  25. Moretzsohn MC, Barbosa AV, Alves-Freitas DM, Teixeira C, Leal-Bertioli SC, Guimarães PM, Pereira RW, Lopes CR, Cavallari MM, Valls JF, Bertioli DJ (2009) A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome. BMC Plant Biol 9(1):40CrossRefPubMedPubMedCentralGoogle Scholar
  26. Moore KM, Knauft DA (1989) The inheritance of high oleic acid in peanut. J Heredity 80:252–253Google Scholar
  27. Moretzsohn MC, Gouvea EG, Inglis PW, Leal-Bertioli SC, Valls JF, Bertioli DJ (2013) A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers. Ann Bot 111(1):113–126Google Scholar
  28. Nielen S, Campos-Fonseca F, Leal-Bertioli S, Guimarães P, Seijo G, Town C, Arrial R, Bertioli D (2010) FIDEL—a retrovirus-like retrotransposon and its distinct evolutionary histories in the A-and B-genome components of cultivated peanut. Chromosome Res 18(2):227–246CrossRefPubMedPubMedCentralGoogle Scholar
  29. Nielen S, Vidigal BS, Leal-Bertioli SC, Ratnaparkhe M, Paterson AH, Garsmeur O, D’Hont A, Guimaraes PM, Bertioli DJ (2012) Matita, a new retroelement from peanut: characterization and evolutionary context in the light of the Arachis A-B genome divergence. Mol Genet Genomics 287(1):21–38CrossRefPubMedGoogle Scholar
  30. Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker KC, Shu S, Udall J, Yoo MJ (2012) Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492(7429):423–427CrossRefPubMedGoogle Scholar
  31. Preuss S, Pikaard CS (2007) rRNA gene silencing and nucleolar dominance: insights into a chromosome-scale epigenetic on/off switch. Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression 1769(5):383–92Google Scholar
  32. Qin C, Yu C, Shen Y, Fang X, Chen L, Min J, Cheng J, Zhao S, Xu M, Luo Y, Yang Y et al (2014) Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci 111(14):5135–5140CrossRefPubMedPubMedCentralGoogle Scholar
  33. Ramos ML, Fleming G, Chu Y, Akiyama Y, Gallo M, Ozias-Akins P (2006) Chromosomal and phylogenetic context for conglutin genes in Arachis based on genomic sequence. Mol Genet Genomics 275(6):578–592CrossRefPubMedGoogle Scholar
  34. Robledo G, Seijo G (2010) Species relationships among the wild B genome of Arachis species (section Arachis) based on FISH mapping of rDNA loci and heterochromatin detection: a new proposal for genome arrangement. Theor Appl Genet 121(6):1033–1046CrossRefPubMedGoogle Scholar
  35. Robledo G, Lavia GI, Seijo G (2009) Species relations among wild Arachis species with the A genome as revealed by FISH mapping of rDNA loci and heterochromatin detection. Theor Appl Genet 118(7):1295–1307CrossRefPubMedGoogle Scholar
  36. Samoluk SS, Chalup L, Robledo G, Seijo JG (2015) Genome sizes in diploid and allopolyploid Arachis L. species (section Arachis). Genet Resour Crop Evol 62(5):747–763CrossRefGoogle Scholar
  37. Schatz MC, Witkowski J, McCombie WR (2012) Current challenges in de novo plant genome sequencing and assembly. Genome Biol 13(4):1CrossRefGoogle Scholar
  38. Seijo JG, Lavia GI, Fernandez A, Kaprovickas A, Ducasse D, Moscone EA (2004) Physical mapping of the 5S and 18S-25S RRNA gene by FISH as evidence that Arachis  duranensis and A. ipaensis are the wild diploid progenitors of A. hypogaea (Leguminosae). Am J Bot 91:1294–1303Google Scholar
  39. Seijo G, Lavia GI, Fernández A, Krapovickas A, Ducasse DA, Bertioli DJ, Moscone EA (2007) Genomic relationships between the cultivated peanut (Arachis hypogaea, Leguminosae) and its close relatives revealed by double GISH. Am J Bot 94(12):1963–1971Google Scholar
  40. Shirasawa K, Koilkonda P, Aoki K, Hirakawa H, Tabata S, Watanabe M, Hasegawa M, Kiyoshima H, Suzuki S, Kuwata C, Naito Y (2012) In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut. BMC Plant Biol 12(1):1CrossRefGoogle Scholar
  41. Shirasawa KE, Bertioli DJ, Varshney RK, Moretzsohn MC, Leal-Bertioli SC, Thudi MA, Pandey MK, Rami JF, Foncéka DA, Gowda MV, Qin HO et al (2013) Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes. DNA Res 20(2):173–184CrossRefPubMedPubMedCentralGoogle Scholar
  42. Soltis DE, Visger CJ, Soltis PS (2014) The polyploidy revolution then and now: Stebbins revisited. Am J Bot 101(7):1057–1078CrossRefPubMedGoogle Scholar
  43. Temsch EM, Greilhuber J (2000) Genome size variation in Arachis hypogaea and A. monticola re-evaluated. Genome 43(3):449–451CrossRefPubMedGoogle Scholar
  44. Varshney RK, Nayak SN, Jackson S, May G (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27(9):522–530CrossRefPubMedGoogle Scholar
  45. Wang K, Wang Z, Li F, Ye W, Wang J, Song G, Yue Z, Cong L, Shang H, Zhu S, Zou C et al (2012) The draft genome of a diploid cotton Gossypium raimondii. Nat Genet 44(10):1098–1103CrossRefPubMedGoogle Scholar
  46. Whitelam GC, Halliday KJ (2008) Annual plant reviews, light and plant development. John Wiley & SonsGoogle Scholar
  47. Woodhouse MR, Cheng F, Pires JC, Lisch D, Freeling M, Wang X (2014) Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids. Proc Natl Acad Sci 111(14):5283–5288Google Scholar
  48. Young ND, Debellé F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, Van de Peer Y et al (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480(7378):520–524PubMedPubMedCentralGoogle Scholar
  49. Zhou X, Xia Y, Ren X, Chen Y, Huang L, Huang S, Liao B, Lei Y, Yan L, Jiang H (2014) Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq). BMC Genom 15(1):1CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Spurthi N. Nayak
    • 1
  • Manish K. Pandey
    • 1
  • Scott A. Jackson
    • 2
  • Xuanqiang Liang
    • 3
  • Rajeev K. Varshney
    • 1
    • 4
    Email author
  1. 1.International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)PatancheruIndia
  2. 2.Center for Applied Genetic Technologies, University of Georgia (UGA)AthensUSA
  3. 3.Crop Research Institute, Guangdong Academy of Agricultural Sciences (GAAS)GuangzhouChina
  4. 4.University of Western Australia (UWA)CrawleyAustralia

Personalised recommendations