nach oben

Erschienen in:

2018 | OriginalPaper | Buchkapitel

Advances in Sequencing and Resequencing in Crop Plants

verfasst von : Pradeep R. Marri, Liang Ye, Yi Jia, Ke Jiang, Steven D. Rounsley

Erschienen in: Plant Genetics and Molecular Biology

Verlag: Springer International Publishing

Einloggen

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config

KI-gestützte Suche

Aus

Abstract

DNA sequencing technologies have changed the face of biological research over the last 20 years. From reference genomes to population level resequencing studies, these technologies have made significant contributions to our understanding of plant biology and evolution. As the technologies have increased in power, the breadth and complexity of the questions that can be asked has increased. Along with this, the challenges of managing unprecedented quantities of sequence data are mounting. This chapter describes a few aspects of the journey so far and looks forward to what may lie ahead.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

über 102.000 Bücher
über 537 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Finance + Banking
Management + Führung
Marketing + Vertrieb
Maschinenbau + Werkstoffe
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 390 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Maschinenbau + Werkstoffe

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Vorheriges Kapitel Plant Genetics and Molecular Biology: An Introduction

Nächstes Kapitel Revolution in Genotyping Platforms for Crop Improvement

Sanger F et al (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74(12):5463–5467CrossRefPubMedPubMedCentral

Mardis ER (2013) Next-generation sequencing platforms. Annu Rev Anal Chem (Palo Alto, Calif) 6:287–303CrossRef

Goodwin S et al (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17(6):333–351CrossRefPubMed

Margulies M et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057):376–380CrossRefPubMedPubMedCentral

Li Z et al (2012) Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph. Brief Funct Genomics 11(1):25–37CrossRefPubMed

Jaffe DB et al (2003) Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res 13(1):91–96CrossRefPubMedPubMedCentral

Myers EW et al (2000) A whole-genome assembly of Drosophila. Science 287(5461):2196–2204CrossRefPubMed

Huang XQ et al (2003) PCAP: a whole-genome assembly program. Genome Res 13(9):2164–2170CrossRefPubMedPubMedCentral

Ewing B et al (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8(3):175–185CrossRefPubMed

10.

Simpson JT et al (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19(6):1117–1123CrossRefPubMedPubMedCentral

11.

Gnerre S et al (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A 108(4):1513–1518CrossRefPubMed

12.

Li R et al (2010) Building the sequence map of the human pan-genome. Nat Biotechnol 28(1):57–63CrossRefPubMed

13.

Li RQ et al (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20(2):265–272CrossRefPubMedPubMedCentral

14.

Fleischmann RD et al (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269(5223):496–512CrossRefPubMed

15.

Fraser CM et al (1995) The minimal gene complement of Mycoplasma genitalium. Science 270(5235):397–403CrossRefPubMed

16.

Sutton GG et al (1995) TIGR assembler: a new tool for assembling large shotgun sequencing projects. Genome Sci Technol 1(1):9–19CrossRef

17.

Hamilton JP, Buell CR (2012) Advances in plant genome sequencing. Plant J 70(1):177–190CrossRefPubMed

18.

Matsumoto T et al (2005) The map-based sequence of the rice genome. Nature 436(7052):793–800CrossRef

19.

Schnable PS et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326(5956):1112–1115CrossRef

20.

Schmutz J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463(7278):178–183CrossRefPubMed

21.

Goff SA et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science 296(5565):92–100CrossRefPubMed

22.

Ming R et al (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452(7190):991–U997CrossRefPubMedPubMedCentral

23.

Paterson AH et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457(7229):551–556CrossRef

24.

Vogel JP et al (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463(7282):763–768CrossRef

25.

Yu J et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science 296(5565):79–92CrossRefPubMed

26.

Michael TP, Jackson S (2013) The first 50 plant genomes. Plant Genome 6(2)

27.

Chalhoub B et al (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345(6199):950–953CrossRefPubMed

28.

Prochnik S et al (2012) The cassava genome: current progress, future directions. Trop Plant Biol 5(1):88–94CrossRefPubMedPubMedCentral

29.

Sato S et al (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485(7400):635–641CrossRef

30.

Wang M et al (2014) The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat Genet 46(9):982–988CrossRefPubMed

31.

International Wheat Genome Sequencing Consortium (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345(6194):1251788CrossRef

32.

Wang XW et al (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43(10):1035–U1157CrossRefPubMed

33.

Wang K et al (2012) The draft genome of a diploid cotton Gossypium raimondii. Nat Genet 44(10):1098–1103CrossRefPubMed

34.

Li FG et al (2014) Genome sequence of the cultivated cotton Gossypium arboreum. Nat Genet 46(6):567–572CrossRefPubMed

35.

Li YH et al (2014) De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat Biotechnol 32(10):1045–1052CrossRefPubMed

36.

Cao J et al (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43(10):956–963CrossRefPubMed

37.

Xu X et al (2012) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 30(1):105–111CrossRef

38.

Chia JM et al (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet 44(7):803–807CrossRefPubMed

39.

Jiao Y et al (2012) Genome-wide genetic changes during modern breeding of maize. Nat Genet 44(7):812–815CrossRefPubMed

40.

Patil G et al (2016) Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean. Sci Rep 6:19199CrossRefPubMedPubMedCentral

41.

Mace ES et al (2013) Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum. Nat Commun 4:2320CrossRefPubMedPubMedCentral

42.

Bradley P et al (2015) Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun 6:10063CrossRefPubMedPubMedCentral

43.

Brozynska M et al (2016) Genomics of crop wild relatives: expanding the gene pool for crop improvement. Plant Biotechnol J 14(4):1070–1085CrossRefPubMed

44.

Leung H et al (2015) Allele mining and enhanced genetic recombination for rice breeding. Rice (N Y) 8(1):34CrossRef

45.

Yang J et al (2015) Extreme-phenotype genome-wide association study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel. Plant J 84(3):587–596CrossRefPubMed

46.

Schatz MC et al (2014) Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol 15(11):506PubMedPubMedCentral

47.

Genomes Project Consortium et al (2010) A map of human genome variation from population-scale sequencing. Nature 467(7319):1061–1073CrossRef

48.

Genomes Project Consortium et al (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491(7422):56–65CrossRef

49.

Genomes Project Consortium et al (2015) A global reference for human genetic variation. Nature 526(7571):68–74CrossRef

50.

Li H et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079CrossRefPubMedPubMedCentral

51.

Danecek P et al (2011) The variant call format and VCFtools. Bioinformatics 27(15):2156–2158CrossRefPubMedPubMedCentral

52.

Knaus BJ, Grunwald NJ (2016) VCFR: a package to manipulate and visualize variant call format data in R. Mol Ecol Resour 17(1):44–53CrossRefPubMed

53.

Cingolani P et al (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6(2):80–92CrossRef

54.

Skinner ME et al (2009) JBrowse: a next-generation genome browser. Genome Res 19(9):1630–1638CrossRefPubMedPubMedCentral

55.

McLaren W et al (2016) The ensembl variant effect predictor. Genome Biol 17(1):122CrossRefPubMedPubMedCentral

56.

Wang K et al (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38(16):e164CrossRefPubMedPubMedCentral

57.

Robinson JT et al (2011) Integrative genomics viewer. Nat Biotechnol 29(1):24–26CrossRefPubMedPubMedCentral

58.

Donlin MJ (2009) Using the generic genome browser (GBrowse). Curr Protoc Bioinformatics Chapter 9: Unit 9.9

59.

Kent WJ et al (2002) The human genome browser at UCSC. Genome Res 12(6):996–1006CrossRefPubMedPubMedCentral

60.

Fiume M et al (2010) Savant: genome browser for high-throughput sequencing data. Bioinformatics 26(16):1938–1944CrossRefPubMedPubMedCentral

61.

Koren S, Phillippy AM (2015) One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr Opin Microbiol 23:110–120CrossRefPubMed

62.

Ming R et al (2015) The pineapple genome and the evolution of CAM photosynthesis. Nat Genet 47(12):1435–1442CrossRefPubMedPubMedCentral

63.

Bankevich A et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19(5):455–477CrossRefPubMedPubMedCentral

64.

Berlin K et al (2015) Assembling large genomes with single-molecule sequencing and locality-sensitive hashing (vol 33, pg 623, 2015). Nat Biotechnol 33(10):1109–1109CrossRefPubMed

65.

English AC et al (2012) Mind the gap: upgrading genomes with Pacific biosciences RS long-read sequencing technology. PLoS One 7(11):e47768CrossRefPubMedPubMedCentral

66.

Koren S et al (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 30(7):692–700CrossRef

67.

Sakai H et al (2015) The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome. Sci Rep 5:16780CrossRefPubMedPubMedCentral

68.

Quick J et al (2016) Real-time, portable genome sequencing for Ebola surveillance. Nature 530(7589):228–232CrossRefPubMedPubMedCentral

69.

Benitez-Paez A et al (2016) Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION (TM) portable nanopore sequencer. Gigascience 5:4CrossRefPubMedPubMedCentral

70.

Ammar R et al (2015) Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes. F1000Res 4:17PubMedPubMedCentral

71.

Chin CS et al (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10(6):563CrossRefPubMed

72.

Gore MA et al (2009) A first-generation haplotype map of maize. Science 326(5956):1115–1117CrossRefPubMed

73.

Li H (2016) BGT: efficient and flexible genotype query across many samples. Bioinformatics 32(4):590–592CrossRefPubMed

74.

Belton JM et al (2012) Hi-C: a comprehensive technique to capture the conformation of genomes. Methods 58(3):268–276CrossRefPubMed

75.

van Berkum NL et al (2010) Hi-C: a method to study the three-dimensional architecture of genomes. J Vis Exp 39

76.

Hirsch CN et al (2014) Insights into the maize pan-genome and pan-transcriptome. Plant Cell 26(1):121–135CrossRefPubMedPubMedCentral

77.

Lu F et al (2015) High-resolution genetic mapping of maize pan-genome sequence anchors. Nat Commun 6:6914CrossRefPubMedPubMedCentral

Titel: Advances in Sequencing and Resequencing in Crop Plants
verfasst von: Pradeep R. Marri
Liang Ye
Yi Jia
Ke Jiang
Steven D. Rounsley
Verlag: Springer International Publishing
Buch: Plant Genetics and Molecular Biology
Print ISBN: 978-3-319-91312-4

Electronic ISBN: 978-3-319-91313-1

Copyright-Jahr: 2018
DOI: https://doi.org/10.1007/10_2017_46

Premium Partner

Marktübersichten

Die im Laufe eines Jahres in der „adhäsion“ veröffentlichten Marktübersichten helfen Anwendern verschiedenster Branchen, sich einen gezielten Überblick über Lieferantenangebote zu verschaffen.

Zur Marktübersicht