Review
doi: 10.1186/gb4015.Current challenges in de novo plant genome sequencing and assembly
Affiliations
- PMID:22546054
- PMCID: PMC3446297
- DOI: 10.1186/gb4015
Item in Clipboard
Review
Current challenges in de novo plant genome sequencing and assembly
Michael C Schatz et al. Genome Biol.2012.
Display options
Format
Display options
Format
Abstract
Genome sequencing is now affordable, but assembling plant genomes de novo remains challenging. We assess the state of the art of assembly and review the best practices for the community.
Figures
Schematic overview of genome assembly.(a)DNA is collected from the biological sample and sequenced.(b)The output from the sequencer consists of many billions of short, unordered DNA fragments from random positions in the genome.(c)The short fragments are compared with each other to discover how they overlap.(d)The overlap relationships are captured in a large assembly graph shown as nodes representing kmers or reads, with edges drawn between overlapping kmers or reads.(e)The assembly graph is refined to correct errors and simplify into the initial set of contigs, shown as large ovals connected by edges.(f)Finally, mates, markers and other long-range information are used to order and orient the initial contigs into large scaffolds, as shown as thin black lines connecting the initial contigs.
Ploidy, heterozygosity and the assembly graph.(a)Schematic representation of a tetraploid genome, such as apple, cotton or cabbage, consisting of haploid chromosomes A to D with homozygosity/heterozygosity shown as different colored blocks.(b)Even without repeats or sequencing error, the assembly graph of the homozygous and heterozygous segments of the genome branch and intertwine in complex patterns. A plant-specific assembler would need to recognize these branching patterns and attempt to reconstruct the individual sequences for chromosomes A to D.
Similar articles
- De novo sequencing of plant genomes using second-generation technologies.Imelfort M, Edwards D.Imelfort M, et al.Brief Bioinform. 2009 Nov;10(6):609-18. doi: 10.1093/bib/bbp039.Brief Bioinform. 2009.PMID:19933209Review.
- Sequencing and Assembling Genomes and Chromosomes of Cereal Crops.Helguera M.Helguera M.Methods Mol Biol. 2020;2072:27-37. doi: 10.1007/978-1-4939-9865-4_4.Methods Mol Biol. 2020.PMID:31541436
- Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy.González VM, Benjak A, Hénaff EM, Mir G, Casacuberta JM, Garcia-Mas J, Puigdomènech P.González VM, et al.BMC Plant Biol. 2010 Nov 12;10:246. doi: 10.1186/1471-2229-10-246.BMC Plant Biol. 2010.PMID:21073723Free PMC article.
- Enrichment of gene-coding sequences in maize by genome filtration.Whitelaw CA, Barbazuk WB, Pertea G, Chan AP, Cheung F, Lee Y, Zheng L, van Heeringen S, Karamycheva S, Bennetzen JL, SanMiguel P, Lakey N, Bedell J, Yuan Y, Budiman MA, Resnick A, Van Aken S, Utterback T, Riedmuller S, Williams M, Feldblyum T, Schubert K, Beachy R, Fraser CM, Quackenbush J.Whitelaw CA, et al.Science. 2003 Dec 19;302(5653):2118-20. doi: 10.1126/science.1090047.Science. 2003.PMID:14684821
- Advances in plant genome sequencing.Hamilton JP, Buell CR.Hamilton JP, et al.Plant J. 2012 Apr;70(1):177-90. doi: 10.1111/j.1365-313X.2012.04894.x.Plant J. 2012.PMID:22449051Review.
Cited by
- Benchmarking variant identification tools for plant diversity discovery.Wu X, Heffelfinger C, Zhao H, Dellaporta SL.Wu X, et al.BMC Genomics. 2019 Sep 9;20(1):701. doi: 10.1186/s12864-019-6057-7.BMC Genomics. 2019.PMID:31500583Free PMC article.
- EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics.Nunn A, Can SN, Otto C, Fasold M, Díez Rodríguez B, Fernández-Pozo N, Rensing SA, Stadler PF, Langenberger D.Nunn A, et al.NAR Genom Bioinform. 2021 Nov 12;3(4):lqab106. doi: 10.1093/nargab/lqab106. eCollection 2021 Dec.NAR Genom Bioinform. 2021.PMID:34805989Free PMC article.
- Applications of Optical Mapping for Plant Genome Assembly and Structural Variation Detection.Yuan Y.Yuan Y.Methods Mol Biol. 2022;2443:245-257. doi: 10.1007/978-1-0716-2067-0_13.Methods Mol Biol. 2022.PMID:35037210
- Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef).Cannarozzi G, Plaza-Wüthrich S, Esfeld K, Larti S, Wilson YS, Girma D, de Castro E, Chanyalew S, Blösch R, Farinelli L, Lyons E, Schneider M, Falquet L, Kuhlemeier C, Assefa K, Tadele Z.Cannarozzi G, et al.BMC Genomics. 2014 Jul 9;15(1):581. doi: 10.1186/1471-2164-15-581.BMC Genomics. 2014.PMID:25007843Free PMC article.
- Next Generation Sequencing Technologies: The Doorway to the Unexplored Genomics of Non-Model Plants.Unamba CI, Nag A, Sharma RK.Unamba CI, et al.Front Plant Sci. 2015 Dec 16;6:1074. doi: 10.3389/fpls.2015.01074. eCollection 2015.Front Plant Sci. 2015.PMID:26734016Free PMC article.Review.
References
- United Nations Food and Agriculture Organization. Dimensions of Need - An atlas of food and agriculture. Staple foods: What do people eat.http://www.fao.org/docrep/u8480e/u8480e07.htm
- Falkowski P, Scholes RJ, Boyle E, Canadell J, Canfield D, Elser J, Gruber N, Hibbard K, Högberg P, Linder S, Mackenzie FT, Moore B, Pedersen T, Rosenthal Y, Seitzinger S, Smetacek V, Steffen W. The global carbon cycle: a test of our knowledge of earth as a system. Science. 2000;290:291–296. doi: 10.1126/science.290.5490.291. - DOI - PubMed
- Fairley P. Introduction: Next generation biofuels. Nature. 2011;474:S2–5. - PubMed
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources