Optical mapping in plant comparative genomics

GigaScience

Volumn 4, Issue 1, 2015, Pages

  Tang, Haibao ^a,b   Lyons, Eric ^b   Town, Christopher D ^c  

^a FUJIAN AGRICULTURE AND FORESTRY UNIVERSITY   (China)

^b UNIVERSITY OF ARIZONA   (United States)

^c J CRAIG VENTER INSTITUTE   (United States)

Author keywords

Comparative genomics; De novo assembly; Optical mapping; Structural variation

Indexed keywords

COMPARATIVE STUDY; CONCEPTUAL FRAMEWORK; GENE FUNCTION; GENE IDENTIFICATION; GENE MAPPING; GENOME ANALYSIS; GENOMICS; HUMAN; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; NONHUMAN; OPTICAL MAPPING; PLANT COMPARATIVE GENOMICS; PLANT GENE; PLANT GENOME; PRIORITY JOURNAL; PROSPECTIVE STUDY; QUALITY CONTROL; REFERENCE DATABASE; REVIEW; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; CHROMOSOMAL MAPPING; DNA FINGERPRINTING; DNA SEQUENCE; GENETICS; PLANT; PLANT CHROMOSOME; PROCEDURES;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; DNA FINGERPRINTING; GENOME, PLANT; PLANTS; SEQUENCE ANALYSIS, DNA;

EID: 84936992187     PISSN: None     EISSN: 2047217X     Source Type: Journal    
DOI: 10.1186/s13742-015-0044-y     Document Type: Review

References (27)

1. Schwartz DC, Li X, Hernandez LI, Ramnarain SP, Huff EJ, Wang YK. Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 1993, 262:110-4. 10.1126/science.8211116, 8211116.
2. Lam ET, Hastie A, Lin C, Ehrlich D, Das SK, Austin MD, et al. Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat Biotechnol 2012, 30:771-6. 10.1038/nbt.2303, 22797562.
3. OpGen [http://www.opgen.com/].
4. BioNanoGenomics [http://www.bionanogenomics.com/].
5. Hall BG, Kirkup BC, Riley MC, Barlow M. Clustering acinetobacter strains by optical mapping. Genome Biol Evol 2013, 5:1176-84. 10.1093/gbe/evt085, 23739739.
6. Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, et al. Assembly and validation of the genome of the nonmodel basal angiosperm Amborella. Science 2013, 342:1516-7. 10.1126/science.1241130, 24357320.
7. Teague B, Waterman MS, Goldstein S, Potamousis K, Zhou S, Reslewic S, et al. High-resolution human genome structure by single-molecule analysis. Proc Natl Acad Sci U S A 2010, 107:10848-53. 10.1073/pnas.0914638107, 20534489.
8. Nagarajan N, Read TD, Pop M. Scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics 2008, 24:1229-35. 10.1093/bioinformatics/btn102, 18356192.
9. Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet 2006, 7:85-97. 10.1038/nrg1767, 16418744.
10. Schatz MC, Witkowski J, McCombie WR. Current challenges in de novo plant genome sequencing and assembly. Genome Biol 2012, 13:243. 10.1186/gb-2012-13-4-243, 22546054.
11. Tang H, Krishnakumar V, Bidwell S, Rosen B, Chan A, Zhou S, et al. An improved genome release (version Mt4.0) for the model legume Medicago truncatula. BMC Genomics 2014, 15:312. 10.1186/1471-2164-15-312, 24767513.
12. Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, Goldstein S, et al. A single molecule scaffold for the maize genome. PLoS Genet 2009, 5:e1000711. 10.1371/journal.pgen.1000711, 19936062.
13. Lin HC, Goldstein S, Mendelowitz L, Zhou S, Wetzel J, Schwartz DC, et al. AGORA: assembly guided by optical restriction alignment. BMC Bioinformatics 2012, 13:189. 10.1186/1471-2105-13-189, 22856673.
14. Valouev A, Schwartz DC, Zhou S, Waterman MS. An algorithm for assembly of ordered restriction maps from single DNA molecules. Proc Natl Acad Sci U S A 2006, 103:15770-5. 10.1073/pnas.0604040103, 17043225.
15. Muggli M, Puglisi S, Boucher C. Efficient indexed alignment of contigs to optical maps. Algorithms in Bioinformatics 2014, 68-81. Springer International Publishing, Berlin-Heidelberg, Brown D, Morgenstern B, 10.1007/978-3-662-44753-6_6.
16. Sarkar D, Goldstein S, Schwartz DC, Newton MA. Statistical significance of optical map alignments. J Comput Biol 2012, 19:478-92. 10.1089/cmb.2011.0221, 22506568.
17. Zhou S, Bechner MC, Place M, Churas CP, Pape L, Leong SA, et al. Validation of rice genome sequence by optical mapping. BMC Genomics 2007, 8:278. 10.1186/1471-2164-8-278, 17697381.
18. Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, et al. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice (N Y) 2013, 6:4.
19. Zhang Q, Chen W, Sun L, Zhao F, Huang B, Yang W, et al. The genome of Prunus mume. Nat Commun 2012, 3:1318. 10.1038/ncomms2290, 23271652.
20. Shearer LA, Anderson LK, de Jong H, Smit S, Goicoechea JL, Roe BA, et al. Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome. G3 (Bethesda) 2014, 4:1395-405. 10.1534/g3.114.011197.
21. Hastie AR, Dong L, Smith A, Finklestein J, Lam ET, Huo N, et al. Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome. PLoS One 2013, 8:e55864. 10.1371/journal.pone.0055864, 23405223.
22. Young ND, Debelle F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 2011, 480:520-4. 10.1038/480162a, 22089132.
23. Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, Platzer A, et al. Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet 2013, 45:884-90. 10.1038/ng.2678, 23793030.
24. Zhang QJ, Zhu T, Xia EH, Shi C, Liu YL, Zhang Y, et al. Rapid diversification of five Oryza AA genomes associated with rice adaptation. Proc Natl Acad Sci U S A 2014, 111:E4954-62. 10.1073/pnas.1418307111, 25368197.
25. Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E. A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 2008, 319:1527-30. 10.1126/science.1153040, 18339939.
26. Chia JM, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, et al. Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet 2012, 44:803-7. 10.1038/ng.2313, 22660545.
27. Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 2014, 345:950-3. 10.1126/science.1253435, 25146293.