Genomic and small RNA sequencing of Miscanthus × giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses

Genome Biology

Volumn 11, Issue 2, 2010, Pages

  Swaminathan, Kankshita ^a   Alabady, Magdy S ^a   Varala, Kranthi ^a   De Paoli, Emanuele ^b   Ho, Isaac ^c   Rokhsar, Dan S ^c,d   Arumuganathan, Aru K ^e   Ming, Ray ^a   Green, Pamela J ^b   Meyers, Blake C ^b   Moose, Stephen P ^a   Hudson, Matthew E ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF DELAWARE   (United States)

^c DOE JOINT GENOME INSTITUTE   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e BENAROYA RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; PLANT RNA;

ANDROPOGON; ARTICLE; CONTROLLED STUDY; GENE DOSAGE; GRASS; INFLORESCENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PLANT GENOME; PLANT LEAF; RHIZOME; RNA SEQUENCE; SORGHUM; TRANSPOSON; CENTROMERE; CLASSIFICATION; DUPLICATE GENE; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE REPEAT; PLANT CHROMOSOME; SEQUENCE ANALYSIS;

ANDROPOGONEAE; MISCANTHUS; POACEAE;

ANDROPOGON; BASE SEQUENCE; CENTROMERE; CHROMOSOMES, PLANT; DNA TRANSPOSABLE ELEMENTS; GENES, DUPLICATE; GENOME, PLANT; MOLECULAR SEQUENCE DATA; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA, PLANT; SEQUENCE ANALYSIS, RNA; SORGHUM;

EID: 77953225899     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2010-11-2-r12     Document Type: Article

References (57)

1. Brown RH. A difference in N use efficiency in C3 and C4 plants and its implications in adaptation and evolution. Crop Sci 1978, 18:93-98.
2. Beadle CL, Long SP. Photosynthesis - is it limiting to biomass production. Biomass 1985, 8:119-168.
3. Moore G, Devos KM, Wang Z, Gale MD. Cereal genome evolution: grasses, line up and form a circle. Curr Biol 1995, 5:737-739. 10.1016/S0960-9822(95)00148-5, 7583118.
4. Paterson AH, Freeling M, Sasaki T. Grains of knowledge: genomics of model cereals. Genome Res 2005, 15:1643-1650. 10.1101/gr.3725905, 16339361.
5. Bennetzen JL. Patterns in grass genome evolution. Curr Opin Plant Biol 2007, 10:176-181. 10.1016/j.pbi.2007.01.010, 17291821.
6. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, et al. The Sorghum bicolor genome and the diversification of the grasses. Nature 2009, 457:551-556. 10.1038/nature07723, 19189423.
7. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, et al. The B73 Maize genome: complexity, diversity and dynamics. Science 2009, 326:1112-1115. 10.1126/science.1178534, 19965430.
8. Vettore AL, da Silva FR, Kemper EL, Souza GM, da Silva AM, Ferro MI, Henrique-Silva F, Giglioti EA, Lemos MV, Coutinho LL, Nobrega MP, Carrer H, França SC, Bacci Júnior M, Goldman MH, Gomes SL, Nunes LR, Camargo LE, Siqueira WJ, Van Sluys MA, Thiemann OH, Kuramae EE, Santelli RV, Marino CL, Targon ML, Ferro JA, Silveira HC, Marini DC, Lemos EG, Monteiro-Vitorello CB, et al. Analysis and functional annotation of an expressed sequence tag collection from tropical crop sugarcane. Genome Res 2003, 13:2725-2735. 403815, 14613979, 10.1101/gr.1532103.
9. Hodkinson TR, Chase MW, Lledó MD, Salamin N, Renvoize SA. Phylogenetics of Miscanthus, Saccharum and related genera (Saccharinae, Andropogoneae, Poaceae) based on DNA sequences from ITS nuclear ribosomal DNA and plastid trnL intron and trnL-F intergenic spacers. J Plant Res 2002, 115:381-392. 10.1007/s10265-002-0049-3, 12579363.
10. Hodkinson TR, Chase MW, Renvoize SA. Characterization of a genetic resource collection for Miscanthus (Saccharinae, Andropogoneae, Poaceae ) using AFLP and ISSR PCR. Ann Bot 2002, 89:627-636. 10.1093/aob/mcf091, 12099538.
11. Hodkinson TR, Chase MW, Takahashi C, Leitch IJ, Bennet MD, Renvoize SA. The use of DNA sequencing (ITS and trnL-F), AFLP, and fluorescent in situ hybridization to study allopolyploid Miscanthus (Poaceae). Am J Bot 2002, 89:279-286.
12. Chen YH, Chen C, Lo CC. Studies on anatomy and morphology in Saccharum-Miscanthus nobilized hybrids: transmission of tillering, ratooning, adaptation and disease resistance from Miscanthus spp. J Agric Assoc China 1993, 164:31-45.
13. Greef JM, Deuter M. Syntaxonomy of Miscanthus × giganteus Greef et Deu. Angewandte Botanik 1993, 67:87-90.
14. Hodkinson TR, Renvoize SA. Nomenclature of Miscanthus giganteus (Poaceae). Kew Bulletin 2001, 56:759-760.
15. Clifton-Brown JC, Lewandowski I, Andersson B, Basch G, Christian DG, Kjeldsen JB, Jørgensen U, Mortensen JV, Riche AB, Schwarz K-U, Tayebi K, Texeira F. Performance of 15 Miscanthus genotypes at five sites in Europe. Agron J 2001, 93:1013-1019.
16. Heaton EA, Dohleman FG, Long SP. Meeting US biofuel goals with less land: the potential of Miscanthus. Global Change Biol 2008, 14:1-15.
17. Linde-Laursen IB. Cytogenetic analysis of Miscanthus 'Giganteus', an interspecific hybrid. Hereditas 1993, 119:297-300.
18. Lafferty J, Lelly T. Cytogenetic studies of different Miscanthus species with potential for agricultural use. Plant Breeding 1994, 113:246-249.
19. Beale CV, Long SP. Can perennial C4-grasses attain high efficiencies of radiant energy conversion in cool climates?. Plant Cell Environ 1995, 18:641-650.
20. Beale CV, Bint DA, Long SP. Leaf photosynthesis in the C4-grass Miscanthus × giganteus, growing in the cool temperate climate of southern England. J Exp Bot 1996, 47:267-273.
21. Naidu S, Al-Shoabi KA, Raines CA, Moose SP, Long SP. Cold-tolerant C4 photosynthesis in Miscanthus × giganteus. Plant Physiol 2003, 132:1688-1697. 167105, 12857847, 10.1104/pp.103.021790.
22. Wang D, Portis AR, Moose SP, Long SP. Cool C4 photosynthesis: Pyruvate Pi Dikinase expression and activity corresponds to the exceptional cold tolerance of carbon assimilation in Miscanthus × giganteus. Plant Physiol 2008, 148:557-567. 2528129, 18539777, 10.1104/pp.108.120709.
23. Swaminathan K, Varala K, Hudson ME. Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey. BMC Genomics 2007, 8:132. 1894642, 17524145, 10.1186/1471-2164-8-132.
24. Wicker T, Schlagenhauf E, Graner A, Close TJ, Keller B, Stein N. 454 sequencing put to the test using the complex genome of barley. BMC Genomics 2006, 7:275. 1633745, 17067373, 10.1186/1471-2164-7-275.
25. Quinn NL, Levenkova N, Chow W, Bouffard P, Boroevich KA, Knight JR, Jarvie TP, Lubieniecki KP, Desany BA, Koop BF, Harkins TT, Davidson WS. Assessing the feasibiality of GS FLX pyrosequencing for sequencing the Atlantic salmon genome. BMC Genomics 2008, 9:404. 2532694, 18755037, 10.1186/1471-2164-9-404.
26. Lu C, Singh Tej S, Luo S, Haudenschild C, Meyers BC, Green PJ. Elucidation of the small RNA component of the transcriptome. Science 2005, 309:1567-1569. 10.1126/science.1114112, 16141074.
27. Rayburn AL, Crawford J, Rayburn CM, Juvik JA. Genome size of three Miscanthus species. Plant Mol Biol Rep 2009, 27:184-188.
28. Bennett MD, Bhandol P, Leitch IJ. Nuclear DNA amounts in angiosperms and their modern uses - 807 new estimates. Ann Bot 2000, 86:859-909.
29. The Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815. 10.1038/35048692, 11130711, The Arabidopsis Genome Initiative.
30. Ouyang S, Buell CR. The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res 2004, 32:D360-363. 308833, 14681434, 10.1093/nar/gkh099.
31. Haberer G, Young S, Bharti AK, Gundlach H, Raymond C, Fuks G, Butler E, Wing RA, Rounsley S, Birren B, Nusbaum C, Mayer KF, Messing J. Structure and architecture of the maize genome. Plant Physiol 2005, 139:1612-1624. 1310546, 16339807, 10.1104/pp.105.068718.
32. International Rice Genome Sequencing Project The map-based sequence of the rice genome. Nature 2005, 436:793-800. 10.1038/nature03895, 16100779, International Rice Genome Sequencing Project.
33. Feschotte C, Jiang N, Wessler SR. Plant transposable elements: where genetics meets genomics. Nat Rev Genet 2002, 3:329-341. 10.1038/nrg793, 11988759.
34. Kim J, Klein PE, Klein RR, Price HJ, Mullet JE, Stelly DM. Chromosome identification and nomenclature of Sorghum bicolor. Genetics 2005, 169:1169-1173. 1449135, 15489512, 10.1534/genetics.104.035980.
35. Comparative Sequencing of Plant Small RNAs. , http://smallrna.udel.edu/project_data.php
36. Nobuta K, Lu C, Shrivastava R, Pillay M, De Paoli E, Accerbi M, Arteaga-Vazquez M, Sidorenko L, Jeong D-H, Yen Y, Green PJ, Chandler VL, Meyers BC. Distinct size distribution of endogenous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci USA 2008, 105:14958-14963. 2567475, 18815367, 10.1073/pnas.0808066105.
37. Stage DE, Eickbush TH. Sequence variation within the rRNA gene loci of 12 Drosophila species. Genome Res 2007, 17:1888-1897. 17989256, 10.1101/gr.6376807, 2099596.
38. Alvarez I, Wendel JW. Ribosomal ITS sequences and plant phylogenetic inference. Mol Phylogenet Evol 2003, 29:417-434. 10.1016/S1055-7903(03)00208-2, 14615184.
39. Baldwin BG. Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: An example from the Compositae. Mol Phylogenet Evol 1992, 1:3-16. 10.1016/1055-7903(92)90030-K, 1342921.
40. Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 2001, 17:754-755. 10.1093/bioinformatics/17.8.754, 11524383.
41. Ronquist F, Huelsenbeck JP. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574. 10.1093/bioinformatics/btg180, 12912839.
42. Hudson ME. Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol Ecol Res 2008, 8:3-17.
43. Feschotte C, Pritham EJ. DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet 2007, 41:331-369. 2167627, 18076328, 10.1146/annurev.genet.40.110405.090448.
44. Hillis DM, Moritz C, Porter CA, Baker RJ. Evidence for biased gene conversion in concerted evolution of ribosomal DNA. Science 1991, 251:308-310. 10.1126/science.1987647, 1987647.
45. Atienza SG, Satovic Z, Petersen KK, Dolstra O, Martin A. Preliminary genetic linkage map of Miscatnhus sinensis with RAPD markers. Theor Appl Genet 2002, 105:946-952. 10.1007/s00122-002-0956-7, 12582920.
46. Toth AL, Varala K, Newman TC, Miguez FE, Hutchison SK, Willoughby DA, Simons JF, Egholm M, Hunt JH, Hudson ME, Robinson GE. Wasp brain gene expression supports an evolutionary link between maternal behavior and eusociality. Science 2007, 318:441-444. 17901299, 10.1126/science.1146647.
47. Fu Y, Hsia AP, Guo L, Schnable PS. Types and frequencies of sequencing errors in methyl-filtered and high C0t maize genome survey sequences. Plant Physiol 2004, 135:2040-2045. 520775, 15299135, 10.1104/pp.104.041640.
48. Fu Y, Emrich SJ, Guo L, Wen TJ, Aluru S, Ashlock DA, Schnable PS. Quality assessment of maize assembled genomic islands (MAGIs) and experimental verification of predicted novel genes. Proc Natl Acad Sci USA 2005, 102:12282-12287. 1186025, 16103354, 10.1073/pnas.0503394102.
49. Bedell JA, Budiman MA, Nunberg A, Citek RW, Robbins D, Jones J, Flick E, Rholfing T, Fries J, Bradford K, McMenamy J, Smith M, Holeman H, Roe BA, Wiley G, Korf IF, Rabinowicz PD, Lakey N, McCombie WR, Jeddeloh JA, Martienssen RA. Sorghum genome sequencing by methylation filtration. PLoS Biol 2005, 3:e13. 539327, 15660154, 10.1371/journal.pbio.0030013.
50. Arumuganathan K, Earle ED. Estimation of nuclear DNA amounts of plants by flow cytometry. Plant Mol Biol Rep 1991, 9:229-241.
51. W.M. Keck Center for Comparative and Functional Genomics. , http://www.biotech.uiuc.edu/centers/Keck
52. Green P. Phrap, SWAT, CrossMatch 2008, University of Washington.
53. Kent WJ. BLAT - The BLAST-Like Alignment Tool. Genome Res 2002, 12:656-664. 187518, 11932250.
54. Schwartz S, Kent WJ, Smit A, Zhang Z, Beartsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res 2003, 13:103-107. 430961, 12529312, 10.1101/gr.809403.
55. Price JH, Dillon SL, Hodnett G, Rooney WL, Ross L, Johnston JS. Genome evolution in the genus Sorghum (Poaceae). Ann Bot 2005, 95:219-227. 10.1093/aob/mci015, 15596469.
56. Wu TD, Watanabe CK. GMAP: A genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 2005, 21:1859-1875. 10.1093/bioinformatics/bti310, 15728110.
57. Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R. Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics 2007, 8:460. 2216043, 18034891, 10.1186/1471-2105-8-460.