Building a model: Developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Straub, Shannon C K ^a   Fishbein, Mark ^b   Livshultz, Tatyana ^c   Foster, Zachary ^a   Parks, Matthew ^a   Weitemier, Kevin ^a   Cronn, Richard C ^d   Liston, Aaron ^a  

^a OREGON STATE UNIVERSITY   (United States)

^b OKLAHOMA STATE UNIVERSITY   (United States)

^c ACADEMY OF NATURAL SCIENCES OF DREXEL UNIVERSITY   (United States)

^d PACIFIC NORTHWEST RESEARCH STATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA; PLANT DNA;

ACCD GENE; ARTICLE; ASCLEPIAS; ASCLEPIAS SYRIACA; CHLOROPLAST; CISTRON; CLPP GENE; CONTROLLED STUDY; DNA POLYMORPHISM; ECOLOGY; EXPRESSED SEQUENCE TAG; GENE MAPPING; GENE SEQUENCE; GENETIC MODEL; GENETIC POLYMORPHISM; MICROSATELLITE MARKER; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT GENE; PLANT GENOME; POPULATION GENETICS; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES COMPARISON; TOBACCO; YCF1 GENE; CELL ORGANELLE; CYTOLOGY; DNA SEQUENCE; ENVIRONMENTAL ASPECTS AND RELATED PHENOMENA; GENETICS; GENOMICS; METHODOLOGY; NUCLEOTIDE REPEAT; OPEN READING FRAME;

APOCYNACEAE; ASCLEPIAS; ASCLEPIAS SYRIACA; ASTERIDS; CATHARANTHUS ROSEUS; HEXAPODA; NICOTIANA TABACUM;

ASCLEPIAS; DNA, PLANT; DNA, RIBOSOMAL; ECOLOGICAL AND ENVIRONMENTAL PROCESSES; EVOLUTION, MOLECULAR; GENOME, PLANT; GENOMICS; OPEN READING FRAMES; ORGANELLES; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA;

EID: 79955505877     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-211     Document Type: Article

References (108)

1. Rokas A, Abbot P. Harnessing genomics for evolutionary insights. Trends Ecol Evol 2009, 24(4):192-200. 10.1016/j.tree.2008.11.004, 19201503.
2. Hudson ME. Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol Ecol Resour 2008, 8(1):3-17. 10.1111/j.1471-8286.2007.02019.x, 21585713.
3. Ekblom R, Galindo J. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity
4. Rasmussen DA, Noor MAF. What can you do with 0.1× genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae). BMC Genomics 2009, 10:382. 10.1186/1471-2164-10-382, 2735751, 19689807.
5. Lee RM, Thimmapuram J, Thinglum KA, Gong G, Hernandez AG, Wright CL, Kim RW, Mikel MA, Tranel PJ. Sampling the Waterhemp (Amaranthus tuberculatus) genome using pyrosequencing technology. Weed Sci 2009, 57(5):463-469.
6. Swaminathan K, Alabady MS, Varala K, De Paoli E, Ho I, Rokhsar DS, Arumuganathan AK, Ming R, Green PJ, Meyers BC, et al. Genomic and small RNA sequencing of Miscanthus × giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses. Genome Biol 2010, 11(2):R12. 10.1186/gb-2010-11-2-r12, 2872872, 20128909.
7. Hribova E, Neumann P, Matsumoto T, Roux N, Macas J, Dolezel J. Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing. BMC Plant Biol 2010, 10:204. 10.1186/1471-2229-10-204, 2956553, 20846365.
8. Macas J, Neumann P, Navratilova A. Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genomics 2007, 8:427. 10.1186/1471-2164-8-427, 2206039, 18031571.
9. Webb KM, Rosenthal BM. Next-generation sequencing of the Trichinella murrelli mitochondrial genome allows comprehensive comparison of its divergence from the principal agent of human trichinellosis, Trichinella spiralis. Infect Genet Evol 2011, 11(1):116-123. 10.1016/j.meegid.2010.10.001, 20946970.
10. Willerslev E, Gilbert MT, Binladen J, Ho S, Campos P, Ratan A, Tomsho L, da Fonseca R, Sher A, Kuznetsova T, et al. Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. BMC Evol Biol 2009, 9(1):95.. 10.1186/1471-2148-9-95, 2694787, 19432984.
11. Dempewolf H, Kane NC, Ostevik KL, Geleta M, Barker MS, Lai Z, Stewart ML, Bekele E, Engels JMM, Cronk QCB, et al. Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass.--the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome. Mol Ecol Resour 2010, 10(6):1048-1058. 10.1111/j.1755-0998.2010.02859.x, 21565115.
12. Meyers S, Liston A. Characterizing the genome of wild relatives of Limnanthes alba (Meadowfoam) using massively parallel sequencing. Acta Horticulturae 2010, 859:309-314.
13. Nock CJ, Waters DL, Edwards MA, Bowen SG, Rice N, Cordeiro GM, Henry RJ. Chloroplast genome sequences from total DNA for plant identification. Plant Biotechnol J 2011, 9:328-333. 10.1111/j.1467-7652.2010.00558.x, 20796245.
14. Givnish TJ, Ames M, McNeal JR, McKain MR, Steele PR, dePamphilis CW, Graham SW, Pires JC, Stevenson DW, Zomlefer WB, et al. Assembling the tree of the monocotyledons: plastome sequence phylogeny and evolution of Poales 1. Ann Mo Bot Gard 2010, 97(4):584-616.
15. Castoe TA, Poole AW, Gu WJ, de Koning APJ, Daza JM, Smith EN, Pollock DD. Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Mol Ecol Resour 2010, 10(2):341-347. 10.1111/j.1755-0998.2009.02750.x, 21565030.
16. Abdelkrim J, Robertson BC, Stanton JAL, Gemmell NJ. Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. Biotechniques 2009, 46(3):185-192. 10.2144/000113084, 19317661.
17. Moore MJ, Soltis PS, Bell CD, Burleigh JG, Soltis DE. Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proc Natl Acad Sci USA 2010, 107(10):4623-4628. 10.1073/pnas.0907801107, 2842043, 20176954.
18. Bai X, Zhang W, Orantes L, Jun T-H, Mittapalli O, Mian MAR, Michel AP. Combining next-generation sequencing strategies for rapid molecular resource development from an invasive aphid species, Aphis glycines. PLoS ONE 2010, 5(6):e11370.. 2894077, 20614011.
19. Rasmann S, Agrawal AA, Cook SC, Erwin AC. Cardenolides, induced responses, and interactions between above- and belowground herbivores of milkweed (Asclepias spp.). Ecology 2009, 90(9):2393-2404. 10.1890/08-1895.1, 19769118.
20. Broyles SB. Hybrid bridges to gene flow: A case study in milkweeds (Asclepias). Evolution 2002, 56(10):1943-1953.
21. Wyatt R, Broyles SB. Ecology and evolution of reproduction in milkweeds. Annu Rev Ecol Syst 1994, 25:423-441.
22. Fishbein M, Venable DL. Evolution of inflorescence design: Theory and data. Evolution 1996, 50(6):2165-2177.
23. Agrawal AA, Fishbein M. Phylogenetic escalation and decline of plant defense strategies. Proc Natl Acad Sci USA 2008, 105(29):10057-10060. 10.1073/pnas.0802368105, 2481309, 18645183.
24. Agrawal AA, Fishbein M. Plant defense syndromes. Ecology 2006, 87(7):S132-S149. 10.1890/0012-9658(2006)87[132:PDS]2.0.CO;2, 16922309.
25. Malcolm SB. Cardenolide-mediated interactions between plants and herbivores. Herbivores: their interactions with secondary plant metabolites Volume I: The chemical participants 1991, 251-296. San Diego: Academic Press, Rosenthal GA, Berenbaum MR, 2.
26. Murata J, Bienzle D, Brandle JE, Sensen CW, De Luca V. Expressed sequence tags from Madagascar periwinkle (Catharanthus roseus). FEBS Lett 2006, 580(18):4501-4507. 10.1016/j.febslet.2006.07.020, 16870181.
27. Murata J, Roepke J, Gordon H, De Luca V. The leaf epidermome of Catharanthus roseus reveals its biochemical specialization. Plant Cell 2008, 20(3):524-542. 10.1105/tpc.107.056630, 2329939, 18326827.
28. Shukla AK, Shasany AK, Gupta MM, Khanuja SPS. Transcriptome analysis in Catharanthus roseus leaves and roots for comparative terpenoid indole alkaloid profiles. J Exp Bot 2006, 57(14):3921-3932. 10.1093/jxb/erl146, 17050644.
29. Abzhanov A, Extavour CG, Groover A, Hodges SA, Hoekstra HE, Kramer EM, Monteiro A. Are we there yet? Tracking the development of new model systems. Trends in Genet 2008, 24(7):353-360.
30. Dolezel J, Bartos J, Voglmayr H, Greilhuber J. Nuclear DNA content and genome size of trout and human. Cytom Part A 2003, 51A(2):127-128.
31. Solexa, Inc Protocol for Whole Genome Sequencing using Solexa Technology. BioTechniques Protocol Guide 2007 2006, 291. New York: BioTechniques, Solexa, Inc.
32. Ratan A. Assembly algorithms for next-generation sequence data. PhD thesis 2009, The Pennsylvania State University, Computer Science and Engineering.
33. Delcher AL, Phillippy A, Carlton J, Salzberg SL. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 2002, 30(11):2478-2483. 10.1093/nar/30.11.2478, 117189, 12034836.
34. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol 2004, 5(2):R12.. 395750, 14759262.
35. Ovcharenko I, Loots GG, Giardine BM, Hou MM, Ma J, Hardison RC, Stubbs L, Miller W. Mulan: Multiple-sequence local alignment and visualization for studying function and evolution. Genome Res 2005, 15(1):184-194. 10.1101/gr.3007205, 540288, 15590941.
36. Katoh K, Kuma K, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 2005, 33(2):511-518. 10.1093/nar/gki198, 548345, 15661851.
37. Wyman SK, Jansen RK, Boore JL. Automatic annotation of organellar genomes with DOGMA. Bioinformatics 2004, 20(17):3252-3255. 10.1093/bioinformatics/bth352, 15180927.
38. Milne I, Bayer M, Cardle L, Shaw P, Stephen G, Wright F, Marshall D. Tablet--next generation sequence assembly visualization. Bioinformatics 2010, 26(3):401-402. 10.1093/bioinformatics/btp666, 2815658, 19965881.
39. Zerbino D, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821-829. 10.1101/gr.074492.107, 2336801, 18349386.
40. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999, 41:95-98.
41. Conant GC, Wolfe KH. GenomeVx: simple web-based creation of editable circular chromosome maps. Bioinformatics 2008, 24(6):861-862. 10.1093/bioinformatics/btm598, 18227121.
42. Sugiyama Y, Watase Y, Nagase M, Makita N, Yagura S, Hirai A, Sugiura M. The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants. Mol Genet Genomics 2005, 272(6):603-615. 10.1007/s00438-004-1075-8, 15583938.
43. Alverson AJ, Wei XX, Rice DW, Stern DB, Barry K, Palmer JD. Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Mol Biol Evol 2010, 27(6):1436-1448. 10.1093/molbev/msq029, 2877997, 20118192.
44. Kent WJ. BLAT - The BLAST-like alignment tool. Genome Res 2002, 12(4):656-664. 187518, 11932250.
45. Knaus B. Short read toolbox. , http://brianknaus.com
46. Gordon A. FASTX-Toolkit. , http://hannonlab.cshl.edu/fastx_toolkit/index.html
47. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
48. Nguyen P, Ma J, Pei D, Obert C, Cheng C, Geiger T. Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire. BMC Genomics 2011, 12(1):106.. 10.1186/1471-2164-12-106, 3045962, 21310087.
49. Gladman S, Seeman T. VelvetOptimiser version 2.1.7. , http://bioinformatics.net.au/software.velvetoptimiser.shtml
50. Cantarel BL, Korf I, Robb SMC, Parra G, Ross E, Moore B, Holt C, Alvarado AS, Yandell M. MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res 2008, 18(1):188-196. 2134774, 18025269.
51. Smit A, Hubley R, Green P. RepeatMasker Open-3.0. , http://www.repeatmasker.org
52. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 2005, 110(1-4):462-467. 10.1159/000084979, 16093699.
53. You FM, Huo NX, Gu YQ, Luo MC, Ma YQ, Hane D, Lazo GR, Dvorak J, Anderson OD. BatchPrimer3: A high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 2008, 9:253. 10.1186/1471-2105-9-253, 2438325, 18510760.
54. He J, Dai XB, Zhao XC. PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results. BMC Bioinformatics 2007, 8:53. 10.1186/1471-2105-8-53, 1800871, 17291345.
55. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
56. Hood GM. PopTools version 3.2.3. , http://www.poptools.org
57. Wu F, Mueller LA, Crouzillat D, Petiard V, Tanksley SD. Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics 2006, 174(3):1407-1420. 10.1534/genetics.106.062455, 1667096, 16951058.
58. Livshultz T, Middleton DJ, Endress ME, Williams JK. Phylogeny of Apocynoideae and the APSA clade (Apocynaceae s.l.). Ann Mo Bot Gard 2007, 94(2):324-359.
59. Angiosperm DNA C-values Database (Release 6.0, Oct. 2005). , http://www.kew.org/cvalues
60. Meve U. Species numbers and progress in Asclepiad taxonomy. Kew Bull 2002, 57(2):459-464.
61. Ravi V, Khurana JP, Tyagi AK, Khurana P. An update on chloroplast genomes. Plant Syst Evol 2008, 271(1-2):101-122.
62. Samson N, Bausher MG, Lee SB, Jansen RK, Daniell H. The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms. Plant Biotechnol J 2007, 5(2):339-353. 10.1111/j.1467-7652.2007.00245.x, 17309688.
63. Jansen RK, Wojciechowski MF, Sanniyasi E, Lee SB, Daniell H. Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae). Mol Phylogenet Evol 2008, 48(3):1204-1217. 10.1016/j.ympev.2008.06.013, 2586962, 18638561.
64. Lee HL, Jansen RK, Chumley TW, Kim KJ. Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Mol Biol Evol 2007, 24(5):1161-1180. 10.1093/molbev/msm036, 17329229.
65. Guisinger MM, Chumley TW, Kuehl JV, Boore JL, Jansen RK. Implications of the plastid genome sequence of Typha (Typhaceae, Poales) for understanding genome evolution in Poaceae. J Mol Evol 2010, 70(2):149-166.
66. Greiner S, Wang X, Rauwolf U, Silber MV, Mayer K, Meurer J, Haberer G, Herrmann RG. The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera, subsection Oenothera: I. Sequence evaluation and plastome evolution. Nucleic Acids Res 2008, 36(7):2366-2378. 10.1093/nar/gkn081, 2367718, 18299283.
67. Guisinger MM, Kuehl JV, Boore JL, Jansen RK. Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: Rearrangements, repeats, and codon usage. Mol Biol Evol 2011, 28(1):583-600. 10.1093/molbev/msq229, 20805190.
68. Jansen RK, Cai Z, Raubeson LA, Daniell H, dePamphilis CW, Leebens-Mack J, Müller KF, Guisinger-Bellian M, Haberle RC, Hansen AK, et al. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci USA 2007, 104(49):19369-19374. 10.1073/pnas.0709121104, 2148296, 18048330.
69. Haberle RC, Fourcade HM, Boore JL, Jansen RK. Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes. J Mol Evol 2008, 66(4):350-361. 10.1007/s00239-008-9086-4, 18330485.
70. Jo Y, Park J, Kim J, Song W, Hur C-G, Lee Y-H, Kang B-C. Complete sequencing and comparative analyses of the pepper (Capsicum annuum L.) plastome revealed high frequency of tandem repeats and large insertion/deletions on pepper plastome. Plant Cell Rep 2010, 1-13.
71. Cai ZQ, Guisinger M, Kim HG, Ruck E, Blazier JC, McMurtry V, Kuehl JV, Boore J, Jansen RK. Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions. J Mol Evol 2008, 67(6):696-704. 10.1007/s00239-008-9180-7, 19018585.
72. Arthofer W, Schuler S, Steiner FM, Schlick-Steiner BC. Chloroplast DNA-based studies in molecular ecology may be compromised by nuclear-encoded plastid sequence. Mol Ecol 2010, 19(18):3853-3856. 10.1111/j.1365-294X.2010.04787.x, 20735742.
73. Parks M, Cronn R, Liston A. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biology 2009, 7:84. 10.1186/1741-7007-7-84, 2793254, 19954512.
74. Neubig K, Whitten W, Carlsward B, Blanco M, Endara L, Williams N, Moore M. Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK. Plant Syst Evol 2009, 277(1):75-84.
75. Kuroda H, Maliga P. The plastid clpP1 protease gene is essential for plant development. Nature 2003, 425(6953):86-89. 10.1038/nature01909, 12955146.
76. Drescher A, Ruf S, Calsa T, Carrer H, Bock R. The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes. Plant J 2000, 22(2):97-104. 10.1046/j.1365-313x.2000.00722.x, 10792825.
77. Kode V, Mudd EA, Iamtham S, Day A. The tobacco plastid accD gene is essential and is required for leaf development. Plant J 2005, 44(2):237-244. 10.1111/j.1365-313X.2005.02533.x, 16212603.
78. Konishi T, Shinohara K, Yamada K, Sasaki Y. Acetyl-CoA carboxylase in higher plants: Most plants other than Gramineae have both the prokaryotic and the eukaryotic forms of this enzyme. Plant Cell Physiol 1996, 37(2):117-122.
79. Gornicki P, Faris J, King I, Podkowinski J, Gill B, Haselkorn R. Plastid-localized acetyl-CoA carboxylase of bread wheat is encoded by a single gene on each of the three ancestral chromosome sets. Proc Natl Acad Sci USA 1997, 94(25):14179-14184. 10.1073/pnas.94.25.14179, 28453, 9391173.
80. Kubo T, Mikami T. Organization and variation of angiosperm mitochondrial genome. Physiol Plant 2007, 129(1):6-13.
81. Knoop V. The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective. Curr Genet 2004, 46(3):123-139.
82. Sanchez-Puerta MV, Cho Y, Mower JP, Alverson AJ, Palmer JD. Frequent, phylogenetically local horizontal transfer of the cox1 group I intron in flowering plant mitochondria. Mol Biol Evol 2008, 25(8):1762-1777. 10.1093/molbev/msn129, 2727383, 18524785.
83. Cusimano N, Zhang L-B, Renner SS. Reevaluation of the cox1 group I intron in Araceae and angiosperms indicates a history dominated by loss rather than horizontal transfer. Mol Biol Evol 2008, 25(2):265-276. 10.1093/molbev/msm241, 18158323.
84. Bennetzen JL. The contributions of retroelements to plant genome organization, function and evolution. Trends Microbiol 1996, 4(9):347-353. 10.1016/0966-842X(96)10042-1, 8885169.
85. Kumar A, Bennetzen JL. Plant retrotransposons. Annu Rev Genet 1999, 33:479-532. 10.1146/annurev.genet.33.1.479, 10690416.
86. Vitte C, Bennetzen JL. Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution. Proc Natl Acad Sci 2006, 103(47):17638-17643. 10.1073/pnas.0605618103, 1693799, 17101966.
87. Vitte C, Panaud O. LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model. Cytogenet Genome Res 2005, 110(1-4):91-107. 10.1159/000084941, 16093661.
88. Cavagnaro P, Chung S-M, Szklarczyk M, Grzebelus D, Senalik D, Atkins A, Simon P. Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences. Mol Genet Genomics 2009, 281(3):273-288. 10.1007/s00438-008-0411-9, 19104839.
89. Cavallini A, Natali L, Zuccolo A, Giordani T, Jurman I, Ferrillo V, Vitacolonna N, Sarri V, Cattonaro F, Ceccarelli M, et al. Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome. Theor Appl Genet 2010, 120(3):491-508. 10.1007/s00122-009-1170-7, 19826774.
90. Datema E, Mueller L, Buels R, Giovannoni J, Visser R, Stiekema W, van Ham R. Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato. BMC Plant Biol 2008, 8(1):34.. 10.1186/1471-2229-8-34, 2324086, 18405374.
91. Whiteford N, Haslam N, Weber G, Prugel-Bennett A, Essex J, Roach P, Bradley M, Neylon C. An analysis of the feasibility of short read sequencing. Nucl Acids Res 2005, 33(19):e171.. 1278949, 16275781.
92. Rogers SO, Bendich AJ. Ribosomal-RNA genes in plants - Variability in copy number and in the intergenic spacer. Plant Mol Biol 1987, 9(5):509-520.
93. Sastri DC, Hilu K, Appels R, Lagudah ES, Playford J, Baum BR. An overview of evolution in plant 5S DNA. Plant Syst Evol 1992, 183(3):169-181.
94. Hillis DM, Dixon MT. Ribosomal DNA: Molecular evolution and phylogenetic inference. Q Rev Biol 1991, 66(4):411-453. 10.1086/417338, 1784710.
95. Volkov R, Kostishin S, Ehrendorfer E, Schweizer D. Molecular organization and evolution of the external transcribed rDNA spacer region in two diploid relatives of Nicotiana tabacum (Solanaceae). Plant Syst Evol 1996, 201(1-4):117-129.
96. Borisjuk NV, Davidjuk YM, Kostishin SS, Miroshnichenco GP, Velasco R, Hemleben V, Volkov RA. Structural analysis of rDNA in the genus Nicotiana. Plant Mol Biol 1997, 35(5):655-660. 10.1023/A:1005856618898, 9349286.
97. Bena G, Jubier M-F, Olivieri I, Lejeune B. Ribosomal external and internal transcribed spacers: Combined use in the phylogenetic analysis of Medicago (Leguminosae). J Mol Evol 1998, 46(3):299-306. 10.1007/PL00006306, 9502673.
98. Volkov RA, Komarova NY, Panchuk II, Hemleben V. Molecular evolution of rDNA external transcribed spacer and phylogeny of sect. Petota (genus Solanum). Mol Phylogenet Evol 2003, 29(2):187-202. 10.1016/S1055-7903(03)00092-7, 13678676.
99. Maggini F, Gelati MT, Spolverini M, Frediani M. The intergenic spacer region of the rDNA in Olea europaea L. Tree Genet Genom 2008, 4(2):293-298.
100. Cronn RC, Zhao XP, Paterson AH, Wendel JF. Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons. J Mol Evol 1996, 42(6):685-705. 10.1007/BF02338802, 8662014.
101. Fujiwara M, Inafuku J, Takeda A, Watanabe A, Fujiwara A, Kohno S, Kubota S. Molecular organization of 5S rDNA in bitterlings (Cyprinidae). Genetica 2009, 135(3):355-365. 10.1007/s10709-008-9294-2, 18648989.
102. Saini A, Jawali N. Molecular evolution of 5S rDNA region in Vigna subgenus Ceratotropis and its phylogenetic implications. Plant Syst Evol 2009, 280(3-4):187-206.
103. Stage DE, Eickbush TH. Sequence variation within the rRNA gene loci of 12 Drosophila species. Genome Res 2007, 17(12):000..
104. Ganley ARD, Kobayashi T. Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data. Genome Res 2007, 17(2):184-191. 10.1101/gr.5457707, 1781350, 17200233.
105. Kolosha VO, Fodor I. Nucleotide sequence of Citrus limon 26S ribosomal-RNA gene and secondary structure model of its RNA. Plant Mol Biol 1990, 14(2):147-161. 10.1007/BF00018556, 2101688.
106. Nei M, Rooney AP. Concerted and birth-and-death evolution of multigene families*. Annu Rev Genet 2005, 39(1):121-152. 10.1146/annurev.genet.39.073003.112240, 1464479, 16285855.
107. Baxter I, Tchieu J, Sussman MR, Boutry M, Palmgren MG, Gribskov M, Harper JF, Axelsen KB. Genomic comparison of P-Type ATPase ion pumps in Arabidopsis and Rice. Plant Physiol 2003, 132(2):618-628. 10.1104/pp.103.021923, 167002, 12805592.
108. Thomson RC, Wang IJ, Johnson JR. Genome-enabled development of DNA markers for ecology, evolution and conservation. Mol Ecol 2010, 19(11):2184-2195. 10.1111/j.1365-294X.2010.04650.x, 20465588.