The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color

Genome Biology

Volumn 14, Issue 6, 2013, Pages

  Motamayor, Juan C ^a   Mockaitis, Keithanne ^b   Schmutz, Jeremy ^a,c   Haiminen, Niina ^d   Livingstone, Donald ^a,e   Cornejo, Omar ^f   Findley, Seth D ^a   Zheng, Ping ^g   Utro, Filippo ^d   Royaert, Stefan ^e   Saski, Christopher ^h   Jenkins, Jerry ^a,c   Podicheti, Ram ^b   Zhao, Meixia ⁱ   Scheffler, Brian E ^j   Stack, Joseph C ^a   Feltus, Frank A ^h   Mustiga, Guiliana M ^a   Amores, Freddy ^k   Phillips, Wilbert ^l   Marelli, Jean P ^m   May, Gregory D ⁿ   Shapiro, Howard ^a   Ma, Jianxin ⁱ   Bustamante, Carlos D ^f   Schnell, Raymond J ^a,e   Main, Dorrie ^g   Gilbert, Don ^b   Parida, Laxmi ^d   Kuhn, David N ^e   more..

^a MARS INC   (United States)

^b INDIANA UNIVERSITY   (United States)

^c HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

^d IBM T J WATSON RESEARCH CENTER   (United States)

^e USDAARS Subtropical Horticulture Research Station   (United States)

^f STANFORD UNIVERSITY   (United States)

^g WASHINGTON STATE UNIVERSITY   (United States)

^h CLEMSON UNIVERSITY   (United States)

ⁱ PURDUE UNIVERSITY   (United States)

^j AGRICULTURAL RESEARCH SERVICE   (United States)

^k Instituto Nacional Autónomo de Investigaciones Agropecuarias INIAP   (Ecuador)

^l CATIE   (Costa Rica)

^m Mars Center for Cocoa Science   (Brazil)

ⁿ NATIONAL CENTER FOR GENOME RESOURCES   (United States)

more..

Author keywords

genetic mapping; genome; haplotype phasing; Matina 1 6; MYB113; pod color; Theobroma cacao L.

Indexed keywords

PROTEIN MYB; SMALL INTERFERING RNA; TRANSCRIPTION FACTOR;

ARTICLE; BRASSICACEAE; CACAO; CULTIVAR; FRUIT COLOR; GENE EXPRESSION; GENE IDENTIFICATION; GENE MAPPING; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC REGULATION; GENETIC TRAIT; HAPLOTYPE; NONHUMAN; PIGMENTATION; PLANT CHROMOSOME; PLANT GENOME; POD; ROSACEAE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; SOLANACEAE; SYNTENY; CHROMOSOME MAP; COLOR; FRUIT; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GENOME SIZE; HIGH THROUGHPUT SEQUENCING; METABOLISM; PLANT GENE; QUANTITATIVE TRAIT; QUANTITATIVE TRAIT LOCUS;

BRASSICACEAE; DICOTYLEDONEAE; ROSACEAE; SOLANACEAE; THEOBROMA CACAO;

CACAO; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; COLOR; FRUIT; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME SIZE; GENOME, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; QUANTITATIVE TRAIT LOCI; QUANTITATIVE TRAIT, HERITABLE; RNA, SMALL INTERFERING; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 84878362237     PISSN: None     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2013-14-6-r53     Document Type: Article

References (117)

1. Motamayor JC, Risterucci AM, Lopez PA, Ortiz CF, Moreno A, Lanaud C. Cacao domestication I: the origin of the cacao cultivated by the Mayas. Heredity 2002, 89:380-386. 10.1038/sj.hdy.6800156, 12399997.
2. Motamayor JC, Lachenaud P, da Silva e Mota JW, Loor R, Kuhn DN, Brown JS, Schnell RJ. Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L). PLoS ONE 2008, 3:e3311. 10.1371/journal.pone.0003311, 2551746, 18827930.
3. Figueira A AL. Theobroma cacao (Cacao). Biotechnology of fruit and nut crops 2005, 639-670. CAB International Biosciences: Wallingford, UK, Litz RE.
4. Foundation TWC The World Cocoa Foundation. Foundation TWC., http://www.worldcocoafoundation.org/learn-about-cocoa/
5. Guiltinan MJ VJ, Zhang D, Figueira A. Genomics of Theobroma cacao, "The Food of the Gods". Genomics of Tropical Crop Plants 2008, 146-170. Springer New York, Moore PH & Ming R.
6. Piasentin F K-RL. Biodiversity conservation and cocoa agroforests. Gro Cocoa 2004, 5:7-8.
7. Bartley BGD. The genetic diversity of cacao and its utilization 2004, Wallingford, UK: CABI Publishing.
8. Motamayor JC, Risterucci AM, Heath M, Lanaud C. Cacao domestication II: progenitor germplasm of the Trinitario cacao cultivar. Heredity 2003, 91:322-330. 10.1038/sj.hdy.6800298, 12939635.
9. Efombagn I, Motamayor J, Sounigo O, Eskes A, Nyassé S, Cilas C, Schnell R, Manzanares-Dauleux M, Kolesnikova-Allen M. Genetic diversity and structure of farm and GenBank accessions of cacao ( Theobroma cacao L.) in Cameroon revealed by microsatellite markers. Tree Genetics & Genomes 2008, 4:821-831.
10. Aikpokpodion P, Motamayor J, Adetimirin V, Adu-Ampomah Y, Ingelbrecht I, Eskes A, Schnell R, Kolesnikova-Allen M. Genetic diversity assessment of sub-samples of cacao, Theobroma cacao L. collections in West Africa using simple sequence repeats marker. Tree Genetics & Genomes 2009, 5:699-711.
11. Argout X, Salse J, Aury J-M, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, Roguet Y, Rodier-Goud M, Barbosa-Neto JF, Sabot F, Kudrna D, Ammiraju JSS, Schuster SC, Carlson JE, Sallet E, Schiex T, Dievart A, Kramer M, Gelley L, Shi Z, Berard A, et al. The genome of Theobroma cacao. Nature Genetics 2011, 43:101-108. 10.1038/ng.736, 21186351.
12. Ranjan A, Ichihashi Y, Sinha N. The tomato genome: implications for plant breeding, genomics and evolution. Genome Biology 2012, 13:167. 3491363, 22943138.
13. Zimmer C. Yet-another-genome syndrome. , http://blogs.discovermagazine.com/loom/2010/04/02/yet-another-genome-syndrome/
14. Brown JS, Phillips-Mora W, Power EJ, Krol C, Cervantes-Martinez C, Motamayor JC, Schnell RJ. Mapping QTLs for resistance to frosty pod and black pod diseases and horticultural traits in Theobroma cacao L. Crop Sci 2007, 47:1851-1858.
15. Royaert S, Phillips-Mora W, Arciniegas Leal A, Cariaga K, Brown J, Kuhn D, Schnell R, Motamayor J. Identification of marker-trait associations for self-compatibility in a segregating mapping population of Theobroma cacao L. Tree Genetics & Genomes 2011, 7:1159-1168.
16. Findley SD, Cannon S, Varala K, Du J, Ma J, Hudson ME, Birchler JA, Stacey G. A fluorescence in situ hybridization system for karyotyping soybean. Genetics 2010, 185:727-744. 10.1534/genetics.109.113753, 2907198, 20421607.
17. Albert PS, Gao Z, Danilova TV, Birchler JA. Diversity of chromosomal karyotypes in maize and its relatives. Cytogenet Genome Res 2010, 129:6-16. 10.1159/000314342, 20551613.
18. Kato A, Lamb JC, Birchler JA. Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci USA 2004, 101:13554-13559. 10.1073/pnas.0403659101, 518793, 15342909.
19. Saski CA, Feltus FA, Staton ME, Blackmon BP, Ficklin SP, Kuhn DN, Schnell RJ, Shapiro H, Motamayor JC. A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6. BMC Genomics 2011, 12:413. 10.1186/1471-2164-12-413, 3173454, 21846342.
20. Ananiev EV, Phillips RL, Rines HW. Chromosome-specific molecular organization of maize (Zea mays L.) centromeric regions. Proc Natl Acad Sci USA 1998, 95:13073-13078. 10.1073/pnas.95.22.13073, 23713, 9789043.
21. Martinez-Zapater JM, Estelle MA, Somerville CR. A highly repeated DNA-sequence in Arabidopsis thaliana. Molecular & General Genetics 1986, 204:417-423.
22. Ma JX, Wing RA, Bennetzen JL, Jackson SA. Plant centromere organization: a dynamic structure with conserved functions. Trends in Genetics 2007, 23:134-139. 10.1016/j.tig.2007.01.004, 17275131.
23. Jaffe DB, B J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Research 2003, 13:91-96. 10.1101/gr.828403, 430950, 12529310.
24. Kuhn DN, Livingstone D, Main D, Zheng P, Saski C, Feltus FA, Mockaitis K, Farmer AD, May GD, Schnell RJ. Identification and mapping of conserved ortholog set (COS) II sequences of cacao and their conversion to SNP markers for marker-assisted selection in Theobroma cacao and comparative genomics studies. Tree Genetics & Genomes 2012, 8:97-111.
25. Feltus FA, Saski CA, Mockaitis K, Haiminen N, Parida L, Smith Z, Ford J, Staton ME, Ficklin SP, Blackmon BP, Cheng CH, Schnell RJ, Kuhn DN, Motamayor JC. Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes. BMC Genomics 2011, 12:379. 10.1186/1471-2164-12-379, 3154204, 21794110.
26. Wang BB, Brendel V. Genomewide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci USA 2006, 103:7175-7180. 10.1073/pnas.0602039103, 1459036, 16632598.
27. The universal protein resource (UniProt) The universal protein resource (UniProt)., http://www.uniprot.org
28. KEGG for linking genomes to life and the environment KEGG for linking genomes to life and the environment., http://www.kegg.jp
29. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003, 13:2178-2189. 10.1101/gr.1224503, 403725, 12952885.
30. Wang K, Wang Z, Li F, Ye W, Wang J, Song G, Yue Z, Cong L, Shang H, Zhu S, Zou C, Li Q, Yuan Y, Lu C, Wei H, Gou C, Zheng Z, Yin Y, Zhang X, Liu K, Wang B, Song C, Shi N, Kohel RJ, Percy RG, Yu JZ, Zhu YX, Wang J, Yu S. The draft genome of a diploid cotton Gossypium raimondii. Nat Genet 2012,
31. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research 2012, 40:D1178-D1186. 10.1093/nar/gkr944, 3245001, 22110026.
32. Eddy SR. Accelerated profile HMM searches. PLoS Computational Biology 2011, 7:e1002195. 10.1371/journal.pcbi.1002195, 3197634, 22039361.
33. Krogh A, Brown M, Mian IS, Sjolander K, Haussler D. Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol 1994, 235:1501-1531. 10.1006/jmbi.1994.1104, 8107089.
34. Eddy SR. Profile hidden Markov models. Bioinformatics 1998, 14:755-763. 10.1093/bioinformatics/14.9.755, 9918945.
35. Kaul S, Koo HL, Jenkins J, Rizzo M, Rooney T, Tallon LJ, Feldblyum T, Nierman W, Benito MI, Lin XY, Town CD, Venter JC, Fraser CM, Tabata S, Nakamura Y, Kaneko T, Sato S, Asamizu E, Kato T, Kotani H, Sasamoto S, Ecker JR, Theologis A, Federspiel NA, Palm CJ, Osborne BI, Shinn P, Conway AB, Vysotskaia VS, Dewar K, et al. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815. 10.1038/35048692, 11130711.
36. Matsumoto T, Wu J, Kanamori H, Katayose Y, Fujisawa M, Namiki N, Mizuno H, Yamamoto K, Antonio BA, Baba T. The map-based sequence of the rice genome. Nature 2005, 436:793-800. 10.1038/nature03895, 16100779.
37. Vogel JP, Garvin DF, Mockler TC, Schmutz J, Rokhsar D, Bevan MW, Barry K, Lucas S, Harmon-Smith M, Lail K, Tice H, Grimwood J, McKenzie N, Huo NX, Gu YQ, Lazo GR, Anderson OD, You FM, Luo MC, Dvorak J, Wright J, Febrer M, Idziak D, Hasterok R, Lindquist E, Wang M, Fox SE, Priest HD, Filichkin SA, Givan SA, et al. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 2010, 463:763-768. 10.1038/nature08747, 20148030.
38. Devos KM, Brown JK, Bennetzen JL. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 2002, 12:1075-1079. 10.1101/gr.132102, 186626, 12097344.
39. Krzywinski M, S J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Research 2009, 19:1639-1645. 10.1101/gr.092759.109, 2752132, 19541911.
40. Freeling M, Lyons E, Pedersen B, Alam M, Ming R, Lisch D. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res 2008, 18:1924-1937. 10.1101/gr.081026.108, 2593585, 18836034.
41. Browning BL, Browning SR. Efficient multilocus association testing for whole genome association studies using localized haplotype clustering. Genet Epidemiol 2007, 31:365-375. 10.1002/gepi.20216, 17326099.
42. Schaid DJ. Evaluating associations of haplotypes with traits. Genet Epidemiol 2004, 27:348-364. 10.1002/gepi.20037, 15543638.
43. Williams AL, Patterson N, Glessner J, Hakonarson H, Reich D. Phasing of many thousands of genotyped samples. Am J Hum Genet 2012, 91:238-251. 10.1016/j.ajhg.2012.06.013, 3415548, 22883141.
44. Jin H, Martin C. Multifunctionality and diversity within the plant MYB-gene family. Plant Mol Biol 1999, 41:577-585. 10.1023/A:1006319732410, 10645718.
45. Amann K, Lezhneva L, Wanner G, Herrmann RG, Meurer J. ACCUMULATION OF PHOTOSYSTEM ONE1, a member of a novel gene family, is required for accumulation of [4Fe-4S] cluster-containing chloroplast complexes and antenna proteins. Plant Cell 2004, 16:3084-3097. 10.1105/tpc.104.024935, 527200, 15494558.
46. Fournier-Level A, Le Cunff L, Gomez C, Doligez A, Ageorges A, Roux C, Bertrand Y, Souquet JM, Cheynier V, This P. Quantitative genetic bases of anthocyanin variation in grape (Vitis vinifera L. ssp. sativa) berry: a quantitative trait locus to quantitative trait nucleotide integrated study. Genetics 2009, 183:1127-1139. 10.1534/genetics.109.103929, 2778965, 19720862.
47. This P, Lacombe T, Cadle-Davidson M, Owens CL. Wine grape (Vitis vinifera L.) color associates with allelic variation in the domestication gene VvmybA1. Theor Appl Genet 2007, 114:723-730. 10.1007/s00122-006-0472-2, 17221259.
48. De Jong WS, Eannetta NT, De Jong DM, Bodis M. Candidate gene analysis of anthocyanin pigmentation loci in the Solanaceae. Theor Appl Genet 2004, 108:423-432. 10.1007/s00122-003-1455-1, 14523517.
49. Zhang B, Hu Z, Zhang Y, Li Y, Zhou S, Chen G. A putative functional MYB transcription factor induced by low temperature regulates anthocyanin biosynthesis in purple kale ( Brassica Oleracea var. acephala f. tricolor). Plant Cell Reports 2012, 31:281-289. 10.1007/s00299-011-1162-3, 21987119.
50. Lin-Wang K, Bolitho K, Grafton K, Kortstee A, Karunairetnam S, McGhie T, Espley R, Hellens R, Allan A. An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae. BMC Plant Biology 2010, 10:50. 10.1186/1471-2229-10-50, 2923524, 20302676.
51. Yanhui C, Xiaoyuan Y, Ku H, Meihua L, Jigang L, Zhaofeng G, Zhiqiang L, Yunfei Z, Xiaoxiao W, Xiaoming Q, Yunping S, Li Z, Xiaohui D, Jingchu L, Xing-Wang D, Zhangliang C, Hongya G, Li-Ji Q. The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family. Plant Mol Biol 2006, 60:107-124. 10.1007/s11103-005-2910-y, 16463103.
52. Fournier-Level A, Lacombe T, Le Cunff L, Boursiquot JM, This P. Evolution of the VvMybA gene family, the major determinant of berry colour in cultivated grapevine (Vitis vinifera L.). Heredity (Edinb) 2010, 104:351-362. 10.1038/hdy.2009.148, 19920856.
53. Bate N, Spurr C, Foster GD, Twell D. Maturation-specific translational enhancement mediated by the 5′-UTR of a late pollen transcript. The Plant Journal 1996, 10:613-623. 10.1046/j.1365-313X.1996.10040613.x, 8893540.
54. Luo QJ, Mittal A, Jia F, Rock CD. An autoregulatory feedback loop involving PAP1 and TAS4 in response to sugars in Arabidopsis. Plant Mol Biol 2012, 80:117-129. 10.1007/s11103-011-9778-9, 3272322, 21533841.
55. Yoshikawa M, Peragine A, Park MY, Poethig RS. A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev 2005, 19:2164-2175. 10.1101/gad.1352605, 1221887,1221887, 16131612.
56. Allen E, Xie Z, Gustafson AM, Carrington JC. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 2005, 121:207-221. 10.1016/j.cell.2005.04.004, 15851028.
57. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 2006, 20:3407-3425. 10.1101/gad.1476406, 1698448, 17182867.
58. Takos A, Jaffe F, Jacob S, Bogs J, Robinson S, Walker A. Light-induced expression of a MYB gene regulates anthocyanin biosynthesis in red apples. Plant Physiol 2006, 142:1216-1232. 10.1104/pp.106.088104, 1630764, 17012405.
59. Gonzalez A, Zhao M, Leavitt JM, Lloyd AM. Regulation of the anthocyanin biosynthetic pathway by the TTG1/bHLH/Myb transcriptional complex in Arabidopsis seedlings. The Plant Journal 2008, 53:814-827. 10.1111/j.1365-313X.2007.03373.x, 18036197.
60. Xia R, Zhu H, An YQ, Beers EP, Liu Z. Apple miRNAs and tasiRNAs with novel regulatory networks. Genome Biol 2012, 13:R47. 10.1186/gb-2012-13-6-r47, 3446319, 22704043.
61. Cacao Genome Database Cacao Genome Database., http://www.cacaogenomedb.org
62. Schnell RJ, Brown JS, Kuhn DN, Cervantes-Martinez C, Olano CT, Motamayor JC. Why would we breed cacao in Florida?. Proc Fla State Hort Soc 2005, 118:189-191.
63. Cope FW. The mechanism of pollen incompatibility in Theobroma cacao. L Heredity 1962, 17:157-182.
64. Iwano M, Takayama S. Self/non-self discrimination in angiosperm self-incompatibility. Curr Opin Plant Biol 2012, 15:78-83. 10.1016/j.pbi.2011.09.003, 21968124.
65. Galbraith DW. Simultaneous flow cytometric quantification of plant nuclear DNA contents over the full range of described angiosperm 2C values. Cytometry A 2009, 75:692-698.
66. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, et al. Genome sequence of the palaeopolyploid soybean. Nature 2010, 463:178-183. 10.1038/nature08670, 20075913.
67. Johnston JS, Bennett MD, Rayburn AL, Galbraith DW, Price HJ. Reference standards for determination of DNA content of plant nuclei. Am J Bot 1999, 86:609-613. 10.2307/2656569, 10330063.
68. Loureiro J, Rodriguez E, Dolezel J, Santos C. Two new nuclear isolation buffers for plant DNA flow cytometry: a test with 37 species. Ann Bot 2007, 100:875-888. 10.1093/aob/mcm152, 2749623, 17684025.
69. Doležel J, Greilhuber J, Suda J. Estimation of nuclear DNA content in plants using flow cytometry. Nature Protocols 2007, 2:2233-2243. 10.1038/nprot.2007.310, 17853881.
70. Arumuganathan K, Earle E. Nuclear DNA content of some important plant species. Plant Molecular Biology Reporter 1991, 9:208-218.
71. SAS Institute. , http://www.sas.com/
72. Van Ooijen JW. Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. Genetics Research 2011, 93:343-349. 10.1017/S0016672311000279, 21878144.
73. Sambrook J, F EF, Maniatis T. Molecular Cloning: A Laboratory Manual 1989, Cold Spring Harbor, NY: Cold Spring Harbor Press.
74. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. Journal of molecular biology 1990, 215:403-410.
75. Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res 2002, 12:656-664. 187518, 11932250.
76. CocoaGen DB CocoaGen DB., http://cocoagendb.cirad.fr/gbrowse/download.html
77. Haas BJ. Analysis of alternative splicing in plants with bioinformatics tools. Curr Top Microbiol Immunol 2008, 326:17-37. 10.1007/978-3-540-76776-3_2, 18630745.
78. The Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. The Arabidopsis Genome Initiative., ftp://ftp.arabidopsis.org/home/tair/Sequences/blast_datasets/TAIR10_blastsets/
79. Jaillon O, Aury J, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyère C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. , ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v7.0/Vvinifera/
80. Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen G-L, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). , ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v7.0/Ptrichocarpa/
81. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, et al. Genome sequence of the palaeopolyploid soybean. , ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v7.0/Gmax/
82. Chan AP, Crabtree J, Zhao Q, Lorenzi H, Orvis J, Puiu D, Melake-Berhan A, Jones KM, Redman J, Chen G, Cahoon EB, Gedil M, Stanke M, Haas BJ, Wortman JR, Fraser-Liggett CM, Ravel J, Rabinowicsz PD. Draft genome sequence of the oilseed species Ricinus communis. , http://castorbean.jcvi.org/downloads.php
83. Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton J-M, Rees DJG, Williams KP, Holt SH, Rojas JJR, Chatterjee M, et al. The genome of woodland strawberry (Fragaria vesca). , https://strawberry.plantandfood.co.nz/gbrowse/navbar/strawberry/download.html
84. 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. Genome sequence and analysis of the tuber crop potato. , http://potatogenomics.plantbiology.msu.edu/index.html
85. The Sorghum bicolor genome and the diversification of grasses The Sorghum bicolor genome and the diversification of grasses., ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v7.0/Sbicolor/
86. Slater GSC, Birney E. Automated generation of heuristics for biological sequence comparison. Bmc Bioinformatics 2005, 6:31. 10.1186/1471-2105-6-31, 553969, 15713233.
87. Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. BioInformatics 2003, 19:ii215-ii225. 10.1093/bioinformatics/btg1080, 14534192.
88. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH. A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics 2007, 8:973-982. 10.1038/nrg2165, 17984973.
89. McCarthy EM, McDonald JF. LTR_STRUC: a novel search and identification program for LTR retrotransposons. BioInformatics 2003, 19:362-367. 10.1093/bioinformatics/btf878, 12584121.
90. Xu Z, Wang H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Research 2007, 35:W265-W268. 10.1093/nar/gkm286, 1933203, 17485477.
91. Ma J, Devos KM, Bennetzen JL. Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res 2004, 14:860-869. 10.1101/gr.1466204, 479113, 15078861.
92. Holligan D, Zhang XY, Jiang N, Pritham EJ, Wessler SR. The transposable element landscape of the model legume Lotus japonicus. Genetics 2006, 174:2215-2228. 10.1534/genetics.106.062752, 1698628, 17028332.
93. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 2005, 110:462-467. 10.1159/000084979, 16093699.
94. Yang LX, Bennetzen JL. Structure-based discovery and description of plant and animal Helitrons. Proc Natl Acad Sci USA 2009, 106:12832-12837. 10.1073/pnas.0905563106, 2722332, 19622734.
95. Chen Y, Zhou FF, Li GJ, Xu Y. MUST: A system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi. Gene 2009, 436:1-7. 10.1016/j.gene.2009.01.019, 19393167.
96. Han YJ, Wessler SR. MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Research 2010, 38.
97. RepeatMasker Open-3.0 RepeatMasker Open-3.0., http://www.repeatmasker.org
98. Mercator: Multiple Whole-Genome Orthology Map Construction Mercator: Multiple Whole-Genome Orthology Map Construction., http://www.biostat.wisc.edu/~cdewey/mercator/
99. Bray N, Pachter L. MAVID: constrained ancestral alignment of multiple sequences. Genome Res 2004, 14:693-699. 10.1101/gr.1960404, 383315, 15060012.
100. McKay SJ, Vergara IA, Stajich JE. Using the Generic Synteny Browser (GBrowse_syn). Current Protocols in Bioinformatics 2002, John Wiley & Sons, Inc.
101. Criollo vs Matina Synteny Criollo vs Matina Synteny., http://www.cacaogenomedb.org/gb-private/gbrowse_syn/tc_criollo_vs_tc_matina/
102. Andras SC, Hartman TP, Marshall JA, Marchant R, Power JB, Cocking EC, Davey MR. A drop-spreading technique to produce cytoplasm-free mitotic preparations from plants with small chromosomes. Chromosome Res 1999, 7:641-647. 10.1023/A:1009288119851, 10628665.
103. Kato A. Air drying method using nitrous oxide for chromosome counting in maize. Biotechnic & Histochemistry 1999, 74:160-166. 10.3109/10520299909047968, 10416789.
104. Gill N, Findley S, Walling JG, Hans C, Ma J, Doyle J, Stacey G, Jackson SA. Molecular and chromosomal evidence for allopolyploidy in soybean. Plant physiology 2009, 151:1167-1174. 10.1104/pp.109.137935, 2773056, 19605552.
105. Utro F, Haiminen N, Livingstone D, Cornejo OE, Royaert S, Schnell RJ, Motamayor JC, Kuhn DN, Parida L. iXora: Exact haplotype inferencing and trait association. BMC Genetics
106. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. BioInformatics 2010, 26:589-595. 10.1093/bioinformatics/btp698, 2828108, 20080505.
107. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. BioInformatics 2009, 25:2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943.
108. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 2010, 20:1297-1303. 10.1101/gr.107524.110, 2928508, 20644199.
109. Depristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, Del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics 2011, 43:491-501. 10.1038/ng.806, 3083463, 21478889.
110. Scheet P, Stephens M. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 2006, 78:629-644. 10.1086/502802, 1424677, 16532393.
111. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular biology and evolution 2011, 28:2731-2739. 10.1093/molbev/msr121, 3203626, 21546353.
112. Patterson N, Price AL, Reich D. Population structure and eigenanalysis. PLoS Genet 2006, 2:e190. 10.1371/journal.pgen.0020190, 1713260, 17194218.
113. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P. Association mapping in structured populations. Am J Hum Genet 2000, 67:170-181. 10.1086/302959, 1287075, 10827107.
114. Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, Eskin E. Efficient control of population structure in model organism association mapping. Genetics 2008, 178:1709-1723. 10.1534/genetics.107.080101, 2278096, 18385116.
115. Chang S, Puryear J, Cairney J. A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter 1993, 11:113-116.
116. Koressaar T, Remm M. Enhancements and modifications of primer design program Primer3. Bioinformatics 2007, 23:1289-1291. 10.1093/bioinformatics/btm091, 17379693.
117. Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Research 2001, 29:e45. 10.1093/nar/29.9.e45, 55695, 11328886.