Abstract
Common bean (Phaseolus vulgaris L.) is a legume that is an important source of dietary protein in developing countries throughout the world. Utilizing the G19833 BAC library for P. vulgaris from Clemson University, 89,017 BAC-end sequences were generated giving 62,588,675 base pairs of genomic sequence covering approximately 9.54% of the genome. Analysis of these sequences in combination with 1,404 shotgun sequences from the cultivar Bat7 revealed that approximately 49.2% of the genome contains repetitive sequence and 29.3% is genic. Compared to other legume BAC-end sequencing projects, it appears that P. vulgaris has higher predicted levels of repetitive sequence, but this may be due to a more intense identification strategy combining both similarity-based matches as well as de novo identification of repeats. In addition, fingerprints for 41,717 BACs were obtained and assembled into a draft physical map consisting of 1,183 clone contigs and 6,385 singletons with ~9x coverage of the genome.
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Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Ammiraju JSS, Luo M, Goicoechea JL, Wang W, Kudrna D, Mueller C, Talag J, Kim HR, Sisneros NB, Blackmon B, Fang E, Tomkins JB, Brar D, MacKill D, McCouch S, Kurata N, Lambert G, Galbraith D, Arumuganathan K, Rao K, Walling JG, Gill N, Yu Y, SanMiguel P, Soderlund C, Jackson S, Wing RA (2006) The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Res 16:140–147
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
Arumuganathan K, Earl ED (1991) Estimation of nuclear DNA content of plants by flow cytometry. Plant Mol Biol 9:229–233
Bao Z, Eddy SR (2002) Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res 12:1269–1276
Bennett MD, Leitch IJ (1995) Nuclear DNA amount in angiosperms. Ann Bot 76:113–176
Blair MW, Pedraza F, Buendia HF, Gaitán-Solís E, Beebe SE, Gepts P, Tohme J (2003) Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.). Theor Appl Genet 107:1362–1374
Boutin SR, Young ND, Olson TC, Yu Z-H, Shoemaker RC, Vallejos CE (1995) Genome conservation among three legume genera detected with DNA markers. Genome 38:928–937
Broughton WJ, Hernandez G, Blair M, Beebe S, Gepts P, Vanderleyden J (2003) Beans (Phaseolus spp.)—model food legumes. Dev Plant Soil Sci 99:55–128
Choi HK, Mun JH, Kin DJ, Zhu H, Baek JM, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR (2004) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA 101:15289–15294
Chou HH, Holmes MH (2001) DNA sequence quality trimming and vector removal. Bioinformatics 17:1093–1094
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676
Costa NM, Low AG, Walker AF, Owen RW, Englyst HN (1994) Effect of baked beans (Phaseolus vulgaris) on steroid metabolism and non-starch polysaccharide output of hypercoholesterolaemic pigs with or without an ileo-rectal anastomosis. Br J Nutr 71:871–886
Doyle JJ, Luckow MA (2003) The rest of the iceberg. Legume diversity and evolution in a phylogenetic context. Plant Phys 131:900–910
Engler FW, Hatfield J, Nelson W, Soderlund CA (2003) Locating sequence on FPC maps and selecting a minimum tiling path. Genome Res 13:2152–2163
Ewing B, Hillier M, Wendle MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–185
Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194
Febrer M, Cheung F, Town CD, Cannon SB, Young ND, Abberton MT, Jenkins G, Milbourne D (2007) Construction, characterization, and preliminary BAC-end sequencing analysis of a bacterial artificial chromosome library of white clover (Trifolium repens L.). Genome 50:412–421
The French-Italian Public Consortium for Grapevine Genome Characterization (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature DOI 10.1038/nature06148
Goff SA, Ricke D, Lan T-H, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun W-L, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. spp. Japonica). Science 296:92–100
Freyre R, Skroch PW, Geffroy V, Adam-Blondon AF, Shirmohamadali A, Johnson WC, Llaca V, Nodari RO, Pereira PA, Tsai SM, Thome J, Dron M, Nienhuis J, Vallejos CE, Gepts P (1998) Towards an integrated linkage map of common bean. 4. Development of a core linkage map and alignment of RFLP maps. Theor Appl Genet 97:847–856
Guo X, Castill-Ramirez S, Gonzalez V, Bustos P, Fernandez-Vazgueq JL, Santamaria RI, Arellano J, Cevallos MA, Davila G (2007) Rapid evolutionary change of common bean (Phaseolus vulgaris L.) plastome, and the genomic diversification of legume chloroplasts. BMC Genomics 8:228
Han K-H, Sekikawa M, Shimada K-I, Sasaki K, Ohba K, Fukushima M (2004) Resistant starch fraction prepared from kintoki bean affects gene expression of genes associated with cholesterol metabolism in rats. Exp Biol and Med 229:787–792
Jackson SA, Rokshar D, Stacey G, Shoemaker RC, Schmutz J, Grimwood J (2006) Toward a reference sequence of the soybean genome: a multiagency effort. Crop Sci 46:S-55–S-61
Kim HR, San Miguel P, Nelson W, Collura K, Wissotski M, Walling JG, Kim JP, Jackson SA, Soderlund C, Wing RA (2007) Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type). Genetics 176:379–390
Lavin M, Herendenn PS, Wojciechowski MF (2005) Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the Tertiary. System Biol 54:530–549
Lee JM, Grant D, Vallejos CE, Shoemaker RC (2001) Genome organization in dicots. II. Arabidopsis as a ‘bridging species’ to resolve genome evolution events among legumes. Theor Appl Genet 103:765–773
Luo MC, Thomas C, You FM, Hsiao J, Ouyang S, Buell CR, Malandro M, McGuire PE, Anderson OE, Dvorak J (2003) High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing restriction fragments by capillary electrophoresis. Genomics 82:378–389
Marek LF, Mudge J, Darnielle L, Grant D, Hamson N, Paz M, Huihuang Y, Denny R, Larson K, Foster-Hartnett D, Cooper A, Danesh D, Larsen D, Schmidt T, Staggs R, Crow JA, Retzel E, Young ND, Shoemaker RC (2001) Soybean genomic survey: BAC-end sequences near RFLP and SSR markers. Genome 44:572–581
McCarthy EM, McDonald JF (2003) LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19:362–367
McClean PE, Lee RK, Otto C, Gepts P, Bassett MJ (2002) Molecular and phenotypic mapping of genes controlling seed coat pattern and color in common bean (Phaseolus vulgaris L.). J Heredity 93:148–152
Menancio-Hautea D, Fatokun CA, Kumar L, Danesh D, Young ND (1993) Comparative genome analysis of mungbean (Vigna radiata L. Wilczek) and cowpea (V. unguiculata L. Walpers) using RFLP mapping data. Theor. Appl. Genet. 86:797–810
Nelson WM, Bharti AK, Butler E, Wei F, Fuks H, Kim HR, Wing RA, Messing J, Soderlund C (2005) Whole-genome validation of high-information-content fingerprinting. Plant Physiol 139:27–38
Pfeil BE, Schlueter JA, Shoemaker RC, Doyle JJ (2005) Placing paleopolyploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families. Syst Biol 54:441–454
Ramirez M, Graham MA, Blanco-Lopez L, Silvente S, Medrano-Soto A, Blair MW, Hernandez G, Vance CP, Lara M (2005) Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Plant Phys 137:1211–1227
Schlueter JA, Lin J-Y, Schlueter SD, Vasylendo-Sanders IF, Deshpande S, Yi J, O’Bleness M, Roe BA, Nelson RT, Scheffler BE, Jackson SA, Shoemaker RC (2007) Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing. BMC Genomics 8:330
Soderlund C, Humphray S, Dunham A, French L (2000) Contigs built with fingerprints, markers, and FPC v4.7. Genome Res 10:1772–1787
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, Cunningham R, Davis J, Degroeve S, Dejardin A, de Pamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehiting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Peple J-C, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson V, Pereda G, Peter R, Philippe G, Pilate G, Poliakov P, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai C-J, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D (2006) The genome of black cottonwood, Populus trichocarpa (Torr & Gray). Science 313:1596–1604
Vallejos CE, Sakiyama NS, Chase CD (1992) A molecular marker-based linkage map of Phaseolus vulgaris L. Genetics 131:733–740
Wei F, Coe E, Nelson W, Bharti A, Engler F, Butler E, Kim H, Goicoechea J, Chen M, Lee S, Fuks G, Sanchez-Villeda H, Schroeder S, Fang, Z, McMullen M, Davis G, Bowers J, Paterson A, Schaeffer M, Gardiner J, Cone K, Messing J, Soderlund C, Wing R (2007) Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genetics 3:1254–1263
Young ND, Cannon SB, Sato S, Kim D, Cook DR, Town CD, Roe BA, Tabata S (2005) Sequencing the gene spaces of Medicago truncatula and Lotus japonicus. Plant Physiol 137:1174–1181
Yu J, Hu S, Wang J, Wong GKS, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. spp. indica). Science 296:79–92
Acknowledgments
The authors would like to thank all of the collaborators in this project for their work and additions to this manuscript. We would also like to acknowledge the technical staff at the AGI BAC/EST Resource, Sequencing and Bioinformatics Centers for their contributions to this project. The project was supported by the USDA Cooperative State Research, Education and Extension Service—National Research Initiative—Plant Genome Program Grant number 06-35300-17266.
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Jessica A. Schlueter, Jose Luis Goicoechea, and Kristi Collura, are the Co-first authors.
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Schlueter, J.A., Goicoechea, J.L., Collura, K. et al. BAC-end Sequence Analysis and a Draft Physical Map of the Common Bean (Phaseolus vulgaris L.) Genome. Tropical Plant Biol. 1, 40–48 (2008). https://doi.org/10.1007/s12042-007-9003-9
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DOI: https://doi.org/10.1007/s12042-007-9003-9