An improved genome release (version Mt4.0) for the model legume Medicago truncatula

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Tang, Haibao ^a   Krishnakumar, Vivek ^a   Bidwell, Shelby ^a   Rosen, Benjamin ^a   Chan, Agnes ^a   Zhou, Shiguo ^b   Gentzbittel, Laurent ^c   Childs, Kevin L ^d   Yandell, Mark ^e   Gundlach, Heidrun ^f   Mayer, Klaus F X ^f   Schwartz, David C ^b   Town, Christopher D ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c UNIVERSITÉ DE TOULOUSE   (France)

^d MICHIGAN STATE UNIVERSITY   (United States)

^e UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^f INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

Gene annotation; Genome assembly; Legume; Medicago; Optical map

Indexed keywords

VEGETABLE PROTEIN;

ARTICLE; BARREL MEDIC; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; GENETIC DATABASE; GENOTYPE; NONHUMAN; PLANT GENE; PLANT GENOME; PREDICTION; RNA SEQUENCE; SEQUENCE ANALYSIS; BACTERIAL ARTIFICIAL CHROMOSOME; GENETICS;

MEDICAGO; MEDICAGO SATIVA; MEDICAGO TRUNCATULA;

CHROMOSOMES, ARTIFICIAL, BACTERIAL; GENOME, PLANT; MEDICAGO TRUNCATULA;

EID: 84899917345     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-312     Document Type: Article

References (42)

1. Bennett MD, Leitch IJ. Nuclear DNA amounts in angiosperms: targets, trends and tomorrow. Ann Bot 2011, 107(3):467-590. 10.1093/aob/mcq258, 3043933, 21257716.
2. Wang D, Griffitts J, Starker C, Fedorova E, Limpens E, Ivanov S, Bisseling T, Long S. A nodule-specific protein secretory pathway required for nitrogen-fixing symbiosis. Science 2010, 327(5969):1126-1129. 10.1126/science.1184096, 20185723.
3. Young ND, Debelle F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KA, Tang H, Rombauts S, Zhao PX, Zhou P, et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 2011, 480(7378):520-524. 3272368, 22089132.
4. Zhou S, Bechner MC, Place M, Churas CP, Pape L, Leong SA, Runnheim R, Forrest DK, Goldstein S, Livny M, Schwartz DC. Validation of rice genome sequence by optical mapping. BMC Genomics 2007, 8:278. 10.1186/1471-2164-8-278, 2048515, 17697381.
5. Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee SS, Kim J, Numa H, Itoh T, Buell CR, Matsumoto T. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 2013, 6(1):4. 10.1186/1939-8433-6-4, 24280374.
6. Li Z, Zhang Z, Yan P, Huang S, Fei Z, Lin K. RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics 2011, 12:540. 10.1186/1471-2164-12-540, 3219749, 22047402.
7. Volkening JD, Bailey DJ, Rose CM, Grimsrud PA, Howes-Podoll M, Venkateshwaran M, Westphall MS, Ane JM, Coon JJ, Sussman MR. A proteogenomic survey of the Medicago truncatula genome. Mol Cell Proteomics: MCP 2012, 11(10):933-944.
8. Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol 2008, 9(1):R7. 10.1186/gb-2008-9-1-r7, 2395244, 18190707.
9. Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sanchez Alvarado A, Yandell M. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res 2008, 18(1):188-196. 2134774, 18025269.
10. Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A 2011, 108(4):1513-1518. 10.1073/pnas.1017351108, 3029755, 21187386.
11. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 2012, 1(1):18. 10.1186/2047-217X-1-18, 3626529, 23587118.
12. Pop M, Kosack DS, Salzberg SL. Hierarchical scaffolding with Bambus. Genome Res 2004, 14(1):149-159. 314292, 14707177.
13. Ben C, Toueni M, Montanari S, Tardin MC, Fervel M, Negahi A, Saint-Pierre L, Mathieu G, Gras MC, Noel D, Prosperi JM, Pilet-Nayel ML, Baranger A, Huguet T, Julier B. Natural diversity in the model legume Medicago truncatula allows identifying distinct genetic mechanisms conferring partial resistance to Verticillium wilt. J Exp Bot 2013, 64(1):317-332. 10.1093/jxb/ers337, 3528038, 23213135.
14. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 2011, 6(5):e19379. 10.1371/journal.pone.0019379, 3087801, 21573248.
15. 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.
16. Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 2011, 27(21):2987-2993. 10.1093/bioinformatics/btr509, 3198575, 21903627.
17. Valouev A, Li L, Liu YC, Schwartz DC, Yang Y, Zhang Y, Waterman MS. Alignment of optical maps. J Comput Biol 2006, 13(2):442-462. 10.1089/cmb.2006.13.442, 16597251.
18. Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, Goldstein S, Pape L, Mehan MR, Churas C, Pasternak S, Forrest DK, Wise R, Ware D, Wing RA, Waterman MS, Livny M, Schwartz DC. A single molecule scaffold for the maize genome. PLoS Genet 2009, 5(11):e1000711. 10.1371/journal.pgen.1000711, 2774507, 19936062.
19. Teague B, Waterman MS, Goldstein S, Potamousis K, Zhou S, Reslewic S, Sarkar D, Valouev A, Churas C, Kidd JM, Kohn S, Runnheim R, Lamers C, Forrest D, Newton MA, Eichler EE, Kent-First M, Surti U, Livny M, Schwartz DC. High-resolution human genome structure by single-molecule analysis. Proc Natl Acad Sci U S A 2010, 107(24):10848-10853. 10.1073/pnas.0914638107, 2890719, 20534489.
20. Zhou P, Silverstein KA, Gao L, Walton JD, Nallu S, Guhlin J, Young ND. Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application). BMC Bioinformatics 2013, 14:335. 10.1186/1471-2105-14-335, 3924332, 24256031.
21. Min XJ, Butler G, Storms R, Tsang A. TargetIdentifier: a webserver for identifying full-length cDNAs from EST sequences. Nucleic Acids Res 2005, 33(Web Server issue):W669-W672. 1160197, 15980559.
22. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. JBrowse: a next-generation genome browser. Genome Res 2009, 19(9):1630-1638. 10.1101/gr.094607.109, 2752129, 19570905.
23. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25(5):955-964. 10.1093/nar/25.5.0955, 146525, 9023104.
24. Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16(6):276-277. 10.1016/S0168-9525(00)02024-2, 10827456.
25. Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD, Salzberg SL, White O. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 2003, 31(19):5654-5666. 10.1093/nar/gkg770, 206470, 14500829.
26. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011, 29(7):644-652. 10.1038/nbt.1883, 3571712, 21572440.
27. Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 2011, 12:323. 10.1186/1471-2105-12-323, 3163565, 21816040.
28. Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res 2011, 21(3):487-493. 10.1101/gr.113985.110, 3044862, 21209072.
29. Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M. Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics 2011, 12:102. 10.1186/1471-2105-12-102, 3088904, 21501495.
30. Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 2007, 23(9):1061-1067. 10.1093/bioinformatics/btm071, 17332020.
31. Kamphuis LG, Williams AH, D'Souza NK, Pfaff T, Ellwood SR, Groves EJ, Singh KB, Oliver RP, Lichtenzveig J. The Medicago truncatula reference accession A17 has an aberrant chromosomal configuration. New Phytol 2007, 174(2):299-303. 10.1111/j.1469-8137.2007.02039.x, 17388892.
32. Julier B, Huguet T, Chardon F, Ayadi R, Pierre JB, Prosperi JM, Barre P, Huyghe C. Identification of quantitative trait loci influencing aerial morphogenesis in the model legume Medicago truncatula. Theor Appl Genet 2007, 114(8):1391-1406. 10.1007/s00122-007-0525-1, 17375280.
33. Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR. Pack-MULE transposable elements mediate gene evolution in plants. Nature 2004, 431(7008):569-573. 10.1038/nature02953, 15457261.
34. Lai J, Li Y, Messing J, Dooner HK. Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc Natl Acad Sci U S A 2005, 102(25):9068-9073. 10.1073/pnas.0502923102, 1157042, 15951422.
35. Foissac S, Gouzy J, Rombauts S, Mathe C, Amselem J, Sterck L, Van de Peer Y, Rouze P, Schiex T. Genome Annotation in Plants and Fungi: EuGene as a Model Platform. Current Bioinformatics, Volume 3 2008, 87-97. (11).
36. 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, 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(7278):178-183. 10.1038/nature08670, 20075913.
37. Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T, Spannagl M, Monaghan E, Nicholson C, Humphray SJ, Schoof H, Mayer KF, Rogers J, Quetier F, Oldroyd GE, Debelle F, Cook DR, Retzel EF, Roe BA, Town CD, Tabata S, Van de Peer Y, Young ND. Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci U S A 2006, 103(40):14959-14964. 10.1073/pnas.0603228103, 1578499, 17003129.
38. Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MT, Azam S, Fan G, Whaley AM, Farmer AD, Sheridan J, Iwata A, Tuteja R, Penmetsa RV, Wu W, Upadhyaya HD, Yang SP, Shah T, Saxena KB, Michael T, McCombie WR, Yang B, Zhang G, Yang H, Wang J, Spillane C, Cook DR, May GD, Xu X, et al. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 2012, 30(1):83-89.
39. Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD, Tar'an B, Millan T, Zhang X, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo MC, et al. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 2013, 31(3):240-246. 10.1038/nbt.2491, 23354103.
40. Thibaud-Nissen F, Campbell M, Hamilton JP, Zhu W, Buell CR. EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome. BMC Genomics 2007, 8:388. 10.1186/1471-2164-8-388, 2151081, 17961238.
41. VandenBosch KA, Frugoli J. Guidelines for genetic nomenclature and community governance for the model legume Medicago truncatula. Mol Plant Microbe Interact 2001, 14(12):1364-1367. 10.1094/MPMI.2001.14.12.1364, 11768530.
42. Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD. A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat Protoc 2012, 7(7):1260-1284. 10.1038/nprot.2012.068, 3648784, 22678431.