A genetic linkage map for the ectomycorrhizal fungus Laccaria bicolor and its alignment to the whole-genome sequence assemblies

New Phytologist

Volumn 180, Issue 2, 2008, Pages 316-328

  Labbe J ^a   Zhang, X ^b,c   Yin, T ^b,c   Schmutz, J ^d   Grimwood, J ^d   Martin, F ^a   Tuskan, G A ^b,c   Le Tacon, F ^a  

^a UNIVERSITÉ DE LORRAINE   (France)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

^c DOE JOINT GENOME INSTITUTE   (United States)

^d STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Gene positioning; Genetic map; Laccaria bicolor; Sequence assemblies

Indexed keywords

DNA; ECTOMYCORRHIZA; FUNGUS; GENE EXPRESSION; GENETIC MARKER; GENOME; IDENTIFICATION METHOD; RECOMBINATION; SYMBIOSIS;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; CHROMOSOME MAP; FUNGAL GENOME; FUNGUS SPORE; GENETIC LINKAGE; GENETIC RECOMBINATION; GENETICS; LACCARIA; MYCORRHIZA; RANDOM AMPLIFIED POLYMORPHIC DNA; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; VARIABLE NUMBER OF TANDEM REPEAT;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; CHROMOSOME MAPPING; GENOME, FUNGAL; LACCARIA; LINKAGE (GENETICS); MINISATELLITE REPEATS; MYCORRHIZAE; POLYMORPHISM, SINGLE NUCLEOTIDE; RANDOM AMPLIFIED POLYMORPHIC DNA TECHNIQUE; RECOMBINATION, GENETIC; SEQUENCE ALIGNMENT; SPORES, FUNGAL;

BASIDIOMYCOTA; FUNGI; LACCARIA; LACCARIA BICOLOR;

EID: 52649109258     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2008.02614.x     Document Type: Article

References (44)

1. Arnau J, Housego AP, Oliver RP. 1994. The use of RAPD markers in genetic analysis of the plant pathogenic fungus Cladosporium fulvum. Current Genetics 25 : 438 444.
2. Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. 2002. ARACHNE: a whole-genome shotgun assembler. Genome Research 12 : 177 189.
3. Callac P, Desmerger C, Kerrigan RW, Imbernn M. 1997. Conservation of genetic linkage with map expansion in distantly related crosses of Agaricus bisporus. FEMS Microbiology Letters 146 : 235 240.
4. Debets F, Swart K, Hoekstra RF, Bos CJ. 1993. Genetic maps of eight linkage groups of Aspergillus niger based on mitotic mapping. Current Genetics 23 : 47 53.
5. Di Battista C, Bouchard D, Martin F, Genere B, Amirault J, Le Tacon F. 2002. Survival after outplanting of the ectomycorrhizal fungus Laccaria bicolor S238N inoculated on Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) cuttings. Annals of Forest Science 59 : 81 92.
6. Di Battista C, Selosse MA, Bouchard D, Stenström E, Le Tacon F. 1996. Variations in symbiotic efficiency, phenotypic characters and ploidy level among different isolates of the ectomycorrhizal basidiomycete Laccaria bicolor strain S238. Mycological Research 100 : 1315 1324.
7. Doudrick RL, Raffle VL, Nelson CD, Furnier GR. 1995. Genetic analysis of homokaryons from basidiome of Laccaria bicolor using RAPD markers. Mycological Research 99 : 1361 1366.
8. Fries N. 1983. Spore germination, homing reaction, and intersterility groups in Laccaria laccata (Agaricales). Mycologia 75 : 221 227.
9. Gale LR, Bryant JD, Calvo S, Giese H, Katan T, O'Donnell K, Suga H, Taga M, Usgaard TR, Ward TJ et al. 2005. Chromosome complement of the fungal plant pathogen Fusarium graminearum based on genetic and physical mapping and cytological observations. Genetics 171 : 985 1001.
10. Grewal SIS, Klar AJS. 1997. Recombinationally repressed region between mat2 and mat3 loci shares homology to centromeric repeats and regulates directionality of mating-type switching in fission yeast. Genetics 146 : 1221 1238.
11. Henrion B, Le Tacon F, Martin F. 1992. Rapid identification of genetic variation of ectomycorrhizal fungi by amplification of ribosomal RNA genes. New Phytologist 122 : 289 298.
12. Hulbert SH, Ilott TW, Legg EJ, Lincoln SE, Lander ES, Michelmore RW. 1988. Genetic analysis of the fungus, Bremia lactucae, using restriction fragment length polymorphisms. Genetics 120 : 947 958.
13. Kerrigan RW. 1993. Meiotic behavior and linkage relationships in the secondarily homothallic fungus Agaricus bisporus. Genetics 133 : 225 236.
14. Koressaar T, Remm M. 2007. Enhancements and modifications of primer design program Primer3. Bioinformatics 23 : 1289 1291.
15. Kosambi DD. 1944. The estimation of map distances from recombination values. Annals of Eugenics 12 : 172 175.
16. Krumsiek J, Arnold R, Rattei T. 2007. Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 23 : 1026 1028.
17. Larraya LM, Perez G, Ritter E, Pisabarro AG, Ramirez L. 2000. Genetic linkage map of the edible basidiomycete Pleurotus ostreatus. Applied and Environmental Microbiology 66 : 5290 5300.
18. Le Tacon F, Alvarez IF, Bouchard D, Henrion B, Jackson JM, Luff S, Parlade JI, Pera J, Stenström E, Villeneuve N et al. 1992. Variation in field response of forest trees to nursery ectomycorrhizal inoculation in Europe. In : Read DJ, Lewis DH, Fitter AH, Alexander IJ, eds. Mycorrhizas in ecosystems. Wallingford, UK : CAB International, 119 134.
19. Lee N, Bakkeren G, Wong K, Sherwood JE, Kronstad JW. 1999. The mating-type and pathogenicity locus of the fungus Ustilago hordei spans a 500-kb region. Proceedings of the National Academy of Sciences, USA 96 : 15026 15031.
20. Lengeler KB, Fox DS, Fraser JA, Allen A, Forrester K, Dietrich FS, Heitman J. 2002. Mating-type locus of Cryptococcus neoformans: a step in the evolution of sex chromosomes. Eukaryotic Cell 1 : 704 718.
21. Lim S, Notley-McRobb L, Lim M, Carter DA. 2005. A comparison of the nature and abundance of microsatellites in 14 fungal genomes. Fungal Genetics and Biology 41 : 1025 1036.
22. Marra R, Huang JC, Fung E, Nielsen K, Heitman J, Vilgalys R, Mitchell TG. 2004. A genetic linkage map of Cryptococcus neoformans variety neoformans serotype D. Genetics 167 : 619 631.
23. Martin F, Aerts A, Ahrén D, Brun A, Danchin EGJ, Duchaussoy F, Gibon J, Kohler A, Lindquist E, Pereda V et al. 2008. Symbiosis insights from the genome of the mycorrhizal basidiomycete Laccaria bicolor. Nature 452 : 88 92.
24. Martin F, Kohler A, Duplessis S. 2007. Living in harmony in the wood underground: ectomycorrhizal genomics. Current Opinion in Plant Biology 10 : 204 210.
25. Martin F, Lammers P, Tuskan GA, DiFazio SP, Podila GK. 2004. Symbiotic sequencing for the Populus mesocosm: DOE tackles the genomes of endomycorrhizal Glomus intraradices and ectomycorrhizal Laccaria bicolor. New Phytologist 161 : 330 335.
26. Martin F, Selosse MA, Le Tacon F. 1999. The nuclear rDNA intergenic spacer of the ectomycorrhizal basidiomycete Laccaria bicolor: structural analysis and allelic polymorphism. Microbiology 145 : 1605 1611.
27. Matheny PB, Curtis JM, Hofstetter V, Aime MC, Moncalvo JM, Ge ZW, Slot JC, Ammirati JF, Baroni TJ, Bougher NL et al. 2007. Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 98 : 982 995.
28. Mueller GJ, Mueller GM, Shih LH, Ammirati JF. 1993. Cytological studies in Laccaria (Agaricales). American Journal of Botany 80 : 316 321.
29. Mueller GM. 1982. The genus Laccaria in North America excluding Mexico. PhD thesis, University of Tennessee, Knoxville, TN, USA.
30. Mueller GM. 1991. The Swedish taxa Laccaria (Agaricales) with notes on their distribution. Nordic Journal of Botany 10 : 665 680.
31. Muraguchi H, Ito Y, Kamada T, Yabagi SO. 2003. A linkage map of the basidiomycete Coprinus cinereus based on RAPD and RFLP. Fungal Genetics and Biology 40 : 93 102.
32. Niculita-Hirzel H, Labbé J, Kohler A, Le Tacon F, Martin F, Sanders I, Kües U. 2008. Gene organization of the mating type regions in the ectomycorrhizal fungus Laccaria bicolor reveals distinct evolution between the two mating type loci New Phytologist 180 : 329 342.
33. Nitta N, Farman ML, Leong SA. 1997. Genome organization of Magnaporthe grisea: integration of genetic maps, clustering of transposable elements and identification of genome duplications and rearrangements. Theoretical and Applied Genetics 95 : 20 22.
34. Park SK, Penas MM, Ramirez L, Pisabarro AG. 2006. Genetic linkage map and expression analysis of genes expressed in the lamellae of the edible basidiomycete Pleurotus ostreatus. Fungal Genetics and Biology 43 : 376 387.
35. Poyatos JF, Hurst LD. 2007. The determinants of gene order conservation in yeasts. Genome Biology 8 : 233 236.
36. Raeder U, Thompson W, Broda P. 1989. RFLP-based genetic map of Phanerochate chrysosporium ME446: lignin peroxidase genes occur in clusters. Molecular Microbiology 3 : 911 918.
37. Selosse MA, Costa G, Di Battista C, Le Tacon F, Martin F. 1996. Meiotic segregation and recombination of the intergenic spacer of the ribosomal DNA in the ectomycorrhizal basidiomycete Laccaria bicolor. Current Genetics 30 : 332 337.
38. Solignac M, Mougel F, Vautrin D, Monnerot M, Cornuet JM. 2007. A third-generation microsatellite-based linkage map of the honey bee, Apis mellifera, and its comparison with the sequence-based physical map. Genome Biology 8 : R66.
39. Tuskan GA, Walla JA, Lundquist JE. 1990. Genetic-geographic variation in western gall rust in North Dakota. Phytopathology 80 : 857 861.
40. Tzeng TH, Lyngholm LK, Ford CF, Bronson CR. 1992. A restriction fragment length polymorphism map and electrophoretic karyotype of the fungal maize pathogen Cochliobolus heterostrophus. Genetics 130 : 81 96.
41. Van Ooijen JW, Voorrips RE. 2001. JoinMap 3.0, software for the calculation of genetic linkage maps. Wageningen, the Netherlands : Plant Research International. [ http://www.plant.wageningen-ur.nl ].
42. Vos P, Hogers R, Bleeker M, Reijans M, Vandelee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M et al. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research 23 : 4407 4414.
43. Yin T, Difazio S, Gunter LE, Riemenschneider D, Tuskan GA. 2004. Large-scale heterospecific distortion in Populus revealed by a dense genetic map. Theoretical and Applied Genetics 109 : 451 463.
44. Yin T, Zhang X, Huang M, Wang M, Zhuge Q, Tu S, Zhu L, Wu R. 2002. Molecular linkage map of the Populus genome. Genome 45 : 541 555.