Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana.

To gain insight into genomic relationships between soybean (Glycine max) and Medicago truncatula, eight groups of bacterial artificial chromosome (BAC) contigs, together spanning 2.60 million base pairs (Mb) in G. max and 1.56 Mb in M. truncatula, were compared through high-resolution physical mapping combined with sequence and hybridization analysis of low-copy BAC ends. Cross-hybridization among G. max and M. truncatula contigs uncovered microsynteny in six of the contig groups and extensive microsynteny in three. Between G. max homoeologous (within genome duplicate) contigs, 85% of coding and 75% of noncoding sequences were conserved at the level of cross-hybridization. By contrast, only 29% of sequences were conserved between G. max and M. truncatula, and some kilobase-scale rearrangements were also observed. Detailed restriction maps were constructed for 11 contigs from the three highly microsyntenic groups, and these maps suggested that sequence order was highly conserved between G. max duplicates and generally conserved between G. max and M. truncatula. One instance of homoeologous BAC contigs in M. truncatula was also observed and examined in detail. A sequence similarity search against the Arabidopsis thaliana genome sequence identified up to three microsyntenic regions in A. thaliana for each of two of the legume BAC contig groups. Together, these results confirm previous predictions of one recent genome-wide duplication in G. max and suggest that M. truncatula also experienced ancient large-scale genome duplications.

[1]  D. Grant,et al.  Genome organization in dicots: genome duplication in Arabidopsis and synteny between soybean and Arabidopsis. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[2]  S. Tanksley,et al.  Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Marek Lf,et al.  BAC contig development by fingerprint analysis in soybean. , 1997 .

[4]  J. Salse,et al.  Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project. , 2002, Nucleic acids research.

[5]  Klaas Vandepoele,et al.  The hidden duplication past of Arabidopsis thaliana , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Daphne Preuss,et al.  Beyond the Arabidopsis Genome: Opportunities for Comparative Genomics1 , 2002, Plant Physiology.

[7]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[8]  K. Theres,et al.  Comparative sequence analysis reveals extensive microcolinearity in the lateral suppressor regions of the tomato, Arabidopsis, and Capsella genomes. , 2001, The Plant cell.

[9]  R. Shoemaker,et al.  Genome duplication in soybean (Glycine subgenus soja). , 1996, Genetics.

[10]  R. Wilson,et al.  High throughput fingerprint analysis of large-insert clones. , 1997, Genome research.

[11]  D. Cook,et al.  Construction of a bacterial artificial chromosome library of Medicago truncatula and identification of clones containing ethylene-response genes , 1999, Theoretical and Applied Genetics.

[12]  R. Tarchini,et al.  The Complete Sequence of 340 kb of DNA around the Rice Adh1–Adh2 Region Reveals Interrupted Colinearity with Maize Chromosome 4 , 2000, Plant Cell.

[13]  D. Cook,et al.  Medicago truncatula--a model in the making! , 1999, Current opinion in plant biology.

[14]  K. Devos,et al.  Genome Relationships: The Grass Model in Current Research , 2000, Plant Cell.

[15]  J. M. Lee,et al.  Genome organization in dicots. II. Arabidopsis as a ’bridging species’ to resolve genome evolution events among legumes , 2001, Theoretical and Applied Genetics.

[16]  B. Keller,et al.  Colinearity and gene density in grass genomes. , 2000, Trends in plant science.

[17]  S. Allouis.  Construction of a bacterial artificial chromosome library and gene targeting in pearl millet. , 2000 .

[18]  R. Shoemaker,et al.  RFLP mapping in soybean: association between marker loci and variation in quantitative traits. , 1990, Genetics.

[19]  P. Schulze-Lefert,et al.  A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome. , 1998, Nucleic acids research.

[20]  J. Bennetzen,et al.  Colinearity and its exceptions in orthologous adh regions of maize and sorghum. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[21]  J. Bennetzen.  Comparative Sequence Analysis of Plant Nuclear Genomes: Microcolinearity and Its Many Exceptions , 2000, Plant Cell.

[22]  A. Kereszt,et al.  A receptor kinase gene regulating symbiotic nodule development , 2002, Nature.

[23]  N. Young,et al.  A bacterial artificial chromosome library for soybean and identification of clones near a major cyst nematode resistance gene , 1998, Theoretical and Applied Genetics.

[24]  T. Bisseling,et al.  Microsynteny between pea and Medicago truncatula in the SYM2 region , 2002, Plant Molecular Biology.

[25]  Brandon S. Gaut,et al.  Evolutionary dynamics of grass genomes , 2002 .

[26]  K. Devos,et al.  Plant comparative genetics after 10 years. , 1998, Science.

[27]  D. Grant,et al.  Soybean genomic survey: BAC-end sequences near RFLP and SSR markers. , 2001, Genome.

[28]  M. Olson,et al.  Multiple-complete-digest restriction fragment mapping: generating sequence-ready maps for large-scale DNA sequencing. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[29]  R. Shoemaker,et al.  BAC contig development by fingerprint analysis in soybean. , 1997, Genome.

[30]  I. Bancroft,et al.  Comparative physical mapping of segments of the genome of Brassica oleracea var. alboglabra that are homoeologous to sequenced regions of chromosomes 4 and 5 of Arabidopsis thaliana. , 2000, The Plant journal : for cell and molecular biology.

[31]  B. Burr,et al.  Gene mapping with recombinant inbreds in maize. , 1988, Genetics.

[32]  R. Shoemaker,et al.  Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana , 2003, Theoretical and Applied Genetics.

[33]  T. Bisseling,et al.  Integration of the FISH pachytene and genetic maps of Medicago truncatula. , 2001, The Plant journal : for cell and molecular biology.

[34]  N. Young,et al.  Comparative genomic analysis of sequences sampled from a small region on soybean (Glycine max) molecular linkage group G. , 2002, Genome.

[35]  Gualtieri G.,et al.  Microsynteny between the Medicago truncatula SYM2-orthologous genomic region and another region located on the same chromosome arm , 2002, Theoretical and Applied Genetics.

[36]  H. Mewes,et al.  Conservation of microstructure between a sequenced region of the genome of rice and multiple segments of the genome of Arabidopsis thaliana. , 2001, Genome research.

[37]  M. Delseny,et al.  Extensive Duplication and Reshuffling in the Arabidopsis Genome , 2000, Plant Cell.