Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays

BackgroundLegumes are the third largest family of flowering plants and are unique among crop species in their ability to fix atmospheric nitrogen. As a result of recent genome sequencing efforts, legumes are now one of a few plant families with extensive genomic and transcriptomic data available in multiple species. The unprecedented complexity and impending completeness of these data create opportunities for new approaches to discovery.ResultsWe report here a transcriptional analysis in six different organ types of syntenic regions totaling approximately 1 Mb between the legume plants barrel medic (Medicago truncatula) and soybean (Glycine max) using oligonucleotide tiling microarrays. This analysis detected transcription of over 80% of the predicted genes in both species. We also identified 499 and 660 transcriptionally active regions from barrel medic and soybean, respectively, over half of which locate outside of the predicted exons. We used the tiling array data to detect differential gene expression in the six examined organ types and found several genes that are preferentially expressed in the nodule. Further investigation revealed that some collinear genes exhibit different expression patterns between the two species.ConclusionThese results demonstrate the utility of genome tiling microarrays in generating transcriptomic data to complement computational annotation of the newly available legume genome sequences. The tiling microarray data was further used to quantify gene expression levels in multiple organ types of two related legume species. Further development of this method should provide a new approach to comparative genomics aimed at elucidating genome organization and transcriptional regulation.

[1]  Lauren M McIntyre,et al.  Common pattern of evolution of gene expression level and protein sequence in Drosophila. , 2004, Molecular biology and evolution.

[2]  Virginia Walbot,et al.  Genetic diversity contribution to errors in short oligonucleotide microarray analysis. , 2006, Plant biotechnology journal.

[3]  J. Ecker,et al.  Applications of DNA tiling arrays for whole-genome analysis. , 2005, Genomics.

[4]  Gordon K. Smyth,et al.  Using DNA microarrays to study gene expression in closely related species , 2007, Bioinform..

[5]  E. Schadt,et al.  Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. , 2005, Trends in genetics : TIG.

[6]  S. P. Fodor,et al.  Large-Scale Transcriptional Activity in Chromosomes 21 and 22 , 2002, Science.

[7]  Joseph R. Ecker,et al.  Corrigendum to ‘‘Applications of DNA tiling arrays for whole-genome analysis’’ [Genomics 85 (2005) 1–15] , 2005 .

[8]  R. Shoemaker,et al.  Paleopolyploidy and gene duplication in soybean and other legumes. , 2006, Current opinion in plant biology.

[9]  Lei Li,et al.  NMPP: a user-customized NimbleGen microarray data processing pipeline , 2006, Bioinform..

[10]  Colin D. Meiklejohn,et al.  Sex-Dependent Gene Expression and Evolution of the Drosophila Transcriptome , 2003, Science.

[11]  M. Luckow,et al.  The Rest of the Iceberg. Legume Diversity and Evolution in a Phylogenetic Context1 , 2003, Plant Physiology.

[12]  Jun Wang,et al.  Genome-wide transcription analyses in rice using tiling microarrays , 2006, Nature Genetics.

[13]  Terence P. Speed,et al.  Expression profiling in primates reveals a rapid evolution of human transcription factors , 2006, Nature.

[14]  N. Young,et al.  Comparative genome analysis of mungbean (Vigna radiata L. Wilczek) and cowpea (V. unguiculata L. Walpers) using RFLP mapping data , 1993, Theoretical and Applied Genetics.

[15]  G. Stacey,et al.  Distinct, crucial roles of flavonoids during legume nodulation. , 2007, Trends in plant science.

[16]  Jun Wang,et al.  Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture , 2005, Genome Biology.

[17]  J. Vincent.  A manual for the practical study of root-nodule bacteria , 1971 .

[18]  Paul J. Rushton,et al.  CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences , 2007, BMC Bioinformatics.

[19]  G. Church,et al.  RNA expression analysis using a 30 base pair resolution Escherichia coli genome array , 2000, Nature Biotechnology.

[20]  J. Hacia,et al.  Comparative analysis of gene-expression patterns in human and African great ape cultured fibroblasts. , 2003, Genome research.

[21]  Wei Zhu,et al.  Improvement of whole-genome annotation of cereals through comparative analyses. , 2007, Genome research.

[22]  D. Buzas,et al.  Promoter trapping in Lotus japonicus reveals novel root and nodule GUS expression domains. , 2005, Plant & cell physiology.

[23]  S. Pääbo,et al.  Intra- and Interspecific Variation in Primate Gene Expression Patterns , 2002, Science.

[24]  G. Helt,et al.  Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution , 2005, Science.

[25]  Mark Gerstein,et al.  Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. , 2005, Trends in genetics : TIG.

[26]  B. Roe,et al.  Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes , 2006, Proceedings of the National Academy of Sciences.

[27]  Dawei Li,et al.  The Genomes of Oryza sativa: A History of Duplications , 2005, PLoS biology.

[28]  G. Stacey,et al.  Endogenous isoflavones are essential for the establishment of symbiosis between soybean and Bradyrhizobium japonicum. , 2006, The Plant journal : for cell and molecular biology.

[29]  H. Spaink,et al.  Lotus japonicus gene Ljsbp is highly conserved among plants and animals and encodes a homologue to the mammalian selenium-binding proteins. , 2002, Molecular plant-microbe interactions : MPMI.

[30]  M. Gerstein,et al.  A Pilot Study of Transcription Unit Analysis in Rice Using Oligonucleotide Tiling-path Microarray , 2005, Plant Molecular Biology.

[31]  Brian W Diers,et al.  A Decade of QTL Mapping for Cyst Nematode Resistance in Soybean , 2004 .

[32]  B. Roe,et al.  Estimating genome conservation between crop and model legume species. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[33]  Thomas E. Royce,et al.  Global Identification of Human Transcribed Sequences with Genome Tiling Arrays , 2004, Science.

[34]  S. Pääbo,et al.  Parallel Patterns of Evolution in the Genomes and Transcriptomes of Humans and Chimpanzees , 2005, Science.

[35]  R. Shoemaker,et al.  Genome conservation among three legume genera detected with DNA markers. , 1995, Genome.

[36]  Mark Gerstein,et al.  Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. , 2005, Genome research.

[37]  Mark Gerstein,et al.  Global Identification and Characterization of Transcriptionally Active Regions in the Rice Genome , 2007, PloS one.

[38]  B. Roe,et al.  Sequencing the Genespaces of Medicago truncatula and Lotus japonicus1 , 2005, Plant Physiology.

[39]  B. Haas,et al.  Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology , 2006, BMC Genomics.

[40]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[41]  H. Ellegren,et al.  From wild wolf to domestic dog: gene expression changes in the brain. , 2004, Brain research. Molecular brain research.

[42]  B. Roe,et al.  Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana , 2005, BMC Plant Biology.

[43]  Joseph M. Dale,et al.  Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome , 2003, Science.

[44]  John M. Walker,et al.  Comparative Genomics , 2007, Methods In Molecular Biology™.

[45]  T. Huguet,et al.  Plant gene expression in effective and ineffective root nodules of alfalfa (Medicago sativa) , 1987, Plant Molecular Biology.