Genome Structure of the Legume, Lotus japonicus

The legume Lotus japonicus has been widely used as a model system to investigate the genetic background of legume-specific phenomena such as symbiotic nitrogen fixation. Here, we report structural features of the L. japonicus genome. The 315.1-Mb sequences determined in this and previous studies correspond to 67% of the genome (472 Mb), and are likely to cover 91.3% of the gene space. Linkage mapping anchored 130-Mb sequences onto the six linkage groups. A total of 10 951 complete and 19 848 partial structures of protein-encoding genes were assigned to the genome. Comparative analysis of these genes revealed the expansion of several functional domains and gene families that are characteristic of L. japonicus. Synteny analysis detected traces of whole-genome duplication and the presence of synteny blocks with other plant genomes to various degrees. This study provides the first opportunity to look into the complex and unique genetic system of legumes.

[1]  J. Poulain,et al.  The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla , 2007, Nature.

[2]  Hedi Peterson,et al.  g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments , 2007, Nucleic Acids Res..

[3]  S. Tabata,et al.  Genome-wide Analyses of the Structural Gene Families Involved in the Legume-specific 5-Deoxyisoflavonoid Biosynthesis of Lotus japonicus , 2007, DNA research : an international journal for rapid publication of reports on genes and genomes.

[4]  Gary Stacey,et al.  Molecular Evolution of Lysin Motif-Type Receptor-Like Kinases in Plants1[W][OA] , 2007, Plant Physiology.

[5]  Bogumil J. Karas,et al.  A Cytokinin Perception Mutant Colonized by Rhizobium in the Absence of Nodule Organogenesis , 2007, Science.

[6]  S. Tabata,et al.  A Gain-of-Function Mutation in a Cytokinin Receptor Triggers Spontaneous Root Nodule Organogenesis , 2007, Science.

[7]  Robert D. Finn,et al.  New developments in the InterPro database , 2007, Nucleic Acids Res..

[8]  L. Parfrey,et al.  Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 in Saccharomyces cerevisiae , 2006, Nucleic acids research.

[9]  S. Tabata,et al.  Genome-wide analysis of ATP-binding cassette (ABC) proteins in a model legume plant, Lotus japonicus: comparison with Arabidopsis ABC protein family. , 2006, DNA research : an international journal for rapid publication of reports on genes and genomes.

[10]  S. Wessler,et al.  The Transposable Element Landscape of the Model Legume Lotus japonicus , 2006, Genetics.

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

[12]  M. Gribskov,et al.  The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) , 2006, Science.

[13]  Jeffrey A. Fawcett,et al.  A SINE Family Widely Distributed in the Plant Kingdom and its Evolutionary History , 2006, Plant Molecular Biology.

[14]  Bogumil J. Karas,et al.  Genetics of symbiosis in Lotus japonicus: recombinant inbred lines, comparative genetic maps, and map position of 35 symbiotic loci. , 2006, Molecular plant-microbe interactions : MPMI.

[15]  Takuji Sasaki,et al.  The map-based sequence of the rice genome , 2005, Nature.

[16]  S. Tabata,et al.  Comparison of the transcript profiles from the root and the nodulating root of the model legume Lotus japonicus by serial analysis of gene expression. , 2005, Molecular plant-microbe interactions : MPMI.

[17]  T. Mizuno,et al.  Pseudo-Response Regulators (PRRs) or True Oscillator Components (TOCs). , 2005, Plant & cell physiology.

[18]  Fredrik Dahl,et al.  Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments , 2005, Nucleic acids research.

[19]  D. Bartel,et al.  Antiquity of MicroRNAs and Their Targets in Land Plantsw⃞ , 2005, The Plant Cell Online.

[20]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt) , 2004, Nucleic Acids Res..

[21]  John Quackenbush,et al.  The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes , 2004, Nucleic Acids Res..

[22]  Takakazu Kaneko,et al.  Comprehensive structural analysis of the genome of red clover (Trifolium pratense L.). , 2005, DNA research : an international journal for rapid publication of reports on genes and genomes.

[23]  D. Bartel,et al.  Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. , 2004, Molecular cell.

[24]  Søren Bak,et al.  Comparative Genomics of Rice and Arabidopsis. Analysis of 727 Cytochrome P450 Genes and Pseudogenes from a Monocot and a Dicot1[w] , 2004, Plant Physiology.

[25]  Klaus F. X. Mayer,et al.  Comparative Analysis of the Receptor-Like Kinase Family in Arabidopsis and Rice , 2004, The Plant Cell Online.

[26]  K. Minamisawa,et al.  Transgenic Lotus japonicus with an ethylene receptor gene Cm-ERS1/H70A enhances formation of infection threads and nodule primordia. , 2004, Plant & cell physiology.

[27]  S. Tabata,et al.  Characteristics of the Lotus Japonicus Gene Repertoire Deduced from Large-Scale Expressed Sequence Tag (EST) Analysis , 2004, Plant Molecular Biology.

[28]  S. Tabata,et al.  Exploitation of colinear relationships between the genomes of Lotus japonicus, Pisum sativum and Arabidopsis thaliana, for positional cloning of a legume symbiosis gene , 2004, Theoretical and Applied Genetics.

[29]  Sam Griffiths-Jones,et al.  The microRNA Registry , 2004, Nucleic Acids Res..

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

[31]  S. Tabata,et al.  Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases , 2003, Nature.

[32]  Erez Y. Levanon,et al.  Widespread occurrence of antisense transcription in the human genome , 2003, Nature Biotechnology.

[33]  K. Fukui,et al.  Development of a quantitative pachytene chromosome map in Oryza sativa by imaging methods. , 2003, Genes & genetic systems.

[34]  S. Wienkoop,et al.  Proteome Analysis. Novel Proteins Identified at the Peribacteroid Membrane from Lotus japonicus Root Nodules1 , 2003, Plant Physiology.

[35]  S. Tabata,et al.  Structural analysis of a Lotus japonicus genome. IV. Sequence features and mapping of seventy-three TAC clones which cover the 7.5 mb regions of the genome. , 2003, DNA research : an international journal for rapid publication of reports on genes and genomes.

[36]  S. Tabata,et al.  Structural analysis of a Lotus japonicus genome. III. Sequence features and mapping of sixty-two TAC clones which cover the 6.7 Mb regions of the genome. , 2003, DNA research : an international journal for rapid publication of reports on genes and genomes.

[37]  S. Tabata,et al.  Structural analysis of a Lotus japonicus genome. V. Sequence features and mapping of sixty-four TAC clones which cover the 6.4 mb regions of the genome. , 2003, DNA research : an international journal for rapid publication of reports on genes and genomes.

[38]  E. Mauceli,et al.  Whole-genome sequence assembly for mammalian genomes: Arachne 2. , 2003, Genome research.

[39]  S. Tabata,et al.  Shoot control of root development and nodulation is mediated by a receptor-like kinase , 2002, Nature.

[40]  M. Ohmori,et al.  HAR1 mediates systemic regulation of symbiotic organ development , 2002, Nature.

[41]  J. Stougaard,et al.  Chromosomal map of the model legume Lotus japonicus. , 2002, Genetics.

[42]  S. Tabata,et al.  A genetic linkage map of the model legume Lotus japonicus and strategies for fast mapping of new loci. , 2002, Genetics.

[43]  M. A. Rosenblad,et al.  Prediction of signal recognition particle RNA genes. , 2002, Nucleic acids research.

[44]  S. Eddy,et al.  Automated de novo identification of repeat sequence families in sequenced genomes. , 2002, Genome research.

[45]  S. Tabata,et al.  A plant receptor-like kinase required for both bacterial and fungal symbiosis , 2002, Nature.

[46]  D. Bouchez,et al.  A Novel Family of Calmodulin-binding Transcription Activators in Multicellular Organisms* , 2002, The Journal of Biological Chemistry.

[47]  J. Sheen,et al.  Two-Component Signal Transduction Pathways in Arabidopsis1 , 2002, Plant Physiology.

[48]  S. Tabata,et al.  Structural analysis of a Lotus japonicus genome. II. Sequence features and mapping of sixty-five TAC clones which cover the 6.5-mb regions of the genome. , 2002, DNA research : an international journal for rapid publication of reports on genes and genomes.

[49]  Y. Nakamura,et al.  Structural analysis of a Lotus japonicus genome. I. Sequence features and mapping of fifty-six TAC clones which cover the 5.4 mb regions of the genome. , 2001, DNA research : an international journal for rapid publication of reports on genes and genomes.

[50]  M Taketa,et al.  Construction of a genetic linkage map of the model legume Lotus japonicus using an intraspecific F2 population. , 2001, DNA research : an international journal for rapid publication of reports on genes and genomes.

[51]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[52]  M. Kawaguchi.  Lotus japonicus `Miyakojima' MG-20: An Early-Flowering Accession Suitable for Indoor Handling , 2000, Journal of Plant Research.

[53]  S. Tabata,et al.  Genome and Chromosome Dimensions of Lotus japonicus , 2000, Journal of Plant Research.

[54]  S. Brunak,et al.  Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. , 2000, Journal of molecular biology.

[55]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[56]  D. M. Roberts,et al.  Water-selective and multifunctional aquaporins from Lotus japonicus nodules , 2000, Planta.

[57]  P. Huijser,et al.  Molecular characterisation of the Arabidopsis SBP-box genes. , 1999, Gene.

[58]  S. Eddy,et al.  A computational screen for methylation guide snoRNAs in yeast. , 1999, Science.

[59]  K. Nakai,et al.  PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. , 1999, Trends in biochemical sciences.

[60]  Yoshihiro Ugawa,et al.  Plant cis-acting regulatory DNA elements (PLACE) database: 1999 , 1999, Nucleic Acids Res..

[61]  V. Brendel,et al.  Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA. , 1998, Nucleic acids research.

[62]  G. Hagen,et al.  The ARF family of transcription factors and their role in plant hormone-responsive transcription , 1998, Cellular and Molecular Life Sciences CMLS.

[63]  M. Borodovsky,et al.  GeneMark.hmm: new solutions for gene finding. , 1998, Nucleic acids research.

[64]  Shigeki Mitaku,et al.  SOSUI: classification and secondary structure prediction system for membrane proteins , 1998, Bioinform..

[65]  M. Adams,et al.  A tool for analyzing and annotating genomic sequences. , 1997, Genomics.

[66]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[67]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[68]  Gapped BLAST and PSI-BLAST: A new , 1997 .

[69]  Peter G. Korning,et al.  Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. , 1996, Nucleic acids research.

[70]  E. Uberbacher,et al.  Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

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

[72]  David Sankoff,et al.  Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison , 1983 .

[73]  Christus,et al.  A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins , 2022 .