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| 1 | SeSaMe:Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi-associated Microorganisms显示文摘Arbuscular mycorrhizal fungi(AMF)are plant root symbionts that play key roles in plant growth and soil fertility.They are obligate biotrophic fungi that form coenocytic multinucleated hyphae and spores.Numerous studies have shown that diverse microorganisms live on the surface of and inside their mycelia,resulting in a metagenome when whole-genome sequencing(WGS)data are obtained from sequencing AMF cultivated in vivo.The metagenome contains not only the AMF sequences,but also those from associated microorganisms.In this study,we introduce a novel bioinformatics program,Spore-associated Symbiotic Microbes(SeSaMe),designed for taxonomic classification of short sequences obtained by next-generation DNA sequencing.A genus-specific usage bias database was created based on amino acid usage and codon usage of a three consecutive codon DNA 9-mer encoding an amino acid trimer in a protein secondary structure.The program distinguishes between coding sequence(CDS)and non-CDS,and classifies a query sequence into a genus group out of 54 genera used as reference.The mean percentages of correct predictions of the CDS and the non-CDS test sets at the genus level were 71% and 50% for bacteria,68% and 73% for fungi(excluding AMF),and 49% and 72% for AMF(Rhizophagus irregularis),respectively.SeSaMe provides not only a means for estimating taxonomic diversity and abundance but also the gene reservoir of the reference taxonomic groups associated with AMF.Therefore,it enables users to study the symbiotic roles of associated microorganisms.It can also be applicable to other microorganisms as well as soil metagenomes.SeSaMe is freely available at www.fungalsesame.org. | Jee Eun Kang Antonio Ciampi Mohamed Hijri | 2020 | Genomics, Proteomics & Bioinformatics2020，18，5： | 2 |
| 2 | Low gene copy number shows that arbuscular mycorrhizal fungi inherit genetically different nuclei显示文摘 | HIJRI M SANDERS IR | 2005 | Nature2005，433，7022： | 1 |
| 3 | Visualization of ribosomal DNA loci in spore interphasic nuclei of glomalean fungi by fluorescence in situ hybridization显示文摘 | Sophie Trouvelot Diederik van Tuinen Mohamed Hijri V. Gianinazzi-Pearson | 1999 | Mycorrhiza1999，，4： | 1 |
| 4 | Visualization of ribosomal DNA loci in spore interphasic nuclei of glomalean fungi by fluorescence in situ hybridization显示文摘 | Trouvelot S Tuinen D V Hijri M | 1999 | Mycorrhiza1999，8，： | 1 |
| 5 | Screening, Identification and Evaluation of Potential Biocontrol Fungal Endophytes against Rhizoctonia s olani AG3 on Potato Plants 显示文摘 | LAHLALI IR HIJRI M | 2010 | FEMS Mierobiol Lett2010，311，： | 1 |
| 6 | Low gene copy number shows that arbuscular mycorrhizal fungi inherit genetically different nuclei显示文摘 | HIJRI M SANDERS I R | 2005 | Nature2005，433，： | 1 |
| 7 | The arbuscular mycorrhlzal fungus, Glomus irregulare, controls the mycotoxin production of Fusarium sambucinum in the pathogenesis of potato显示文摘 | Ismail Y McCormick S Hijri M | 2013 | FEMS Microbiology Letters2013，348，1： | 1 |
| 8 | Communities of arbuscularmycorrhizalfungi in arable soils are not necessarily low in diversity 显示文摘 | Hijri I Sykorova Z | 2006 | Molecular Ecology2006，15，： | 1 |
| 9 | Molecular identification of arbuscular mycorrhizal fungi in roots : Perspectives and problems 显示文摘 | Dirk Redecker Isabelle Hijri Andres Wiemken | 2003 | Folia Geobotanica2003，38，： | 1 |
| 10 | Epiparasitic plants specialized on arbuscular myeorrhizal fungi显示文摘 | Bidartondo M I Redecker D Hijri I | 2002 | Nature2002，419，6905： | 1 |
| 11 | Molecular identification of arbuscular mycorrhizal fungi in roots: Perspectives and prob- lems显示文摘 | Redecker D Hijri I Wiemken A | 2003 | Folia Geobotanica2003，38，2： | 1 |
| 12 | Epiparasitic plants specialized on arbuscular mycorrhizal fungi显示文摘 | Bidartondo M I Redecker D Hijri I | 2002 | Nature2002，419，： | 1 |
| 13 | Effect of arbuscular myeorrhizal fungi on trace metal uptake by sunflower plants grown on cadmium contaminated soil 显示文摘 | Hassan S E Hijri M St-Arnaud M | 2013 | New Biotechnology2013，30，6： | 1 |
| 14 | Effect of arbuscular mycorrhizal fungi on trace metal uptake by sunflower plants grown on cadmium contaminated soil显示文摘 | HASSAN S E HIJRI M ST-ARNAUD M | 2013 | New Biotechnology2013，30，6： | 1 |
| 15 | Epiparasitic plants specialized on arbuscular mycorrhizal fungi显示文摘 | Bidartondo M I Redecker D Hijri I | 2002 | Nature2002，419，： | 1 |
| 16 | Screening,identification and evaluation of poten- tial biocontrol fungal endophytes against Rhizocton solani AG3 on potato plants显示文摘 | LAI4LMJ R HIJRI M | 2010 | Research letter2010，311，： | 1 |
| 17 | Molecular characterization of chromosome termini of the arbuscular mycorrhizal fungus Glomus intraradices (Glomeromycota)显示文摘 | Hijri M Niculita H Sanders I R | 2007 | Fungal Genetics and Biology2007，44，： | 1 |
| 18 | SeSaMe PS Function:Functional Analysis of the Whole Metagenome Sequencing Data of the Arbuscular Mycorrhizal Fungi显示文摘In this study,we introduce a novel bioinformatics program,Spore-associated Symbiotic Microbes Position-specific Function(SeSaMe PS Function),for position-specific functional analysis of short sequences derived from metagenome sequencing data of the arbuscular mycorrhizal fungi.The unique advantage of the program lies in databases created based on genus-specific sequence properties derived from protein secondary structure,namely amino acid usages,codon usages,and codon contexts of 3-codon DNA 9-mers.SeSaMe PS Function searches a query sequence against reference sequence database,identifies 3-codon DNA 9-mers with structural roles,and creates a comparative dataset containing the codon usage biases of the 3-codon DNA 9-mers from 54 bacterial and fungal genera.The program applies correlation principal component analysis in conjunction with K-means clustering method to the comparative dataset.3-codon DNA 9-mers clustered as a sole member or with only a few members are often structurally and functionally distinctive sites that provide useful insights into important molecular interactions.The program provides a versatile means for studying functions of short sequences from metagenome sequencing and has a wide spectrum of applications.SeSaMe PS Function is freely accessible at www.fungalsesame.org. | Jee Eun Kang Antonio Ciampi Mohamed Hijri | 2020 | Genomics, Proteomics & Bioinformatics2020，18，5： | 0 |
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