scholarly journals Genomics of Phytopathogenic Fungi and the Development of Bioinformatic Resources

2002 ◽  
Vol 15 (5) ◽  
pp. 421-427 ◽  
Author(s):  
Darren M. Soanes ◽  
Wendy Skinner ◽  
John Keon ◽  
John Hargreaves ◽  
Nicholas J. Talbot
Keyword(s):  
Relational Database ◽  
Expressed Sequence Tags ◽  
Magnaporthe Grisea ◽  
Mycosphaerella Graminicola ◽  
Phytopathogenic Fungi ◽  
Current Status ◽  
Gene Sequences ◽  
Fungal Genomics ◽  
Est Sequence ◽  
Expressed Sequence

Genomic resources available to researchers studying phytopathogenic fungi are limited. Here, we briefly review the genomic and bioinformatic resources available and the current status of fungal genomics. We also describe a relational database containing sequences of expressed sequence tags (ESTs) from three phytopathogenic fungi, Blumeria graminis, Magnaporthe grisea, and Mycosphaerella graminicola, and the methods and underlying principles required for its construction. The database contains significant annotation for each EST sequence and is accessible at http://cogeme.ex.ac.uk . An easy-to-use interface allows the user to identify gene sequences by using simple text queries or homology searches. New querying functions and large sequence sets from a variety of phytopathogenic species will be incorporated in due course.

Analysis of expressed sequence tags from the wheat leaf blotch pathogen Mycosphaerella graminicola (anamorph Septoria tritici)

2005 ◽  
Vol 42 (5) ◽  
pp. 376-389 ◽  
Author(s):  
John Keon ◽  
John Antoniw ◽  
Jason Rudd ◽  
Wendy Skinner ◽  
John Hargreaves ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Mycosphaerella Graminicola ◽  
Septoria Tritici ◽  
Leaf Blotch ◽  
Wheat Leaf ◽  
Expressed Sequence

EST mining for structure and expression of genes in the region of the wheat high-molecular-weight glutenin loci

Genome ◽  
2009 ◽  
Vol 52 (8) ◽  
pp. 726-740 ◽  
Author(s):  
O. D. Anderson
Keyword(s):  
Expressed Sequence Tags ◽  
Genomic Region ◽  
Chromatin Domain ◽  
Gene Sequences ◽  
Orthologous Genes ◽  
Coding Regions ◽  
Expression Of Genes ◽  
Depth Analysis ◽  
Genes Encoding ◽  
Expressed Sequence

An in-depth analysis was carried out with expressed sequence tags (ESTs) for genes in and near the HMW-GS loci. Considerations for using ESTs are discussed, including the occurrence of chimeric and aberrant HMW-GS ESTs. Complete gene sequences demonstrated the feasibility of constructing accurate full-length coding regions from EST assemblies and found, or supported, errors in several previously reported HMW-GS gene sequences. New complete HMW-GS gene sequences are reported for the cultivars Chinese Spring and Glenlea. The Ay subunit gene, which is considered null in cultivated wheats, was shown to transcribe in at least two germplasms. Analyses support the conclusion that of the five known genes within this genomic region, the two HMW-GS genes and the globulin gene are highly expressed. The other two genes, encoding a receptor kinase and a protein kinase, have one and no identifiable wheat EST, respectively, although ESTs are found for the orthologous genes in barley. The ESTs of all five genes within the HMW-GS region are either definitely associated with the endosperm or possibly originate from imbibed seed, suggesting the four distinct gene classes in this region are part of a seed or endosperm chromatin domain. EST resources were also used to determine relative abundance of ESTs for all classes of wheat prolamines and indicated differential levels of expression both among germplasms and among the three genomes of hexaploid wheats.

scholarly journals Gene Discovery and Gene Expression in the Rice Blast Fungus, Magnaporthe grisea: Analysis of Expressed Sequence Tags

2004 ◽  
Vol 17 (12) ◽  
pp. 1337-1347 ◽  
Author(s):  
Daniel J. Ebbole ◽  
Yuan Jin ◽  
Michael Thon ◽  
Huaqin Pan ◽  
Eric Bhattarai ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expressed Sequence Tags ◽  
Magnaporthe Grisea ◽  
Large Fraction ◽  
Cell Types ◽  
Growth Conditions ◽  
Mitogen Activated Protein Kinase ◽  
Cdna Libraries ◽  
Fungal Genes ◽  
Expressed Sequence

Over 28,000 expressed sequence tags (ESTs) were produced from cDNA libraries representing a variety of growth conditions and cell types. Several Magnaporthe grisea strains were used to produce the libraries, including a nonpathogenic strain bearing a mutation in the PMK1 mitogen-activated protein kinase. Approximately 23,000 of the ESTs could be clustered into 3,050 contigs, leaving 5,127 singleton sequences. The estimate of 8,177 unique sequences indicates that over half of the genes of the fungus are represented in the ESTs. Analysis of EST frequency reveals growth and cell type-specific patterns of gene expression. This analysis establishes criteria for identification of fungal genes involved in pathogenesis. A large fraction of the genes represented by ESTs have no known function or described homologs. Manual annotation of the most abundant cDNAs with no known homologs allowed us to identify a family of metallothionein proteins present in M. grisea, Neurospora crassa, and Fusarium graminearum. In addition, multiply represented ESTs permitted the identification of alternatively spliced mRNA species. Alternative splicing was rare, and in most cases, the alternate mRNA forms were unspliced, although alternative 5′ splice sites were also observed.

scholarly journals The genome and genes of Epichloe festucae

2007 ◽  
Vol 13 ◽  
pp. 461-465
Author(s):  
U. Hesse ◽  
P. Maynard ◽  
S. Macmil ◽  
G. Wiley ◽  
K. Andreeva ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Sequence Data ◽  
Gene Prediction ◽  
454 Sequencing ◽  
Inflorescence Development ◽  
Fungal Genomics ◽  
Epichloë Festucae ◽  
Sexual State ◽  
Expressed Sequence ◽  
Lolium Pratense

The ascomycete Epichloë festucae is a model endophyte that 1) switches between mutualistic and antagonistic states, 2) is seed transmissible, 3) has a sexual state amenable to genetic analysis, and 4) is rich in bioprotective alkaloids. This fungus grows systemically and intercellularly throughout the life of its host plant. On each reproductive tiller the fungus either infects benignly and transmits clonally in seeds, or produces its sexual state (stroma) and chokes inflorescence development. The E. festucae genome was estimated at 29 Mb in six chromosomes. The genome sequence was assembled from cloned insert end reads (4.2 x coverage) and preassembled pyrosequencing reads (454-sequencing: 20 x raw, 1.7 x assembled), giving 3967 supercontigs, of which 1004 were larger than 2 kb and covered 92% of the genome. Gene prediction with FGENESH identified ~10,000 putative genes. We also sequenced 25,000 ESTs from each of two normalised libraries — one of choked inflorescences, the other of benignly infected inflorescences — yielding 5077 E. festucae unigenes, annotated by BLAST and InterPro. Sequence data and annotations are stored in a database for visualisation and inspection with the GBrowse browser. The genomic sequences can be queried by BLAST at http://www.genome.ou.edu/blast/ ef_blastall.html. Keywords: bioinformatics, DNA sequence, Epichloë festucae, expressed sequence tags, Festucae pratensis, fungal genomics, Lolium pratense

Tc8, a Tourist-like Transposon in Caenorhabditis elegans

Genetics ◽  
2001 ◽  
Vol 158 (3) ◽  
pp. 1081-1088 ◽  
Author(s):  
Quang Hien Le ◽  
Kime Turcotte ◽  
Thomas Bureau
Keyword(s):  
Caenorhabditis Elegans ◽  
Expressed Sequence Tags ◽  
Large Family ◽  
Insertion Sequences ◽  
Normal Plant ◽  
Nematode Caenorhabditis Elegans ◽  
Plant Genomes ◽  
Plant Genes ◽  
Expressed Sequence ◽  
Eukaryotic Genomes

Abstract Members of the Tourist family of miniature inverted-repeat transposable elements (MITEs) are very abundant among a wide variety of plants, are frequently found associated with normal plant genes, and thus are thought to be important players in the organization and evolution of plant genomes. In Arabidopsis, the recent discovery of a Tourist member harboring a putative transposase has shed new light on the mobility and evolution of MITEs. Here, we analyze a family of Tourist transposons endogenous to the genome of the nematode Caenorhabditis elegans (Bristol N2). One member of this large family is 7568 bp in length, harbors an ORF similar to the putative Tourist transposase from Arabidopsis, and is related to the IS5 family of bacterial insertion sequences (IS). Using database searches, we found expressed sequence tags (ESTs) similar to the putative Tourist transposases in plants, insects, and vertebrates. Taken together, our data suggest that Tourist-like and IS5-like transposons form a superfamily of potentially active elements ubiquitous to prokaryotic and eukaryotic genomes.

scholarly journals VfODB: a comprehensive database of ESTs, EST-SSRs, mtSSRs, microRNA-target markers and genetic maps in Vicia faba

AoB Plants ◽  
2020 ◽  
Vol 12 (6) ◽  
Author(s):  
Morad M Mokhtar ◽  
Ebtissam H A Hussein ◽  
Salah El-Din S El-Assal ◽  
Mohamed A M Atia
Keyword(s):  
Vicia Faba ◽  
Faba Bean ◽  
Expressed Sequence Tags ◽  
Genetic Linkage ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Microrna Target ◽  
Genetic Linkage Maps ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract Faba bean (Vicia faba) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibres. Molecular markers tools represent an invaluable tool for faba bean breeders towards rapid crop improvement. Although there have historically been few V. faba genome resources available, several transcriptomes and mitochondrial genome sequence data have been released. These data in addition to previously developed genetic linkage maps represent a great resource for developing functional markers and maps that can accelerate the faba bean breeding programmes. Here, we present the Vicia faba Omics database (VfODB) as a comprehensive database integrating germplasm information, expressed sequence tags (ESTs), expressed sequence tags-simple sequence repeats (EST-SSRs), and mitochondrial-simple sequence repeats (mtSSRs), microRNA-target markers and genetic maps in faba bean. In addition, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps. Collectively, we developed 31 536 EST markers, 9071 EST-SSR markers and 3023 microRNA-target markers based on V. faba RefTrans V2 mining. By mapping 7940 EST and 2282 EST-SSR markers against the KEGG pathways database we successfully developed 107 functional maps. Also, 40 mtSSR markers were developed based on mitochondrial genome mining. On the data curation level, we retrieved 3461 markers representing 12 types of markers (CAPS, EST, EST-SSR, Gene marker, INDEL, Isozyme, ISSR, RAPD, SCAR, RGA, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets. VfODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.

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