Life Sciences Commons^™

Telomere Roles In Fungal Genome Evolution And Adaptation, Mostafa Rahnama, Baohua Wang, Jane Dostart, Olga Novikova, Daniel Yackzan, Andrew T. Yackzan, Haley Bruss, Maray Baker, Haven Jacob, Xiaofei Zhang, April Lamb, Alex Stewart, Melanie Heist, Joey Hoover, Patrick Calie, Li Chen, Jinze Liu, Mark L. Farman

Plant Pathology Faculty Publications

Telomeres form the ends of linear chromosomes and usually comprise protein complexes that bind to simple repeated sequence motifs that are added to the 3′ ends of DNA by the telomerase reverse transcriptase (TERT). One of the primary functions attributed to telomeres is to solve the “end-replication problem” which, if left unaddressed, would cause gradual, inexorable attrition of sequences from the chromosome ends and, eventually, loss of viability. Telomere-binding proteins also protect the chromosome from 5′ to 3′ exonuclease action, and disguise the chromosome ends from the double-strand break repair machinery whose illegitimate action potentially generates catastrophic chromosome aberrations. Telomeres …

Introduction To The Toxins Special Issue On Ergot Alkaloids, Christopher L. Schardl

Plant Pathology Faculty Publications

No abstract provided.

Mites In The Promoters Of Effector Genes Allow Prediction Of Novel Virulence Genes In Fusarium Oxysporum, Sarah M. Schmidt, Petra M. Houterman, Ines Schreiver, Lisong Ma, Stefan G. Amyotte, Biju Chellappan, Sjef Boeren, Frank L. W. Takken, Martijn Rep

Plant Pathology Faculty Publications

BACKGROUND: The plant-pathogenic fungus Fusarium oxysporum f.sp.lycopersici (Fol) has accessory, lineage-specific (LS) chromosomes that can be transferred horizontally between strains. A single LS chromosome in the Fol4287 reference strain harbors all known Fol effector genes. Transfer of this pathogenicity chromosome confers virulence to a previously non-pathogenic recipient strain. We hypothesize that expression and evolution of effector genes is influenced by their genomic context.

RESULTS: To gain a better understanding of the genomic context of the effector genes, we manually curated the annotated genes on the pathogenicity chromosome and identified and classified transposable elements. Both retro- and DNA transposons are present …

Discovery Of Novel Dsrna Viral Sequences By In Silico Cloning And Implications For Viral Diversity, Host Range And Evolution, Huiquan Liu, Yanping Fu, Jiatao Xie, Jiasen Cheng, Said A. Ghabrial, Guoqing Li, Xianhong Yi, Daohong Jiang

Plant Pathology Faculty Publications

Genome sequence of viruses can contribute greatly to the study of viral evolution, diversity and the interaction between viruses and hosts. Traditional molecular cloning methods for obtaining RNA viral genomes are time-consuming and often difficult because many viruses occur in extremely low titers. DsRNA viruses in the families, Partitiviridae, Totiviridae, Endornaviridae, Chrysoviridae, and other related unclassified dsRNA viruses are generally associated with symptomless or persistent infections of their hosts. These characteristics indicate that samples or materials derived from eukaryotic organisms used to construct cDNA libraries and EST sequencing might carry these viruses, which were not easily detected by the researchers. …

Evolutionary Genomics Of Mycovirus-Related Dsrna Viruses Reveals Cross-Family Horizontal Gene Transfer And Evolution Of Diverse Viral Lineages, Huiquan Liu, Yanping Fu, Jiatao Xie, Jiasen Cheng, Said A. Ghabrial, Guoqing Li, Youliang Peng, Xianhong Yi, Daohong Jiang

Plant Pathology Faculty Publications

BACKGROUND: Double-stranded (ds) RNA fungal viruses are typically isometric single-shelled particles that are classified into three families, Totiviridae, Partitiviridae and Chrysoviridae, the members of which possess monopartite, bipartite and quadripartite genomes, respectively. Recent findings revealed that mycovirus-related dsRNA viruses are more diverse than previously recognized. Although an increasing number of viral complete genomic sequences have become available, the evolution of these diverse dsRNA viruses remains to be clarified. This is particularly so since there is little evidence for horizontal gene transfer (HGT) among dsRNA viruses.

RESULTS: In this study, we report the molecular properties of two novel dsRNA mycoviruses that …

Widespread Horizontal Gene Transfer From Circular Single-Stranded Dna Viruses To Eukaryotic Genomes, Huiquan Liu, Yanping Fu, Bo Li, Xiao Yu, Jiatao Xie, Jiasen Cheng, Said A. Ghabrial, Guoqing Li, Xianhong Yi, Daohong Jiang

Plant Pathology Faculty Publications

BACKGROUND: In addition to vertical transmission, organisms can also acquire genes from other distantly related species or from their extra-chromosomal elements (plasmids and viruses) via horizontal gene transfer (HGT). It has been suggested that phages represent substantial forces in prokaryotic evolution. In eukaryotes, retroviruses, which can integrate into host genome as an obligate step in their replication strategy, comprise approximately 8% of the human genome. Unlike retroviruses, few members of other virus families are known to transfer genes to host genomes.

RESULTS: Here we performed a systematic search for sequences related to circular single-stranded DNA (ssDNA) viruses in publicly available …

Abundant Degenerate Miniature Inverted-Repeat Transposable Elements In Genomes Of Epichloid Fungal Endophytes Of Grasses, Damien J Fleetwood, Anar K Khan, Richard D Johnson, Carolyn A Young, Shipra Mittal, Ruth E Wrenn, Uljana Hesse, Simon J Foster, Christopher L. Schardl, Barry Scott

Plant Pathology Faculty Publications

Miniature inverted-repeat transposable elements (MITEs) are abundant repeat elements in plant and animal genomes; however, there are few analyses of these elements in fungal genomes. Analysis of the draft genome sequence of the fungal endophyte Epichloë festucae revealed 13 MITE families that make up almost 1% of the E. festucae genome, and relics of putative autonomous parent elements were identified for three families. Sequence and DNA hybridization analyses suggest that at least some of the MITEs identified in the study were active early in the evolution of Epichloë but are not found in closely related genera. Analysis of MITE integration …

The Combined Effect Of Environmental And Host Factors On The Emergence Of Viral Rna Recombinants, Hannah M. Jaag, Peter D. Nagy

Plant Pathology Faculty Publications

Viruses are masters of evolution due to high frequency mutations and genetic recombination. In spite of the significance of viral RNA recombination that promotes the emergence of drug-resistant virus strains, the role of host and environmental factors in RNA recombination is poorly understood. Here we report that the host Met22p/Hal2p bisphosphate-3'-nucleotidase regulates the frequency of viral RNA recombination and the efficiency of viral replication. Based on Tomato bushy stunt virus (TBSV) and yeast as a model host, we demonstrate that deletion of MET22 in yeast or knockdown of AHL, SAL1 and FRY1 nucleotidases/phosphatases in plants leads to increased TBSV recombination …

Distinct Evolutionary Histories Of The Dna-A And Dna-B Components Of Bipartite Begomoviruses, Rob W. Briddon, Basavaprabhu L. Patil, Basavaraj Bagewadi, Muhammad Shah Nawaz-Ul-Rehman, Claude M. Fauquet

Plant Pathology Faculty Publications

BACKGROUND: Viruses of the genus Begomovirus (family Geminiviridae) have genomes consisting of either one or two genomic components. The component of bipartite begomoviruses known as DNA-A is homologous to the genomes of all geminiviruses and encodes proteins required for replication, control of gene expression, overcoming host defenses, encapsidation and insect transmission. The second component, referred to as DNA-B, encodes two proteins with functions in intra- and intercellular movement in host plants. The origin of the DNA-B component remains unclear. The study described here was initiated to investigate the relationship between the DNA-A and DNA-B components of bipartite begomoviruses with a …

Evolution Of A Subtilisin-Like Protease Gene Family In The Grass Endophytic Fungus Epichloë Festucae, Michelle K. Bryant, Christopher L. Schardl, Uljana Hesse, Barry Scott

Plant Pathology Faculty Publications

BACKGROUND: Subtilisin-like proteases (SLPs) form a superfamily of enzymes that act to degrade protein substrates. In fungi, SLPs can play either a general nutritive role, or may play specific roles in cell metabolism, or as pathogenicity or virulence factors.

RESULTS: Fifteen different genes encoding SLPs were identified in the genome of the grass endophytic fungus Epichloë festucae. Phylogenetic analysis indicated that these SLPs belong to four different subtilisin families: proteinase K, kexin, pyrolysin and subtilisin. The pattern of intron loss and gain is consistent with this phylogeny. E. festucae is exceptional in that it contains two kexin-like genes. Phylogenetic analysis …

'Paclims': A Component Lim System For High-Throughput Functional Genomic Analysis, Nicole Donofrio, Ravi Rajagopalon, Douglas Brown, Stephen Diener, Donald Windham, Shelly Nolin, Anna Floyd, Thomas Mitchell, Natalia Galadima, Sara Tucker, Marc J. Orbach, Gayatri Patel, Mark Farman, Vishal Pampanwar, Cari Soderlund, Yong-Hwan Lee, Ralph A. Dean

Plant Pathology Faculty Publications

BACKGROUND: Recent advances in sequencing techniques leading to cost reduction have resulted in the generation of a growing number of sequenced eukaryotic genomes. Computational tools greatly assist in defining open reading frames and assigning tentative annotations. However, gene functions cannot be asserted without biological support through, among other things, mutational analysis. In taking a genome-wide approach to functionally annotate an entire organism, in this application the approximately 11,000 predicted genes in the rice blast fungus (Magnaporthe grisea), an effective platform for tracking and storing both the biological materials created and the data produced across several participating institutions was required.

RESULTS: …