Untitled

Thon, Michael R.; Pan, Huaqin; Diener, Stephen; Papalas, John A.; Taro, Audrey; Mitchell, Thomas K.; Dean, Ralph A.

doi:10.1186/gb-2006-7-2-r16

Cited by 83 publications

(48 citation statements)

References 39 publications

(43 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The TEs in the three outlier BACs show greater clustering/organization than expected by chance. Distinct TE clusters are usually marked by increased rates of gene duplications and higher sequence diversity of genes associated with the clusters [90]. We also observe nested TE structures in our analysis.…”

Section: Discussionsupporting

confidence: 62%

Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome

Gill

Buti

Kane

et al. 2014

Biology

View full text Add to dashboard Cite

Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence.

show abstract

Section: Discussionsupporting

confidence: 62%

Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome

Gill

Buti

Kane

et al. 2014

Biology

View full text Add to dashboard Cite

show abstract

“…The abundance of transposon relic sequences adds to the evolutionary potential of the EAS cluster. In Magnaporthe oryzae, transposable element clusters correlate with increased recombination rate, loss of synteny, gene duplication, and sequence divergence from orthologous genes (51). Inter-and intrachromasomal recombination mediated by these repeat sequences in the N. lolii genome could be important in generating genetic diversity.…”

Section: Discussionmentioning

confidence: 99%

A Complex Ergovaline Gene Cluster in Epichloë Endophytes of Grasses

Fleetwood

Scott

Lane

et al. 2007

Appl Environ Microbiol

127

View full text Add to dashboard Cite

Clavicipitaceous fungal endophytes of the genera Epichloë and Neotyphodium form symbioses with grasses of the subfamily Pooideae, in which they can synthesize an array of bioprotective alkaloids. Some strains produce the ergopeptine alkaloid ergovaline, which is implicated in livestock toxicoses caused by ingestion of endophyteinfected grasses. Cloning and analysis of a nonribosomal peptide synthetase (NRPS) gene from Neotyphodium lolii revealed a putative gene cluster for ergovaline biosynthesis containing a single-module NRPS gene, lpsB, and other genes orthologous to genes in the ergopeptine gene cluster of Claviceps purpurea and the clavine cluster of Aspergillus fumigatus. Despite conservation of gene sequence, gene order is substantially different between the N. lolii, C. purpurea, and A. fumigatus ergot alkaloid gene clusters. Southern analysis indicated that the N. lolii cluster was linked with previously identified ergovaline biosynthetic genes dmaW and lpsA. The ergovaline genes are closely associated with transposon relics, including retrotransposons and autonomous and nonautonomous DNA transposons. All genes in the cluster were highly expressed in planta, but expression was very low or undetectable in mycelia from axenic culture. This work provides a genetic foundation for elucidating biochemical steps in the ergovaline pathway, the ecological role of individual ergot alkaloid compounds, and the regulation of their synthesis in planta.

show abstract

“…Likewise, mutations arising from mobile element insertions in conserved blocks can cause synteny loss [21]. TE clusters from WM276 were shown to be responsible for synteny breaks at 5 genome points (Additional files 4, 5, 6, 7 and 8).…”

Section: Resultsmentioning

confidence: 99%

sRNAs as possible regulators of retrotransposon activity in Cryptococcus gattii VGII

et al. 2017

View full text Add to dashboard Cite

BackgroundThe absence of Argonaute genes in the fungal pathogen Cryptococcus gattii R265 and other VGII strains indicates that yeasts of this genotype cannot have a functional RNAi pathway, an evolutionarily conserved gene silencing mechanism performed by small RNAs. The success of the R265 strain as a pathogen that caused the Pacific Northwest and Vancouver Island outbreaks may imply that RNAi machinery loss could be beneficial under certain circumstances during evolution. As a result, a hypermutant phenotype would be created with high rates of genome retrotransposition, for instance. This study therefore aimed to evaluate in silicio the effect of retrotransposons and their control mechanisms by small RNAs on genomic stability and synteny loss of C. gattii R265 through retrotransposons sequence comparison and orthology analysis with other 16 C. gattii genomic sequences available.ResultsRetrotransposon mining identified a higher sequence count to VGI genotype compared to VGII, VGIII, and VGIV. However, despite the lower retrotransposon number, VGII exhibited increased synteny loss and genome rearrangement events. RNA-Seq analysis indicated highly expressed retrotransposons as well as sRNA production.ConclusionsGenome rearrangement and synteny loss may suggest a greater retrotransposon mobilization caused by RNAi pathway absence, but the effective presence of sRNAs that matches retrotransposon sequences means that an alternative retrotransposon silencing mechanism could be active in genomic integrity maintenance of C. gattii VGII strains.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3688-4) contains supplementary material, which is available to authorized users.

show abstract

Untitled

Abstract: Analysis of the Magnaporthe oryzae chromosome 7 and comparison with syntenic regions in other fungal genomes suggests that transposable elements create localized segments with increased rates of chromosomal rearrangements, gene duplications and gene evolution.

Cited by 83 publications

References 39 publications

Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome

Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome

A Complex Ergovaline Gene Cluster in Epichloë Endophytes of Grasses

sRNAs as possible regulators of retrotransposon activity in Cryptococcus gattii VGII

Contact Info

Product

Resources

About