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Full-Text Articles in Genetics and Genomics
Draft Genome Sequence Of A Dictyoglomus Sp. From An Enrichment Culture Of A New Zealand Geothermal Spring, Anna-Louise Reysenbach, John A. Donaho, John F. Kelley, Emily St. John, Christina Turner, Mircea Podar, Matthew B. Stott
Draft Genome Sequence Of A Dictyoglomus Sp. From An Enrichment Culture Of A New Zealand Geothermal Spring, Anna-Louise Reysenbach, John A. Donaho, John F. Kelley, Emily St. John, Christina Turner, Mircea Podar, Matthew B. Stott
Biology Faculty Publications and Presentations
A draft genome of a novel Dictyoglomus sp., NZ13-RE01, was obtained from a New Zealand hot spring enrichment culture. The 1,927,012-bp genome is similar in both size and G+C content to other Dictyoglomus spp. Like its relatives, Dictyoglomus sp. NZ13-RE01 encodes many genes involved in complex carbohydrate metabolism.
Identification Of Novel Mites (Miniature Inverted-Repeat Transposable Elements) In Coxiella Burnetii: Implications For Protein And Small Rna Evolution, Shaun Wachter, Rahul Raghavan, Jenny Wachter, Michael F. Minnick
Identification Of Novel Mites (Miniature Inverted-Repeat Transposable Elements) In Coxiella Burnetii: Implications For Protein And Small Rna Evolution, Shaun Wachter, Rahul Raghavan, Jenny Wachter, Michael F. Minnick
Biology Faculty Publications and Presentations
Background: Coxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. C. burnetii’s genome contains an abundance of pseudogenes and numerous selfish genetic elements. MITEs (miniature invertedrepeat transposable elements) are non-autonomous transposons that occur in all domains of life and are thought to be insertion sequences (ISs) that have lost their transposase function. Like most transposable elements (TEs), MITEs are thought to play an active role in evolution by altering gene function and expression through insertion and deletion activities. However, information regarding bacterial MITEs is limited. Results: We describe two MITE families discovered during research on small non-coding …
Genome Rearrangements Can Make And Break Small Rna Genes, Rahul Raghavan, Fenil R. Kacharia, Jess A. Millar, Christine Demko Sislak, Howard Ochman
Genome Rearrangements Can Make And Break Small Rna Genes, Rahul Raghavan, Fenil R. Kacharia, Jess A. Millar, Christine Demko Sislak, Howard Ochman
Biology Faculty Publications and Presentations
Small RNAs (sRNAs) are short, transcribed regulatory elements that are typically encoded in the intergenic regions (IGRs) of bacterial genomes. Several sRNAs, first recognized in Escherichia coli, are conserved among enteric bacteria, but because of the regulatory roles of sRNAs, differences in sRNA repertoires might be responsible for features that differentiate closely related species. We scanned the E. coli MG1655 and Salmonella enterica Typhimurium genomes for nonsyntenic IGRs as a potential source of uncharacterized, species-specific sRNAs and found that genome rearrangements have reconfigured several IGRs causing the disruption and formation of sRNAs. Within an IGR that is present in …
A Selective Force Favoring Increased G+C Content In Bacterial Genes, Rahul Raghavan, Yogeshwar D. Kelkar, Howard Ochman
A Selective Force Favoring Increased G+C Content In Bacterial Genes, Rahul Raghavan, Yogeshwar D. Kelkar, Howard Ochman
Biology Faculty Publications and Presentations
Bacteria display considerable variation in their overall base compositions, which range from 13% to over 75% G+C. This variation in genomic base compositions has long been considered to be a strictly neutral character, due solely to differences in the mutational process; however, recent sequence comparisons indicate that mutational input alone cannot produce the observed base compositions, implying a role for natural selection. Because bacterial genomes have high gene content, forces that operate on the base composition of individual genes could help shape the overall genomic base composition. To explore this possibility, we tested whether genes that encode the same protein …
Genome-Wide Detection Of Novel Regulatory Rnas In E. Coli, Rahul Raghavan, Eduardo Groisman, Howard Ochman
Genome-Wide Detection Of Novel Regulatory Rnas In E. Coli, Rahul Raghavan, Eduardo Groisman, Howard Ochman
Biology Faculty Publications and Presentations
The intergenic regions in bacterial genomes can contain regulatory leader sequences and small RNAs (sRNAs), which both serve to modulate gene expression. Computational analyses have predicted the presence of hundreds of these noncoding regulatory RNAs in Escherichia coli; however, only about 80 have been experimentally validated. By applying a deep-sequencing approach, we detected and quantified the vast majority of the previously validated regulatory elements and identified 10 new sRNAs and nine new regulatory leader sequences in the intergenic regions of E. coli. Half of the newly discovered sRNAs displayed enhanced stability in the presence of the RNA-binding protein …