Genetics and Genomics | Open Access Articles

Physical Mapping Of The Anopheles (Nyssorhynchus) Darlingi Genomic Scaffolds, Míriam Silva Rafael, Leticia Cegatti Bridi, Igor V. Sharakhov, Osvaldo Marinotti, Maria V. Sharakhova, Vladimir A. Timoshevskiy, Giselle Moura Guimarães-Marques, Valéria Silva Santos, Carlos Gustavo Nunes Da Silva, Spartaco Astolfi-Filho, Wanderli Pedro Tadei

Biology Faculty Publications

The genome assembly of Anopheles darlingi consists of 2221 scaffolds (N50 = 115,072 bp) and has a size spanning 136.94 Mbp. This assembly represents one of the smallest genomes among Anopheles species. Anopheles darlingi genomic DNA fragments of ~37 Kb were cloned, end-sequenced, and used as probes for fluorescence in situ hybridization (FISH) with salivary gland polytene chromosomes. In total, we mapped nine DNA probes to scaffolds and autosomal arms. Comparative analysis of the An. darlingi scaffolds with homologous sequences of the Anopheles albimanus and Anopheles gambiae genomes identified chromosomal rearrangements among these species. Our results confirmed that physical mapping …

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Genome Of The Tropical Plant Marchantia Inflexa: Implications For Sex Chromosome Evolution And Dehydration Tolerance, Rose A. Marks, Jeramiah J. Smith, Quentin Cronk, Christopher J. Grassa, D. Nicholas Mcletchie

Biology Faculty Publications

We present a draft genome assembly for the tropical liverwort, Marchantia inflexa, which adds to a growing body of genomic resources for bryophytes and provides an important perspective on the evolution and diversification of land plants. We specifically address questions related to sex chromosome evolution, sexual dimorphisms, and the genomic underpinnings of dehydration tolerance. This assembly leveraged the recently published genome of related liverwort, M. polymorpha, to improve scaffolding and annotation, aid in the identification of sex-linked sequences, and quantify patterns of sequence differentiation within Marchantia. We find that genes on sex chromosomes are under greater …

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Cluster M Mycobacteriophages Bongo, Pegleg, And Rey With Unusually Large Repertoires Of Trna Isotopes, Welkin H. Pope, Kirk R. Anders, Madison Baird, Charles A. Bowman, Michelle M. Boyle, Gregory W. Broussard, Tiffany Chow, Kari L. Clase, Shannon Cooper, Kathleen A. Cornely, Randall J. Dejong, Veronique A. Delesalle, Lisa Deng, David Dunbar, Nicholas P. Edgington, Christina M. Ferreira, Kathleen Weston Hafer, Grant A. Hartzog, J. Robert Hatherill, Lee E. Hughes, Khristina Ipapo, Gregory P. Krukonis, Christopher G. Meier, Denise L. Monti, Matthew R. Olm, Shallee T. Page, Craig L. Peebles, Claire A. Rinehart, Michael R. Rubin, Daniel A. Russell, Erin R. Sanders, Morgan Schoer, Christopher D. Shaffer, James Wherley, Edwin Vazquez, Han Yuan, Daiyuan Zhang, Steven G. Cresawn, Deborah Jacobs-Sera, Roger W. Hendrix, Graham F. Hatfull

Biology Faculty Publications

Genomic analysis of a large set of phages infecting the common hostMycobacterium smegmatis mc²155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average …

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Engaging Students In A Bioinformatics Activity To Introduce Gene Structure And Function, Barbara J. May

Biology Faculty Publications

Bioinformatics spans many fields of biological research and plays a vital role in mining and analyzing data. Therefore, there is an ever-increasing need for students to understand not only what can be learned from this data, but also how to use basic bioinformatics tools. This activity is designed to provide secondary and undergraduate biology students to a hands-on activity meant to explore and understand gene structure with the use of basic bioinformatic tools. Students are provided an “unknown” sequence from which they are asked to use a free online gene finder program to identify the gene. Students then predict the …

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Genomeblast: A Web Tool For Small Genome Comparison, Guoqing Lu, Liying Jiang, Resa M. K. Helikar, Thaine W. Rowley, Luwen Zhang, Xianfeng Chen, Etsuko N. Moriyama

Biology Faculty Publications

Background: Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inference of phylogenetic relationships in a given set of genomes.

Results: GenomeBlast is a Web tool developed for comparative analysis of multiple small genomes. A new parameter called "coverage" was introduced and used along with sequence identity to evaluate global similarity between genes. With GenomeBlast, the following results can be obtained: (1) unique genes in each …

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Biology Faculty Publications

Genome Of The Tropical Plant Marchantia Inflexa: Implications For Sex Chromosome Evolution And Dehydration Tolerance, Rose A. Marks, Jeramiah J. Smith, Quentin Cronk, Christopher J. Grassa, D. Nicholas Mcletchie

Biology Faculty Publications

Biology Faculty Publications

Engaging Students In A Bioinformatics Activity To Introduce Gene Structure And Function, Barbara J. May

Biology Faculty Publications

Genomeblast: A Web Tool For Small Genome Comparison, Guoqing Lu, Liying Jiang, Resa M. K. Helikar, Thaine W. Rowley, Luwen Zhang, Xianfeng Chen, Etsuko N. Moriyama

Biology Faculty Publications