Biology Commons^™

Improved Chromosome-Level Genome Assembly Of The Glanville Fritillary Butterfly (Melitaea Cinxia) Integrating Pacific Biosciences Long Reads And A High-Density Linkage Map, Olli-Pekka Smolander, Daniel Blande, Virpi Ahola, Pasi Rastas, Jaakko Tanskanen, Juhana Kammonen, Vicencio Oostra, Lorenzo Pellegrini, Suvi Ikonen, Tad Dallas, Michelle F. Dileo, Anne Duplouy, Iihan Cem Duru, Pauliina Halimaa, Aapo Kahilainen, Suyog S. Kuwar, Sirpa O. Kärenlampi, Elvira Lafuente, Shiqi Luo, Jenny Makkonen, Abhilash Nair, Narua De La Paz Celorio-Mancera, Ville Pennanen, Annukka Ruokolainen, Tarja Sundell, Arja I. Tervahauta, Victoria Twort, Erik Van Bergen, Janina Österman-Udd, Lars Paulin, Mikko J. Frilander, Petri Auvinen, Marjo Saastamoinen

Faculty Publications

Background

The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses.

Results

The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92–94% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and …

Complex Gene Loss And Duplication Events Have Facilitated The Evolution Of Multiple Loricrin Genes In Diverse Bird Species, Anthony C. Davis, Matthew J. Greenwold, Roger H. Sawyer

Faculty Publications

The evolution of a mechanically resilient epidermis was a key adaptation in the transition of amniotes to a fully terrestrial lifestyle. Skin appendages usually form via a specialized type of programmed cell death known as cornification which is characterized by the formation of an insoluble cornified envelope (CE). Many of the substrates of cornification are encoded by linked genes located at a conserved genetic locus known as the epidermal differentiation complex (EDC). Loricrin is the main protein component of the mammalian CE and is encoded for by a gene located within the EDC. Recently, genes resembling mammalian loricrin, along with …

Compositional Traits In Sorghum Bicolor Characterized By Transcriptome, Ionome And Genome-Wide Association Analysis, Nadia Shakoor

Theses and Dissertations

To address the challenge of global mineral malnutrition, current biofortification research in crop plants aims to improve mineral concentration and micronutrient bioavailablity via genetic and traditional breeding methods. Many staple food crops are also used as biofuels, and the chemical and mineral composition of these energy crops directly affect biomass quality and subsequent energy output. Identification of genes and QTL that impact mineral and compositional traits in the grain and biomass of major cereals, including sorghum, is fundamental to developing breeding and selection methods aimed at increasing bioavailable minerals and improving biofuel suitability and seed nutritional quality. A combinatorial strategy …

Correction Of The Caulobacter Crescentus Na1000 Genome Annotation, Bert Ely, Latia Etheredge Scott

Faculty Publications

Bacterial genome annotations are accumulating rapidly in the GenBank database and the use of automated annotation technologies to create these annotations has become the norm. However, these automated methods commonly result in a small, but significant percentage of genome annotation errors. To improve accuracy and reliability, we analyzed the Caulobacter crescentus NA1000 genome utilizing computer programs Artemis and MICheck to manually examine the third codon position GC content, alignment to a third codon position GC frame plot peak, and matches in the GenBank database. We identified 11 new genes, modified the start site of 113 genes, and changed the reading …

Genetic Diversity Of Peanut (Arachis Hypogaea L.) And Its Wild Relatives Based On The Analysis Of Hypervariable Regions Of The Genome, Marcio De Carvalho Moretzsohn, Mark S. Hopkins, Sharon E. Mitchell, Stephen Kresovich, Jose Francisco Montenegro Valls, Marcio Elias Ferreira

Faculty Publications

Background: The genus Arachis is native to a region that includes Central Brazil and neighboring countries. Little is known about the genetic variability of the Brazilian cultivated peanut (Arachis hypogaea, genome AABB) germplasm collection at the DNA level. The understanding of the genetic diversity of cultivated and wild species of peanut (Arachis spp.) is essential to develop strategies of collection, conservation and use of the germplasm in variety development. The identity of the ancestor progenitor species of cultivated peanut has also been of great interest. Several species have been suggested as putative AA and BB genome donors …