An investigation of maize B chromosome-derived minichromosomes

Title from PDF of title page (University of Missouri--Columbia, viewed on August 29, 2012).The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file.Dissertation advisor: Dr. James BirchlerIncludes bibliographical references.Vita.Ph. D. University of Missouri-Columbia 2012."May 2012"The maize (Zea mays) B chromosome is a supernumerary chromosome with a selfish inheritance characterized by nondisjunction at the second pollen mitosis, univalent survival in meiosis, and preferential fertilization of the egg. The apparent lack of known genes allows this inheritance to accumulate the B chromosome to multiple copies in the genome with relatively little effect. By bombarding telomere-containing constructs with selection markers into maize embryos with B chromosomes, multiple B chromosome truncations of varying sizes were found. Using these B-derived minichromosomes, we were able to address minichromosome pairing and accumulation limits, which led to the observation of dosage dependent nondisjunction of the B chromosome and the discovery of an asynchronous endoreduplicating chromosome. Because the stacking of multiple genes in crop plants is becoming more prevalent, establishing a system of multiple minichromosomes could ease the development and increase the capabilities of transgenic plants.Includes bibliographical reference

The Complete Nucleotide Sequence of Barley Yellow Dwarf Virus-PAV from Wheat in Turkey

We report the sequence of an assembled genome of Barley yellow dwarf virus-PAV (BYDV-PAV) from Turkey. This 5,672 nucleotide RNA encodes seven known open reading frames and a possible eighth. This genome from wheat is closely related to BYDV-PAVs in Pakistan, Brazil, and Australia, including one sequenced 34 years ago.Scientific and Technological Research Council of Turkey, International Postdoctoral Research Scholarship Program (TUBITAK-BIDEB); Tekirdag Namik Kemal University, The Scientific Research Projects Coordination Unit (NKU-BAP) [NKUBAP.03.GA.21.289]; Iowa State University Plant Sciences Institute; DARPA Insect Allies Program; Iowa Agriculture and Home Economics Experiment Station, Ames, IA - Hatch Act [4308]; State of Iowa fundsThis study was funded by the Scientific and Technological Research Council of Turkey, International Postdoctoral Research Scholarship Program (TUBITAK-BIDEB), and Tekirdag Namik Kemal University, The Scientific Research Projects Coordination Unit (NKU-BAP, Project No: NKUBAP.03.GA.21.289) to H.I., and the Iowa State University Plant Sciences Institute and the DARPA Insect Allies Program funding to W.A.M. This paper of the Iowa Agriculture and Home Economics Experiment Station, Ames, IA, Project No. 4308 was supported in part by Hatch Act and State of Iowa funds

The draft genome of Ditylenchus dipsaci.

Ditylenchus dipsaci is a devastating pest to many crops worldwide. We present the first genome sequence for this species, produced with PacBio sequencing and assembled with CANU. Ditylenchus dipsaci is a devastating pest to many crops worldwide. We present the first genome sequence for this species, produced with PacBio sequencing and assembled with CANU

A pseudomolecule assembly of the Rocky Mountain elk genome

Rocky Mountain elk (Cervus canadensis) populations have significant economic implications to the cattle industry, as they are a major reservoir for Brucella abortus in the Greater Yellowstone area. Vaccination attempts against intracellular bacterial diseases in elk populations have not been successful due to a negligible adaptive cellular immune response. A lack of genomic resources has impeded attempts to better understand why vaccination does not induce protective immunity. To overcome this limitation, PacBio, Illumina, and Hi-C sequencing with a total of 686-fold coverage was used to assemble the elk genome into 35 pseudomolecules. A robust gene annotation was generated resulting in 18,013 gene models and 33,422 mRNAs. The accuracy of the assembly was assessed using synteny to the red deer and cattle genomes identifying several chromosomal rearrangements, fusions and fissions. Because this genome assembly and annotation provide a foundation for genome-enabled exploration of Cervus species, we demonstrate its utility by exploring the conservation of immune system-related genes. We conclude by comparing cattle immune system-related genes to the elk genome, revealing eight putative gene losses in elk

CenH3 evolution in diploids and polyploids of three angiosperm genera

BACKGROUND: Centromeric DNA sequences alone are neither necessary nor sufficient for centromere specification. The centromere specific histone, CenH3, evolves rapidly in many species, perhaps as a coevolutionary response to rapidly evolving centromeric DNA. To gain insight into CenH3 evolution, we characterized patterns of nucleotide and protein diversity among diploids and allopolyploids within three diverse angiosperm genera, Brassica, Oryza, and Gossypium (cotton), with a focus on evidence for diversifying selection in the various domains of the CenH3 gene. In addition, we compare expression profiles and alternative splicing patterns for CenH3 in representatives of each genus. RESULTS: All three genera retain both duplicated CenH3 copies, while Brassica and Gossypium exhibit pronounced homoeologous expression level bias. Comparisons among genera reveal shared and unique aspects of CenH3 evolution, variable levels of diversifying selection in different CenH3 domains, and that alternative splicing contributes significantly to CenH3 diversity. CONCLUSIONS: Since the N terminus is subject to diversifying selection but the DNA binding domains do not appear to be, rapidly evolving centromere sequences are unlikely to be the primary driver of CenH3 sequence diversification. At present, the functional explanation for the diversity generated by both conventional protein evolution in the N terminal domain, as well as alternative splicing, remains unexplained. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-014-0383-3) contains supplementary material, which is available to authorized users