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Polyploid Genomics HALEY HALE What is Polyploidy? The heritable condition of possessing more than 2 sets of chromosomes1 ◦ Commonly associated with genome plasticity ◦ Other genomic alterations observed with polyploid formation: ◦ ◦ ◦ ◦ ◦ Chromosomal rearrangements New Transposable Element Activity DNA Mutation Duplicate Gene Deletion Gene Expression & Epigenetic changes What is Polyploidy? The heritable condition of possessing more than 2 sets of chromosomes1 Common in plants and some fish/amphibians ◦ But also found in insects, leeches, reptiles, and mammals… ◦ Tolerance to polyploidization varies NO BIG DEAL! What is Polyploidy? Terms: ◦ Genome ◦ Complete set of DNA What is Polyploidy? Terms: ◦ Genome ◦ Complete set of DNA ◦ Sub-Genome ◦ A subset of a genome ABC What is Polyploidy? Terms: ◦ Genome ◦ Complete set of DNA ◦ Sub-Genome ◦ A subset of a genome ◦ Homoelogues ◦ Multiple distinct copies of genes Mechanisms of Polyploidy Autopolyploidy ◦ Polyploidy arising WITHIN a species ◦ Results from a mutation in chromosome number Mechanisms of Polyploidy Allopolyploidy ◦ Polyploidy arising due to HYBRIDIZATION between species ◦ Results from concurrent hybridizations and mutations in chromosome number Advantages to 3 Polyploidy Heterosis ◦ Causes polyploids to be more vigorous than their diploid progenitors Gene Redundancy ◦ Sheilds polyploids from the deleterious effect of mutations Asexual Reproduction ◦ Enables polyploids to reproduce without a mate Disadvantages to 3 Polyploidy Changes in cellular architecture and regulatory implications ◦ Increases in genome size usually leads to increases in cell volume Difficulties in mitosis ◦ Leads to loss of chromosomes resulting in aneuploid cells Difficulties in meiosis ◦ Leads to aneuploid gametes Regulatory changes in gene expression Epigenetic Instability ◦ Polyploidy can disturb the regulatory adaptations that were selected in the parents Polyploidy and Speciation Paleopolyploidization ◦ Most organisms derived from polyploid ancestors2 Cycling of polyploidization and diploidization3 has occurred throughout life ◦ Polyploidization ◦ The multiplication of the entire genome ◦ Diploidization ◦ Gradual conversion from polyploidy to diploidy through genetic changes that differentiate duplicated loci Determining Ploidy Flow cytometry Microscopy Karyotype Analysis 8 Level Challenges to Genome Sequencing/Analysis Polyploids consist of two or more homeologous subgenomes4 ◦ Difficult to assign individual sequences to their associated subgenome Homeologues are difficult to amplify using PCR3 ◦ More than 1 copy will give multiple peaks at sites that differ within and between homologues Indels will cause subsequent undecipherable peaks in the sequence Genomes are usually large… making sequencing VERY costly Sequencing Methods Bacterial cloning to separate gene copies3 ◦ Time consuming and expensive Designed primers specific to each known homeologue3 Extraction of DNA from a mixture of individuals from a single population3 Physical separation of chromosomes5 Use of genome sequence of diploid ancestors4 Sequencing Methods Bacterial cloning to separate gene copies3 Designed primers specific to each known homeologue3 ◦ Requires existing knowledge of homeologue sequence ◦ Poa3 ◦ Used a barcoded mixture of targeted gene regions via 454 sequencing and next-gen methods Extraction of DNA from a mixture of individuals from a single population3 Physical separation of chromosomes5 Use of genome sequence of diploid ancestors4 Sequencing Methods Bacterial cloning to separate gene copies3 Designed primers specific to each known homeologue3 Extraction of DNA from a mixture of individuals from a single population3 Physical separation of chromosomes5 Use of genome sequence of diploid ancestors4 ◦ Tragopogon6 ◦ Used 454 and Illumina expressed sequence tag sequencing of parental diploid species ◦ HANDS – HSP base Assignment using NGS data through Diploid Similarity ◦ Involves comparative alignments of polyploid reads and diploid progenitor reads to a suitable reference sequence ◦ Applicable to allopolyploid genomes ◦ Wheat genome Sequencing/Analyzing the Wheat Genome4 Bread Wheat – T. aestivum ◦ Allohexaploid – 6n ◦ A, B, & D subgenomes (AABBDD) ◦ Diverged in sequence from their common ancestor – Homeolog-Specific Polymorphisms (HSPs) Sequencing/Analyzing the Wheat Genome4 Sequencing ◦ BAC-by-BAC: Hierarchical Shotgun Sequencing ◦ A physical map of the target genome is established using BAC clones ◦ A set of overlapping clones are ordered along the chromosomes of the target genome ◦ Individually mapped clones are subjected to shotgun sequencing ◦ DNA from each clone is fragmented randomly and sequenced ◦ Sequences are aligned and analyzed (HANDS) 7 SHEsisPlus New 2016 software designed for genetic analysis of polyploids Used for Gene Association Studies Sources 1. Griffin, P. C., Robin, C., Hoffmann, A. A. 2011. A next-gen sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses. BMC Biology 9:19 2. Van de Peer, Y., & Meyer, A. Chapter 6: Large-scale gene and ancient genome duplications. In The Evolution of the Genome, ed. T. R. Gregory, 330-363 (San Diego, Elsevier, 2005) 3. Comai, L. 2005. The Advantages And Disadvantages Of Being Polyploid. Nature Reviews 6:836-846 4. Mithani, A., Belfield, E. J., Brown, C., Jiang, C., Leach, L. J., Harberd, N.P. 2013. HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids. BMC Genomics 14: 653 5. Aversano, R., Ercolano, M., Caruso, I., Fasano, C., Rosellini, D., Carputo, D. 2012. Molecular Tools for Exploring Polyploid Genomes in Plants. Int. J. Mol. Sci. 13: 10316-10335 6. Buggs, R. J., Chamala, S., Wu, W., Gao, L., May, G. D., Schnable, P. S., Soltis, D. E., Barbazuk, W. B. 2010. Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by nextgeneration sequencing and Sequenom iPLEX MassARRAY genotyping. Molecular Ecology 1: 132-146 7. Shen, J., Li, Z., Chen, J., Song, Z., Zhou, Z., Shi, Y. 2016. SHEsisPlus, a toolset for genetic studies on polyploid species. Scientific Reports 6: 24095 8. Aikpokpodion, P. O., Otu, P. A., Uyoh, A. E. 2012 . Karytype Analysis and Ploidy Determination Using Flow Cytometry in African Bitter Milk Plant “Utazi”, Gongronema latifolium Benth. Cytologia 77: 43-52 Extra Resources •Schmid, M., Evans, B. J., Bogart, J. P. 2015. Polyploidy in Amphibia. Cytogenet Genome Res 145: 315330 •Mable, B. K., Alexandrou, M. A., Taylor, M. I. 2011. Genome duplication in amphibians and fish: an extended synthesis. Journal of Zoology 284: 151-182 • Page, J. T., Gingle, A. R., Udall, J. A. 2013. PolyCat: A Resource for Genome Categorization of Sequencing Reads From Allopolyploid Organisms. Genes|Genomes|Genetics 3: 517-525 •Margarido, G. R. A., Heckerman, D. 2015. ConPADE: Genome Assembly Ploidy Estimation from NextGeneration Sequencing Data. PLOS Computational Biology •http://www.wheatgenome.org/