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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:
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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
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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
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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
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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)
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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/