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Allotetraploid
kjenike edited this page Feb 21, 2023
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An allotetraploid usually is formed from the hybridization of two different species, which means there are two sets of distinct chromosomes.
The GenomeScope 2.0 paper (https://www.nature.com/articles/s41467-020-14998-3) describes the difference between allotetraploids and autotetraploids. Figure 2 from that paper is below to give a better representation of how these two broad types of polyploids arise.
And, from the same paper, figure 6a, we can see an example allotetraploid
This particular histogram was made from reads from Gossypium barbadense.
Introduction
k-mer spectra analysis
- 📖 Introduction to K-mer spectra analysis
- 📖 Basics of genome modeling
- ⚒ manual model fitting (for better understanding of the underlying model)
- ⚒ simple diploid
- ⚒ demonstrating the effect of sequencing error rate on k-mer coverage
- 📖 Common difficulties in characterisation of diploid genomes using k mer spectra analysis
- ⚒ low coverage (pitfall) - to be merged
- ⚒ very homozygous diploid
- ⚒ highly heterozygous diploid
- ⚒ Genome size of a repetitive genome (pitfall)
- ⚒ Wrong ploidy (pitfall)
- 📖 Characterization of polyploid genomes using k mer spectra analysis
- ⚒ Autotetraploid
- ⚒ Allotetraploid
- ⚒ Estimating ploidy (smudgeplot)
- 📖 Genome modeling as a quality control
- ⚒ Contamination (pitfall)
- ⚒ k-mers in an assembly (Mercury/KAT)
- 📖 Analysing genome skimming data
Separation of chromosomes
- 📖Separate sub-genomes of an allopolyploid
- 📖Separating chromosomes by comparison of sequencing libraries
Species assignment using short k-mers
Others