Abstract
BACKGROUND: The centromere is one of the key regions of the eukaryotic chromosome. While maintaining its function, centromeric DNA may differ among closely related species. Here, we explored the composition and structure of the pericentromeres (a chromosomal region including a functional centromere) of Hieracium alpinum (Asteraceae), a member of one of the most diverse genera in the plant kingdom. Previously, we identified a pericentromere-specific tandem repeat that made it possible to distinguish reads within the Oxford Nanopore library attributed to the pericentromeres, separating them into a discrete subset and allowing comparison of the repeatome composition of this subset with the remaining genome. RESULTS: We found that the main satellite DNA (satDNA) monomer forms long arrays of linear and block types in the pericentromeric heterochromatin of H. alpinum, and very often, single reads contain forward and reverse arrays and mirror each other. Beside the major, two new minor satDNA families were discovered. In addition to satDNAs, high amounts of LTR retrotransposons (TEs) with dominant of Tekay lineage, were detected in the pericentromeres. We were able to reconstruct four main TEs of the Ty3-gypsy and Ty1-copia superfamilies and compare their relative positions with satDNAs. The latter showed that the conserved domains (CDs) of the TE proteins are located between the newly discovered satDNAs, which appear to be parts of ancient Tekay LTRs that we were able to reconstruct. The dominant satDNA monomer shows a certain similarity to the GAG CD of the Angela retrotransposon. CONCLUSIONS: The species-specific pericentromeric arrays of the H. alpinum genome are heterogeneous, exhibiting both linear and block type structures. High amounts of forward and reverse arrays of the main satDNA monomer point to multiple microinversions that could be the main mechanism for rapid structural evolution stochastically creating the uniqueness of an individual pericentromeric structure. The traces of TEs insertion waves remain in pericentromeres for a long time, thus "keeping memories" of past genomic events. We counted at least four waves of TEs insertions. In pericentromeres, TEs particles can be transformed into satDNA, which constitutes a background pool of minor families that, under certain conditions, can replace the dominant one(s).
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Claims 12
Claim · model-written summary
The main satDNA monomer forms long linear and block arrays in pericentromeric heterochromatin.
- Taxon
- H. alpinum
Hieracium alpinume0 - Gene
- satDNAe0
- Outcome
- long arrays of linear and block typese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“main satellite DNA (satDNA) monomer forms long arrays of linear and block types in the pericentromeric heterochromatin of H. alpinum”
Claim · model-written summary
Single reads often contain forward and reverse arrays that mirror each other.
- Outcome
- forward and reverse arrayse0
Not reportedTaxon
Verbatim
e0“single reads contain forward and reverse arrays and mirror each other”
Claim · model-written summary
Two new minor satDNA families were discovered.
Not reportedTaxon
Verbatim
e0“two new minor satDNA families were discovered”
Claim · model-written summary
Pericentromeres contain high amounts of LTR retrotransposons dominated by the Tekay lineage.
Not reportedTaxon
Verbatim
e0“high amounts of LTR retrotransposons (TEs) with dominant of Tekay lineage, were detected in the pericentromeres”
Claim · model-written summary
Four main transposable elements from Ty3-gypsy and Ty1-copia were reconstructed.
Not reportedTaxon
Verbatim
e0“reconstruct four main TEs of the Ty3-gypsy and Ty1-copia superfamilies”
Claim · model-written summary
Conserved TE protein domains occur between newly discovered satDNAs.
- Outcome
- conserved domains (CDs) of the TE proteinse0
Not reportedTaxon
Verbatim
e0“conserved domains (CDs) of the TE proteins are located between the newly discovered satDNAs”
Claim · model-written summary
New satDNAs appear to derive from ancient Tekay LTRs.
Not reportedTaxon
Verbatim
e0“newly discovered satDNAs, which appear to be parts of ancient Tekay LTRs”
Claim · model-written summary
The dominant satDNA monomer resembles the GAG domain of Angela retrotransposon.
Not reportedTaxonDirection
Verbatim
e0“dominant satDNA monomer shows a certain similarity to the GAG CD of the Angela retrotransposon”
Claim · model-written summary
Pericentromeric arrays are heterogeneous with linear and block structures.
- Taxon
- H. alpinumHieracium alpinume0
- Outcome
- heterogeneouse0
- Qualifier
- linear and block type structurese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“pericentromeric arrays of the H. alpinum genome are heterogeneous, exhibiting both linear and block type structures”
Claim · model-written summary
Forward and reverse satDNA arrays suggest microinversions drove structural evolution.
Not reportedTaxon
Verbatim
e0“High amounts of forward and reverse arrays of the main satDNA monomer point to multiple microinversions that could be the main mechanism for rapid structural evolution”
Claim · model-written summary
At least four waves of transposable element insertion were counted.
Not reportedTaxon
Verbatim
e0“We counted at least four waves of TEs insertions”
Claim · model-written summary
Pericentromeric transposable elements can become minor-family satDNA that can replace dominant families.
Not reportedTaxon
Verbatim
e0“TEs particles can be transformed into satDNA, which constitutes a background pool of minor families that, under certain conditions, can replace the dominant one(s)”