PMID- 33224172
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20240330
IS  - 1664-462X (Print)
IS  - 1664-462X (Electronic)
IS  - 1664-462X (Linking)
VI  - 11
DP  - 2020
TI  - Characterization and Dynamics of Repeatomes in Closely Related Species of 
      Hieracium (Asteraceae) and Their Synthetic and Apomictic Hybrids.
PG  - 591053
LID - 10.3389/fpls.2020.591053 [doi]
LID - 591053
AB  - The repetitive content of the plant genome (repeatome) often represents its 
      largest fraction and is frequently correlated with its size. Transposable 
      elements (TEs), the main component of the repeatome, are an important driver in 
      the genome diversification due to their fast-evolving nature. Hybridization and 
      polyploidization events are hypothesized to induce massive bursts of TEs 
      resulting, among other effects, in an increase of copy number and genome size. 
      Little is known about the repeatome dynamics following hybridization and 
      polyploidization in plants that reproduce by apomixis (asexual reproduction via 
      seeds). To address this, we analyzed the repeatomes of two diploid parental 
      species, Hieracium intybaceum and H. prenanthoides (sexual), their diploid F1 
      synthetic and their natural triploid hybrids (H. pallidiflorum and H. picroides, 
      apomictic). Using low-coverage next-generation sequencing (NGS) and a graph-based 
      clustering approach, we detected high overall similarity across all major 
      repeatome categories between the parental species, despite their large 
      phylogenetic distance. Medium and highly abundant repetitive elements comprise 
       approximately 70% of Hieracium genomes; most prevalent were Ty3/Gypsy chromovirus Tekay and 
      Ty1/Copia Maximus-SIRE elements. No TE bursts were detected, neither in synthetic 
      nor in natural hybrids, as TE abundance generally followed theoretical 
      expectations based on parental genome dosage. Slight over- and 
      under-representation of TE cluster abundances reflected individual differences in 
      genome size. However, in comparative analyses, apomicts displayed an 
      overabundance of pararetrovirus clusters not observed in synthetic hybrids. 
      Substantial deviations were detected in rDNAs and satellite repeats, but these 
      patterns were sample specific. rDNA and satellite repeats (three of them were 
      newly developed as cytogenetic markers) were localized on chromosomes by 
      fluorescence in situ hybridization (FISH). In a few cases, low-abundant repeats 
      (5S rDNA and certain satellites) showed some discrepancy between NGS data and 
      FISH results, which is due partly to the bias of low-coverage sequencing and 
      partly to low amounts of the satellite repeats or their sequence divergence. 
      Overall, satellite DNA (including rDNA) was markedly affected by hybridization, 
      but independent of the ploidy or reproductive mode of the progeny, whereas bursts 
      of TEs did not play an important role in the evolutionary history of Hieracium.
CI  - Copyright (c) 2020 Zagorski, Hartmann, Bertrand, Pastova, Slavikova, Josefiova and 
      Fehrer.
FAU - Zagorski, Danijela
AU  - Zagorski D
AD  - Institute of Botany, Czech Academy of Sciences, Pruhonice, Czechia.
FAU - Hartmann, Matthias
AU  - Hartmann M
AD  - Institute of Botany, Czech Academy of Sciences, Pruhonice, Czechia.
FAU - Bertrand, Yann J K
AU  - Bertrand YJK
AD  - Institute of Botany, Czech Academy of Sciences, Pruhonice, Czechia.
FAU - Pastova, Ladislava
AU  - Pastova L
AD  - Institute of Botany, Czech Academy of Sciences, Pruhonice, Czechia.
FAU - Slavikova, Renata
AU  - Slavikova R
AD  - Institute of Botany, Czech Academy of Sciences, Pruhonice, Czechia.
FAU - Josefiova, Jirina
AU  - Josefiova J
AD  - Institute of Botany, Czech Academy of Sciences, Pruhonice, Czechia.
FAU - Fehrer, Judith
AU  - Fehrer J
AD  - Institute of Botany, Czech Academy of Sciences, Pruhonice, Czechia.
LA  - eng
PT  - Journal Article
DEP - 20201102
PL  - Switzerland
TA  - Front Plant Sci
JT  - Frontiers in plant science
JID - 101568200
PMC - PMC7667050
OTO - NOTNLM
OT  - RepeatExplorer
OT  - apomixis
OT  - hawkweed
OT  - hybridization
OT  - next-generation sequencing
OT  - polyploidization
OT  - repeatome
EDAT- 2020/11/24 06:00
MHDA- 2020/11/24 06:01
PMCR- 2020/01/01
CRDT- 2020/11/23 05:37
PHST- 2020/08/03 00:00 [received]
PHST- 2020/10/09 00:00 [accepted]
PHST- 2020/11/23 05:37 [entrez]
PHST- 2020/11/24 06:00 [pubmed]
PHST- 2020/11/24 06:01 [medline]
PHST- 2020/01/01 00:00 [pmc-release]
AID - 10.3389/fpls.2020.591053 [doi]
PST - epublish
SO  - Front Plant Sci. 2020 Nov 2;11:591053. doi: 10.3389/fpls.2020.591053. eCollection 
      2020.