PMID- 34490015
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20210908
IS  - 1664-462X (Print)
IS  - 1664-462X (Electronic)
IS  - 1664-462X (Linking)
VI  - 12
DP  - 2021
TI  - Differentially Amplified Repetitive Sequences Among Aegilops tauschii Subspecies 
      and Genotypes.
PG  - 716750
LID - 10.3389/fpls.2021.716750 [doi]
LID - 716750
AB  - Genomic repetitive sequences commonly show species-specific sequence type, 
      abundance, and distribution patterns, however, their intraspecific 
      characteristics have been poorly described. We quantified the genomic repetitive 
      sequences and performed single nucleotide polymorphism (SNP) analysis between 29 
      Ae. tauschii genotypes and subspecies using publicly available raw genomic 
      Illumina sequence reads and used fluorescence in situ hybridization (FISH) to 
      experimentally analyze some repeats. The majority of the identified repetitive 
      sequences had similar contents and proportions between anathera, meyeri, and 
      strangulata subspecies. However, two Ty3/gypsy retrotransposons (CL62 and CL87) 
      showed significantly higher abundances, and CL1, CL119, CL213, CL217 tandem 
      repeats, and CL142 retrotransposon (Ty1/copia type) showed significantly lower 
      abundances in subspecies strangulata compared with the subspecies anathera and 
      meyeri. One tandem repeat and 45S ribosomal DNA (45S rDNA) abundances showed a 
      high variation between genotypes but their abundances were not subspecies 
      specific. Phylogenetic analysis using the repeat abundances of the aforementioned 
      clusters placed the strangulata subsp. in a distinct clade but could not 
      discriminate anathera and meyeri. A near complete differentiation of anathera and 
      strangulata subspecies was observed using SNP analysis; however, var. meyeri 
      showed higher genetic diversity. FISH using major tandem repeats couldn't detect 
      differences between subspecies, although (GAA)(10) signal patterns generated two 
      different karyotype groups. Taken together, the different classes of repetitive 
      DNA sequences have differentially accumulated between strangulata and the other 
      two subspecies of Ae. tauschii that is generally in agreement with spike 
      morphology, implying that factors affecting repeatome evolution are variable even 
      among highly closely related lineages.
CI  - Copyright (c) 2021 Ebrahimzadegan, Orooji, Ma and Mirzaghaderi.
FAU - Ebrahimzadegan, Rahman
AU  - Ebrahimzadegan R
AD  - Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of 
      Kurdistan, Sanandaj, Iran.
FAU - Orooji, Fatemeh
AU  - Orooji F
AD  - Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of 
      Kurdistan, Sanandaj, Iran.
FAU - Ma, Pengtao
AU  - Ma P
AD  - College of Life Sciences, Yantai University, Yantai, China.
FAU - Mirzaghaderi, Ghader
AU  - Mirzaghaderi G
AD  - Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of 
      Kurdistan, Sanandaj, Iran.
LA  - eng
PT  - Journal Article
DEP - 20210819
PL  - Switzerland
TA  - Front Plant Sci
JT  - Frontiers in plant science
JID - 101568200
PMC - PMC8417419
OTO - NOTNLM
OT  - repetitive sequence abundance
OT  - satellite repeat
OT  - speciation
OT  - tandem repeat
OT  - wheat
COIS- The authors declare that the research was conducted in the absence of any 
      commercial or financial relationships that could be construed as a potential 
      conflict of interest.
EDAT- 2021/09/08 06:00
MHDA- 2021/09/08 06:01
PMCR- 2021/01/01
CRDT- 2021/09/07 07:44
PHST- 2021/05/29 00:00 [received]
PHST- 2021/07/27 00:00 [accepted]
PHST- 2021/09/07 07:44 [entrez]
PHST- 2021/09/08 06:00 [pubmed]
PHST- 2021/09/08 06:01 [medline]
PHST- 2021/01/01 00:00 [pmc-release]
AID - 10.3389/fpls.2021.716750 [doi]
PST - epublish
SO  - Front Plant Sci. 2021 Aug 19;12:716750. doi: 10.3389/fpls.2021.716750. 
      eCollection 2021.