PMID- 30084890
OWN - NLM
STAT- MEDLINE
DCOM- 20190816
LR  - 20190816
IS  - 1095-8290 (Electronic)
IS  - 0305-7364 (Print)
IS  - 0305-7364 (Linking)
VI  - 122
IP  - 2
DP  - 2018 Aug 1
TI  - Analysis of retrotransposon abundance, diversity and distribution in holocentric 
      Eleocharis (Cyperaceae) genomes.
PG  - 279-290
LID - 10.1093/aob/mcy066 [doi]
AB  - BACKGROUND AND AIMS: Long terminal repeat-retrotransposons (LTR-RTs) comprise a 
      large portion of plant genomes, with massive repeat blocks distributed across the 
      chromosomes. Eleocharis species have holocentric chromosomes, and show a positive 
      correlation between chromosome numbers and the amount of nuclear DNA. To evaluate 
      the role of LTR-RTs in karyotype diversity in members of Eleocharis (subgenus 
      Eleocharis), the occurrence and location of different members of the Copia and 
      Gypsy superfamilies were compared, covering interspecific variations in ploidy 
      levels (considering chromosome numbers), DNA C-values and chromosomal 
      arrangements. METHODS: The DNA C-value was estimated by flow cytometry. Genomes 
      of Eleocharis elegans and E. geniculata were partially sequenced using Illumina 
      MiSeq assemblies, which were a source for searching for conserved proteins of 
      LTR-RTs. POL domains were used for recognition, comparing families and for probe 
      production, considering different families of Copia and Gypsy superfamilies. 
      Probes were obtained by PCR and used in fluorescence in situ hybridization (FISH) 
      against chromosomes of seven Eleocharis species. KEY RESULTS: A positive 
      correlation between ploidy levels and the amount of nuclear DNA was observed, but 
      with significant variations between samples with the same ploidy levels, 
      associated with repetitive DNA fractions. LTR-RTs were abundant in E. elegans and 
      E. geniculata genomes, with a predominance of Copia Sirevirus and Gypsy 
      Athila/Tat clades. FISH using LTR-RT probes exhibited scattered and clustered 
      signals, but with differences in the chromosomal locations of Copia and Gypsy. 
      The diversity in LTR-RT locations suggests that there is no typical chromosomal 
      distribution pattern for retrotransposons in holocentric chromosomes, except the 
      CRM family with signals distributed along chromatids. CONCLUSIONS: These data 
      indicate independent fates for each LTR-RT family, including accumulation between 
      and within chromosomes and genomes. Differential activity and small changes in 
      LTR-RTs suggest a secondary role in nuclear DNA variation, when compared with 
      ploidy changes.
FAU - de Souza, Thaissa B
AU  - de Souza TB
AD  - Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, 
      Center for Biological Sciences, State University of Londrina, Londrina, Parana, 
      Brazil.
FAU - Chaluvadi, Srinivasa R
AU  - Chaluvadi SR
AD  - Department of Genetics, University of Georgia, Athens, GA, USA.
FAU - Johnen, Lucas
AU  - Johnen L
AD  - Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, 
      Center for Biological Sciences, State University of Londrina, Londrina, Parana, 
      Brazil.
FAU - Marques, Andre
AU  - Marques A
AD  - Laboratory of Genetic Resources, Campus Arapiraca, Federal University of Alagoas, 
      Arapiraca, Brazil.
FAU - Gonzalez-Elizondo, M Socorro
AU  - Gonzalez-Elizondo MS
AD  - CIIDIR, Instituto Politecnico Nacional, Durango, Mexico.
FAU - Bennetzen, Jeffrey L
AU  - Bennetzen JL
AD  - Department of Genetics, University of Georgia, Athens, GA, USA.
FAU - Vanzela, Andre L L
AU  - Vanzela ALL
AD  - Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, 
      Center for Biological Sciences, State University of Londrina, Londrina, Parana, 
      Brazil.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Ann Bot
JT  - Annals of botany
JID - 0372347
RN  - 0 (Retroelements)
MH  - Chromosomes, Plant/*genetics
MH  - Eleocharis/*genetics
MH  - Flow Cytometry
MH  - *Genetic Variation
MH  - Genome Size
MH  - Genome, Plant/*genetics
MH  - In Situ Hybridization, Fluorescence
MH  - Ploidies
MH  - Retroelements/*genetics
MH  - Species Specificity
MH  - Terminal Repeat Sequences/genetics
PMC - PMC6070107
EDAT- 2018/08/08 06:00
MHDA- 2019/08/17 06:00
PMCR- 2018/05/04
CRDT- 2018/08/08 06:00
PHST- 2018/02/09 00:00 [received]
PHST- 2018/04/18 00:00 [accepted]
PHST- 2018/08/08 06:00 [entrez]
PHST- 2018/08/08 06:00 [pubmed]
PHST- 2019/08/17 06:00 [medline]
PHST- 2018/05/04 00:00 [pmc-release]
AID - 4993082 [pii]
AID - mcy066 [pii]
AID - 10.1093/aob/mcy066 [doi]
PST - ppublish
SO  - Ann Bot. 2018 Aug 1;122(2):279-290. doi: 10.1093/aob/mcy066.