PMID- 30770721
OWN - NLM
STAT- MEDLINE
DCOM- 20190225
LR  - 20200225
IS  - 1471-2229 (Electronic)
IS  - 1471-2229 (Linking)
VI  - 19
IP  - 1
DP  - 2019 Feb 15
TI  - Molecular cytogenetic analysis of genome-specific repetitive elements in Citrus 
      clementina Hort. Ex Tan. and its taxonomic implications.
PG  - 77
LID - 10.1186/s12870-019-1676-3 [doi]
LID - 77
AB  - BACKGROUND: Clementine mandarin (Citrus clementina Hort. ex Tan.) is one of the 
      most famous and widely grown citrus cultivars worldwide. Variations in relation 
      to the composition and distribution of repetitive DNA sequences that dominate 
      greatly in eukaryote genomes are considered to be species-, genome-, or even 
      chromosome-specific. Repetitive DNA-based fluorescence in situ hybridization 
      (FISH) is a powerful tool for molecular cytogenetic study. However, to date few 
      studies have involved in the repetitive elements and cytogenetic karyotype of 
      Clementine. RESULTS: A graph-based similarity sequence read clustering 
      methodology was performed to analyze the repetitive DNA families in the 
      Clementine genome. The bioinformatics analysis showed that repetitive DNAs 
      constitute 41.95% of the Clementine genome, and the majority of repetitive 
      elements are retrotransposons and satellite DNAs. Sequential multicolor FISH 
      using a probe mix that contained CL17, four satellite DNAs, two rDNAs and an 
      oligonucleotide of (TTTAGGG)(3) was performed with Clementine somatic metaphase 
      chromosomes. An integrated karyotype of Clementine was established based on 
      unequivocal and reproducible chromosome discriminations. The distribution 
      patterns of these probes in several Citrus, Poncirus and Fortunella species were 
      summarized through extensive FISH analyses. Polymorphism and heterozygosity were 
      commonly observed in the three genera. Some asymmetrical FISH loci in Clementine 
      were in agreement with its hybrid origin. CONCLUSIONS: The composition and 
      abundance of repetitive elements in the Clementine genome were reanalyzed. 
      Multicolor FISH-based karyotyping provided direct visual proof of the 
      heterozygous nature of Clementine chromosomes with conspicuous asymmetrical FISH 
      hybridization signals. We detected some similar and variable distribution 
      patterns of repetitive DNAs in Citrus, Poncirus, and Fortunella, which revealed 
      notable conservation among these genera, as well as obvious polymorphism and 
      heterozygosity, indicating the potential utility of these repetitive element 
      markers for the study of taxonomic, phylogenetic and evolutionary relationships 
      in the future.
FAU - Deng, Honghong
AU  - Deng H
AD  - College of Horticulture and Landscape Architecture, Southwest University, 
      Chongqing, 400715, China.
FAU - Xiang, Suqiong
AU  - Xiang S
AD  - College of Horticulture and Landscape Architecture, Southwest University, 
      Chongqing, 400715, China.
FAU - Guo, Qigao
AU  - Guo Q
AD  - College of Horticulture and Landscape Architecture, Southwest University, 
      Chongqing, 400715, China.
FAU - Jin, Weiwei
AU  - Jin W
AD  - National Maize Improvement Center, College of Agronomy and Biotechnology, China 
      Agricultural University, Beijing, 100193, China.
FAU - Cai, Zexi
AU  - Cai Z
AD  - National Maize Improvement Center, College of Agronomy and Biotechnology, China 
      Agricultural University, Beijing, 100193, China. caizexi123@cau.edu.cn.
FAU - Liang, Guolu
AU  - Liang G
AD  - College of Horticulture and Landscape Architecture, Southwest University, 
      Chongqing, 400715, China. lianggl@swu.edu.cn.
LA  - eng
GR  - CYB14050/Program for Chongqing Graduate Student Innovation/
GR  - 201606990048/China Scholarship Council/
GR  - 31272138/National Natural Science Foundation of China/
GR  - 2014BAD16B0102(1)/National Sci-tech Support Plan/
PT  - Journal Article
DEP - 20190215
PL  - England
TA  - BMC Plant Biol
JT  - BMC plant biology
JID - 100967807
RN  - 0 (DNA, Satellite)
RN  - 0 (Retroelements)
SB  - IM
MH  - Citrus/*classification/genetics
MH  - Cytogenetic Analysis
MH  - DNA, Satellite/genetics
MH  - Genome, Plant/*genetics
MH  - In Situ Hybridization, Fluorescence
MH  - Karyotype
MH  - Phylogeny
MH  - Polymorphism, Genetic/*genetics
MH  - Repetitive Sequences, Nucleic Acid/*genetics
MH  - Retroelements/genetics
PMC - PMC6377768
OTO - NOTNLM
OT  - Hybrid identification
OT  - Karyotype
OT  - Multicolor FISH
OT  - Repetitive DNA sequences
OT  - Satellite DNA
OT  - rDNA
COIS- AUTHOR'S INFORMATION: Guolu Liang and Zexi Cai are the co-corresponding author 
      for this manuscript. ETHICS APPROVAL AND CONSENT TO PARTICIPATE: Not applicable 
      CONSENT FOR PUBLICATION: Not applicable COMPETING INTERESTS: The authors declare 
      that they have no competing interests. PUBLISHER'S NOTE: Springer Nature remains 
      neutral with regard to jurisdictional claims in published maps and institutional 
      affiliations.
EDAT- 2019/02/17 06:00
MHDA- 2019/02/26 06:00
PMCR- 2019/02/15
CRDT- 2019/02/17 06:00
PHST- 2018/03/30 00:00 [received]
PHST- 2019/02/07 00:00 [accepted]
PHST- 2019/02/17 06:00 [entrez]
PHST- 2019/02/17 06:00 [pubmed]
PHST- 2019/02/26 06:00 [medline]
PHST- 2019/02/15 00:00 [pmc-release]
AID - 10.1186/s12870-019-1676-3 [pii]
AID - 1676 [pii]
AID - 10.1186/s12870-019-1676-3 [doi]
PST - epublish
SO  - BMC Plant Biol. 2019 Feb 15;19(1):77. doi: 10.1186/s12870-019-1676-3.