PMID- 31727905
OWN - NLM
STAT- MEDLINE
DCOM- 20201102
LR  - 20210110
IS  - 2045-2322 (Electronic)
IS  - 2045-2322 (Linking)
VI  - 9
IP  - 1
DP  - 2019 Nov 14
TI  - Identification and characterization of abundant repetitive sequences in Allium 
      cepa.
PG  - 16756
LID - 10.1038/s41598-019-52995-9 [doi]
LID - 16756
AB  - Species of the genus Allium are well known for their large genomes. Allium cepa 
      is of great economic significance. Among vegetables, it ranks second after tomato 
      in terms of the global production value. However, there is limited genomics 
      information available on A. cepa. In this study, we sequenced the A. cepa genome 
      at low-coverage and annotated repetitive sequences by using a combination of 
      next-generation sequencing (NGS) and bioinformatics tools. Nearly 92% of 16 Gb 
      haploid onion genome were defined as repetitive sequences, organized in 162 
      clusters of at least 0.01 percent of the genome. Of these, a proportion 
      representing 40.5% of the genome were further analyzed in detail to obtain an 
      overview of representative repetitive elements present in the A. cepa genome. Few 
      representative satellite repeats were studied by fluorescence in situ 
      hybridization (FISH) and southern blotting. These results provided a basis for 
      evolutionary cytogenomics within the Allium genus.
FAU - Fu, Jiaping
AU  - Fu J
AD  - Institute of Economic Crops, Hubei Academy of Agriculture Sciences, Wuhan, 
      430064, China.
FAU - Zhang, Hao
AU  - Zhang H
AD  - State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, 
      Wuhan, 430072, China.
FAU - Guo, Fengling
AU  - Guo F
AD  - Institute of Economic Crops, Hubei Academy of Agriculture Sciences, Wuhan, 
      430064, China.
FAU - Ma, Lu
AU  - Ma L
AUID- ORCID: 0000-0001-5271-0686
AD  - Shenzhen Tobeacon Technology Co. Ltd., Shenzhen, 518049, China.
FAU - Wu, Jinping
AU  - Wu J
AD  - Institute of Economic Crops, Hubei Academy of Agriculture Sciences, Wuhan, 
      430064, China.
FAU - Yue, Mengxia
AU  - Yue M
AD  - State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, 
      Wuhan, 430072, China.
FAU - Zheng, Xueke
AU  - Zheng X
AD  - State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, 
      Wuhan, 430072, China.
FAU - Qiu, Zhengming
AU  - Qiu Z
AD  - Institute of Economic Crops, Hubei Academy of Agriculture Sciences, Wuhan, 
      430064, China. 13808640602@163.com.
FAU - Li, Lijia
AU  - Li L
AD  - State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, 
      Wuhan, 430072, China. ljli@whu.edu.cn.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20191114
PL  - England
TA  - Sci Rep
JT  - Scientific reports
JID - 101563288
RN  - 0 (DNA, Plant)
SB  - IM
MH  - Chromosome Mapping
MH  - DNA, Plant/genetics
MH  - Genome Size
MH  - High-Throughput Nucleotide Sequencing
MH  - In Situ Hybridization, Fluorescence
MH  - Onions/*genetics
MH  - *Repetitive Sequences, Nucleic Acid
MH  - Whole Genome Sequencing/*methods
PMC - PMC6856378
COIS- The authors declare no competing interests.
EDAT- 2019/11/16 06:00
MHDA- 2020/11/03 06:00
PMCR- 2019/11/14
CRDT- 2019/11/16 06:00
PHST- 2019/02/27 00:00 [received]
PHST- 2019/10/26 00:00 [accepted]
PHST- 2019/11/16 06:00 [entrez]
PHST- 2019/11/16 06:00 [pubmed]
PHST- 2020/11/03 06:00 [medline]
PHST- 2019/11/14 00:00 [pmc-release]
AID - 10.1038/s41598-019-52995-9 [pii]
AID - 52995 [pii]
AID - 10.1038/s41598-019-52995-9 [doi]
PST - epublish
SO  - Sci Rep. 2019 Nov 14;9(1):16756. doi: 10.1038/s41598-019-52995-9.