PMID- 28775768
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20240326
IS  - 1759-8753 (Print)
IS  - 1759-8753 (Electronic)
VI  - 8
DP  - 2017
TI  - Targeted identification of TE insertions in a Drosophila genome through 
      hemi-specific PCR.
PG  - 10
LID - 10.1186/s13100-017-0092-1 [doi]
LID - 10
AB  - BACKGROUND: Transposable elements (TEs) are major components of eukaryotic 
      genomes and drivers of genome evolution, producing intraspecific polymorphism and 
      interspecific differences through mobilization and non-homologous recombination. 
      TE insertion sites are often highly variable within species, creating a need for 
      targeted genome re-sequencing (TGS) methods to identify TE insertion sites. 
      METHODS: We present a hemi-specific PCR approach for TGS of P-elements in 
      Drosophila genomes on the Illumina platform. We also present a computational 
      framework for identifying new insertions from TGS reads. Finally, we describe a 
      new method for estimating the frequency of TE insertions from WGS data, which is 
      based precise insertion sites provided by TGS annotations. RESULTS: By comparing 
      our results to TE annotations based on whole genome re-sequencing (WGS) data for 
      the same Drosophilamelanogaster strain, we demonstrate that TGS is powerful for 
      identifying true insertions, even in repeat-rich heterochromatic regions. We also 
      demonstrate that TGS offers enhanced annotation of precise insertion sites, which 
      facilitates estimation of TE insertion frequency. CONCLUSIONS: TGS by 
      hemi-specific PCR is a powerful approach for identifying TE insertions of 
      particular TE families in species with a high-quality reference genome, at 
      greatly reduced cost as compared to WGS. It may therefore be ideal for population 
      genomic studies of particular TE families. Additionally, TGS and WGS can be used 
      as complementary approaches, with TGS annotations identifying more annotated 
      insertions with greater precision for a target TE family, and WGS data allowing 
      for estimates of TE insertion frequencies, and a broader picture of the location 
      of non-target TEs across the genome.
FAU - Zhang, Shuo
AU  - Zhang S
AD  - Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd. 
      Suite 342, Houston, TX 77204 USA. ISNI: 0000 0004 1569 9707. GRID: grid.266436.3
FAU - Kelleher, Erin S
AU  - Kelleher ES
AUID- ORCID: 0000-0002-1827-067X
AD  - Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd. 
      Suite 342, Houston, TX 77204 USA. ISNI: 0000 0004 1569 9707. GRID: grid.266436.3
LA  - eng
PT  - Journal Article
DEP - 20170728
PL  - England
TA  - Mob DNA
JT  - Mobile DNA
JID - 101519891
PMC - PMC5534036
COIS- ETHICS APPROVAL AND CONSENT TO PARTICIPATE: Not applicable. CONSENT FOR 
      PUBLICATION: Not applicable. COMPETING INTERESTS: Not applicable. PUBLISHER'S 
      NOTE: Springer Nature remains neutral with regard to jurisdictional claims in 
      published maps and institutional affiliations.
EDAT- 2017/08/05 06:00
MHDA- 2017/08/05 06:01
PMCR- 2017/07/28
CRDT- 2017/08/05 06:00
PHST- 2017/04/14 00:00 [received]
PHST- 2017/07/10 00:00 [accepted]
PHST- 2017/08/05 06:00 [entrez]
PHST- 2017/08/05 06:00 [pubmed]
PHST- 2017/08/05 06:01 [medline]
PHST- 2017/07/28 00:00 [pmc-release]
AID - 92 [pii]
AID - 10.1186/s13100-017-0092-1 [doi]
PST - epublish
SO  - Mob DNA. 2017 Jul 28;8:10. doi: 10.1186/s13100-017-0092-1. eCollection 2017.