English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

Background  Transposable elements (TEs) are fragments of DNA that can insert into new chromosomal locations. They represent a great proportion of eukaryotic genomes. The identification and characterization of TEs facilitates understanding the transpositional activity of TEs with their effects on the orchid genome structure.    Results  We combined the draft whole-genome sequences of  Phalaenopsis equestris  with BAC end sequences, Roche 454, and Illumina/Solexa, and identified long terminal repeat (LTR) retrotransposons in these genome sequences by using LTRfinder and classified by using Gepard software. Among the 10 families  Gypsy -like retrotransposons, three families  Gypsy1 ,  Gypsy2 , and  Gypsy3 , contained the most copies among these predicted elements. In addition, six high-copy retrotransposons were identified according to their reads in the sequenced raw data. The 12-kb  Orchid-rt1  contains 18,000 copies representing 220 Mbp of the  P. equestris  genome. Southern blot and slot blot assays showed that these four retrotransposons  Gypsy1 ,  Gypsy2 ,  Gypsy3 , and  Orchid-rt1  contained high copies in the large-genome-size/large-chromosome species  P. violacea  and  P. bellina . Both  Orchid-rt1  and  Gypsy1  displayed various ratios of copy number for the LTR sequences versus coding sequences among four  Phalaenopsis  species, including  P. violacea  and  P. bellina  and small-genome-size/small-chromosome  P. equestris  and  P. ahprodite  subsp.  formosana , which suggests that  Orchid-rt1  and  Gypsy1  have been through various mutations and homologous recombination events. FISH results showed amplification of  Orchid-rt1  in the euchromatin regions among the four  Phalaenopsis  species. The expression levels of  Peq018599  encoding copper transporter 1 is highly upregulated with the insertion of  Orchid-rt1 , while it is down regulated for  Peq009948  and  Peq014239  encoding for a 26S proteasome non-ATP regulatory subunit 4 homolog and auxin-responsive factor AUX/IAA-related. In addition, insertion of  Orchid-rt1  in these three genes are all in their intron regions.    Conclusion   Orchid-rt1  and  Gypsy1–3  have amplified within  Phalaenopsis  orchids concomitant with the expanded genome sizes, and  Orchid-rt1  and  Gypsy1  may have gone through various mutations and homologous recombination events. Insertion of  Orchid-rt1  is in the introns and affects gene expression levels.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-020-07221-6.

Identification of high-copy number long terminal repeat retrotransposons and their expansion in Phalaenopsis orchids