title: Characterization of three active transposable elements recently inserted in three independent DFR-A alleles and one high-copy DNA transposon isolated from the Pink allele of the ANS gene in onion (Allium cepa L.).
abstract: Intact retrotransposon and DNA transposons inserted in a single gene were characterized in onions (Allium cepa) and their transcription and copy numbers were estimated in this study. While analyzing diverse onion germplasm, large insertions in the DFR-A gene encoding dihydroflavonol 4-reductase (DFR) involved in the anthocyanin biosynthesis pathway were found in two accessions. A 5,070-bp long terminal repeat (LTR) retrotransposon inserted in the active DFR-A (R4) allele was identified from one of the large insertions and designated AcCOPIA1. An intact ORF encoded typical domains of copia-like LTR retrotransposons. However, AcCOPIA1 contained atypical 'TG' and 'TA' dinucleotides at the ends of the LTRs. A 4,615-bp DNA transposon was identified in the other large insertion. This DNA transposon, designated AcCACTA1, contained an ORF coding for a transposase showing homology with the CACTA superfamily transposable elements (TEs). Another 5,073-bp DNA transposon was identified from the DFR-A (TRN) allele. This DNA transposon, designated AchAT1, belonged to the hAT superfamily with short 4-bp terminal inverted repeats (TIRs). Finally, a 6,258-bp non-autonomous DNA transposon, designated AcPINK, was identified in the ANS-p allele encoding anthocyanidin synthase, the next downstream enzyme to DFR in the anthocyanin biosynthesis pathway. AcPINK also possessed very short 3-bp TIRs. Active transcription of AcCOPIA1, AcCACTA1, and AchAT1 was observed through RNA-Seq analysis and RT-PCR. The copy numbers of AcPINK estimated by mapping the genomic DNA reads produced by NextSeq 500 were predominantly high compared with the other TEs. A series of evidence indicated that these TEs might have transposed in these onion genes very recently, providing a stepping stone for elucidation of enormously large-sized onion genome structure.
authors.affiliation: Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Gwangju, 500-757, Republic of Korea, dronion@jnu.ac.kr.
authors.forename: Sunggil
authors.initials: S
authors.lastname: Kim
authors.forename: Jee Young
authors.initials: JY
authors.lastname: Park
authors.forename: Tae-Jin
authors.initials: TJ
authors.lastname: Yang
mesh_terms: D000429:Alcohol Oxidoreductases / Q000235:genetics*; D000483:Alleles; D000595:Amino Acid Sequence; D001483:Base Sequence; D004251:DNA Transposable Elements / Q000235:genetics*; D018076:DNA, Complementary / Q000235:genetics; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D019697:Onions / Q000201:enzymology / Q000235:genetics*; D010105:Oxygenases / Q000235:genetics*; D010802:Phylogeny; D010860:Pigments, Biological / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics; D018626:Retroelements / Q000235:genetics*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D020079:Terminal Repeat Sequences / Q000235:genetics; D019895:Transposases / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D018076:DNA, Complementary; D010860:Pigments, Biological; D010940:Plant Proteins; D018626:Retroelements; D000429:Alcohol Oxidoreductases; C056570:dihydroflavanol 4-reductase; D010105:Oxygenases; C118159:anthocyanidin synthase; D019895:Transposases