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首页> 外文期刊>Molecular genetics and genomics: MGG >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.)
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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.)

机译：从洋葱中ANS基因的粉红等位基因中分离出的三个独立的DFR-A等位基因和一个高拷贝DNA转座子中最近插入的三个活性转座子的特性

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摘要

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 steppingstone for elucidation of enormously large-sized onion genome structure.
机译：完整的逆转录转座子和插入到单个基因中的DNA转座子在洋葱（葱属洋葱）中进行了表征，并在本研究中估计了它们的转录和拷贝数。在分析各种洋葱种质时，在两个种质中发现了大量插入花青素生物合成途径的编码二氢黄酮醇4-还原酶（DFR）的DFR-A基因。从一个大的插入片段中鉴定出一个插入到活动DFR-A（R4）等位基因中的5,070 bp长的末端重复序列（LTR）反转录转座子，并命名为AcCOPIA1。完整的ORF编码的Copia样LTR反转录转座子的典型域。但是，AcCOPIA1在LTR的末端包含非典型的'TG'和'TA'二核苷酸。在另一个大插入片段中鉴定出一个4,615-bp DNA转座子。这种DNA转座子，称为AcCACTA1，包含一个ORF编码的转座酶，该转座酶显示出与CACTA超家族可转座元件（TEs）的同源性。从DFR-A（TRN）等位基因中鉴定出另一个5,073-bp DNA转座子。该DNA转座子称为AchAT1，属于具有短4 bp末端反向重复序列（TIR）的hAT超家族。最后，在编码花青素合酶的ANS-p等位基因中鉴定出了一个6,258 bp的非自治DNA转座子，称为AcPINK，该花色素苷合酶是花青素生物合成途径中DFR的下一个下游酶。 AcPINK还拥有非常短的3 bp TIR。通过RNA-Seq分析和RT-PCR观察到AcCOPIA1，AcCACTA1和AchAT1的主动转录。与其他TE相比，通过映射NextSeq 500产生的基因组DNA读数估算出的AcPINK的拷贝数主要很高。一系列证据表明，这些TEs可能在最近的这些洋葱基因中已经发生了转座，为阐明巨大的洋葱基因组结构提供了垫脚石。

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