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. 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. 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.

中文翻译：

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高拷贝数长末端重复逆转录转座子的鉴定及其在蝴蝶兰中的扩增

转座因子（TEs）是可插入新染色体位置的DNA片段。它们代表了很大比例的真核基因组。TEs的鉴定和表征有助于了解TEs的转座活性及其对兰花基因组结构的影响。我们将蝴蝶兰的全基因组序列草稿与BAC末端序列，Roche 454和Illumina / Solexa进行了组合，并使用LTRfinder在这些基因组序列中鉴定了长末端重复（LTR）逆转座子，并使用Gepard软件进行了分类。在10个类吉普赛样逆转录转座子中，三个家族Gypsy1，Gypsy2和Gypsy3包含了这些预测元素中最多的拷贝。此外，根据序列原始数据中的读物，鉴定了六个高复制逆转录转座子。12 kb的Orchid-rt1包含18,000个拷贝，代表P. equestris基因组的220 Mbp。Southern印迹法和狭缝印迹法检测表明，这四个逆转录转座子Gypsy1，Gypsy2，Gypsy3和Orchid-rt1在大基因组大小/大染色体物种紫罗兰和贝氏假单胞菌中含有高拷贝。Orchid-rt1和Gypsy1都在包括蝴蝶兰（P. violacea）和贝利纳螺旋体（P. bellina）以及小基因组大小/小染色体P. equestris和P. ahprodite亚种的4种蝴蝶兰中显示LTR序列与编码序列的拷贝数比率不同。 。formosana，这表明Orchid-rt1和Gypsy1已经经历了各种突变和同源重组事件。FISH结果表明，兰花4种蝴蝶兰的常染色质区域中的Orchid-rt1扩增。编码铜转运蛋白1的Peq018599的表达水平随Orchid-rt1的插入而上调，而对编码26S蛋白酶体非ATP调节亚基4同源物和生长素应答因子AUX / IAA-的Peq009948和Peq014239则下调。有关。另外，在这三个基因中插入兰花-rt1都在其内含子区域。兰花蝴蝶兰中的Orchid-rt1和Gypsy1-3随着基因组大小的扩展而扩增，而Orchid-rt1和Gypsy1可能经历了各种突变和同源重组事件。Orchid-rt1的插入位于内含子中，并影响基因表达水平。而下调编码Peq009948和Peq014239的26S蛋白酶体非ATP调节亚基4同源物和生长素反应性因子AUX / IAA相关。另外，在这三个基因中插入兰花-rt1都在其内含子区域。兰花蝴蝶兰中的Orchid-rt1和Gypsy1-3随着基因组大小的扩展而扩增，而Orchid-rt1和Gypsy1可能经历了各种突变和同源重组事件。Orchid-rt1的插入位于内含子中，并影响基因表达水平。而下调编码Peq009948和Peq014239的26S蛋白酶体非ATP调节亚基4同源物和生长素反应性因子AUX / IAA相关。另外，在这三个基因中插入兰花-rt1都在其内含子区域。兰花蝴蝶兰中的Orchid-rt1和Gypsy1-3随着基因组大小的扩展而扩增，而Orchid-rt1和Gypsy1可能经历了各种突变和同源重组事件。Orchid-rt1的插入位于内含子中，并影响基因表达水平。Orchid-rt1和Gypsy1可能经历了各种突变和同源重组事件。Orchid-rt1的插入位于内含子中，并影响基因表达水平。Orchid-rt1和Gypsy1可能经历了各种突变和同源重组事件。Orchid-rt1的插入位于内含子中，并影响基因表达水平。