Rey-Baños Rita, Sáenz de Miera Luis E, García Pedro, Pérez de la Vega Marcelino
Área de Genética, Dpto. de Biología Molecular, Universidad de León, León, Spain.
PLoS One. 2017 Apr 27;12(4):e0176728. doi: 10.1371/journal.pone.0176728. eCollection 2017.
Retrotransposons with long terminal repeats (LTR-RTs) are widespread mobile elements in eukaryotic genomes. We obtained a total of 81 partial LTR-RT sequences from lentil corresponding to internal retrotransposon components and LTRs. Sequences were obtained by PCR from genomic DNA. Approximately 37% of the LTR-RT internal sequences presented premature stop codons, pointing out that these elements must be non-autonomous. LTR sequences were obtained using the iPBS technique which amplifies sequences between LTR-RTs. A total of 193 retrotransposon-derived genetic markers, mainly iPBS, were used to obtain a genetic linkage map from 94 F7 inbred recombinant lines derived from the cross between the cultivar Lupa and the wild ancestor L. culinaris subsp. orientalis. The genetic map included 136 markers located in eight linkage groups. Clusters of tightly linked retrotransposon-derived markers were detected in linkage groups LG1, LG2, and LG6, hence denoting a non-random genomic distribution. Phylogenetic analyses identified the LTR-RT families in which internal and LTR sequences are included. Ty3-gypsy elements were more frequent than Ty1-copia, mainly due to the high Ogre element frequency in lentil, as also occurs in other species of the tribe Vicieae. LTR and internal sequences were used to analyze in silico their distribution among the contigs of the lentil draft genome. Up to 8.8% of the lentil contigs evidenced the presence of at least one LTR-RT similar sequence. A statistical analysis suggested a non-random distribution of these elements within of the lentil genome. In most cases (between 97% and 72%, depending on the LTR-RT type) none of the internal sequences flanked by the LTR sequence pair was detected, suggesting that defective and non-autonomous LTR-RTs are very frequent in lentil. Results support that LTR-RTs are abundant and widespread throughout of the lentil genome and that they are a suitable source of genetic markers useful to carry out further genetic analyses.
具有长末端重复序列的逆转座子（LTR-RTs）是真核生物基因组中广泛存在的可移动元件。我们从兵豆中总共获得了81个与内部逆转座子组件和LTRs相对应的部分LTR-RT序列。序列通过从基因组DNA进行PCR获得。大约37%的LTR-RT内部序列存在过早终止密码子，这表明这些元件一定是非自主的。LTR序列是使用iPBS技术获得的，该技术可扩增LTR-RTs之间的序列。总共193个逆转座子衍生的遗传标记，主要是iPBS，用于从94个F7自交重组系构建遗传连锁图谱，这些重组系来源于品种卢帕与野生祖先东方兵豆亚种之间的杂交。遗传图谱包括位于8个连锁群中的136个标记。在连锁群LG1、LG2和LG6中检测到紧密连锁的逆转座子衍生标记簇，因此表明其基因组分布是非随机的。系统发育分析确定了包含内部和LTR序列的LTR-RT家族。Ty3-gypsy元件比Ty1-copia更常见，主要是因为兵豆中Ogre元件频率较高，在蚕豆族的其他物种中也是如此。LTR和内部序列用于在计算机上分析它们在兵豆基因组草图重叠群中的分布。高达8.8%的兵豆重叠群证明存在至少一个LTR-RT相似序列。统计分析表明这些元件在兵豆基因组内的分布是非随机的。在大多数情况下（根据LTR-RT类型，介于97%和72%之间），未检测到由LTR序列对侧翼的任何内部序列，这表明有缺陷的和非自主的LTR-RTs在兵豆中非常常见。结果支持LTR-RTs在整个兵豆基因组中丰富且广泛存在，并且它们是进行进一步遗传分析的合适遗传标记来源。
