DataSheet_1_Different Families of Retrotransposons and DNA Transposons Are Actively Transcribed and May Have Transposed Recently in Physcomitrium (Physcomitrella) patens.docx

Similarly to other plant genomes of similar size, more than half of the genome of P. patens is covered by Transposable Elements (TEs). However, the composition and distribution of P. patens TEs is quite peculiar, with Long Terminal Repeat (LTR)-retrotransposons, which form patches of TE-rich regions interleaved with gene-rich regions, accounting for the vast majority of the TE space. We have already shown that RLG1, the most abundant TE in P. patens, is expressed in non-stressed protonema tissue. Here we present a non-targeted analysis of the TE expression based on RNA-Seq data and confirmed by qRT-PCR analyses that shows that, at least four LTR-RTs (RLG1, RLG2, RLC4 and tRLC5) and one DNA transposon (PpTc2) are expressed in P. patens. These TEs are expressed during development or under stresses that P. patens frequently faces, such as dehydratation/rehydratation stresses, suggesting that TEs have ample possibilities to transpose during P. patens life cycle. Indeed, an analysis of the TE polymorphisms among four different P. patens accessions shows that different TE families have recently transposed in this species and have generated genetic variability that may have phenotypic consequences, as a fraction of the TE polymorphisms are within or close to genes. Among the transcribed and mobile TEs, tRLC5 is particularly interesting as it concentrates in a single position per chromosome that could coincide with the centromere, and its expression is specifically induced in young sporophyte, where meiosis takes place.

与相似大小的其他植物基因组类似，超过半数的拟南芥（P. patens）基因组被转座元件（TEs）所覆盖。然而，拟南芥TEs的组成与分布颇具特色，其中长末端重复（LTR）-反转录转座子形成了TE富集区域与基因富集区域交错的斑驳地带，占据了TE空间的绝大部分。我们已证明，在拟南芥中，RLG1是最丰富的TE，其在非胁迫性的原球茎组织中表达。在本研究中，我们基于RNA-Seq数据进行的非靶向TE表达分析，并通过qRT-PCR分析得到证实，发现至少四种LTR-RTs（RLG1、RLG2、RLC4和tRLC5）以及一种DNA转座子（PpTc2）在拟南芥中表达。这些TEs在发育过程中或在拟南芥常遭遇的压力条件下（如脱水/复水压力）表达，这表明TEs在拟南芥的生命周期中具有充足的转座可能性。实际上，对四个不同拟南芥品种的TE多态性分析显示，不同的TE家族近期在此物种中发生了转座，并产生了可能具有表型后果的遗传变异，因为部分TE多态性位于基因内部或附近。在转录和移动的TEs中，tRLC5尤为引人注目，因为它在每个染色体上的单一位置集中，可能对应着着丝点，并且其表达在年轻的配子体中特异性诱导，而减数分裂就在这里进行。