Sequencing the giga-genomes of several pine species has enabled comparative genomic analyses of these outcrossing tree species. Previous studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occupy the large intergenic spaces in conifer genomes. In this study, we analyzed the distribution of TEs in gene regions of the assembled genomes of Pinus taeda and Pinus lambertiana using high-performance computing resources. The quality of draft genomes and the genome annotation have significant consequences for the investigation of TEs and these aspects are discussed. Several TE families frequently inserted into genes or their flanks were identified in both species’ genomes. Potentially important sequence motifs were identified in TEs that could bind additional regulatory factors, promoting gene network formation with faster or enhanced transcription initiation. Node genes that contain many TEs were observed in multiple potential transposable element-associated networks. This study demonstrated the increased accumulation of TEs in the introns of stress-responsive genes of pines and suggests the possibility of rewiring them into responsive networks and sub-networks interconnected with node genes containing multiple TEs. Many such regulatory influences could lead to the adaptive environmental response clines that are characteristic of naturally spread pine populations.

中文翻译：

---

松树参考基因组的比较研究揭示了转座因子互连基因网络

对几种松树物种的 giga 基因组进行测序使这些异交树种的比较基因组分析成为可能。先前的研究揭示了占据针叶树基因组中大的基因间空间的转座因子 (TE) 的广泛分布和非凡的多样性。在这项研究中，我们使用高性能计算资源分析了火炬松和兰伯松组装基因组基因区域中 TE 的分布。基因组草图的质量和基因组注释对 TE 的研究具有重要影响，并讨论了这些方面。在这两个物种的基因组中发现了几个经常插入基因或其侧翼的 TE 家族。在 TE 中发现了潜在的重要序列基序，这些基序可以结合其他调节因子，以更快或增强的转录起始促进基因网络的形成。在多个潜在的转座元件相关网络中观察到包含许多 TE 的节点基因。这项研究证明了松树应激反应基因内含子中 TE 的积累增加，并表明将它们重新连接到与包含多个 TE 的节点基因互连的响应网络和子网络中的可能性。许多这样的监管影响可能导致适应性环境反应基因，这是自然传播的松树种群的特征。这项研究证明了松树应激反应基因内含子中 TE 的积累增加，并表明将它们重新连接到与包含多个 TE 的节点基因互连的响应网络和子网络中的可能性。许多这样的监管影响可能导致适应性环境反应基因，这是自然传播的松树种群的特征。这项研究证明了松树应激反应基因内含子中 TE 的积累增加，并表明将它们重新连接到与包含多个 TE 的节点基因互连的响应网络和子网络中的可能性。许多这样的监管影响可能导致适应性环境反应基因，这是自然传播的松树种群的特征。