Evaluating the contribution of transposons to agricultural domestication

脊椎动物和转座子有着共同的进化史。事实上，整个脊椎动物的进化都发生在转座子相互作用的背景下，因为转座子的起源被认为大大早于脊椎动物的起源。因此，脊椎动物基因组通常包含非常大比例的活性转座子和突变转座子残体（例如，转座子占人类总基因组含量的50%）。直到最近，转座子在很大程度上被认为是散布在宿主基因组中的“垃圾DNA”。虽然已知活性元件可引起插入突变，但很少有人认识到转座子在宿主进化中发挥了有意义的作用。然而，自基因组学革命以来，转座子在宿主基因组复杂性的进化中扮演着非常重要的角色，发挥着关键的调节作用，并直接提供蛋白质编码序列作为宿主新功能的原料。鉴于来自脊椎动物系统发育的大量高质量基因组，我们现在处于一个强有力的位置，可以更多地了解宿主基因组在进化过程中利用转座子的复杂性。这为在生物学的一系列重要领域开发新的应用提供了巨大的潜力。该项目将通过对重要家畜品种及其野生祖先的详细比较基因组学分析，解决转座子对农业驯化的贡献这一令人兴奋的问题。在本项目中，来自大量农业上重要的家畜物种的基因组数据将与高产、低产品种和野生祖先物种的数据相辅相成，对转座子含量、整合历史以及与宿主基因本体的相互作用进行尖端的生物信息学分析。这将为转座子在驯化过程中的作用和转座子的活性提供一个新的和详细的图景。特别感兴趣的将是转座子参与与生产性状相关的基因组区域，以及确定包含转座子热点的区域，其中嵌套插入为进化过程（如适应性行走和新宿主表型的表达）提供了基础。这个跨学科项目将涉及在几所著名大学的培训，包括埃克塞特大学（埃克塞特大学Alex Hayward博士）的尖端生物信息学和系统发育方法，以及卡迪夫大学（Pablo Orozco terWengel博士）的种群基因组学和牲畜基因组学。该项目将为驯化的遗传结构和进化基础提供非常新颖的见解，在农业中具有相当大的应用潜力，以提高牲畜生产系统的复原力和可持续性。

Vertebrates and transposons share an ancient co-evolutionary history. Indeed, the whole of vertebrate evolution has occurred within the context of transposon interactions, since the origin of transposons is believed to significantly predate the origin of the vertebrates. Consequently, vertebrate genomes typically contain very large proportions of both active transposons and mutated transposon remnants (e.g. transposons account for ~50% of total genome content in humans). Until recently, transposons were largely considered to be 'junk DNA' that littered the host genome. While active elements were known to cause insertional mutagenesis, there was very little appreciation that transposons played a meaningful role in host evolution. However, since the genomics revolution, it has become apparent that transposons are highly important players in the evolution of host genomic complexity, playing key regulatory roles as well as directly contributing protein coding sequence as raw material for novel host functions. Given an abundance of high quality genomes from across vertebrate phylogeny, we are now in a powerful position to learn more about the intricacies by which transposons are harnessed by host genomes during evolution. This offers great potential for developing novel applications across a range of important areas in biology. This project will address the exciting question of the contribution of transposons to agricultural domestication, using a detailed comparative genomics analysis of important livestock breeds and their wild ancestors. In this project, genomic data from a large number of agriculturally important livestock species, will be complemented with data from high and low producing breeds and wild ancestral species, to perform cutting-edge bioinformatic analyses of transposon content, integration history, and interactions with host gene ontology. This will provide a new and detailed picture of transposon activity and the contribution of transposons during domestication. Of particular interest will be transposon involvement in genomic regions linked to production traits, and regions identified to contain transposon hotspots, where nested insertions have provided the substrate for evolutionary processes such as adaptive walks and the expression of new host phenotypes. This cross-disciplinary project will involve training at several prestigious universities, including cutting-edge bioinformatic and phylogenetic approaches at Exeter (Dr Alex Hayward, University of Exeter), and population genomics and livestock genomics at Cardiff (Dr Pablo Orozco terWengel). The project will provide highly novel insights into the genetic architecture and evolutionary basis of domestication, with considerable potential for applications in agriculture, to increase the resilience and sustainability of livestock production systems.