Evaluating the contribution of transposons to agricultural domestication

脊椎动物和转座子有着古老的共同进化史。事实上，脊椎动物的整个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明显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跃转座子和突变的转座子残留物(例如，转座子约占人类基因组总含量的50%)。直到最近，转座子在很大程度上还被认为是散落在宿主基因组中的“垃圾DNA”。虽然已知活性元件会导致插入突变，但很少有人认识到转座子在宿主进化中起到了有意义的作用。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，并直接贡献蛋白质编码序列作为新宿主功能的原料。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大的地位，可以更多地了解在进化过程中宿主基因组利用转座子的错综复杂的情况。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。该项目将利用对重要家畜品种及其野生祖先的详细比较基因组分析，解决转座子对农业驯化的贡献这一令人兴奋的问题。在这个项目中，来自大量农业上重要的家畜物种的基因组数据将与来自高产和低产品种以及野生祖先物种的数据相辅相成，以执行转座子含量、整合历史以及与宿主基因本体论的相互作用的尖端生物信息学分析。这将为转座子的活性和转座子在驯化过程中的作用提供一个新的和详细的图景。特别令人感兴趣的是转座子参与与生产性状相关的基因组区域，以及被确定为包含转座子热点的区域，其中嵌套插入为进化过程提供了底物，如适应性行走和新寄主表型的表达。这一跨学科项目将涉及几所著名大学的培训，包括埃克塞特大学的尖端生物信息学和系统发育方法(埃克塞特大学的Alex Hayward博士)，以及加的夫的人口基因组学和牲畜基因组学(Pablo Orozco terWengel博士)。该项目将对驯化的遗传结构和进化基础提供高度新颖的见解，在农业中具有相当大的应用潜力，以提高畜牧业生产系统的弹性和可持续性。

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.