PhD defence: Qing Liu

Title: The chromosome-level genome of the migratory locust provides novel insights on chromatin changes during phase change of locusts

Supervisor: Guojie Zhang

Defence committee: David Nash, Fangqing Zhao (Beijing Institutes of Life Science), Lan Jiang (Beijing Institute of Genomics, Chinese Academy of Sciences)

Summary: Affecting the morphology and behaviour by changes in environmental conditions indicates that the life cycle of the migratory locust is a typical instance of phenotypic plasticity. Responding to change of the density of population in the field, locusts exhibit strikingly different phases: amiable solitarious and notorious gregarious. Density-dependent phenotypic plasticity of locusts is fully in line with the characteristics of epigenomics. However, the specific regulatory roles of histone modification in locust phase change remain open questions, due to the absence of a high contiguous genome assembly and a highly confident genome annotation, which is necessary for epigenomic researches in locusts.

This PhD thesis is an attempt to explore the regulatory roles of histone modification in phase change of the migratory locust. In the first chapter, we generated a chromosome-scale genome assembly of the migratory locust, an insect with 12 chromosomes and a genome size of 6.95 Gb. We performed the annotation of protein-coding genes and transposable elements and identified the X chromosome of locusts using a chromosome quotient method. Taking advantage of the great improvement in completeness of genomic transposable element copies, we deepen the analyses of transposable elements and tracked the historical proliferation of TEs in the migratory locust genome.

In the second chapter, we generated high-resolution transcription initiation datasets to define a comprehensive atlas of core promoters in locusts, contributing to the expansion of non-Drosophila taxonomic representation and revealing distinct genomic features to deepen the understanding of transcription initiation in insects. We found widespread higher expression activities in distant core promoters in locusts, implying an important role of distant transcription initiation in locusts. We further compared core promoters in the seven arthropod species across a broad range of genome sizes to reinforce our results on the emergence of distant core promoters in large-sized genomes, and we also revealed the changes in abundance and divergence of TFBSs of distant transcription initiation in the context of genome size.

In the third chapter, we generated the first genome-wide epigenomic maps of chromatin architecture in the locust genome at a key nymph stage in which developmental direction into solitarious or gregarious phase is critical. By comprehensive analyses of the open chromatin, DNA accessibility, histone modification and transcriptome, we characterized the chromatin architecture of protein-coding genes and cis-regulatory elements including enhancers and promoters. Our results revealed a regulatory role of chromatin architecture in maintenance of phase-related transcriptional programs in the migratory locust.

The defence is held online via Zoom: https://ucph-ku.zoom.us/j/63662823335?pwd=c0RtR1UwM3Z6NHdqZ281U3NaaFhoZz09