Portrait of author

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

Date: 01-09-2021    Supervisor: Le Kang and Guojie Zhang



This thesis is an attempt to explore the regulatory roles of histone modification in phase changes in the migratory locust. In the first chapter, we generate a chromosome-scale genome assembly of the migratory locust, an insect with 12 chromosomes and a genome size of 6.95 Gb. We perform the annotation of protein-coding genes and transposable elements and identify the X chromosome of this species via a chromosome quotient method. By taking advantage of the great improvement that has been achieved in ensuring the completeness of genomic transposable element copies, we deepen the analyses of transposable elements (TEs) and track their historical proliferation in the migratory locust genome.

In the second chapter, we generate high-resolution transcription initiation datasets to define a comprehensive atlas of core promoters in locusts. We find widespread high expression activities in distant core promoters in locusts, implying an important role of distant transcription initiation in locusts. We further compare core promoters in 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. We also reveal the changes in abundance and divergence of the TFBSs of distant transcription initiation in the context of genome size. These results contribute to the expansion of non-Drosophila taxonomic representation and revealing distinct genomic features to deepen our understanding of transcription initiation in insects.

In the third chapter, we provide the first genome-wide epigenomic maps of chromatin architecture in the locust genome at a key nymphal 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 characterize the chromatin architecture of protein-coding genes and cis-regulatory elements including enhancers and promoters. Our results reveal a regulatory role of chromatin architecture in the maintenance of phase-related transcriptional programs in the migratory locust.