Genomic studies in Pseudolycoriella hygida (Sciaridae)

• Ano de defesa: 2024
• Autor(a) principal: Trinca, Vitor
• Tipo de documento: Tese
• Tipo de acesso: Acesso aberto
• Idioma: eng
• Instituição de defesa: Biblioteca Digitais de Teses e Dissertações da USP
• Palavras-chave em Português: Análise de transcriptoma; Análises filogenéticas; Comportamentos alimentares de sciarídeos; Developmentally regulated gene expression; Expressão gênica regulada no desenvolvimento; Genoma nuclear; Nuclear genome; Phylogenetic analyses; Salivary gland secretion; Sciarids feeding habits; Secreção da glândula salivar; Transcriptome analysis
• Link de acesso: https://www.teses.usp.br/teses/disponiveis/17/17136/tde-13052024-143522/

The order Diptera, which includes true flies, can be subdivided into basal and higher Diptera. Basal Diptera encompasses the infraorders Tipulomorpha, Culicomorpha, Psychodomorpha, and Bibionomorpha, while the higher Diptera belong to the suborder Brachycera. The availability of genomes for Diptera is uneven, with a focus on higher Diptera, which account for 76% of genome assemblies. Studies on species of the Sciaridae family (Bibionomorpha) have contributed to the understanding of both processes of general occurrence in metazoans, as well as those specific to sciarids, notably gene amplification in DNA puff-forming regions and the mechanism of sexual determination. Our laboratory employs the species Pseudolycoriella hygida (Bibionomorpha: Sciaridae) as a model organism. This thesis is divided into three chapters. The first chapter presents the assembly and annotation of three sciarid mitogenomes, highlighting that the mitogenome of P. hygida (37 kb) is the largest described in the order Diptera to date. Gene rearrangements characteristic of sciarid subfamilies were found, and phylogenetic analyses revealed the position of P. hygida within the Sciaridae family. The second chapter describes the nuclear genome of P. hygida, that comprises 609 Mb distributed in 6,452 scaffolds, that is presented at the chromosomal level, with approximately 90% of the genome distributed among the four largest scaffolds corresponding to chromosomes A, B, C, and X. A total of 17,881 protein-coding genes were predicted, with 92.9% of them functionally annotated. Bioinformatic and biochemical analyses revealed the presence of active carbohydrate-active enzymes (CAZymes) in the saliva. Comparative analyses with other sciarids and Lucilia cuprina (Diptera: Calliphoridae) indicated that sciarids do not present significant differences in the annotated CAZymes, regardless of their feeding habits. However, the comparison of sciarid CAZymes against L. cuprina showed groups of CAZymes exclusively encoded in sciarid genomes capable of degrading carbohydrates present in plant and fungal cell walls. In the third chapter, we present the characterization of RNAseq libraries from salivary glands of early fourth-instar larvae and at different ages during DNA puff formation. The analyses revealed that 10,769 genes are expressed in this tissue, and 1,687 genes are differentially expressed among the ages analyzed. Notably, these genes are associated to categories such as translation, proteolysis, and plasma membrane transport, emphasizing the secretory role of salivary gland cells. The study also investigated the gene expression profile during the opening of DNA puffs, identifying candidate genes residing in DNA puff-forming regions. In summary, this thesis contributes to the field of Diptera genomics, expands our knowledge about P. hygida offers new perspectives on sciarid biology.