Genomic signatures of plasticity and diversity in the phenotypic development

• Grant number: 20/13719-7
• Support Opportunities: Research Grants - Young Investigators Grants
• Start date: May 01, 2022
• End date: April 30, 2027
• Field of knowledge: Biological Sciences - Zoology - Physiology of Recent Groups
• Principal Investigator: Flávia Cristina de Paula Freitas
• Grantee: Flávia Cristina de Paula Freitas
• Host Institution: Instituto de Biologia (IB). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• City of the host institution: Campinas
• Associated researchers: Alexandre dos Santos Cristino ; Alexandre Rossi Paschoal ; Francis de Morais Franco Nunes ; Marco Antonio Del Lama
• Associated scholarship(s): 25/10137-0 - Investigation of the D-Serine/NMDAR Pathway in Ovary Formation of Frieseomelitta varia, BP.MS; 24/22812-1 - Integration of transcriptome and chromatin accessibility data to reconstruct the cis-regulatory network of honeybee ovary development, BP.MS; 24/02856-4 - Morphological and transcriptomic analysis of the ovaries in the development of workers of the stingless bee Melipona quadrifasciata, BP.MS; + associated scholarships 23/12650-1 - Determination of the number and duration of the larval stages of the stingless bee Frieseomelitta varia, BP.IC; 23/12693-2 - Investigation of the mevalonate pathway role in the ovaries of honey bees and stingless bees., BP.IC; 23/11435-0 - Comparative analysis of queen and worker ovary morphology in the larval and pupal development of Frieseomelitta varia, BP.IC; 22/15906-4 - Comparative analysis of the cis-regulatory network of the ovary development in queens of honey bees and stingless bees, BP.MS; 22/05232-6 - Genomic signatures of plasticity and diversity in the phenotypic development, BP.JP - associated scholarships

Abstract

One of the most intriguing properties of the genome is its plasticity in triggering alternative genetic programs in response to different molecular signals or environmental factors. This property is crucial for differentiating the zygote into hundreds of cell types during embryonic development. The modulation of genome plasticity is a complex biological process, an outcome of the integration of different levels of regulation and molecular interactions that take place in the cell. Studies of complex biological processes such as genomic plasticity in development benefit from integrative and comparative genomic methods. This project aims to identify the aspects that give the genome the ability to trigger alternative genetic programs in response to different environmental factors. For this, the development of eussocial bees, in which the same genome is capable of guiding the formation of a fertile queen or a worker incapable of mating in response to the type and amount of food received during larval development, will be used as a model. To identify the genomic aspects related to plasticity, data from different levels of regulation will be integrated, such as regulatory genomic sequences (obtained through ATAC-seq) and the transcriptome (RNA-seq). This approach will be used to reconstruct the regulatory network for the development of the ovaries of eussocial bees Apis mellifera, Frieseomelitta varia and Melipona quadrifasciata which differ in terms of reproductive capacity. The comparison of the regulatory network of ovary development in these three species will identify changes in the regulation modules that allowed the appearance of ovaries with different reproductive capacities. These differences include the total activation capacity of the ovaries in workers of M. quadrifasciata, the optional activation in workers of A. mellifera and the permanent sterility in workers of F. varia. These eussocial bees offer an excellent opportunity to unravel the relationship between genome, transcriptome and physiomorphology because they have had their genomes sequenced and because they differ in terms of the phenotypic plasticity of the ovaries. This diversity makes their ovaries an interesting model for understanding the genomic and molecular aspects underlying phenotypic plasticity and the emergence of new physiomorphologies. In addition to providing elements for understanding the regulatory mechanisms that explain the evolutionary history of bees, this project will contribute to (1) the establishment of a new line of research at the host institution, entitled Integrative and Comparative Genomics of Development, (2) assembly a meliponary and the acquisition of equipment for the foundation of a new research group at the host institution; (3) improvements in the functional annotation of the genome of A. mellifera, F. varia and M. quadrifasciata species; (4) training in genomics for undergraduate and graduate students participating in this project. (AU)