Genomic Biology of Limb and Gonad Development in the Spanish Mole (Talpa occidentalis)

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In this study we propose to use the mole (Talpa occidentalis) as a model to study how evolution operates in particular developmental processes and how this is reflected by specific changes in the species genome. The identification of the genetic causes underlying these adaptations can provide basic principles about how evolution operates and can provide insights into the molecular mechanisms of human disease. Moles have perfectly adapted to their fossorial lifestyle. In this evolutionary process they developed some exceptional features including polydactyly of the fore- and hindlimbs. Furthermore, female moles are true hermaphrodites, i.e. they have functioning ovaries and testes. We aim at unravelling the genomic origin of these unique features. In our preliminary work we managed to compile a complete genome sequence of the Spanish mole thereby providing the frame work for any future molecular work. The 2 Gb large genome was assembled and compared to other species. We found regions of interest such as a triplication of Cyp19a1, a gene invovled in the steroid pathway. In addition, we performed RNA-seq of gonadal tissue comparing male testis and the testicular and ovarian part of the female gonad. Our data indicate that changes in the steroid pathway may be involved in sex reversal in moles. Our first aim is to improve our mole genome data by PacBio sequencing a technology that provides extra-long read lengths that simplify and improve genome assembly. We will analyze the genome for structural variations by identifying breaks in synteny in comparison to other species. Two other mole species that do not show the ovotestis phenotype will be genome sequenced and compared to Talpa occidentalis. To identify regions involved in gene regulation, genome wide maps of histone modifications will be created in limb and gonadal tissue. In our second aim we will investigate the biology of digit development in the mole. We will study the developmental mechanisms of polydactyly and the involvement of candidate pathways such as hedgehog and Hox in this process. For this purpose we will perform in situ hybridizations in mole embryos. Genomic analysis of regulatory domains of identified misexpressed genes and the distribution of histone marks will reveal possible phenotype related differences. Chromosome conformation capture (4C) experiments will be performed at selected loci and compared to the mouse. Identified genomic changes will be tested in a cohort of patients with polydactyly. In the third aim we want to unravel the genomic origin of female sex reversal in moles. We will use RNA-seq at additional stages to identify candidate target genes that could be responsible for the ovotestes in female moles. Comparison of genomes and histone marks will help to identify regulatory elements and evolutionary changes that are related to the ovotestis phenotype. Identified changes will be tested in a cohort of patients with disorders of sexual development.