Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects
Karageorgiou, Charikleia (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Gámez Visairas, Víctor (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Tarrío, Rosa (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Rodríguez-Trelles, Francisco (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)

Fecha:	2019
Resumen:	Background: Drosophila subobscura has long been a central model in evolutionary genetics. Presently, its use is hindered by the lack of a reference genome. To bridge this gap, here we used PacBio long-read technology, together with the available wealth of genetic marker information, to assemble and annotate a high-quality nuclear and complete mitochondrial genome for the species. With the obtained assembly, we performed the first synteny analysis of genome structure evolution in the subobscura subgroup. Results: We generated a highly-contiguous ~ 129 Mb-long nuclear genome, consisting of six pseudochromosomes corresponding to the six chromosomes of a female haploid set, and a complete 15,764 bp-long mitogenome, and provide an account of their numbers and distributions of codifying and repetitive content. All 12 identified paracentric inversion differences in the subobscura subgroup would have originated by chromosomal breakage and repair, with some associated duplications, but no evidence of direct gene disruptions by the breakpoints. Between lineages, inversion fixation rates were 10 times higher in continental D. subobscura than in the two small oceanic-island endemics D. guanche and D. madeirensis. Within D. subobscura, we found contrasting ratios of chromosomal divergence to polymorphism between the A sex chromosome and the autosomes. Conclusions: We present the first high-quality, long-read sequencing of a D. subobscura genome. Our findings generally support genome structure evolution in this species being driven indirectly, through the inversions' recombination-suppression effects in maintaining sets of adaptive alleles together in the face of gene flow. The resources developed will serve to further establish the subobscura subgroup as model for comparative genomics and evolutionary indicator of global change.
Ayudas:	Ministerio de Economía y Competitividad CGL2017-89160-P Agència de Gestió d'Ajuts Universitaris i de Recerca 2017/SGR-1379
Derechos:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Lengua:	Anglès
Documento:	Article ; recerca ; Versió publicada
Materia:	Genome structure evolution ; Inversion originating mechanisms ; Inversion fixation and polymorphism ; Spatiotemporally fluctuating selection ; Adaptation ; Global change
Publicado en:	BMC genomics, Vol. 20 (March 2019) , art. 223, ISSN 1471-2164

DOI: 10.1186/s12864-019-5590-8
PMID: 30885123

21 p, 1.7 MB

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