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Dense gene physical maps of the non-model species Drosophila subobscura

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Abstract

The comparative analysis of genetic and physical maps as well as of whole genome sequences had revealed that in the Drosophila genus, most structural rearrangements occurred within chromosomal elements as a result of paracentric inversions. Genome sequence comparison would seem the best method to estimate rates of chromosomal evolution, but the high-quality reference genomes required for this endeavor are still scanty. Here, we have obtained dense physical maps for Muller elements A, C, and E of Drosophila subobscura, a species with an extensively studied rich and adaptive chromosomal polymorphism. These maps are based on 462 markers: 115, 236, and 111 markers for elements A, C, and E, respectively. The availability of these dense maps will facilitate genome assembly and will thus greatly contribute to obtaining a good reference genome, which is a required step for D. subobscura to attain the model species status. The comparative analysis of these physical maps and those obtained from the D. pseudoobscura and D. melanogaster genomes allowed us to infer the number of fixed inversions and chromosomal evolutionary rates for each pairwise comparison. For all three elements, rates inferred from the more closely related species were higher than those inferred from the more distantly related species, which together with results of relative-rate tests point to an acceleration in the D. subobscura lineage at least for elements A and E.

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Abbreviations

BAC :

Bacteria artificial chromosome

BP :

Breakpoints

BSI :

Barcelona Subobscura Initiative

ch cu :

cherry curled

Ma :

Million years

Mb :

Megabases

P1 :

P1-derived artificial chromosome

YAC :

Yeast artificial chromosome

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Acknowledgments

We thank David Salguero for his excellent technical assistance. We also thank Servei de Genòmica, Serveis Cientifico-Tècnics, Universitat de Barcelona, for automated sequencing facilities. This paper was prepared with full knowledge and support of the Barcelona Subobscura Initiative (BSI). This work was supported by grants BFU2012-35168 and BFU2014-63732 from Ministerio de Economía y Competitividad, Spain, and 2014SGR-1055 from Comissió Interdepartamental de Recerca i Innovació Tecnològica, Generalitat de Catalunya, Spain to MA.

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  1. Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain

    Dorcas J. Orengo, Eva Puerma, Montserrat Papaceit, Carmen Segarra & Montserrat Aguadé

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  1. Dorcas J. Orengo
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  2. Eva Puerma
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  3. Montserrat Papaceit
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Correspondence to Montserrat Aguadé.

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Responsible Editor: Fengtang Yang

Dorcas J. Orengo and Eva Puerma contributed equally to this work

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Orengo, D.J., Puerma, E., Papaceit, M. et al. Dense gene physical maps of the non-model species Drosophila subobscura . Chromosome Res 25, 145–154 (2017). https://doi.org/10.1007/s10577-016-9549-1

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