The molecular characterization of fixed inversions breakpoints unveils the ancestral character of the Drosophila guanche chromosomal arrangements

Dorcas J Orengo,Eva Puerma,Montserrat Aguadé

doi:10.1038/s41598-018-37121-5

Abstract

Cytological studies revealed that the number of chromosomes and their organization varies across species. The increasing availability of whole genome sequences of multiple species across specific phylogenies has confirmed and greatly extended these cytological observations. In the Drosophila genus, the ancestral karyotype consists of five rod-like acrocentric chromosomes (Muller elements A to E) and one dot-like chromosome (element F), each exhibiting a generally conserved gene content. Chromosomal fusions and paracentric inversions are thus the major contributors, respectively, to chromosome number variation among species and to gene order variation within chromosomal element. The subobscura cluster of Drosophila consists in three species that retain the genus ancestral karyotype and differ by a reduced number of fixed inversions. Here, we have used cytological information and the D. guanche genome sequence to identify and molecularly characterize the breakpoints of inversions that became fixed since the D. guanche-D. subobscura split. Our results have led us to propose a modified version of the D. guanche cytological map of its X chromosome, and to establish that (i) most inversions became fixed in the D. subobscura lineage and (ii) the order in which the four X chromosome overlapping inversions occurred and became fixed.

Highlights

The last decade witnessed an accelerated development of whole genome sequencing technologies and the concomitant development of the bioinformatics and analytical tools required for genome assembly and annotation as well as for whole genomes evolutionary comparisons both within species and across phylogenies
Comparison of the banding pattern of the three species of the subobscura cluster and those of six other species of the obscura group did not allow the establishment of how the different members of the subobscura cluster are related to the other six species, except for the J and E chromosomes, for which the subobscura cluster ancestor would have the arrangement presently found in D. guanche[27]
Concerning the three species of the subobscura cluster, polytene chromosomes in hybrids between D. madeirensis and either D. subobscura or D. guanche[12,13,22] revealed that at the cytological level (i) D. madeirensis only differed from the standard arrangement of the D. subobscura chromosomes by two A chromosome inversions and three autosomal inversions[12,22], (ii) for the A chromosome, the differences exhibited by D. madeirensis relative to D. subobscura are shared by D. guanche[13], and (iii) the most centromere-proximal A chromosome inversion present in D. madeirensis differed from the D. subobscura polymorphic A1 inversion[12]

Summary

Introduction

The last decade witnessed an accelerated development of whole genome sequencing technologies and the concomitant development of the bioinformatics and analytical tools required for genome assembly and annotation as well as for whole genomes evolutionary comparisons both within species and across phylogenies. Of inversion breakpoints through genome comparison at short time scales [i.e., either between closely related species such as Drosophila melanogaster, D. simulans and D. yakuba[8], or within species9] allowed the detailed characterization of inversion breakpoints, which revealed that inversions could originate by the staggered breaks mechanism in addition to the cut-and-paste and ectopic recombination mechanisms Both the cytological and genome-based approaches to identify inversions and to finely localize their breakpoints through banding pattern and genome comparison, respectively, have limitations. The time elapsed since the divergence of the species under study would constitute a second limitation to identify fixed inversions as chromosomal changes accumulate through time This accumulation implies that the banding pattern comparison might render the cytological identification of homologous fragments uncertain or even impossible when distantly related species are compared. The breakpoints of several of the D. subobscura polymorphic inversions have been molecularly identified and characterized through chromosome walking, which has revealed that the staggered breaks mechanism that generates duplications in the derived arrangement is the prevalent mechanism originating inversions in this species[15,16,17,18,19,20], like it is in D. melanogaster[9,21]

Methods

Results

Conclusion