Abstract
Chromosomal inversions are structural changes that alter gene order but generally not gene content in the affected region. In Drosophila, extensive cytological studies revealed the widespread character of inversion polymorphism, with evidence for its adaptive character. In Drosophila subobscura, polymorphism affects both its four large autosomal elements and its X (A) chromosome. The characterization of eight of these autosomal inversions breakpoints revealed that most of them originated through the staggered-breaks mechanism. Here, we have performed chromosomal walks to identify the breakpoints of two X-chromosome widely distributed inversions —A2 and A1— of D. subobscura. Inversion A2 is considered a warm-adapted arrangement that exhibits parallel latitudinal clines in the species ancestral distribution area and in both American subcontinents, whereas inversion A1 is only present in the Palearctic region where it presents an east-west cline. The duplication detected at the A2 inversion breakpoints is consistent with its origin by the staggered-breaks mechanism. Inversion A1 breakpoints could not be molecularly identified even though they could be narrowly delimited. This result points to chromosome walking limitations when using as a guide the genome of other species. Limitations stem from the rate of evolution by paracentric inversions, which in Drosophila is highest for the X chromosome.
Highlights
Chromosomal inversions and gene duplications are two types of structural variation that have greatly contributed to genome evolution and organismal adaptation
Four markers that had been previously mapped close to the inversion breakpoints were used to start chromosomal walks towards the breakpoints using the D. pseudoobscura and D. melanogaster genomes as a guide: markers P90 and P236 for the proximal breakpoint, and markers Marf and Usp[7] for the distal breakpoint[30,32]
Four markers previously mapped near the inversion breakpoints were used for chromosome walking using the D. pseudoobscura and D. melanogaster genomes as a guide: markers cm and Cyp4g1 for the proximal breakpoint, and markers dod and RpS6 for the distal breakpoint[30]
Summary
Chromosomal inversions and gene duplications are two types of structural variation that have greatly contributed to genome evolution and organismal adaptation. Breakpoints were identified by chromosome walking, a procedure that requires the availability of the genome sequence of either the species under study or that of a closely related species to design probes that are physically mapped by in situ hybridization on polytene chromosomes[11,16,17,18,19,20] These experimental procedures have allowed the identification and characterization of the breakpoints of three autosomal inversions of D. melanogaster[14,15,16] that were later identified by computational methods[12]. The breakpoints characterization revealed that most of the studied inversions (seven of eight) had originated through the staggered-breaks mechanism, with the duplicated fragment ranging in this case from 60 bp to ~7.8 kb
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