Multiple intrasyntenic rearrangements and rapid speciation in voles

Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom

Ancestral sequence reconstruction is a fundamental aspect of molecular evolution studies and can trace small-scale sequence modifications through the evolution of genomes and species. In contrast, fine-grained reconstructions of ancestral genome organizations are still in their infancy, limiting our ability to draw comprehensive views of genome and karyotype evolution. Here we reconstruct the detailed gene contents and organizations of 624 ancestral vertebrate, plant, fungi, metazoan and protist genomes, 183 of which are near-complete chromosomal gene order reconstructions. Reconstructed ancestral genomes are similar to their descendants in terms of gene content as expected and agree precisely with reference cytogenetic and in silico reconstructions when available. By comparing successive ancestral genomes along the phylogenetic tree, we estimate the intra- and interchromosomal rearrangement history of all major vertebrate clades at high resolution. This freely available resource introduces the possibility to follow evolutionary processes at genomic scales in chronological order, across multiple clades and without relying on a single extant species as reference.

Comparison of detection methods and genome quality when quantifying nuclear mitochondrial insertions in vertebrate genomes

The integration of mitochondrial genome fragments into the nuclear genome is well documented, and the transfer of these mitochondrial nuclear pseudogenes (numts) is thought to be an ongoing evolutionary process. With the increasing number of eukaryotic genomes available, genome-wide distributions of numts are often surveyed. However, inconsistencies in genome quality can reduce the accuracy of numt estimates, and methods used for identification can be complicated by the diverse sizes and ages of numts. Numts have been previously characterized in rodent genomes and it was postulated that they might be more prevalent in a group of voles with rapidly evolving karyotypes. Here, we examine 37 rodent genomes, and an additional 26 vertebrate genomes, while also considering numt detection methods. We identify numts using DNA:DNA and protein:translated-DNA similarity searches and compare numt distributions among rodent and vertebrate taxa to assess whether some groups are more susceptible to transfer. A combination of protein sequence comparisons (protein:translated-DNA) and BLASTN genomic DNA searches detect 50% more numts than genomic DNA:DNA searches alone. In addition, higher-quality RefSeq genomes produce lower estimates of numts than GenBank genomes, suggesting that lower quality genome assemblies can overestimate numts abundance. Phylogenetic analysis shows that mitochondrial transfers are not associated with karyotypic diversity among rodents. Surprisingly, we did not find a strong correlation between numt counts and genome size. Estimates using DNA: DNA analyses can underestimate the amount of mitochondrial DNA that is transferred to the nucleus.

Intraspecies multiple chromosomal variations including rare tandem fusion in the Russian Far Eastern endemic evoron vole Alexandromysevoronensis (Rodentia, Arvicolinae)

The vole Alexandromysevoronensis (Kovalskaya et Sokolov, 1980) with its two chromosomal races, "Evoron" (2n = 38-41, NF = 54-59) and "Argi" (2n = 34, 36, 37, NF = 51-56) is the endemic vole found in the Russian Far East. For the "Argi" chromosomal race, individuals from two isolated populations in mountain regions were investigated here for the first time using GTG-, GTC-, NOR methods. In the area under study, 8 new karyotype variants have been registered. The karyotype with 2n = 34 has a rare tandem fusion of three autosomes: two biarmed (Mev6 and Mev7) and one acrocentric (Mev14) to form a large biarmed chromosome (Mev6/7/14), all of which reveal a heterozygous state. For A.evoronensis, the variation in the number of chromosomes exceeded the known estimate of 2n = 34, 36 and amounted to 2n = 34, 36, 38-41. The combination of all the variations of chromosomes for the species made it possible to describe 20 variants of the A.evoronensis karyotype, with 11 chromosomes being involved in multiple structural rearrangements. In the "Evoron" chromosomal race 4 chromosomes (Mev1, Mev4, Mev17, and Mev18) and in the "Argi" chromosomal race 9 chromosomes (Mev6, Mev7, Mev14, Mev13, Mev11, Mev15, Mev17, Mev18, and Mev19) were observed. Tandem and Robertsonian rearrangements (Mev17/18 and Mev17.18) were revealed in both chromosomal races "Evoron" and "Argi".

Molecular Composition of Heterochromatin and Its Contribution to Chromosome Variation in the Microtus thomasi/Microtus atticus Species Complex

The voles of the Microtus thomasi/M. atticus species complex demonstrate a remarkable variability in diploid chromosomal number (2n = 38–44 chromosomes) and sex chromosome morphology. In the current study, we examined by in situ hybridization the topology of four satellite DNA motifs (Msat-160, Mth-Alu900, Mth-Alu2.2, TTAGGG telomeric sequences) and two transposons (LINE, SINE) on the karyotypes of nine chromosome races (i.e., populations with unique cytogenetic traits) of Microtus thomasi, and two chromosomal races of M. atticus. According to the topology of the repetitive DNA motifs, we were able to identify six types of biarmed chromosomes formed from either Robertsonian or/and tandem fusions. In addition, we identified 14 X chromosome variants and 12 Y chromosome variants, and we were able to reconstruct their evolutionary relations, caused mainly by distinct mechanisms of amplification of repetitive DNA elements, including the telomeric sequences. Our study used the model of the Microtus thomasi/M. atticus species complex to explore how repetitive centromeric content can alter from chromosomal rearrangements and can shape the morphology of sex chromosomes, resulting in extensive inter-species cytogenetic variability.

Evolutionary rearrangements of X chromosomes in voles (Arvicolinae, Rodentia)

Euchromatic segments of the X chromosomes of placental mammals are the most conservative elements of the karyotype, only rarely subjected to either inter- or intrachromosomal rearrangements. Here, using microdissection-derived set of region-specific probes of Terricola savii we detailed the evolutionary rearrangements found in X chromosomes in 20 vole species (Arvicolinae, Rodentia). We show that the evolution of X chromosomes in this taxon was accompanied by multiple para- and pericentric inversions and centromere shifts. The contribution of intrachromosomal rearrangements to the karyotype evolution of Arvicolinae species was approximately equivalent in both the separate autosomal conserved segments and the X chromosomes. Intrachromosmal rearrangements and structural reorganization of the X chromosomes was likely accompanied by an accumulation, distribution, and evolution of repeated sequences.

The molecular genealogy of sequential overlapping inversions implies both homologous chromosomes of a heterokaryotype in an inversion origin

Cytological and molecular studies have revealed that inversion chromosomal polymorphism is widespread across taxa and that inversions are among the most common structural changes fixed between species. Two major mechanisms have been proposed for the origin of inversions considering that breaks occur at either repetitive or non-homologous sequences. While inversions originating through the first mechanism might have a multiple origin, those originating through the latter mechanism would have a unique origin. Variation at regions flanking inversion breakpoints can be informative on the origin and history of inversions given the reduced recombination in heterokaryotypes. Here, we have analyzed nucleotide variation at a fragment flanking the most centromere-proximal shared breakpoint of several sequential overlapping inversions of the E chromosome of Drosophila subobscura —inversions E₁, E₂, E₉ and E₃. The molecular genealogy inferred from variation at this shared fragment does not exhibit the branching pattern expected according to the sequential origin of inversions. The detected discordance between the molecular and cytological genealogies has led us to consider a novel possibility for the origin of an inversion, and more specifically that one of these inversions originated on a heterokaryotype for chromosomal arrangements. Based on this premise, we propose three new models for inversions origin.