Large-scale comparative analysis of cytogenetic markers across Lepidoptera

Abstract

Fluorescence in situ hybridization (FISH) allows identification of particular chromosomes and their rearrangements. Using FISH with signal enhancement via antibody amplification and enzymatically catalysed reporter deposition, we evaluated applicability of universal cytogenetic markers, namely 18S and 5S rDNA genes, U1 and U2 snRNA genes, and histone H3 genes, in the study of the karyotype evolution in moths and butterflies. Major rDNA underwent rather erratic evolution, which does not always reflect chromosomal changes. In contrast, the hybridization pattern of histone H3 genes was well conserved, reflecting the stable organisation of lepidopteran genomes. Unlike 5S rDNA and U1 and U2 snRNA genes which we failed to detect, except for 5S rDNA in a few representatives of early diverging lepidopteran lineages. To explain the negative FISH results, we used quantitative PCR and Southern hybridization to estimate the copy number and organization of the studied genes in selected species. The results suggested that their detection was hampered by long spacers between the genes and/or their scattered distribution. Our results question homology of 5S rDNA and U1 and U2 snRNA loci in comparative studies. We recommend the use of histone H3 in studies of karyotype evolution.

The role of repetitive DNA in re-patterning of major rDNA clusters in Lepidoptera

“…Therefore, we physically mapped partial sequences of 18S and 28S rDNA to test whether rDNA spreads as a whole unit in the studied species. In H. humuli and C. ohridella, both 18S and 28S rDNA signals co-localized and covered significant portion of one chromosome pair (Figure 1a, b) as reported earlier (Provazníková et al, 2021). Seven and eleven rDNA loci were highlighted by both probes in A. urticae and I. io, respectively (Figure 1c, d), which is in agreement with known distribution of their major rDNA (Nguyen et al, 2010;Provazníková et al, 2021).…”

“…We cannot distinguish with certainty whether the rDNA spread occurred via ectopic recombination or integration of ecc-rDNA. Yet we argue that preferential spread of rDNA into terminal regions of lepidopteran chromosomes (Nguyen et al, 2010;Provazníková et al, 2021) favours ectopic recombination as its efficiency depends on proximity of homologous sequences to telomeres (Goldman and Lichten, 1996;Nguyen et al, 2010), whereas ecc-rDNA could be integrated anywhere in the genome as long as a homologous sequence is present.…”

“…However, these were not autonomous and their sequence diverged from those found in the rest of the genome. Thus, it seems unlikely that MEs could mediate spread of rDNA observed in some Lepidoptera (Provazníková et al, 2021) via transposition.…”

“…Thus, spread of rDNA clusters is not clearly associated with large scale chromosome rearrangements such as chromosome fissions or fusions. Unusual distribution of rDNA was observed in the ghost moth, Hepialus humuli (Hepialidae), and the horse chestnut leaf miner, Cameraria ohridella (Gracillariidae), in which signal of the 18S rDNA probe covered about one half and one fourth of a single NOR-bearing chromosome, respectively (Provazníková et al, 2021). It was proposed that the dynamic rDNA repatterning is due to ectopic recombination, i.e.…”

Insights into the Karyotype Evolution of Charinidae, the Early-Diverging Clade of Whip Spiders (Arachnida: Amblypygi)

“…The major rDNA cluster (45S rDNA) is by far the most utilized molecular chromosomal marker across diverse eukaryotic organisms, and especially in non-model groups [72][73][74]. The major rDNA cluster visualized either by 18S or 28S rDNA probes has already been localized in some spiders [36,46,73,[75][76][77], scorpions [45,76,[78][79][80][81][82], pseudoscorpions [83], harvestmen [84][85][86][87], ticks [73,88,89], and an amblypygid [18].…”