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Heterochromatin Is Not the Only Place for satDNAs: The High Diversity of satDNAs in the Euchromatin of the Beetle Chrysolina americana (Coleoptera, Chrysomelidae) - PubMed

  • ️Mon Jan 01 2024

Heterochromatin Is Not the Only Place for satDNAs: The High Diversity of satDNAs in the Euchromatin of the Beetle Chrysolina americana (Coleoptera, Chrysomelidae)

José M Rico-Porras et al. Genes (Basel). 2024.

Abstract

The satellitome of the beetle Chrysolina americana Linneo, 1758 has been characterized through chromosomal analysis, genomic sequencing, and bioinformatics tools. C-banding reveals the presence of constitutive heterochromatin blocks enriched in A+T content, primarily located in pericentromeric regions. Furthermore, a comprehensive satellitome analysis unveils the extensive diversity of satellite DNA families within the genome of C. americana. Using fluorescence in situ hybridization techniques and the innovative CHRISMAPP approach, we precisely map the localization of satDNA families on assembled chromosomes, providing insights into their organization and distribution patterns. Among the 165 identified satDNA families, only three of them exhibit a remarkable amplification and accumulation, forming large blocks predominantly in pericentromeric regions. In contrast, the remaining, less abundant satDNA families are dispersed throughout euchromatic regions, challenging the traditional association of satDNA with heterochromatin. Overall, our findings underscore the complexity of repetitive DNA elements in the genome of C. americana and emphasize the need for further exploration to elucidate their functional significance and evolutionary implications.

Keywords: CHRISMAPP; Chrysomelidae; chromosome in silico mapping; euchromatin; fluorescence in situ hybridization; genome evolution; heterochromatin; karyotype; repetitive DNA; satellite DNA; satellitome.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1

(A) Male mitotic metaphase and (B) karyotype of C. americana. The karyotype consists of 11 pairs of autosomes and the sex pair, a metacentric X chromosome and a dot-shaped Y chromosome. Pair one exhibits significant heteromorphism due to the size of the secondary constriction located on the long arm (*). (C) Meiotic metaphase with 11 autosomal bivalents and the sex chromosomes in an Xyp “parachute” shape. (D) Mitotic metaphase after the C-banding technique and subsequent DAPI staining (inverted image). Heterochromatin blocks are observed in the pericentromeric regions of all chromosomes except for the Y chromosome. Arrows indicate some chromosomes displaying two heterochromatin blocks.

Figure 2
Figure 2

FISH using the CameSat001-141 satDNA (labeled in red) as a probe on both mitotic (A) and meiotic (B) chromosomes of C. americana. Similarly, FISH was conducted using the CameSat002-187 satellite DNA (labeled in green) on mitotic (C) and meiotic (D) chromosomes. Double FISH using both the probes on mitotic (E) and meiotic (F) chromosomes. Arrows indicate the chromosomes or the bivalents that did not display a hybridization signal with CameSat001. Arrowheads indicate the Y chromosome, which did not exhibit a hybridization signal with either of the two probes.

Figure 3
Figure 3

Male mitotic metaphase (A) and karyotype (B) of C. americana following FISH with the CameSat003-10 family, showing the presence of positive hybridization signals on the pericentromeric regions of four pairs of autosomes, including the submetacentric pair 6.

Figure 4
Figure 4

C. americana pseudochromosomes showing the distribution of different satDNA families obtained through the CHRISMAPP approach. For each chromosome, two schemes are displayed, the top one illustrates the distribution of the five most abundant satDNA families, while the bottom one shows the distribution of the remaining satDNA families (from CameSat006-2670 to CamaSat165-105). Asterisks indicate the presence of short arrays of the CameSat001-141, CameSat002-187, and CameSat003-10.

Figure 5
Figure 5

DAPI staining (A) and FISH on male mitotic chromosomes of C. americana using a probe specific to the CameSat004-322 family with one amplification round (B), revealing positive hybridization signals on all chromosomes mainly accumulated at the terminal region or the chromosome arms. (C) Hybridization using CameSat004-322 as a probe with two amplification rounds. Arrowhead shows the Y chromosome.

Figure 6
Figure 6

DAPI staining (A) and FISH (B) on male mitotic chromosomes of C. americana, using a specific probe for the CameSat005-499 satDNA family. (C) Merged image revealing positive hybridization signals in the euchromatin of all chromosomes. Arrowhead shows the Y chromosome. (D) Selected chromosomes after DAPI staining, FISH with the CameSat005-499 satDNA, and merged images. Arrows indicate the DAPI-positive heterochromatic regions that are free of hybridization signals.

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