Abstract
The W chromosome of most lepidopteran species represents the largest heterochromatin entity in the female genome. Although satellite DNA is a typical component of constitutive heterochromatin, there are only a few known satellite DNAs (satDNAs) located on the W chromosome in moths and butterflies. In this study, we isolated and characterized new satDNA (PiSAT1) from microdissected W chromosomes of the Indian meal moth, Plodia interpunctella. Even though the PiSAT1 is mainly localized near the female-specific segment of the W chromosome, short arrays of this satDNA also occur on autosomes and/or the Z chromosome. Probably due to the predominant location in the non-recombining part of the genome, PiSAT1 exhibits a relatively large nucleotide variability in its monomers. However, at least a part of all predicted functional motifs is located in conserved regions. Moreover, we detected polyadenylated transcripts of PiSAT1 in all developmental stages and in both sexes (female and male larvae, pupae and adults). Our results suggest a potential structural and functional role of PiSAT1 in the P. interpunctella genome, which is consistent with accumulating evidence for the important role of satDNAs in eukaryotic genomes.
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Abbreviations
- BAC:
-
Bacterial artificial chromosome
- cDNA:
-
Complementary DNA
- CGH:
-
Comparative genomic hybridization
- DABCO:
-
1,4-Diazabicyclo(2.2.2)-octane
- DAPI:
-
4′,6-Diamidino-2-phenylindole
- FISH:
-
Fluorescence in situ hybridization
- gDNA:
-
Genomic DNA
- LTR:
-
Long terminal repeats
- mtDNA:
-
Mitochondrial DNA
- ncRNA:
-
Non-coding RNA
- ORF:
-
Open reading frame
- PCR:
-
Polymerase chain reaction
- RNAi:
-
RNA interference
- satDNA:
-
Satellite DNA
- SDS:
-
Sodium dodecyl sulphate
- SSC:
-
Saline-sodium citrate buffer
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Acknowledgements
We thank Marie Korchová for the care of P. interpunctella cultures. Our thanks belong to Martina Žurovcová, Hanka Zikmundová, Sander Visser and M.Z. for providing P. interpunctella specimens to establish laboratory rearing. We are also thankful to Professor Steve Paterson for providing important information about the P. interpunctella genome assembly. This research was funded by grant 14-22765S of the Czech Science Foundation (GACR). Current support from GACR grants 17-17211S (M.D.) and 17-13713S (M.Z. and F.M.) is also gratefully acknowledged. S.K. acknowledges support from the Ministry of Education, Youth and Sports of the Czech Republic (CEITEC 2020 project LQ1601).
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Online resource 1
Highly polyploid nuclei from female Malpighian tubules of Plodia interpunctella with heterochromatic body formed by multiple copies of W chromosome (indicated by arrows). Scale bars = 20 μm. (a) Part of polyploid nucleus from spreading preparation stained by Giemsa. (a) Part of Malpighian tubule from squash preparation stained by lactic acetic orcein. (PDF 351 kb)
Online resource 2
Alignment of PiSAT1 monomers against the consensus sequence. Sequences are listed in alphabetical order. PiSAT1a-d (GenBank accession number KY450690) are monomers from the original W chromosome-derived clone, PiSAT1 monomer 1-17 (GenBank accession numbers KY450691-KY450707) are additionally PCR isolated sequences, monomers obtained from Plodia interpunctella genome are named according to the respective scaffold. Red bars indicate places of alignment with indels longer than 2 bp. Grey bars refer to conserved regions of monomers based on sliding window analysis. *PiSAT1 monomers with deletions longer than 2 bp. +PiSAT1 monomers with insertions longer than 2 bp. (PDF 1090 kb)
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Dalíková, M., Zrzavá, M., Kubíčková, S. et al. W-enriched satellite sequence in the Indian meal moth, Plodia interpunctella (Lepidoptera, Pyralidae). Chromosome Res 25, 241–252 (2017). https://doi.org/10.1007/s10577-017-9558-8
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DOI: https://doi.org/10.1007/s10577-017-9558-8