Houseflies provide a good experimental model to study the initial evolutionary stages of a primary sex-determining locus because they possess different recently evolved proto-Y chromosomes that contain male-determining loci (M) with the same male-determining gene, Mdmd. We investigate M-loci genomically and cytogenetically revealing distinct molecular architectures among M-loci. M on chromosome V (MV) has two intact Mdmd copies in a palindrome. M on chromosome III (MIII) has tandem duplications containing 88 Mdmd copies (only one intact) and various repeats, including repeats that are XY-prevalent. M on chromosome II (MII) and the Y (MY) share MIII-like architecture, but with fewer repeats. MY additionally shares MV-specific sequence arrangements. Based on these data and karyograms using two probes, one derives from MIII and one Mdmd-specific, we infer evolutionary histories of polymorphic M-loci, which have arisen from unique translocations of Mdmd, embedded in larger DNA fragments, and diverged independently into regions of varying complexity.

Department of Biology and Biochemistry University of Houston Houston TX USA

Department of Biology Georgetown University Washington DC USA

Department of Cell and Molecular Biology National Bioinformatics Infrastructure Sweden Science for Life Laboratory Uppsala University Uppsala Sweden

Department of Developmental Biology Johann Friedrich Blumenbach Institute of Zoology and Anthropology Göttingen Center of Molecular Biosciences University of Göttingen Göttingen Germany

Department of Genetics Rutgers The State University of New Jersey Piscataway NJ USA

Department of Human Genetics Leiden University Medical Center Leiden The Netherlands

Department of Molecular Life Sciences University of Zürich Zürich Switzerland

Department of Organismal Biology Systematic Biology Evolutionary Biology Centre Uppsala University Uppsala Sweden

Groningen Institute for Evolutionary Life Sciences University of Groningen Groningen The Netherlands

Institute of Entomology Biology Centre of the Czech Academy of Sciences České Budějovice Czech Republic

SIB Swiss Institute of Bioinformatics University of Zurich Zürich Switzerland

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Wilkins AS. Moving up the hierarchy: a hypothesis on the evolution of a genetic sex determination pathway. Bioessays. 1995;17:71–77. doi: 10.1002/bies.950170113. PubMed DOI

Saccone G. A history of the genetic and molecular identification of genes and their functions controlling insect sex determination. Insect Biochem. Mol. Biol. 2022;151:103873. doi: 10.1016/j.ibmb.2022.103873. PubMed DOI

Steinemann M, Steinemann S. Enigma of Y chromosome degeneration: neo-Y and neo-X chromosomes of Drosophila miranda a model for sex chromosome evolution. Genetica. 1998;102:409. doi: 10.1023/A:1017058119760. PubMed DOI

Charlesworth B, Charlesworth D. The degeneration of Y chromosomes. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2000;355:1563–1572. doi: 10.1098/rstb.2000.0717. PubMed DOI PMC

Carvalho AB, Koerich LB, Clark AG. Origin and evolution of Y chromosomes: drosophila tales. Trends Genet. 2009;25:270–277. doi: 10.1016/j.tig.2009.04.002. PubMed DOI PMC

Bachtrog D. Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration. Nat. Rev. Genet. 2013;14:113–124. doi: 10.1038/nrg3366. PubMed DOI PMC

Nei M. Linkage modification and sex difference in recombination. Genetics. 1969;63:681. doi: 10.1093/genetics/63.3.681. PubMed DOI PMC

Dübendorfer A, Hediger M, Burghardt G, Bopp D. Musca domestica, a window on the evolution of sex-determining mechanisms in insects. Int. J. Dev. Biol. 2002;46:75–79. PubMed

Hamm RL, Meisel RP, Scott JG. The evolving puzzle of autosomal versus Y-linked male determination in Musca domestica. G3. 2015;5:371–384. doi: 10.1534/g3.114.014795. PubMed DOI PMC

Meisel RP, Scott JG, Clark AG. Transcriptome differences between alternative sex determining genotypes in the house fly, Musca domestica. Genome Biol. Evol. 2015;7:2051–2061. doi: 10.1093/gbe/evv128. PubMed DOI PMC

Son JH, et al. Minimal effects of proto-Y chromosomes on house fly gene expression in spite of evidence that selection maintains stable polygenic sex determination. Genetics. 2019;213:313–327. doi: 10.1534/genetics.119.302441. PubMed DOI PMC

Adhikari, K. et al. Temperature‐dependent effects of house fly proto‐Y chromosomes on gene expression could be responsible for fitness differences that maintain polygenic sex determination. Mol. Ecol. 30, 5704–5720 (2021). PubMed

Sharma A, et al. Male sex in houseflies is determined by Mdmd, a paralog of the generic splice factor gene CWC22. Science. 2017;356:642–645. doi: 10.1126/science.aam5498. PubMed DOI

Franco MG, Rubini PG, Vecchi M. Sex-determinants and their distribution in various populations of Musca domestica L. of Western Europe. Genet. Res. 1982;40:279–293. doi: 10.1017/S0016672300019157. PubMed DOI

Denholm I, Franco MG, Rubini PG, Vecchi M. Identification of a male determinant on the X chromosome of housefly (Musca domestica L.) populations in South-East England. Genet. Res. 1983;42:311–322. doi: 10.1017/S0016672300021790. DOI

Tomita T, Wada Y. Multifactorial sex determination in natural populations of the housefly (Musca domestica) in Japan. Jpn. J. Genet. 1989;64:373–382. doi: 10.1266/jjg.64.373. DOI

Hamm RL, Shono T, Scott JG. A cline in frequency of autosomal males is not associated with insecticide resistance in house fly (Diptera: Muscidae) J. Econ. Entomol. 2005;98:171–176. doi: 10.1093/jee/98.1.171. PubMed DOI

Kozielska M, Feldmeyer B, Pen I, Weissing FJ, Beukeboom LW. Are autosomal sex-determining factors of the housefly (Musca domestica) spreading north? Genet. Res. 2008;90:157–165. doi: 10.1017/S001667230700907X. PubMed DOI

Feldmeyer B, et al. Climatic variation and the geographical distribution of sex-determining mechanisms in the housefly. Evol. Ecol. Res. 2008;10:797–809.

Li, X., Lin, F., van de Zande, L. & Beukeboom, L. W. Strong variation in frequencies of male and female determiners between neighboring housefly populations. Insect Sci. 29, 1470–1482 (2022) PubMed PMC

Meisel RP, Gonzales CA, Luu H. The house fly Y Chromosome is young and minimally differentiated from its ancient X Chromosome partner. Genome Res. 2017;27:1417–1426. doi: 10.1101/gr.215509.116. PubMed DOI PMC

Scott JG, et al. Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment. Genome Biol. 2014;15:466. doi: 10.1186/s13059-014-0466-3. PubMed DOI PMC

Picard CJ, Johnston JS, Tarone AM. Genome sizes of forensically relevant Diptera. J. Med. Entomol. 2012;49:192–197. doi: 10.1603/ME11075. PubMed DOI

Rozen S, et al. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature. 2003;423:873–876. doi: 10.1038/nature01723. PubMed DOI

Hughes JF, et al. Chimpanzee and human y chromosomes are remarkably divergent in structure and gene content. Nature. 2010;463:536–539. doi: 10.1038/nature08700. PubMed DOI PMC

Hughes JF, et al. Strict evolutionary conservation followed rapid gene loss on human and rhesus y chromosomes. Nature. 2012;483:82–87. doi: 10.1038/nature10843. PubMed DOI PMC

Tomaszkiewicz M, et al. A time- and cost-effective strategy to sequence mammalian Y chromosomes: an application to the de novo assembly of gorilla Y. Genome Res. 2016;26:530–540. doi: 10.1101/gr.199448.115. PubMed DOI PMC

Trombetta B, Cruciani F. Y chromosome palindromes and gene conversion. Hum. Genet. 2017;136:605–619. doi: 10.1007/s00439-017-1777-8. PubMed DOI

Geraldes A, Rambo T, Wing RA, Ferrand N, Nachman MW. Extensive gene conversion drives the concerted evolution of paralogous copies of the SRY gene in European rabbits. Mol. Biol. Evol. 2010;27:2437–2440. doi: 10.1093/molbev/msq139. PubMed DOI PMC

Davis JK, Thomas PJ, Thomas JW. AW-linked palindrome and gene conversion in New World sparrows and blackbirds. Chromosome Res. 2010;18:543–553. doi: 10.1007/s10577-010-9134-y. PubMed DOI PMC

Fiston-Lavier A-S, Anxolabehere D, Quesneville H. A model of segmental duplication formation in Drosophila melanogaster. Genome Res. 2007;17:1458–1470. doi: 10.1101/gr.6208307. PubMed DOI PMC

Hediger M, et al. Molecular characterization of the key switch F provides a basis for understanding the rapid divergence of the sex-determining pathway in the housefly. Genetics. 2010;184:155–170. doi: 10.1534/genetics.109.109249. PubMed DOI PMC

Hediger M, Niessen M, Müller-Navia J, Nöthiger R, Dübendorfer A. Distribution of heterochromatin on the mitotic chromosomes of Musca domestica L. in relation to the activity of male-determining factors. Chromosoma. 1998;107:267–271. doi: 10.1007/s004120050307. PubMed DOI

Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXivpreprintarXiv:1303.3997 (2013).

Danecek P, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021;10:giab008. doi: 10.1093/gigascience/giab008. PubMed DOI PMC

Li H, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–2079. doi: 10.1093/bioinformatics/btp352. PubMed DOI PMC

Carabajal Paladino LZ, Nguyen P, Šíchová J, Marec F. Mapping of single-copy genes by TSA-FISH in the codling moth, Cydia pomonella. BMC Genet. 2014;15:S15. doi: 10.1186/1471-2156-15-S2-S15. PubMed DOI PMC

Aljanabi SM, Martinez I. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res. 1997;25:4692–4693. doi: 10.1093/nar/25.22.4692. PubMed DOI PMC

Li X, et al. Chromosomal mapping of tandem repeats in the yesso scallop, patinopecten yessoensis (jay, 1857), utilizing fluorescence in situ hybridization. Comp. Cytogenet. 2016;10:157–169. doi: 10.3897/CompCytogen.v10i1.7391. PubMed DOI PMC

Chakraborty, M., Baldwin-Brown, J. G., Long, A. D. & Emerson, J. J. Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage. Nucleic Acids Res. 44, e147 (2016). PubMed PMC

Koren S, et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017;27:722–736. doi: 10.1101/gr.215087.116. PubMed DOI PMC

Chin C-S, et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods. 2013;10:563. doi: 10.1038/nmeth.2474. PubMed DOI

Nurk S, et al. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Res. 2020;30:1291–1305. doi: 10.1101/gr.263566.120. PubMed DOI PMC

Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 2019;37:540–546. doi: 10.1038/s41587-019-0072-8. PubMed DOI

Walker, B. J. et al. Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE9, e112963 (2014). PubMed PMC

Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29:1072–1075. doi: 10.1093/bioinformatics/btt086. PubMed DOI PMC

Seppey, M., Manni, M. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness. in Gene prediction: methods and protocols (Springer, 2019). PubMed

Smit, A. F. A., Hubley, R. & Green, P. RepeatMasker Open-4.0. http://www.repeatmasker.org (2013–2015).

Hao Z, et al. RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms. PeerJ Comput. Sci. 2020;6:1–11. doi: 10.7717/peerj-cs.251. PubMed DOI PMC

Seibt KM, Schmidt T, Heitkam T. FlexiDot: highly customizable, ambiguity-aware dotplots for visual sequence analyses. Bioinformatics. 2018;34:3575–3577. doi: 10.1093/bioinformatics/bty395. PubMed DOI

Wickham H. ggplot2. Wiley Interdiscip. Rev. Comput. Stat. 2011;3:180–185. doi: 10.1002/wics.147. DOI

Li H. New strategies to improve minimap2 alignment accuracy. Bioinformatics. 2021;37:4572–4574. doi: 10.1093/bioinformatics/btab705. PubMed DOI PMC

Robinson JT, Thorvaldsdóttir H, Turner D, Mesirov JP. igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV) Bioinformatics. 2023;39:btac830. doi: 10.1093/bioinformatics/btac830. PubMed DOI PMC

Visser, S., Voleníková, A., Nguyen, P., Verhulst, E. C. & Marec, F. A conserved role of the duplicated Masculinizer gene in sex determination of the Mediterranean flour moth, Ephestia kuehniella. PLoS Genet. 17, e1009420 (2021). PubMed PMC