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Lavanchy G, Brandt A, Bastardot M, Dumas Z, Labédan M, Massy M, Toubiana W, Tran Van P, Luchetti A, Scali V, Mantovani B, Schwander T. Evolution of alternative reproductive systems in Bacillus stick insects. Evolution 2024; 78:1109-1120. [PMID: 38501929 DOI: 10.1093/evolut/qpae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/22/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
Reproduction is a key feature of all organisms, yet the way in which it is achieved varies greatly across the tree of life. One striking example of this variation is the stick insect genus Bacillus, in which five different reproductive modes have been described: sex, facultative and obligate parthenogenesis, and two highly unusual reproductive modes: hybridogenesis and androgenesis. Under hybridogenesis, the entire genome from the paternal species is eliminated and replaced each generation by mating with the corresponding species. Under androgenesis, an egg is fertilized, but the developing diploid offspring bear two paternal genomes and no maternal genome, as a consequence of unknown mechanisms. Here, we reevaluate the previous descriptions of Bacillus lineages and the proposed F1 hybrid ancestries of the hybridogenetic and obligately parthenogenetic lineages (based on allozymes and karyotypes) from Sicily, where all these reproductive modes are found. We generate a chromosome-level genome assembly for a facultative parthenogenetic species (B. rossius) and combine extensive field sampling with RADseq and mtDNA data. We identify and genetically corroborate all previously described species and confirm the ancestry of hybrid lineages. All hybrid lineages have fully retained their F1 hybrid constitution throughout the genome, indicating that the elimination of the paternal genome in hybridogens is always complete and that obligate parthenogenesis in Bacillus hybrid species is not associated with an erosion of heterozygosity as known in other hybrid asexuals. Our results provide a stepping stone toward understanding the transitions between reproductive modes and the proximate mechanisms of genome elimination.
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Affiliation(s)
- Guillaume Lavanchy
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Alexander Brandt
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Marc Bastardot
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Marjorie Labédan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Morgane Massy
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - William Toubiana
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Andrea Luchetti
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, University of Bologna, Bologna, Italy
| | - Valerio Scali
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, University of Bologna, Bologna, Italy
| | - Barbara Mantovani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, University of Bologna, Bologna, Italy
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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Coffing GC, Tittes S, Small ST, Songco-Casey JO, Piscopo DM, Pungor JR, Miller AC, Niell CM, Kern AD. Cephalopod Sex Determination and its Ancient Evolutionary Origin Revealed by Chromosome-level Assembly of the California Two-Spot Octopus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.21.581452. [PMID: 38463997 PMCID: PMC10925132 DOI: 10.1101/2024.02.21.581452] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Sex chromosomes are critical elements of sexual reproduction in many animal and plant taxa, however they show incredible diversity and rapid turnover even within clades. Here, using a chromosome-level assembly generated with long read sequencing, we report the first evidence for genetic sex determination in cephalopods. We have uncovered a sex chromosome in California two-spot octopus (Octopus bimaculoides) in which males/females show ZZ/ZO karyotypes respectively. We show that the octopus Z chromosome is an evolutionary outlier with respect to divergence and repetitive element content as compared to other chromosomes and that it is present in all coleoid cephalopods that we have examined. Our results suggest that the cephalopod Z chromosome originated between 455 and 248 million years ago and has been conserved to the present, making it the among the oldest conserved animal sex chromosomes known.
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Affiliation(s)
- Gabrielle C. Coffing
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Silas Tittes
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Scott T. Small
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Jeremea O. Songco-Casey
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Denise M. Piscopo
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Judit R. Pungor
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Adam C. Miller
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Cristopher M. Niell
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Andrew D. Kern
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
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Mora P, Hospodářská M, Voleníková AC, Koutecký P, Štundlová J, Dalíková M, Walters JR, Nguyen P. Sex-biased gene content is associated with sex chromosome turnover in Danaini butterflies. Mol Ecol 2024:e17256. [PMID: 38180347 DOI: 10.1111/mec.17256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/01/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024]
Abstract
Sex chromosomes play an outsized role in adaptation and speciation, and thus deserve particular attention in evolutionary genomics. In particular, fusions between sex chromosomes and autosomes can produce neo-sex chromosomes, which offer important insights into the evolutionary dynamics of sex chromosomes. Here, we investigate the evolutionary origin of the previously reported Danaus neo-sex chromosome within the tribe Danaini. We assembled and annotated genomes of Tirumala septentrionis (subtribe Danaina), Ideopsis similis (Amaurina), Idea leuconoe (Euploeina) and Lycorea halia (Itunina) and identified their Z-linked scaffolds. We found that the Danaus neo-sex chromosome resulting from the fusion between a Z chromosome and an autosome corresponding to the Melitaea cinxia chromosome (McChr) 21 arose in a common ancestor of Danaina, Amaurina and Euploina. We also identified two additional fusions as the W chromosome further fused with the synteny block McChr31 in I. similis and independent fusion occurred between ancestral Z chromosome and McChr12 in L. halia. We further tested a possible role of sexually antagonistic selection in sex chromosome turnover by analysing the genomic distribution of sex-biased genes in I. leuconoe and L. halia. The autosomes corresponding to McChr21 and McChr31 involved in the fusions are significantly enriched in female- and male-biased genes, respectively, which could have hypothetically facilitated fixation of the neo-sex chromosomes. This suggests a role of sexual antagonism in sex chromosome turnover in Lepidoptera. The neo-Z chromosomes of both I. leuconoe and L. halia appear fully compensated in somatic tissues, but the extent of dosage compensation for the ancestral Z varies across tissues and species.
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Affiliation(s)
- Pablo Mora
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Monika Hospodářská
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | | | - Petr Koutecký
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Jana Štundlová
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Martina Dalíková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - James R Walters
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Petr Nguyen
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
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Lasne C, Elkrewi M, Toups MA, Layana L, Macon A, Vicoso B. The Scorpionfly (Panorpa cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome. Mol Biol Evol 2023; 40:msad245. [PMID: 37988296 PMCID: PMC10715201 DOI: 10.1093/molbev/msad245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/05/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
Many insects carry an ancient X chromosome-the Drosophila Muller element F-that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 My. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure to that of several dipteran species as well as more distantly related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the 2 homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.
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Affiliation(s)
- Clementine Lasne
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Marwan Elkrewi
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Melissa A Toups
- Department of Life and Environmental Sciences, Bournemouth University, Poole, UK
| | - Lorena Layana
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Ariana Macon
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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