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Aharonoff A, Kim J, Washington A, Ercan S. SMC-mediated dosage compensation in C. elegans evolved in the presence of an ancestral nematode mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595224. [PMID: 38826443 PMCID: PMC11142195 DOI: 10.1101/2024.05.21.595224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Mechanisms of X chromosome dosage compensation have been studied extensively in a few model species representing clades of shared sex chromosome ancestry. However, the diversity within each clade as a function of sex chromosome evolution is largely unknown. Here, we anchor ourselves to the nematode Caenorhabditis elegans, for which a well-studied mechanism of dosage compensation occurs through a specialized structural maintenance of chromosomes (SMC) complex, and explore the diversity of dosage compensation in the surrounding phylogeny of nematodes. Through phylogenetic analysis of the C. elegans dosage compensation complex and a survey of its epigenetic signatures, including X-specific topologically associating domains (TADs) and X-enrichment of H4K20me1, we found that the condensin-mediated mechanism evolved recently in the lineage leading to Caenorhabditis through an SMC-4 duplication. Intriguingly, an independent duplication of SMC-4 and the presence of X-specific TADs in Pristionchus pacificus suggest that condensin-mediated dosage compensation arose more than once. mRNA-seq analyses of gene expression in several nematode species indicate that dosage compensation itself is ancestral, as expected from the ancient XO sex determination system. Indicative of the ancestral mechanism, H4K20me1 is enriched on the X chromosomes in Oscheius tipulae, which does not contain X-specific TADs or SMC-4 paralogs. Together, our results indicate that the dosage compensation system in C. elegans is surprisingly new, and condensin may have been co-opted repeatedly in nematodes, suggesting that the process of evolving a chromosome-wide gene regulatory mechanism for dosage compensation is constrained. Significance statement X chromosome dosage compensation mechanisms evolved in response to Y chromosome degeneration during sex chromosome evolution. However, establishment of dosage compensation is not an endpoint. As sex chromosomes change, dosage compensation strategies may have also changed. In this study, we performed phylogenetic and epigenomic analyses surrounding Caenorhabditis elegans and found that the condensin-mediated dosage compensation mechanism in C. elegans is surprisingly new, and has evolved in the presence of an ancestral mechanism. Intriguingly, condensin-based dosage compensation may have evolved more than once in the nematode lineage, the other time in Pristionchus. Together, our work highlights a previously unappreciated diversity of dosage compensation mechanisms within a clade, and suggests constraints in evolving new mechanisms in the presence of an existing one.
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Affiliation(s)
- Avrami Aharonoff
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003
| | - Jun Kim
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003
| | - Aaliyah Washington
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003
| | - Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003
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van’t Hof AE, Whiteford S, Yung CJ, Yoshido A, Zrzavá M, de Jong MA, Tan KL, Zhu D, Monteiro A, Brakefield PM, Marec F, Saccheri IJ. Zygosity-based sex determination in a butterfly drives hypervariability of Masculinizer. SCIENCE ADVANCES 2024; 10:eadj6979. [PMID: 38701204 PMCID: PMC11067997 DOI: 10.1126/sciadv.adj6979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024]
Abstract
Nature has devised many ways of producing males and females. Here, we report on a previously undescribed mechanism for Lepidoptera that functions without a female-specific gene. The number of alleles or allele heterozygosity in a single Z-linked gene (BaMasc) is the primary sex-determining switch in Bicyclus anynana butterflies. Embryos carrying a single BaMasc allele develop into WZ (or Z0) females, those carrying two distinct alleles develop into ZZ males, while (ZZ) homozygotes initiate female development, have mismatched dosage compensation, and die as embryos. Consequently, selection against homozygotes has favored the evolution of spectacular allelic diversity: 205 different coding sequences of BaMasc were detected in a sample of 246 females. The structural similarity of a hypervariable region (HVR) in BaMasc to the HVR in Apis mellifera csd suggests molecular convergence between deeply diverged insect lineages. Our discovery of this primary switch highlights the fascinating diversity of sex-determining mechanisms and underlying evolutionary drivers.
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Affiliation(s)
- Arjen E. van’t Hof
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 České Budějovice, Czech Republic
| | - Sam Whiteford
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Carl J. Yung
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Atsuo Yoshido
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 České Budějovice, Czech Republic
| | - Magda Zrzavá
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Maaike A. de Jong
- Netherlands eScience Center, Science Park 402, 1098 XH Amsterdam, Netherlands
| | - Kian-Long Tan
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Dantong Zhu
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | | | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 České Budějovice, Czech Republic
| | - Ilik J. Saccheri
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
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3
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Webster TH, Vannan A, Pinto BJ, Denbrock G, Morales M, Dolby GA, Fiddes IT, DeNardo DF, Wilson MA. Lack of Dosage Balance and Incomplete Dosage Compensation in the ZZ/ZW Gila Monster (Heloderma suspectum) Revealed by De Novo Genome Assembly. Genome Biol Evol 2024; 16:evae018. [PMID: 38319079 PMCID: PMC10950046 DOI: 10.1093/gbe/evae018] [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: 06/15/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/07/2024] Open
Abstract
Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes. Here, we report the assembly and analysis of the Gila monster genome. We generated a de novo draft genome assembly for a male using 10X Genomics technology. We further generated and analyzed short-read whole genome sequencing and whole transcriptome sequencing data for three males and three females. By comparing female and male genomic data, we identified four putative Z chromosome scaffolds. These putative Z chromosome scaffolds are homologous to Z-linked scaffolds identified in the Komodo dragon. Further, by analyzing RNAseq data, we observed evidence of incomplete dosage compensation between the Gila monster Z chromosome and autosomes and a lack of balance in Z-linked expression between the sexes. In particular, we observe lower expression of the Z in females (ZW) than males (ZZ) on a global basis, though we find evidence suggesting local gene-by-gene compensation. This pattern has been observed in most other ZZ/ZW systems studied to date and may represent a general pattern for female heterogamety in vertebrates.
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Affiliation(s)
- Timothy H Webster
- Department of Anthropology, University of Utah, Salt Lake City, UT, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Annika Vannan
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
| | - Grant Denbrock
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Matheo Morales
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Greer A Dolby
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Dale F DeNardo
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ, USA
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4
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Kimura A, Go AC, Markow T, Ranz JM. Evidence of Nonrandom Patterns of Functional Chromosome Organization in Danaus plexippus. Genome Biol Evol 2024; 16:evae054. [PMID: 38488057 PMCID: PMC10972686 DOI: 10.1093/gbe/evae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 05/01/2024] Open
Abstract
Our understanding on the interplay between gene functionality and gene arrangement at different chromosome scales relies on a few Diptera and the honeybee, species with quality reference genome assemblies, accurate gene annotations, and abundant transcriptome data. Using recently generated 'omic resources in the monarch butterfly Danaus plexippus, a species with many more and smaller chromosomes relative to Drosophila species and the honeybee, we examined the organization of genes preferentially expressed at broadly defined developmental stages (larva, pupa, adult males, and adult females) at both fine and whole-chromosome scales. We found that developmental stage-regulated genes do not form more clusters, but do form larger clusters, than expected by chance, a pattern consistent across the gene categories examined. Notably, out of the 30 chromosomes in the monarch genome, 12 of them, plus the fraction of the chromosome Z that corresponds to the ancestral Z in other Lepidoptera, were found enriched for developmental stage-regulated genes. These two levels of nonrandom gene organization are not independent as enriched chromosomes for developmental stage-regulated genes tend to harbor disproportionately large clusters of these genes. Further, although paralogous genes were overrepresented in gene clusters, their presence is not enough to explain two-thirds of the documented cases of whole-chromosome enrichment. The composition of the largest clusters often included paralogs from more than one multigene family as well as unrelated single-copy genes. Our results reveal intriguing patterns at the whole-chromosome scale in D. plexippus while shedding light on the interplay between gene expression and chromosome organization beyond Diptera and Hymenoptera.
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Affiliation(s)
- Ashlyn Kimura
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92647, USA
| | - Alwyn C Go
- Department of Biology, University of Winnipeg, Winnipeg, MB R3B 2E9, Canada
| | - Therese Markow
- Unidad de Genómica Avanzada (Langebio), CINVESTAV, Irapuato, GTO 36824, México
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - José M Ranz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92647, 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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6
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Chen X, Wang Z, Zhang C, Hu J, Lu Y, Zhou H, Mei Y, Cong Y, Guo F, Wang Y, He K, Liu Y, Li F. Unraveling the complex evolutionary history of lepidopteran chromosomes through ancestral chromosome reconstruction and novel chromosome nomenclature. BMC Biol 2023; 21:265. [PMID: 37981687 PMCID: PMC10658929 DOI: 10.1186/s12915-023-01762-4] [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: 04/12/2023] [Accepted: 11/06/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Lepidoptera is one of the most species-rich animal groups, with substantial karyotype variations among species due to chromosomal rearrangements. Knowledge of the evolutionary patterns of lepidopteran chromosomes still needs to be improved. RESULTS Here, we used chromosome-level genome assemblies of 185 lepidopteran insects to reconstruct an ancestral reference genome and proposed a new chromosome nomenclature. Thus, we renamed over 5000 extant chromosomes with this system, revealing the historical events of chromosomal rearrangements and their features. Additionally, our findings indicate that, compared with autosomes, the Z chromosome in Lepidoptera underwent a fast loss of conserved genes, rapid acquisition of lineage-specific genes, and a low rate of gene duplication. Moreover, we presented evidence that all available 67 W chromosomes originated from a common ancestor chromosome, with four neo-W chromosomes identified, including one generated by fusion with an autosome and three derived through horizontal gene transfer. We also detected nearly 4000 inter-chromosomal gene movement events. Notably, Geminin is transferred from the autosome to the Z chromosome. When located on the autosome, Geminin shows female-biased expression, but on the Z chromosome, it exhibits male-biased expression. This contributes to the sexual dimorphism of body size in silkworms. CONCLUSIONS Our study sheds light on the complex evolutionary history of lepidopteran chromosomes based on ancestral chromosome reconstruction and novel chromosome nomenclature.
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Affiliation(s)
- Xi Chen
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zuoqi Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Chaowei Zhang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Jingheng Hu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yueqi Lu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Hang Zhou
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yuyang Cong
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fangyuan Guo
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Kang He
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Ying Liu
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.
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Mulhair PO, Crowley L, Boyes DH, Lewis OT, Holland PWH. Opsin Gene Duplication in Lepidoptera: Retrotransposition, Sex Linkage, and Gene Expression. Mol Biol Evol 2023; 40:msad241. [PMID: 37935057 PMCID: PMC10642689 DOI: 10.1093/molbev/msad241] [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: 08/16/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Color vision in insects is determined by signaling cascades, central to which are opsin proteins, resulting in sensitivity to light at different wavelengths. In certain insect groups, lineage-specific evolution of opsin genes, in terms of copy number, shifts in expression patterns, and functional amino acid substitutions, has resulted in changes in color vision with subsequent behavioral and niche adaptations. Lepidoptera are a fascinating model to address whether evolutionary change in opsin content and sequence evolution are associated with changes in vision phenotype. Until recently, the lack of high-quality genome data representing broad sampling across the lepidopteran phylogeny has greatly limited our ability to accurately address this question. Here, we annotate opsin genes in 219 lepidopteran genomes representing 33 families, reconstruct their evolutionary history, and analyze shifts in selective pressures and expression between genes and species. We discover 44 duplication events in opsin genes across ∼300 million years of lepidopteran evolution. While many duplication events are species or family specific, we find retention of an ancient long-wavelength-sensitive (LW) opsin duplication derived by retrotransposition within the speciose superfamily Noctuoidea (in the families Nolidae, Erebidae, and Noctuidae). This conserved LW retrogene shows life stage-specific expression suggesting visual sensitivities or other sensory functions specific to the early larval stage. This study provides a comprehensive order-wide view of opsin evolution across Lepidoptera, showcasing high rates of opsin duplications and changes in expression patterns.
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Affiliation(s)
- Peter O Mulhair
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Liam Crowley
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | | | - Owen T Lewis
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
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8
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Freedman MG, Kronforst MR. Migration genetics take flight: genetic and genomic insights into monarch butterfly migration. CURRENT OPINION IN INSECT SCIENCE 2023; 59:101079. [PMID: 37385346 PMCID: PMC10592233 DOI: 10.1016/j.cois.2023.101079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/01/2023]
Abstract
Monarch butterflies have emerged as a model system in migration genetics. Despite inherent challenges associated with studying the integrative phenotypes that characterize migration, recent research has highlighted genes and transcriptional networks underlying aspects of the monarch's migratory syndrome. Circadian clock genes and the vitamin A synthesis pathway regulate reproductive diapause initiation, while diapause termination appears to involve calcium and insulin signaling. Comparative approaches have highlighted genes that distinguish migratory and nonmigratory monarch populations, as well as genes associated with natural variation in propensity to initiate diapause. Population genetic techniques demonstrate that seasonal migration can collapse patterns of spatial structure at continental scales, whereas loss of migration can drive differentiation between even nearby populations. Finally, population genetics can be applied to reconstruct the monarch's evolutionary history and search for contemporary demographic changes, which can provide relevant context for understanding recently observed declines in overwintering North American monarch numbers.
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9
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Charlesworth D, Hastings A, Graham C. Can a Y Chromosome Degenerate in an Evolutionary Instant? A Commentary on Fong et al. 2023. Genome Biol Evol 2023; 15:evad105. [PMID: 37290043 PMCID: PMC10480580 DOI: 10.1093/gbe/evad105] [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: 04/04/2023] [Revised: 05/29/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023] Open
Abstract
It is well known that the Y chromosomes of Drosophila and mammals and the W chromosomes of birds carry only small fractions of the genes carried by the homologous X or Z chromosomes, and this "genetic degeneration" is associated with loss of recombination between the sex chromosome pair. However, it is still not known how much evolutionary time is needed to reach such nearly complete degeneration. The XY pair of species in a group of closely related poecilid fish is homologous but has been found to have either nondegenerated or completely degenerated Y chromosomes. We evaluate evidence described in a recent paper and show that the available data cast doubt on the view that degeneration has been extraordinarily rapid in the latter (Micropoecilia species).
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Affiliation(s)
- Deborah Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Abigail Hastings
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Chay Graham
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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10
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Liu Y, Chen X, Yin Y, Li X, He K, Zhao X, Li X, Luo X, Mei Y, Wang Z, Shu R, Cheng Z, Gebretsadik KG, Luo C, Wang R, Lv Y, Chen A, Li F. A chromosome-level genome assembly of tomato pinworm, Tuta absoluta. Sci Data 2023; 10:390. [PMID: 37330594 PMCID: PMC10276875 DOI: 10.1038/s41597-023-02299-5] [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: 03/12/2023] [Accepted: 06/09/2023] [Indexed: 06/19/2023] Open
Abstract
The tomato pinworm, Tuta absoluta, or Phthorimaea absouta, is native to South America, but quickly spread to other regions of world, including Europe, Africa, and Asia, devastating to global tomato production. However, a lack of high-quality genome resources makes it difficult to understand its high invasiveness and ecological adaptation. Here, we sequenced the genome of the tomato pinworm using Nanopore platforms, yielding a genome assembly of 564.5 Mb with contig N50 of 3.33 Mb. BUSCO analysis demonstrated that this genome assembly has a high-level completeness of 98.0% gene coverage. In total, 310 Mb are repeating sequences accounting for 54.8% of genome assembly, and 21,979 protein-coding genes are annotated. Next, we used the Hi-C technique to anchor 295 contigs to 29 chromosomes, yielding a chromosome-level genome assembly with a scaffold N50 of 20.7 Mb. In sum, the high-quality genome assembly of the tomato pinworm is a useful gene resource that contributes to a better understanding of the biological characteristics of its invasiveness and will help in developing an efficient control policy.
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Affiliation(s)
- Ying Liu
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China.
| | - Xi Chen
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanqiong Yin
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Xiaowei Li
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Kang He
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xueqing Zhao
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Xiangyong Li
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Xiyan Luo
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Yang Mei
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zuoqi Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Runguo Shu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ziqi Cheng
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Kifle Gebreegziabiher Gebretsadik
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
- Tigray Agricultural Research Institute (TARI), Mek'ele, Tigray, +492, Ethiopia
| | - Chen Luo
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Ran Wang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yaobin Lv
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Aidong Chen
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China.
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
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11
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Mongue AJ, Martin SH, Manweiler REV, Scullion H, Koehn JL, de Roode JC, Walters JR. Genome sequence of Ophryocystis elektroscirrha, an apicomplexan parasite of monarch butterflies: cryptic diversity and response to host-sequestered plant chemicals. BMC Genomics 2023; 24:278. [PMID: 37226080 DOI: 10.1186/s12864-023-09350-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/29/2023] [Indexed: 05/26/2023] Open
Abstract
Apicomplexa are ancient and diverse organisms which have been poorly characterized by modern genomics. To better understand the evolution and diversity of these single-celled eukaryotes, we sequenced the genome of Ophryocystis elektroscirrha, a parasite of monarch butterflies, Danaus plexippus. We contextualize our newly generated resources within apicomplexan genomics before answering longstanding questions specific to this host-parasite system. To start, the genome is miniscule, totaling only 9 million bases and containing fewer than 3,000 genes, half the gene content of two other sequenced invertebrate-infecting apicomplexans, Porospora gigantea and Gregarina niphandrodes. We found that O. elektroscirrha shares different orthologs with each sequenced relative, suggesting the true set of universally conserved apicomplexan genes is very small indeed. Next, we show that sequencing data from other potential host butterflies can be used to diagnose infection status as well as to study diversity of parasite sequences. We recovered a similarly sized parasite genome from another butterfly, Danaus chrysippus, that was highly diverged from the O. elektroscirrha reference, possibly representing a distinct species. Using these two new genomes, we investigated potential evolutionary response by parasites to toxic phytochemicals their hosts ingest and sequester. Monarch butterflies are well-known to tolerate toxic cardenolides thanks to changes in the sequence of their Type II ATPase sodium pumps. We show that Ophryocystis completely lacks Type II or Type 4 sodium pumps, and related proteins PMCA calcium pumps show extreme sequence divergence compared to other Apicomplexa, demonstrating new avenues of research opened by genome sequencing of non-model Apicomplexa.
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Affiliation(s)
- Andrew J Mongue
- Department of Entomology and Nematology, University of Florida, Gainesville, USA.
| | - Simon H Martin
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Rachel E V Manweiler
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, USA
| | - Helena Scullion
- Department of Entomology and Nematology, University of Florida, Gainesville, USA
| | - Jordyn L Koehn
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, USA
| | | | - James R Walters
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, USA
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12
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Gauthier J, Meier J, Legeai F, McClure M, Whibley A, Bretaudeau A, Boulain H, Parrinello H, Mugford ST, Durbin R, Zhou C, McCarthy S, Wheat CW, Piron-Prunier F, Monsempes C, François MC, Jay P, Noûs C, Persyn E, Jacquin-Joly E, Meslin C, Montagné N, Lemaitre C, Elias M. First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): Comparative models for mimicry genetic studies. Mol Ecol Resour 2023; 23:872-885. [PMID: 36533297 DOI: 10.1111/1755-0998.13749] [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: 06/20/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
The ithomiine butterflies (Nymphalidae: Danainae) represent the largest known radiation of Müllerian mimetic butterflies. They dominate by number the mimetic butterfly communities, which include species such as the iconic neotropical Heliconius genus. Recent studies on the ecology and genetics of speciation in Ithomiini have suggested that sexual pheromones, colour pattern and perhaps hostplant could drive reproductive isolation. However, no reference genome was available for Ithomiini, which has hindered further exploration on the genetic architecture of these candidate traits, and more generally on the genomic patterns of divergence. Here, we generated high-quality, chromosome-scale genome assemblies for two Melinaea species, M. marsaeus and M. menophilus, and a draft genome of the species Ithomia salapia. We obtained genomes with a size ranging from 396 to 503 Mb across the three species and scaffold N50 of 40.5 and 23.2 Mb for the two chromosome-scale assemblies. Using collinearity analyses we identified massive rearrangements between the two closely related Melinaea species. An annotation of transposable elements and gene content was performed, as well as a specialist annotation to target chemosensory genes, which is crucial for host plant detection and mate recognition in mimetic species. A comparative genomic approach revealed independent gene expansions in ithomiines and particularly in gustatory receptor genes. These first three genomes of ithomiine mimetic butterflies constitute a valuable addition and a welcome comparison to existing biological models such as Heliconius, and will enable further understanding of the mechanisms of adaptation in butterflies.
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Affiliation(s)
| | - Joana Meier
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Fabrice Legeai
- BIPAA, IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France
- Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Melanie McClure
- Institut Systématique Évolution Biodiversité (ISYEB), Centre National de la Recherche Scientifique, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
- Laboratoire Écologie, Évolution, Interactions des Systèmes Amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, Cayenne, France
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anthony Bretaudeau
- BIPAA, IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France
- Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Hélène Boulain
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Hugues Parrinello
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Sam T Mugford
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Chenxi Zhou
- Department of Genetics, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Shane McCarthy
- Department of Genetics, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | | | - Florence Piron-Prunier
- Institut Systématique Évolution Biodiversité (ISYEB), Centre National de la Recherche Scientifique, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | - Christelle Monsempes
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Marie-Christine François
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Paul Jay
- Ecologie Systématique Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | | | - Emma Persyn
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
- CIRAD, UMR PVBMT, St Pierre, France
| | - Emmanuelle Jacquin-Joly
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Camille Meslin
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Nicolas Montagné
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | | | - Marianne Elias
- Institut Systématique Évolution Biodiversité (ISYEB), Centre National de la Recherche Scientifique, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
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13
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Webster TH, Vannan A, Pinto BJ, Denbrock G, Morales M, Dolby GA, Fiddes IT, DeNardo DF, Wilson MA. Incomplete dosage balance and dosage compensation in the ZZ/ZW Gila monster ( Heloderma suspectum) revealed by de novo genome assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538436. [PMID: 37163099 PMCID: PMC10168389 DOI: 10.1101/2023.04.26.538436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes. Here, we report the assembly and analysis of the Gila monster genome. We generated a de novo draft genome assembly for a male using 10X Genomics technology. We further generated and analyzed short-read whole genome sequencing and whole transcriptome sequencing data for three males and three females. By comparing female and male genomic data, we identified four putative Z-chromosome scaffolds. These putative Z-chromosome scaffolds are homologous to Z-linked scaffolds identified in the Komodo dragon. Further, by analyzing RNAseq data, we observed evidence of incomplete dosage compensation between the Gila monster Z chromosome and autosomes and a lack of balance in Z-linked expression between the sexes. In particular, we observe lower expression of the Z in females (ZW) than males (ZZ) on a global basis, though we find evidence suggesting local gene-by-gene compensation. This pattern has been observed in most other ZZ/ZW systems studied to date and may represent a general pattern for female heterogamety in vertebrates.
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Affiliation(s)
- Timothy H. Webster
- Department of Anthropology, University of Utah, Salt Lake City, UT
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Annika Vannan
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Brendan J. Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
| | - Grant Denbrock
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Matheo Morales
- School of Life Sciences, Arizona State University, Tempe, AZ
- Department of Genetics, Yale University, New Haven, CT
| | - Greer A. Dolby
- School of Life Sciences, Arizona State University, Tempe, AZ
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ
| | | | - Dale F. DeNardo
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ
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14
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Zhao L, Li XD, Jiang T, Wang H, Dan Z, Xu SQ, Guan DL. The Chromosome-Level Genome of Hestina assimilis (Lepidoptera: Nymphalidae) Reveals the Evolution of Saprophagy-Related Genes in Brush-Footed Butterflies. Int J Mol Sci 2023; 24:ijms24032087. [PMID: 36768416 PMCID: PMC9917059 DOI: 10.3390/ijms24032087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/06/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Most butterflies feed on nectar, while some saprophagous butterflies forage on various non-nectar foods. To date, little is known about the genomic and molecular shifts associated with the evolution of the saprophagous feeding strategy. Here, we assembled the high-quality chromosome-level genome of Hestina assimilis to explore its saprophagous molecular and genetic mechanisms. This chromosome-level genome of H. assimilis is 412.82 Mb, with a scaffold N50 of 15.70 Mb. In total, 98.11% of contigs were anchored to 30 chromosomes. Compared with H. assimilis and other Nymphalidae butterflies, the genes of metabolism and detoxification experienced expansions. We annotated 80 cytochrome P450 (CYP) genes in the H. assimilis genome, among which genes belonging to the CYP4 subfamily were significantly expanded (p < 0.01). These P450 genes were unevenly distributed and mainly concentrated on chromosomes 6-9. We identified 33 olfactory receptor (OR), 20 odorant-binding protein (OBP), and six gustatory receptor (GR) genes in the H. assimilis genome, which were fewer than in the nectarivorous Danaus plexippus. A decreased number of OBP, OR, and GR genes implied that H. assimilis should resort less to olfaction and gustation than their nectarivorous counterparts, which need highly specialized olfactory and gustatory functions. Moreover, we found one site under positive selection occurred in residue 996 (phenylalanine) of GR genes exclusive to H. assimilis, which is conservative in most lineages. Our study provides support for the adaptive evolution of feeding habits in butterflies.
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Affiliation(s)
- Lu Zhao
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Xiao-Dong Li
- School of Chemistry and Bioengineering, Hechi University, Yizhou 546300, China
| | - Tao Jiang
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Hang Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Zhicuo Dan
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Sheng-Quan Xu
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
- Correspondence: (S.-Q.X.); (D.-L.G.)
| | - De-Long Guan
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
- School of Chemistry and Bioengineering, Hechi University, Yizhou 546300, China
- Correspondence: (S.-Q.X.); (D.-L.G.)
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15
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Hu QL, Ye YX, Zhuo JC, Huang HJ, Li JM, Zhang CX. Chromosome-level Assembly, Dosage Compensation and Sex-biased Gene Expression in the Small Brown Planthopper, Laodelphax striatellus. Genome Biol Evol 2022; 14:evac160. [PMID: 36317697 PMCID: PMC9651030 DOI: 10.1093/gbe/evac160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2022] [Indexed: 01/19/2024] Open
Abstract
In insects, sex chromosome differentiation often results in unequal gene dosages between sexes. Dosage compensation mechanisms evolve to balance gene expression, but the degree and mechanism of regulation often vary by insect species. In hemipteran species, the small brown planthopper (SBPH), Laodelphax striatellus, is an injurious crop pest, with a sex chromosome type XX in females and XO in males. This species offers the opportunity to study dosage compensation and sex-biased gene expression. In this study, we generated a chromosome-level genome of SBPH using Oxford Nanopore Technologies and high-throughput chromatin conformation capture (Hi-C) technology. We also sequenced RNA-seq data from 16 tissue samples to annotate the genome and analyze gene dosage compensation. We finally obtained a 510.2 megabases (Mb) genome with 99.12% of the scaffolds anchored on 15 chromosomes (14 autosomes and 1 X chromosome) and annotated 16,160 protein-coding genes based on full-length cDNA sequencing data. Furthermore, we found complete dosage compensation in all L. striatellus somatic tissues, but lack of dosage compensation in gonad tissue testis. We also found that female-biased genes were significantly enriched on the X chromosome in all tissues, whereas male-biased genes in gonad tissues were enriched on autosomes. This study not only provides a high-quality genome assembly but also lays a foundation for a better understanding of the sexual regulatory network in hemipteran insects.
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Affiliation(s)
- Qing-Ling Hu
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yu-Xuan Ye
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
| | - Ji-Chong Zhuo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Hai-Jian Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Chuan-Xi Zhang
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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16
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Shipilina D, Näsvall K, Höök L, Vila R, Talavera G, Backström N. Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly. Genomics 2022; 114:110481. [PMID: 36115505 DOI: 10.1016/j.ygeno.2022.110481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/01/2022] [Accepted: 09/10/2022] [Indexed: 01/14/2023]
Abstract
Characterization of gene family expansions and crossing over is crucial for understanding how organisms adapt to the environment. Here, we develop a high-density linkage map and detailed genome annotation of the painted lady butterfly (Vanessa cardui) - a non-diapausing, highly polyphagous species famous for its long-distance migratory behavior and almost cosmopolitan distribution. Our results reveal a complex interplay between regional recombination rate variation, gene duplications and transposable element activity shaping the genome structure of the painted lady. We identify several lineage specific gene family expansions. Their functions are mainly associated with protein and fat metabolism, detoxification, and defense against infection - critical processes for the painted lady's unique life-history. Furthermore, the detailed recombination maps allow us to characterize the regional recombination landscape, data that reveal a strong effect of chromosome size on the recombination rate, a limited impact of GC-biased gene conversion and a positive association between recombination and short interspersed elements.
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Affiliation(s)
- Daria Shipilina
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden; Swedish Collegium for Advanced Study, Thunbergsvägen 2, 75236 Uppsala, Sweden.
| | - Karin Näsvall
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Lars Höök
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Roger Vila
- The Butterfly Diversity and Evolution Lab, Institut de Biologia Evolutiva, Passeig Martim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona, Passeig del Migdia s/n, 08038 Barcelona, Spain
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
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17
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Tomihara K, Kawamoto M, Suzuki Y, Katsuma S, Kiuchi T. Masculinizer-induced dosage compensation is achieved by transcriptional downregulation of both copies of Z-linked genes in the silkworm, Bombyx mori. Biol Lett 2022; 18:20220116. [PMID: 36069069 PMCID: PMC9449812 DOI: 10.1098/rsbl.2022.0116] [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: 03/09/2022] [Accepted: 08/15/2022] [Indexed: 11/12/2022] Open
Abstract
The evolution of dosage compensation produces similar expression of sex-linked and autosomal genes in the heterogametic sex. The silkworm (Bombyx mori), a lepidopteran insect, has a female heterogametic WZ sex determination system. A Z-linked gene, Masculinizer (Masc), is the primary determinant of maleness and dosage compensation in B. mori. However, it remains unknown whether one of the two Z chromosomes is inactivated or both Z chromosomes are suppressed in B. mori males. Hence, we performed transcriptome analysis using hybrids between two B. mori strains and analysed allele-specific expression to distinguish these alternatives. Our analysis revealed that genes on both the maternal and paternal Z chromosomes are transcriptionally upregulated in Masc knocked down males. We therefore conclude that both Z chromosomes are transcriptionally downregulated in B. mori males, similar to the system in Caenorhabditis elegans.
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Affiliation(s)
- Kenta Tomihara
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Munetaka Kawamoto
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takashi Kiuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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18
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Montgomery SA, Hisanaga T, Wang N, Axelsson E, Akimcheva S, Sramek M, Liu C, Berger F. Polycomb-mediated repression of paternal chromosomes maintains haploid dosage in diploid embryos of Marchantia. eLife 2022; 11:79258. [PMID: 35996955 PMCID: PMC9402228 DOI: 10.7554/elife.79258] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/18/2022] [Indexed: 02/06/2023] Open
Abstract
Complex mechanisms regulate gene dosage throughout eukaryotic life cycles. Mechanisms controlling gene dosage have been extensively studied in animals, however it is unknown how generalizable these mechanisms are to diverse eukaryotes. Here, we use the haploid plant Marchantia polymorpha to assess gene dosage control in its short-lived diploid embryo. We show that throughout embryogenesis, paternal chromosomes are repressed resulting in functional haploidy. The paternal genome is targeted for genomic imprinting by the Polycomb mark H3K27me3 starting at fertilization, rendering the maternal genome in control of embryogenesis. Maintaining haploid gene dosage by this new form of imprinting is essential for embryonic development. Our findings illustrate how haploid-dominant species can regulate gene dosage through paternal chromosome inactivation and initiates the exploration of the link between life cycle history and gene dosage in a broader range of organisms.
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Affiliation(s)
- Sean Akira Montgomery
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Tetsuya Hisanaga
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Nan Wang
- Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Svetlana Akimcheva
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Milos Sramek
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Chang Liu
- Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
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19
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Kim KW, De-Kayne R, Gordon IJ, Omufwoko KS, Martins DJ, Ffrench-Constant R, Martin SH. Stepwise evolution of a butterfly supergene via duplication and inversion. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210207. [PMID: 35694743 PMCID: PMC9189502 DOI: 10.1098/rstb.2021.0207] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Supergenes maintain adaptive clusters of alleles in the face of genetic mixing. Although usually attributed to inversions, supergenes can be complex, and reconstructing the precise processes that led to recombination suppression and their timing is challenging. We investigated the origin of the BC supergene, which controls variation in warning coloration in the African monarch butterfly, Danaus chrysippus. By generating chromosome-scale assemblies for all three alleles, we identified multiple structural differences. Most strikingly, we find that a region of more than 1 million bp underwent several segmental duplications at least 7.5 Ma. The resulting duplicated fragments appear to have triggered four inversions in surrounding parts of the chromosome, resulting in stepwise growth of the region of suppressed recombination. Phylogenies for the inversions are incongruent with the species tree and suggest that structural polymorphisms have persisted for at least 4.1 Myr. In addition to the role of duplications in triggering inversions, our results suggest a previously undescribed mechanism of recombination suppression through independent losses of divergent duplicated tracts. Overall, our findings add support for a stepwise model of supergene evolution involving a variety of structural changes. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
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Affiliation(s)
- Kang-Wook Kim
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rishi De-Kayne
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ian J Gordon
- Centre of Excellence in Biodiversity and Natural Resource Management, University of Rwanda, Huye Campus, Huye, Rwanda
| | | | - Dino J Martins
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, USA.,Mpala Research Centre, Nanyuki, Kenya
| | | | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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20
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Law STS, Nong W, So WL, Baril T, Swale T, Chan CB, Tobe SS, Kai ZP, Bendena WG, Hayward A, Hui JHL. Chromosomal-level reference genome of the moth Heortia vitessoides (Lepidoptera: Crambidae), a major pest of agarwood-producing trees. Genomics 2022; 114:110440. [PMID: 35905835 DOI: 10.1016/j.ygeno.2022.110440] [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: 05/20/2022] [Revised: 07/13/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022]
Abstract
The moth Heortia vitessoides Moore (Lepidoptera: Crambidae) is a major pest of ecologically, commercially and culturally important agarwood-producing trees in the genus Aquilaria. In particular, H. vitessoides is one of the most destructive defoliating pests of the incense tree Aquilaria sinesis, which produces a valuable fragrant wood used as incense and in traditional Chinese medicine [33]. Nevertheless, a genomic resource for H. vitessoides is lacking. Here, we present a chromosomal-level assembly for H. vitessoides, consisting of a 517 megabase (Mb) genome assembly with high physical contiguity (scaffold N50 of 18.2 Mb) and high completeness (97.9% complete BUSCO score). To aid gene annotation, 8 messenger RNA transcriptomes from different developmental stages were generated, and a total of 16,421 gene models were predicted. Expansion of gene families involved in xenobiotic metabolism and development were detected, including duplications of cytosolic sulfotransferase (SULT) genes shared among lepidopterans. In addition, small RNA sequencing of 5 developmental stages of H. vitessoides facilitated the identification of 85 lepidopteran conserved microRNAs, 94 lineage-specific microRNAs, as well as several microRNA clusters. A large proportion of the H. vitessoides genome consists of repeats, with a 29.12% total genomic contribution from transposable elements, of which long interspersed nuclear elements (LINEs) are the dominant component (17.41%). A sharp decrease in the genome-wide percentage of LINEs with lower levels of genetic distance to family consensus sequences suggests that LINE activity has peaked in H. vitessoides. In contrast, opposing patterns suggest a substantial recent increase in DNA and LTR element activity. Together with annotations of essential sesquiterpenoid hormonal pathways, neuropeptides, microRNAs and transposable elements, the high-quality genomic and transcriptomic resources we provide for the economically important moth H. vitessoides provide a platform for the development of genomic approaches to pest management, and contribute to addressing fundamental research questions in Lepidoptera.
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Affiliation(s)
- Sean T S Law
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai Lok So
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | | | | | - Chi Bun Chan
- School of Biological Science, The University of Hong Kong, Hong Kong, China
| | - Stephen S Tobe
- Department of Cell and Systems Biology, University of Toronto, Canada
| | - Zhen-Peng Kai
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | | | | | - Jerome H L Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
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21
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Meisel RP, Asgari D, Schlamp F, Unckless RL. Induction and inhibition of Drosophila X chromosome gene expression are both impeded by the dosage compensation complex. G3 (BETHESDA, MD.) 2022; 12:6632659. [PMID: 35792851 PMCID: PMC9434221 DOI: 10.1093/g3journal/jkac165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/16/2022] [Indexed: 12/24/2022]
Abstract
Sex chromosomes frequently differ from the autosomes in the frequencies of genes with sexually dimorphic or tissue-specific expression. Multiple hypotheses have been put forth to explain the unique gene content of the X chromosome, including selection against male-beneficial X-linked alleles, expression limits imposed by the haploid dosage of the X in males, and interference by the dosage compensation complex on expression in males. Here, we investigate these hypotheses by examining differential gene expression in Drosophila melanogaster following several treatments that have widespread transcriptomic effects: bacterial infection, viral infection, and abiotic stress. We found that genes that are induced (upregulated) by these biotic and abiotic treatments are frequently under-represented on the X chromosome, but so are those that are repressed (downregulated) following treatment. We further show that whether a gene is bound by the dosage compensation complex in males can largely explain the paucity of both up- and downregulated genes on the X chromosome. Specifically, genes that are bound by the dosage compensation complex, or close to a dosage compensation complex high-affinity site, are unlikely to be up- or downregulated after treatment. This relationship, however, could partially be explained by a correlation between differential expression and breadth of expression across tissues. Nonetheless, our results suggest that dosage compensation complex binding, or the associated chromatin modifications, inhibit both up- and downregulation of X chromosome gene expression within specific contexts, including tissue-specific expression. We propose multiple possible mechanisms of action for the effect, including a role of Males absent on the first, a component of the dosage compensation complex, as a dampener of gene expression variance in both males and females. This effect could explain why the Drosophila X chromosome is depauperate in genes with tissue-specific or induced expression, while the mammalian X has an excess of genes with tissue-specific expression.
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Affiliation(s)
- Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd, Houston, TX 77204-5001, USA
| | - Danial Asgari
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd, Houston, TX 77204-5001, USA
| | - Florencia Schlamp
- Department of Medicine, NYU Grossman School of Medicine, 435 E 30th St, New York, NY 10016, USA
| | - Robert L Unckless
- Department of Molecular Biosciences, University of Kansas, 4055 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
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22
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Evolution of sexual systems, sex chromosomes and sex-linked gene transcription in flatworms and roundworms. Nat Commun 2022; 13:3239. [PMID: 35688815 PMCID: PMC9187692 DOI: 10.1038/s41467-022-30578-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/06/2022] [Indexed: 12/02/2022] Open
Abstract
Many species with separate male and female individuals (termed ‘gonochorism’ in animals) have sex-linked genome regions. Here, we investigate evolutionary changes when genome regions become completely sex-linked, by analyses of multiple species of flatworms (Platyhelminthes; among which schistosomes recently evolved gonochorism from ancestral hermaphroditism), and roundworms (Nematoda) which have undergone independent translocations of different autosomes. Although neither the evolution of gonochorism nor translocations fusing ancestrally autosomal regions to sex chromosomes causes inevitable loss of recombination, we document that formerly recombining regions show genomic signatures of recombination suppression in both taxa, and become strongly genetically degenerated, with a loss of most genes. Comparisons with hermaphroditic flatworm transcriptomes show masculinisation and some defeminisation in schistosome gonad gene expression. We also find evidence that evolution of sex-linkage in nematodes is accompanied by transcriptional changes and dosage compensation. Our analyses also identify sex-linked genes that could assist future research aimed at controlling some of these important parasites. Transitions between hermaphroditic and separate sexes are relatively understudied in animals compared to pants. Here, Wang et al. reconstruct the evolution of separate sexes in the flatworms and complex changes of sex chromosomes in the roundworms.
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23
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The evolution of gene regulation on sex chromosomes. Trends Genet 2022; 38:844-855. [DOI: 10.1016/j.tig.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 11/20/2022]
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24
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Nakajima Y, Ogura A. Genomics and effective trait candidates of edible insects. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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Dosage compensation in Bombyx mori is achieved by partial repression of both Z chromosomes in males. Proc Natl Acad Sci U S A 2022; 119:e2113374119. [PMID: 35239439 PMCID: PMC8915793 DOI: 10.1073/pnas.2113374119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genes on sex chromosomes (i.e. human chX) are regulated differently in males and females to balance gene expression levels between sexes (XY vs. XX). This sex-specific regulation is called dosage compensation (DC). DC is achieved by altering the shape and compaction of sex chromosomes specifically in one sex. In this study, we use Oligopaints to examine DC in silkworms. This study visualizes this phenomenon in a species with ZW sex chromosomes, which evolved independently of XY. Our data support a long-standing model for how DC mechanisms evolved across species, and we show potential similarity between DC in silkworms and nematodes, suggesting that this type of DC may have emerged multiple independent times throughout evolution. Interphase chromatin is organized precisely to facilitate accurate gene expression. The structure–function relationship of chromatin is epitomized in sex chromosome dosage compensation (DC), where sex-linked gene expression is balanced between males and females via sex-specific alterations to three-dimensional chromatin structure. Studies in ZW-bearing species suggest that DC is absent or incomplete in most lineages except butterflies and moths, where male (ZZ) Z chromosome (chZ) expression is reduced by half to equal females (ZW). However, whether one chZ is inactivated (as in mammals) or both are partially repressed (as in Caenorhabditis elegans) is unclear. Using Oligopaints in the silkworm, Bombyx mori, we visualize autosomes and chZ in somatic cells from both sexes. We find that B. mori chromosomes are highly compact relative to Drosophila. We show that in B. mori males, both chZs are similar in size and shape and are more compact than autosomes or the female chZ after DC establishment, suggesting both male chZs are partially and equally downregulated. We also find that in the early stages of DC in females, chZ chromatin becomes more accessible and Z-linked expression increases. Concomitant with these changes, the female chZ repositions toward the nuclear center, revealing nonsequencing-based support for Ohno’s hypothesis. These studies visualizing interphase genome organization and chZ structure in Lepidoptera uncover intriguing similarities between DC in B. mori and C. elegans, despite these lineages harboring evolutionarily distinct sex chromosomes (ZW/XY), suggesting a possible role for holocentricity in DC mechanisms.
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26
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Singh KS, De-Kayne R, Omufwoko KS, Martins DJ, Bass C, Ffrench-Constant R, Martin SH. Genome assembly of Danaus chrysippus and comparison with the Monarch Danaus plexippus. G3 (BETHESDA, MD.) 2022; 12:6491253. [PMID: 35100331 PMCID: PMC9210279 DOI: 10.1093/g3journal/jkab449] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/21/2021] [Indexed: 02/07/2023]
Abstract
Milkweed butterflies in the genus Danaus are studied in a diverse range of research fields including the neurobiology of migration, biochemistry of plant detoxification, host–parasite interactions, evolution of sex chromosomes, and speciation. We have assembled a nearly chromosomal genome for Danaus chrysippus (known as the African Monarch, African Queen, and Plain Tiger) using long-read sequencing data. This species is of particular interest for the study of genome structural change and its consequences for evolution. Comparison with the genome of the North American Monarch Danaus plexippus reveals generally strong synteny but highlights 3 inversion differences. The 3 chromosomes involved were previously found to carry peaks of intraspecific differentiation in D. chrysippus in Africa, suggesting that these inversions may be polymorphic and associated with local adaptation. The D. chrysippus genome is over 40% larger than that of D. plexippus, and nearly all of the additional ∼100 Megabases of DNA comprises repeats. Future comparative genomic studies within this genus will shed light on the evolution of genome architecture.
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Affiliation(s)
- Kumar Saurabh Singh
- Bioinformatics Group, Wageningen University, Wageningen 6708 PB, The Netherlands
| | - Rishi De-Kayne
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | | | - Dino J Martins
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.,Mpala Research Centre, Nanyuki, P O Box 555 10400, Kenya
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, Penryn TR10 9FE, UK
| | | | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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27
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Baril T, Hayward A. Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus. Mob DNA 2022; 13:5. [PMID: 35172896 PMCID: PMC8848866 DOI: 10.1186/s13100-022-00263-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/06/2022] [Indexed: 01/10/2023] Open
Abstract
Background Lepidoptera (butterflies and moths) are an important model system in ecology and evolution. A high-quality chromosomal genome assembly is available for the monarch butterfly (Danaus plexippus), but it lacks an in-depth transposable element (TE) annotation, presenting an opportunity to explore monarch TE dynamics and the impact of TEs on shaping the monarch genome. Results We find 6.21% of the monarch genome is comprised of TEs, a reduction of 6.85% compared to the original TE annotation performed on the draft genome assembly. Monarch TE content is low compared to two closely related species with available genomes, Danaus chrysippus (33.97% TE) and Danaus melanippus (11.87% TE). The biggest TE contributions to genome size in the monarch are LINEs and Penelope-like elements, and three newly identified families, r2-hero_dPle (LINE), penelope-1_dPle (Penelope-like), and hase2-1_dPle (SINE), collectively contribute 34.92% of total TE content. We find evidence of recent TE activity, with two novel Tc1 families rapidly expanding over recent timescales (tc1-1_dPle, tc1-2_dPle). LINE fragments show signatures of genomic deletions indicating a high rate of TE turnover. We investigate associations between TEs and wing colouration and immune genes and identify a three-fold increase in TE content around immune genes compared to other host genes. Conclusions We provide a detailed TE annotation and analysis for the monarch genome, revealing a considerably smaller TE contribution to genome content compared to two closely related Danaus species with available genome assemblies. We identify highly successful novel DNA TE families rapidly expanding over recent timescales, and ongoing signatures of both TE expansion and removal highlight the dynamic nature of repeat content in the monarch genome. Our findings also suggest that insect immune genes are promising candidates for future interrogation of TE-mediated host adaptation. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00263-5.
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Affiliation(s)
- Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK.
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK.
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28
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Pocius VM, Majewska AA, Freedman MG. The Role of Experiments in Monarch Butterfly Conservation: A Review of Recent Studies and Approaches. ANNALS OF THE ENTOMOLOGICAL SOCIETY OF AMERICA 2022; 115:10-24. [PMID: 35069967 PMCID: PMC8764570 DOI: 10.1093/aesa/saab036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Indexed: 06/14/2023]
Abstract
Monarch butterflies (Danaus plexippus) (Lepidoptera Danaidae Danaus plexippus (Linnaeus)) are an iconic species of conservation concern due to declines in the overwintering colonies over the past twenty years. Because of this downward trend in overwintering numbers in both California and Mexico, monarchs are currently considered 'warranted-but-precluded' for listing under the Endangered Species Act. Monarchs have a fascinating life history and have become a model system in chemical ecology, migration biology, and host-parasite interactions, but many aspects of monarch biology important for informing conservation practices remain unresolved. In this review, we focus on recent advances using experimental and genetic approaches that inform monarch conservation. In particular, we emphasize three areas of broad importance, which could have an immediate impact on monarch conservation efforts: 1) breeding habitat and host plant use, 2) natural enemies and exotic caterpillar food plants, and 3) the utility of genetic and genomic approaches for understanding monarch biology and informing ongoing conservation efforts. We also suggest future studies in these areas that could improve our understanding of monarch behavior and conservation.
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Affiliation(s)
- Victoria M Pocius
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | | | - Micah G Freedman
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
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29
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Manni M, Berkeley MR, Seppey M, Zdobnov EM. BUSCO: Assessing Genomic Data Quality and Beyond. Curr Protoc 2021; 1:e323. [PMID: 34936221 DOI: 10.1002/cpz1.323] [Citation(s) in RCA: 243] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Evaluation of the quality of genomic "data products" such as genome assemblies or gene sets is of critical importance in order to recognize possible issues and correct them during the generation of new data. It is equally essential to guide subsequent or comparative analyses with existing data, as the correct interpretation of the results necessarily requires knowledge about the quality level and reliability of the inputs. Using datasets of near universal single-copy orthologs derived from OrthoDB, BUSCO can estimate the completeness and redundancy of genomic data by providing biologically meaningful metrics based on expected gene content. These can complement technical metrics such as contiguity measures (e.g., number of contigs/scaffolds, and N50 values). Here, we describe the use of the BUSCO tool suite to assess different data types that can range from genome assemblies of single isolates and assembled transcriptomes and annotated gene sets to metagenome-assembled genomes where the taxonomic origin of the species is unknown. BUSCO is the only tool capable of assessing all these types of sequences from both eukaryotic and prokaryotic species. The protocols detail the various BUSCO running modes and the novel workflows introduced in versions 4 and 5, including the batch analysis on multiple inputs, the auto-lineage workflow to run assessments without specifying a dataset, and a workflow for the evaluation of (large) eukaryotic genomes. The protocols further cover the BUSCO setup, guidelines to interpret the results, and BUSCO "plugin" workflows for performing common operations in genomics using BUSCO results, such as building phylogenomic trees and visualizing syntenies. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Assessing an input sequence with a BUSCO dataset specified manually Basic Protocol 2: Assessing an input sequence with a dataset automatically selected by BUSCO Basic Protocol 3: Assessing multiple inputs Alternate Protocol: Decreasing analysis runtime when assessing a large number of small genomes with BUSCO auto-lineage workflow and Snakemake Support Protocol 1: BUSCO setup Support Protocol 2: Visualizing BUSCO results Support Protocol 3: Building phylogenomic trees.
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Affiliation(s)
- Mosè Manni
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Matthew R Berkeley
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Mathieu Seppey
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
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30
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Cicconardi F, Lewis JJ, Martin SH, Reed RD, Danko CG, Montgomery SH. Chromosome Fusion Affects Genetic Diversity and Evolutionary Turnover of Functional Loci but Consistently Depends on Chromosome Size. Mol Biol Evol 2021; 38:4449-4462. [PMID: 34146107 PMCID: PMC8476138 DOI: 10.1093/molbev/msab185] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Major changes in chromosome number and structure are linked to a series of evolutionary phenomena, including intrinsic barriers to gene flow or suppression of recombination due to chromosomal rearrangements. However, chromosome rearrangements can also affect the fundamental dynamics of molecular evolution within populations by changing relationships between linked loci and altering rates of recombination. Here, we build chromosome-level assembly Eueides isabella and, together with a recent chromosome-level assembly of Dryas iulia, examine the evolutionary consequences of multiple chromosome fusions in Heliconius butterflies. These assemblies pinpoint fusion points on 10 of the 20 autosomal chromosomes and reveal striking differences in the characteristics of fused and unfused chromosomes. The ten smallest autosomes in D. iulia and E. isabella, which have each fused to a longer chromosome in Heliconius, have higher repeat and GC content, and longer introns than predicted by their chromosome length. When fused, these characteristics change to become more in line with chromosome length. The fusions also led to reduced diversity, which likely reflects increased background selection and selection against introgression between diverging populations, following a reduction in per-base recombination rate. We further show that chromosome size and fusion impact turnover rates of functional loci at a macroevolutionary scale. Together these results provide further evidence that chromosome fusion in Heliconius likely had dramatic effects on population level processes shaping rates of neutral and adaptive divergence. These effects may have impacted patterns of diversification in Heliconius, a classic example of an adaptive radiation.
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Affiliation(s)
- Francesco Cicconardi
- School of Biological Sciences, University of Bristol Bristol—Life Sciences Building, Bristol, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - James J Lewis
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
- Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Robert D Reed
- Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Stephen H Montgomery
- School of Biological Sciences, University of Bristol Bristol—Life Sciences Building, Bristol, United Kingdom
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31
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Rovatsos M, Gamble T, Nielsen SV, Georges A, Ezaz T, Kratochvíl L. Do male and female heterogamety really differ in expression regulation? Lack of global dosage balance in pygopodid geckos. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200102. [PMID: 34304587 PMCID: PMC8310713 DOI: 10.1098/rstb.2020.0102] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2020] [Indexed: 12/25/2022] Open
Abstract
Differentiation of sex chromosomes is thought to have evolved with cessation of recombination and subsequent loss of genes from the degenerated partner (Y and W) of sex chromosomes, which in turn leads to imbalance of gene dosage between sexes. Based on work with traditional model species, theory suggests that unequal gene copy numbers lead to the evolution of mechanisms to counter this imbalance. Dosage compensation, or at least achieving dosage balance in expression of sex-linked genes between sexes, has largely been documented in lineages with male heterogamety (XX/XY sex determination), while ZZ/ZW systems are assumed to be usually associated with the lack of chromosome-wide gene dose regulatory mechanisms. Here, we document that although the pygopodid geckos evolved male heterogamety with a degenerated Y chromosome 32-72 Ma, one species in particular, Burton's legless lizard (Lialis burtonis), does not possess dosage balance in the expression of genes in its X-specific region. We summarize studies on gene dose regulatory mechanisms in animals and conclude that there is in them no significant dichotomy between male and female heterogamety. We speculate that gene dose regulatory mechanisms are likely to be related to the general mechanisms of sex determination instead of type of heterogamety. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Michail Rovatsos
- Department of Ecology, Charles University, Prague, CZ 12844, Czech Republic
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
- Milwaukee Public Museum, 800 W. Wells Street, Milwaukee, WI 53233, USA
- Bell Museum of Natural History, University of Minnesota, Saint Paul, MN 55108, USA
| | - Stuart V. Nielsen
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Lukáš Kratochvíl
- Department of Ecology, Charles University, Prague, CZ 12844, Czech Republic
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32
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Mongue AJ, Hansen ME, Walters JR. Support for faster and more adaptive Z chromosome evolution in two divergent lepidopteran lineages. Evolution 2021; 76:332-345. [PMID: 34463346 PMCID: PMC9291949 DOI: 10.1111/evo.14341] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 07/21/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022]
Abstract
The rateof divergence for Z or X chromosomes is usually observed to be greater than autosomes, but the proposed evolutionary causes for this pattern vary, as do empirical results from diverse taxa. Even among moths and butterflies (Lepidoptera), which generally share a single-origin Z chromosome, the handful of available studies give mixed support for faster or more adaptive evolution of the Z chromosome, depending on the species assayed. Here, we examine the molecular evolution of Z chromosomes in two additional lepidopteran species: the Carolina sphinx moth and the monarch butterfly, the latter of which possesses a recent chromosomal fusion yielding a segment of newly Z-linked DNA. We find evidence for both faster and more adaptive Z chromosome evolution in both species, although this effect is strongest in the neo-Z portion of the monarch sex chromosome. The neo-Z is less male-biased than expected of a Z chromosome, and unbiased and female-biased genes drive the signal for adaptive evolution here. Together these results suggest that male-biased gene accumulation and haploid selection have opposing effects on long-term rates of adaptation and may help explain the discrepancies in previous findings as well as the repeated evolution of neo-sex chromosomes in Lepidoptera.
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Affiliation(s)
- Andrew J Mongue
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, 66045.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH93FL, United Kingdom
| | - Megan E Hansen
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, 66045
| | - James R Walters
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, 66045
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33
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Keller Valsecchi CI, Marois E, Basilicata MF, Georgiev P, Akhtar A. Distinct mechanisms mediate X chromosome dosage compensation in Anopheles and Drosophila. Life Sci Alliance 2021; 4:4/9/e202000996. [PMID: 34266874 PMCID: PMC8321682 DOI: 10.26508/lsa.202000996] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 12/14/2022] Open
Abstract
CRISPR knockout of msl-2 and epigenome analyses in Anopheles reveal that X chromosome dosage compensation in mosquitos and Drosophila is achieved by two different molecular mechanisms. Sex chromosomes induce potentially deleterious gene expression imbalances that are frequently corrected by dosage compensation (DC). Three distinct molecular strategies to achieve DC have been previously described in nematodes, fruit flies, and mammals. Is this a consequence of distinct genomes, functional or ecological constraints, or random initial commitment to an evolutionary trajectory? Here, we study DC in the malaria mosquito Anopheles gambiae. The Anopheles and Drosophila X chromosomes evolved independently but share a high degree of homology. We find that Anopheles achieves DC by a mechanism distinct from the Drosophila MSL complex–histone H4 lysine 16 acetylation pathway. CRISPR knockout of Anopheles msl-2 leads to embryonic lethality in both sexes. Transcriptome analyses indicate that this phenotype is not a consequence of defective X chromosome DC. By immunofluorescence and ChIP, H4K16ac does not preferentially enrich on the male X. Instead, the mosquito MSL pathway regulates conserved developmental genes. We conclude that a novel mechanism confers X chromosome up-regulation in Anopheles. Our findings highlight the pluralism of gene-dosage buffering mechanisms even under similar genomic and functional constraints.
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Affiliation(s)
| | - Eric Marois
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS) UPR9022, Inserm U1257, Strasbourg, France
| | - M Felicia Basilicata
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Institute of Molecular Biology (IMB), Mainz, Germany
| | - Plamen Georgiev
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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34
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Charlesworth D. The timing of genetic degeneration of sex chromosomes. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200093. [PMID: 34247501 DOI: 10.1098/rstb.2020.0093] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genetic degeneration is an extraordinary feature of sex chromosomes, with the loss of functions of Y-linked genes in species with XY systems, and W-linked genes in ZW systems, eventually affecting almost all genes. Although degeneration is familiar to most biologists, important aspects are not yet well understood, including how quickly a Y or W chromosome can become completely degenerated. I review the current understanding of the time-course of degeneration. Degeneration starts after crossing over between the sex chromosome pair stops, and theoretical models predict an initially fast degeneration rate and a later much slower one. It has become possible to estimate the two quantities that the models suggest are the most important in determining degeneration rates-the size of the sex-linked region, and the time when recombination became suppressed (which can be estimated using Y-X or W-Z sequence divergence). However, quantifying degeneration is still difficult. I review evidence on gene losses (based on coverage analysis) or loss of function (by classifying coding sequences into functional alleles and pseudogenes). I also review evidence about whether small genome regions degenerate, or only large ones, whether selective constraints on the genes in a sex-linked region also strongly affect degeneration rates, and about how long it takes before all (or almost all) genes are lost. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, EH9 3LF, UK
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35
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Lewis JJ, Cicconardi F, Martin SH, Reed RD, Danko CG, Montgomery SH. The Dryas iulia Genome Supports Multiple Gains of a W Chromosome from a B Chromosome in Butterflies. Genome Biol Evol 2021; 13:evab128. [PMID: 34117762 PMCID: PMC8290107 DOI: 10.1093/gbe/evab128] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2021] [Indexed: 12/17/2022] Open
Abstract
In butterflies and moths, which exhibit highly variable sex determination mechanisms, the homogametic Z chromosome is deeply conserved and is featured in many genome assemblies. The evolution and origin of the female W sex chromosome, however, remains mostly unknown. Previous studies have proposed that a ZZ/Z0 sex determination system is ancestral to Lepidoptera, and that W chromosomes may originate from sex-linked B chromosomes. Here, we sequence and assemble the female Dryas iulia genome into 32 highly contiguous ordered and oriented chromosomes, including the Z and W sex chromosomes. We then use sex-specific Hi-C, ATAC-seq, PRO-seq, and whole-genome DNA sequence data sets to test if features of the D. iulia W chromosome are consistent with a hypothesized B chromosome origin. We show that the putative W chromosome displays female-associated DNA sequence, gene expression, and chromatin accessibility to confirm the sex-linked function of the W sequence. In contrast with expectations from studies of homologous sex chromosomes, highly repetitive DNA content on the W chromosome, the sole presence of domesticated repetitive elements in functional DNA, and lack of sequence homology with the Z chromosome or autosomes is most consistent with a B chromosome origin for the W, although it remains challenging to rule out extensive sequence divergence. Synteny analysis of the D. iulia W chromosome with other female lepidopteran genome assemblies shows no homology between W chromosomes and suggests multiple, independent origins of the W chromosome from a B chromosome likely occurred in butterflies.
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Affiliation(s)
- James J Lewis
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Francesco Cicconardi
- School of Biological Sciences, University of Bristol, United Kingdom
- Department of Zoology, University of Cambridge, United Kingdom
| | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, USA
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36
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Gonzalez de la Rosa PM, Thomson M, Trivedi U, Tracey A, Tandonnet S, Blaxter M. A telomere-to-telomere assembly of Oscheius tipulae and the evolution of rhabditid nematode chromosomes. G3-GENES GENOMES GENETICS 2021; 11:6026964. [PMID: 33561231 PMCID: PMC8022731 DOI: 10.1093/g3journal/jkaa020] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/25/2020] [Indexed: 12/20/2022]
Abstract
Eukaryotic chromosomes have phylogenetic persistence. In many taxa, each chromosome has a single functional centromere with essential roles in spindle attachment and segregation. Fusion and fission can generate chromosomes with no or multiple centromeres, leading to genome instability. Groups with holocentric chromosomes (where centromeric function is distributed along each chromosome) might be expected to show karyotypic instability. This is generally not the case, and in Caenorhabditis elegans, it has been proposed that the role of maintenance of a stable karyotype has been transferred to the meiotic pairing centers, which are found at one end of each chromosome. Here, we explore the phylogenetic stability of nematode chromosomes using a new telomere-to-telomere assembly of the rhabditine nematode Oscheius tipulae generated from nanopore long reads. The 60-Mb O. tipulae genome is resolved into six chromosomal molecules. We find the evidence of specific chromatin diminution at all telomeres. Comparing this chromosomal O. tipulae assembly with chromosomal assemblies of diverse rhabditid nematodes, we identify seven ancestral chromosomal elements (Nigon elements) and present a model for the evolution of nematode chromosomes through rearrangement and fusion of these elements. We identify frequent fusion events involving NigonX, the element associated with the rhabditid X chromosome, and thus sex chromosome-associated gene sets differ markedly between species. Despite the karyotypic stability, gene order within chromosomes defined by Nigon elements is not conserved. Our model for nematode chromosome evolution provides a platform for investigation of the tensions between local genome rearrangement and karyotypic evolution in generating extant genome architectures.
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Affiliation(s)
| | - Marian Thomson
- Edinburgh Genomics, School of Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Urmi Trivedi
- Edinburgh Genomics, School of Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Sophie Tandonnet
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP 05508-090, Brazil
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
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A de novo transcriptional atlas in Danaus plexippus reveals variability in dosage compensation across tissues. Commun Biol 2021; 4:791. [PMID: 34172835 PMCID: PMC8233437 DOI: 10.1038/s42003-021-02335-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 06/09/2021] [Indexed: 02/06/2023] Open
Abstract
A detailed knowledge of gene function in the monarch butterfly is still lacking. Here we generate a genome assembly from a Mexican nonmigratory population and used RNA-seq data from 14 biological samples for gene annotation and to construct an atlas portraying the breadth of gene expression during most of the monarch life cycle. Two thirds of the genes show expression changes, with long noncoding RNAs being particularly finely regulated during adulthood, and male-biased expression being four times more common than female-biased. The two portions of the monarch heterochromosome Z, one ancestral to the Lepidoptera and the other resulting from a chromosomal fusion, display distinct association with sex-biased expression, reflecting sample-dependent incompleteness or absence of dosage compensation in the ancestral but not the novel portion of the Z. This study presents extended genomic and transcriptomic resources that will facilitate a better understanding of the monarch's adaptation to a changing environment.
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38
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Muyle A, Bachtrog D, Marais GAB, Turner JMA. Epigenetics drive the evolution of sex chromosomes in animals and plants. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200124. [PMID: 33866802 DOI: 10.1098/rstb.2020.0124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We review how epigenetics affect sex chromosome evolution in animals and plants. In a few species, sex is determined epigenetically through the action of Y-encoded small RNAs. Epigenetics is also responsible for changing the sex of individuals through time, even in species that carry sex chromosomes, and could favour species adaptation through breeding system plasticity. The Y chromosome accumulates repeats that become epigenetically silenced which leads to an epigenetic conflict with the expression of Y genes and could accelerate Y degeneration. Y heterochromatin can be lost through ageing, which activates transposable elements and lowers male longevity. Y chromosome degeneration has led to the evolution of meiotic sex chromosome inactivation in eutherians (placentals) and marsupials, and dosage compensation mechanisms in animals and plants. X-inactivation convergently evolved in eutherians and marsupials via two independently evolved non-coding RNAs. In Drosophila, male X upregulation by the male specific lethal (MSL) complex can spread to neo-X chromosomes through the transposition of transposable elements that carry an MSL-binding motif. We discuss similarities and possible differences between plants and animals and suggest future directions for this dynamic field of research. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Aline Muyle
- University of California Irvine, Irvine, CA 92697, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Gabriel A B Marais
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622 Villeurbanne, France.,LEAF- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Portugal
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39
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Gershman A, Romer TG, Fan Y, Razaghi R, Smith WA, Timp W. De novo genome assembly of the tobacco hornworm moth (Manduca sexta). G3 (BETHESDA, MD.) 2021; 11:jkaa047. [PMID: 33561252 PMCID: PMC8022704 DOI: 10.1093/g3journal/jkaa047] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/20/2020] [Indexed: 01/24/2023]
Abstract
The tobacco hornworm, Manduca sexta, is a lepidopteran insect that is used extensively as a model system for studying insect biology, development, neuroscience, and immunity. However, current studies rely on the highly fragmented reference genome Msex_1.0, which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. We present a new reference genome for M. sexta, JHU_Msex_v1.0, applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly is 470 Mb and is ∼20× more continuous than the original assembly, with scaffold N50 > 14 Mb. We annotated the assembly by lifting over existing annotations and supplementing with additional supporting RNA-based data for a total of 25,256 genes. The new reference assembly is accessible in annotated form for public use. We demonstrate that improved continuity of the M. sexta genome improves resequencing studies and benefits future research on M. sexta as a model organism.
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Affiliation(s)
- Ariel Gershman
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Tatiana G Romer
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Yunfan Fan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Roham Razaghi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Wendy A Smith
- Department of Biology, Northeastern University, Boston, MA, 02215, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, 21287, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
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40
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Nguyen DHM, Panthum T, Ponjarat J, Laopichienpong N, Kraichak E, Singchat W, Ahmad SF, Muangmai N, Peyachoknagul S, Na-Nakorn U, Srikulnath K. An Investigation of ZZ/ZW and XX/XY Sex Determination Systems in North African Catfish ( Clarias gariepinus, ). Front Genet 2021; 11:562856. [PMID: 33584785 PMCID: PMC7874028 DOI: 10.3389/fgene.2020.562856] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 12/07/2020] [Indexed: 12/30/2022] Open
Abstract
An investigation of sex-specific loci may provide important insights into fish sex determination strategies. This may be useful for biotechnological purposes, for example, to produce all-male or all-female fish for commercial breeding. The North African catfish species, Clarias gariepinus, has been widely adopted for aquaculture because its superior growth and disease resistance render the species suitable for hybridization with other catfish to improve the productivity and quality of fish meat. This species has either a ZZ/ZW or XX/XY sex determination system. Here, we investigate and characterize these systems using high-throughput genome complexity reduction sequencing as Diversity Arrays Technology. This approach was effective in identifying moderately sex-linked loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA) markers in 30 perfectly sexed individuals of C. gariepinus. However, SNPs based markers were not found in this study. In total, 41 loci met the criteria for being moderately male-linked (with male vs. female ratios 80:20 and 70:30), while 25 loci were found to be moderately linked to female sex. No strictly male- or female-linked loci were detected. Seven moderately male-linked loci were partially homologous to some classes of transposable elements and three moderately male-linked loci were partially homologous to functional genes. Our data showed that the male heterogametic XX/XY sex determination system should co-exist with the ZZ/ZW system in C. gariepinus. Our finding of the co-existence of XX/XY and ZZ/ZW systems can be applied to benefit commercial breeding of this species in Thailand. This approach using moderately sex-linked loci provides a solid baseline for revealing sex determination mechanisms and identify potential sex determination regions in catfish, allowing further investigation of genetic improvements in breeding programs.
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Affiliation(s)
- Dung Ho My Nguyen
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Jatupong Ponjarat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | | | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Uthairat Na-Nakorn
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand.,Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, Thailand.,Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand.,Amphibian Research Center, Hiroshima University, Higashihiroshima, Japan
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41
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Zhao X, Xu H, He K, Shi Z, Chen X, Ye X, Mei Y, Yang Y, Li M, Gao L, Xu L, Xiao H, Liu Y, Lu Z, Li F. A chromosome-level genome assembly of rice leaffolder, Cnaphalocrocis medinalis. Mol Ecol Resour 2020; 21:561-572. [PMID: 33051980 DOI: 10.1111/1755-0998.13274] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/21/2020] [Accepted: 10/01/2020] [Indexed: 12/01/2022]
Abstract
The rice leaffolder, Cnaphalocrocis medinalis Guenée (Crambidae, Lepidoptera), is an important agricultural pest that causes serious losses to rice production in rice-growing regions with high humidity and temperature. However, a lack of genomic resources limits in-depth understanding of its biological characteristics and ecological adaptation. Here, we sequenced the genome of rice leaffolder using the Illumina and PacBio platforms, yielding a genome assembly of 528.3 Mb with a contig N50 of 524.6 kb. A high percentage (96.4%) of Benchmarking Universal Single-Copy Orthologs (BUSCOs) were successfully detected, suggesting high-level completeness of the genome assembly. In total, 39.5% of the genome consists of repeat sequences and 15,045 protein-coding genes were annotated. Comparative phylogenomic analysis showed that some gene families associated with hormone biosynthesis expanded in rice leaffolder. Next, we used the Hi-C technique to produce a chromosome-level genome assembly with a scaffold N50 of 16.1 Mb by anchoring 3,248 scaffolds to 31 chromosomes. The rice leaffolder genome showed high chromosomal synteny with the genome of four other lepidopteran insects. By comparing coverage ratios from the genome resequencing of male and female pupae, we identified near intact Z and W chromosomes. The W chromosome is estimated as 20.75 Mb, which is the most complete known W chromosome in Lepidoptera. The protein-coding genes on the W chromosome were significantly enriched in metabolic pathways. In all, the high-quality genome assembly and the near-intact W chromosome of rice leaffolder should be a useful resource for the fields of insect migration, chromosome evolution and pest control.
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Affiliation(s)
- Xianxin Zhao
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs, Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Hongxing Xu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agroproducts, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Kang He
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs, Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zhenmin Shi
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs, Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xi Chen
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs, Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xinhai Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs, Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs, Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yajun Yang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agroproducts, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Meizhen Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs, Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Libin Gao
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs, Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Le Xu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs, Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Huamei Xiao
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs, Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.,College of Life Sciences and Resource Environment, Key Laboratory of Crop Growth and Development Regulation of Jiangxi Province, Yichun University, Yichun, China
| | - Ying Liu
- Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Zhongxian Lu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agroproducts, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs, Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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42
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Belyi A, Argyridou E, Parsch J. The Influence of Chromosomal Environment on X-Linked Gene Expression in Drosophila melanogaster. Genome Biol Evol 2020; 12:2391-2402. [PMID: 33104185 PMCID: PMC7719225 DOI: 10.1093/gbe/evaa227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2020] [Indexed: 12/14/2022] Open
Abstract
Sex chromosomes often differ from autosomes with respect to their gene expression and regulation. In Drosophila melanogaster, X-linked genes are dosage compensated by having their expression upregulated in the male soma, a process mediated by the X-chromosome-specific binding of the dosage compensation complex (DCC). Previous studies of X-linked gene expression found a negative correlation between a gene’s male-to-female expression ratio and its distance to the nearest DCC binding site in somatic tissues, including head and brain, which suggests that dosage compensation influences sex-biased gene expression. A limitation of the previous studies, however, was that they focused on endogenous X-linked genes and, thus, could not disentangle the effects of chromosomal position from those of gene-specific regulation. To overcome this limitation, we examined the expression of an exogenous reporter gene inserted at many locations spanning the X chromosome. We observed a negative correlation between the male-to-female expression ratio of the reporter gene and its distance to the nearest DCC binding site in somatic tissues, but not in gonads. A reporter gene’s location relative to a DCC binding site had greater influence on its expression than the local regulatory elements of neighboring endogenous genes, suggesting that intra-chromosomal variation in the strength of dosage compensation is a major determinant of sex-biased gene expression. Average levels of sex-biased expression did not differ between head and brain, but there was greater positional effect variation in the brain, which may explain the observed excess of endogenous sex-biased genes located on the X chromosome in this tissue.
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Affiliation(s)
- Aleksei Belyi
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Eliza Argyridou
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - John Parsch
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
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43
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Lee J, Nishiyama T, Shigenobu S, Yamaguchi K, Suzuki Y, Shimada T, Katsuma S, Kiuchi T. The genome sequence of Samia ricini, a new model species of lepidopteran insect. Mol Ecol Resour 2020; 21:327-339. [PMID: 32985129 DOI: 10.1111/1755-0998.13259] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 08/24/2020] [Accepted: 09/01/2020] [Indexed: 01/15/2023]
Abstract
Samia ricini, a gigantic saturniid moth, has the potential to be a novel lepidopteran model species. Samia ricini is far more resistant to diseases than the current model species Bombyx mori, and therefore can be more easily reared. In addition, genetic resources available for S. ricini rival those for B. mori: at least 26 ecoraces of S. ricini are reported and S. ricini can hybridize with wild Samia species, which are distributed throughout Asian countries, and produce fertile progenies. Physiological traits such as food preference, integument colour and larval spot pattern differ among S. ricini strains and wild Samia species so that those traits can be targeted in forward genetic analyses. To facilitate genetic research in S. ricini, we determined its whole genome sequence. The assembled genome of S. ricini was 458 Mb with 155 scaffolds, and the scaffold N50 length of the assembly was ~ 21 Mb. In total, 16,702 protein coding genes were predicted. While the S. ricini genome was mostly collinear with that of B. mori with some rearrangements and few S. ricini-specific genes were discovered, chorion genes and fibroin genes seemed to have expanded in the S. ricini lineage. As the first step of genetic analyses, causal genes for "Blue," "Yellow," "Spot," and "Red cocoon" phenotypes were mapped to chromosomes.
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Affiliation(s)
- Jung Lee
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Department of Life Science, Faculty of Science/Graduate School of Science, Gakushuin University, Tokyo, Japan
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Toru Shimada
- Department of Life Science, Faculty of Science/Graduate School of Science, Gakushuin University, Tokyo, Japan
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takashi Kiuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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44
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Talla V, Pierce AA, Adams KL, de Man TJB, Nallu S, Villablanca FX, Kronforst MR, de Roode JC. Genomic evidence for gene flow between monarchs with divergent migratory phenotypes and flight performance. Mol Ecol 2020; 29:2567-2582. [PMID: 32542770 DOI: 10.1111/mec.15508] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 06/05/2020] [Indexed: 12/24/2022]
Abstract
Monarch butterflies are known for their spectacular annual migration in eastern North America, with millions of monarchs flying up to 4,500 km to overwintering sites in central Mexico. Monarchs also live west of the Rocky Mountains, where they travel shorter distances to overwinter along the Pacific Coast. It is often assumed that eastern and western monarchs form distinct evolutionary units, but genomic studies to support this notion are lacking. We used a tethered flight mill to show that migratory eastern monarchs have greater flight performance than western monarchs, consistent with their greater migratory distances. However, analysing more than 20 million SNPs in 43 monarch genomes, we found no evidence for genomic differentiation between eastern and western monarchs. Genomic analysis also showed identical and low levels of genetic diversity, and demographic analyses indicated similar effective population sizes and ongoing gene flow between eastern and western monarchs. Gene expression analysis of a subset of candidate genes during active flight revealed differential gene expression related to nonmuscular motor activity. Our results demonstrate that eastern and western monarchs maintain migratory differences despite ongoing gene flow, and suggest that migratory differences between eastern and western monarchs are not driven by select major-effects alleles. Instead, variation in migratory distance and destination may be driven by environmentally induced differential gene expression or by many alleles of small effect.
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Affiliation(s)
- Venkat Talla
- Department of Biology, Emory University, Atlanta, GA, USA
| | | | - Kandis L Adams
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Tom J B de Man
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Sumitha Nallu
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Francis X Villablanca
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA, USA
| | - Marcus R Kronforst
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
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45
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Lenormand T, Fyon F, Sun E, Roze D. Sex Chromosome Degeneration by Regulatory Evolution. Curr Biol 2020; 30:3001-3006.e5. [PMID: 32559446 DOI: 10.1016/j.cub.2020.05.052] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/07/2020] [Accepted: 05/14/2020] [Indexed: 12/31/2022]
Abstract
In many species, the Y (or W) sex chromosome is degenerate. Current theory proposes that this degeneration follows the arrest of recombination and results from the accumulation of deleterious mutations due to selective interference-the inefficacy of natural selection on non-recombining genomic regions. This theory requires very few assumptions, but it does not robustly predict fast erosion of the Y (or W) in large populations or the stepwise degeneration of several small non-recombining strata. We propose a new mechanism for Y/W erosion that works over faster timescales, in large populations, and for small non-recombining regions (down to a single sex-linked gene). The mechanism is based on the instability and divergence of cis-regulatory sequences in non-recombining genome regions, which become selectively haploidized to mask deleterious mutations on coding sequences. This haploidization is asymmetric, because cis-regulators on the X cannot be silenced (otherwise there would be no expression in females). This process causes rapid Y/W degeneration and simultaneous evolution of dosage compensation, provided that autosomal trans-regulatory sequences with sex-limited effects are available to compensate for cis-regulatory divergence. Although this "degeneration by regulatory evolution" does not require selective interference, both processes may act in concert to further accelerate Y degeneration.
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Affiliation(s)
- Thomas Lenormand
- CEFE, Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier 34293, France; Radcliffe Institute, Harvard University, Cambridge, MA 02138, USA.
| | - Frederic Fyon
- CEFE, Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier 34293, France
| | - Eric Sun
- Radcliffe Institute, Harvard University, Cambridge, MA 02138, USA
| | - Denis Roze
- CNRS, UMI 3614, Roscoff 29680, France; Sorbonne Université, Station Biologique de Roscoff, France
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46
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Abstract
Diverse dosage compensation mechanisms have evolved across species to equalize gene expression between sexes and between the sex chromosomes and autosomes. New results show that two opposite modes of dosage compensation can occur within one species, the monarch butterfly.
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Affiliation(s)
- Jingyue Duan
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Erica N Larschan
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI 02912, USA.
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