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Yu XR, Chen X, Bai QR, Mu MY, Tang LD, Smagghe G, Zang LS. Chromosome-level genome assembly and sex chromosome identification of the pink stem borer, Sesamia inferens (Lepidoptera: Noctuidae). Sci Data 2024; 11:810. [PMID: 39039110 PMCID: PMC11263549 DOI: 10.1038/s41597-024-03625-1] [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: 12/19/2023] [Accepted: 07/09/2024] [Indexed: 07/24/2024] Open
Abstract
The pink stem borer, Sesamia inferens Walker (Lepidoptera: Noctuidae), is one of the most notorious pest insects of rice and maize crops in the world. Here, we generated a high-quality chromosome-level genome assembly of S. inferens, using a combination of Illumina, PacBio HiFi and Hi-C technologies. The total assembly size was 973.18 Mb with a contig N50 of 33.39 Mb, anchored to 31 chromosomes, revealing a karyotype of 30 + Z. The BUSCO analysis indicated a high completeness of 98.90% (n = 5286), including 5172 (97.8%) single-copy BUSCOs and 58 (1.1%) duplicated BUSCOs. The genome contains 58.59% (564.58 Mb) repeat elements and 26628 predicted protein-coding genes. The chromosome-level genome assembly of S. inferens provides in-depth knowledge and will be a helpful resource for the Lepidoptera and pest control research communities.
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Affiliation(s)
- Xiao-Rui Yu
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Xu Chen
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Qing-Rong Bai
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
| | | | - Liang-De Tang
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Guy Smagghe
- Institute of Entomology, Guizhou University, Guiyang, 550025, China
| | - Lian-Sheng Zang
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
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2
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Decroly T, Vila R, Lohse K, Mackintosh A. Rewinding the Ratchet: Rare Recombination Locally Rescues Neo-W Degeneration and Generates Plateaus of Sex-Chromosome Divergence. Mol Biol Evol 2024; 41:msae124. [PMID: 38950035 PMCID: PMC11232697 DOI: 10.1093/molbev/msae124] [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: 01/19/2024] [Revised: 04/26/2024] [Accepted: 05/28/2024] [Indexed: 07/03/2024] Open
Abstract
Natural selection is less efficient in the absence of recombination. As a result, nonrecombining sequences, such as sex chromosomes, tend to degenerate over time. Although the outcomes of recombination arrest are typically observed after many millions of generations, recent neo-sex chromosomes can give insight into the early stages of this process. Here, we investigate the evolution of neo-sex chromosomes in the Spanish marbled white butterfly, Melanargia ines, where a Z-autosome fusion has turned the homologous autosome into a nonrecombining neo-W chromosome. We show that these neo-sex chromosomes are likely limited to the Iberian population of M. ines, and that they arose around the time when this population split from North-African populations, around 1.5 million years ago. Recombination arrest of the neo-W chromosome has led to an excess of premature stop-codons and frame-shift mutations, and reduced gene expression compared to the neo-Z chromosome. Surprisingly, we identified two regions of ∼1 Mb at one end of the neo-W that are both less diverged from the neo-Z and less degraded than the rest of the chromosome, suggesting a history of rare but repeated genetic exchange between the two neo-sex chromosomes. These plateaus of neo-sex chromosome divergence suggest that neo-W degradation can be locally reversed by rare recombination between neo-W and neo-Z chromosomes.
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Affiliation(s)
- Thomas Decroly
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, ESP-08003 Barcelona, Spain
| | - Konrad Lohse
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Alexander Mackintosh
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
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3
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Rueda-M N, Pardo-Diaz C, Montejo-Kovacevich G, McMillan WO, Kozak KM, Arias CF, Ready J, McCarthy S, Durbin R, Jiggins CD, Meier JI, Salazar C. Genomic evidence reveals three W-autosome fusions in Heliconius butterflies. PLoS Genet 2024; 20:e1011318. [PMID: 39024186 PMCID: PMC11257349 DOI: 10.1371/journal.pgen.1011318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/24/2024] [Indexed: 07/20/2024] Open
Abstract
Sex chromosomes are evolutionarily labile in many animals and sometimes fuse with autosomes, creating so-called neo-sex chromosomes. Fusions between sex chromosomes and autosomes have been proposed to reduce sexual conflict and to promote adaptation and reproductive isolation among species. Recently, advances in genomics have fuelled the discovery of such fusions across the tree of life. Here, we discovered multiple fusions leading to neo-sex chromosomes in the sapho subclade of the classical adaptive radiation of Heliconius butterflies. Heliconius butterflies generally have 21 chromosomes with very high synteny. However, the five Heliconius species in the sapho subclade show large variation in chromosome number ranging from 21 to 60. We find that the W chromosome is fused with chromosome 4 in all of them. Two sister species pairs show subsequent fusions between the W and chromosomes 9 or 14, respectively. These fusions between autosomes and sex chromosomes make Heliconius butterflies an ideal system for studying the role of neo-sex chromosomes in adaptive radiations and the degeneration of sex chromosomes over time. Our findings emphasize the capability of short-read resequencing to detect genomic signatures of fusion events between sex chromosomes and autosomes even when sex chromosomes are not explicitly assembled.
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Affiliation(s)
- Nicol Rueda-M
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Carolina Pardo-Diaz
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | | | - Krzysztof M. Kozak
- Smithsonian Tropical Research Institute, Panama City, Panama
- Museum of Vertebrate Zoology, Berkeley, California, United States of America
| | - Carlos F. Arias
- Smithsonian Tropical Research Institute, Panama City, Panama
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, Washington DC, United States of America
| | - Jonathan Ready
- Institute for Biological Sciences, Federal University of Pará - UFPA, Belém, Brazil
- Centre for Advanced Studies of Biodiversity - CEABIO, Belém, Brazil
| | - Shane McCarthy
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Richard Durbin
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Joana I. Meier
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
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4
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Dai W, Mank JE, Ban L. Gene gain and loss from the Asian corn borer W chromosome. BMC Biol 2024; 22:102. [PMID: 38693535 PMCID: PMC11064298 DOI: 10.1186/s12915-024-01902-4] [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: 01/17/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024] Open
Abstract
BACKGROUND Sex-limited chromosomes Y and W share some characteristics, including the degeneration of protein-coding genes, enrichment of repetitive elements, and heterochromatin. However, although many studies have suggested that Y chromosomes retain genes related to male function, far less is known about W chromosomes and whether they retain genes related to female-specific function. RESULTS Here, we built a chromosome-level genome assembly of the Asian corn borer, Ostrinia furnacalis Guenée (Lepidoptera: Crambidae, Pyraloidea), an economically important pest in corn, from a female, including both the Z and W chromosome. Despite deep conservation of the Z chromosome across Lepidoptera, our chromosome-level W assembly reveals little conservation with available W chromosome sequence in related species or with the Z chromosome, consistent with a non-canonical origin of the W chromosome. The W chromosome has accumulated significant repetitive elements and experienced rapid gene gain from the remainder of the genome, with most genes exhibiting pseudogenization after duplication to the W. The genes that retain significant expression are largely enriched for functions in DNA recombination, the nucleosome, chromatin, and DNA binding, likely related to meiotic and mitotic processes within the female gonad. CONCLUSIONS Overall, our chromosome-level genome assembly supports the non-canonical origin of the W chromosome in O. furnacalis, which experienced rapid gene gain and loss, with the retention of genes related to female-specific function.
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Affiliation(s)
- Wenting Dai
- Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Liping Ban
- Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
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Wright CJ, Stevens L, Mackintosh A, Lawniczak M, Blaxter M. Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera. Nat Ecol Evol 2024; 8:777-790. [PMID: 38383850 PMCID: PMC11009112 DOI: 10.1038/s41559-024-02329-4] [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: 10/09/2023] [Accepted: 01/12/2024] [Indexed: 02/23/2024]
Abstract
Chromosomes are a central unit of genome organization. One-tenth of all described species on Earth are butterflies and moths, the Lepidoptera, which generally possess 31 chromosomes. However, some species display dramatic variation in chromosome number. Here we analyse 210 chromosomally complete lepidopteran genomes and show that the chromosomes of extant lepidopterans are derived from 32 ancestral linkage groups, which we term Merian elements. Merian elements have remained largely intact through 250 million years of evolution and diversification. Against this stable background, eight lineages have undergone extensive reorganization either through numerous fissions or a combination of fusion and fission events. Outside these lineages, fusions are rare and fissions are rarer still. Fusions often involve small, repeat-rich Merian elements and the sex-linked element. Our results reveal the constraints on genome architecture in Lepidoptera and provide a deeper understanding of chromosomal rearrangements in eukaryotic genome evolution.
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Affiliation(s)
| | - Lewis Stevens
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK.
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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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Ma L, Liu Q, Wei S, Liu S, Tian L, Song F, Duan Y, Cai W, Li H. Chromosome-level genome assembly of bean flower thrips Megalurothrips usitatus (Thysanoptera: Thripidae). Sci Data 2023; 10:252. [PMID: 37137922 PMCID: PMC10156705 DOI: 10.1038/s41597-023-02164-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
Bean flower thrips Megalurothrips usitatus is a staple pest of cowpea and other legumes and causes dramatic economic losses. Its small size allows for easy concealment, and large reproductive capacity easily leads to infestations. Despite the importance of a genome in developing novel management strategies, genetic studies on M. usitatus remain limited. Thus, we generated a chromosome-level M. usitatus genome using a combination of PacBio long read and Hi-C technologies. The assembled genome was 238.14 Mb with a scaffold N50 of 13.85 Mb. The final genome was anchored into 16 pseudo-chromosomes containing 14,000 genes, of which 91.74% were functionally annotated. Comparative genomic analyses revealed that expanded gene families were enriched in fatty acid metabolism and detoxification metabolism (ABC transporters), and contracted gene families were strongly associated with chitin-based cuticle development and sensory perception of taste. In conclusion, this high-quality genome provides an invaluable resource for us to understand the thrips' ecology and genetics, contributing to pest management.
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Affiliation(s)
- Ling Ma
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Qiaoqiao Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Shujun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Shanlin Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Li Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Yuange Duan
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
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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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10
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Höök L, Näsvall K, Vila R, Wiklund C, Backström N. High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.). Chromosome Res 2023; 31:2. [PMID: 36662301 PMCID: PMC9859909 DOI: 10.1007/s10577-023-09713-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/21/2023]
Abstract
Karyotypes are generally conserved between closely related species and large chromosome rearrangements typically have negative fitness consequences in heterozygotes, potentially driving speciation. In the order Lepidoptera, most investigated species have the ancestral karyotype and gene synteny is often conserved across deep divergence, although examples of extensive genome reshuffling have recently been demonstrated. The genus Leptidea has an unusual level of chromosome variation and rearranged sex chromosomes, but the extent of restructuring across the rest of the genome is so far unknown. To explore the genomes of the wood white (Leptidea) species complex, we generated eight genome assemblies using a combination of 10X linked reads and HiC data, and improved them using linkage maps for two populations of the common wood white (L. sinapis) with distinct karyotypes. Synteny analysis revealed an extensive amount of rearrangements, both compared to the ancestral karyotype and between the Leptidea species, where only one of the three Z chromosomes was conserved across all comparisons. Most restructuring was explained by fissions and fusions, while translocations appear relatively rare. We further detected several examples of segregating rearrangement polymorphisms supporting a highly dynamic genome evolution in this clade. Fusion breakpoints were enriched for LINEs and LTR elements, which suggests that ectopic recombination might be an important driver in the formation of new chromosomes. Our results show that chromosome count alone may conceal the extent of genome restructuring and we propose that the amount of genome evolution in Lepidoptera might still be underestimated due to lack of taxonomic sampling.
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Affiliation(s)
- L. Höök
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - K. Näsvall
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - R. Vila
- Butterfly Diversity and Evolution Lab, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - C. Wiklund
- Department of Zoology, Division of Ecology, Stockholm University, Stockholm, Sweden
| | - N. Backström
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
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11
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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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12
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Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots. Nat Commun 2022; 13:944. [PMID: 35177601 PMCID: PMC8854603 DOI: 10.1038/s41467-022-28585-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 01/26/2022] [Indexed: 12/13/2022] Open
Abstract
The karyotype of most birds has remained considerably stable during more than 100 million years’ evolution, except for some groups, such as parrots. The evolutionary processes and underlying genetic mechanism of chromosomal rearrangements in parrots, however, are poorly understood. Here, using chromosome-level assemblies of four parrot genomes, we uncover frequent chromosome fusions and fissions, with most of them occurring independently among lineages. The increased activities of chromosomal rearrangements in parrots are likely associated with parrot-specific loss of two genes, ALC1 and PARP3, that have known functions in the repair of double-strand breaks and maintenance of genome stability. We further find that the fusion of the ZW sex chromosomes and chromosome 11 has created a pair of neo-sex chromosomes in the ancestor of parrots, and the chromosome 25 has been further added to the sex chromosomes in monk parakeet. Together, the combination of our genomic and cytogenetic analyses characterizes the complex evolutionary history of chromosomal rearrangements and sex chromosomes in parrots. Parrots have undergone substantial karyotype evolution compared to most other birds. Here, Huang et al. analyze chromosome-level genome assemblies for four parrot species and elucidate the complex evolutionary history of parrot chromosomes.
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13
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Ranz JM, González PM, Su RN, Bedford SJ, Abreu-Goodger C, Markow T. Multiscale analysis of the randomization limits of the chromosomal gene organization between Lepidoptera and Diptera. Proc Biol Sci 2022; 289:20212183. [PMID: 35042416 PMCID: PMC8767184 DOI: 10.1098/rspb.2021.2183] [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] [Received: 10/01/2021] [Accepted: 12/13/2021] [Indexed: 11/12/2022] Open
Abstract
How chromosome gene organization and gene content evolve among distantly related and structurally malleable genomes remains unresolved. This is particularly the case when considering different insect orders. We have compared the highly contiguous genome assemblies of the lepidopteran Danaus plexippus and the dipteran Drosophila melanogaster, which shared a common ancestor around 290 Ma. The gene content of 23 out of 30 D. plexippus chromosomes was significantly associated with one or two of the six chromosomal elements of the Drosophila genome, denoting common ancestry. Despite the phylogenetic distance, 9.6% of the 1-to-1 orthologues still reside within the same ancestral genome neighbourhood. Furthermore, the comparison D. plexippus-Bombyx mori indicated that the rates of chromosome repatterning are lower in Lepidoptera than in Diptera, although still within the same order of magnitude. Concordantly, 14 developmental gene clusters showed a higher tendency to retain full or partial clustering in D. plexippus, further supporting that the physical association between the SuperHox and NK clusters existed in the ancestral bilaterian. Our results illuminate the scope and limits of the evolution of the gene organization and content of the ancestral chromosomes to the Lepidoptera and Diptera while helping reconstruct portions of the genome in their most recent common ancestor.
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Affiliation(s)
- José M. Ranz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine CA 92647, USA
| | - Pablo M. González
- Unidad de Genómica Avanzada (Langebio), CINVESTAV, Irapuato GTO 36824, México
| | - Ryan N. Su
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine CA 92647, USA
| | - Sarah J. Bedford
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine CA 92647, USA
| | - Cei Abreu-Goodger
- Unidad de Genómica Avanzada (Langebio), CINVESTAV, Irapuato GTO 36824, México
| | - 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
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14
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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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15
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Hejníčková M, Dalíková M, Potocký P, Tammaru T, Trehubenko M, Kubíčková S, Marec F, Zrzavá M. Degenerated, Undifferentiated, Rearranged, Lost: High Variability of Sex Chromosomes in Geometridae (Lepidoptera) Identified by Sex Chromatin. Cells 2021; 10:cells10092230. [PMID: 34571879 PMCID: PMC8468057 DOI: 10.3390/cells10092230] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 02/04/2023] Open
Abstract
Sex chromatin is a conspicuous body that occurs in polyploid nuclei of most lepidopteran females and consists of numerous copies of the W sex chromosome. It is also a cytogenetic tool used to rapidly assess the W chromosome presence in Lepidoptera. However, certain chromosomal features could disrupt the formation of sex chromatin and lead to the false conclusion that the W chromosome is absent in the respective species. Here we tested the sex chromatin presence in 50 species of Geometridae. In eight selected species with either missing, atypical, or normal sex chromatin patterns, we performed a detailed karyotype analysis by means of comparative genomic hybridization (CGH) and fluorescence in situ hybridization (FISH). The results showed a high diversity of W chromosomes and clarified the reasons for atypical sex chromatin, including the absence or poor differentiation of W, rearrangements leading to the neo-W emergence, possible association with the nucleolus, and the existence of multiple W chromosomes. In two species, we detected intraspecific variability in the sex chromatin status and sex chromosome constitution. We show that the sex chromatin is not a sufficient marker of the W chromosome presence, but it may be an excellent tool to pinpoint species with atypical sex chromosomes.
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Affiliation(s)
- Martina Hejníčková
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (M.H.); (M.D.); (M.T.)
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (P.P.); (F.M.)
| | - Martina Dalíková
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (M.H.); (M.D.); (M.T.)
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (P.P.); (F.M.)
| | - Pavel Potocký
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (P.P.); (F.M.)
| | - Toomas Tammaru
- Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014 Tartu, Estonia;
| | - Marharyta Trehubenko
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (M.H.); (M.D.); (M.T.)
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (P.P.); (F.M.)
| | - Svatava Kubíčková
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic;
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (P.P.); (F.M.)
| | - Magda Zrzavá
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (M.H.); (M.D.); (M.T.)
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic; (P.P.); (F.M.)
- Correspondence:
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16
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Baiz MD, Tucker PK, Mueller JL, Cortés-Ortiz L. X-Linked Signature of Reproductive Isolation in Humans is Mirrored in a Howler Monkey Hybrid Zone. J Hered 2021; 111:419-428. [PMID: 32725191 PMCID: PMC7525826 DOI: 10.1093/jhered/esaa021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Indexed: 12/13/2022] Open
Abstract
Reproductive isolation is a fundamental step in speciation. While sex chromosomes have been linked to reproductive isolation in many model systems, including hominids, genetic studies of the contribution of sex chromosome loci to speciation for natural populations are relatively sparse. Natural hybrid zones can help identify genomic regions contributing to reproductive isolation, like hybrid incompatibility loci, since these regions exhibit reduced introgression between parental species. Here, we use a primate hybrid zone (Alouatta palliata × Alouatta pigra) to test for reduced introgression of X-linked SNPs compared to autosomal SNPs. To identify X-linked sequence in A. palliata, we used a sex-biased mapping approach with whole-genome re-sequencing data. We then used genomic cline analysis with reduced-representation sequence data for parental A. palliata and A. pigra individuals and hybrids (n = 88) to identify regions with non-neutral introgression. We identified ~26 Mb of non-repetitive, putatively X-linked genomic sequence in A. palliata, most of which mapped collinearly to the marmoset and human X chromosomes. We found that X-linked SNPs had reduced introgression and an excess of ancestry from A. palliata as compared to autosomal SNPs. One outlier region with reduced introgression overlaps a previously described "desert" of archaic hominin ancestry on the human X chromosome. These results are consistent with a large role for the X chromosome in speciation across animal taxa and further, suggest shared features in the genomic basis of the evolution of reproductive isolation in primates.
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Affiliation(s)
- Marcella D Baiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI.,Department of Biology, Pennsylvania State University, University Park, PA
| | - Priscilla K Tucker
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Jacob L Mueller
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | - Liliana Cortés-Ortiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI
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17
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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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18
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Tan WH, Talla V, Mongue AJ, de Roode JC, Gerardo NM, Walters JR. Population genomics reveals variable patterns of immune gene evolution in monarch butterflies (Danaus plexippus). Mol Ecol 2021; 30:4381-4391. [PMID: 34245613 DOI: 10.1111/mec.16071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/27/2022]
Abstract
Humoral and cellular immune responses provide animals with major defences against harmful pathogens. While it is often assumed that immune genes undergo rapid diversifying selection, this assumption has not been tested in many species. Moreover, it is likely that different classes of immune genes experience different levels of evolutionary constraint, resulting in varying selection patterns. We examined the evolutionary patterns for a set of 91 canonical immune genes of North American monarch butterflies (Danaus plexippus), using as an outgroup the closely related soldier butterfly (Danaus eresimus). As a comparison to these immune genes, we selected a set of control genes that were paired with each immune for approximate size and genomic location. As a whole, these immune genes had a significant but modest reduction in Tajima's D relative to paired-control genes, but otherwise did not show distinct patterns of population genetic variation or evolutionary rates. When further partitioning these immune genes into four functional classes (recognition, signalling, modulation, and effector), we found distinct differences among these groups. Relative to control genes, recognition genes exhibit increased nonsynonymous diversity and divergence, suggesting reduced constraints on evolution, and supporting the notion that coevolution with pathogens results in diversifying selection. In contrast, signalling genes showed an opposite pattern of reduced diversity and divergence, suggesting evolutionary constraints and conservation. Modulator and effector genes showed no statistical differences from controls. These results are consistent with patterns found in immune genes in fruit flies and Pieris butterflies, suggesting that consistent selective pressures on different classes of immune genes broadly govern the evolution of innate immunity among insects.
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Affiliation(s)
- Wen-Hao Tan
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Venkat Talla
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Andrew J Mongue
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | | | | | - James R Walters
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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19
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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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20
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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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21
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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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22
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Sember A, Pappová M, Forman M, Nguyen P, Marec F, Dalíková M, Divišová K, Doležálková-Kaštánková M, Zrzavá M, Sadílek D, Hrubá B, Král J. Patterns of Sex Chromosome Differentiation in Spiders: Insights from Comparative Genomic Hybridisation. Genes (Basel) 2020; 11:E849. [PMID: 32722348 PMCID: PMC7466014 DOI: 10.3390/genes11080849] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 01/21/2023] Open
Abstract
Spiders are an intriguing model to analyse sex chromosome evolution because of their peculiar multiple X chromosome systems. Y chromosomes were considered rare in this group, arising after neo-sex chromosome formation by X chromosome-autosome rearrangements. However, recent findings suggest that Y chromosomes are more common in spiders than previously thought. Besides neo-sex chromosomes, they are also involved in the ancient X1X2Y system of haplogyne spiders, whose origin is unknown. Furthermore, spiders seem to exhibit obligatorily one or two pairs of cryptic homomorphic XY chromosomes (further cryptic sex chromosome pairs, CSCPs), which could represent the ancestral spider sex chromosomes. Here, we analyse the molecular differentiation of particular types of spider Y chromosomes in a representative set of ten species by comparative genomic hybridisation (CGH). We found a high Y chromosome differentiation in haplogyne species with X1X2Y system except for Loxosceles spp. CSCP chromosomes exhibited generally low differentiation. Possible mechanisms and factors behind the observed patterns are discussed. The presence of autosomal regions marked predominantly or exclusively with the male or female probe was also recorded. We attribute this pattern to intraspecific variability in the copy number and distribution of certain repetitive DNAs in spider genomes, pointing thus to the limits of CGH in this arachnid group. In addition, we confirmed nonrandom association of chromosomes belonging to particular CSCPs at spermatogonial mitosis and spermatocyte meiosis and their association with multiple Xs throughout meiosis. Taken together, our data suggest diverse evolutionary pathways of molecular differentiation in different types of spider Y chromosomes.
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Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic;
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Michaela Pappová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Martin Forman
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Petr Nguyen
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (P.N.); (M.D.); (M.Z.)
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic;
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic;
| | - Martina Dalíková
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (P.N.); (M.D.); (M.Z.)
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic;
| | - Klára Divišová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Marie Doležálková-Kaštánková
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic;
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Magda Zrzavá
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (P.N.); (M.D.); (M.Z.)
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic;
| | - David Sadílek
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
| | - Barbora Hrubá
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Jiří Král
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
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23
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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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24
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Meisel RP. Evolution of Sex Determination and Sex Chromosomes: A Novel Alternative Paradigm. Bioessays 2020; 42:e1900212. [DOI: 10.1002/bies.201900212] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 05/11/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Richard P. Meisel
- Department of Biology and Biochemistry University of Houston 3455 Cullen Blvd Houston TX 77204‐5001 USA
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25
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Deng Z, Zhang Y, Zhang M, Huang J, Li C, Ni X, Li X. Characterization of the First W-Specific Protein-Coding Gene for Sex Identification in Helicoverpa armigera. Front Genet 2020; 11:649. [PMID: 32636875 PMCID: PMC7317607 DOI: 10.3389/fgene.2020.00649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 05/28/2020] [Indexed: 12/11/2022] Open
Abstract
Helicoverpa armigera is a globally-important crop pest with a WZ (female)/ZZ (male) sex chromosome system. The absence of discernible sexual dimorphism in its egg and larval stages makes it impossible to address any sex-related theoretical and applied questions before pupation unless a W-specific sequence marker is available for sex diagnosis. To this end, we used one pair of morphologically pre-sexed pupae to PCR-screen 17 non-transposon transcripts selected from 4855 W-linked candidate reads identified by mapping a publicly available egg transcriptome of both sexes to the male genome of this species and detected the read SRR1015458.67499 only in the female pupa. Subsequent PCR screenings of this read and the previously reported female-specific RAPD (random amplified polymorphic DNA) marker AF18 with ten more pairs of pre-sexed pupae and different annealing positions and/or temperatures as well as its co-occurrence with the female-specific transcript splicing isoforms of doublesex gene of H. armigera (Hadsx) and amplification and sequencing of their 5′ unknown flanking sequences in three additional pairs of pre-sexed pupae verified that SRR1015458.67499 is a single copy protein-coding gene unique to W chromosome (named GUW1) while AF18 is a multicopy MITE transposon located on various chromosomes. Test application of GUW1 as a marker to sex 30 neonates of H. armigera yielded a female/male ratio of 1.14: 1.00. Both GUW1 and Hadsx splicing isoforms assays revealed that the H. armigera embryo cell line QB-Ha-E-1 is a male cell line. Taken together, GUW1 is not only a reliable DNA marker for sexing all stages of H. armigera and its cell lines, but also represents the first W-specific protein-coding gene in lepidopterans.
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Affiliation(s)
- Zhongyuan Deng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yakun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Min Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jinyong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Changyou Li
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Xinzhi Ni
- Agricultural Research Service, U.S. Department of Agriculture, Crop Genetics and Breeding Research Unit, University of Georgia - Tifton Campus, Tifton, GA, United States
| | - Xianchun Li
- Department of Entomology and BIO5 Institute, University of Arizona, Tucson, AZ, United States
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26
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Yoshido A, Šíchová J, Pospíšilová K, Nguyen P, Voleníková A, Šafář J, Provazník J, Vila R, Marec F. Evolution of multiple sex-chromosomes associated with dynamic genome reshuffling in Leptidea wood-white butterflies. Heredity (Edinb) 2020; 125:138-154. [PMID: 32518391 PMCID: PMC7426936 DOI: 10.1038/s41437-020-0325-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022] Open
Abstract
Sex-chromosome systems tend to be highly conserved and knowledge about their evolution typically comes from macroevolutionary inference. Rapidly evolving complex sex-chromosome systems represent a rare opportunity to study the mechanisms of sex-chromosome evolution at unprecedented resolution. Three cryptic species of wood-white butterflies—Leptidea juvernica, L. sinapis and L. reali—have each a unique set of multiple sex-chromosomes with 3–4 W and 3–4 Z chromosomes. Using a transcriptome-based microarray for comparative genomic hybridisation (CGH) and a library of bacterial artificial chromosome (BAC) clones, both developed in L. juvernica, we identified Z-linked Leptidea orthologs of Bombyx mori genes and mapped them by fluorescence in situ hybridisation (FISH) with BAC probes on multiple Z chromosomes. In all three species, we determined synteny blocks of autosomal origin and reconstructed the evolution of multiple sex-chromosomes. In addition, we identified W homologues of Z-linked orthologs and characterised their molecular differentiation. Our results suggest that the multiple sex-chromosome system evolved in a common ancestor as a result of dynamic genome reshuffling through repeated rearrangements between the sex chromosomes and autosomes, including translocations, fusions and fissions. Thus, the initial formation of neo-sex chromosomes could not have played a role in reproductive isolation between these Leptidea species. However, the subsequent species-specific fissions of several neo-sex chromosomes could have contributed to their reproductive isolation. Then, significantly increased numbers of Z-linked genes and independent neo-W chromosome degeneration could accelerate the accumulation of genetic incompatibilities between populations and promote their divergence resulting in speciation.
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Affiliation(s)
- Atsuo Yoshido
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Jindra Šíchová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Kristýna Pospíšilová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Anna Voleníková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Jan Provazník
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Pg. Marítim de la Barceloneta 37, 08003, Barcelona, Spain
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic.
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27
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Martin SH, Singh KS, Gordon IJ, Omufwoko KS, Collins S, Warren IA, Munby H, Brattström O, Traut W, Martins DJ, Smith DAS, Jiggins CD, Bass C, ffrench-Constant RH. Whole-chromosome hitchhiking driven by a male-killing endosymbiont. PLoS Biol 2020; 18:e3000610. [PMID: 32108180 PMCID: PMC7046192 DOI: 10.1371/journal.pbio.3000610] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/23/2020] [Indexed: 12/30/2022] Open
Abstract
Neo-sex chromosomes are found in many taxa, but the forces driving their emergence and spread are poorly understood. The female-specific neo-W chromosome of the African monarch (or queen) butterfly Danaus chrysippus presents an intriguing case study because it is restricted to a single 'contact zone' population, involves a putative colour patterning supergene, and co-occurs with infection by the male-killing endosymbiont Spiroplasma. We investigated the origin and evolution of this system using whole genome sequencing. We first identify the 'BC supergene', a broad region of suppressed recombination across nearly half a chromosome, which links two colour patterning loci. Association analysis suggests that the genes yellow and arrow in this region control the forewing colour pattern differences between D. chrysippus subspecies. We then show that the same chromosome has recently formed a neo-W that has spread through the contact zone within approximately 2,200 years. We also assembled the genome of the male-killing Spiroplasma, and find that it shows perfect genealogical congruence with the neo-W, suggesting that the neo-W has hitchhiked to high frequency as the male-killer has spread through the population. The complete absence of female crossing-over in the Lepidoptera causes whole-chromosome hitchhiking of a single neo-W haplotype, carrying a single allele of the BC supergene and dragging multiple non-synonymous mutations to high frequency. This has created a population of infected females that all carry the same recessive colour patterning allele, making the phenotypes of each successive generation highly dependent on uninfected male immigrants. Our findings show how hitchhiking can occur between the physically unlinked genomes of host and endosymbiont, with dramatic consequences.
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Affiliation(s)
- Simon H. Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Kumar Saurabh Singh
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, United Kingdom
| | - Ian J. Gordon
- Center of Excellence in Biodiversity and Natural Resource Management, University of Rwanda, Huye, Rwanda
| | - Kennedy Saitoti Omufwoko
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States of America
- Mpala Research Centre, Nanyuki, Kenya
| | - Steve Collins
- African Butterfly Research Institute, Nairobi, Kenya
| | - Ian A. Warren
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Hannah Munby
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Oskar Brattström
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Walther Traut
- Institut für Biologie, Universität Lübeck, Lübeck, Germany
| | - Dino J. Martins
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States of America
- Mpala Research Centre, Nanyuki, Kenya
| | | | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, United Kingdom
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28
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Hejníčková M, Koutecký P, Potocký P, Provazníková I, Voleníková A, Dalíková M, Visser S, Marec F, Zrzavá M. Absence of W Chromosome in Psychidae Moths and Implications for the Theory of Sex Chromosome Evolution in Lepidoptera. Genes (Basel) 2019; 10:E1016. [PMID: 31817557 PMCID: PMC6947638 DOI: 10.3390/genes10121016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 11/17/2022] Open
Abstract
Moths and butterflies (Lepidoptera) are the largest group with heterogametic females. Although the ancestral sex chromosome system is probably Z0/ZZ, most lepidopteran species have the W chromosome. When and how the W chromosome arose remains elusive. Existing hypotheses place the W origin either at the common ancestor of Ditrysia and Tischeriidae, or prefer independent origins of W chromosomes in these two groups. Due to their phylogenetic position at the base of Ditrysia, bagworms (Psychidae) play an important role in investigating the W chromosome origin. Therefore, we examined the W chromosome status in three Psychidae species, namely Proutiabetulina, Taleporiatubulosa, and Diplodomalaichartingella, using both classical and molecular cytogenetic methods such as sex chromatin assay, comparative genomic hybridization (CGH), and male vs. female genome size comparison by flow cytometry. In females of all three species, no sex chromatin was found, no female-specific chromosome regions were revealed by CGH, and a Z-chromosome univalent was observed in pachytene oocytes. In addition, the genome size of females was significantly smaller than males. Overall, our study provides strong evidence for the absence of the W chromosome in Psychidae, thus supporting the hypothesis of two independent W chromosome origins in Tischeriidae and in advanced Ditrysia.
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Affiliation(s)
- Martina Hejníčková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Petr Koutecký
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Pavel Potocký
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005 České Budějovice, Czech Republic
| | - Irena Provazníková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Anna Voleníková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Martina Dalíková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Sander Visser
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005 České Budějovice, Czech Republic
| | - Magda Zrzavá
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
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29
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Gu L, Reilly PF, Lewis JJ, Reed RD, Andolfatto P, Walters JR. Dichotomy of Dosage Compensation along the Neo Z Chromosome of the Monarch Butterfly. Curr Biol 2019; 29:4071-4077.e3. [PMID: 31735674 DOI: 10.1016/j.cub.2019.09.056] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 10/25/2022]
Abstract
Mechanisms of sex chromosome dosage compensation (SCDC) differ strikingly among animals. In Drosophila flies, chromosome-wide transcription is doubled from the single X chromosome in hemizygous (XY) males, whereas in Caenorhabditis nematodes, expression is halved for both X copies in homozygous (XX) females [1, 2]. Unlike other female-heterogametic (WZ female and ZZ male) animals, moths and butterflies exhibit sex chromosome dosage compensation patterns typically seen only in male-heterogametic species [3]. The monarch butterfly carries a newly derived Z chromosome segment that arose from an autosomal fusion with the ancestral Z [4]. Using a highly contiguous genome assembly, we show that gene expression is balanced between sexes along the entire Z chromosome but with distinct modes of compensation on the two segments. On the ancestral Z segment, depletion of H4K16ac corresponds to nearly halving of biallelic transcription in males, a pattern convergent to nematodes. Conversely, the newly derived Z segment shows a Drosophila-like mode of compensation, with enriched H4K16ac levels corresponding to doubled monoallelic transcription in females. Our work reveals that, contrary to the expectation of co-opting regulatory mechanisms readily in place, the evolution of plural modes of dosage compensation is also possible along a single sex chromosome within a species.
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Affiliation(s)
- Liuqi Gu
- Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS 66045, USA.
| | - Patrick F Reilly
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - James J Lewis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - James R Walters
- Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS 66045, USA.
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30
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Schemberger MO, Nascimento VD, Coan R, Ramos É, Nogaroto V, Ziemniczak K, Valente GT, Moreira-Filho O, Martins C, Vicari MR. DNA transposon invasion and microsatellite accumulation guide W chromosome differentiation in a Neotropical fish genome. Chromosoma 2019; 128:547-560. [DOI: 10.1007/s00412-019-00721-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/25/2019] [Accepted: 08/06/2019] [Indexed: 11/28/2022]
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31
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Hill J, Rastas P, Hornett EA, Neethiraj R, Clark N, Morehouse N, de la Paz Celorio-Mancera M, Cols JC, Dircksen H, Meslin C, Keehnen N, Pruisscher P, Sikkink K, Vives M, Vogel H, Wiklund C, Woronik A, Boggs CL, Nylin S, Wheat CW. Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution. SCIENCE ADVANCES 2019; 5:eaau3648. [PMID: 31206013 PMCID: PMC6561736 DOI: 10.1126/sciadv.aau3648] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 05/03/2019] [Indexed: 05/04/2023]
Abstract
Chromosome evolution presents an enigma in the mega-diverse Lepidoptera. Most species exhibit constrained chromosome evolution with nearly identical haploid chromosome counts and chromosome-level gene collinearity among species more than 140 million years divergent. However, a few species possess radically inflated chromosomal counts due to extensive fission and fusion events. To address this enigma of constraint in the face of an exceptional ability to change, we investigated an unprecedented reorganization of the standard lepidopteran chromosome structure in the green-veined white butterfly (Pieris napi). We find that gene content in P. napi has been extensively rearranged in large collinear blocks, which until now have been masked by a haploid chromosome number close to the lepidopteran average. We observe that ancient chromosome ends have been maintained and collinear blocks are enriched for functionally related genes suggesting both a mechanism and a possible role for selection in determining the boundaries of these genome-wide rearrangements.
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Affiliation(s)
- Jason Hill
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Corresponding author. (J.H.); (C.W.W.)
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Emily A. Hornett
- Department of Zoology, University of Cambridge, Cambridge, UK
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Ramprasad Neethiraj
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Nathan Clark
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Nathan Morehouse
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | | | - Jofre Carnicer Cols
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, 08028 Barcelona, Spain
- CREAF, Global Ecology Unit, Autonomous University of Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Heinrich Dircksen
- Functional Morphology, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Camille Meslin
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- INRA, Department of Sensory Ecology, Institute of Ecology and Environmental Sciences of Paris, Route de Saint-Cyr, 78026 Versailles Cedex, France
| | - Naomi Keehnen
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Peter Pruisscher
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Kristin Sikkink
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN 55108, USA
- Department of Biology, University of Mississippi, University, MS 38677, USA
| | - Maria Vives
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, 08028 Barcelona, Spain
- CREAF, Global Ecology Unit, Autonomous University of Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Christer Wiklund
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Alyssa Woronik
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
- Center for Developmental Genetics, Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Carol L. Boggs
- Department of Biological Sciences University of South Carolina, Columbia, SC 29208, USA
| | - Sören Nylin
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Christopher W. Wheat
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
- Corresponding author. (J.H.); (C.W.W.)
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Carabajal Paladino LZ, Provazníková I, Berger M, Bass C, Aratchige NS, López SN, Marec F, Nguyen P. Sex Chromosome Turnover in Moths of the Diverse Superfamily Gelechioidea. Genome Biol Evol 2019; 11:1307-1319. [PMID: 31028711 PMCID: PMC6486803 DOI: 10.1093/gbe/evz075] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2019] [Indexed: 01/22/2023] Open
Abstract
Sex chromosomes play a central role in genetics of speciation and their turnover was suggested to promote divergence. In vertebrates, sex chromosome-autosome fusions resulting in neo-sex chromosomes occur frequently in male heterogametic taxa (XX/XY), but are rare in groups with female heterogamety (WZ/ZZ). We examined sex chromosomes of seven pests of the diverse lepidopteran superfamily Gelechioidea and confirmed the presence of neo-sex chromosomes in their karyotypes. Two synteny blocks, which correspond to autosomes 7 (LG7) and 27 (LG27) in the ancestral lepidopteran karyotype exemplified by the linkage map of Biston betularia (Geometridae), were identified as sex-linked in the tomato leafminer, Tuta absoluta (Gelechiidae). Testing for sex-linkage performed in other species revealed that while LG7 fused to sex chromosomes in a common ancestor of all Gelechioidea, the second fusion between the resulting neo-sex chromosome and the other autosome is confined to the tribe Gnoreschemini (Gelechiinae). Our data accentuate an emerging pattern of high incidence of neo-sex chromosomes in Lepidoptera, the largest clade with WZ/ZZ sex chromosome system, which suggest that the paucity of neo-sex chromosomes is not an intrinsic feature of female heterogamety. Furthermore, LG7 contains one of the major clusters of UDP-glucosyltransferases, which are involved in the detoxification of plant secondary metabolites. Sex chromosome evolution in Gelechioidea thus supports an earlier hypothesis postulating that lepidopteran sex chromosome-autosome fusions can be driven by selection for association of Z-linked preference or host-independent isolation genes with larval performance and thus can contribute to ecological specialization and speciation of moths.
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Affiliation(s)
- Leonela Z Carabajal Paladino
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- The Pirbright Institute, Surrey, United Kingdom
| | - Irena Provazníková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Madeleine Berger
- Rothamsted Research, Department of Biointeractions and Crop Protection, Herts, United Kingdom
| | - Chris Bass
- University of Exeter, College of Life and Environmental Sciences, Biosciences, Penryn, Cornwall, United Kingdom
| | - Nayanie S Aratchige
- Coconut Research Institute of Sri Lanka, Crop Protection Division, Bandirippuwa Estate, Lunuwila, Sri Lanka
| | - Silvia N López
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Microbiología y Zoología Agrícola, Hurlingham, Buenos Aires, Argentina
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
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Insights into the Structure of the Spruce Budworm ( Choristoneura fumiferana) Genome, as Revealed by Molecular Cytogenetic Analyses and a High-Density Linkage Map. G3-GENES GENOMES GENETICS 2018; 8:2539-2549. [PMID: 29950429 PMCID: PMC6071596 DOI: 10.1534/g3.118.200263] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genome structure characterization can contribute to a better understanding of processes such as adaptation, speciation, and karyotype evolution, and can provide useful information for refining genome assemblies. We studied the genome of an important North American boreal forest pest, the spruce budworm, Choristoneura fumiferana, through a combination of molecular cytogenetic analyses and construction of a high-density linkage map based on single nucleotide polymorphism (SNP) markers obtained through a genotyping-by-sequencing (GBS) approach. Cytogenetic analyses using fluorescence in situ hybridization methods confirmed the haploid chromosome number of n = 30 in both sexes of C. fumiferana and showed, for the first time, that this species has a WZ/ZZ sex chromosome system. Synteny analysis based on a comparison of the Bombyx mori genome and the C. fumiferana linkage map revealed the presence of a neo-Z chromosome in the latter species, as previously reported for other tortricid moths. In this neo-Z chromosome, we detected an ABC transporter C2 (ABCC2) gene that has been associated with insecticide resistance. Sex-linkage of the ABCC2 gene provides a genomic context favorable to selection and rapid spread of resistance against Bacillus thuringiensis serotype kurstaki (Btk), the main insecticide used in Canada to control spruce budworm populations. Ultimately, the linkage map we developed, which comprises 3586 SNP markers distributed over 30 linkage groups for a total length of 1720.41 cM, will be a valuable tool for refining our draft assembly of the spruce budworm genome.
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Fraïsse C, Picard MAL, Vicoso B. The deep conservation of the Lepidoptera Z chromosome suggests a non-canonical origin of the W. Nat Commun 2017; 8:1486. [PMID: 29133797 PMCID: PMC5684275 DOI: 10.1038/s41467-017-01663-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/12/2017] [Indexed: 12/22/2022] Open
Abstract
Moths and butterflies (Lepidoptera) usually have a pair of differentiated WZ sex chromosomes. However, in most lineages outside of the division Ditrysia, as well as in the sister order Trichoptera, females lack a W chromosome. The W is therefore thought to have been acquired secondarily. Here we compare the genomes of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment of a B chromosome). We show that the gene content of the Z is highly conserved across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome fusion). Our comparative genomics analysis therefore supports the secondary acquisition of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme stability of well-differentiated sex chromosomes.
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Affiliation(s)
- Christelle Fraïsse
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, 3400, Austria
| | - Marion A L Picard
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, 3400, Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, 3400, Austria.
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Mongue AJ, Walters JR. The Z chromosome is enriched for sperm proteins in two divergent species of Lepidoptera. Genome 2017; 61:248-253. [PMID: 28961403 DOI: 10.1139/gen-2017-0068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genes that promote sexual conflict, such as those with a sex-limited fitness benefit, are expected to accumulate differentially on sex chromosomes relative to autosomes. Few tests of this hypothesis exist for male homogametic (ZZ) taxa, however, and most use RNA expression data to identify such genes. Here, we employ a different identification method by using proteomic analysis of sperm cells to identify genes with a sex-limited benefit. We tested for a bias in genomic location of sperm protein genes in two species of Lepidoptera. An excess of sperm protein genes was identified on the Z chromosomes of both the Carolina sphinx moth (Manduca sexta) and the monarch butterfly (Danaus plexippus). Taking into consideration a Z-autosome fusion in monarchs, we discover that the ancestrally sex-linked portion of the genome is the source of this enrichment, while the newly sex-linked portion still appears similar to autosomes in relative abundance of sperm protein genes. Together, these results point to an enrichment of male-beneficial genes on the Z chromosome and demonstrate the usefulness of proteomic datasets in sexual conflict research.
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Affiliation(s)
- Andrew J Mongue
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - James R Walters
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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