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Kalita AI, Keller Valsecchi CI. Dosage compensation in non-model insects - progress and perspectives. Trends Genet 2024:S0168-9525(24)00207-5. [PMID: 39341686 DOI: 10.1016/j.tig.2024.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 08/26/2024] [Accepted: 08/28/2024] [Indexed: 10/01/2024]
Abstract
In many multicellular eukaryotes, heteromorphic sex chromosomes are responsible for determining the sexual characteristics and reproductive functions of individuals. Sex chromosomes can cause a dosage imbalance between sexes, which in some species is re-equilibrated by dosage compensation (DC). Recent genomic advances have extended our understanding of DC mechanisms in insects beyond model organisms such as Drosophila melanogaster. We review current knowledge of insect DC, focusing on its conservation and divergence across orders, the evolutionary dynamics of neo-sex chromosomes, and the diversity of molecular mechanisms. We propose a framework to uncover DC regulators in non-model insects that relies on integrating evolutionary, genomic, and functional approaches. This comprehensive approach will facilitate a deeper understanding of the evolution and essentiality of gene regulatory mechanisms.
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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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Brůna T, Li H, Guhlin J, Honsel D, Herbold S, Stanke M, Nenasheva N, Ebel M, Gabriel L, Hoff KJ. Galba: genome annotation with miniprot and AUGUSTUS. BMC Bioinformatics 2023; 24:327. [PMID: 37653395 PMCID: PMC10472564 DOI: 10.1186/s12859-023-05449-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/21/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes. In addition, no transcriptome data is available for some genomes. RESULTS Various gene annotation tools have been developed but each has its limitations. Here, we introduce GALBA, a fully automated pipeline that utilizes miniprot, a rapid protein-to-genome aligner, in combination with AUGUSTUS to predict genes with high accuracy. Accuracy results indicate that GALBA is particularly strong in the annotation of large vertebrate genomes. We also present use cases in insects, vertebrates, and a land plant. GALBA is fully open source and available as a docker image for easy execution with Singularity in high-performance computing environments. CONCLUSIONS Our pipeline addresses the critical need for accurate gene annotation in newly sequenced genomes, and we believe that GALBA will greatly facilitate genome annotation for diverse organisms.
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Affiliation(s)
- Tomáš Brůna
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, 02215 MA USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, 02215 MA USA
| | - Joseph Guhlin
- Genomics Aotearoa and Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, Dunedin, 9016 New Zealand
| | - Daniel Honsel
- Institute of Computer Science, University of Göttingen, 37077 Göttingen, Germany
| | - Steffen Herbold
- Faculty for Computer Science and Mathematics, University of Passau, 94032 Passau, Germany
| | - Mario Stanke
- Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Natalia Nenasheva
- Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Matthis Ebel
- Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Lars Gabriel
- Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Katharina J. Hoff
- Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
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Brůna T, Li H, Guhlin J, Honsel D, Herbold S, Stanke M, Nenasheva N, Ebel M, Gabriel L, Hoff KJ. GALBA: Genome Annotation with Miniprot and AUGUSTUS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536199. [PMID: 37090650 PMCID: PMC10120627 DOI: 10.1101/2023.04.10.536199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes. In addition, no transcriptome data is available for some genomes. Various gene annotation tools have been developed but each has its limitations. Here, we introduce GALBA, a fully automated pipeline that utilizes miniprot, a rapid protein- to-genome aligner, in combination with AUGUSTUS to predict genes with high accuracy. Accuracy results indicate that GALBA is particularly strong in the annotation of large vertebrate genomes. We also present use cases in insects, vertebrates, and a previously unannotated land plant. GALBA is fully open source and available as a docker image for easy execution with Singularity in high-performance computing environments. Our pipeline addresses the critical need for accurate gene annotation in newly sequenced genomes, and we believe that GALBA will greatly facilitate genome annotation for diverse organisms.
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Affiliation(s)
- Tomáš Brůna
- US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA & Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph Guhlin
- Genomics Aotearoa and Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9016, New Zealand
| | - Daniel Honsel
- Institute of Computer Science, University of Göttingen, 37077 Göttingen, Germany
| | - Steffen Herbold
- Faculty for Computer Science and Mathematics, University of Passau, 94032 Passau, Germany
| | - Mario Stanke
- Institute of Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Natalia Nenasheva
- Institute of Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Matthis Ebel
- Institute of Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Lars Gabriel
- Institute of Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Katharina J. Hoff
- Institute of Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
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Hu QL, Ye YX, Zhuo JC, Huang HJ, Li JM, Zhang CX. Chromosome-level Assembly, Dosage Compensation and Sex-biased Gene Expression in the Small Brown Planthopper, Laodelphax striatellus. Genome Biol Evol 2022; 14:evac160. [PMID: 36317697 PMCID: PMC9651030 DOI: 10.1093/gbe/evac160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2022] [Indexed: 01/19/2024] Open
Abstract
In insects, sex chromosome differentiation often results in unequal gene dosages between sexes. Dosage compensation mechanisms evolve to balance gene expression, but the degree and mechanism of regulation often vary by insect species. In hemipteran species, the small brown planthopper (SBPH), Laodelphax striatellus, is an injurious crop pest, with a sex chromosome type XX in females and XO in males. This species offers the opportunity to study dosage compensation and sex-biased gene expression. In this study, we generated a chromosome-level genome of SBPH using Oxford Nanopore Technologies and high-throughput chromatin conformation capture (Hi-C) technology. We also sequenced RNA-seq data from 16 tissue samples to annotate the genome and analyze gene dosage compensation. We finally obtained a 510.2 megabases (Mb) genome with 99.12% of the scaffolds anchored on 15 chromosomes (14 autosomes and 1 X chromosome) and annotated 16,160 protein-coding genes based on full-length cDNA sequencing data. Furthermore, we found complete dosage compensation in all L. striatellus somatic tissues, but lack of dosage compensation in gonad tissue testis. We also found that female-biased genes were significantly enriched on the X chromosome in all tissues, whereas male-biased genes in gonad tissues were enriched on autosomes. This study not only provides a high-quality genome assembly but also lays a foundation for a better understanding of the sexual regulatory network in hemipteran insects.
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Affiliation(s)
- Qing-Ling Hu
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yu-Xuan Ye
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
| | - Ji-Chong Zhuo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Hai-Jian Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Chuan-Xi Zhang
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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Kim KW, De-Kayne R, Gordon IJ, Omufwoko KS, Martins DJ, Ffrench-Constant R, Martin SH. Stepwise evolution of a butterfly supergene via duplication and inversion. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210207. [PMID: 35694743 PMCID: PMC9189502 DOI: 10.1098/rstb.2021.0207] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Supergenes maintain adaptive clusters of alleles in the face of genetic mixing. Although usually attributed to inversions, supergenes can be complex, and reconstructing the precise processes that led to recombination suppression and their timing is challenging. We investigated the origin of the BC supergene, which controls variation in warning coloration in the African monarch butterfly, Danaus chrysippus. By generating chromosome-scale assemblies for all three alleles, we identified multiple structural differences. Most strikingly, we find that a region of more than 1 million bp underwent several segmental duplications at least 7.5 Ma. The resulting duplicated fragments appear to have triggered four inversions in surrounding parts of the chromosome, resulting in stepwise growth of the region of suppressed recombination. Phylogenies for the inversions are incongruent with the species tree and suggest that structural polymorphisms have persisted for at least 4.1 Myr. In addition to the role of duplications in triggering inversions, our results suggest a previously undescribed mechanism of recombination suppression through independent losses of divergent duplicated tracts. Overall, our findings add support for a stepwise model of supergene evolution involving a variety of structural changes. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
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Affiliation(s)
- Kang-Wook Kim
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rishi De-Kayne
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ian J Gordon
- Centre of Excellence in Biodiversity and Natural Resource Management, University of Rwanda, Huye Campus, Huye, Rwanda
| | | | - Dino J Martins
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, USA.,Mpala Research Centre, Nanyuki, Kenya
| | | | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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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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8
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Alfieri JM, Wang G, Jonika MM, Gill CA, Blackmon H, Athrey GN. A Primer for Single-Cell Sequencing in Non-Model Organisms. Genes (Basel) 2022; 13:380. [PMID: 35205423 PMCID: PMC8872538 DOI: 10.3390/genes13020380] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/12/2022] [Accepted: 02/17/2022] [Indexed: 02/05/2023] Open
Abstract
Single-cell sequencing technologies have led to a revolution in our knowledge of the diversity of cell types, connections between biological levels of organization, and relationships between genotype and phenotype. These advances have mainly come from using model organisms; however, using single-cell sequencing in non-model organisms could enable investigations of questions inaccessible with typical model organisms. This primer describes a general workflow for single-cell sequencing studies and considerations for using non-model organisms (limited to multicellular animals). Importantly, single-cell sequencing, when further applied in non-model organisms, will allow for a deeper understanding of the mechanisms between genotype and phenotype and the basis for biological variation.
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Affiliation(s)
- James M. Alfieri
- Department of Biology, Texas A&M University, College Station, TX 77843, USA; (M.M.J.); (H.B.)
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX 77843, USA;
- Department of Poultry Science, Texas A&M University, College Station, TX 77843, USA
| | - Guosong Wang
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA; (G.W.); (C.A.G.)
| | - Michelle M. Jonika
- Department of Biology, Texas A&M University, College Station, TX 77843, USA; (M.M.J.); (H.B.)
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843, USA
| | - Clare A. Gill
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA; (G.W.); (C.A.G.)
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843, USA
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, TX 77843, USA; (M.M.J.); (H.B.)
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX 77843, USA;
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843, USA
| | - Giridhar N. Athrey
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX 77843, USA;
- Department of Poultry Science, Texas A&M University, College Station, TX 77843, USA
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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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