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Simmons JR, Estrem B, Zagoskin MV, Oldridge R, Zadegan SB, Wang J. Chromosome fusion and programmed DNA elimination shape karyotypes of nematodes. Curr Biol 2024; 34:2147-2161.e5. [PMID: 38688284 PMCID: PMC11111355 DOI: 10.1016/j.cub.2024.04.022] [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: 11/30/2023] [Revised: 02/21/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
An increasing number of metazoans undergo programmed DNA elimination (PDE), where a significant amount of DNA is selectively lost from the somatic genome during development. In some nematodes, PDE leads to the removal and remodeling of the ends of all germline chromosomes. In several species, PDE also generates internal breaks that lead to sequence loss and increased numbers of somatic chromosomes. The biological significance of these karyotype changes associated with PDE and the origin and evolution of nematode PDE remain largely unknown. Here, we assembled the single germline chromosome of the nematode Parascaris univalens and compared the karyotypes, chromosomal gene organization, and PDE features among other nematodes. We show that PDE in Parascaris converts an XX/XY sex-determination system in the germline into an XX/XO system in the somatic cells. Comparisons of Ascaris, Parascaris, and Baylisascaris ascarid chromosomes suggest that PDE existed in the ancestor of these nematodes, and their current distinct germline karyotypes were derived from fusion events of smaller ancestral chromosomes. The DNA breaks involved in PDE resolve these fused germline chromosomes into their pre-fusion karyotypes. These karyotype changes may lead to alterations in genome architecture and gene expression in the somatic cells. Cytological and genomic analyses further suggest that satellite DNA and the heterochromatic chromosome arms are dynamic and may play a role during meiosis. Overall, our results show that chromosome fusion and PDE have been harnessed in these ascarids to sculpt their karyotypes, altering the genome organization and serving specific functions in the germline and somatic cells.
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Affiliation(s)
- James R Simmons
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Brandon Estrem
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Maxim V Zagoskin
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Ryan Oldridge
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Sobhan Bahrami Zadegan
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jianbin Wang
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA; UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA.
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Al-Yazeedi T, Adams S, Tandonnet S, Turner A, Kim J, Lee J, Pires-daSilva A. The contribution of an X chromosome QTL to non-Mendelian inheritance and unequal chromosomal segregation in Auanema freiburgense. Genetics 2024; 227:iyae032. [PMID: 38431281 PMCID: PMC11075566 DOI: 10.1093/genetics/iyae032] [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: 12/24/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024] Open
Abstract
Auanema freiburgense is a nematode with males, females, and selfing hermaphrodites. When XO males mate with XX females, they typically produce a low proportion of XO offspring because they eliminate nullo-X spermatids. This process ensures that most sperm carry an X chromosome, increasing the likelihood of X chromosome transmission compared to random segregation. This occurs because of an unequal distribution of essential cellular organelles during sperm formation, likely dependent on the X chromosome. Some sperm components are selectively segregated into the X chromosome's daughter cell, while others are discarded with the nullo-X daughter cell. Intriguingly, the interbreeding of 2 A. freiburgense strains results in hybrid males capable of producing viable nullo-X sperm. Consequently, when these hybrid males mate with females, they yield a high percentage of male offspring. To uncover the genetic basis of nullo-spermatid elimination and X chromosome drive, we generated a genome assembly for A. freiburgense and genotyped the intercrossed lines. This analysis identified a quantitative trait locus spanning several X chromosome genes linked to the non-Mendelian inheritance patterns observed in A. freiburgense. This finding provides valuable clues to the underlying factors involved in asymmetric organelle partitioning during male meiotic division and thus non-Mendelian transmission of the X chromosome and sex ratios.
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Affiliation(s)
- Talal Al-Yazeedi
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Sally Adams
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Sophie Tandonnet
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Anisa Turner
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Jun Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Junho Lee
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
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Sullivan W. Remarkable chromosomes and karyotypes: A top 10 list. Mol Biol Cell 2024; 35:pe1. [PMID: 38517328 PMCID: PMC11064663 DOI: 10.1091/mbc.e23-12-0498] [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: 12/20/2023] [Revised: 02/23/2024] [Accepted: 03/01/2024] [Indexed: 03/23/2024] Open
Abstract
Chromosomes and karyotypes are particularly rich in oddities and extremes. Described below are 10 remarkable chromosomes and karyotypes sprinkled throughout the tree of life. These include variants in chromosome number, structure, and dynamics both natural and engineered. This versatility highlights the robustness and tolerance of the mitotic and meiotic machinery to dramatic changes in chromosome and karyotype architecture. These examples also illustrate that the robustness comes at a cost, enabling the evolution of chromosomes that subvert mitosis and meiosis.
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Affiliation(s)
- William Sullivan
- Department of MCD Biology, University of California, Santa Cruz, CA 95064
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Grishanin A. Chromatin diminution as a tool to study some biological problems. COMPARATIVE CYTOGENETICS 2024; 18:27-49. [PMID: 38369988 PMCID: PMC10870232 DOI: 10.3897/compcytogen.17.112152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/21/2024] [Indexed: 02/20/2024]
Abstract
This work reveals the opportunities to obtain additional information about some biological problems through studying species that possess chromatin diminution. A brief review of the hypothesized biological significance of chromatin diminution is discussed. This article analyzes the biological role of chromatin diminution as it relates to the C-value enigma. It is proposed to consider chromatin diminution as a universal mechanism of genome reduction, reducing the frequency of recombination events in the genome, which leads to specialization and adaptation of the species to more narrow environmental conditions. A hypothesis suggesting the role of non-coding DNA in homologous recombination in eukaryotes is proposed. Cyclopskolensis Lilljeborg, 1901 (Copepoda, Crustacea) is proposed as a model species for studying the mechanisms of transformation of the chromosomes and interphase nuclei structure of somatic line cells due to chromatin diminution. Chromatin diminution in copepods is considered as a stage of irreversible differentiation of embryonic cells during ontogenesis. The process of speciation in cyclopoids with chromatin diminution is considered.
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Affiliation(s)
- Andrey Grishanin
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, 152742 Borok, Yaroslavl Prov., RussiaRussian Academy of SciencesBorokRussia
- Department of Biophisics, Faculty of Natural and Engineering Sciences, Dubna State University, Universitetskaya 19, 141980, Dubna, Moscow Prov., RussiaDubna State UniversityDubnaRussia
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Simmons JR, Estrem B, Zagoskin MV, Oldridge R, Zadegan SB, Wang J. Chromosome fusion and programmed DNA elimination shape karyotypes of parasitic nematodes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572835. [PMID: 38187595 PMCID: PMC10769430 DOI: 10.1101/2023.12.21.572835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
A growing list of metazoans undergo programmed DNA elimination (PDE), where a significant amount of DNA is selectively lost from the somatic genome during development. In some nematodes, PDE leads to the removal and remodeling of the ends of all germline chromosomes. In several species, PDE also generates internal breaks that lead to sequence loss and an increased number of somatic chromosomes. The biological significance of these karyotype changes associated with PDE and the origin and evolution of nematode PDE remain largely unknown. Here, we assembled the single germline chromosome of the horse parasite Parascaris univalens and compared the karyotypes, chromosomal gene organization, and PDE features among ascarid nematodes. We show that PDE in Parascaris converts an XX/XY sex-determination system in the germline into an XX/XO system in the somatic cells. Comparisons of Ascaris, Parascaris, and Baylisascaris ascarid chromosomes suggest that PDE existed in the ancestor of these parasites, and their current distinct germline karyotypes were derived from fusion events of smaller ancestral chromosomes. The DNA breaks involved in PDE resolve these fused germline chromosomes into their pre-fusion karyotypes, leading to alterations in genome architecture and gene expression in the somatic cells. Cytological and genomic analyses further suggest that satellite DNA and the heterochromatic chromosome arms play a dynamic role in the Parascaris germline chromosome during meiosis. Overall, our results show that chromosome fusion and PDE have been harnessed in these ascarids to sculpt their karyotypes, altering the genome organization and serving specific functions in the germline and somatic cells.
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Affiliation(s)
- James R. Simmons
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Brandon Estrem
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Maxim V. Zagoskin
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Ryan Oldridge
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Sobhan Bahrami Zadegan
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Jianbin Wang
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996, USA
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, 37996, USA
- Lead Contact
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Cutter AD. Sexual conflict, heterochrony and tissue specificity as evolutionary problems of adaptive plasticity in development. Proc Biol Sci 2023; 290:20231854. [PMID: 37817601 PMCID: PMC10565415 DOI: 10.1098/rspb.2023.1854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/15/2023] [Indexed: 10/12/2023] Open
Abstract
Differential gene expression represents a fundamental cause and manifestation of phenotypic plasticity. Adaptive phenotypic plasticity in gene expression as a trait evolves when alleles that mediate gene regulation serve to increase organismal fitness by improving the alignment of variation in gene expression with variation in circumstances. Among the diverse circumstances that a gene encounters are distinct cell types, developmental stages and sexes, as well as an organism's extrinsic ecological environments. Consequently, adaptive phenotypic plasticity provides a common framework to consider diverse evolutionary problems by considering the shared implications of alleles that produce context-dependent gene expression. From this perspective, adaptive plasticity represents an evolutionary resolution to conflicts of interest that arise from any negatively pleiotropic effects of expression of a gene across ontogeny, among tissues, between the sexes, or across extrinsic environments. This view highlights shared properties within the general relation of fitness, trait expression and context that may nonetheless differ substantively in the grain of selection within and among generations to influence the likelihood of adaptive plasticity as an evolutionary response. Research programmes that historically have focused on these separate issues may use the insights from one another by recognizing their shared dependence on context-dependent gene regulatory evolution.
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Affiliation(s)
- Asher D. Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
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Crane YM, Crane CF, Cambron SE, Springmeyer LJ, Schemerhorn BJ. Molecular characterization of eliminated chromosomes in Hessian fly (Mayetiola destructor (Say)). CHROMOSOME RESEARCH : AN INTERNATIONAL JOURNAL ON THE MOLECULAR, SUPRAMOLECULAR AND EVOLUTIONARY ASPECTS OF CHROMOSOME BIOLOGY 2023; 31:3. [PMID: 36692656 PMCID: PMC9873768 DOI: 10.1007/s10577-023-09718-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 01/25/2023]
Abstract
Like other cecidomyiid Diptera, Hessian fly has stable S chromosomes and dispensable E chromosomes that are retained only in the germ line. Amplified fragment length polymorphisms (AFLP), suppressive subtractive hybridization (SSH), fluorescent in-situ hybridization (FISH), and sequencing were used to investigate similarities and differences between S and E chromosomes. More than 99.9% of AFLP bands were identical between separated ovary and somatic tissue, but one band was unique to ovary and resembled Worf, a non-LTR retrotransposon. Arrayed clones, derived by SSH of somatic from ovarian DNA, showed no clones that were unique to ovary. FISH with BAC clones revealed a diagnostic banding pattern of BAC positions on both autosomes and both sex chromosomes, and each E chromosome shared a pattern with one of the S chromosomes. Sequencing analysis showed that E chromosomes are nearly identical to S chromosomes, since no sequence could be confirmed to belong only to E chromosomes. There were a few questionably E-specific sequences that are candidates for further investigation. Thus, the E chromosomes appear to be derived from S chromosomes by the acquisition or conversion of sequences that produce the negatively heteropycnotic region around the centromere.
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Affiliation(s)
- Yan M Crane
- USDA Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA.,Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA
| | - Charles F Crane
- USDA Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA.,Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Sue E Cambron
- USDA Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA.,Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA
| | - Lucy J Springmeyer
- USDA Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA
| | - Brandon J Schemerhorn
- USDA Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA. .,Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA.
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Dockendorff TC, Estrem B, Reed J, Simmons JR, Zadegan SB, Zagoskin MV, Terta V, Villalobos E, Seaberry EM, Wang J. The nematode Oscheius tipulae as a genetic model for programmed DNA elimination. Curr Biol 2022; 32:5083-5098.e6. [PMID: 36379215 PMCID: PMC9729473 DOI: 10.1016/j.cub.2022.10.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/05/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022]
Abstract
Programmed DNA elimination (PDE) is a notable exception to the paradigm of genome integrity. In metazoa, PDE often occurs coincident with germline to somatic cell differentiation. During PDE, portions of genomic DNA are lost, resulting in reduced somatic genomes. Prior studies have described the sequences lost, as well as chromosome behavior, during metazoan PDE. However, a system for studying the mechanisms and consequences of PDE in metazoa is lacking. Here, we present a functional and genetic model for PDE in the free-living Rhabditidae nematode Oscheius tipulae, a family that also includes Caenorhabditis elegans. O. tipulae was recently suggested to eliminate DNA. Using staged embryos and DNA FISH, we showed that O. tipulae PDE occurs during embryogenesis at the 8-16 cell stages. We identified a conserved motif, named Sequence For Elimination (SFE), for all 12 break sites on the six chromosomes at the junctions of retained and eliminated DNA. SFE mutants exhibited a "fail-to-eliminate" phenotype only at the modified sites. END-seq revealed that breaks can occur at multiple positions within the SFE, with extensive end resection followed by telomere addition to both retained and eliminated ends. We identified many functional SFEs at the chromosome ends through END-seq in the wild-type embryos, genome sequencing of SFE mutants, and comparative genomics of 23 wild isolates. We suggest that these alternative SFEs provide flexibility in the sequences eliminated and a fail-safe mechanism for PDE. These studies establish O. tipulae as a new, attractive model for studying the mechanisms and consequences of PDE in a metazoan.
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Affiliation(s)
- Thomas C Dockendorff
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Brandon Estrem
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jordan Reed
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - James R Simmons
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Sobhan Bahrami Zadegan
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
| | - Maxim V Zagoskin
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Vincent Terta
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Eduardo Villalobos
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Erin M Seaberry
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jianbin Wang
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA; UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA.
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