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Yamaya K, Wang B, Memar N, Odiba A, Woglar A, Gartner A, Villeneuve A. Disparate roles for C. elegans DNA translocase paralogs RAD-54.L and RAD-54.B in meiotic prophase germ cells. Nucleic Acids Res 2023; 51:9183-9202. [PMID: 37548405 PMCID: PMC10516670 DOI: 10.1093/nar/gkad638] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/06/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023] Open
Abstract
RAD54 family DNA translocases partner with RAD51 recombinases to ensure stable genome inheritance, exhibiting biochemical activities both in promoting recombinase removal and in stabilizing recombinase association with DNA. Understanding how such disparate activities of RAD54 paralogs align with their biological roles is an ongoing challenge. Here we investigate the in vivo functions of Caenorhabditis elegans RAD54 paralogs RAD-54.L and RAD-54.B during meiotic prophase, revealing distinct contributions to the dynamics of RAD-51 association with DNA and to the progression of meiotic double-strand break repair (DSBR). While RAD-54.L is essential for RAD-51 removal from meiotic DSBR sites to enable recombination progression, RAD-54.B is largely dispensable for meiotic DSBR. However, RAD-54.B is required to prevent hyperaccumulation of RAD-51 on unbroken DNA during the meiotic sub-stage when DSBs and early recombination intermediates form. Moreover, DSB-independent hyperaccumulation of RAD-51 foci in the absence of RAD-54.B is RAD-54.L-dependent, revealing a hidden activity of RAD-54.L in promoting promiscuous RAD-51 association that is antagonized by RAD-54.B. We propose a model wherein a division of labor among RAD-54 paralogs allows germ cells to ramp up their capacity for efficient homologous recombination that is crucial to successful meiosis while counteracting potentially deleterious effects of unproductive RAD-51 association with unbroken DNA.
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Affiliation(s)
- Kei Yamaya
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bin Wang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, 530007 Nanning, China
| | - Nadin Memar
- IBS Center for Genomic Integrity and Department for Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Arome Solomon Odiba
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, 530007 Nanning, China
| | - Alexander Woglar
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Swiss Institute for Experimental Cancer Research (ISREC) and School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Anton Gartner
- IBS Center for Genomic Integrity and Department for Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Anne M Villeneuve
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
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Inwood SN, Skelly J, Guhlin JG, Harrop TWR, Goldson SL, Dearden PK. Chromosome-level genome assemblies of two parasitoid biocontrol wasps reveal the parthenogenesis mechanism and an associated novel virus. BMC Genomics 2023; 24:440. [PMID: 37543591 PMCID: PMC10403939 DOI: 10.1186/s12864-023-09538-4] [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: 05/22/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND Biocontrol is a key technology for the control of pest species. Microctonus parasitoid wasps (Hymenoptera: Braconidae) have been released in Aotearoa New Zealand as biocontrol agents, targeting three different pest weevil species. Despite their value as biocontrol agents, no genome assemblies are currently available for these Microctonus wasps, limiting investigations into key biological differences between the different species and strains. METHODS AND FINDINGS Here we present high-quality genomes for Microctonus hyperodae and Microctonus aethiopoides, assembled with short read sequencing and Hi-C scaffolding. These assemblies have total lengths of 106.7 Mb for M. hyperodae and 129.2 Mb for M. aethiopoides, with scaffold N50 values of 9 Mb and 23 Mb respectively. With these assemblies we investigated differences in reproductive mechanisms, and association with viruses between Microctonus wasps. Meiosis-specific genes are conserved in asexual Microctonus, with in-situ hybridisation validating expression of one of these genes in the ovaries of asexual Microctonus aethiopoides. This implies asexual reproduction in these Microctonus wasps involves meiosis, with the potential for sexual reproduction maintained. Investigation of viral gene content revealed candidate genes that may be involved in virus-like particle production in M. aethiopoides, as well as a novel virus infecting M. hyperodae, for which a complete genome was assembled. CONCLUSION AND SIGNIFICANCE These are the first published genomes for Microctonus wasps which have been deployed as biocontrol agents, in Aotearoa New Zealand. These assemblies will be valuable resources for continued investigation and monitoring of these biocontrol systems. Understanding the biology underpinning Microctonus biocontrol is crucial if we are to maintain its efficacy, or in the case of M. hyperodae to understand what may have influenced the significant decline of biocontrol efficacy. The potential for sexual reproduction in asexual Microctonus is significant given that empirical modelling suggests this asexual reproduction is likely to have contributed to biocontrol decline. Furthermore the identification of a novel virus in M. hyperodae highlights a previously unknown aspect of this biocontrol system, which may contribute to premature mortality of the host pest. These findings have potential to be exploited in future in attempt to increase the effectiveness of M. hyperodae biocontrol.
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Affiliation(s)
- Sarah N Inwood
- Bioprotection Aotearoa and Biochemistry Department, University of Otago, Dunedin, Aotearoa, New Zealand
| | - John Skelly
- Bioprotection Aotearoa and Biochemistry Department, University of Otago, Dunedin, Aotearoa, New Zealand
- Humble Bee Bio, Wellington, Aotearoa, New Zealand
| | - Joseph G Guhlin
- Genomics Aotearoa, University of Otago, Dunedin, Aotearoa, New Zealand
| | - Thomas W R Harrop
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Stephen L Goldson
- Biocontrol and Biosecurity Group, AgResearch Limited, Lincoln, Aotearoa, New Zealand
| | - Peter K Dearden
- Bioprotection Aotearoa and Biochemistry Department, University of Otago, Dunedin, Aotearoa, New Zealand.
- Genomics Aotearoa, University of Otago, Dunedin, Aotearoa, New Zealand.
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Inwood SN, Harrop TWR, Dearden PK. The venom composition and parthenogenesis mechanism of the parasitoid wasp Microctonus hyperodae, a declining biocontrol agent. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 153:103897. [PMID: 36584929 DOI: 10.1016/j.ibmb.2022.103897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
A biocontrol system in New Zealand using the endoparasitoid Microctonus hyperodae is failing, despite once being one of the most successful examples of classical biocontrol worldwide. Though it is of significant economic importance as a control agent, little is known about the genetics of M. hyperodae. In this study, RNA-seq was used to characterise two key traits of M. hyperodae in this system, the venom, critical for the initial success of biocontrol, and the asexual reproduction mode, which influenced biocontrol decline. Expanded characterisation of M. hyperodae venom revealed candidates involved in manipulating the host environment to source nutrition for the parasitoid egg, preventing a host immune response against the egg, as well as two components that may stimulate the host's innate immune system. Notably lacking from the venom-specific expression list was calreticulin, as it also had high expression in the ovaries. In-situ hybridisation revealed this ovarian expression was localised to the follicle cells, which may result in the deposition of calreticulin into the egg exochorion. Investigating the asexual reproduction of M. hyperodae revealed core meiosis-specific genes had conserved expression patterns with the highest expression in the ovaries, suggesting M. hyperodae parthenogenesis involves meiosis and that the potential for sexual reproduction may have been retained. Upregulation of genes involved in endoreduplication provides a potential mechanism for the restoration of diploidy in eggs after meiosis.
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Affiliation(s)
- Sarah N Inwood
- Bioprotection Aotearoa, Genomics Aotearoa, and the Biochemistry Department, University of Otago, Dunedin, Aotearoa, New Zealand
| | - Thomas W R Harrop
- Bioprotection Aotearoa, Genomics Aotearoa, and the Biochemistry Department, University of Otago, Dunedin, Aotearoa, New Zealand; Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peter K Dearden
- Bioprotection Aotearoa, Genomics Aotearoa, and the Biochemistry Department, University of Otago, Dunedin, Aotearoa, New Zealand.
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Slater GP, Smith NMA, Harpur BA. Prospects in Connecting Genetic Variation to Variation in Fertility in Male Bees. Genes (Basel) 2021; 12:1251. [PMID: 34440424 PMCID: PMC8392204 DOI: 10.3390/genes12081251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 12/20/2022] Open
Abstract
Bees are economically and ecologically important pollinating species. Managed and native bee species face increasing pressures from human-created stressors such as habitat loss, pesticide use, and introduced pathogens. There has been increasing attention towards how each of these factors impacts fertility, especially sperm production and maintenance in males. Here, we turn our attention towards another important factor impacting phenotypic variation: genetics. Using honey bees as a model, we explore the current understanding of how genetic variation within and between populations contributes to variation in sperm production, sperm maintenance, and insemination success among males. We conclude with perspectives and future directions in the study of male fertility in honey bees and non-Apis pollinators more broadly, which still remain largely understudied.
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Affiliation(s)
- Garett P. Slater
- Department of Entomology, Purdue University, 901 W State St., West Lafayette, IN 47907, USA;
| | - Nicholas M. A. Smith
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD 4072, Australia;
| | - Brock A. Harpur
- Department of Entomology, Purdue University, 901 W State St., West Lafayette, IN 47907, USA;
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A comparative genomic approach using mouse and fruit fly data to discover genes involved in testis function in hymenopterans with a focus on Nasonia vitripennis. BMC Ecol Evol 2021; 21:90. [PMID: 34011283 PMCID: PMC8132408 DOI: 10.1186/s12862-021-01825-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 05/12/2021] [Indexed: 11/18/2022] Open
Abstract
Background Spermatogenesis appears to be a relatively well-conserved process even among distantly related animal taxa such as invertebrates and vertebrates. Although Hymenopterans share many characteristics with other organisms, their complex haplodiploid reproduction system is still relatively unknown. However, they serve as a complementary insect model to Drosophila for studying functional male fertility. In this study, we used a comparative method combining taxonomic, phenotypic data and gene expression to identify candidate genes that could play a significant role in spermatogenesis in hymenopterans. Results Of the 546 mouse genes predominantly or exclusively expressed in the mouse testes, 36% had at least one ortholog in the fruit fly. Of these genes, 68% had at least one ortholog in one of the six hymenopteran species we examined. Based on their gene expression profiles in fruit fly testes, 71 of these genes were hypothesized to play a marked role in testis function. Forty-three of these 71 genes had an ortholog in at least one of the six hymenopteran species examined, and their enriched GO terms were related to the G2/M transition or to cilium organization, assembly, or movement. Second, of the 379 genes putatively involved in male fertility in Drosophila, 224 had at least one ortholog in each of the six Hymenoptera species. Finally, we showed that 199 of these genes were expressed in early pupal testis in Nasonia vitripennis; 86 exhibited a high level of expression, and 54 displayed modulated expression during meiosis. Conclusions In this study combining phylogenetic and experimental approaches, we highlighted genes that may have a major role in gametogenesis in hymenopterans; an essential prerequisite for further research on functional importance of these genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01825-6.
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Wu C, Twort VG, Newcomb RD, Buckley TR. Divergent Gene Expression Following Duplication of Meiotic Genes in the Stick Insect Clitarchus hookeri. Genome Biol Evol 2021; 13:6245840. [PMID: 33885769 DOI: 10.1093/gbe/evab060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2021] [Indexed: 01/02/2023] Open
Abstract
Some animal groups, such as stick insects (Phasmatodea), have repeatedly evolved alternative reproductive strategies, including parthenogenesis. Genomic studies have found modification of the genes underlying meiosis exists in some of these animals. Here we examine the evolution of copy number, evolutionary rate, and gene expression in candidate meiotic genes of the New Zealand geographic parthenogenetic stick insect Clitarchus hookeri. We characterized 101 genes from a de novo transcriptome assembly from female and male gonads that have homology with meiotic genes from other arthropods. For each gene we determined copy number, the pattern of gene duplication relative to other arthropod orthologs, and the potential for meiosis-specific expression. There are five genes duplicated in C. hookeri, including one also duplicated in the stick insect Timema cristinae, that are not or are uncommonly duplicated in other arthropods. These included two sister chromatid cohesion associated genes (SA2 and SCC2), a recombination gene (HOP1), an RNA-silencing gene (AGO2) and a cell-cycle regulation gene (WEE1). Interestingly, WEE1 and SA2 are also duplicated in the cyclical parthenogenetic aphid Acyrthosiphon pisum and Daphnia duplex, respectively, indicating possible roles in the evolution of reproductive mode. Three of these genes (SA2, SCC2, and WEE1) have one copy displaying gonad-specific expression. All genes, with the exception of WEE1, have significantly different nonsynonymous/synonymous ratios between the gene duplicates, indicative of a shift in evolutionary constraints following duplication. These results suggest that stick insects may have evolved genes with novel functions in gamete production by gene duplication.
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Affiliation(s)
- Chen Wu
- School of Biological Sciences, The University of Auckland, New Zealand.,Manaaki Whenua-Landcare Research, Auckland, New Zealand.,New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Victoria G Twort
- School of Biological Sciences, The University of Auckland, New Zealand.,Manaaki Whenua-Landcare Research, Auckland, New Zealand.,Zoology Unit, Finnish Museum of Natural History, LUOMUS, University of Helsinki, Finland
| | - Richard D Newcomb
- School of Biological Sciences, The University of Auckland, New Zealand.,New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Thomas R Buckley
- School of Biological Sciences, The University of Auckland, New Zealand.,Manaaki Whenua-Landcare Research, Auckland, New Zealand
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Cao LJ, Song W, Yue L, Guo SK, Chen JC, Gong YJ, Hoffmann AA, Wei SJ. Chromosome-level genome of the peach fruit moth Carposina sasakii (Lepidoptera: Carposinidae) provides a resource for evolutionary studies on moths. Mol Ecol Resour 2020; 21:834-848. [PMID: 33098233 DOI: 10.1111/1755-0998.13288] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/05/2020] [Accepted: 10/16/2020] [Indexed: 01/22/2023]
Abstract
The peach fruit moth (PFM), Carposina sasakii Matsumura, is a major phytophagous orchard pest widely distributed across Northeast Asia. Here, we report the chromosome-level genome for the PFM, representing the first genome for the family Carposinidae, from the lepidopteran superfamily Copromorphoidea. The genome was assembled into 404.83 Mb sequences using PacBio long-read and Illumina short-read sequences, including 275 contigs, with a contig N50 length of 2.62 Mb. All contigs were assembled into 31 linkage groups assisted by the Hi-C technique, including 30 autosomes and a Z chromosome. BUSCO analysis showed that 98.3% of genes were complete and 0.4% of genes were fragmented, while 1.3% of genes were missing in the assembled genome. In total, 21,697 protein-coding genes were predicted, of which 84.80% were functionally annotated. Because of the importance of diapause triggered by photoperiod in PFM, five circadian genes in the PFM as well as in the other related species were annotated, and potential genes related to diapause and photoperiodic reaction were also identified from transcriptome sequencing. In addition, manual annotation of detoxification gene families was undertaken and showed a higher number of glutathione S-transferase (GST) gene in PFM than in most other lepidopterans, in contrast to a lower number of uridine diphosphate (UDP)-glycosyltransferase (UGT) gene, carboxyl/cholinesterases (CCE) gene and cytochrome P450 monooxygenase (P450) gene, suggesting different detoxication pathways in this moth. The high-quality genome provides a resource for comparative evolutionary studies of this moth and its relatives within the context of radiations across Lepidoptera.
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Affiliation(s)
- Li-Jun Cao
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wei Song
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Lei Yue
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shao-Kun Guo
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jin-Cui Chen
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ya-Jun Gong
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ary Anthony Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Vic, Australia
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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The genome of the sea anemone Actinia equina (L.): Meiotic toolkit genes and the question of sexual reproduction. Mar Genomics 2020; 53:100753. [PMID: 32057717 DOI: 10.1016/j.margen.2020.100753] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/05/2020] [Accepted: 02/05/2020] [Indexed: 12/15/2022]
Abstract
The beadlet anemone Actinia equina (L.) (Cnidaria: Anthozoa: Actiniaria: Actiniidae) is one of the most familiar organisms of the North European intertidal zone. Once considered a single, morphologically variable species across northern Europe, it is now recognised as one member of a variable species complex. Previous studies of distribution, aggression, allozymes and mitochondrial DNA suggest that the diversity in form and colour within A. equina may hide still unrecognised species diversity. To empower further study of A. equina population genetics and systematics, we sequenced (PacBio Sequel) the genome of a single A. equina individual to produce a high-quality genome assembly (contig N50 = 492,607 bp, 1485 contigs, number of protein coding genes = 47,671, 97% BUSCO completeness). There is debate as to whether A. equina reproduces solely asexually, since no reliable, consistent evidence of sexual reproduction has been found. To gain further insight, we examined the genome for evidence of a 'meiotic toolkit' - genes believed to be found consistently in sexually reproducing organisms - and demonstrate that the A. equina genome appears not to have this full complement. Additionally, Smudgeplot analysis, coupled with high haplotype diversity, indicates this genome assembly to be of ambiguous ploidy, suggesting that A. equina may not be diploid. The suggested polyploid nature of this species coupled with the deficiency in meiotic toolkit genes, indicates that further field and laboratory studies of this species is warranted to understand how this species reproduces and what role ploidy may play in speciation within this speciose genus.
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Saunders DS. Dormancy, Diapause, and the Role of the Circadian System in Insect Photoperiodism. ANNUAL REVIEW OF ENTOMOLOGY 2020; 65:373-389. [PMID: 31594413 DOI: 10.1146/annurev-ento-011019-025116] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Whole-animal experiments devised to investigate possible association between photoperiodic time measurement and the circadian system (Bünning's hypothesis) are compared with more recent molecular investigations of circadian clock genes. In Sarcophaga argyrostoma and some other species, experimental cycles of light and darkness revealed a photoperiodic oscillator, set to constant phase at dusk and measuring night length repeatedly during extended periods of darkness. In some species, however, extreme dampening revealed an unrepetitive (i.e., hourglass-like) response. Rhythms of clock gene transcript abundance may also show similar phase relationships to the light cycle, and gene silencing of important clock genes indicates that they play a crucial role in photoperiodism either alone or in concert. However, the multiplicity of peripheral oscillators in the insect circadian system indicates that more complex mechanisms might also be important.
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Tvedte ES, Forbes AA, Logsdon JM. Retention of Core Meiotic Genes Across Diverse Hymenoptera. J Hered 2018; 108:791-806. [PMID: 28992199 DOI: 10.1093/jhered/esx062] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 07/13/2017] [Indexed: 12/20/2022] Open
Abstract
The cellular mechanisms of meiosis are critical for proper gamete formation in sexual organisms. Functional studies in model organisms have identified genes essential for meiosis, yet the extent to which this core meiotic machinery is conserved across non-model systems is not fully understood. Moreover, it is unclear whether deviation from canonical modes of sexual reproduction is accompanied by modifications in the genetic components involved in meiosis. We used a robust approach to identify and catalogue meiosis genes in Hymenoptera, an insect order typically characterized by haplodiploid reproduction. Using newly available genome data, we searched for 43 genes involved in meiosis in 18 diverse hymenopterans. Seven of eight genes with roles specific to meiosis were found across a majority of surveyed species, suggesting the preservation of core meiotic machinery in haplodiploid hymenopterans. Phylogenomic analyses of the inventory of meiosis genes and the identification of shared gene duplications and losses provided support for the grouping of species within Proctotrupomorpha, Ichneumonomorpha, and Aculeata clades, along with a paraphyletic Symphyta. The conservation of meiosis genes across Hymenoptera provides a framework for studying transitions between reproductive modes in this insect group.
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Affiliation(s)
- Eric S Tvedte
- Department of Biology, University of Iowa, Iowa City, IA 52242
| | - Andrew A Forbes
- Department of Biology, University of Iowa, Iowa City, IA 52242
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA 52242
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12
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Sekiné K, Furusawa T, Hatakeyama M. The boule gene is essential for spermatogenesis of haploid insect male. Dev Biol 2015; 399:154-163. [PMID: 25592223 DOI: 10.1016/j.ydbio.2014.12.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/18/2014] [Accepted: 12/22/2014] [Indexed: 11/15/2022]
Abstract
boule (bol), a member of the Deleted in Azoospermia (DAZ) gene family plays an important role in meiosis (reductional maturation divisions) in a spermatogenesis-specific manner in animals by regulating translation of the downstream cell division cycle 25 (cdc25) phosphatase mRNA. Orthologues of bol are conserved among animals and found in the genomes of hymenopteran insects, in which the general mode of reproduction is haplodiploidy: female is diploid and male is haploid. In this mode of reproduction, haploid males produce haploid sperm through non-reductional maturation divisions. The question thus arises of whether the bol gene actually functions during spermatogenesis in these haploid males. In this study, we identified two transcriptional isoforms of bol orthologue (Ar bol and Ar bol-2), and one cdc25 orthologue (Ar cdc25) in the hymenopteran sawfly, Athalia rosae. Ar bol was expressed exclusively in the testis when maturation divisions occurred, while Ar bol-2 was expressed ubiquitously. Knockdown of all bol transcripts (both Ar bol and Ar bol-2) resulted in a lack of mature sperm, whereas males with sole knockdown of Ar bol-2 were able to produce a small number of mature sperm. The cell cycle was arrested before maturation divisions in the testis in which all bol transcripts were knocked down, as revealed by flow cytometry. Although no mature sperm was produced, sperm elongation was partially observed when Ar cdc25 alone was knocked down. These results indicate that Ar bol is essential for the entry and progression of maturation divisions and sperm differentiation in haploid males.
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Affiliation(s)
- Kazuki Sekiné
- Division of Insect Sciences, National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Tadashi Furusawa
- Division of Animal Sciences, National Institute of Agrobiological Sciences, 2, Ikenodai, Tsukuba, Ibaraki 305-8602, Japan
| | - Masatsugu Hatakeyama
- Division of Insect Sciences, National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki 305-8634, Japan.
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Chi J, Mahé F, Loidl J, Logsdon J, Dunthorn M. Meiosis gene inventory of four ciliates reveals the prevalence of a synaptonemal complex-independent crossover pathway. Mol Biol Evol 2013; 31:660-72. [PMID: 24336924 DOI: 10.1093/molbev/mst258] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
To establish which meiosis genes are present in ciliates, and to look for clues as to which recombination pathways may be treaded by them, four genomes were inventoried for 11 meiosis-specific and 40 meiosis-related genes. We found that the set of meiosis genes shared by Tetrahymena thermophila, Paramecium tetraurelia, Ichthyophthirius multifiliis, and Oxytricha trifallax is consistent with the prevalence of a Mus81-dependent class II crossover pathway that is considered secondary in most model eukaryotes. There is little evidence for a canonical class I crossover pathway that requires the formation of a synaptonemal complex (SC). This gene inventory suggests that meiotic processes in ciliates largely depend on mitotic repair proteins for executing meiotic recombination. We propose that class I crossovers and SCs were reduced sometime during the evolution of ciliates. Consistent with this reduction, we provide microscopic evidence for the presence only of degenerate SCs in Stylonychia mytilus. In addition, lower nonsynonymous to synonymous mutation rates of some of the meiosis genes suggest that, in contrast to most other nuclear genes analyzed so far, meiosis genes in ciliates are largely evolving at a slower rate than those genes in fungi and animals.
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Affiliation(s)
- Jingyun Chi
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
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Hanson SJ, Schurko AM, Hecox-Lea B, Welch DBM, Stelzer CP, Logsdon JM. Inventory and phylogenetic analysis of meiotic genes in monogonont rotifers. J Hered 2013; 104:357-70. [PMID: 23487324 PMCID: PMC3622358 DOI: 10.1093/jhered/est011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 12/17/2012] [Accepted: 02/11/2013] [Indexed: 12/22/2022] Open
Abstract
A long-standing question in evolutionary biology is how sexual reproduction has persisted in eukaryotic lineages. As cyclical parthenogens, monogonont rotifers are a powerful model for examining this question, yet the molecular nature of sexual reproduction in this lineage is currently understudied. To examine genes involved in meiosis, we generated partial genome assemblies for 2 distantly related monogonont species, Brachionus calyciflorus and B. manjavacas. Here we present an inventory of 89 meiotic genes, of which 80 homologs were identified and annotated from these assemblies. Using phylogenetic analysis, we show that several meiotic genes have undergone relatively recent duplication events that appear to be specific to the monogonont lineage. Further, we compare the expression of "meiosis-specific" genes involved in recombination and all annotated copies of the cell cycle regulatory gene CDC20 between obligate parthenogenetic (OP) and cyclical parthenogenetic (CP) strains of B. calyciflorus. We show that "meiosis-specific" genes are expressed in both CP and OP strains, whereas the expression of one of the CDC20 genes is specific to cyclical parthenogenesis. The data presented here provide insights into mechanisms of cyclical parthenogenesis and establish expectations for studies of obligate asexual relatives of monogononts, the bdelloid rotifer lineage.
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Affiliation(s)
- Sara J Hanson
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
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15
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Yokoo R, Zawadzki KA, Nabeshima K, Drake M, Arur S, Villeneuve AM. COSA-1 reveals robust homeostasis and separable licensing and reinforcement steps governing meiotic crossovers. Cell 2012; 149:75-87. [PMID: 22464324 DOI: 10.1016/j.cell.2012.01.052] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 10/27/2011] [Accepted: 01/15/2012] [Indexed: 11/30/2022]
Abstract
Crossovers (COs) between homologous chromosomes ensure their faithful segregation during meiosis. We identify C. elegans COSA-1, a cyclin-related protein conserved in metazoa, as a key component required to convert meiotic double-strand breaks (DSBs) into COs. During late meiotic prophase, COSA-1 localizes to foci that correspond to the single CO site on each homolog pair and indicate sites of eventual concentration of other conserved CO proteins. Chromosomes gain and lose competence to load CO proteins during meiotic progression, with competence to load COSA-1 requiring prior licensing. Our data further suggest a self-reinforcing mechanism maintaining CO designation. Modeling of a nonlinear dose-response relationship between IR-induced DSBs and COSA-1 foci reveals efficient conversion of DSBs into COs when DSBs are limiting and a robust capacity to limit cytologically differentiated CO sites when DSBs are in excess. COSA-1 foci serve as a unique live cell readout for investigating CO formation and CO interference.
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Affiliation(s)
- Rayka Yokoo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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16
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Chen M, Zou M, Yang L, He S. Basal jawed vertebrate phylogenomics using transcriptomic data from Solexa sequencing. PLoS One 2012; 7:e36256. [PMID: 22558409 PMCID: PMC3338709 DOI: 10.1371/journal.pone.0036256] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 03/29/2012] [Indexed: 11/18/2022] Open
Abstract
The traditionally accepted relationships among basal jawed vertebrates have been challenged by some molecular phylogenetic analyses based on mitochondrial sequences. Those studies split extant gnathostomes into two monophyletic groups: tetrapods and piscine branch, including Chondrichthyes, Actinopterygii and sarcopterygian fishes. Lungfish and bichir are found in a basal position on the piscine branch. Based on transcriptomes of an armored bichir (Polypterus delhezi) and an African lungfish (Protopterus sp.) we generated, expressed sequences and whole genome sequences available from public databases, we obtained 111 genes to reconstruct the phylogenetic tree of basal jawed vertebrates and estimated their times of divergence. Our phylogenomic study supports the traditional relationship. We found that gnathostomes are divided into Chondrichthyes and the Osteichthyes, both with 100% support values (posterior probabilities and bootstrap values). Chimaeras were found to have a basal position among cartilaginous fishes with a 100% support value. Osteichthyes were divided into Actinopterygii and Sarcopterygii with 100% support value. Lungfish and tetrapods form a monophyletic group with 100% posterior probability. Bichir and two teleost species form a monophyletic group with 100% support value. The previous tree, based on mitochondrial data, was significantly rejected by an approximately unbiased test (AU test, p = 0). The time of divergence between lungfish and tetrapods was estimated to be 391.8 Ma and the divergence of bichir from pufferfish and medaka was estimated to be 330.6 Ma. These estimates closely match the fossil record. In conclusion, our phylogenomic study successfully resolved the relationship of basal jawed vertebrates based on transtriptomes, EST and whole genome sequences.
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Affiliation(s)
- Ming Chen
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Graduate University of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Ming Zou
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Graduate University of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Lei Yang
- Laboratory of Integrated Biodiversity, Conservation, and Genomics, Department of Biology, Saint Louis University, St. Louis, Missouri, United States of America
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- * E-mail:
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17
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Saunders DS, Bertossa RC. Deciphering time measurement: the role of circadian 'clock' genes and formal experimentation in insect photoperiodism. JOURNAL OF INSECT PHYSIOLOGY 2011; 57:557-566. [PMID: 21295039 DOI: 10.1016/j.jinsphys.2011.01.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 01/18/2011] [Accepted: 01/19/2011] [Indexed: 05/30/2023]
Abstract
This review examines possible role(s) of circadian 'clock' genes in insect photoperiodism against a background of many decades of formal experimentation and model building. Since ovarian diapause in the genetic model organism Drosophila melanogaster has proved to be weak and variable, recent attention has been directed to species with more robust photoperiodic responses. However, no obvious consensus on the problem of time measurement in insect photoperiodism has yet to emerge and a variety of mechanisms are indicated. In some species, expression patterns of clock genes and formal experiments based on the canonical properties of the circadian system have suggested that a damped oscillator version of Pittendrigh's external coincidence model is appropriate to explain the measurement of seasonal changes in night length. In other species extreme dampening of constituent oscillators may give rise to apparently hourglass-like photoperiodic responses, and in still others there is evidence for dual oscillator (dawn and dusk) photoperiodic mechanisms of the internal coincidence type. Although the exact role of circadian rhythmicity and of clock genes in photoperiodism is yet to be settled, Bünning's general hypothesis (Bünning, 1936) remains the most persuasive unifying principle. Observed differences between photoperiodic clocks may be reflections of underlying differences in the clock genes in their circadian feedback loops.
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Dorus S, Wilkin EC, Karr TL. Expansion and functional diversification of a leucyl aminopeptidase family that encodes the major protein constituents of Drosophila sperm. BMC Genomics 2011; 12:177. [PMID: 21466698 PMCID: PMC3078892 DOI: 10.1186/1471-2164-12-177] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 04/05/2011] [Indexed: 11/12/2022] Open
Abstract
Background The evolutionary diversification of gene families through gene creation (and loss) is a dynamic process believed to be critical to the evolution of functional novelty. Previous identification of a closely related family of eight annotated metalloprotease genes of the M17 Merops family in the Drosophila sperm proteome (termed, Sperm-LeucylAminoPeptidases, S-LAPs 1-8) led us to hypothesize that this gene family may have experienced such a diversification during insect evolution. Results To assess putative functional activities of S-LAPs, we (i) demonstrated that all S-LAPs are specifically expressed in the testis, (ii) confirmed their presence in sperm by two-dimensional gel electrophoresis and mass spectrometry, (iii) determined that they represent a major portion of the total protein in sperm and (iv) identified aminopeptidase enzymatic activity in sperm extracts using LAP-specific substrates. Functionally significant divergence at the canonical M17 active site indicates that the largest phylogenetic group of S-LAPs lost catalytic activity and likely acquired novel, as yet undetermined, functions in sperm prior to the expansion of the gene family. Conclusions Comparative genomic and phylogenetic analyses revealed the dramatic expansion of the S-LAP gene family during Drosophila evolution and copy number heterogeneity in the genomes of related insects. This finding, in conjunction with the loss of catalytic activity and potential neofunctionalization amongst some family members, extends empirical support for pervasive "revolving door" turnover in the evolution of reproductive gene family composition and function.
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Affiliation(s)
- Steve Dorus
- Centers for Evolutionary Medicine and Informatics and Infectious Diseases and Vaccinology, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5001, USA.
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Brown S. The Nasonia genome sequence: finding gems in the jewel (wasp) box. INSECT MOLECULAR BIOLOGY 2010; 19 Suppl 1:v-vii. [PMID: 20167012 DOI: 10.1111/j.1365-2583.2009.00989.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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