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Bett VK, Macon A, Vicoso B, Elkrewi M. Chromosome-Level Assembly of Artemia franciscana Sheds Light on Sex Chromosome Differentiation. Genome Biol Evol 2024; 16:evae006. [PMID: 38245839 PMCID: PMC10827361 DOI: 10.1093/gbe/evae006] [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: 09/21/2023] [Revised: 11/27/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024] Open
Abstract
Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, is still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of A. franciscana (Kellogg 1906), from the Great Salt Lake, United States. The genome is 1 GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.
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Affiliation(s)
| | - Ariana Macon
- Institute of Science and Technology Austria (ISTA), Klosterneuburg 3400, Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria (ISTA), Klosterneuburg 3400, Austria
| | - Marwan Elkrewi
- Institute of Science and Technology Austria (ISTA), Klosterneuburg 3400, Austria
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2
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Mrnjavac A, Khudiakova KA, Barton NH, Vicoso B. Slower-X: reduced efficiency of selection in the early stages of X chromosome evolution. Evol Lett 2023; 7:4-12. [PMID: 37065438 PMCID: PMC10091493 DOI: 10.1093/evlett/qrac004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/08/2022] [Accepted: 12/17/2022] [Indexed: 02/04/2023] Open
Abstract
Abstract
Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated.
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Affiliation(s)
- Andrea Mrnjavac
- Institute of Science and Technology Austria , Am Campus 1, 3400 Klosterneuburg , Austria
| | - Ksenia A Khudiakova
- Institute of Science and Technology Austria , Am Campus 1, 3400 Klosterneuburg , Austria
| | - Nicholas H Barton
- Institute of Science and Technology Austria , Am Campus 1, 3400 Klosterneuburg , Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria , Am Campus 1, 3400 Klosterneuburg , Austria
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3
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Nikolakis ZL, Adams RH, Wade KJ, Lund AJ, Carlton EJ, Castoe TA, Pollock DD. Prospects for genomic surveillance for selection in schistosome parasites. FRONTIERS IN EPIDEMIOLOGY 2022; 2:932021. [PMID: 38455290 PMCID: PMC10910990 DOI: 10.3389/fepid.2022.932021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/12/2022] [Indexed: 03/09/2024]
Abstract
Schistosomiasis is a neglected tropical disease caused by multiple parasitic Schistosoma species, and which impacts over 200 million people globally, mainly in low- and middle-income countries. Genomic surveillance to detect evidence for natural selection in schistosome populations represents an emerging and promising approach to identify and interpret schistosome responses to ongoing control efforts or other environmental factors. Here we review how genomic variation is used to detect selection, how these approaches have been applied to schistosomes, and how future studies to detect selection may be improved. We discuss the theory of genomic analyses to detect selection, identify experimental designs for such analyses, and review studies that have applied these approaches to schistosomes. We then consider the biological characteristics of schistosomes that are expected to respond to selection, particularly those that may be impacted by control programs. Examples include drug resistance, host specificity, and life history traits, and we review our current understanding of specific genes that underlie them in schistosomes. We also discuss how inherent features of schistosome reproduction and demography pose substantial challenges for effective identification of these traits and their genomic bases. We conclude by discussing how genomic surveillance for selection should be designed to improve understanding of schistosome biology, and how the parasite changes in response to selection.
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Affiliation(s)
- Zachary L. Nikolakis
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
| | - Richard H. Adams
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, GA, United States
| | - Kristen J. Wade
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Andrea J. Lund
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado, Anschutz, Aurora, CO, United States
| | - Elizabeth J. Carlton
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado, Anschutz, Aurora, CO, United States
| | - Todd A. Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
| | - David D. Pollock
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States
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4
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Charlesworth D. Evolution: A can of (flat)worms. Curr Biol 2022; 32:R918-R921. [PMID: 36099896 DOI: 10.1016/j.cub.2022.07.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
A recent paper suggests that the flatworm Schmidtea mediterranea has an autosome that is 'primed' to evolve into a sex chromosome. However, this chromosome could be a balanced-lethal system and may illuminate these puzzling systems.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Ecology and Evolution, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK.
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5
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Elkrewi M, Khauratovich U, Toups MA, Bett VK, Mrnjavac A, Macon A, Fraisse C, Sax L, Huylmans AK, Hontoria F, Vicoso B. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. Genetics 2022; 222:6670797. [PMID: 35977389 PMCID: PMC9526061 DOI: 10.1093/genetics/iyac123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.
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Affiliation(s)
- Marwan Elkrewi
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria
| | - Uladzislava Khauratovich
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.,Department of Chromosome Biology, Max Perutz Labs, University of Vienna, 1030, Austria
| | - Melissa A Toups
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.,Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, BH12 5BB, UK
| | | | - Andrea Mrnjavac
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria
| | - Ariana Macon
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria
| | - Christelle Fraisse
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.,CNRS, Univ. Lille, UMR 8198-Evo-Eco-Paleo, F-59000 Lille, France
| | - Luca Sax
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.,Lewis and Clark College, Portland, OR 97219, USA
| | - Ann Kathrin Huylmans
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.,Institute of Organismic and Molecular Evolution, Johannes Guttenberg Universität Mainz, Mainz, 55122, Germany
| | - Francisco Hontoria
- Instituto de Acuicultura de Torre de la Sal (IATS-CSIC), Ribera de Cabanes, 12595, Spain
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria
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6
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Xu X, Wang Y, Wang C, Guo G, Yu X, Dai Y, Liu Y, Wei G, He X, Jin G, Zhang Z, Guan Q, Pain A, Wang S, Zhang W, Young ND, Gasser RB, McManus DP, Cao J, Zhou Q, Zhang Q. Chromosome-level genome assembly defines female-biased genes associated with sex determination and differentiation in the human blood fluke Schistosoma japonicum. Mol Ecol Resour 2022; 23:205-221. [PMID: 35844053 DOI: 10.1111/1755-0998.13689] [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: 10/10/2021] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 12/01/2022]
Abstract
Schistosomiasis is a neglected tropical disease of humans caused by blood flukes of the genus Schistosoma, the only dioecious parasitic flatworm. Although aspects of sex determination, differentiation and reproduction have been studied in some Schistosoma species, almost nothing is known for Schistosoma japonicum, the causative agent of schistosomiasis japonica. This mainly reflects the lack of high-quality genomic and transcriptomic resources for this species. As current genomes for S. japonicum are highly fragmented, we assembled and report a chromosome-level reference genome (seven autosomes, the Z-chromosome and partial W-chromosome), achieving a substantially enhanced gene annotation. Utilizing this genome, we discovered that the sex chromosomes of S. japonicum and its congener S. mansoni independently suppressed recombination during evolution, forming five and two evolutionary strata, respectively. By exploring the W-chromosome and sex-specific transcriptomes, we identified 35 W-linked genes and 257 female-preferentially transcribed genes (FTGs) from our chromosomal assembly and uncovered a signature for sex determination and differentiation in S. japonicum. These FTGs clustering within autosomes or the Z-chromosome exhibit a highly dynamic transcription profile during the pairing of female and male schistosomula, thereby representing a critical phase for the maturation of the female worms and suggesting distinct layers of regulatory control of gene transcription at this development stage. Collectively, these data provide a valuable resource for further functional genomic characterization of S. japonicum, shed light on the evolution of sex chromosomes in this highly virulent human blood fluke, and provide a pathway to identify novel targets for development of intervention tools against schistosomiasis.
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Affiliation(s)
- Xindong Xu
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Yifeng Wang
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Changhong Wang
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Gangqiang Guo
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Xinyu Yu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Yang Dai
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Yaobao Liu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Guiying Wei
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Xiaohui He
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Ge Jin
- Novogene Bioinformatics Institute, Beijing, China
| | - Ziqiu Zhang
- Novogene Bioinformatics Institute, Beijing, China
| | - Qingtian Guan
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Shengyue Wang
- National Research Center for Translational Medicine, State Key Laboratory of Medical Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University (SJTU) School of Medicine, Shanghai, China
| | - Wenbao Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Donald P McManus
- Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jun Cao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China.,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.,Center for Reproductive Medicine, the Second Affiliated Hospital School of Medicine and Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Qingfeng Zhang
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
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7
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Evolution of sexual systems, sex chromosomes and sex-linked gene transcription in flatworms and roundworms. Nat Commun 2022; 13:3239. [PMID: 35688815 PMCID: PMC9187692 DOI: 10.1038/s41467-022-30578-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/06/2022] [Indexed: 12/02/2022] Open
Abstract
Many species with separate male and female individuals (termed ‘gonochorism’ in animals) have sex-linked genome regions. Here, we investigate evolutionary changes when genome regions become completely sex-linked, by analyses of multiple species of flatworms (Platyhelminthes; among which schistosomes recently evolved gonochorism from ancestral hermaphroditism), and roundworms (Nematoda) which have undergone independent translocations of different autosomes. Although neither the evolution of gonochorism nor translocations fusing ancestrally autosomal regions to sex chromosomes causes inevitable loss of recombination, we document that formerly recombining regions show genomic signatures of recombination suppression in both taxa, and become strongly genetically degenerated, with a loss of most genes. Comparisons with hermaphroditic flatworm transcriptomes show masculinisation and some defeminisation in schistosome gonad gene expression. We also find evidence that evolution of sex-linkage in nematodes is accompanied by transcriptional changes and dosage compensation. Our analyses also identify sex-linked genes that could assist future research aimed at controlling some of these important parasites. Transitions between hermaphroditic and separate sexes are relatively understudied in animals compared to pants. Here, Wang et al. reconstruct the evolution of separate sexes in the flatworms and complex changes of sex chromosomes in the roundworms.
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8
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Kelemen RK, Elkrewi M, Lindholm AK, Vicoso B. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. Proc Biol Sci 2022; 289:20211985. [PMID: 35135349 PMCID: PMC8826135 DOI: 10.1098/rspb.2021.1985] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The t-haplotype of mice is a classical model for autosomal transmission distortion. A largely non-recombining variant of the proximal region of chromosome 17, it is transmitted to more than 90% of the progeny of heterozygous males through the disabling of sperm carrying a standard chromosome. While extensive genetic and functional work has shed light on individual genes involved in drive, much less is known about the evolution and function of the rest of its hundreds of genes. Here, we characterize the sequence and expression of dozens of t-specific transcripts and of their chromosome 17 homologues. Many genes showed reduced expression of the t-allele, but an equal number of genes showed increased expression of their t-copy, consistent with increased activity or a newly evolved function. Genes on the t-haplotype had a significantly higher non-synonymous substitution rate than their homologues on the standard chromosome, with several genes harbouring dN/dS ratios above 1. Finally, the t-haplotype has acquired at least two genes from other chromosomes, which show high and tissue-specific expression. These results provide a first overview of the gene content of this selfish element, and support a more dynamic evolutionary scenario than expected of a large genomic region with almost no recombination.
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Affiliation(s)
- Reka K. Kelemen
- Institute of Science and Technology Austria, Am Campus, 1, 3400 Klosterneuburg, Austria
| | - Marwan Elkrewi
- Institute of Science and Technology Austria, Am Campus, 1, 3400 Klosterneuburg, Austria
| | - Anna K. Lindholm
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse, 190, 8057 Zurich, Switzerland
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Am Campus, 1, 3400 Klosterneuburg, Austria
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