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Nie Y, Liu X, Zhao L, Huang Y. Repetitive element expansions contribute to genome size gigantism in Pamphagidae: A comparative study (Orthoptera, Acridoidea). Genomics 2024; 116:110896. [PMID: 39025318 DOI: 10.1016/j.ygeno.2024.110896] [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: 03/25/2024] [Revised: 07/10/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
Pamphagidae is a family of Acridoidea that inhabits the desert steppes of Eurasia and Africa. This study employed flow cytometry to estimate the genome size of eight species in the Pamphagidae. The results indicate that the genome size of the eight species ranged from 13.88 pg to 14.66 pg, with an average of 14.26 pg. This is the largest average genome size recorded for the Orthoptera families, as well as for the entire Insecta. Furthermore, the study explored the role of repetitive sequences in the genome, including their evolutionary dynamics and activity, using low-coverage next-generation sequencing data. The genome is composed of 14 different types of repetitive sequences, which collectively make up between 59.9% and 68.17% of the total genome. The Pamphagidae family displays high levels of transposable element (TE) activity, with the number of TEs increasing and accumulating since the family's emergence. The study found that the types of repetitive sequences contributing to the TE outburst events are similar across species. Additionally, the study identified unique repetitive elements for each species. The differences in repetitive sequences among the eight Pamphagidae species correspond to their phylogenetic relationships. The study sheds new light on genome gigantism in the Pamphagidae and provides insight into the correlation between genome size and repetitive sequences within the family.
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Affiliation(s)
- Yimeng Nie
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xuanzeng Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Lina Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
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Taraveau F, Bru D, Quembo CJ, Jourdan-Pineau H. Development of microsatellite markers for the soft tick Ornithodoros phacochoerus. Parasit Vectors 2024; 17:301. [PMID: 38992704 PMCID: PMC11238500 DOI: 10.1186/s13071-024-06382-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Soft ticks of the genus Ornithodoros are responsible for the maintenance and transmission of the African swine fever (ASF) virus in the sylvatic and domestic viral cycles in Southern Africa. They are also the main vectors of the Borrelia species causing relapsing fevers. Currently, no genetic markers are available for Afrotropical Ornithodoros ticks. As ASF spreads globally, such markers are needed to assess the role of ticks in the emergence of new outbreaks. The aim of this study is to design microsatellite markers that could be used for ticks of the Ornithodoros moubata complex, particularly Ornithodoros phacochoerus, to assess population structure and tick movements in ASF endemic areas. METHODS A total of 151 markers were designed using the O. moubata and O. porcinus genomes after elimination of repeated sequences in the genomes. All designed markers were tested on O. phacochoerus and O. porcinus DNA to select the best markers. RESULTS A total of 24 microsatellite markers were genotyped on two populations of O. phacochoerus and on individuals from four other Ornithodoros species. Nineteen markers were selected to be as robust as possible for population genetic studies on O. phacochoerus. CONCLUSIONS The microsatellite markers developed here represent the first genetic tool to study nidicolous populations of O. phacochoerus.
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Affiliation(s)
- Florian Taraveau
- UMR ASTRE, CIRAD, INRAE, Campus de Baillarguet, 34398, Montpellier, France.
| | - David Bru
- UMR ASTRE, CIRAD, INRAE, Campus de Baillarguet, 34398, Montpellier, France
| | - Carlos João Quembo
- Central Region Office-Regional Veterinary Laboratory, Agricultural Research Institute of Mozambique, Chimoio, EN6.CP42, Mozambique
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Haq IU, Muhammad M, Yuan H, Ali S, Abbasi A, Asad M, Ashraf HJ, Khurshid A, Zhang K, Zhang Q, Liu C. Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda. Life (Basel) 2022; 12:521. [PMID: 35455012 PMCID: PMC9026859 DOI: 10.3390/life12040521] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 11/29/2022] Open
Abstract
Spodoptera frugiperda (fall armyworm) is a member of the superfamily Noctuoidea that accounts for more than a third of all Lepidoptera and includes a considerable number of agricultural and forest pest species. Spodoptera frugiperda is a polyphagous species that is a significant agricultural pest worldwide, emphasizing its economic importance. Spodoptera frugiperda's genome size, assembly, phylogenetic classification, and transcriptome analysis have all been previously described. However, the different studies reported different compositions of repeated DNA sequences that occupied the whole assembled genome, and the Spodoptera frugiperda genome also lacks the comprehensive study of dynamic satellite DNA. We conducted a comparative analysis of repetitive DNA across geographically distant populations of Spodoptera frugiperda, particularly satellite DNA, using publicly accessible raw genome data from eight different geographical regions. Our results showed that most transposable elements (TEs) were commonly shared across all geographically distant samples, except for the Maverick and PIF/Harbinger elements, which have divergent repeat copies. The TEs age analysis revealed that most TEs families consist of young copies 1-15 million years old; however, PIF/Harbinger has some older/degenerated copies of 30-35 million years old. A total of seven satellite DNA families were discovered, accounting for approximately 0.65% of the entire genome of the Spodoptera frugiperda fall armyworm. The repeat profiling analysis of satellite DNA families revealed differential read depth coverage or copy numbers. The satellite DNA families range in size from the lowest 108 bp SfrSat06-108 families to the largest (1824 bp) SfrSat07-1824 family. We did not observe a statistically significant correlation between monomer length and K2P divergence, copy number, or abundance of each satellite family. Our findings suggest that the satellite DNA families identified in Spodoptera frugiperda account for a considerable proportion of the genome's repetitive fraction. The satellite DNA families' repeat profiling revealed a point mutation along the reference sequences. Limited TEs differentiation exists among geographically distant populations of Spodoptera frugiperda.
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Affiliation(s)
- Inzamam Ul Haq
- College of Plant Protection, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou 730070, China; (I.U.H.); (A.K.); (K.Z.); (Q.Z.)
| | - Majid Muhammad
- College of Life Sciences, Shaanxi Normal University, Xi’an 710100, China; (M.M.); (H.Y.)
| | - Huang Yuan
- College of Life Sciences, Shaanxi Normal University, Xi’an 710100, China; (M.M.); (H.Y.)
| | - Shahbaz Ali
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan 64200, Pakistan;
| | - Asim Abbasi
- Department of Zoology, Bahawalpur Campus, University of Central Punjab, Bahawalpur 63100, Pakistan;
| | - Muhammad Asad
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Hafiza Javaria Ashraf
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Aroosa Khurshid
- College of Plant Protection, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou 730070, China; (I.U.H.); (A.K.); (K.Z.); (Q.Z.)
| | - Kexin Zhang
- College of Plant Protection, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou 730070, China; (I.U.H.); (A.K.); (K.Z.); (Q.Z.)
| | - Qiangyan Zhang
- College of Plant Protection, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou 730070, China; (I.U.H.); (A.K.); (K.Z.); (Q.Z.)
| | - Changzhong Liu
- College of Plant Protection, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou 730070, China; (I.U.H.); (A.K.); (K.Z.); (Q.Z.)
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Comparative Analysis of Transposable Elements in Genus Calliptamus Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation. INSECTS 2021; 12:insects12090837. [PMID: 34564277 PMCID: PMC8466570 DOI: 10.3390/insects12090837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/01/2021] [Accepted: 09/14/2021] [Indexed: 12/15/2022]
Abstract
Simple Summary Calliptamus is a genus of grasshoppers belonging to the family Acrididae. The genus Calliptamus includes approximately 17 recognized species. Calliptamus abbreviatus, Calliptamus italicus, and Calliptamus barbarus are three species that are widely found in northern China. These species are polyphagous, feeding on a variety of wild plants as well as crops, particularly legumes. The genome sizes, phylogenetic position, and transcriptome analysis of the genus Calliptamus were already known previous to this research. The repeatome analysis of these species was missing, which is directly linked to the larger genome sizes of the grasshoppers. Here, we classified repetitive DNA sequences at the level of superfamilies and sub-families, and found that LINE, TcMar-Tc1 and Ty3-gypsy LTR retrotransposons dominated the repeatomes of all genomes, accounting for 16–34% of the total genomes of these species. Satellite DNA dynamic evolutionary changes in all three genomes played a role in genome size evolution. This study would be a valuable source for future genome assemblies. Abstract Transposable elements (TEs) play a significant role in both eukaryotes and prokaryotes genome size evolution, structural changes, duplication, and functional variabilities. However, the large number of different repetitive DNA has hindered the process of assembling reference genomes, and the genus level TEs diversification of the grasshopper massive genomes is still under investigation. The genus Calliptamus diverged from Peripolus around 17 mya and its species divergence dated back about 8.5 mya, but their genome size shows rather large differences. Here, we used low-coverage Illumina unassembled short reads to investigate the effects of evolutionary dynamics of satDNAs and TEs on genome size variations. The Repeatexplorer2 analysis with 0.5X data resulted in 52%, 56%, and 55% as repetitive elements in the genomes of Calliptamus barbarus, Calliptamus italicus, and Calliptamus abbreviatus, respectively. The LINE and Ty3-gypsy LTR retrotransposons and TcMar-Tc1 dominated the repeatomes of all genomes, accounting for 16–35% of the total genomes of these species. Comparative analysis unveiled that most of the transposable elements (TEs) except satDNAs were highly conserved across three genomes in the genus Calliptamus grasshoppers. Out of a total of 20 satDNA families, 17 satDNA families were commonly shared with minor variations in abundance and divergence between three genomes, and 3 were Calliptamus barbarus specific. Our findings suggest that there is a significant amplification or contraction of satDNAs at genus phylogeny which is the main cause that made genome size different.
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Shah A, Hoffman JI, Schielzeth H. Comparative Analysis of Genomic Repeat Content in Gomphocerine Grasshoppers Reveals Expansion of Satellite DNA and Helitrons in Species with Unusually Large Genomes. Genome Biol Evol 2020; 12:1180-1193. [PMID: 32539114 PMCID: PMC7486953 DOI: 10.1093/gbe/evaa119] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic organisms vary widely in genome size and much of this variation can be explained by differences in the abundance of repetitive elements. However, the phylogenetic distributions and turnover rates of repetitive elements are largely unknown, particularly for species with large genomes. We therefore used de novo repeat identification based on low coverage whole-genome sequencing to characterize the repeatomes of six species of gomphocerine grasshoppers, an insect clade characterized by unusually large and variable genome sizes. Genome sizes of the six species ranged from 8.4 to 14.0 pg DNA per haploid genome and thus include the second largest insect genome documented so far (with the largest being another acridid grasshopper). Estimated repeat content ranged from 79% to 96% and was strongly correlated with genome size. Averaged over species, these grasshopper repeatomes comprised significant amounts of DNA transposons (24%), LINE elements (21%), helitrons (13%), LTR retrotransposons (12%), and satellite DNA (8.5%). The contribution of satellite DNA was particularly variable (ranging from <1% to 33%) as was the contribution of helitrons (ranging from 7% to 20%). The age distribution of divergence within clusters was unimodal with peaks ∼4-6%. The phylogenetic distribution of repetitive elements was suggestive of an expansion of satellite DNA in the lineages leading to the two species with the largest genomes. Although speculative at this stage, we suggest that the expansion of satellite DNA could be secondary and might possibly have been favored by selection as a means of stabilizing greatly expanded genomes.
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Affiliation(s)
- Abhijeet Shah
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
- Institute of Ecology and Evolution, Friedrich Schiller University Jena, Jena, Germany
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
| | - Holger Schielzeth
- Institute of Ecology and Evolution, Friedrich Schiller University Jena, Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany
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Schielzeth H, Dieker P. The green-brown polymorphism of the club-legged grasshopper Gomphocerus sibiricus is heritable and appears genetically simple. BMC Evol Biol 2020; 20:63. [PMID: 32487064 PMCID: PMC7268444 DOI: 10.1186/s12862-020-01630-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/18/2020] [Indexed: 11/24/2022] Open
Abstract
Background Local coexistence of distinct, genetically determined color morphs can be unstable and transitional. Stable, long-term coexistence requires some form of balancing selection to protect morphs from getting lost by directional selection or genetic drift. However, not all phenotypic polymorphism need to have a genetic basis. We here report on the genetic basis of two color polymorphisms in the club-legged grasshopper Gomphocerus sibiricus: a green-brown polymorphism that is phylogenetically and geographically widespread among orthopteran insects and a pied-brown pattern polymorphism that is shared among many gomphocerine grasshoppers. Results We found a remarkably clear outcome of matings within and between morph that suggest not only that the green-brown polymorphism is heritable in this species, but that results can be most parsimoniously explained by a single autosomal locus with two alleles in which the green allele is dominant over the brown allele. A few individuals did not match this pattern and suggest the existence of genetic modifiers and/or developmental phenocopies. We also show that the pied-brown polymorphism is highly heritable, although the evidence for the involvement of one or more loci is less clear-cut. Conclusions Overall, our data demonstrate that the two polymorphisms are heritable in the club-legged grasshopper and appear genetically simple, at least with respect to green morphs. The results are consistent with the idea that the synthesis or transport of a pigment involved in the production of green coloration (likely biliverdin) is lost by homozygosity for loss-of-function alleles in brown individuals. The apparently simple genetic architecture of the green-brown polymorphism offer potential for studying balancing selection in the field and for genetic mapping in this species.
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Affiliation(s)
- Holger Schielzeth
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University Jena, Dornburger Straße 159, 07743, Jena, Germany.
| | - Petra Dieker
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University Jena, Dornburger Straße 159, 07743, Jena, Germany.,Present Address: Thünen Institute of Biodiversity, Bundesallee 65, 38116, Braunschweig, Germany
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Trochez-Solarte JD, Ruiz-Erazo X, Almanza-Pinzon M, Zambrano-Gonzalez G. Role of microsatellites in genetic analysis of Bombyx mori silkworm: a review. F1000Res 2019; 8:1424. [PMID: 32148760 PMCID: PMC7043130 DOI: 10.12688/f1000research.20052.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/24/2019] [Indexed: 11/23/2022] Open
Abstract
In the genome of
Bombyx mori Linnaeus (1758), the microsatellites, or simple sequence repeats (SSR), feature among their particular characteristics a high adenine and thymine (A/T) content, low number of repeats, low frequency, and a grouping in "families" with similar flanking regions. Such characteristics may be the result of a complex interaction between factors that limit the size and dispersion of SSR loci—such as their high association with transposons—and mean that microsatellites within this taxon suitable as molecular markers are relatively rare. The determination of genetic profiles in populations and cell lines has not been affected owing to the high level of polymorphism, nor has the analysis of diversity, structure and genetic relationships. However, the scarcity of suitable microsatellites has restricted their application in genetic mapping, limiting them to preliminary identification of gene location of genes or quantitative trait loci (QTLs) related to thermotolerance, resistance to viruses, pigmentation patterns, body development and the weight of the cocoon, the cortex, the pupa and the filament. The review confirms that, as markers, microsatellites are versatile and perform well. They could thus be useful both to advance research in emerging countries with few resources seeking to promote sericulture in their territories, and to advance in the genetic and molecular knowledge of characteristics of productive and biological interest, given the latest technological developments in terms of the sequencing, identification, isolation and genotyping of SSR loci.
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Affiliation(s)
- Julian David Trochez-Solarte
- Agropecuary Sciences Department, Production Integrated Systems Research Group (SISINPRO), Faculty of Agricultural Sciences, University of Cauca, Popayán, Cauca, 190017, Colombia
| | - Ximena Ruiz-Erazo
- Agropecuary Sciences Department, Production Integrated Systems Research Group (SISINPRO), Faculty of Agricultural Sciences, University of Cauca, Popayán, Cauca, 190017, Colombia
| | - Martha Almanza-Pinzon
- Agropecuary Sciences Department, Production Integrated Systems Research Group (SISINPRO), Faculty of Agricultural Sciences, University of Cauca, Popayán, Cauca, 190017, Colombia
| | - Giselle Zambrano-Gonzalez
- Biology Department, Geology, Ecology and Conservation Research Group (GECO), Faculty of Natural Sciences and Education, University of Cauca, Popayán, Cauca, 190002, Colombia
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da Silva AF, Dezordi FZ, Loreto ELS, Wallau GL. Drosophila parasitoid wasps bears a distinct DNA transposon profile. Mob DNA 2018; 9:23. [PMID: 30002736 PMCID: PMC6035795 DOI: 10.1186/s13100-018-0127-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/19/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The majority of Eukaryotic genomes are composed of a small portion of stable (non-mobile) genes and a large fraction of parasitic mobile elements such as transposable elements and endogenous viruses: the Mobilome. Such important component of many genomes are normally underscored in genomic analysis and detailed characterized mobilomes only exists for model species. In this study, we used a combination of de novo and homology approaches to characterize the Mobilome of two non-model parasitoid wasp species. RESULTS The different methodologies employed for TE characterization recovered TEs with different features as TE consensus number and size. Moreover, some TEs were detected only by one or few methodologies. RepeatExplorer and dnaPipeTE estimated a low TE content of 5.86 and 4.57% for Braconidae wasp and 5.22% and 7.42% for L. boulardi species, respectively. Both mobilomes are composed by a miscellaneous of ancient and recent elements. Braconidae wasps presented a large diversity of Maverick/Polintons Class II TEs while other TE superfamilies were more equally diverse in both species. Phylogenetic analysis of reconstructed elements showed that vertical transfer is the main mode of transmission. CONCLUSION Different methodologies should be used complementarity in order to achieve better mobilome characterization. Both wasps genomes have one of the lower mobilome estimates among all Hymenoptera genomes studied so far and presented a higher proportion of Class II than Class I TEs. The large majority of superfamilies analyzed phylogenetically showed that the elements are being inherited by vertical transfer. Overall, we achieved a deep characterization of the mobilome in two non-model parasitoid wasps improving our understanding of their evolution.
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Affiliation(s)
- Alexandre Freitas da Silva
- Pós Graduação em Biociências e Biotecnologia em Saúde, Instituto Aggeu Magalhães (IAM), Recife, Pernambuco Brazil
| | - Filipe Zimmer Dezordi
- Pós Graduação em Biociências e Biotecnologia em Saúde, Instituto Aggeu Magalhães (IAM), Recife, Pernambuco Brazil
| | - Elgion Lucio Silva Loreto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM), Fundação Oswaldo Cruz (FIOCRUZ/PE), Recife, Pernambuco Brazil
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