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Yuan R, Zheng B, Li Z, Ma X, Shu X, Qu Q, Ye X, Li S, Tang P, Chen X. The chromosome-level genome of Chinese praying mantis Tenodera sinensis (Mantodea: Mantidae) reveals its biology as a predator. Gigascience 2022; 12:giad090. [PMID: 37882605 PMCID: PMC10600911 DOI: 10.1093/gigascience/giad090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/17/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND The Chinese praying mantis, Tenodera sinensis (Saussure), is a carnivorous insect that preys on a variety of arthropods and small vertebrates, including pest species. Several studies have been conducted to understand its behavior and physiology. However, there is limited knowledge about the genetic information underlying its genome evolution, digestive demands, and predatory behaviors. FINDINGS Here we have assembled the chromosome-level genome of T. sinensis, representing the first sequenced genome of the family Mantidae, with a genome size of 2.54 Gb and scaffold N50 of 174.78 Mb. Our analyses revealed that 98.6% of BUSCO genes are present, resulting in a well-annotated assembly compared to other insect genomes, containing 25,022 genes. The reconstructed phylogenetic analysis showed the expected topology placing the praying mantis in an appropriate position. Analysis of transposon elements suggested the Gypsy/Dirs family, which belongs to long terminal repeat (LTR) transposons, may be a key factor resulting in the larger genome size. The genome shows expansions in several digestion and detoxification associated gene families, including trypsin and glycosyl hydrolase (GH) genes, ATP-binding cassette (ABC) transporter, and carboxylesterase (CarE), reflecting the possible genomic basis of digestive demands. Furthermore, we have found 1 ultraviolet-sensitive opsin and 2 long-wavelength-sensitive (LWS) opsins, emphasizing the core role of LWS opsins in regulating predatory behaviors. CONCLUSIONS The high-quality genome assembly of the praying mantis provides a valuable repository for studying the evolutionary patterns of the mantis genomes and the gene expression profiles of insect predators.
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Affiliation(s)
- Ruizhong Yuan
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Boying Zheng
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Zekai Li
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Xingzhou Ma
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Xiaohan Shu
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572025, China
| | - Qiuyu Qu
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572025, China
| | - Xiqian Ye
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Sheng Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
- Guangmeiyuan R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Meizhou 514779, China
| | - Pu Tang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Xuexin Chen
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572025, China
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2
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Bhattarai UR, Katuwal M, Poulin R, Gemmell NJ, Dowle E. Genome assembly and annotation of the European earwig Forficula auricularia (subspecies B). G3 GENES|GENOMES|GENETICS 2022; 12:6668290. [PMID: 35972389 PMCID: PMC9526046 DOI: 10.1093/g3journal/jkac199] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 07/06/2022] [Indexed: 11/14/2022]
Abstract
The European earwig Forficula auricularia is an important model for studies of maternal care, sexual selection, sociality, and host–parasite interactions. However, detailed genetic investigations of this species are hindered by a lack of genomic resources. Here, we present a high-quality hybrid genome assembly for Forficula auricularia using Nanopore long-reads and 10× linked-reads. The final assembly is 1.06 Gb in length with 31.03% GC content. It consists of 919 scaffolds with an N50 of 12.55 Mb. Half of the genome is present in only 20 scaffolds. Benchmarking Universal Single-Copy Orthologs scores are ∼90% from 3 sets of single-copy orthologs (eukaryotic, insect, and arthropod). The total repeat elements in the genome are 64.62%. The MAKER2 pipeline annotated 12,876 protein-coding genes and 21,031 mRNAs. Phylogenetic analysis revealed the assembled genome as that of species B, one of the 2 known genetic subspecies of Forficula auricularia. The genome assembly, annotation, and associated resources will be of high value to a large and diverse group of researchers working on dermapterans.
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Affiliation(s)
| | - Mandira Katuwal
- Department of Anatomy, University of Otago , Dunedin 9016, New Zealand
| | - Robert Poulin
- Department of Zoology, University of Otago , Dunedin 9016, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, University of Otago , Dunedin 9016, New Zealand
| | - Eddy Dowle
- Department of Anatomy, University of Otago , Dunedin 9016, New Zealand
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3
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Sicat JPA, Visendi P, Sewe SO, Bouvaine S, Seal SE. Characterization of transposable elements within the Bemisia tabaci species complex. Mob DNA 2022; 13:12. [PMID: 35440097 PMCID: PMC9017028 DOI: 10.1186/s13100-022-00270-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/30/2022] [Indexed: 12/24/2022] Open
Abstract
Background Whiteflies are agricultural pests that cause negative impacts globally to crop yields resulting at times in severe economic losses and food insecurity. The Bemisia tabaci whitefly species complex is the most damaging in terms of its broad crop host range and its ability to serve as vector for over 400 plant viruses. Genomes of whiteflies belonging to this species complex have provided valuable genomic data; however, transposable elements (TEs) within these genomes remain unexplored. This study provides the first accurate characterization of TE content within the B. tabaci species complex. Results This study identified that an average of 40.61% of the genomes of three whitefly species (MEAM1, MEDQ, and SSA-ECA) consists of TEs. The majority of the TEs identified were DNA transposons (22.85% average) while SINEs (0.14% average) were the least represented. This study also compared the TE content of the three whitefly genomes with three other hemipteran genomes and found significantly more DNA transposons and less LINEs in the whitefly genomes. A total of 63 TE superfamilies were identified to be present across the three whitefly species (39 DNA transposons, six LTR, 16 LINE, and two SINE). The sequences of the identified TEs were clustered which generated 5766 TE clusters. A total of 2707 clusters were identified as uniquely found within the whitefly genomes while none of the generated clusters were from both whitefly and non-whitefly TE sequences. This study is the first to characterize TEs found within different B. tabaci species and has created a standardized annotation workflow that could be used to analyze future whitefly genomes. Conclusion This study is the first to characterize the landscape of TEs within the B. tabaci whitefly species complex. The characterization of these elements within the three whitefly genomes shows that TEs occupy significant portions of B. tabaci genomes, with DNA transposons representing the vast majority. This study also identified TE superfamilies and clusters of TE sequences of potential interest, providing essential information, and a framework for future TE studies within this species complex. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00270-6.
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Affiliation(s)
- Juan Paolo A Sicat
- Natural Resources Institute, University of Greenwich, Central Avenue, Gillingham, Chatham, ME4 4TB, UK.
| | - Paul Visendi
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Steven O Sewe
- Natural Resources Institute, University of Greenwich, Central Avenue, Gillingham, Chatham, ME4 4TB, UK
| | - Sophie Bouvaine
- Natural Resources Institute, University of Greenwich, Central Avenue, Gillingham, Chatham, ME4 4TB, UK
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Gillingham, Chatham, ME4 4TB, UK
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4
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Pezenti LF, Levy SM, de Souza RF, Sosa-Gómez DR, da Rosa R. Testes morphology and the identification of transcripts of the hormonal pathways of the velvetbean caterpillar Anticarsia gemmatalis Hübner, 1818 (Lepidoptera: Erebidae). ARTHROPOD STRUCTURE & DEVELOPMENT 2021; 65:101111. [PMID: 34571334 DOI: 10.1016/j.asd.2021.101111] [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: 06/24/2021] [Revised: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Anticarsia gemmatalis is one of the main defoliating pests of soybeans in Brazil. In the current study, we characterized the histomorphology of the testes and the spermatogenesis process in A. gemmatalis. We also identified transcripts involved in the biosynthesis, metabolism, and signaling of juvenile and ecdysteroid hormones, in order to provide information about potential mechanisms of regulation of hormonal pathways in this species. Our analyses revealed that the A. gemmatalis larvae have a pair of kidney-shaped testicles. These are divided into four testicular follicles, where there are germ cell cysts at different stages of development. In the pupal stage, the testicles are fused, so adults have a single spherical testis, with a variable number of follicles. The A. gemmatalis has centripetal spermatogenesis and exhibits spermatic dimorphism. We identified 31 transcripts that encode proteins involved in juvenile hormone and ecdysteroid pathways, such as mevalonate kinase, CYP14A1, ecdysone receptor, among others. Our results on the morphology of the testes and spermatogenesis process, as well as identification of the genes involved in hormonal pathways in A. gemmatalis, provide important data for understanding the biology of this agricultural pest, which can be used as a basis for further research in other economically important lepidopterans.
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Affiliation(s)
- Larissa Forim Pezenti
- Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil; Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Sheila Michele Levy
- Laboratório de Insetos, Departamento de Histologia, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Rogério Fernandes de Souza
- Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Daniel Ricardo Sosa-Gómez
- Empresa Brasileira de Pesquisa Agropecuária/Centro Nacional de Pesquisa de Soja (Embrapa Soja), Londrina, Paraná, Brazil.
| | - Renata da Rosa
- Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
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5
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Sieriebriennikov B, Reinberg D, Desplan C. A molecular toolkit for superorganisms. Trends Genet 2021; 37:846-859. [PMID: 34116864 PMCID: PMC8355152 DOI: 10.1016/j.tig.2021.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 12/16/2022]
Abstract
Social insects, such as ants, bees, wasps, and termites, draw biologists' attention due to their distinctive lifestyles. As experimental systems, they provide unique opportunities to study organismal differentiation, division of labor, longevity, and the evolution of development. Ants are particularly attractive because several ant species can be propagated in the laboratory. However, the same lifestyle that makes social insects interesting also hampers the use of molecular genetic techniques. Here, we summarize the efforts of the ant research community to surmount these hurdles and obtain novel mechanistic insight into the biology of social insects. We review current approaches and propose novel ones involving genomics, transcriptomics, chromatin and DNA methylation profiling, RNA interference (RNAi), and genome editing in ants and discuss future experimental strategies.
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Affiliation(s)
- Bogdan Sieriebriennikov
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA; Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.
| | - Claude Desplan
- Department of Biology, New York University, New York, NY, USA.
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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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7
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Genome Size Estimation of Callipogon relictus Semenov (Coleoptera: Cerambycidae), an Endangered Species and a Korea Natural Monument. INSECTS 2021; 12:insects12020111. [PMID: 33513896 PMCID: PMC7910860 DOI: 10.3390/insects12020111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 11/24/2022]
Abstract
Simple Summary The longhorned beetle Calipogon relictus has been considered as a class I endangered species since 2012 in Korea. In an attempt towards beetle conservation, we estimated its genome size at 1.8 ± 0.2 Gb, representing one of the largest cerambycid genomes. This study provides useful insight at the genome level and facilitates the development of an effective conservation strategy. Abstract We estimated the genome size of a relict longhorn beetle, Callipogon relictus Semenov (Cerambycidae: Prioninae)—the Korean natural monument no. 218 and a Class I endangered species—using a combination of flow cytometry and k-mer analysis. The two independent methods enabled accurate estimation of the genome size in Cerambycidae for the first time. The genome size of C. relictus was 1.8 ± 0.2 Gb, representing one of the largest cerambycid genomes studied to date. An accurate estimation of genome size of a critically endangered longhorned beetle is a major milestone in our understanding and characterization of the C. relictus genome. Ultimately, the findings provide useful insight into insect genomics and genome size evolution, particularly among beetles.
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8
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Verlinden H, Sterck L, Li J, Li Z, Yssel A, Gansemans Y, Verdonck R, Holtof M, Song H, Behmer ST, Sword GA, Matheson T, Ott SR, Deforce D, Van Nieuwerburgh F, Van de Peer Y, Vanden Broeck J. First draft genome assembly of the desert locust, Schistocerca gregaria. F1000Res 2020; 9:775. [PMID: 33163158 PMCID: PMC7607483 DOI: 10.12688/f1000research.25148.2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/13/2021] [Indexed: 12/31/2022] Open
Abstract
Background: At the time of publication, the most devastating desert locust crisis in decades is affecting East Africa, the Arabian Peninsula and South-West Asia. The situation is extremely alarming in East Africa, where Kenya, Ethiopia and Somalia face an unprecedented threat to food security and livelihoods. Most of the time, however, locusts do not occur in swarms, but live as relatively harmless solitary insects. The phenotypically distinct solitarious and gregarious locust phases differ markedly in many aspects of behaviour, physiology and morphology, making them an excellent model to study how environmental factors shape behaviour and development. A better understanding of the extreme phenotypic plasticity in desert locusts will offer new, more environmentally sustainable ways of fighting devastating swarms. Methods: High molecular weight DNA derived from two adult males was used for Mate Pair and Paired End Illumina sequencing and PacBio sequencing. A reliable reference genome of Schistocerca gregaria was assembled using the ABySS pipeline, scaffolding was improved using LINKS. Results: In total, 1,316 Gb Illumina reads and 112 Gb PacBio reads were produced and assembled. The resulting draft genome consists of 8,817,834,205 bp organised in 955,015 scaffolds with an N50 of 157,705 bp, making the desert locust genome the largest insect genome sequenced and assembled to date. In total, 18,815 protein-encoding genes are predicted in the desert locust genome, of which 13,646 (72.53%) obtained at least one functional assignment based on similarity to known proteins. Conclusions: The desert locust genome data will contribute greatly to studies of phenotypic plasticity, physiology, neurobiology, molecular ecology, evolutionary genetics and comparative genomics, and will promote the desert locust's use as a model system. The data will also facilitate the development of novel, more sustainable strategies for preventing or combating swarms of these infamous insects.
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Affiliation(s)
- Heleen Verlinden
- Laboratory of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, 3000, Belgium
| | - Lieven Sterck
- Laboratory of Bioinformatics and Evolutionary Genomics, Ghent University, Ghent, 9000, Belgium.,Center for Plant Systems Biology, Ghent University - VIB, Ghent, 9052, Belgium
| | - Jia Li
- Laboratory of Bioinformatics and Evolutionary Genomics, Ghent University, Ghent, 9000, Belgium.,Center for Plant Systems Biology, Ghent University - VIB, Ghent, 9052, Belgium
| | - Zhen Li
- Laboratory of Bioinformatics and Evolutionary Genomics, Ghent University, Ghent, 9000, Belgium.,Center for Plant Systems Biology, Ghent University - VIB, Ghent, 9052, Belgium
| | - Anna Yssel
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, 9000, Belgium.,NXTGNT, Ghent University, Ghent, 9000, Belgium
| | - Rik Verdonck
- Laboratory of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, 3000, Belgium.,Station d' Ecologie Théorique et Expérimentale, UMR 5321 CNRS et Université Paul Sabatier, Moulis, 09200, France
| | - Michiel Holtof
- Laboratory of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, 3000, Belgium
| | - Hojun Song
- Department of Entomology, Texas A&M University, College Station, Texas, TX 77843-2475, USA
| | - Spencer T Behmer
- Department of Entomology, Texas A&M University, College Station, Texas, TX 77843-2475, USA
| | - Gregory A Sword
- Department of Entomology, Texas A&M University, College Station, Texas, TX 77843-2475, USA
| | - Tom Matheson
- Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, LE1 7RH, UK
| | - Swidbert R Ott
- Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, LE1 7RH, UK
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, 9000, Belgium.,NXTGNT, Ghent University, Ghent, 9000, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, 9000, Belgium.,NXTGNT, Ghent University, Ghent, 9000, Belgium
| | - Yves Van de Peer
- Laboratory of Bioinformatics and Evolutionary Genomics, Ghent University, Ghent, 9000, Belgium.,Center for Plant Systems Biology, Ghent University - VIB, Ghent, 9052, Belgium.,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Jozef Vanden Broeck
- Laboratory of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, 3000, Belgium
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9
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Verlinden H, Sterck L, Li J, Li Z, Yssel A, Gansemans Y, Verdonck R, Holtof M, Song H, Behmer ST, Sword GA, Matheson T, Ott SR, Deforce D, Van Nieuwerburgh F, Van de Peer Y, Vanden Broeck J. First draft genome assembly of the desert locust, Schistocerca gregaria. F1000Res 2020; 9:775. [PMID: 33163158 DOI: 10.12688/f1000research.25148.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/20/2020] [Indexed: 12/22/2022] Open
Abstract
Background: At the time of publication, the most devastating desert locust crisis in decades is affecting East Africa, the Arabian Peninsula and South-West Asia. The situation is extremely alarming in East Africa, where Kenya, Ethiopia and Somalia face an unprecedented threat to food security and livelihoods. Most of the time, however, locusts do not occur in swarms, but live as relatively harmless solitary insects. The phenotypically distinct solitarious and gregarious locust phases differ markedly in many aspects of behaviour, physiology and morphology, making them an excellent model to study how environmental factors shape behaviour and development. A better understanding of the extreme phenotypic plasticity in desert locusts will offer new, more environmentally sustainable ways of fighting devastating swarms. Methods: High molecular weight DNA derived from two adult males was used for Mate Pair and Paired End Illumina sequencing and PacBio sequencing. A reliable reference genome of Schistocerca gregaria was assembled using the ABySS pipeline, scaffolding was improved using LINKS. Results: In total, 1,316 Gb Illumina reads and 112 Gb PacBio reads were produced and assembled. The resulting draft genome consists of 8,817,834,205 bp organised in 955,015 scaffolds with an N50 of 157,705 bp, making the desert locust genome the largest insect genome sequenced and assembled to date. In total, 18,815 protein-encoding genes are predicted in the desert locust genome, of which 13,646 (72.53%) obtained at least one functional assignment based on similarity to known proteins. Conclusions: The desert locust genome data will contribute greatly to studies of phenotypic plasticity, physiology, neurobiology, molecular ecology, evolutionary genetics and comparative genomics, and will promote the desert locust's use as a model system. The data will also facilitate the development of novel, more sustainable strategies for preventing or combating swarms of these infamous insects.
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Affiliation(s)
- Heleen Verlinden
- Laboratory of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, 3000, Belgium
| | - Lieven Sterck
- Laboratory of Bioinformatics and Evolutionary Genomics, Ghent University, Ghent, 9000, Belgium.,Center for Plant Systems Biology, Ghent University - VIB, Ghent, 9052, Belgium
| | - Jia Li
- Laboratory of Bioinformatics and Evolutionary Genomics, Ghent University, Ghent, 9000, Belgium.,Center for Plant Systems Biology, Ghent University - VIB, Ghent, 9052, Belgium
| | - Zhen Li
- Laboratory of Bioinformatics and Evolutionary Genomics, Ghent University, Ghent, 9000, Belgium.,Center for Plant Systems Biology, Ghent University - VIB, Ghent, 9052, Belgium
| | - Anna Yssel
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, 9000, Belgium.,NXTGNT, Ghent University, Ghent, 9000, Belgium
| | - Rik Verdonck
- Laboratory of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, 3000, Belgium.,Station d' Ecologie Théorique et Expérimentale, UMR 5321 CNRS et Université Paul Sabatier, Moulis, 09200, France
| | - Michiel Holtof
- Laboratory of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, 3000, Belgium
| | - Hojun Song
- Department of Entomology, Texas A&M University, College Station, Texas, TX 77843-2475, USA
| | - Spencer T Behmer
- Department of Entomology, Texas A&M University, College Station, Texas, TX 77843-2475, USA
| | - Gregory A Sword
- Department of Entomology, Texas A&M University, College Station, Texas, TX 77843-2475, USA
| | - Tom Matheson
- Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, LE1 7RH, UK
| | - Swidbert R Ott
- Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, LE1 7RH, UK
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, 9000, Belgium.,NXTGNT, Ghent University, Ghent, 9000, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, 9000, Belgium.,NXTGNT, Ghent University, Ghent, 9000, Belgium
| | - Yves Van de Peer
- Laboratory of Bioinformatics and Evolutionary Genomics, Ghent University, Ghent, 9000, Belgium.,Center for Plant Systems Biology, Ghent University - VIB, Ghent, 9052, Belgium.,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Jozef Vanden Broeck
- Laboratory of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, 3000, Belgium
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10
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da Fonseca RR, Couto A, Machado AM, Brejova B, Albertin CB, Silva F, Gardner P, Baril T, Hayward A, Campos A, Ribeiro ÂM, Barrio-Hernandez I, Hoving HJ, Tafur-Jimenez R, Chu C, Frazão B, Petersen B, Peñaloza F, Musacchia F, Alexander GC, Osório H, Winkelmann I, Simakov O, Rasmussen S, Rahman MZ, Pisani D, Vinther J, Jarvis E, Zhang G, Strugnell JM, Castro LFC, Fedrigo O, Patricio M, Li Q, Rocha S, Antunes A, Wu Y, Ma B, Sanges R, Vinar T, Blagoev B, Sicheritz-Ponten T, Nielsen R, Gilbert MTP. A draft genome sequence of the elusive giant squid, Architeuthis dux. Gigascience 2020; 9:giz152. [PMID: 31942620 PMCID: PMC6962438 DOI: 10.1093/gigascience/giz152] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/27/2019] [Accepted: 12/05/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked. FINDINGS We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. CONCLUSIONS This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.
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Affiliation(s)
- Rute R da Fonseca
- Center for Macroecology, Evolution and Climate (CMEC), GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Alvarina Couto
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo 36310, Spain
| | - Andre M Machado
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos, 4450'208 Matosinhos, Portugal
| | - Brona Brejova
- Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48 Bratislava, Slovak Republic
| | - Carolin B Albertin
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Filipe Silva
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos, 4450'208 Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Paul Gardner
- Department of Biochemistry, University of Otago, 710 Cumberland Street, North Dunedin, Dunedin 9016, New Zealand
| | - Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK
| | - Alex Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK
| | - Alexandre Campos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos, 4450'208 Matosinhos, Portugal
| | - Ângela M Ribeiro
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos, 4450'208 Matosinhos, Portugal
| | - Inigo Barrio-Hernandez
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Henk-Jan Hoving
- GEOMAR Helmholtz Centre for Ocean Research Kiel,Wischhofstraße 1-3, 24148 Kiel, Germany
| | - Ricardo Tafur-Jimenez
- Instituto del Mar del Perú, Esq. Gamarra y Gral. Valle, Chucuito Apartado 22, Callao, Peru
| | - Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Barbara Frazão
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos, 4450'208 Matosinhos, Portugal
- IPMA, Fitoplâncton Lab, Rua C do Aeroporto, 1749-077, Lisboa, Portugal
| | - Bent Petersen
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Batu 3 1/2, Butik Air Nasi, 08100 Bedong, Kedah, Malaysia
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen,Øster Farimagsgade 5, 1353 Copenhagen, Denmark
| | - Fernando Peñaloza
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, México
| | - Francesco Musacchia
- Genomic Medicine, Telethon Institute of Genetics and Medicine, Via Campi Flegrei, 34, 80078 Pozzuoli, Naples, Italy
| | - Graham C Alexander
- GCB Sequencing and Genomic Technologies Shared Resource, Duke University CIEMAS, 101 Science Drive, Durham, NC 27708, USA
| | - Hugo Osório
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- Faculty of Medicine of the University of Porto, Alameda Prof. Hernani Monteiro, 4200-319 Porto, Portugal
| | - Inger Winkelmann
- Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Oleg Simakov
- Department of Molecular Evolution and Development, University of Vienna, Althanstrasse 14 (UZA1), A-1090 Vienna, Austria
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - M Ziaur Rahman
- Bioinformatics Solutions Inc, 470 Weber St N Suite 204, Waterloo, ON N2L 6J2, Canada
| | - Davide Pisani
- School of Biological Sciences and School of Earth Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TG, UK
| | - Jakob Vinther
- School of Biological Sciences and School of Earth Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TG, UK
| | - Erich Jarvis
- Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu Kunming, Yunnan 650223, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu Kunming, Yunnan 650223, China
| | - Jan M Strugnell
- Centre for Sustainable Tropical Fisheries & Aquaculture, James Cook University, Townsville, Douglas QLD 4814, Australia
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne Victoria 3086, Australia
| | - L Filipe C Castro
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos, 4450'208 Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Olivier Fedrigo
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Qiye Li
- BGI-Shenzhen, Shenzhen, China
| | - Sara Rocha
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo 36310, Spain
- Biomedical Research Center (CINBIO), University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
| | - Agostinho Antunes
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos, 4450'208 Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Yufeng Wu
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Bin Ma
- School of Computer Science, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada
| | - Remo Sanges
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Tomas Vinar
- Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48 Bratislava, Slovak Republic
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Thomas Sicheritz-Ponten
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Batu 3 1/2, Butik Air Nasi, 08100 Bedong, Kedah, Malaysia
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen,Øster Farimagsgade 5, 1353 Copenhagen, Denmark
| | - Rasmus Nielsen
- Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Departments of Integrative Biology and Statistics, University of California, 3040 Valley Life Sciences, Berkeley, CA 94720-3200, USA
| | - M Thomas P Gilbert
- Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Høgskolering 1, 7491 Trondheim, Norway
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11
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Yao Q, Dong Y, Chen J, Quan L, Zhang W, Chen B. Transcriptome Analysis of Female and Male Conopomorpha sinensis (Lepidoptera: Gracilariidae) Adults With a Focus on Hormone and Reproduction. JOURNAL OF ECONOMIC ENTOMOLOGY 2019; 112:2966-2975. [PMID: 31504646 DOI: 10.1093/jee/toz225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Indexed: 06/10/2023]
Abstract
Conopomorpha sinensis Bradley is the dominant borer pest of litchi and longan in the Asian-pacific area. Reduction or interference of reproduction and mating of adult moths is one of the most used strategies to control C. sinensis. Insect reproduction is a critical biological process closely related to endocrine control. Conopomorpha sinensis genome and transcriptome information is limited, hampering both our understanding of the molecular mechanisms underlying hormone activity and reproduction and the development of control strategies for this borer pest. To explore the sex differences in gene expression profiles influencing these biological processes, de novo transcriptomes were assembled from female and male adult C. sinensis specimens. This analysis yielded 184,422 unigenes with an average length of 903 bp and 405,961 transcripts after sequencing and assembly. About 45.06, 22.41, 19.53, 34.05, 35.82, 36.42, and 19.85% of the unigenes had significant matches in seven public databases. Subsequently, gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis revealed comprehensive information about the function of each gene and identified enriched categories and pathways that were associated with the 2,890 female-biased genes and 2,964 male-biased genes. In addition, we identified some important unigenes related to hormone activity and reproduction among the sex-differentially expressed genes (DEGs), including unigenes coding for ecdysone-induced protein 78C, juvenile hormone (JH)-regulated gene fatty acyl-CoA reductase, vitellogenin, etc. Our findings provide a more comprehensive portrait of the sex differences involved in the relationship of two important physiological features-hormone activity and reproduction in C. sinensis and members of the family Gracillariidae.
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Affiliation(s)
- Qiong Yao
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Yizhi Dong
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Jing Chen
- Department of Biochemistry and Molecular Biology, College of Basic Medical Science, Zunyi Medical University, Zunyi, Guizhou, China
| | - Linfa Quan
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol and Institute of Entomology, Sun-Yat-sen University, Guangzhou, China
| | - Bingxu Chen
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
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12
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Sang Y, Gao B, Diaby M, Zong W, Chen C, Shen D, Wang S, Wang Y, Ivics Z, Song C. Incomer, a DD36E family of Tc1/mariner transposons newly discovered in animals. Mob DNA 2019; 10:45. [PMID: 31788035 PMCID: PMC6875036 DOI: 10.1186/s13100-019-0188-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/11/2019] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The Tc1/mariner superfamily might represent the most diverse and widely distributed group of DNA transposons. Several families have been identified; however, exploring the diversity of this superfamily and updating its classification is still ongoing in the life sciences. RESULTS Here we identified a new family of Tc1/mariner transposons, named Incomer (IC), which is close to, but distinct from the known family DD34E/Tc1. ICs have a total length of about 1.2 kb, and harbor a single open reading frame encoding a ~ 346 amino acid transposase with a DD36E motif and flanked by short terminal inverted repeats (TIRs) (22-32 base pairs, bp). This family is absent from prokaryotes, and is mainly distributed among vertebrates (141 species of four classes), including Agnatha (one species of jawless fish), Actinopterygii (132 species of ray-finned fish), Amphibia (four species of frogs), and Mammalia (four species of bats), but have a restricted distribution in invertebrates (four species in Insecta and nine in Arachnida). All ICs in bats (Myotis lucifugus, Eptesicus fuscus, Myotis davidii, and Myotis brandtii) are present as truncated copies in these genomes, and most of them are flanked by relatively long TIRs (51-126 bp). High copy numbers of miniature inverted-repeat transposable elements (MITEs) derived from ICs were also identified in bat genomes. Phylogenetic analysis revealed that ICs are more closely related to DD34E/Tc1 than to other families of Tc1/mariner (e.g., DD34D/mariner and DD × D/pogo), and can be classified into four distinct clusters. The host and IC phylogenies and pairwise distance comparisons between RAG1 genes and all consensus sequences of ICs support the idea that multiple episodes of horizontal transfer (HT) of ICs have occurred in vertebrates. In addition, the discovery of intact transposases, perfect TIRs and target site duplications of ICs suggests that this family may still be active in Insecta, Arachnida, frogs, and fish. CONCLUSIONS Exploring the diversity of Tc1/mariner transposons and revealing their evolutionary profiles will help provide a better understanding of the evolution of DNA transposons and their impact on genomic evolution. Here, a newly discovered family (DD36E/Incomer) of Tc1/mariner transposons is described in animals. It displays a similar structural organization and close relationship with the known DD34E/Tc1 elements, but has a relatively narrow distribution, indicating that DD36E/IC might have originated from the DD34E/Tc1 family. Our data also support the hypothesis of horizontal transfer of IC in vertebrates, even invading one lineage of mammals (bats). This study expands our understanding of the diversity of Tc1/mariner transposons and updates the classification of this superfamily.
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Affiliation(s)
- Yatong Sang
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Bo Gao
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225 Langen, Germany
| | - Mohamed Diaby
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Wencheng Zong
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Cai Chen
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Dan Shen
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Saisai Wang
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yali Wang
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225 Langen, Germany
| | - Chengyi Song
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
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13
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Morgan-Richards M, Langton-Myers SS, Trewick SA. Loss and gain of sexual reproduction in the same stick insect. Mol Ecol 2019; 28:3929-3941. [PMID: 31386772 PMCID: PMC6852293 DOI: 10.1111/mec.15203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 06/17/2019] [Accepted: 07/30/2019] [Indexed: 01/10/2023]
Abstract
The outcome of competition between different reproductive strategies within a single species can be used to infer selective advantage of the winning strategy. Where multiple populations have independently lost or gained sexual reproduction it is possible to investigate whether the advantage is contingent on local conditions. In the New Zealand stick insect Clitarchus hookeri, three populations are distinguished by recent change in reproductive strategy and we determine their likely origins. One parthenogenetic population has established in the United Kingdom and we provide evidence that sexual reproduction has been lost in this population. We identify the sexual population from which the parthenogenetic population was derived, but show that the UK females have a post‐mating barrier to fertilisation. We also demonstrate that two sexual populations have recently arisen in New Zealand within the natural range of the mtDNA lineage that otherwise characterizes parthenogenesis in this species. We infer independent origins of males at these two locations using microsatellite genotypes. In one population, a mixture of local and nonlocal alleles suggested males were the result of invasion. Males in another population were most probably the result of loss of an X chromosome that produced a male phenotype in situ. Two successful switches in reproductive strategy suggest local competitive advantage for outcrossing over parthenogenetic reproduction. Clitarchus hookeri provides remarkable evidence of repeated and rapid changes in reproductive strategy, with competitive outcomes dependent on local conditions.
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Affiliation(s)
| | | | - Steven A Trewick
- Wildlife & Ecology, Massey University, Palmerston North, New Zealand
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14
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Veenstra JA. Two Lys-vasopressin-like peptides, EFLamide, and other phasmid neuropeptides. Gen Comp Endocrinol 2019; 278:3-11. [PMID: 29705195 DOI: 10.1016/j.ygcen.2018.04.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/23/2018] [Accepted: 04/25/2018] [Indexed: 10/25/2022]
Abstract
Phasmid neuropeptide genes were identified in the genomes of two phasmids, Timema cristinae and Clitarchus hookeri. The two species belong to two sisters groups, the Timematodea and Euphasmatodea respectively. Neuropeptide genes were identified using the BLAST+ program on the genome assemblies and the absence of some neuropeptides was confirmed by the concomitant absence of their G-protein coupled receptors. Both genomes were assembled using short reads and the average coverage of the genome is more than 166 times for both species. This makes it virtually impossible that there would not be a single short read for at least one of the conserved transmembrane regions of a GPCR coded by such a genome. Hence, when not a single read can be found for a specific GPCR, it can be concluded that the particular gene is absent from that species. Most previously identified insect neuropeptides are used by these two species. Of the three arthropod allatostatin C related peptides, only allatostatins CC and CCC are present. Both species lack leucokinin, while sulfakinin and dilp8 signaling is absent from Clitarchus, but present in Timema. Interestingly, whereas Timema has lost a vasopressin-related peptide, the gene coding such a peptide is amplified in the Clitarchus genome. Furthermore, while Clitarchus has a specific tryptopyrokinin gene, Timema does not and in this species tryptopyrokinin is coded only by the pyrokinin and periviscerokinin genes. Finally, both species have genes coding EFLamide and its GPCR; in phasmids these genes codes for one (Clitarchus) or two (Timema) EFLamide paracopies.
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Affiliation(s)
- Jan A Veenstra
- INCIA, UMR 5287 CNRS, Université de Bordeaux, allée Geoffroy St Hillaire, CS 50023, 33 615 Pessac Cedex, France.
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15
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Tvedte ES, Logsdon JM, Forbes AA. Sex loss in insects: causes of asexuality and consequences for genomes. CURRENT OPINION IN INSECT SCIENCE 2019; 31:77-83. [PMID: 31109677 DOI: 10.1016/j.cois.2018.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/03/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
Boasting a staggering diversity of reproductive strategies, insects provide attractive models for the comparative study of the causes and consequences of transitions to asexuality. We provide an overview of some contemporary studies of reproductive systems in insects and compile an initial database of asexual insect genome resources. Insect systems have already yielded some important insights into various mechanisms by which sex is lost, including genetic, endosymbiont-mediated, and hybridization. Studies of mutation and substitution after loss of sex provide the strongest empirical support for hypothesized effects of asexuality, whereas there is mixed evidence for ecological hypotheses such as increased parasite load and altered niche breadth in asexuals. Most hypotheses have been explored in a select few taxa (e.g. stick insects, aphids), such that much of the great taxonomic breadth of insects remain understudied. Given the variation in the proximate causes of asexuality in insects, we argue for expanding the taxonomic breadth of study systems. Despite some challenges for investigating sex in insects, the increasing cost-effectiveness of genomic sequencing makes data generation for closely-related asexual and sexual lineages increasingly feasible.
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Affiliation(s)
- Eric S Tvedte
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States.
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA, United States
| | - Andrew A Forbes
- Department of Biology, University of Iowa, Iowa City, IA, United States
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16
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Peona V, Weissensteiner MH, Suh A. How complete are “complete” genome assemblies?-An avian perspective. Mol Ecol Resour 2018; 18:1188-1195. [DOI: 10.1111/1755-0998.12933] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/11/2018] [Accepted: 07/06/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Valentina Peona
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Matthias H. Weissensteiner
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
- Division of Evolutionary Biology; Faculty of Biology; Ludwig-Maximilian University of Munich; Planegg-Martinsried Germany
| | - Alexander Suh
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
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17
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Brand P, Lin W, Johnson BR. The Draft Genome of the Invasive Walking Stick, Medauroidea extradendata, Reveals Extensive Lineage-Specific Gene Family Expansions of Cell Wall Degrading Enzymes in Phasmatodea. G3 (BETHESDA, MD.) 2018; 8:1403-1408. [PMID: 29588379 PMCID: PMC5940134 DOI: 10.1534/g3.118.200204] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 03/21/2018] [Indexed: 12/12/2022]
Abstract
Plant cell wall components are the most abundant macromolecules on Earth. The study of the breakdown of these molecules is thus a central question in biology. Surprisingly, plant cell wall breakdown by herbivores is relatively poorly understood, as nearly all early work focused on the mechanisms used by symbiotic microbes to breakdown plant cell walls in insects such as termites. Recently, however, it has been shown that many organisms make endogenous cellulases. Insects, and other arthropods, in particular have been shown to express a variety of plant cell wall degrading enzymes in many gene families with the ability to break down all the major components of the plant cell wall. Here we report the genome of a walking stick, Medauroidea extradentata, an obligate herbivore that makes uses of endogenously produced plant cell wall degrading enzymes. We present a draft of the 3.3Gbp genome along with an official gene set that contains a diversity of plant cell wall degrading enzymes. We show that at least one of the major families of plant cell wall degrading enzymes, the pectinases, have undergone a striking lineage-specific gene family expansion in the Phasmatodea. This genome will be a useful resource for comparative evolutionary studies with herbivores in many other clades and will help elucidate the mechanisms by which metazoans breakdown plant cell wall components.
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Affiliation(s)
- Philipp Brand
- Department of Evolution and Ecology, Center for Population Biology, University of California, Davis, California 95619
| | - Wei Lin
- Department of Entomology and Nematology, University of California, Davis, California 95616
| | - Brian R Johnson
- Department of Entomology and Nematology, University of California, Davis, California 95616
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