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Kitchen SA, Naragon TH, Brückner A, Ladinsky MS, Quinodoz SA, Badroos JM, Viliunas JW, Kishi Y, Wagner JM, Miller DR, Yousefelahiyeh M, Antoshechkin IA, Eldredge KT, Pirro S, Guttman M, Davis SR, Aardema ML, Parker J. The genomic and cellular basis of biosynthetic innovation in rove beetles. Cell 2024; 187:3563-3584.e26. [PMID: 38889727 PMCID: PMC11246231 DOI: 10.1016/j.cell.2024.05.012] [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: 06/07/2023] [Revised: 02/29/2024] [Accepted: 05/06/2024] [Indexed: 06/20/2024]
Abstract
How evolution at the cellular level potentiates macroevolutionary change is central to understanding biological diversification. The >66,000 rove beetle species (Staphylinidae) form the largest metazoan family. Combining genomic and cell type transcriptomic insights spanning the largest clade, Aleocharinae, we retrace evolution of two cell types comprising a defensive gland-a putative catalyst behind staphylinid megadiversity. We identify molecular evolutionary steps leading to benzoquinone production by one cell type via a mechanism convergent with plant toxin release systems, and synthesis by the second cell type of a solvent that weaponizes the total secretion. This cooperative system has been conserved since the Early Cretaceous as Aleocharinae radiated into tens of thousands of lineages. Reprogramming each cell type yielded biochemical novelties enabling ecological specialization-most dramatically in symbionts that infiltrate social insect colonies via host-manipulating secretions. Our findings uncover cell type evolutionary processes underlying the origin and evolvability of a beetle chemical innovation.
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Affiliation(s)
- Sheila A Kitchen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Thomas H Naragon
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Adrian Brückner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mark S Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sofia A Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jean M Badroos
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Joani W Viliunas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yuriko Kishi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Julian M Wagner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - David R Miller
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mina Yousefelahiyeh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Igor A Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - K Taro Eldredge
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stacy Pirro
- Iridian Genomes, 613 Quaint Acres Dr., Silver Spring, MD 20904, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Steven R Davis
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, NJ 07043, USA
| | - Joseph Parker
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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2
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Kim B, Jhang SY, Koh B, Kim S, Chi WJ, Park JM, Lim CE, Hong Y, Kim H, Yu J, Cho S. Chromosome-level genome assembly of Korean holoparasitic plants, Orobanche coerulescens. Sci Data 2024; 11:714. [PMID: 38956398 PMCID: PMC11219998 DOI: 10.1038/s41597-024-03207-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/02/2024] [Indexed: 07/04/2024] Open
Abstract
Orobanche coerulescens is a parasitic plant that cannot complete its life cycle without a host and is incapable of photosynthesis. The habitats of O. coerulescens span the coasts of Korea and its volcanic islands, Ulleungdo and Dokdo. Those on the volcanic islands exhibit morphological differences and have distinct hosts compared to those on the peninsula. The family of Orobanchaceae, encompassing both autotrophic and parasitic species, serves as a model for evolutionary studies of parasitic states. However, there are limited genome assemblies for the Orobanche genus. In our study, we produced approximately 100x ONT long reads to construct a chromosome-level genome of O. coerulescens. The resulting assembly has a total size of 3,648 Mb with an N50 value of 195 Mb, and 82.0% of BUSCO genes were identified as complete. Results of the repeat annotation revealed that 86.3% of the genome consisted of repeat elements, and 29,395 protein-coding genes were annotated. This chromosome-level genome will be an important biological resource for conserving biodiversity and further understanding parasitic plants.
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Affiliation(s)
- Bongsang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
- eGnome, Inc, Seoul, Republic of Korea.
| | - So Yun Jhang
- eGnome, Inc, Seoul, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Bomin Koh
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc, Seoul, Republic of Korea
| | - Soonok Kim
- National Institute of Biological Resources, Incheon, Republic of Korea
| | - Won-Jae Chi
- National Institute of Biological Resources, Incheon, Republic of Korea
| | - Jeong-Mi Park
- National Institute of Biological Resources, Incheon, Republic of Korea
| | - Chae Eun Lim
- National Institute of Biological Resources, Incheon, Republic of Korea
| | - Yoonjee Hong
- National Institute of Biological Resources, Incheon, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc, Seoul, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | | | - Seoae Cho
- eGnome, Inc, Seoul, Republic of Korea
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3
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Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fürst-Jansen JMR, Dadras A, Zegers JMS, Rieseberg TP, Dhabalia Ashok A, Darienko T, Bierenbroodspot MJ, Gramzow L, Petroll R, Haas FB, Fernandez-Pozo N, Nousias O, Li T, Fitzek E, Grayburn WS, Rittmeier N, Permann C, Rümpler F, Archibald JM, Theißen G, Mower JP, Lorenz M, Buschmann H, von Schwartzenberg K, Boston L, Hayes RD, Daum C, Barry K, Grigoriev IV, Wang X, Li FW, Rensing SA, Ben Ari J, Keren N, Mosquna A, Holzinger A, Delaux PM, Zhang C, Huang J, Mutwil M, de Vries J, Yin Y. Genomes of multicellular algal sisters to land plants illuminate signaling network evolution. Nat Genet 2024; 56:1018-1031. [PMID: 38693345 PMCID: PMC11096116 DOI: 10.1038/s41588-024-01737-3] [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: 04/21/2023] [Accepted: 03/25/2024] [Indexed: 05/03/2024]
Abstract
Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.
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Affiliation(s)
- Xuehuan Feng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jinfang Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Zhejiang Lab, Hangzhou, China
| | - Iker Irisarri
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany
- Section Phylogenomics, Centre for Molecular biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Museum Hamburg, Hamburg, Germany
| | - Huihui Yu
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE, USA
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Yunnan, China
| | - Bo Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Zahin Ali
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Sophie de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, France
| | - Janine M R Fürst-Jansen
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Armin Dadras
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Jaccoline M S Zegers
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Tim P Rieseberg
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Amra Dhabalia Ashok
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Tatyana Darienko
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Maaike J Bierenbroodspot
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Lydia Gramzow
- University of Jena, Matthias Schleiden Institute/Genetics, Jena, Germany
| | - Romy Petroll
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Fabian B Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Institute for Mediterranean and Subtropical Horticulture 'La Mayora', Málaga, Spain
| | - Orestis Nousias
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Tang Li
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Elisabeth Fitzek
- Computational Biology, Department of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - W Scott Grayburn
- Northern Illinois University, Molecular Core Lab, Department of Biological Sciences, DeKalb, IL, USA
| | - Nina Rittmeier
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Innsbruck, Austria
| | - Charlotte Permann
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Innsbruck, Austria
| | - Florian Rümpler
- University of Jena, Matthias Schleiden Institute/Genetics, Jena, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Günter Theißen
- University of Jena, Matthias Schleiden Institute/Genetics, Jena, Germany
| | - Jeffrey P Mower
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE, USA
| | - Maike Lorenz
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Experimental Phycology and Culture Collection of Algae at Goettingen University, Goettingen, Germany
| | - Henrik Buschmann
- University of Applied Sciences Mittweida, Faculty of Applied Computer Sciences and Biosciences, Section Biotechnology and Chemistry, Molecular Biotechnology, Mittweida, Germany
| | - Klaus von Schwartzenberg
- Universität Hamburg, Institute of Plant Science and Microbiology, Microalgae and Zygnematophyceae Collection Hamburg and Aquatic Ecophysiology and Phycology, Hamburg, Germany
| | - Lori Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Richard D Hayes
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Xiyin Wang
- North China University of Science and Technology, Tangshan, China
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- University of Freiburg, Centre for Biological Signalling Studies (BIOSS), Freiburg, Germany
| | - Julius Ben Ari
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Noa Keren
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Assaf Mosquna
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Andreas Holzinger
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Innsbruck, Austria
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, France
| | - Chi Zhang
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE, USA
- University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, NE, USA
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC, USA
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Marek Mutwil
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Jan de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany.
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany.
- University of Goettingen, Goettingen Center for Molecular Biosciences, Goettingen, Germany.
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.
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4
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Yıldız Akkamış H, Kaya EC, Tek AL. Discovery and genome-wide characterization of a novel miniature inverted repeat transposable element reveal genome-specific distribution in Glycine. Genes Genomics 2024:10.1007/s13258-024-01519-5. [PMID: 38676850 DOI: 10.1007/s13258-024-01519-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Miniature inverted repeat transposable elements (MITEs) are a dynamic component responsible for genome evolution. Tourist MITEs are derived from and mobilized by elements from the harbinger superfamily. OBJECTIVE In this study, a novel family of Tourist-like MITE was characterized in wild soybean species Glycine falcata. The new GftoMITE1 was initially discovered as an insertional polymorphism of the centromere-specific histone H3 (CenH3) gene in G. falcata. METHODS Using polymerase chain reaction, cloning and sequencing approaches, we showed a high number of copies of the GftoMITE1 family. Extensive bioinformatic analyses revealed the genome-level distribution and locus-specific mapping of GftoMITE1 members in Glycine species. RESULTS Our results provide the first extensive characterization of the GftoMITE1 family and contribute to the understanding of the evolution of MITEs in the Glycine genus. Genome-specific GftoMITE1 was prominent in perennial wild soybean species, but not in annual cultivated soybean (Glycine max) or its progenitor (Glycine soja). CONCLUSIONS We discuss that the GftoMITE1 family reveals a single rapid amplification in G. falcata and could have potential implications for gene regulation and soybean breeding as an efficient genetic marker for germplasm utilization in the future.
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Affiliation(s)
- Hümeyra Yıldız Akkamış
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240, Niğde, Turkey
| | - Emir Can Kaya
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240, Niğde, Turkey
| | - Ahmet L Tek
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240, Niğde, Turkey.
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5
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Garza AB, Lerat E, Girgis HZ. Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats. Mob DNA 2024; 15:8. [PMID: 38627766 PMCID: PMC11020628 DOI: 10.1186/s13100-024-00317-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 03/08/2024] [Indexed: 04/20/2024] Open
Abstract
Plant genomes include large numbers of transposable elements. One particular type of these elements is flanked by two Long Terminal Repeats (LTRs) and can translocate using RNA. Such elements are known as LTR-retrotransposons; they are the most abundant type of transposons in plant genomes. They have many important functions involving gene regulation and the rise of new genes and pseudo genes in response to severe stress. Additionally, LTR-retrotransposons have several applications in biotechnology. Due to the abundance and the importance of LTR-retrotransposons, multiple computational tools have been developed for their detection. However, none of these tools take advantages of the availability of related genomes; they process one chromosome at a time. Further, recently nested LTR-retrotransposons (multiple elements of the same family are inserted into each other) cannot be annotated accurately - or cannot be annotated at all - by the currently available tools. Motivated to overcome these two limitations, we built Look4LTRs, which can annotate LTR-retrotransposons in multiple related genomes simultaneously and discover recently nested elements. The methodology of Look4LTRs depends on techniques imported from the signal-processing field, graph algorithms, and machine learning with a minimal use of alignment algorithms. Four plant genomes were used in developing Look4LTRs and eight plant genomes for evaluating it in contrast to three related tools. Look4LTRs is the fastest while maintaining better or comparable F1 scores (the harmonic average of recall and precision) to those obtained by the other tools. Our results demonstrate the added benefit of annotating LTR-retrotransposons in multiple related genomes simultaneously and the ability to discover recently nested elements. Expert human manual examination of six elements - not included in the ground truth - revealed that three elements belong to known families and two elements are likely from new families. With respect to examining recently nested LTR-retrotransposons, three out of five were confirmed to be valid elements. Look4LTRs - with its speed, accuracy, and novel features - represents a true advancement in the annotation of LTR-retrotransposons, opening the door to many studies focused on understanding their functions in plants.
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Affiliation(s)
- Anthony B Garza
- Bioinformatics Toolsmith Laboratory, Department of Electrical Engineering and Computer Science, Texas A &M University-Kingsville, Kingsville, Texas, USA
| | - Emmanuelle Lerat
- The Biometrics and Evolutionary Biology Laboratory, University Lyon 1, Lyon, France
| | - Hani Z Girgis
- Bioinformatics Toolsmith Laboratory, Department of Electrical Engineering and Computer Science, Texas A &M University-Kingsville, Kingsville, Texas, USA.
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Bhattarai UR, Poulin R, Gemmell NJ, Dowle E. Genome assembly and annotation of the mermithid nematode Mermis nigrescens. G3 (BETHESDA, MD.) 2024; 14:jkae023. [PMID: 38301266 PMCID: PMC10989877 DOI: 10.1093/g3journal/jkae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/03/2024]
Abstract
Genetic studies of nematodes have been dominated by Caenorhabditis elegans as a model species. A lack of genomic resources has limited the expansion of genetic research to other groups of nematodes. Here, we report a draft genome assembly of a mermithid nematode, Mermis nigrescens. Mermithidae are insect parasitic nematodes with hosts including a wide range of terrestrial arthropods. We sequenced, assembled, and annotated the whole genome of M. nigrescens using nanopore long reads and 10X Chromium link reads. The assembly is 524 Mb in size consisting of 867 scaffolds. The N50 value is 2.42 Mb, and half of the assembly is in the 30 longest scaffolds. The assembly BUSCO score from the eukaryotic database (eukaryota_odb10) indicates that the genome is 86.7% complete and 5.1% partial. The genome has a high level of heterozygosity (6.6%) with a repeat content of 83.98%. mRNA-seq reads from different sized nematodes (≤2 cm, 3.5-7 cm, and >7 cm body length) representing different developmental stages were also generated and used for the genome annotation. Using ab initio and evidence-based gene model predictions, 12,313 protein-coding genes and 24,186 mRNAs were annotated. These genomic resources will help researchers investigate the various aspects of the biology and host-parasite interactions of mermithid nematodes.
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Affiliation(s)
- Upendra R Bhattarai
- Department of Anatomy, University of Otago, Dunedin 9016, New Zealand
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - 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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Minnick MF. Functional Roles and Genomic Impact of Miniature Inverted-Repeat Transposable Elements (MITEs) in Prokaryotes. Genes (Basel) 2024; 15:328. [PMID: 38540387 PMCID: PMC10969869 DOI: 10.3390/genes15030328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 06/14/2024] Open
Abstract
Prokaryotic genomes are dynamic tapestries that are strongly influenced by mobile genetic elements (MGEs), including transposons (Tn's), plasmids, and bacteriophages. Of these, miniature inverted-repeat transposable elements (MITEs) are undoubtedly the least studied MGEs in bacteria and archaea. This review explores the diversity and distribution of MITEs in prokaryotes and describes what is known about their functional roles in the host and involvement in genomic plasticity and evolution.
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Affiliation(s)
- Michael F Minnick
- Program in Cellular, Molecular and Microbial Biology, Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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8
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Li T, Zheng J, Nousias O, Yan Y, Meinhardt LW, Goenaga R, Zhang D, Yin Y. The American Cherimoya Genome Reveals Insights into the Intra-Specific Divergence, the Evolution of Magnoliales, and a Putative Gene Cluster for Acetogenin Biosynthesis. PLANTS (BASEL, SWITZERLAND) 2024; 13:636. [PMID: 38475482 DOI: 10.3390/plants13050636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024]
Abstract
Annona cherimola (cherimoya) is a species renowned for its delectable fruit and medicinal properties. In this study, we developed a chromosome-level genome assembly for the cherimoya 'Booth' cultivar from the United States. The genome assembly has a size of 794 Mb with a N50 = 97.59 Mb. The seven longest scaffolds account for 87.6% of the total genome length, which corresponds to the seven pseudo-chromosomes. A total of 45,272 protein-coding genes (≥30 aa) were predicted with 92.9% gene content completeness. No recent whole genome duplications were identified by an intra-genome collinearity analysis. Phylogenetic analysis supports that eudicots and magnoliids are more closely related to each other than to monocots. Moreover, the Magnoliales was found to be more closely related to the Laurales than the Piperales. Genome comparison revealed that the 'Booth' cultivar has 200 Mb less repeats than the Spanish cultivar 'Fino de Jete', despite their highly similar (>99%) genome sequence identity and collinearity. These two cultivars were diverged during the early Pleistocene (1.93 Mya), which suggests a different origin and domestication of the cherimoya. Terpene/terpenoid metabolism functions were found to be enriched in Magnoliales, while TNL (Toll/Interleukin-1-NBS-LRR) disease resistance gene has been lost in Magnoliales during evolution. We have also identified a gene cluster that is potentially responsible for the biosynthesis of acetogenins, a class of natural products found exclusively in Annonaceae. The cherimoya genome provides an invaluable resource for supporting characterization, conservation, and utilization of Annona genetic resources.
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Affiliation(s)
- Tang Li
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA
| | - Jinfang Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA
| | - Orestis Nousias
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA
| | - Yuchen Yan
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA
| | - Lyndel W Meinhardt
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Ricardo Goenaga
- Tropical Agriculture Research Station, United States Department of Agriculture, Agriculture Research Service, Mayaguez 00680, Puerto Rico
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA
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9
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Loreto ELS, Melo ESD, Wallau GL, Gomes TMFF. The good, the bad and the ugly of transposable elements annotation tools. Genet Mol Biol 2024; 46:e20230138. [PMID: 38373163 PMCID: PMC10876081 DOI: 10.1590/1678-4685-gmb-2023-0138] [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: 05/09/2023] [Accepted: 11/26/2023] [Indexed: 02/21/2024] Open
Abstract
Transposable elements are repetitive and mobile DNA segments that can be found in virtually all organisms investigated to date. Their complex structure and variable nature are particularly challenging from the genomic annotation point of view. Many softwares have been developed to automate and facilitate TEs annotation at the genomic level, but they are highly heterogeneous regarding documentation, usability and methods. In this review, we revisited the existing software for TE genomic annotation, concentrating on the most often used ones, the methodologies they apply, and usability. Building on the state of the art of TE annotation software we propose best practices and highlight the strengths and weaknesses from the available solutions.
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Affiliation(s)
- Elgion L S Loreto
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal de Santa Maria, Departamento de Bioquímica e Biologia Molecular, Santa Maria, RS, Brazil
| | - Elverson S de Melo
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Entomologia, Recife, PE, Brazil
| | - Gabriel L Wallau
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Entomologia, Recife, PE, Brazil
| | - Tiago M F F Gomes
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
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10
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Stuart KC, Johnson RN, Major RE, Atsawawaranunt K, Ewart KM, Rollins LA, Santure AW, Whibley A. The genome of a globally invasive passerine, the common myna, Acridotheres tristis. DNA Res 2024; 31:dsae005. [PMID: 38366840 PMCID: PMC10917472 DOI: 10.1093/dnares/dsae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/18/2024] Open
Abstract
In an era of global climate change, biodiversity conservation is receiving increased attention. Conservation efforts are greatly aided by genetic tools and approaches, which seek to understand patterns of genetic diversity and how they impact species health and their ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions regarding adaptive potential, with a particular focus on how changes in genetic diversity and effective population size interact with novel selection regimes. The common myna (Acridotheres tristis) is a globally invasive passerine and is an excellent model species for research both into the persistence of low-diversity populations and the mechanisms of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna. We describe the genomic landscape of this species, including genome wide allelic diversity, methylation, repeats, and recombination rate, as well as an examination of gene family evolution. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, and reveal artefactual impacts of genetic bottlenecks on demographic analysis.
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Affiliation(s)
- Katarina C Stuart
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Rebecca N Johnson
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Richard E Major
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
| | | | - Kyle M Ewart
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
- School of Life and Environmental Sciences,University of Sydney, Sydney, Australia
| | - Lee A Rollins
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa, New Zealand
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11
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Gao D. Introduction of Plant Transposon Annotation for Beginners. BIOLOGY 2023; 12:1468. [PMID: 38132293 PMCID: PMC10741241 DOI: 10.3390/biology12121468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Transposons are mobile DNA sequences that contribute large fractions of many plant genomes. They provide exclusive resources for tracking gene and genome evolution and for developing molecular tools for basic and applied research. Despite extensive efforts, it is still challenging to accurately annotate transposons, especially for beginners, as transposon prediction requires necessary expertise in both transposon biology and bioinformatics. Moreover, the complexity of plant genomes and the dynamic evolution of transposons also bring difficulties for genome-wide transposon discovery. This review summarizes the three major strategies for transposon detection including repeat-based, structure-based, and homology-based annotation, and introduces the transposon superfamilies identified in plants thus far, and some related bioinformatics resources for detecting plant transposons. Furthermore, it describes transposon classification and explains why the terms 'autonomous' and 'non-autonomous' cannot be used to classify the superfamilies of transposons. Lastly, this review also discusses how to identify misannotated transposons and improve the quality of the transposon database. This review provides helpful information about plant transposons and a beginner's guide on annotating these repetitive sequences.
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Affiliation(s)
- Dongying Gao
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210, USA
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12
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Rigou S, Schmitt A, Alempic JM, Lartigue A, Vendloczki P, Abergel C, Claverie JM, Legendre M. Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses. Mol Biol Evol 2023; 40:msad244. [PMID: 37950899 PMCID: PMC10664404 DOI: 10.1093/molbev/msad244] [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: 02/25/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/13/2023] Open
Abstract
Pithoviridae are amoeba-infecting giant viruses possessing the largest viral particles known so far. Since the discovery of Pithovirus sibericum, recovered from a 30,000-yr-old permafrost sample, other pithoviruses, and related cedratviruses, were isolated from various terrestrial and aquatic samples. Here, we report the isolation and genome sequencing of 2 Pithoviridae from soil samples, in addition to 3 other recent isolates. Using the 12 available genome sequences, we conducted a thorough comparative genomic study of the Pithoviridae family to decipher the organization and evolution of their genomes. Our study reveals a nonuniform genome organization in 2 main regions: 1 concentrating core genes and another gene duplications. We also found that Pithoviridae genomes are more conservative than other families of giant viruses, with a low and stable proportion (5% to 7%) of genes originating from horizontal transfers. Genome size variation within the family is mainly due to variations in gene duplication rates (from 14% to 28%) and massive invasion by inverted repeats. While these repeated elements are absent from cedratviruses, repeat-rich regions cover as much as a quarter of the pithoviruses genomes. These regions, identified using a dedicated pipeline, are hotspots of mutations, gene capture events, and genomic rearrangements that contribute to their evolution.
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Affiliation(s)
- Sofia Rigou
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Alain Schmitt
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Jean-Marie Alempic
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Audrey Lartigue
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Peter Vendloczki
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Chantal Abergel
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Jean-Michel Claverie
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Matthieu Legendre
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
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13
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Purayil GP, Almarzooqi AY, El-Tarabily KA, You FM, AbuQamar SF. Fully resolved assembly of Fusarium proliferatum DSM106835 genome. Sci Data 2023; 10:705. [PMID: 37845258 PMCID: PMC10579329 DOI: 10.1038/s41597-023-02610-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/28/2023] [Indexed: 10/18/2023] Open
Abstract
In the United Arab Emirates, sudden decline syndrome (SDS) is a destructive disease of date palm caused by the soil-borne fungal pathogen Fusarium proliferatum (Fp) DSM106835. Here, a high-resolution genome assembly of Fp DSM106835 was generated using PacBio HiFi sequencing with Omni-C data to provide a high-quality chromatin-organised reference genome with 418 scaffolds, totalling 58,468,907 bp in length and an N50 value of 4,383,091 bp from which 15,580 genes and 16,321 transcripts were predicted. The assembly achieved a complete BUSCO score of 99.2% for 758 orthologous genes. Compared to seven other Fp strains, Fp DSM106835 exhibited the highest continuity with a cumulative size of 44.26 Mbp for the first ten scaffolds/contigs, surpassing the assemblies of all examined Fp strains. Our findings of the high-quality genome of Fp DSM106835 provide an important resource to investigate its genetics, biology and evolutionary history. This study also contributes to fulfill the gaps in fungal knowledge, particularly the genes/metabolites associated with pathogenicity during the plant-pathogen interaction responsible for SDS.
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Affiliation(s)
- Gouthaman P Purayil
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Amal Y Almarzooqi
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates.
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
| | - Synan F AbuQamar
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates.
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14
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Lee C, Polo RO, Zaheer R, Van Domselaar G, Zovoilis A, McAllister TA. Evaluation of metagenomic assembly methods for the detection and characterization of antimicrobial resistance determinants and associated mobilizable elements. J Microbiol Methods 2023; 213:106815. [PMID: 37699502 DOI: 10.1016/j.mimet.2023.106815] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/14/2023]
Abstract
Antimicrobial resistance genes (ARGs) can be transferred between members of a bacterial population by mobile genetic elements (MGE). Understanding the risk of these transfer events is important in monitoring and predicting antimicrobial resistance (AMR), especially in the context of a One Health Continuum. However, there is no universally accepted method for detection of ARGs and MGEs, and especially for determining their linkages. This study used publicly available shotgun metagenomic DNA short-read (Illumina, 100 bp paired-end) sequence data from samples across the One Health Continuum (including beef cattle composite feces from feedlots, catch basin water at feedlots, agricultural soil from feedlot manured surrounding fields, and urban/municipal sewage influent from two municipal wastewater treatment plants) to develop a workflow to identify and associate ARGs and MGEs. ARG- and MGE-based targeted-assemblies with available short-read data were unable to meet this analysis goal. In contrast, de novo assembly of contigs provided enough sequence context to associate ARGs and MGEs, without compromising discovery rate. However, to estimate the relative abundance of these elements, unassembled sequence data must still be used.
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Affiliation(s)
- Catrione Lee
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada; Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T3M 2L7, Canada
| | - Rodrigo Ortega Polo
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Government of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada
| | - Athanasios Zovoilis
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T3M 2L7, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada.
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15
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Liao X, Zhu W, Zhou J, Li H, Xu X, Zhang B, Gao X. Repetitive DNA sequence detection and its role in the human genome. Commun Biol 2023; 6:954. [PMID: 37726397 PMCID: PMC10509279 DOI: 10.1038/s42003-023-05322-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 09/04/2023] [Indexed: 09/21/2023] Open
Abstract
Repetitive DNA sequences playing critical roles in driving evolution, inducing variation, and regulating gene expression. In this review, we summarized the definition, arrangement, and structural characteristics of repeats. Besides, we introduced diverse biological functions of repeats and reviewed existing methods for automatic repeat detection, classification, and masking. Finally, we analyzed the type, structure, and regulation of repeats in the human genome and their role in the induction of complex diseases. We believe that this review will facilitate a comprehensive understanding of repeats and provide guidance for repeat annotation and in-depth exploration of its association with human diseases.
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Affiliation(s)
- Xingyu Liao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Wufei Zhu
- Department of Endocrinology, Yichang Central People's Hospital, The First College of Clinical Medical Science, China Three Gorges University, 443000, Yichang, P.R. China
| | - Juexiao Zhou
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Haoyang Li
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Xiaopeng Xu
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Bin Zhang
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia.
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16
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Burkes-Patton S, Cooper EA, Schlueter J. RepBox: a toolbox for the identification of repetitive elements. BMC Bioinformatics 2023; 24:317. [PMID: 37608271 PMCID: PMC10463291 DOI: 10.1186/s12859-023-05419-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 07/18/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) are short, mobile DNA elements that are known to play important roles in the genomes of many eukaryotic species. The identification and categorization of these elements is a critical task for many genomic studies, and the continued increase in the number of de novo assembled genomes demands new tools to improve the efficiency of this process. For this reason, we developed RepBox, a suite of Python scripts that combine several pre-existing family-specific TE detection methods into a single user-friendly pipeline. RESULTS Based on comparisons of RepBox with the standard TE detection software RepeatModeler, we find that RepBox consistently classifies more elements and is also able to identify a more diverse array of TE families than the existing methods in plant genomes. CONCLUSIONS The performance of RepBox on two different plant genomes indicates that our toolbox represents a significant improvement over existing TE detection methods, and should facilitate future TE annotation efforts in additional species.
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Affiliation(s)
- Shelvasha Burkes-Patton
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Elizabeth A Cooper
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
- North Carolina Research Campus, Kannapolis, NC, 28081, USA
| | - Jessica Schlueter
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
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17
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Sheng Y, Wang H, Ou Y, Wu Y, Ding W, Tao M, Lin S, Deng Z, Bai L, Kang Q. Insertion sequence transposition inactivates CRISPR-Cas immunity. Nat Commun 2023; 14:4366. [PMID: 37474569 PMCID: PMC10359306 DOI: 10.1038/s41467-023-39964-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/06/2023] [Indexed: 07/22/2023] Open
Abstract
CRISPR-Cas immunity systems safeguard prokaryotic genomes by inhibiting the invasion of mobile genetic elements. Here, we screened prokaryotic genomic sequences and identified multiple natural transpositions of insertion sequences (ISs) into cas genes, thus inactivating CRISPR-Cas defenses. We then generated an IS-trapping system, using Escherichia coli strains with various ISs and an inducible cas nuclease, to monitor IS insertions into cas genes following the induction of double-strand DNA breakage as a physiological host stress. We identified multiple events mediated by different ISs, especially IS1 and IS10, displaying substantial relaxed target specificity. IS transposition into cas was maintained in the presence of DNA repair machinery, and transposition into other host defense systems was also detected. Our findings highlight the potential of ISs to counter CRISPR activity, thus increasing bacterial susceptibility to foreign DNA invasion.
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Affiliation(s)
- Yong Sheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
| | - Hengyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
| | - Yixin Ou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
- Haihe Laboratory of Synthetic Biology, 300308, Tianjin, P. R. China
| | - Yingying Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
- National Engineering Research Center of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilization (South), Ministry of Agriculture and Rural Affairs, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, 201403, Shanghai, P. R. China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
| | - Meifeng Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
- Haihe Laboratory of Synthetic Biology, 300308, Tianjin, P. R. China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
- Haihe Laboratory of Synthetic Biology, 300308, Tianjin, P. R. China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China.
- Haihe Laboratory of Synthetic Biology, 300308, Tianjin, P. R. China.
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China.
| | - Qianjin Kang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China.
- Haihe Laboratory of Synthetic Biology, 300308, Tianjin, P. R. China.
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18
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Martelossi J, Nicolini F, Subacchi S, Pasquale D, Ghiselli F, Luchetti A. Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution. BMC Biol 2023; 21:145. [PMID: 37365567 DOI: 10.1186/s12915-023-01632-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) can represent one of the major sources of genomic variation across eukaryotes, providing novel raw materials for species diversification and innovation. While considerable effort has been made to study their evolutionary dynamics across multiple animal clades, molluscs represent a substantially understudied phylum. Here, we take advantage of the recent increase in mollusc genomic resources and adopt an automated TE annotation pipeline combined with a phylogenetic tree-based classification, as well as extensive manual curation efforts, to characterize TE repertories across 27 bivalve genomes with a particular emphasis on DDE/D class II elements, long interspersed nuclear elements (LINEs), and their evolutionary dynamics. RESULTS We found class I elements as highly dominant in bivalve genomes, with LINE elements, despite less represented in terms of copy number per genome, being the most common retroposon group covering up to 10% of their genome. We mined 86,488 reverse transcriptases (RVT) containing LINE coming from 12 clades distributed across all known superfamilies and 14,275 class II DDE/D-containing transposons coming from 16 distinct superfamilies. We uncovered a previously underestimated rich and diverse bivalve ancestral transposon complement that could be traced back to their most recent common ancestor that lived ~ 500 Mya. Moreover, we identified multiple instances of lineage-specific emergence and loss of different LINEs and DDE/D lineages with the interesting cases of CR1- Zenon, Proto2, RTE-X, and Academ elements that underwent a bivalve-specific amplification likely associated with their diversification. Finally, we found that this LINE diversity is maintained in extant species by an equally diverse set of long-living and potentially active elements, as suggested by their evolutionary history and transcription profiles in both male and female gonads. CONCLUSIONS We found that bivalves host an exceptional diversity of transposons compared to other molluscs. Their LINE complement could mainly follow a "stealth drivers" model of evolution where multiple and diversified families are able to survive and co-exist for a long period of time in the host genome, potentially shaping both recent and early phases of bivalve genome evolution and diversification. Overall, we provide not only the first comparative study of TE evolutionary dynamics in a large but understudied phylum such as Mollusca, but also a reference library for ORF-containing class II DDE/D and LINE elements, which represents an important genomic resource for their identification and characterization in novel genomes.
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Affiliation(s)
- Jacopo Martelossi
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Filippo Nicolini
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
- Fano Marine Center, Department of Biological, Geological and Environmental Sciences, University of Bologna, Viale Adriatico 1/N, 61032, Fano, Italy
| | - Simone Subacchi
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Daniela Pasquale
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Fabrizio Ghiselli
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy.
| | - Andrea Luchetti
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
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19
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Devos KM, Qi P, Bahri BA, Gimode DM, Jenike K, Manthi SJ, Lule D, Lux T, Martinez-Bello L, Pendergast TH, Plott C, Saha D, Sidhu GS, Sreedasyam A, Wang X, Wang H, Wright H, Zhao J, Deshpande S, de Villiers S, Dida MM, Grimwood J, Jenkins J, Lovell J, Mayer KFX, Mneney EE, Ojulong HF, Schatz MC, Schmutz J, Song B, Tesfaye K, Odeny DA. Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet. Nat Commun 2023; 14:3694. [PMID: 37344528 DOI: 10.1038/s41467-023-38915-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/19/2023] [Indexed: 06/23/2023] Open
Abstract
Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a 'poor man's crop', finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts.
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Affiliation(s)
- Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA.
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
| | - Peng Qi
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Bochra A Bahri
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Pathology, University of Georgia, Griffin, GA, 30223, USA
| | - Davis M Gimode
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
| | - Katharine Jenike
- Departments of Computer Science, Biology and Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Samuel J Manthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
- Department of Horticulture, University of Georgia, Athens, GA, 30602, USA
| | - Dagnachew Lule
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Oromia Agricultural Research Institute, P.O. Box 81265, Addis Ababa, Ethiopia
- Ethiopian Agricultural Transformation Agency, Addis Ababa, Bole, Ethiopia
| | - Thomas Lux
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Liliam Martinez-Bello
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- UR Ventures, University of Rochester, Rochester, NY, 14627, USA
| | - Thomas H Pendergast
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Dipnarayan Saha
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- ICAR-Central Research Institute for Jute and Allied Fibers, Kolkata, West Bengal, 700120, India
| | - Gurjot S Sidhu
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Hao Wang
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Hallie Wright
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Jianxin Zhao
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Santosh Deshpande
- ICRISAT, Patancheru, 502 324, T.S., India
- Hytech Seed India Pvt. Ltd., Ravalkol Village, Medcahl-Malkajgiri Dist-, 501 401, Hubballi, T.S, India
| | - Santie de Villiers
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, 80108, Kenya
- Pwani University Biosciences Research Center (PUBReC), Kilifi, 80108, Kenya
| | - Mathews M Dida
- Department of Crop and Soil Science, Maseno University, P.O. 333, Maseno, Kenya
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - John Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Emmarold E Mneney
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar Es Salaam, Tanzania
- Biotechnology Society of Tanzania, P.O. Box 10257, Dar es Salaam, Tanzania
| | - Henry F Ojulong
- ICRISAT, Matopos Research Station, P.O. Box 776, Bulawayo, Zimbabwe
| | - Michael C Schatz
- Departments of Computer Science, Biology and Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bo Song
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Bio and Emerging Technology Institute, Addis Ababa, Ethiopia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
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20
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Kitchen SA, Naragon TH, Brückner A, Ladinsky MS, Quinodoz SA, Badroos JM, Viliunas JW, Wagner JM, Miller DR, Yousefelahiyeh M, Antoshechkin IA, Eldredge KT, Pirro S, Guttman M, Davis SR, Aardema ML, Parker J. The genomic and cellular basis of biosynthetic innovation in rove beetles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542378. [PMID: 37398185 PMCID: PMC10312436 DOI: 10.1101/2023.05.29.542378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
How evolution at the cellular level potentiates change at the macroevolutionary level is a major question in evolutionary biology. With >66,000 described species, rove beetles (Staphylinidae) comprise the largest metazoan family. Their exceptional radiation has been coupled to pervasive biosynthetic innovation whereby numerous lineages bear defensive glands with diverse chemistries. Here, we combine comparative genomic and single-cell transcriptomic data from across the largest rove beetle clade, Aleocharinae. We retrace the functional evolution of two novel secretory cell types that together comprise the tergal gland-a putative catalyst behind Aleocharinae's megadiversity. We identify key genomic contingencies that were critical to the assembly of each cell type and their organ-level partnership in manufacturing the beetle's defensive secretion. This process hinged on evolving a mechanism for regulated production of noxious benzoquinones that appears convergent with plant toxin release systems, and synthesis of an effective benzoquinone solvent that weaponized the total secretion. We show that this cooperative biosynthetic system arose at the Jurassic-Cretaceous boundary, and that following its establishment, both cell types underwent ∼150 million years of stasis, their chemistry and core molecular architecture maintained almost clade-wide as Aleocharinae radiated globally into tens of thousands of lineages. Despite this deep conservation, we show that the two cell types have acted as substrates for the emergence of adaptive, biochemical novelties-most dramatically in symbiotic lineages that have infiltrated social insect colonies and produce host behavior-manipulating secretions. Our findings uncover genomic and cell type evolutionary processes underlying the origin, functional conservation and evolvability of a chemical innovation in beetles.
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21
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Martelossi J, Forni G, Iannello M, Savojardo C, Martelli PL, Casadio R, Mantovani B, Luchetti A, Rota-Stabelli O. Wood feeding and social living: Draft genome of the subterranean termite Reticulitermes lucifugus (Blattodea; Termitoidae). INSECT MOLECULAR BIOLOGY 2023; 32:118-131. [PMID: 36366787 DOI: 10.1111/imb.12818] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Termites (Insecta, Blattodea, Termitoidae) are a widespread and diverse group of eusocial insects known for their ability to digest wood matter. Herein, we report the draft genome of the subterranean termite Reticulitermes lucifugus, an economically important species and among the most studied taxa with respect to eusocial organization and mating system. The final assembly (~813 Mb) covered up to 88% of the estimated genome size and, in agreement with the Asexual Queen Succession Mating System, it was found completely homozygous. We predicted 16,349 highly supported gene models and 42% of repetitive DNA content. Transposable elements of R. lucifugus show similar evolutionary dynamics compared to that of other termites, with two main peaks of activity localized at 25% and 8% of Kimura divergence driven by DNA, LINE and SINE elements. Gene family turnover analyses identified multiple instances of gene duplication associated with R. lucifugus diversification, with significant lineage-specific gene family expansions related to development, perception and nutrient metabolism pathways. Finally, we analysed P450 and odourant receptor gene repertoires in detail, highlighting the large diversity and dynamical evolutionary history of these proteins in the R. lucifugus genome. This newly assembled genome will provide a valuable resource for further understanding the molecular basis of termites biology as well as for pest control.
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Affiliation(s)
- Jacopo Martelossi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Giobbe Forni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Mariangela Iannello
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Castrense Savojardo
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Pier Luigi Martelli
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Rita Casadio
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Andrea Luchetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Omar Rota-Stabelli
- Center Agriculture Food Environment C3A, University of Trento/Fondazione Edmund Mach, Trento, Italy
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22
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Oggenfuss U, Croll D. Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen. PLoS Pathog 2023; 19:e1011130. [PMID: 36787337 PMCID: PMC9970103 DOI: 10.1371/journal.ppat.1011130] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 02/27/2023] [Accepted: 01/18/2023] [Indexed: 02/15/2023] Open
Abstract
The activity of transposable elements (TEs) contributes significantly to pathogen genome evolution. TEs often destabilize genome integrity but may also confer adaptive variation in pathogenicity or resistance traits. De-repression of epigenetically silenced TEs often initiates bursts of transposition activity that may be counteracted by purifying selection and genome defenses. However, how these forces interact to determine the expansion routes of TEs within a pathogen species remains largely unknown. Here, we analyzed a set of 19 telomere-to-telomere genomes of the fungal wheat pathogen Zymoseptoria tritici. Phylogenetic reconstruction and ancestral state estimates of individual TE families revealed that TEs have undergone distinct activation and repression periods resulting in highly uneven copy numbers between genomes of the same species. Most TEs are clustered in gene poor niches, indicating strong purifying selection against insertions near coding sequences, or as a consequence of insertion site preferences. TE families with high copy numbers have low sequence divergence and strong signatures of defense mechanisms (i.e., RIP). In contrast, small non-autonomous TEs (i.e., MITEs) are less impacted by defense mechanisms and are often located in close proximity to genes. Individual TE families have experienced multiple distinct burst events that generated many nearly identical copies. We found that a Copia element burst was initiated from recent copies inserted substantially closer to genes compared to older copies. Overall, TE bursts tended to initiate from copies in GC-rich niches that escaped inactivation by genomic defenses. Our work shows how specific genomic environments features provide triggers for TE proliferation in pathogen genomes.
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Affiliation(s)
- Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- * E-mail:
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23
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Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fürst-Jansen JM, Dadras A, Zegers JM, Rieseberg TP, Ashok AD, Darienko T, Bierenbroodspot MJ, Gramzow L, Petroll R, Haas FB, Fernandez-Pozo N, Nousias O, Li T, Fitzek E, Grayburn WS, Rittmeier N, Permann C, Rümpler F, Archibald JM, Theißen G, Mower JP, Lorenz M, Buschmann H, von Schwartzenberg K, Boston L, Hayes RD, Daum C, Barry K, Grigoriev IV, Wang X, Li FW, Rensing SA, Ari JB, Keren N, Mosquna A, Holzinger A, Delaux PM, Zhang C, Huang J, Mutwil M, de Vries J, Yin Y. Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526407. [PMID: 36778228 PMCID: PMC9915684 DOI: 10.1101/2023.01.31.526407] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The filamentous and unicellular algae of the class Zygnematophyceae are the closest algal relatives of land plants. Inferring the properties of the last common ancestor shared by these algae and land plants allows us to identify decisive traits that enabled the conquest of land by plants. We sequenced four genomes of filamentous Zygnematophyceae (three strains of Zygnema circumcarinatum and one strain of Z. cylindricum) and generated chromosome-scale assemblies for all strains of the emerging model system Z. circumcarinatum. Comparative genomic analyses reveal expanded genes for signaling cascades, environmental response, and intracellular trafficking that we associate with multicellularity. Gene family analyses suggest that Zygnematophyceae share all the major enzymes with land plants for cell wall polysaccharide synthesis, degradation, and modifications; most of the enzymes for cell wall innovations, especially for polysaccharide backbone synthesis, were gained more than 700 million years ago. In Zygnematophyceae, these enzyme families expanded, forming co-expressed modules. Transcriptomic profiling of over 19 growth conditions combined with co-expression network analyses uncover cohorts of genes that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.
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Affiliation(s)
- Xuehuan Feng
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Jinfang Zheng
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Iker Irisarri
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
- Section Phylogenomics, Centre for Molecular biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Museum Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Huihui Yu
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE 68588, USA
| | - Bo Zheng
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Zahin Ali
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Sophie de Vries
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, 31326, France
| | - Janine M.R. Fürst-Jansen
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Armin Dadras
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Jaccoline M.S. Zegers
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tim P. Rieseberg
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Amra Dhabalia Ashok
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tatyana Darienko
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Maaike J. Bierenbroodspot
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Lydia Gramzow
- University of Jena, Matthias Schleiden Institute / Genetics, 07743, Jena, Germany
| | - Romy Petroll
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Fabian B. Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (UMA-CSIC)
| | - Orestis Nousias
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Tang Li
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Elisabeth Fitzek
- Computational Biology, Department of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - W. Scott Grayburn
- Northern Illinois University, Molecular Core Lab, Department of Biological Sciences, DeKalb, IL 60115, USA
| | - Nina Rittmeier
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Sternwartestraße 15, A-6020 Innsbruck, Austria
| | - Charlotte Permann
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Sternwartestraße 15, A-6020 Innsbruck, Austria
| | - Florian Rümpler
- University of Jena, Matthias Schleiden Institute / Genetics, 07743, Jena, Germany
| | - John M. Archibald
- Dalhousie University, Department of Biochemistry and Molecular Biology, 5850 College Street, Halifax NS B3H 4R2, Canada
| | - Günter Theißen
- University of Jena, Matthias Schleiden Institute / Genetics, 07743, Jena, Germany
| | - Jeffrey P. Mower
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE 68588, USA
| | - Maike Lorenz
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Experimental Phycology and Culture Collection of Algae at Goettingen University (EPSAG), Nikolausberger Weg 18, 37073 Goettingen, Germany
| | - Henrik Buschmann
- University of Applied Sciences Mittweida, Faculty of Applied Computer Sciences and Biosciences, Section Biotechnology and Chemistry, Molecular Biotechnology, Technikumplatz 17, 09648 Mittweida, Germany
| | - Klaus von Schwartzenberg
- Universität Hamburg, Institute of Plant Science and Microbiology, Microalgae and Zygnematophyceae Collection Hamburg (MZCH) and Aquatic Ecophysiology and Phycology, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Lori Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Richard D. Hayes
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V. Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Xiyin Wang
- North China University of Science and Technology
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Cornell University, Plant Biology Section, Ithaca, NY, USA
| | - Stefan A. Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- University of Freiburg, Centre for Biological Signalling Studies (BIOSS), Freiburg, Germany
| | - Julius Ben Ari
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot 7610000, Israel
| | - Noa Keren
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot 7610000, Israel
| | - Assaf Mosquna
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot 7610000, Israel
| | - Andreas Holzinger
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Sternwartestraße 15, A-6020 Innsbruck, Austria
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, 31326, France
| | - Chi Zhang
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE 68588, USA
- University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, NE 68588, USA
| | - Jinling Huang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Marek Mutwil
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jan de Vries
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
- University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
| | - Yanbin Yin
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
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24
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Xu R, Martelossi J, Smits M, Iannello M, Peruzza L, Babbucci M, Milan M, Dunham JP, Breton S, Milani L, Nuzhdin SV, Bargelloni L, Passamonti M, Ghiselli F. Multi-tissue RNA-Seq Analysis and Long-read-based Genome Assembly Reveal Complex Sex-specific Gene Regulation and Molecular Evolution in the Manila Clam. Genome Biol Evol 2022; 14:6889380. [PMID: 36508337 PMCID: PMC9803972 DOI: 10.1093/gbe/evac171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 11/26/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
The molecular factors and gene regulation involved in sex determination and gonad differentiation in bivalve molluscs are unknown. It has been suggested that doubly uniparental inheritance (DUI) of mitochondria may be involved in these processes in species such as the ubiquitous and commercially relevant Manila clam, Ruditapes philippinarum. We present the first long-read-based de novo genome assembly of a Manila clam, and a RNA-Seq multi-tissue analysis of 15 females and 15 males. The highly contiguous genome assembly was used as reference to investigate gene expression, alternative splicing, sequence evolution, tissue-specific co-expression networks, and sexual contrasting SNPs. Differential expression (DE) and differential splicing (DS) analyses revealed sex-specific transcriptional regulation in gonads, but not in somatic tissues. Co-expression networks revealed complex gene regulation in gonads, and genes in gonad-associated modules showed high tissue specificity. However, male gonad-associated modules showed contrasting patterns of sequence evolution and tissue specificity. One gene set was related to the structural organization of male gametes and presented slow sequence evolution but high pleiotropy, whereas another gene set was enriched in reproduction-related processes and characterized by fast sequence evolution and tissue specificity. Sexual contrasting SNPs were found in genes overrepresented in mitochondrial-related functions, providing new candidates for investigating the relationship between mitochondria and sex in DUI species. Together, these results increase our understanding of the role of DE, DS, and sequence evolution of sex-specific genes in an understudied taxon. We also provide resourceful genomic data for studies regarding sex diagnosis and breeding in bivalves.
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Affiliation(s)
- Ran Xu
- Corresponding authors: E-mail: (R.X.); E-mail: (F.G.)
| | | | | | | | - Luca Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Joseph P Dunham
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA,SeqOnce Biosciences Inc., Pasadena, CA, USA
| | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Sergey V Nuzhdin
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
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Monshi FI, Katsube-Tanaka T. 2S albumin g13 polypeptide, less related to Fag e 2, can be eliminated in common buckwheat (Fagopyrum esculentum Moench) seeds. FOOD CHEMISTRY: MOLECULAR SCIENCES 2022; 5:100138. [PMID: 36187231 PMCID: PMC9523277 DOI: 10.1016/j.fochms.2022.100138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/06/2022]
Abstract
2S albumin (g11, g13, g14, and g28) is an important allergen in common buckwheat. g13 is hydrophobic, scarce, and less related to g14 than g11/g28 is related to g14. g13_null allele homozygote produced no g13 protein in seeds. Insert-like sequence of g13_null allele resided frequently in buckwheat genome. g13_null homozygote lowered allergenicity in common buckwheat.
2S albumin (g11, g13, g14, and g28) is an important allergen in common buckwheat (Fagopyrum esculentum). g13 is hydrophobic, rare in seeds, and may show distinct allergenicity from the others; therefore, we tried to eliminate this protein. Phylogenetic and property distance analyses indicated g13 is less related to g14 (Fag e 2) than g11/g28 is related to g14, particularly in the second domain containing the II and III α-helices. A null allele with a 531 bp insertion in the coding region was found for g13 at an allele frequency of 2 % in natural populations of common buckwheat. The g13_null allele homozygote accumulated no g13 protein. A BLAST search for the 531 bp insertion suggested the insert-like sequence resided frequently in the buckwheat genome, including the self-incompatibility responsible gene ELF3 in Fagopyrum tataricum. The g13_null insert-like sequence could, therefore, help in producing hypoallergenic cultivars, and expand the genetic diversity of buckwheat.
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26
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Yim WC, Swain ML, Ma D, An H, Bird KA, Curdie DD, Wang S, Ham HD, Luzuriaga-Neira A, Kirkwood JS, Hur M, Solomon JKQ, Harper JF, Kosma DK, Alvarez-Ponce D, Cushman JC, Edger PP, Mason AS, Pires JC, Tang H, Zhang X. The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome. THE PLANT CELL 2022; 34:4143-4172. [PMID: 35961044 PMCID: PMC9614464 DOI: 10.1093/plcell/koac249] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 06/24/2022] [Indexed: 05/05/2023]
Abstract
Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. Brassica carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.
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Affiliation(s)
| | | | - Dongna Ma
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65201, USA
| | - Kevin A Bird
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - David D Curdie
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Samuel Wang
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Hyun Don Ham
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | | | - Jay S Kirkwood
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA
| | - Manhoi Hur
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA
| | - Juan K Q Solomon
- Department of Agriculture, Veterinary & Rangeland Sciences, University of Nevada, Reno, Nevada 89557, USA
| | - Jeffrey F Harper
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Dylan K Kosma
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | | | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Annaliese S Mason
- Plant Breeding Department, INRES, The University of Bonn, Bonn 53115, Germany
| | - J Chris Pires
- Division of Biological Sciences, Bond Life Sciences Center, , University of Missouri, Columbia, Missouri 65211, USA
| | - Haibao Tang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingtan Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
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27
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Depotter JRL, Ökmen B, Ebert MK, Beckers J, Kruse J, Thines M, Doehlemann G. High Nucleotide Substitution Rates Associated with Retrotransposon Proliferation Drive Dynamic Secretome Evolution in Smut Pathogens. Microbiol Spectr 2022; 10:e0034922. [PMID: 35972267 PMCID: PMC9603552 DOI: 10.1128/spectrum.00349-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/22/2022] [Indexed: 11/20/2022] Open
Abstract
Transposable elements (TEs) play a pivotal role in shaping diversity in eukaryotic genomes. The covered smut pathogen on barley, Ustilago hordei, encountered a recent genome expansion. Using long reads, we assembled genomes of 6 U. hordei strains and 3 sister species, to study this genome expansion. We found that larger genome sizes can mainly be attributed to a higher genome fraction of long terminal repeat retrotransposons (LTR-RTs). In the studied smut genomes, LTR-RTs fractions are the largest in U. hordei and are positively correlated with the mating-type locus sizes, which is up to ~560 kb in U. hordei. Furthermore, LTR-RTs were found to be associated with higher nucleotide substitution levels, as these occur in specific genome regions of smut species with a recent LTR-RT proliferation. Moreover, genes in genome regions with higher nucleotide substitution levels generally reside closer to LTR-RTs than other genome regions. Genome regions with many nucleotide substitutions encountered an especially high fraction of CG substitutions, which is not observed for LTR-RT sequences. The high nucleotide substitution levels particularly accelerate the evolution of secretome genes, as their more accessory nature results in substitutions that often lead to amino acid alterations. IMPORTANCE Genomic alteration can be generated through various means, in which transposable elements (TEs) can play a pivotal role. Their mobility causes mutagenesis in itself and can disrupt the function of the sequences they insert into. They also impact genome evolution as their repetitive nature facilitates nonhomologous recombination. Furthermore, TEs have been linked to specific epigenetic genome organizations. We report a recent TE proliferation in the genome of the barley covered smut fungus, Ustilago hordei. This proliferation is associated with a distinct nucleotide substitution regime that has a higher rate and a higher fraction of CG substitutions. This different regime shapes the evolution of genes in subjected genome regions. We hypothesize that TEs may influence the error-rate of DNA polymerase in a hitherto unknown fashion.
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Affiliation(s)
- J. R. L. Depotter
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - B. Ökmen
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - M. K. Ebert
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - J. Beckers
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - J. Kruse
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany
| | - M. Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany
| | - G. Doehlemann
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
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28
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Scarlett VT, Lovell JT, Shao M, Phillips J, Shu S, Lusinska J, Goodstein DM, Jenkins J, Grimwood J, Barry K, Chalhoub B, Schmutz J, Hasterok R, Catalán P, Vogel JP. Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium. Genetics 2022; 223:6758249. [PMID: 36218464 PMCID: PMC9910409 DOI: 10.1093/genetics/iyac146] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
The "genomic shock" hypothesis posits that unusual challenges to genome integrity such as whole genome duplication may induce chaotic genome restructuring. Decades of research on polyploid genomes have revealed that this is often, but not always the case. While some polyploids show major chromosomal rearrangements and derepression of transposable elements in the immediate aftermath of whole genome duplication, others do not. Nonetheless, all polyploids show gradual diploidization over evolutionary time. To evaluate these hypotheses, we produced a chromosome-scale reference genome for the natural allotetraploid grass Brachypodium hybridum, accession "Bhyb26." We compared 2 independently derived accessions of B. hybridum and their deeply diverged diploid progenitor species Brachypodium stacei and Brachypodium distachyon. The 2 B. hybridum lineages provide a natural timecourse in genome evolution because one formed 1.4 million years ago, and the other formed 140 thousand years ago. The genome of the older lineage reveals signs of gradual post-whole genome duplication genome evolution including minor gene loss and genome rearrangement that are missing from the younger lineage. In neither B. hybridum lineage do we find signs of homeologous recombination or pronounced transposable element activation, though we find evidence supporting steady post-whole genome duplication transposable element activity in the older lineage. Gene loss in the older lineage was slightly biased toward 1 subgenome, but genome dominance was not observed at the transcriptomic level. We propose that relaxed selection, rather than an abrupt genomic shock, drives evolutionary novelty in B. hybridum, and that the progenitor species' similarity in transposable element load may account for the subtlety of the observed genome dominance.
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Affiliation(s)
- Virginia T Scarlett
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Mingqin Shao
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Jeremy Phillips
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Shengqiang Shu
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - David M Goodstein
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kerrie Barry
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - Jeremy Schmutz
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA,Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | | | - John P Vogel
- Corresponding author: U.S. Dept. of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA.
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Genome-wide identification and development of miniature inverted-repeat transposable elements and intron length polymorphic markers in tea plant (Camellia sinensis). Sci Rep 2022; 12:16233. [PMID: 36171247 PMCID: PMC9519581 DOI: 10.1038/s41598-022-20400-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
Marker-assisted breeding and tagging of important quantitative trait loci for beneficial traits are two important strategies for the genetic improvement of plants. However, the scarcity of diverse and informative genetic markers covering the entire tea genome limits our ability to achieve such goals. In the present study, we used a comparative genomic approach to mine the tea genomes of Camellia sinensis var. assamica (CSA) and C. sinensis var. sinensis (CSS) to identify the markers to differentiate tea genotypes. In our study, 43 and 60 Camellia sinensis miniature inverted-repeat transposable element (CsMITE) families were identified in these two sequenced tea genomes, with 23,170 and 37,958 putative CsMITE sequences, respectively. In addition, we identified 4912 non-redundant, Camellia sinensis intron length polymorphic (CsILP) markers, 85.8% of which were shared by both the CSS and CSA genomes. To validate, a subset of randomly chosen 10 CsMITE markers and 15 CsILP markers were tested and found to be polymorphic among the 36 highly diverse tea genotypes. These genome-wide markers, which were identified for the first time in tea plants, will be a valuable resource for genetic diversity analysis as well as marker-assisted breeding of tea genotypes for quality improvement.
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30
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Ubi BE, Gorafi YSA, Yaakov B, Monden Y, Kashkush K, Tsujimoto H. Exploiting the miniature inverted-repeat transposable elements insertion polymorphisms as an efficient DNA marker system for genome analysis and evolutionary studies in wheat and related species. FRONTIERS IN PLANT SCIENCE 2022; 13:995586. [PMID: 36119578 PMCID: PMC9479669 DOI: 10.3389/fpls.2022.995586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Transposable elements (TEs) constitute ~80% of the complex bread wheat genome and contribute significantly to wheat evolution and environmental adaptation. We studied 52 TE insertion polymorphism markers to ascertain their efficiency as a robust DNA marker system for genetic studies in wheat and related species. Significant variation was found in miniature inverted-repeat transposable element (MITE) insertions in relation to ploidy with the highest number of "full site" insertions occurring in the hexaploids (32.6 ± 3.8), while the tetraploid and diploid progenitors had 22.3 ± 0.6 and 15.0 ± 3.5 "full sites," respectively, which suggested a recent rapid activation of these transposons after the formation of wheat. Constructed phylogenetic trees were consistent with the evolutionary history of these species which clustered mainly according to ploidy and genome types (SS, AA, DD, AABB, and AABBDD). The synthetic hexaploids sub-clustered near the tetraploid species from which they were re-synthesized. Preliminary genotyping in 104 recombinant inbred lines (RILs) showed predominantly 1:1 segregation for simplex markers, with four of these markers already integrated into our current DArT-and SNP-based linkage map. The MITE insertions also showed stability with no single excision observed. The MITE insertion site polymorphisms uncovered in this study are very promising as high-potential evolutionary markers for genomic studies in wheat.
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Affiliation(s)
- Benjamin Ewa Ubi
- Molecular Breeding Laboratory, Arid Land Research Center, Tottori University, Tottori, Japan
- Department of Biotechnology, Ebonyi State University, Abakaliki, Abakaliki, Ebonyi, Nigeria
| | - Yasir Serag Alnor Gorafi
- International Platform for Dryland Research and Education, Tottori University, Tottori, Japan
- Agricultural Research Corporation, Wad Medani, Sudan
| | - Beery Yaakov
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Hisashi Tsujimoto
- Molecular Breeding Laboratory, Arid Land Research Center, Tottori University, Tottori, Japan
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31
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Riehl K, Riccio C, Miska EA, Hemberg M. TransposonUltimate: software for transposon classification, annotation and detection. Nucleic Acids Res 2022; 50:e64. [PMID: 35234904 PMCID: PMC9226531 DOI: 10.1093/nar/gkac136] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 12/17/2022] Open
Abstract
Most genomes harbor a large number of transposons, and they play an important role in evolution and gene regulation. They are also of interest to clinicians as they are involved in several diseases, including cancer and neurodegeneration. Although several methods for transposon identification are available, they are often highly specialised towards specific tasks or classes of transposons, and they lack common standards such as a unified taxonomy scheme and output file format. We present TransposonUltimate, a powerful bundle of three modules for transposon classification, annotation, and detection of transposition events. TransposonUltimate comes as a Conda package under the GPL-3.0 licence, is well documented and it is easy to install through https://github.com/DerKevinRiehl/TransposonUltimate. We benchmark the classification module on the large TransposonDB covering 891,051 sequences to demonstrate that it outperforms the currently best existing solutions. The annotation and detection modules combine sixteen existing softwares, and we illustrate its use by annotating Caenorhabditis elegans, Rhizophagus irregularis and Oryza sativa subs. japonica genomes. Finally, we use the detection module to discover 29 554 transposition events in the genomes of 20 wild type strains of C. elegans. Databases, assemblies, annotations and further findings can be downloaded from (https://doi.org/10.5281/zenodo.5518085).
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Affiliation(s)
- Kevin Riehl
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Cristian Riccio
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Eric A Miska
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, 75 Francis Street, Boston, MA 02215, USA
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32
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Tempel S, Bedo J, Talla E. From a large-scale genomic analysis of insertion sequences to insights into their regulatory roles in prokaryotes. BMC Genomics 2022; 23:451. [PMID: 35725380 PMCID: PMC9208149 DOI: 10.1186/s12864-022-08678-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/07/2022] [Indexed: 12/03/2022] Open
Abstract
Background Insertion sequences (ISs) are mobile repeat sequences and most of them can copy themselves to new host genome locations, leading to genome plasticity and gene regulation in prokaryotes. In this study, we present functional and evolutionary relationships between IS and neighboring genes in a large-scale comparative genomic analysis. Results IS families were located in all prokaryotic phyla, with preferential occurrence of IS3, IS4, IS481, and IS5 families in Alpha-, Beta-, and Gammaproteobacteria, Actinobacteria and Firmicutes as well as in eukaryote host-associated organisms and autotrophic opportunistic pathogens. We defined the concept of the IS-Gene couple (IG), which allowed to highlight the functional and regulatory impacts of an IS on the closest gene. Genes involved in transcriptional regulation and transport activities were found overrepresented in IG. In particular, major facilitator superfamily (MFS) transporters, ATP-binding proteins and transposases raised as favorite neighboring gene functions of IS hotspots. Then, evolutionary conserved IS-Gene sets across taxonomic lineages enabled the classification of IS-gene couples into phylum, class-to-genus, and species syntenic IS-Gene couples. The IS5, IS21, IS4, IS607, IS91, ISL3 and IS200 families displayed two to four times more ISs in the phylum and/or class-to-genus syntenic IGs compared to other IS families. This indicates that those families were probably inserted earlier than others and then subjected to horizontal transfer, transposition and deletion events over time. In phylum syntenic IG category, Betaproteobacteria, Crenarchaeota, Calditrichae, Planctomycetes, Acidithiobacillia and Cyanobacteria phyla act as IS reservoirs for other phyla, and neighboring gene functions are mostly related to transcriptional regulators. Comparison of IS occurrences with predicted regulatory motifs led to ~ 26.5% of motif-containing ISs with 2 motifs per IS in average. These results, concomitantly with short IS-Gene distances, suggest that those ISs would interfere with the expression of neighboring genes and thus form strong candidates for an adaptive pairing. Conclusions All together, our large-scale study provide new insights into the IS genetic context and strongly suggest their regulatory roles. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08678-3.
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Affiliation(s)
- Sebastien Tempel
- Aix Marseille University, CNRS, LCB, Laboratoire de Chimie Bactérienne, 13009, Marseille, France.
| | - Justin Bedo
- Bioinformatics Division, the Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, VIC, 3052, Australia.,School of Computing and Information Systems, the University of Melbourne, Parkville, VIC, 3010, Australia
| | - Emmanuel Talla
- Aix Marseille University, CNRS, LCB, Laboratoire de Chimie Bactérienne, 13009, Marseille, France.
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33
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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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34
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Storer JM, Hubley R, Rosen J, Smit AFA. Methodologies for the De novo Discovery of Transposable Element Families. Genes (Basel) 2022; 13:709. [PMID: 35456515 PMCID: PMC9025800 DOI: 10.3390/genes13040709] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 02/07/2023] Open
Abstract
The discovery and characterization of transposable element (TE) families are crucial tasks in the process of genome annotation. Careful curation of TE libraries for each organism is necessary as each has been exposed to a unique and often complex set of TE families. De novo methods have been developed; however, a fully automated and accurate approach to the development of complete libraries remains elusive. In this review, we cover established methods and recent developments in de novo TE analysis. We also present various methodologies used to assess these tools and discuss opportunities for further advancement of the field.
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Affiliation(s)
| | | | | | - Arian F. A. Smit
- Institute for Systems Biology, Seattle, WA 98109, USA; (J.M.S.); (R.H.); (J.R.)
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Villarroel CA, González-González A, Alvarez-Baca JK, Villarreal P, Ballesteros GI, Figueroa CC, Cubillos FA, Ramírez CC. Genome sequencing of a predominant clonal lineage of the grain aphid Sitobion avenae. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 143:103742. [PMID: 35183733 DOI: 10.1016/j.ibmb.2022.103742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/15/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
The English grain aphid, Sitobion avenae, is a cosmopolitan pest that feeds on cereals, provoking substantial yield losses by injuring plant tissue and by vectoring plant viruses. Here we report a highly complete, de novo draft genome of the grain aphid using long-read sequencing. We generated an assembly of 2740 contigs with a N50 of 450 kb. We compared this draft genome with that of other aphid species, inspecting gene family evolution, genome-wide positive selection, and searched for horizontal gene transfer events. In addition, we described a recent copy number variant expansion of gene families involving aconitase, ABC transporter, and esterase genes that could be associated with resistance to insecticides and plant chemical defenses. This S. avenae genome obtained from a predominant invasive genotype can provide a framework for studying the spatial-temporal success of these clonal lineages in invaded agroecosystems.
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Affiliation(s)
- Carlos A Villarroel
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile; Instituto de Investigación Interdisciplinaria (I3), Universidad de Talca, Talca, Chile; Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
| | | | | | - Pablo Villarreal
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile; Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile
| | - Gabriel I Ballesteros
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile; Instituto de Investigación Interdisciplinaria (I3), Universidad de Talca, Talca, Chile
| | - Christian C Figueroa
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile; Centro de Ecología Molecular y Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Francisco A Cubillos
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile; Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile
| | - Claudio C Ramírez
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile; Centro de Ecología Molecular y Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
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Miniature Inverted-Repeat Transposable Elements (MITEs) in the Two Lepidopteran Genomes of Helicoverpa armigera and Helicoverpa zea. INSECTS 2022; 13:insects13040313. [PMID: 35447755 PMCID: PMC9033116 DOI: 10.3390/insects13040313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/10/2022] [Accepted: 03/20/2022] [Indexed: 02/04/2023]
Abstract
Simple Summary Miniature inverted-repeat transposable elements (MITEs) are non-autonomous transposable elements that play important roles in genome organization and evolution. Helicoverpa armigera and Helicoverpa zea shows a high number of reported cases of insecticide resistance worldwide, having evolved resistance against pyrethroids, organophosphates, carbamates, organochlorines, and recently to macrocyclic lactone spinosad and several Bacillus thuringiensis toxins. In the present study, we conducted a genome screening of MITEs in the H. armigera and H. zea genomes using bioinformatics approaches, and the results revealed a total of 3570 and 7405 MITE sequences in the H. armigera and H. zea genomes, respectively. Among these MITEs, we highlighted eleven MITE insertions in the H. armigera defensome genes and only one MITE insertion in those of H. zea. Abstract Miniature inverted-repeat transposable elements MITEs are ubiquitous, non-autonomous class II transposable elements. The moths, Helicoverpa armigera and Helicoverpa zea, are recognized as the two most serious pest species within the genus. Moreover, these pests have the ability to develop insecticide resistance. In the present study, we conducted a genome-wide analysis of MITEs present in H. armigera and H. zea genomes using the bioinformatics tool, MITE tracker. Overall, 3570 and 7405 MITE sequences were identified in H. armigera and H. zea genomes, respectively. Comparative analysis of identified MITE sequences in the two genomes led to the identification of 18 families, comprising 140 MITE members in H. armigera and 161 MITE members in H. zea. Based on target site duplication (TSD) sequences, the identified families were classified into three superfamilies (PIF/harbinger, Tc1/mariner and CACTA). Copy numbers varied from 6 to 469 for each MITE family. Finally, the analysis of MITE insertion sites in defensome genes showed intronic insertions of 11 MITEs in the cytochrome P450, ATP-binding cassette transporter (ABC) and esterase genes in H. armigera whereas for H. zea, only one MITE was retrieved in the ABC-C2 gene. These insertions could thus be involved in the insecticide resistance observed in these pests.
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Gisby JS, Catoni M. The widespread nature of Pack-TYPE transposons reveals their importance for plant genome evolution. PLoS Genet 2022; 18:e1010078. [PMID: 35202390 PMCID: PMC8903248 DOI: 10.1371/journal.pgen.1010078] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 03/08/2022] [Accepted: 02/06/2022] [Indexed: 11/29/2022] Open
Abstract
Pack-TYPE transposable elements (TEs) are a group of non-autonomous DNA transposons found in plants. These elements can efficiently capture and shuffle coding DNA across the host genome, accelerating the evolution of genes. Despite their relevance for plant genome plasticity, the detection and study of Pack-TYPE TEs are challenging due to the high similarity these elements have with genes. Here, we produced an automated annotation pipeline designed to study Pack-TYPE elements and used it to successfully annotate and analyse more than 10,000 new Pack-TYPE TEs in the rice and maize genomes. Our analysis indicates that Pack-TYPE TEs are an abundant and heterogeneous group of elements. We found that these elements are associated with all main superfamilies of Class II DNA transposons in plants and likely share a similar mechanism to capture new chromosomal DNA sequences. Furthermore, we report examples of the direct contribution of these TEs to coding genes, suggesting a generalised and extensive role of Pack-TYPE TEs in plant genome evolution. Transposable Elements (TEs) are genetic DNA sequences able to move across the genome, and their transposition activity is associated with genome plasticity and gene evolution. However, most of these elements exhibit “selfish” behaviour, meaning that they mainly transpose their own DNA sequence and only exceptionally might rearrange the DNA of coding genes. Pack-TYPE TEs, found in plants, represent an important exception, and they can efficiently capture and shuffle DNA sequences captured from the genome, accelerating the evolution of genes. We provide here the first automatic pipeline designed explicitly for the annotation of Pack-TYPE TEs. We used our approach to systematically investigate Pack-TYPE TEs in the rice and maize reference genomes, and annotated thousands of new elements in these species. We demonstrate that Pack-TYPE elements are abundant in plants and we report several examples of coding genes originated as a consequence of the mobilization of these elements.
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Affiliation(s)
- Jack S. Gisby
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- * E-mail: (JSG); (MC)
| | - Marco Catoni
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- Institute for Sustainable Plant Protection, National Research Council of Italy, Torino, Italy
- * E-mail: (JSG); (MC)
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Crescente JM, Zavallo D, Del Vas M, Asurmendi S, Helguera M, Fernandez E, Vanzetti LS. Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat. BMC Genomics 2022; 23:154. [PMID: 35193500 PMCID: PMC8862332 DOI: 10.1186/s12864-022-08364-4] [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: 04/16/2021] [Accepted: 02/03/2022] [Indexed: 12/15/2022] Open
Abstract
Background Plant miRNAs are a class of small non-coding RNAs that can repress gene expression at the post-transcriptional level by targeting RNA degradation or promoting translational repression. There is increasing evidence that some miRNAs can derive from a group of non-autonomous class II transposable elements called Miniature Inverted-repeat Transposable Elements (MITEs). Results We used public small RNA and degradome libraries from Triticum aestivum to screen for microRNAs production and predict their cleavage target sites. In parallel, we also created a comprehensive wheat MITE database by identifying novel elements and compiling known ones. When comparing both data sets, we found high homology between MITEs and 14% of all the miRNAs production sites detected. Furthermore, we show that MITE-derived miRNAs have preference for targeting degradation sites with MITE insertions in the 3’ UTR regions of the transcripts. Conclusions Our results revealed that MITE-derived miRNAs can underlay the origin of some miRNAs and potentially shape a regulatory gene network. Since MITEs are found in millions of insertions in the wheat genome and are closely linked to genic regions, this kind of regulatory network could have a significant impact on the post-transcriptional control of gene expression. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08364-4).
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Affiliation(s)
- Juan M Crescente
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires, CP C1425FQB, Argentina.
| | - Diego Zavallo
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA - Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Los Reseros y Nicolás Repetto, Hurlingham, CP 1686, Argentina
| | - Mariana Del Vas
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA - Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Los Reseros y Nicolás Repetto, Hurlingham, CP 1686, Argentina
| | - Sebastián Asurmendi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA - Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Los Reseros y Nicolás Repetto, Hurlingham, CP 1686, Argentina
| | - Marcelo Helguera
- Instituto Nacional de Tecnología Agropecuaria (INTA). EEA INTA Marcos Juárez, Ruta 12 s/n, Marcos Juarez, CP 2850, Argentina
| | - Elmer Fernandez
- Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas (CIDIE-CONICET), Universidad Católica de Córdoba, Córdoba, Argentina.,Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Leonardo S Vanzetti
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires, CP C1425FQB, Argentina.,Instituto Nacional de Tecnología Agropecuaria (INTA). EEA INTA Marcos Juárez, Ruta 12 s/n, Marcos Juarez, CP 2850, Argentina
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Finding and Characterizing Repeats in Plant Genomes. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2443:327-385. [PMID: 35037215 DOI: 10.1007/978-1-0716-2067-0_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Plant genomes contain a particularly high proportion of repeated structures of various types. This chapter proposes a guided tour of the available software that can help biologists to scan automatically for these repeats in sequence data or check hypothetical models intended to characterize their structures. Since transposable elements (TEs) are a major source of repeats in plants, many methods have been used or developed for this broad class of sequences. They are representative of the range of tools available for other classes of repeats and we have provided two sections on this topic (for the analysis of genomes or directly of sequenced reads), as well as a selection of the main existing software. It may be hard to keep up with the profusion of proposals in this dynamic field and the rest of the chapter is devoted to the foundations of an efficient search for repeats and more complex patterns. We first introduce the key concepts of the art of indexing and mapping or querying sequences. We end the chapter with the more prospective issue of building models of repeat families. We present the Machine Learning approach first, seeking to build predictors automatically for some families of ET, from a set of sequences known to belong to this family. A second approach, the linguistic (or syntactic) approach, allows biologists to describe themselves and check the validity of models of their favorite repeat family.
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Liu Z, Roesti M, Marques D, Hiltbrunner M, Saladin V, Peichel CL. Chromosomal fusions facilitate adaptation to divergent environments in threespine stickleback. Mol Biol Evol 2021; 39:6462204. [PMID: 34908155 PMCID: PMC8826639 DOI: 10.1093/molbev/msab358] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chromosomal fusions are hypothesized to facilitate adaptation to divergent environments, both by bringing together previously unlinked adaptive alleles and by creating regions of low recombination that facilitate the linkage of adaptive alleles; but, there is little empirical evidence to support this hypothesis. Here, we address this knowledge gap by studying threespine stickleback (Gasterosteus aculeatus), in which ancestral marine fish have repeatedly adapted to freshwater across the northern hemisphere. By comparing the threespine and ninespine stickleback (Pungitius pungitius) genomes to a de novo assembly of the fourspine stickleback (Apeltes quadracus) and an outgroup species, we find two chromosomal fusion events involving the same chromosomes have occurred independently in the threespine and ninespine stickleback lineages. On the fused chromosomes in threespine stickleback, we find an enrichment of quantitative trait loci underlying traits that contribute to marine versus freshwater adaptation. By comparing whole-genome sequences of freshwater and marine threespine stickleback populations, we also find an enrichment of regions under divergent selection on these two fused chromosomes. There is elevated genetic diversity within regions under selection in the freshwater population, consistent with a simulation study showing that gene flow can increase diversity in genomic regions associated with local adaptation and our demographic models showing gene flow between the marine and freshwater populations. Integrating our results with previous studies, we propose that these fusions created regions of low recombination that enabled the formation of adaptative clusters, thereby facilitating freshwater adaptation in the face of recurrent gene flow between marine and freshwater threespine sticklebacks.
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Affiliation(s)
- Zuyao Liu
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - David Marques
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland.,Natural History Museum Basel, Basel, Switzerland
| | - Melanie Hiltbrunner
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Verena Saladin
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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Evolutionary assembly of cooperating cell types in an animal chemical defense system. Cell 2021; 184:6138-6156.e28. [PMID: 34890552 DOI: 10.1016/j.cell.2021.11.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/29/2021] [Accepted: 11/10/2021] [Indexed: 12/21/2022]
Abstract
How the functions of multicellular organs emerge from the underlying evolution of cell types is poorly understood. We deconstructed evolution of an organ novelty: a rove beetle gland that secretes a defensive cocktail. We show how gland function arose via assembly of two cell types that manufacture distinct compounds. One cell type, comprising a chemical reservoir within the abdomen, produces alkane and ester compounds. We demonstrate that this cell type is a hybrid of cuticle cells and ancient pheromone and adipocyte-like cells, executing its function via a mosaic of enzymes from each parental cell type. The second cell type synthesizes benzoquinones using a chimera of conserved cellular energy and cuticle formation pathways. We show that evolution of each cell type was shaped by coevolution between the two cell types, yielding a potent secretion that confers adaptive value. Our findings illustrate how cooperation between cell types arises, generating new, organ-level behaviors.
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42
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Zidi M, Denis F, Klai K, Chénais B, Caruso A, Djebbi S, Mezghani M, Casse N. Genome-wide characterization of Mariner-like transposons and their derived MITEs in the Whitefly Bemisia tabaci (Hemiptera: Aleyrodidae). G3 (BETHESDA, MD.) 2021; 11:jkab287. [PMID: 34849769 PMCID: PMC8664452 DOI: 10.1093/g3journal/jkab287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/28/2021] [Indexed: 12/02/2022]
Abstract
The whitefly, Bemisia tabaci is a hemipteran pest of vegetable crops vectoring a broad category of viruses. Currently, this insect pest showed a high adaptability and resistance to almost all the chemical compounds commonly used for its control. In many cases, transposable elements (TEs) contributed to the evolution of host genomic plasticity. This study focuses on the annotation of Mariner-like elements (MLEs) and their derived Miniature Inverted repeat Transposable Elements (MITEs) in the genome of B. tabaci. Two full-length MLEs belonging to mauritiana and irritans subfamilies were detected and named Btmar1.1 and Btmar2.1, respectively. Additionally, 548 defective MLE sequences clustering mainly into 19 different Mariner lineages of mauritiana and irritans subfamilies were identified. Each subfamily showed a significant variation in MLE copy number and size. Furthermore, 71 MITEs were identified as MLEs derivatives that could be mobilized via the potentially active transposases encoded by Btmar 1.1 and Btmar2.1. The vast majority of sequences detected in the whitefly genome present unusual terminal inverted repeats (TIRs) of up to 400 bp in length. However, some exceptions are sequences without TIRs. This feature of the MLEs and their derived MITEs in B. tabaci genome that distinguishes them from all the other MLEs so far described in insects, which have TIRs size ranging from 20 to 40 bp. Overall, our study provides an overview of MLEs, especially those with large TIRs, and their related MITEs, as well as diversity of their families, which will provide a better understanding of the evolution and adaptation of the whitefly genome.
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Affiliation(s)
- Marwa Zidi
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
| | - Françoise Denis
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
- Laboratoire BOREA MNHN, CNRS FRE 2030, SU, IRD 207, UCN, UA, 75231 Paris, France
| | - Khouloud Klai
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
| | - Benoît Chénais
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
| | - Aurore Caruso
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
| | - Salma Djebbi
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - Maha Mezghani
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - Nathalie Casse
- Biologie des Organismes, Stress, Santé, Environnement, Le Mans Université, F-72085 Le Mans, France
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Parisot N, Vargas-Chávez C, Goubert C, Baa-Puyoulet P, Balmand S, Beranger L, Blanc C, Bonnamour A, Boulesteix M, Burlet N, Calevro F, Callaerts P, Chancy T, Charles H, Colella S, Da Silva Barbosa A, Dell'Aglio E, Di Genova A, Febvay G, Gabaldón T, Galvão Ferrarini M, Gerber A, Gillet B, Hubley R, Hughes S, Jacquin-Joly E, Maire J, Marcet-Houben M, Masson F, Meslin C, Montagné N, Moya A, Ribeiro de Vasconcelos AT, Richard G, Rosen J, Sagot MF, Smit AFA, Storer JM, Vincent-Monegat C, Vallier A, Vigneron A, Zaidman-Rémy A, Zamoum W, Vieira C, Rebollo R, Latorre A, Heddi A. The transposable element-rich genome of the cereal pest Sitophilus oryzae. BMC Biol 2021; 19:241. [PMID: 34749730 PMCID: PMC8576890 DOI: 10.1186/s12915-021-01158-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/27/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. RESULTS We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino acids required for insect development and cuticle biosynthesis. CONCLUSIONS Here we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.
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Affiliation(s)
- Nicolas Parisot
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Carlos Vargas-Chávez
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Present Address: Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Clément Goubert
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, New York, 14853, USA
- Present Address: Human Genetics, McGill University, Montreal, QC, Canada
| | | | - Séverine Balmand
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Louis Beranger
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Caroline Blanc
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Aymeric Bonnamour
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Matthieu Boulesteix
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
| | - Nelly Burlet
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
| | - Federica Calevro
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Patrick Callaerts
- Department of Human Genetics, Laboratory of Behavioral and Developmental Genetics, KU Leuven, University of Leuven, B-3000, Leuven, Belgium
| | - Théo Chancy
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Hubert Charles
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
| | - Stefano Colella
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, INRAE, SupAgro, Univ Montpellier, Montpellier, France
| | - André Da Silva Barbosa
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Elisa Dell'Aglio
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Alex Di Genova
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
- Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
| | - Gérard Febvay
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Toni Gabaldón
- Life Sciences, Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Mechanisms of Disease, Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Institut Catalan de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Alexandra Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Benjamin Gillet
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Lyon, France
| | | | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Lyon, France
| | - Emmanuelle Jacquin-Joly
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Justin Maire
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Florent Masson
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Camille Meslin
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Nicolas Montagné
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Andrés Moya
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), València, Spain
| | | | - Gautier Richard
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653, Le Rheu, France
| | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA, USA
| | - Marie-France Sagot
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
| | | | | | | | - Agnès Vallier
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Aurélien Vigneron
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: Department of Evolutionary Ecology, Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, 55128, Mainz, Germany
| | - Anna Zaidman-Rémy
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Waël Zamoum
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France.
- ERABLE European Team, INRIA, Rhône-Alpes, France.
| | - Rita Rebollo
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France.
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain.
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), València, Spain.
| | - Abdelaziz Heddi
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France.
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Ben Amara W, Quesneville H, Khemakhem MM. A Genomic Survey of Mayetiola destructor Mobilome Provides New Insights into the Evolutionary History of Transposable Elements in the Cecidomyiid Midges. PLoS One 2021; 16:e0257996. [PMID: 34634072 PMCID: PMC8504770 DOI: 10.1371/journal.pone.0257996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 09/16/2021] [Indexed: 11/19/2022] Open
Abstract
The availability of the Whole-Genome Sequence of the wheat pest Mayetiola destructor offers the opportunity to investigate the Transposable Elements (TEs) content and their relationship with the genes involved in the insect virulence. In this study, de novo annotation carried out using REPET pipeline showed that TEs occupy approximately 16% of the genome and are represented by 1038 lineages. Class II elements were the most frequent and most TEs were inactive due to the deletions they have accumulated. The analyses of TEs ages revealed a first burst at 20% of divergence from present that mobilized many TE families including mostly Tc1/mariner and Gypsy superfamilies and a second burst at 2% of divergence, which involved mainly the class II elements suggesting new TEs invasions. Additionally, 86 TEs insertions involving recently transposed elements were identified. Among them, several MITEs and Gypsy retrotransposons were inserted in the vicinity of SSGP and chemosensory genes. The findings represent a valuable resource for more in-depth investigation of the TE impact onto M. destructor genome and their possible influence on the expression of the virulence and chemosensory genes and consequently the behavior of this pest towards its host plants.
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Affiliation(s)
- Wiem Ben Amara
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hadi Quesneville
- INRAE, URGI, Université Paris-Saclay, Versailles, France
- INRAE, BioinfOmics, Plant Bioinformatics Facility, Université Paris-Saclay, Versailles, France
| | - Maha Mezghani Khemakhem
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
- * E-mail:
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45
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Havelka M, Sawayama E, Saito T, Yoshitake K, Saka D, Ineno T, Asakawa S, Takagi M, Goto R, Matsubara T. Chromosome-Scale Genome Assembly and Transcriptome Assembly of Kawakawa Euthynnus affinis; A Tuna-Like Species. Front Genet 2021; 12:739781. [PMID: 34616435 PMCID: PMC8489456 DOI: 10.3389/fgene.2021.739781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Miloš Havelka
- South Ehime Fisheries Research Center, Ehime University, Ainan, Japan
| | - Eitaro Sawayama
- Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Japan
| | - Taiju Saito
- South Ehime Fisheries Research Center, Ehime University, Ainan, Japan
| | - Kazutoshi Yoshitake
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Daiki Saka
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Toshinao Ineno
- Aquaculture Research Institute, Kindai University, Shingu, Japan
| | - Shuichi Asakawa
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Motohiro Takagi
- South Ehime Fisheries Research Center, Ehime University, Ainan, Japan
| | - Rie Goto
- South Ehime Fisheries Research Center, Ehime University, Ainan, Japan
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Alabi N, Wu Y, Bossdorf O, Rieseberg LH, Colautti RI. Genome Report: A draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics. G3-GENES GENOMES GENETICS 2021; 11:6380431. [PMID: 34599816 PMCID: PMC8664459 DOI: 10.1093/g3journal/jkab339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 09/10/2021] [Indexed: 11/24/2022]
Abstract
The emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here, we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara and Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC3-3-20) collected from the native range near Venice, Italy, and sequenced paired-end and mate pair libraries at ∼70 × coverage. A de novo assembly resulted in a highly continuous draft genome (N50 = 121 Mb; L50 = 2) with 99.7% of the 1.1 Gb genome mapping to scaffolds of at least 50 Kb in length. A total of 64,770 predicted genes in the annotated genome include 99% of plant BUSCO genes and 98% of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe, we found that almost one-third of BUSCO genes (390/1440) mapped to two or more scaffolds despite <2% genome-wide average heterozygosity. The continuity and gene space quality of our draft assembly will enable molecular and functional genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation strategies.
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Affiliation(s)
- Nikolay Alabi
- Biology Department, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Yihan Wu
- Biology Department, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Oliver Bossdorf
- Institute of Ecology and Evolution, University of Tübingen, 72074 Tübingen, Germany
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Robert I Colautti
- Biology Department, Queen's University, Kingston, Ontario K7L 3N6, Canada
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Stitz M, Chaparro C, Lu Z, Olzog VJ, Weinberg CE, Blom J, Goesmann A, Grunau C, Grevelding CG. Satellite-Like W-Elements: Repetitive, Transcribed, and Putative Mobile Genetic Factors with Potential Roles for Biology and Evolution of Schistosoma mansoni. Genome Biol Evol 2021; 13:6361599. [PMID: 34469545 PMCID: PMC8490949 DOI: 10.1093/gbe/evab204] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2021] [Indexed: 12/17/2022] Open
Abstract
A large portion of animal and plant genomes consists of noncoding DNA. This part includes tandemly repeated sequences and gained attention because it offers exciting insights into genome biology. We investigated satellite-DNA elements of the platyhelminth Schistosoma mansoni, a parasite with remarkable biological features. Schistosoma mansoni lives in the vasculature of humans causing schistosomiasis, a disease of worldwide importance. Schistosomes are the only trematodes that have evolved separate sexes, and the sexual maturation of the female depends on constant pairing with the male. The schistosome karyotype comprises eight chromosome pairs, males are homogametic (ZZ) and females are heterogametic (ZW). Part of the repetitive DNA of S. mansoni are W-elements (WEs), originally discovered as female-specific satellite DNAs in the heterochromatic block of the W-chromosome. Based on new genome and transcriptome data, we performed a reanalysis of the W-element families (WEFs). Besides a new classification of 19 WEFs, we provide first evidence for stage-, sex-, pairing-, gonad-, and strain-specific/preferential transcription of WEs as well as their mobile nature, deduced from autosomal copies of full-length and partial WEs. Structural analyses suggested roles as sources of noncoding RNA-like hammerhead ribozymes, for which we obtained functional evidence. Finally, the variable WEF occurrence in different schistosome species revealed remarkable divergence. From these results, we propose that WEs potentially exert enduring influence on the biology of S. mansoni. Their variable occurrence in different strains, isolates, and species suggests that schistosome WEs may represent genetic factors taking effect on variability and evolution of the family Schistosomatidae.
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Affiliation(s)
- Maria Stitz
- Institute of Parasitology, BFS, Justus Liebig University Giessen, Giessen, Germany
| | - Cristian Chaparro
- IHPE, CNRS, IFREMER, UPVD, University Montpellier, Perpignan, France
| | - Zhigang Lu
- Institute of Parasitology, BFS, Justus Liebig University Giessen, Giessen, Germany
| | | | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Germany
| | - Christoph Grunau
- IHPE, CNRS, IFREMER, UPVD, University Montpellier, Perpignan, France
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48
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Liao X, Li M, Hu K, Wu FX, Gao X, Wang J. A sensitive repeat identification framework based on short and long reads. Nucleic Acids Res 2021; 49:e100. [PMID: 34214175 PMCID: PMC8464074 DOI: 10.1093/nar/gkab563] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 06/08/2021] [Accepted: 06/18/2021] [Indexed: 12/11/2022] Open
Abstract
Numerous studies have shown that repetitive regions in genomes play indispensable roles in the evolution, inheritance and variation of living organisms. However, most existing methods cannot achieve satisfactory performance on identifying repeats in terms of both accuracy and size, since NGS reads are too short to identify long repeats whereas SMS (Single Molecule Sequencing) long reads are with high error rates. In this study, we present a novel identification framework, LongRepMarker, based on the global de novo assembly and k-mer based multiple sequence alignment for precisely marking long repeats in genomes. The major characteristics of LongRepMarker are as follows: (i) by introducing barcode linked reads and SMS long reads to assist the assembly of all short paired-end reads, it can identify the repeats to a greater extent; (ii) by finding the overlap sequences between assemblies or chomosomes, it locates the repeats faster and more accurately; (iii) by using the multi-alignment unique k-mers rather than the high frequency k-mers to identify repeats in overlap sequences, it can obtain the repeats more comprehensively and stably; (iv) by applying the parallel alignment model based on the multi-alignment unique k-mers, the efficiency of data processing can be greatly optimized and (v) by taking the corresponding identification strategies, structural variations that occur between repeats can be identified. Comprehensive experimental results show that LongRepMarker can achieve more satisfactory results than the existing de novo detection methods (https://github.com/BioinformaticsCSU/LongRepMarker).
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Affiliation(s)
- Xingyu Liao
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Min Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Kang Hu
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Fang-Xiang Wu
- Department of Mechanical Engineering and Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK S7N5A9, Canada
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Jianxin Wang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
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Lin L, Sharma A, Yu Q. Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome. BMC PLANT BIOLOGY 2021; 21:424. [PMID: 34537020 PMCID: PMC8449440 DOI: 10.1186/s12870-021-03194-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Miniature inverted-repeat transposable elements (MITEs) are non-autonomous DNA transposable elements that play important roles in genome organization and evolution. Genome-wide identification and characterization of MITEs provide essential information for understanding genome structure and evolution. RESULTS We performed genome-wide identification and characterization of MITEs in the pineapple genome. The top two MITE families, accounting for 29.39% of the total MITEs and 3.86% of the pineapple genome, have insertion preference in (TA) n dinucleotide microsatellite regions. We therefore named these MITEs A. comosus microsatellite-associated MITEs (Ac-mMITEs). The two Ac-mMITE families, Ac-mMITE-1 and Ac-mMITE-2, shared sequence similarity in the terminal inverted repeat (TIR) regions, suggesting that these two Ac-mMITE families might be derived from a common or closely related autonomous elements. The Ac-mMITEs are frequently clustered via adjacent insertions. Among the 21,994 full-length Ac-mMITEs, 46.1% of them were present in clusters. By analyzing the Ac-mMITEs without (TA) n microsatellite flanking sequences, we found that Ac-mMITEs were likely derived from Mutator-like DNA transposon. Ac-MITEs showed highly polymorphic insertion sites between cultivated pineapples and their wild relatives. To better understand the evolutionary history of Ac-mMITEs, we filtered and performed comparative analysis on the two distinct groups of Ac-mMITEs, microsatellite-targeting MITEs (mt-MITEs) that are flanked by dinucleotide microsatellites on both sides and mutator-like MITEs (ml-MITEs) that contain 9/10 bp TSDs. Epigenetic analysis revealed a lower level of host-induced silencing on the mt-MITEs in comparison to the ml-MITEs, which partially explained the significantly higher abundance of mt-MITEs in pineapple genome. The mt-MITEs and ml-MITEs exhibited differential insertion preference to gene-related regions and RNA-seq analysis revealed their differential influences on expression regulation of nearby genes. CONCLUSIONS Ac-mMITEs are the most abundant MITEs in the pineapple genome and they were likely derived from Mutator-like DNA transposon. Preferential insertion in (TA) n microsatellite regions of Ac-mMITEs occurred recently and is likely the result of damage-limiting strategy adapted by Ac-mMITEs during co-evolution with their host. Insertion in (TA) n microsatellite regions might also have promoted the amplification of mt-MITEs. In addition, mt-MITEs showed no or negligible impact on nearby gene expression, which may help them escape genome control and lead to their amplification.
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Affiliation(s)
- Lianyu Lin
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Anupma Sharma
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA.
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50
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A Practical Guide on Computational Tools and Databases for Transposable Elements in Plants. Methods Mol Biol 2021. [PMID: 33900590 DOI: 10.1007/978-1-0716-1134-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
In the age of big data, obtaining precise information about the research topic of interesting is extremely important. Keeping this in mind, this chapter focuses on providing a practical knowledge guide about computational tools and databases of transposable elements (TE) in plants. For that, we organize and present this text in three sections: (1) a discussion about tools and databases on this theme; (2) hands-on of how to use a few of them; (3) an exploratory data analysis on public TE data. Finally, we are going deep to present the main challenges and possible solutions to improve resources and tools.
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