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Hu XM, Zheng S, Zhang Q, Wan X, Li J, Mao R, Yang R, Xiong K. PANoptosis signaling enables broad immune response in psoriasis: From pathogenesis to new therapeutic strategies. Comput Struct Biotechnol J 2024; 23:64-76. [PMID: 38125299 PMCID: PMC10730955 DOI: 10.1016/j.csbj.2023.11.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
Background Accumulating evidence suggests that regulated cell death, such as pyroptosis, apoptosis, and necroptosis, is deeply involved in the pathogenesis of psoriasis. As a newly recognized form of systematic cell death, PANoptosis is involved in a variety of inflammatory disorders through amplifying inflammatory and immune cascades, but its role in psoriasis remains elusive. Objectives To reveal the role of PANoptosis in psoriasis for a potential therapeutic strategy. Methods Multitranscriptomic analysis and experimental validation were used to identify PANoptosis signaling in psoriasis. RNA-seq and scRNA-seq analyses were performed to establish a PANoptosis-mediated immune response in psoriasis, which revealed hub genes through WGCNA and predicted disulfiram as a potential drug. The effect and mechanism of disulfiram were verified in imiquimod (IMQ)-induced psoriasis. Results Here, we found a highlighted PANoptosis signature in psoriasis patients through multitranscriptomic analysis and experimental validation. Based on this, two distinct PANoptosis patterns (non/high) were identified, which were the options for clinical classification. The high-PANoptosis-related group had a higher response rate to immune cell infiltration (such as M1 macrophages and keratinocytes). Subsequently, WGCNA showed the hub genes (e.g., S100A12, CYCS, NOD2, STAT1, HSPA4, AIM2, MAPK7), which were significantly associated with clinical phenotype, PANoptosis signature, and identified immune response in psoriasis. Finally, we explored disulfiram (DSF) as a candidate drug for psoriasis through network pharmacology, which ameliorated IMQ-mediated psoriatic symptoms through antipyroptosis-mediated inflammation and enhanced apoptotic progression. By analyzing the specific ligand-receptor interaction pairs within and between cell lineages, we speculated that DSF might exert its effects by targeting keratinocytes directly or targeting M1 macrophages to downregulate the proliferation of keratinocytes. Conclusions PANoptosis with its mediated immune cell infiltration provides a roadmap for research on the pathogenesis and therapeutic strategies of psoriasis.
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Affiliation(s)
- Xi-min Hu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Shengyuan Zheng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Qi Zhang
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Xinxing Wan
- Department of Endocrinology, Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Ji Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Rui Mao
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Ronghua Yang
- Department of Burn and Plastic Surgery, Guangzhou First People's Hospital, South China University of Technology, Guangzhou 510000, China
| | - Kun Xiong
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha 410013, China
- Hunan Key Laboratory of Ophthalmology, Xiangya Hospital, Central South University, Changsha 410008, China
- Key Laboratory of Emergency and Trauma, Ministry of Education, College of Emergency and Trauma, Hainan Medical University, Haikou 571199, China
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2
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Kang H, Han AR, Zhang A, Jeong H, Koh W, Lee JM, Lee H, Jo HY, Maria-Solano MA, Bhalla M, Kwon J, Roh WS, Yang J, An HJ, Choi S, Kim HM, Lee CJ. GolpHCat (TMEM87A), a unique voltage-dependent cation channel in Golgi apparatus, contributes to Golgi-pH maintenance and hippocampus-dependent memory. Nat Commun 2024; 15:5830. [PMID: 38992057 PMCID: PMC11239671 DOI: 10.1038/s41467-024-49297-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/30/2024] [Indexed: 07/13/2024] Open
Abstract
Impaired ion channels regulating Golgi pH lead to structural alterations in the Golgi apparatus, such as fragmentation, which is found, along with cognitive impairment, in Alzheimer's disease. However, the causal relationship between altered Golgi structure and cognitive impairment remains elusive due to the lack of understanding of ion channels in the Golgi apparatus of brain cells. Here, we identify that a transmembrane protein TMEM87A, renamed Golgi-pH-regulating cation channel (GolpHCat), expressed in astrocytes and neurons that contributes to hippocampus-dependent memory. We find that GolpHCat displays unique voltage-dependent currents, which is potently inhibited by gluconate. Additionally, we gain structural insights into the ion conduction through GolpHCat at the molecular level by determining three high-resolution cryogenic-electron microscopy structures of human GolpHCat. GolpHCat-knockout mice show fragmented Golgi morphology and altered protein glycosylation and functions in the hippocampus, leading to impaired spatial memory. These findings suggest a molecular target for Golgi-related diseases and cognitive impairment.
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Affiliation(s)
- Hyunji Kang
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
- IBS School, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Ah-Reum Han
- Center for Biomolecular and Cellular Structure, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Aihua Zhang
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Heejin Jeong
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Korea
| | - Wuhyun Koh
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Jung Moo Lee
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Hayeon Lee
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Hee Young Jo
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Korea
| | - Miguel A Maria-Solano
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Mridula Bhalla
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Jea Kwon
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Woo Suk Roh
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Jimin Yang
- Center for Biomolecular and Cellular Structure, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Korea
| | - Sun Choi
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, Seoul, 03760, Republic of Korea.
| | - Ho Min Kim
- Center for Biomolecular and Cellular Structure, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea.
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
| | - C Justin Lee
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea.
- IBS School, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
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Kosugi M, Ohtani S, Hara K, Toyoda A, Nishide H, Ozawa SI, Takahashi Y, Kashino Y, Kudoh S, Koike H, Minagawa J. Characterization of the far-red light absorbing light-harvesting chlorophyll a/ b binding complex, a derivative of the distinctive Lhca gene family in green algae. FRONTIERS IN PLANT SCIENCE 2024; 15:1409116. [PMID: 38916036 PMCID: PMC11194369 DOI: 10.3389/fpls.2024.1409116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/22/2024] [Indexed: 06/26/2024]
Abstract
Prasiola crispa, an aerial green alga, exhibits remarkable adaptability to the extreme conditions of Antarctica by forming layered colonies capable of utilizing far-red light for photosynthesis. Despite a recent report on the structure of P. crispa's unique light-harvesting chlorophyll (Chl)-binding protein complex (Pc-frLHC), which facilitates far-red light absorption and uphill excitation energy transfer to photosystem II, the specific genes encoding the subunits of Pc-frLHC have not yet been identified. Here, we report a draft genome sequence of P. crispa strain 4113, originally isolated from soil samples on Ongul Island, Antarctica. We obtained a 92 Mbp sequence distributed in 1,045 scaffolds comprising 10,244 genes, reflecting 87.1% of the core eukaryotic gene set. Notably, 26 genes associated with the light-harvesting Chl a/b binding complex (LHC) were identified, including four Pc-frLHC genes, with similarity to a noncanonical Lhca gene with four transmembrane helices, such as Ot_Lhca6 in Ostreococcus tauri and Cr_LHCA2 in Chlamydomonas reinhardtii. A comparative analysis revealed that Pc-frLHC shares homology with certain Lhca genes found in Coccomyxa and Trebouxia species. This similarity indicates that Pc-frLHC has evolved from an ancestral Lhca gene with four transmembrane helices and branched out within the Trebouxiaceae family. Furthermore, RNA-seq analysis conducted during the initiation of Pc-frLHC gene induction under red light illumination indicated that Pc-frLHC genes were induced independently from other genes associated with photosystems or LHCs. Instead, the genes of transcription factors, helicases, chaperones, heat shock proteins, and components of blue light receptors were identified to coexpress with Pc-frLHC. Those kinds of information could provide insights into the expression mechanisms of Pc-frLHC and its evolutional development.
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Affiliation(s)
- Makiko Kosugi
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Japan
| | - Shuji Ohtani
- Faculty of Education, Shimane University, Matsue, Japan
| | - Kojiro Hara
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Hiroyo Nishide
- Data Integration and Analysis Facility, National Institute for Basic Biology, National Institutes of Natural Science, Okazaki, Japan
| | - Shin-Ichiro Ozawa
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Yuichiro Takahashi
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan
| | | | - Sakae Kudoh
- National Institute of Polar Research, Research Organization of Information and Systems, Tokyo, Japan
- Department of Polar Science, School of Multidisciplinary Science, The Graduate University for Advanced Studies, SOKENDAI, Tokyo, Japan
| | - Hiroyuki Koike
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Jun Minagawa
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Okazaki, Japan
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Bowles AMC, Williams TA, Donoghue PCJ, Campbell DA, Williamson CJ. Metagenome-assembled genome of the glacier alga Ancylonema yields insights into the evolution of streptophyte life on ice and land. THE NEW PHYTOLOGIST 2024. [PMID: 38840553 DOI: 10.1111/nph.19860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/03/2024] [Indexed: 06/07/2024]
Abstract
Contemporary glaciers are inhabited by streptophyte algae that balance photosynthesis and growth with tolerance of low temperature, desiccation and UV radiation. These same environmental challenges have been hypothesised as the driving force behind the evolution of land plants from streptophyte algal ancestors in the Cryogenian (720-635 million years ago). We sequenced, assembled and analysed the metagenome-assembled genome of the glacier alga Ancylonema nordenskiöldii to investigate its adaptations to life in ice, and whether this represents a vestige of Cryogenian exaptations. Phylogenetic analysis confirms the placement of glacier algae within the sister lineage to land plants, Zygnematophyceae. The metagenome-assembled genome is characterised by an expansion of genes involved in tolerance of high irradiance and UV light, while lineage-specific diversification is linked to the novel screening pigmentation of glacier algae. We found no support for the hypothesis of a common genomic basis for adaptations to ice and to land in streptophytes. Comparative genomics revealed that the reductive morphological evolution in the ancestor of Zygnematophyceae was accompanied by reductive genome evolution. This first genome-scale data for glacier algae suggests an Ancylonema-specific adaptation to the cryosphere, and sheds light on the genome evolution of land plants and Zygnematophyceae.
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Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, UK
| | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, UK
| | - Douglas A Campbell
- Department of Biology, Mount Allison University, Sackville, NB, E4L 1H3, Canada
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Ahadaf S, Azzouz S, Galiou OE, Errahmouni MA, Mentag R, Arakrak A, Laglaoui A. Genomic Insights Into Enterococcus mundtii 203: A Promising Probiotic Candidate Isolated From Camel Feces. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10284-6. [PMID: 38733462 DOI: 10.1007/s12602-024-10284-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2024] [Indexed: 05/13/2024]
Abstract
Enterococcus, a common commensal organism in the human gut, exhibits a dual nature with certain strains offering probiotic benefits, while others are associated with nosocomial infections. In this study, we conducted a comprehensive examination of the genome of Enterococcus mundtii strain 203 to assess its probiotic potential and safety profile. The complete genome sequencing, assembly, and annotation were performed, followed by bioinformatics analysis. Our investigation reveals a detailed characterization of the Enterococcus mundtii 203 genome, originally isolated from camel feces, with a size of 3,053,234 bases and a GC content of 38.4%. Importantly, our analysis suggests that this strain poses no risk as a human pathogen due to the absence of antibiotic resistance determinants and virulence factors. The genome harbors a multitude of genes responsible for lactic acid production, bioactive peptide synthesis, adhesion molecule expression, resistance to harsh gut conditions, and enhancement of host metabolism. These findings underline the potential probiotic functionality of Enterococcus mundtii 203, positioning it as a promising candidate. Notably, our study did not identify any sequences related to insertion elements or CRISPR-Cas fragments.
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Affiliation(s)
- Soumaya Ahadaf
- Biotechnology and Biomolecular Engineering Research Team, Department of Biology, Faculty of Science and Technology, Abdelmalek Essaâdi University, Tetouan, Morocco
| | - Safae Azzouz
- Biotechnology and Biomolecular Engineering Research Team, Department of Biology, Faculty of Science and Technology, Abdelmalek Essaâdi University, Tetouan, Morocco
| | - Ouiam El Galiou
- Biotechnology and Biomolecular Engineering Research Team, Department of Biology, Faculty of Science and Technology, Abdelmalek Essaâdi University, Tetouan, Morocco
| | - Mohamed Akram Errahmouni
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, 10090, Rabat, Morocco
| | - Rachid Mentag
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, 10090, Rabat, Morocco
| | - Abdelhay Arakrak
- Biotechnology and Biomolecular Engineering Research Team, Department of Biology, Faculty of Science and Technology, Abdelmalek Essaâdi University, Tetouan, Morocco
| | - Amin Laglaoui
- Biotechnology and Biomolecular Engineering Research Team, Department of Biology, Faculty of Science and Technology, Abdelmalek Essaâdi University, Tetouan, Morocco.
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6
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Balamurugan C, Steenwyk JL, Goldman GH, Rokas A. The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi. G3 (BETHESDA, MD.) 2024; 14:jkae063. [PMID: 38507596 PMCID: PMC11075534 DOI: 10.1093/g3journal/jkae063] [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: 12/27/2023] [Revised: 12/27/2023] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Fungi biosynthesize diverse secondary metabolites, small organic bioactive molecules with key roles in fungal ecology. Fungal secondary metabolites are often encoded by physically clustered genes known as biosynthetic gene clusters (BGCs). Fungi in the genus Penicillium produce a cadre of secondary metabolites, some of which are useful (e.g. the antibiotic penicillin and the cholesterol-lowering drug mevastatin) and others harmful (e.g. the mycotoxin patulin and the immunosuppressant gliotoxin) to human affairs. Fungal genomes often also encode resistance genes that confer protection against toxic secondary metabolites. Some Penicillium species, such as Penicillium decumbens, are known to produce gliotoxin, a secondary metabolite with known immunosuppressant activity. To investigate the evolutionary conservation of homologs of the gliotoxin BGC and of genes involved in gliotoxin resistance in Penicillium, we analyzed 35 Penicillium genomes from 23 species. Homologous, lesser fragmented gliotoxin BGCs were found in 12 genomes, mostly fragmented remnants of the gliotoxin BGC were found in 21 genomes, whereas the remaining 2 Penicillium genomes lacked the gliotoxin BGC altogether. In contrast, broad conservation of homologs of resistance genes that reside outside the BGC across Penicillium genomes was observed. Evolutionary rate analysis revealed that BGCs with higher numbers of genes evolve slower than BGCs with few genes, suggestive of constraint and potential functional significance or more recent decay. Gene tree-species tree reconciliation analyses suggested that the history of homologs in the gliotoxin BGC across the genus Penicillium likely involved multiple duplications, losses, and horizontal gene transfers. Our analyses suggest that genes encoded in BGCs can have complex evolutionary histories and be retained in genomes long after the loss of secondary metabolite biosynthesis.
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Affiliation(s)
- Charu Balamurugan
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Gustavo H Goldman
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo CEP 14040-903, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
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Raimondeau P, Ksouda S, Marande W, Fuchs AL, Gryta H, Theron A, Puyoou A, Dupin J, Cheptou PO, Vautrin S, Valière S, Manzi S, Baali-Cherif D, Chave J, Christin PA, Besnard G. A hemizygous supergene controls homomorphic and heteromorphic self-incompatibility systems in Oleaceae. Curr Biol 2024; 34:1977-1986.e8. [PMID: 38626764 DOI: 10.1016/j.cub.2024.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/29/2024] [Accepted: 03/18/2024] [Indexed: 04/18/2024]
Abstract
Self-incompatibility (SI) has evolved independently multiple times and prevents self-fertilization in hermaphrodite angiosperms. Several groups of Oleaceae such as jasmines exhibit distylous flowers, with two compatibility groups each associated with a specific floral morph.1 Other Oleaceae species in the olive tribe have two compatibility groups without associated morphological variation.2,3,4,5 The genetic basis of both homomorphic and dimorphic SI systems in Oleaceae is unknown. By comparing genomic sequences of three olive subspecies (Olea europaea) belonging to the two compatibility groups, we first locate the genetic determinants of SI within a 700-kb hemizygous region present only in one compatibility group. We then demonstrate that the homologous hemizygous region also controls distyly in jasmine. Phylogenetic analyses support a common origin of both systems, following a segmental genomic duplication in a common ancestor. Examination of the gene content of the hemizygous region in different jasmine and olive species suggests that the mechanisms determining compatibility groups and floral phenotypes (whether homomorphic or dimorphic) in Oleaceae rely on the presence/absence of two genes involved in gibberellin and brassinosteroid regulation.
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Affiliation(s)
- Pauline Raimondeau
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France; Yale Institute of Biospheric Studies, New Haven, CT 06520, USA
| | - Sayam Ksouda
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - William Marande
- INRAE, Centre National de Ressources Génomiques Végétales, 31326 Castanet-Tolosan, France
| | - Anne-Laure Fuchs
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Hervé Gryta
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Anthony Theron
- INRAE, Centre National de Ressources Génomiques Végétales, 31326 Castanet-Tolosan, France
| | - Aurore Puyoou
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Julia Dupin
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Pierre-Olivier Cheptou
- CEFE (Centre d'Ecologie Fonctionnelle et Evolutive), UMR 5175, CNRS, Université de Montpellier, Université Paul Valéry, EPHE, IRD, 34293 Montpellier, France
| | - Sonia Vautrin
- INRAE, Centre National de Ressources Génomiques Végétales, 31326 Castanet-Tolosan, France
| | - Sophie Valière
- INRAE, US 1426, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France
| | - Sophie Manzi
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Djamel Baali-Cherif
- Laboratoire de Recherche sur les Zones Arides, USTHB/ENSA, 16000 Alger, Algeria
| | - Jérôme Chave
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Guillaume Besnard
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France.
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Xu Y, Wang C, Li Z, Zheng X, Kang Z, Lu P, Zhang J, Cao P, Chen Q, Liu X. A chromosome-level haplotype-resolved genome assembly of oriental tobacco budworm (Helicoverpa assulta). Sci Data 2024; 11:461. [PMID: 38710675 DOI: 10.1038/s41597-024-03264-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 04/15/2024] [Indexed: 05/08/2024] Open
Abstract
Oriental tobacco budworm (Helicoverpa assulta) and cotton bollworm (Helicoverpa armigera) are two closely related species within the genus Helicoverpa. They have similar appearances and consistent damage patterns, often leading to confusion. However, the cotton bollworm is a typical polyphagous insect, while the oriental tobacco budworm belongs to the oligophagous insects. In this study, we used Nanopore, PacBio, and Illumina platforms to sequence the genome of H. assulta and used Hifiasm to create a haplotype-resolved draft genome. The Hi-C technique helped anchor 33 primary contigs to 32 chromosomes, including two sex chromosomes, Z and W. The final primary haploid genome assembly was approximately 415.19 Mb in length. BUSCO analysis revealed a high degree of completeness, with 99.0% gene coverage in this genome assembly. The repeat sequences constituted 38.39% of the genome assembly, and we annotated 17093 protein-coding genes. The high-quality genome assembly of the oriental tobacco budworm serves as a valuable genetic resource that enhances our comprehension of how they select hosts in a complex odour environment. It will also aid in developing an effective control policy.
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Affiliation(s)
- Yalong Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy (BLSA), Beijing, 102209, China
| | - Chen Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy (BLSA), Beijing, 102209, China
| | - Zefeng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy (BLSA), Beijing, 102209, China
| | - Xueao Zheng
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy (BLSA), Beijing, 102209, China
| | - Zhengzhong Kang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy (BLSA), Beijing, 102209, China
| | - Peng Lu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy (BLSA), Beijing, 102209, China
| | - Jianfeng Zhang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy (BLSA), Beijing, 102209, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
- Beijing Life Science Academy (BLSA), Beijing, 102209, China
| | - Qiansi Chen
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China.
- Beijing Life Science Academy (BLSA), Beijing, 102209, China.
| | - Xiaoguang Liu
- Institution Henan International Laboratory for Green Pest Control, Henan Engineering Laboratory of Pest Biological Control, College of Plant Protection, Henan Agricultural University, Zhengzhou, 450000, China.
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9
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Formaggioni A, Cavalli G, Hamada M, Sakamoto T, Plazzi F, Passamonti M. The Evolution and Characterization of the RNA Interference Pathways in Lophotrochozoa. Genome Biol Evol 2024; 16:evae098. [PMID: 38713108 PMCID: PMC11114477 DOI: 10.1093/gbe/evae098] [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: 10/23/2023] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024] Open
Abstract
In animals, three main RNA interference mechanisms have been described so far, which respectively maturate three types of small noncoding RNAs (sncRNAs): miRNAs, piRNAs, and endo-siRNAs. The diversification of these mechanisms is deeply linked with the evolution of the Argonaute gene superfamily since each type of sncRNA is typically loaded by a specific Argonaute homolog. Moreover, other protein families play pivotal roles in the maturation of sncRNAs, like the DICER ribonuclease family, whose DICER1 and DICER2 paralogs maturate respectively miRNAs and endo-siRNAs. Within Metazoa, the distribution of these families has been only studied in major groups, and there are very few data for clades like Lophotrochozoa. Thus, we here inferred the evolutionary history of the animal Argonaute and DICER families including 43 lophotrochozoan species. Phylogenetic analyses along with newly sequenced sncRNA libraries suggested that in all Trochozoa, the proteins related to the endo-siRNA pathway have been lost, a part of them in some phyla (i.e. Nemertea, Bryozoa, Entoprocta), while all of them in all the others. On the contrary, early diverging phyla, Platyhelminthes and Syndermata, showed a complete endo-siRNA pathway. On the other hand, miRNAs were revealed the most conserved and ubiquitous mechanism of the metazoan RNA interference machinery, confirming their pivotal role in animal cell regulation.
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Affiliation(s)
- Alessandro Formaggioni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Gianmarco Cavalli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Mayuko Hamada
- Ushimado Marine Institute, Okayama University, Okayama, Japan
| | | | - Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
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10
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Barua D, Płecha M, Muszewska A. A minimal Fanconi Anemia complex in early diverging fungi. Sci Rep 2024; 14:9922. [PMID: 38688950 PMCID: PMC11061109 DOI: 10.1038/s41598-024-60318-w] [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: 01/02/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
Fanconi Anemia (FA) pathway resolves DNA interstrand cross links (ICL). The FA pathway was initially recognized in vertebrates, but was later confirmed in other animals and speculated in fungi. FA proteins FANCM, FANCL and FANCJ are present in Saccharomyces cerevisiae but, their mechanism of interaction to resolve ICL is still unclear. Unlike Dikarya, early diverging fungi (EDF) possess more traits shared with animals. We traced the evolutionary history of the FA pathway across Opisthokonta. We scanned complete proteomes for FA-related homologs to establish their taxonomic distribution and analyzed their phylogenetic trees. We checked transcription profiles of FA genes to test if they respond to environmental conditions and their genomic localizations for potential co-localization. We identified fungal homologs of the activation and ID complexes, 5 out of 8 core proteins, all of the endonucleases, and deubiquitination proteins. All fungi lack FANCC, FANCF and FANCG proteins responsible for post-replication repair and chromosome stability in animals. The observed taxonomic distribution can be attributed to a gradual degradation of the FA pathway from EDF to Dikarya. One of the key differences is that EDF have the ID complex recruiting endonucleases to the site of ICL. Moreover, 21 out of 32 identified FA genes are upregulated in response to different growth conditions. Several FA genes are co-localized in fungal genomes which also could facilitate co-expression. Our results indicate that a minimal FA pathway might still be functional in Mucoromycota with a gradual loss of components in Dikarya ancestors.
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Affiliation(s)
- Drishtee Barua
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Magdalena Płecha
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland.
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11
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Katsavou E, Sarafoglou C, Balabanidou V, Skoufa E, Nauen R, Linka M, Geibel S, Denecke S, Vontas J. Characterisation of lepidopteran geranylgeranyl diphosphate synthase as a putative pesticide target. INSECT MOLECULAR BIOLOGY 2024; 33:147-156. [PMID: 37962063 DOI: 10.1111/imb.12885] [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: 06/04/2023] [Accepted: 10/11/2023] [Indexed: 11/15/2023]
Abstract
Geranylgeranyl pyrophosphate (diphosphate) synthase (GGPPS) plays an important role in various physiological processes in insects, such as isoprenoid biosynthesis and protein prenylation. Here, we functionally characterised the GGPPS from the major agricultural lepidopteran pests Spodoptera frugiperda and Helicoverpa armigera. Partial disruption of GGPPS by CRISPR in S. frugiperda decreased embryo hatching rate and larval survival, suggesting that this gene is essential. Functional expression in vitro of Helicoverpa armigera GGPPS in Escherichia coli revealed a catalytically active enzyme. Next, we developed and optimised an enzyme assay to screen for potential inhibitors, such as the zoledronate and the minodronate, which showed a dose-dependent inhibition. Phylogenetic analysis of GGPPS across insects showed that GGPPS is highly conserved but also revealed several residues likely to be involved in substrate binding, which were substantially different in bee pollinator and human GGPPS. Considering the essentiality of GGPPS and its putative binding residue variability qualifies a GGPPS as a novel pesticide target. The developed assay may contribute to the identification of novel insecticide leads.
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Affiliation(s)
- Evangelia Katsavou
- Pesticide Science Laboratory, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Chara Sarafoglou
- Department of Biology, University of Crete, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Vasileia Balabanidou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Evangelia Skoufa
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Ralf Nauen
- R&D Pest Control, Crop Science Division, Bayer AG, Monheim am Rhein, Germany
| | - Marc Linka
- R&D Pest Control, Crop Science Division, Bayer AG, Monheim am Rhein, Germany
| | - Sven Geibel
- R&D Pest Control, Crop Science Division, Bayer AG, Monheim am Rhein, Germany
| | - Shane Denecke
- Department of Biology, University of Crete, Crete, Greece
- Department of Pathobiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John Vontas
- Pesticide Science Laboratory, Department of Crop Science, Agricultural University of Athens, Athens, Greece
- Department of Biology, University of Crete, Crete, Greece
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12
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Wright CJ, Stevens L, Mackintosh A, Lawniczak M, Blaxter M. Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera. Nat Ecol Evol 2024; 8:777-790. [PMID: 38383850 PMCID: PMC11009112 DOI: 10.1038/s41559-024-02329-4] [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: 10/09/2023] [Accepted: 01/12/2024] [Indexed: 02/23/2024]
Abstract
Chromosomes are a central unit of genome organization. One-tenth of all described species on Earth are butterflies and moths, the Lepidoptera, which generally possess 31 chromosomes. However, some species display dramatic variation in chromosome number. Here we analyse 210 chromosomally complete lepidopteran genomes and show that the chromosomes of extant lepidopterans are derived from 32 ancestral linkage groups, which we term Merian elements. Merian elements have remained largely intact through 250 million years of evolution and diversification. Against this stable background, eight lineages have undergone extensive reorganization either through numerous fissions or a combination of fusion and fission events. Outside these lineages, fusions are rare and fissions are rarer still. Fusions often involve small, repeat-rich Merian elements and the sex-linked element. Our results reveal the constraints on genome architecture in Lepidoptera and provide a deeper understanding of chromosomal rearrangements in eukaryotic genome evolution.
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Affiliation(s)
| | - Lewis Stevens
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK.
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13
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Koren S, Bao Z, Guarracino A, Ou S, Goodwin S, Jenike KM, Lucas J, McNulty B, Park J, Rautiainen M, Rhie A, Roelofs D, Schneiders H, Vrijenhoek I, Nijbroek K, Ware D, Schatz MC, Garrison E, Huang S, McCombie WR, Miga KH, Wittenberg AH, Phillippy AM. Gapless assembly of complete human and plant chromosomes using only nanopore sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585294. [PMID: 38529488 PMCID: PMC10962732 DOI: 10.1101/2024.03.15.585294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The combination of ultra-long Oxford Nanopore (ONT) sequencing reads with long, accurate PacBio HiFi reads has enabled the completion of a human genome and spurred similar efforts to complete the genomes of many other species. However, this approach for complete, "telomere-to-telomere" genome assembly relies on multiple sequencing platforms, limiting its accessibility. ONT "Duplex" sequencing reads, where both strands of the DNA are read to improve quality, promise high per-base accuracy. To evaluate this new data type, we generated ONT Duplex data for three widely-studied genomes: human HG002, Solanum lycopersicum Heinz 1706 (tomato), and Zea mays B73 (maize). For the diploid, heterozygous HG002 genome, we also used "Pore-C" chromatin contact mapping to completely phase the haplotypes. We found the accuracy of Duplex data to be similar to HiFi sequencing, but with read lengths tens of kilobases longer, and the Pore-C data to be compatible with existing diploid assembly algorithms. This combination of read length and accuracy enables the construction of a high-quality initial assembly, which can then be further resolved using the ultra-long reads, and finally phased into chromosome-scale haplotypes with Pore-C. The resulting assemblies have a base accuracy exceeding 99.999% (Q50) and near-perfect continuity, with most chromosomes assembled as single contigs. We conclude that ONT sequencing is a viable alternative to HiFi sequencing for de novo genome assembly, and has the potential to provide a single-instrument solution for the reconstruction of complete genomes.
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Affiliation(s)
- Sergey Koren
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhigui Bao
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, BadenWürttemberg, Germany
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Human Technopole, Milan, Italy
| | - Shujun Ou
- Ohio State University, Columbus, OH, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Katharine M. Jenike
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Julian Lucas
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Brandy McNulty
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jimin Park
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Mikko Rautiainen
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arang Rhie
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dick Roelofs
- KeyGene, Agro Business Park 90, 6708 PW Wageningen, Netherlands
| | | | - Ilse Vrijenhoek
- KeyGene, Agro Business Park 90, 6708 PW Wageningen, Netherlands
| | - Koen Nijbroek
- KeyGene, Agro Business Park 90, 6708 PW Wageningen, Netherlands
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | | | - Karen H. Miga
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | - Adam M. Phillippy
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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14
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Pan X, Ren L, Yang Y, Xu Y, Ning L, Zhang Y, Luo H, Zou Q, Zhang Y. MCSdb, a database of proteins residing in membrane contact sites. Sci Data 2024; 11:281. [PMID: 38459036 PMCID: PMC10923927 DOI: 10.1038/s41597-024-03104-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 02/29/2024] [Indexed: 03/10/2024] Open
Abstract
Organelles do not act as autonomous discrete units but rather as interconnected hubs that engage in extensive communication by forming close contacts called "membrane contact sites (MCSs)". And many proteins have been identified as residing in MCS and playing important roles in maintaining and fulfilling specific functions within these microdomains. However, a comprehensive compilation of these MCS proteins is still lacking. Therefore, we developed MCSdb, a manually curated resource of MCS proteins and complexes from publications. MCSdb documents 7010 MCS protein entries and 263 complexes, involving 24 organelles and 44 MCSs across 11 species. Additionally, MCSdb orchestrates all data into different categories with multitudinous information for presenting MCS proteins. In summary, MCSdb provides a valuable resource for accelerating MCS functional interpretation and interorganelle communication deciphering.
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Affiliation(s)
- Xianrun Pan
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Liping Ren
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Yu Yang
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Yi Xu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Lin Ning
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yibing Zhang
- Glasgow College, University of Electronic Science and Technology of China, Chengdu, China
| | - Huaichao Luo
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China.
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.
| | - Yang Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
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15
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Thiébaut A, Altenhoff AM, Campli G, Glover N, Dessimoz C, Waterhouse RM. DrosOMA: the Drosophila Orthologous Matrix browser. F1000Res 2024; 12:936. [PMID: 38434623 PMCID: PMC10905159 DOI: 10.12688/f1000research.135250.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/12/2024] [Indexed: 03/05/2024] Open
Abstract
Background Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and gene family origins, trajectories, and dynamics, as well as enabling the tracing of speciation, duplication, and loss events, and facilitating the transfer of gene functional information across species. Genomic data are available for an increasing number of species from the genus Drosophila, however, a dedicated resource exploiting these data to provide the research community with browsable results from genus-wide orthology delineation has been lacking. Methods Using the OMA Orthologous Matrix orthology inference approach and browser deployment framework, we catalogued orthologues across a selected set of Drosophila species with high-quality annotated genomes. We developed and deployed a dedicated instance of the OMA browser to facilitate intuitive exploration, visualisation, and downloading of the genus-wide orthology delineation results. Results DrosOMA - the Drosophila Orthologous Matrix browser, accessible from https://drosoma.dcsr.unil.ch/ - presents the results of orthology delineation for 36 drosophilids from across the genus and four outgroup dipterans. It enables querying and browsing of the orthology data through a feature-rich web interface, with gene-view, orthologous group-view, and genome-view pages, including comprehensive gene name and identifier cross-references together with available functional annotations and protein domain architectures, as well as tools to visualise local and global synteny conservation. Conclusions The DrosOMA browser demonstrates the deployability of the OMA browser framework for building user-friendly orthology databases with dense sampling of a selected taxonomic group. It provides the Drosophila research community with a tailored resource of browsable results from genus-wide orthology delineation.
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Affiliation(s)
- Antonin Thiébaut
- Department of Ecology and Evolution, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Adrian M. Altenhoff
- Department of Computer Science, SIB Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Giulia Campli
- Department of Ecology and Evolution, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Natasha Glover
- Department of Computational Biology, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Christophe Dessimoz
- Department of Computational Biology, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Robert M. Waterhouse
- Department of Ecology and Evolution, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
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16
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Carhuaricra-Huaman D, Setubal JC. Protein-Coding Gene Families in Prokaryote Genome Comparisons. Methods Mol Biol 2024; 2802:33-55. [PMID: 38819555 DOI: 10.1007/978-1-0716-3838-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
The identification of orthologous genes is relevant for comparative genomics, phylogenetic analysis, and functional annotation. There are many computational tools for the prediction of orthologous groups as well as web-based resources that offer orthology datasets for download and online analysis. This chapter presents a simple and practical guide to the process of orthologous group prediction, using a dataset of 10 prokaryotic proteomes as example. The orthology methods covered are OrthoMCL, COGtriangles, OrthoFinder2, and OMA. The authors compare the number of orthologous groups predicted by these various methods, and present a brief workflow for the functional annotation and reconstruction of phylogenies from inferred single-copy orthologous genes. The chapter also demonstrates how to explore two orthology databases: eggNOG6 and OrthoDB.
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Affiliation(s)
- Dennis Carhuaricra-Huaman
- Programa de Pós-Graduação Interunidades em Bioinformática, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, SP, Brazil
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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17
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Singleton M, Eisen M. Leveraging genomic redundancy to improve inference and alignment of orthologous proteins. G3 (BETHESDA, MD.) 2023; 13:jkad222. [PMID: 37770067 PMCID: PMC10700111 DOI: 10.1093/g3journal/jkad222] [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: 07/28/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
Identifying protein sequences with common ancestry is a core task in bioinformatics and evolutionary biology. However, methods for inferring and aligning such sequences in annotated genomes have not kept pace with the increasing scale and complexity of the available data. Thus, in this work, we implemented several improvements to the traditional methodology that more fully leverage the redundancy of closely related genomes and the organization of their annotations. Two highlights include the application of the more flexible k-clique percolation algorithm for identifying clusters of orthologous proteins and the development of a novel technique for removing poorly supported regions of alignments with a phylogenetic hidden Markov model (phylo-HMM). In making the latter, we wrote a fully documented Python package Homomorph that implements standard HMM algorithms and created a set of tutorials to promote its use by a wide audience. We applied the resulting pipeline to a set of 33 annotated Drosophila genomes, generating 22,813 orthologous groups and 8,566 high-quality alignments.
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Affiliation(s)
- Marc Singleton
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Michael Eisen
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
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18
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Porter R, Černoša A, Fernández-Sanmartín P, Cortizas AM, Aranda E, Luo Y, Zalar P, Podlogar M, Gunde-Cimerman N, Gostinčar C. Degradation of polypropylene by fungi Coniochaeta hoffmannii and Pleurostoma richardsiae. Microbiol Res 2023; 277:127507. [PMID: 37793281 DOI: 10.1016/j.micres.2023.127507] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023]
Abstract
The urgent need for better disposal and recycling of plastics has motivated a search for microbes with the ability to degrade synthetic polymers. While microbes capable of metabolizing polyurethane and polyethylene terephthalate have been discovered and even leveraged in enzymatic recycling approaches, microbial degradation of additive-free polypropylene (PP) remains elusive. Here we report the isolation and characterization of two fungal strains with the potential to degrade pure PP. Twenty-seven fungal strains, many isolated from hydrocarbon contaminated sites, were screened for degradation of commercially used textile plastic. Of the candidate strains, two identified as Coniochaeta hoffmannii and Pleurostoma richardsiae were found to colonize the plastic fibers using scanning electron microscopy (SEM). Further experiments probing degradation of pure PP films were performed using C. hoffmannii and P. richardsiae and analyzed using SEM, Raman spectroscopy and Fourier transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR). The results showed that the selected fungi were active against pure PP, with distinct differences in the bonds targeted and the degree to which each was altered. Whole genome and transcriptome sequencing was conducted for both strains and the abundance of carbohydrate active enzymes, GC content, and codon usage bias were analyzed in predicted proteomes for each. Enzymatic assays were conducted to assess each strain's ability to degrade naturally occurring compounds as well as synthetic polymers. These investigations revealed potential adaptations to hydrocarbon-rich environments and provide a foundation for further investigation of PP degrading activity in C. hoffmannii and P. richardsiae.
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Affiliation(s)
- Rachel Porter
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Anja Černoša
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Paola Fernández-Sanmartín
- CRETUS, EcoPast Research Group (GI-1553), Departamento de Edafoloxía e Química Agrícola, Faculty of Biology, Universidade de Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Spain
| | - Antonio Martínez Cortizas
- CRETUS, EcoPast Research Group (GI-1553), Departamento de Edafoloxía e Química Agrícola, Faculty of Biology, Universidade de Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Spain
| | - Elisabet Aranda
- University of Granada, Institute of Water Research, Environmental Microbiology Group, Ramón y Cajal n4, 18071 Granada, Spain
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao 266555, China
| | - Polona Zalar
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Matejka Podlogar
- Department for Nanostructured Materials, Jožef Stefan Institute, Jamova cesta 39, Ljubljana, Slovenia
| | - Nina Gunde-Cimerman
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Cene Gostinčar
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia.
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19
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Alencar RM, Sepulveda CCP, Martinez-Villegas L, Bahia AC, Santana RA, de Souza IB, D'Elia GMA, Duarte APM, de Lacerda MVG, Monteiro WM, Secundino NFC, Pimenta PFP, Koerich LB. Unravelling the genome of the brackish water malaria vector Anopheles aquasalis. Sci Rep 2023; 13:20472. [PMID: 37993652 PMCID: PMC10665375 DOI: 10.1038/s41598-023-47830-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023] Open
Abstract
Malaria is a severe public health problem in several developing tropical and subtropical countries. Anopheles aquasalis is the primary coastal malaria vector in Central and South America and the Caribbean Islands, and it has the peculiar feature of living in water with large changes in salinity. Recent research has recognised An. aquasalis as an important model for studying the interactions of murine and human Plasmodium parasites. This study presents the complete genome of An. aquasalis and offers insights into its evolution and physiology. The genome is similar in size and gene content to other Neotropical anophelines, with 162 Mb and 12,446 protein-coding genes. There are 1387 single-copy orthologs at the Diptera level (eg. An. gambiae, An. darlingi and Drosophila melanogaster). An. aquasalis diverged from An. darlingi, the primary malaria vector in inland South America, nearly 20 million years ago. Proteins related to ion transport and metabolism belong to the most abundant gene families with 660 genes. We identified gene families relevant to osmosis control (e.g., aquaporins, vacuolar-ATPases, Na+/K+-ATPases, and carbonic anhydrases). Evolutionary analysis suggests that all osmotic regulation genes are under strong purifying selection. We also observed low copy number variation in insecticide resistance and immunity-related genes for all known classical pathways. The data provided by this study offers candidate genes for further studies of parasite-vector interactions and for studies on how anophelines of brackish water deal with the high fluctuation in water salinity. We also established data and insights supporting An. aquasalis as an emerging Neotropical malaria vector model for genetic and molecular studies.
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Affiliation(s)
- Rodrigo Maciel Alencar
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Cesar Camilo Prado Sepulveda
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Luis Martinez-Villegas
- Instituto de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, FIOCRUZ, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil
| | - Ana Cristina Bahia
- Laboratório de Bioquímica de Insetos e Parasitos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, CEP 21.941-170, Brazil
| | - Rosa Amélia Santana
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
- Instituto de Pesquisa Leônidas & Maria Deane, Fundação Oswaldo Cruz, Manaus, Amazonas, CEP 69.027-070, Brazil
| | - Igor Belém de Souza
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Gigliola Mayara Ayres D'Elia
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Ana Paula Marques Duarte
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Marcus Vinicius Guimarães de Lacerda
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Instituto de Pesquisa Leônidas & Maria Deane, Fundação Oswaldo Cruz, Manaus, Amazonas, CEP 69.027-070, Brazil
- University of Texas Medical Branch, Galveston, United States of America
| | - Wuelton Marcelo Monteiro
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Nágila Francinete Costa Secundino
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
- Instituto de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, FIOCRUZ, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil
| | - Paulo Filemon Paolucci Pimenta
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil.
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil.
- Instituto de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil.
- Programa de Pós-Graduação em Ciências da Saúde, FIOCRUZ, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil.
| | - Leonardo Barbosa Koerich
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 31.270-901, Brazil.
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20
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Wang GS, Cai Q, Hao YJ, Bau T, Chen ZH, Li MX, David N, Kraisitudomsook N, Yang ZL. Phylogenetic and taxonomic updates of Agaricales, with an emphasis on Tricholomopsis. Mycology 2023; 15:180-209. [PMID: 38813470 PMCID: PMC11133883 DOI: 10.1080/21501203.2023.2263031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/20/2023] [Indexed: 05/31/2024] Open
Abstract
The order Agaricales was divided into eight suborders. However, the phylogenetic relationships among some suborders are largely unresolved, and the phylogenetic positions and delimitations of some taxa, such as Sarcomyxaceae and Tricholomopsis, remain unsettled. In this study, sequence data of 38 genomes were generated through genome skimming on an Illumina sequencing system. To anchor the systematic position of Sarcomyxaceae and Tricholomopsis, a phylogenetic analysis based on 555 single-copy orthologous genes from the aforementioned genomes and 126 publicly accessible genomes was performed. The results fully supported the clustering of Tricholomopsis with Phyllotopsis and Pleurocybella within Phyllotopsidaceae, which formed a divergent monophyletic major lineage together with Pterulaceae, Radulomycetaceae, and Macrotyphula in Agaricales. The analysis also revealed that Sarcomyxaceae formed a unique major clade. Therefore, two new suborders, Phyllotopsidineae and Sarcomyxineae, are proposed for the two major lineages. Analyses of 450 single-copy orthologous genes and four loci suggested that Tricholomopsis consisted of at least four clades. Tricholomopsis is subsequently subdivided into four distinct sections. Seventeen Tricholomopsis species in China, including six new species, are reported. Conoloma is established to accommodate T. mucronata. The substrate preference of Tricholomopsis species and the transitions of the pileate ornamentations among the species within the genus are discussed.
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Affiliation(s)
- Geng-Shen Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qing Cai
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yan-Jia Hao
- School of Horticulture, Anhui Agricultural University, Hefei, China
| | - Tolgor Bau
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Zuo-Hong Chen
- Life Science College, Hunan Normal University, Changsha, China
| | - Mei-Xiang Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Navarro David
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, Marseille, France
- INRAE, Aix Marseille Université, CIRM-CF, Marseille, France
| | - Nattapol Kraisitudomsook
- Department of Biology, Faculty of Science and Technology, Muban Chombueng Rajabhat University, Ratchaburi, Thailand
| | - Zhu-Liang Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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21
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Sokołowska B, Orłowska M, Okrasińska A, Piłsyk S, Pawłowska J, Muszewska A. What can be lost? Genomic perspective on the lipid metabolism of Mucoromycota. IMA Fungus 2023; 14:22. [PMID: 37932857 PMCID: PMC10629195 DOI: 10.1186/s43008-023-00127-4] [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: 12/02/2022] [Accepted: 10/23/2023] [Indexed: 11/08/2023] Open
Abstract
Mucoromycota is a phylum of early diverging fungal (EDF) lineages, of mostly plant-associated terrestrial fungi. Some strains have been selected as promising biotechnological organisms due to their ability to produce polyunsaturated fatty acids and efficient conversion of nutrients into lipids. Others get their lipids from the host plant and are unable to produce even the essential ones on their own. Following the advancement in EDF genome sequencing, we carried out a systematic survey of lipid metabolism protein families across different EDF lineages. This enabled us to explore the genomic basis of the previously documented ability to produce several types of lipids within the fungal tree of life. The core lipid metabolism genes showed no significant diversity in distribution, however specialized lipid metabolic pathways differed in this regard among different fungal lineages. In total 165 out of 202 genes involved in lipid metabolism were present in all tested fungal lineages, while remaining 37 genes were found to be absent in some of fungal lineages. Duplications were observed for 69 genes. For the first time we demonstrate that ergosterol is not being produced by several independent groups of plant-associated fungi due to the losses of different ERG genes. Instead, they possess an ancestral pathway leading to the synthesis of cholesterol, which is absent in other fungal lineages. The lack of diacylglycerol kinase in both Mortierellomycotina and Blastocladiomycota opens the question on sterol equilibrium regulation in these organisms. Early diverging fungi retained most of beta oxidation components common with animals including Nudt7, Nudt12 and Nudt19 pointing at peroxisome divergence in Dikarya. Finally, Glomeromycotina and Mortierellomycotina representatives have a similar set of desaturases and elongases related to the synthesis of complex, polyunsaturated fatty acids pointing at an ancient expansion of fatty acid metabolism currently being explored by biotechnological studies.
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Affiliation(s)
- Blanka Sokołowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
- Faculty of Biology, Biological and Chemical Research Centre, Institute of Evolutionary Biology, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Małgorzata Orłowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
- Faculty of Biology, Biological and Chemical Research Centre, Institute of Evolutionary Biology, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Alicja Okrasińska
- Faculty of Biology, Biological and Chemical Research Centre, Institute of Evolutionary Biology, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Sebastian Piłsyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Julia Pawłowska
- Faculty of Biology, Biological and Chemical Research Centre, Institute of Evolutionary Biology, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland.
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22
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Kearney SK, Berger A, Baker E. Aon: a service to augment Alliance Genome Resource data with additional species. BMC Res Notes 2023; 16:297. [PMID: 37891644 PMCID: PMC10604687 DOI: 10.1186/s13104-023-06577-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
OBJECTIVE Cross-species comparative genomics requires access to accurate homology data across the entire range of annotated genes. The Alliance of Genome Resources (AGR) provides an open-source and comprehensive database of homology data calculated using a wide array of algorithms at differing stringencies to elucidate orthologous relationships. However, the current AGR application program interface (API) is limited to five homology endpoints for nine species. While AGR provides a robust resource for several canonical species, its utility can be greatly enhanced by increased filtering and data processing options and incorporating additional species. RESULTS Here, we describe a novel API tool, AON, that expands access to the AGR orthology resource by creating a data structure that supports 50 additional endpoints. More importantly, it provides users with a framework for adding bespoke endpoints, custom species, and additional orthology data. We demonstrate AON's functionality by incorporating the service into the GeneWeaver ecosystem for supporting cross-species data analysis.
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Affiliation(s)
- Sophie K Kearney
- Department of Computer Science, Baylor University, One Bear Place Box 97356, Waco, 76798, USA
| | | | - Erich Baker
- Department of Computer Science, Baylor University, One Bear Place Box 97356, Waco, 76798, USA.
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23
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Gadagkar SR, Baeza JA, Buss K, Johnson N. De-novo whole genome assembly of the orange jewelweed, Impatiens capensis Meerb. (Balsaminaceae) using nanopore long-read sequencing. PeerJ 2023; 11:e16328. [PMID: 37901463 PMCID: PMC10601903 DOI: 10.7717/peerj.16328] [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: 12/21/2022] [Accepted: 09/30/2023] [Indexed: 10/31/2023] Open
Abstract
The plant family Balsaminaceae comprises only two genera, and they are a study in contrasts. While Impatiens is an impressively prolific genus, with over 1,000 species and more being discovered each year, its sister genus, Hydrocera, has one solitary species, H. triflora. The two genera also differ in geographic distribution and habitat type (Impatiens species are widely distributed in much of the Old World and N. America, while H. triflora is confined to wetlands specific to S. India, Sri Lanka, and SE Asia). Other contrasting features include plant habit, habitat, floral architecture, mode of seed dispersal, and a host of other traits. The family Balsaminaceae is therefore an excellent model for studying speciation and character evolution as well as understanding the proximal and evolutionary forces that have driven the two genera to adopt such contrasting evolutionary paths. Various species of the Impatiens genus are also commercially important in the ornamental flower industry and as sources of phytochemicals that are of medicinal and other commercial value. As a preliminary step towards studying the genomic basis of the contrasting features of the two genera, we have sequenced and assembled, de novo, the genome of an iconic Impatiens species from N. America, namely I. capensis, and report our findings here.
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Affiliation(s)
- Sudhindra R. Gadagkar
- Biomedical Sciences Program, Midwestern University, Glendale, Arizona, United States of America
- College of Veterinary Medicine, Midwestern University, Glendale, Arizona, United States of America
- Arizona College of Osteopathic Medicine, Midwestern University, Glendale, Arizona, United States of America
| | - J. Antonio Baeza
- Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo, Chile
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
- Smithsonian Marine Station at Fort Pierce, Fort Pierce, Florida, United States of America
| | - Kristina Buss
- Bioinformatics Core, Arizona State University, Tempe, Arizona, United States of America
| | - Nate Johnson
- Biomedical Sciences Program, Midwestern University, Glendale, Arizona, United States of America
- College of Veterinary Medicine, Midwestern University, Glendale, Arizona, United States of America
- Arizona College of Osteopathic Medicine, Midwestern University, Glendale, Arizona, United States of America
- Center for Biology and Society, Arizona State University, Tempe, Arizona, United States of America
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24
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Huang N, Li H. compleasm: a faster and more accurate reimplementation of BUSCO. Bioinformatics 2023; 39:btad595. [PMID: 37758247 PMCID: PMC10558035 DOI: 10.1093/bioinformatics/btad595] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 08/21/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023] Open
Abstract
MOTIVATION Evaluating the gene completeness is critical to measuring the quality of a genome assembly. An incomplete assembly can lead to errors in gene predictions, annotation, and other downstream analyses. Benchmarking Universal Single-Copy Orthologs (BUSCO) is a widely used tool for assessing the completeness of genome assembly by testing the presence of a set of single-copy orthologs conserved across a wide range of taxa. However, BUSCO is slow particularly for large genome assemblies. It is cumbersome to apply BUSCO to a large number of assemblies. RESULTS Here, we present compleasm, an efficient tool for assessing the completeness of genome assemblies. Compleasm utilizes the miniprot protein-to-genome aligner and the conserved orthologous genes from BUSCO. It is 14 times faster than BUSCO for human assemblies and reports a more accurate completeness of 99.6% than BUSCO's 95.7%, which is in close agreement with the annotation completeness of 99.5% for T2T-CHM13. AVAILABILITY AND IMPLEMENTATION https://github.com/huangnengCSU/compleasm.
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Affiliation(s)
- Neng Huang
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, United States
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, United States
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States
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25
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Neely BA, Ellisor DL, Davis WC. Proteomics as a Metrological Tool to Evaluate Genome Annotation Accuracy Following De Novo Genome Assembly: A Case Study Using the Atlantic Bottlenose Dolphin ( Tursiops truncatus). Genes (Basel) 2023; 14:1696. [PMID: 37761836 PMCID: PMC10531373 DOI: 10.3390/genes14091696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The last decade has witnessed dramatic improvements in whole-genome sequencing capabilities coupled to drastically decreased costs, leading to an inundation of high-quality de novo genomes. For this reason, the continued development of genome quality metrics is imperative. Using the 2016 Atlantic bottlenose dolphin NCBI RefSeq annotation and mass spectrometry-based proteomic analysis of six tissues, we confirmed 10,402 proteins from 4711 protein groups, constituting nearly one-third of the possible predicted proteins. Since the identification of larger proteins with more identified peptides implies reduced database fragmentation and improved gene annotation accuracy, we propose the metric NP10, which attempts to capture this quality improvement. The NP10 metric is calculated by first stratifying proteomic results by identifying the top decile (or 10th 10-quantile) of identified proteins based on the number of peptides per protein and then returns the median molecular weight of the resulting proteins. When using the 2016 versus 2012 Tursiops truncatus genome annotation to search this proteomic data set, there was a 21% improvement in NP10. This metric was further demonstrated by using a publicly available proteomic data set to compare human genome annotations from 2004, 2013 and 2016, which showed a 33% improvement in NP10. These results demonstrate that proteomics may be a useful metrological tool to benchmark genome accuracy, though there is a need for reference proteomic datasets across species to facilitate the evaluation of new de novo and existing genome.
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Affiliation(s)
- Benjamin A. Neely
- National Institute of Standards and Technology, NIST Charleston, 331 Fort Johnson Road, Charleston, SC 29412, USA; (D.L.E.); (W.C.D.)
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26
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Wang Z, Ma X, Zhu J, Zheng B, Yuan R, Lu Z, Shu X, Fang Y, Tian S, Qu Q, Ye X, Tang P, Chen X. Chromosome-level genome assembly of Chouioia cunea Yang, the parasitic wasp of the fall webworm. Sci Data 2023; 10:485. [PMID: 37495588 PMCID: PMC10372138 DOI: 10.1038/s41597-023-02388-5] [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: 04/17/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023] Open
Abstract
Chouioia cunea Yang 1989 is a parasitic wasp of many lepidopteran insects during their pupal stage, and has been successfully used to control pests such as the fall webworm Hyphantria cunea. Here we reported the chromosome-level genome of C. cunea by using short (MGI-SEQ), long (Oxford Nanopore), chromatin-linked (Hi-C) sequencing reads and transcriptomic data, representing the first chromosome-level genome of parasitic wasps of the family Eulophidae. The total assembly length is 171.99 Mb, containing 6 pesudo-chromosomes with a GC content of 36.89% and the scaffold/contig N50 length of 31.70/26.52 Mb. The BUSCO completeness of the assembly was estimated to be 98.7%. A total of 12,258 protein-coding genes (PCGs), 10,547 3'-UTRs, and 10,671 5'-UTRs were annotated. This high-quality genome is an important step toward a better understanding of the genomes of the Eulophidae (Chalcidoidea), and will serve as a valuable resource for analyses of phylogenetic relationships and the evolution of Hymenoptera.
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Affiliation(s)
- Ziqi Wang
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xingzhou Ma
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jiachen Zhu
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Boying Zheng
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ruizhong Yuan
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhaohe Lu
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiaohan Shu
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yu Fang
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shiji Tian
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Qiuyu Qu
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiqian Ye
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Pu Tang
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China.
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Xuexin Chen
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China.
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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27
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Shaw C, Hess M, Weimer BC. Microbial-Derived Tryptophan Metabolites and Their Role in Neurological Disease: Anthranilic Acid and Anthranilic Acid Derivatives. Microorganisms 2023; 11:1825. [PMID: 37512997 PMCID: PMC10384668 DOI: 10.3390/microorganisms11071825] [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: 06/21/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
The gut microbiome provides the host access to otherwise indigestible nutrients, which are often further metabolized by the microbiome into bioactive components. The gut microbiome can also shift the balance of host-produced compounds, which may alter host health. One precursor to bioactive metabolites is the essential aromatic amino acid tryptophan. Tryptophan is mostly shunted into the kynurenine pathway but is also the primary metabolite for serotonin production and the bacterial indole pathway. Balance between tryptophan-derived bioactive metabolites is crucial for neurological homeostasis and metabolic imbalance can trigger or exacerbate neurological diseases. Alzheimer's, depression, and schizophrenia have been linked to diverging levels of tryptophan-derived anthranilic, kynurenic, and quinolinic acid. Anthranilic acid from collective microbiome metabolism plays a complex but important role in systemic host health. Although anthranilic acid and its metabolic products are of great importance for host-microbe interaction in neurological health, literature examining the mechanistic relationships between microbial production, host regulation, and neurological diseases is scarce and at times conflicting. This narrative review provides an overview of the current understanding of anthranilic acid's role in neurological health and disease, with particular focus on the contribution of the gut microbiome, the gut-brain axis, and the involvement of the three major tryptophan pathways.
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Affiliation(s)
- Claire Shaw
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, University of California Davis, Davis, CA 95616, USA
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA 95616, USA
| | - Matthias Hess
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA 95616, USA
| | - Bart C Weimer
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, University of California Davis, Davis, CA 95616, USA
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28
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Pownall ME, Miao L, Vejnar CE, M’Saad O, Sherrard A, Frederick MA, Benitez MD, Boswell CW, Zaret KS, Bewersdorf J, Giraldez AJ. Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin. Science 2023; 381:92-100. [PMID: 37410825 PMCID: PMC10372697 DOI: 10.1126/science.ade5308] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 05/17/2023] [Indexed: 07/08/2023]
Abstract
Nanoscale chromatin organization regulates gene expression. Although chromatin is notably reprogrammed during zygotic genome activation (ZGA), the organization of chromatin regulatory factors during this universal process remains unclear. In this work, we developed chromatin expansion microscopy (ChromExM) to visualize chromatin, transcription, and transcription factors in vivo. ChromExM of embryos during ZGA revealed how the pioneer factor Nanog interacts with nucleosomes and RNA polymerase II (Pol II), providing direct visualization of transcriptional elongation as string-like nanostructures. Blocking elongation led to more Pol II particles clustered around Nanog, with Pol II stalled at promoters and Nanog-bound enhancers. This led to a new model termed "kiss and kick", in which enhancer-promoter contacts are transient and released by transcriptional elongation. Our results demonstrate that ChromExM is broadly applicable to study nanoscale nuclear organization.
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Affiliation(s)
- Mark E. Pownall
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Liyun Miao
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Charles E. Vejnar
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Ons M’Saad
- Department of Cell Biology, Yale University School of Medicine; New Haven, CT 06510, USA
- Department of Biomedical Engineering, Yale University; New Haven, CT 06510, USA
| | - Alice Sherrard
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Megan A. Frederick
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria D.J. Benitez
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Curtis W. Boswell
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Kenneth S. Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine; New Haven, CT 06510, USA
- Kavli Institute for Neuroscience, Yale University School of Medicine; New Haven, CT 06510, USA
- Department of Biomedical Engineering, Yale University; New Haven, CT 06510, USA
- Department of Physics, Yale University; New Haven, CT 06510, USA
- Nanobiology Institute, Yale University; West Haven, CT 06477, USA
| | - Antonio J. Giraldez
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
- Yale Stem Cell Center, Yale University School of Medicine; New Haven, CT 06510, USA
- Yale Cancer Center, Yale University School of Medicine; New Haven, CT 06510, USA
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29
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Scheunert A, Lautenschlager U, Ott T, Oberprieler C. Nano-Strainer: A workflow for the identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads. Ecol Evol 2023; 13:e10190. [PMID: 37475726 PMCID: PMC10354226 DOI: 10.1002/ece3.10190] [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: 12/23/2022] [Revised: 05/18/2023] [Accepted: 06/01/2023] [Indexed: 07/22/2023] Open
Abstract
In modern plant systematics, target enrichment enables simultaneous analysis of hundreds of genes. However, when dealing with reticulate or polyploidization histories, few markers may suffice, but often are required to be single-copy, a condition that is not necessarily met with commercial capture kits. Also, large genome sizes can render target capture ineffective, so that amplicon sequencing would be preferable; however, knowledge about suitable loci is often missing. Here, we present a comprehensive workflow for the identification of putative single-copy nuclear markers in a genus of interest, by mining a small dataset from target capture using a few representative taxa. The proposed pipeline assesses sequence variability contained in the data from targeted loci and assigns reads to their respective genes, via a combined BLAST/clustering procedure. Cluster consensus sequences are then examined based on four pre-defined criteria presumably indicative for absence of paralogy. This is done by calculating four specialized indices; loci are ranked according to their performance in these indices, and top-scoring loci are considered putatively single- or low copy. The approach can be applied to any probe set. As it relies on long reads, the present contribution also provides template workflows for processing Nanopore-based target capture data. Obtained markers are further tested and then entered into amplicon sequencing. For the detection of possibly remaining paralogy in these data, which might occur in groups with rampant paralogy, we also employ the long-read assembly tool canu. In diploid representatives of the young Compositae genus Leucanthemum, characterized by high levels of polyploidy, our approach resulted in successful amplification of 13 loci. Modifications to remove traces of paralogy were made in seven of these. A species tree from the markers correctly reproduced main relationships in the genus, however, at low resolution. The presented workflow has the potential to valuably support phylogenetic research, for example in polyploid plant groups.
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Affiliation(s)
- Agnes Scheunert
- Evolutionary and Systematic Botany Group, Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
| | - Ulrich Lautenschlager
- Evolutionary and Systematic Botany Group, Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
| | - Tankred Ott
- Evolutionary and Systematic Botany Group, Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
| | - Christoph Oberprieler
- Evolutionary and Systematic Botany Group, Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
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30
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Huang N, Li H. miniBUSCO: a faster and more accurate reimplementation of BUSCO. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.03.543588. [PMID: 37333158 PMCID: PMC10274665 DOI: 10.1101/2023.06.03.543588] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Motivation Assembly completeness evaluation of genome assembly is a critical assessment of the accuracy and reliability of genomic data. An incomplete assembly can lead to errors in gene predictions, annotation, and other downstream analyses. BUSCO is one of the most widely used tools for assessing the completeness of genome assembly by comparing the presence of a set of single-copy orthologs conserved across a wide range of taxa. However, the runtime of BUSCO can be long, particularly for some large genome assemblies. It is a challenge for researchers to quickly iterate the genome assemblies or analyze a large number of assemblies. Results Here, we present miniBUSCO, an efficient tool for assessing the completeness of genome assemblies. miniBUSCO utilizes the protein-to-genome aligner miniprot and the datasets of conserved orthologous genes from BUSCO. Our evaluation of the real human assembly indicates that miniBUSCO achieves a 14-fold speedup over BUSCO. Furthermore, miniBUSCO reports a more accurate completeness of 99.6% than BUSCO's completeness of 95.7%, which is in close agreement with the annotation completeness of 99.5% for T2T-CHM13. Availability https://github.com/huangnengCSU/minibusco . Contact hli@ds.dfci.harvard.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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31
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Shu X, Yuan R, Zheng B, Wang Z, Ye X, Tang P, Chen X. Chromosome-level genome assembly of Microplitis manilae Ashmead, 1904 (Hymenoptera: Braconidae). Sci Data 2023; 10:266. [PMID: 37164995 PMCID: PMC10172384 DOI: 10.1038/s41597-023-02190-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/27/2023] [Indexed: 05/12/2023] Open
Abstract
Microplitis manilae Ashmead (Hymenoptera: Braconidae) is an important parasitoid of agricultural pests in lepidopteran species. So far, two extant genome assembles from the genus Microplitis are fragmented. Here, we offered a high-quality genome assembly of M. manilae at the chromosome level with high accuracy and contiguity, assembled by ONT long-read, MGI-SEQ short-read, and Hi-C sequencing methods. The final assembled genome size was 282.85 Mb, with 268.17 Mb assigned to 11 pseudochromosomes. The scaffold N50 length was 25.23 Mb, and the complete BUSCO score was 98.61%. The genome contained 152.37 Mb of repetitive elements, representing 53.87% of the total genome size. We predicted 15,689 protein-coding genes, of which 13,580 genes were annotated functionally. Gene family evolution investigations of M. manilae revealed 615 expanded and 635 contracted gene families. The high-quality genome of M. manilae reported in this paper will be a useful genomic resource for research on parasitoid wasps in the future.
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Affiliation(s)
- Xiaohan Shu
- Hainan Institute, Zhejiang University, Sanya, 572025, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ruizhong Yuan
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Boying Zheng
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhizhi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiqian Ye
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Pu Tang
- Hainan Institute, Zhejiang University, Sanya, 572025, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China.
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Xuexin Chen
- Hainan Institute, Zhejiang University, Sanya, 572025, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
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32
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Feugere L, Bates A, Emagbetere T, Chapman E, Malcolm LE, Bulmer K, Hardege J, Beltran-Alvarez P, Wollenberg Valero KC. Heat induces multiomic and phenotypic stress propagation in zebrafish embryos. PNAS NEXUS 2023; 2:pgad137. [PMID: 37228511 PMCID: PMC10205475 DOI: 10.1093/pnasnexus/pgad137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 04/11/2023] [Indexed: 05/27/2023]
Abstract
Heat alters biology from molecular to ecological levels, but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here, we provide a comprehensive picture of the molecular signatures of this process, by integrating multiomic and phenotypic data. In individual zebrafish embryos, repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slowdown in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulfur-containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response, extracellular signaling, glycosaminoglycan/keratan sulfate, and lipid metabolism. Consequently, non-heat-exposed receivers (exposed to stress metabolites only) experienced accelerated catch-up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most, mediated by apelin signaling. Our results prove the concept of indirect heat-induced stress propagation toward naive receivers, inducing phenotypes comparable with those resulting from direct heat exposure, but utilizing distinct molecular pathways. Group-exposing a nonlaboratory zebrafish line, we independently confirm that the glycosaminoglycan biosynthesis-related gene chs1 and the mucus glycoprotein gene prg4a, functionally connected to the candidate stress metabolite classes sugars and phosphocholine, are differentially expressed in receivers. This hints at the production of Schreckstoff-like cues in receivers, leading to further stress propagation within groups, which may have ecological and animal welfare implications for aquatic populations in a changing climate.
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Affiliation(s)
- Lauric Feugere
- Department of Biological and Marine Sciences, University of Hull, Kingston upon Hull HU6 7RX, UK
| | - Adam Bates
- Department of Biological and Marine Sciences, University of Hull, Kingston upon Hull HU6 7RX, UK
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Timothy Emagbetere
- Department of Biological and Marine Sciences, University of Hull, Kingston upon Hull HU6 7RX, UK
| | - Emma Chapman
- Department of Biological and Marine Sciences, University of Hull, Kingston upon Hull HU6 7RX, UK
| | - Linsey E Malcolm
- Biomedical Institute for Multimorbidities, Centre for Biomedicine, Hull York Medical School, University of Hull, Kingston upon Hull HU6 7RX, UK
| | - Kathleen Bulmer
- Biomedical Institute for Multimorbidities, Centre for Biomedicine, Hull York Medical School, University of Hull, Kingston upon Hull HU6 7RX, UK
| | - Jörg Hardege
- Department of Biological and Marine Sciences, University of Hull, Kingston upon Hull HU6 7RX, UK
| | - Pedro Beltran-Alvarez
- Biomedical Institute for Multimorbidities, Centre for Biomedicine, Hull York Medical School, University of Hull, Kingston upon Hull HU6 7RX, UK
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33
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Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, Goodman DB, Goodman L, Keough KC, Kirilenko B, Kowalczyk A, Lawless C, Lind AL, Meadows JRS, Moreira LR, Redlich RW, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown AR, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev SV, Lawler AJ, Marinescu VD, Morrill KM, Osmanski A, Paulat NS, Phan BN, Reilly SK, Schäffer DE, Steiner C, Supple MA, Wilder AP, Wirthlin ME, Xue JR, Birren BW, Gazal S, Hubley RM, Koepfli KP, Marques-Bonet T, Meyer WK, Nweeia M, Sabeti PC, Shapiro B, Smit AFA, Springer MS, Teeling EC, Weng Z, Hiller M, Levesque DL, Lewin HA, Murphy WJ, Navarro A, Paten B, Pollard KS, Ray DA, Ruf I, Ryder OA, Pfenning AR, Lindblad-Toh K, Karlsson EK. Evolutionary constraint and innovation across hundreds of placental mammals. Science 2023; 380:eabn3943. [PMID: 37104599 PMCID: PMC10250106 DOI: 10.1126/science.abn3943] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/16/2022] [Indexed: 04/29/2023]
Abstract
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.
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Affiliation(s)
- Matthew J. Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Irene M. Kaplow
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | | | - Michael X. Dong
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Xue Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Patrick F. Sullivan
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Allyson G. Hindle
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Gregory Andrews
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Joel C. Armstrong
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Matteo Bianchi
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Ana M. Breit
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
| | - Mark Diekhans
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Cornelia Fanter
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Nicole M. Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Daniel B. Goodman
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Kathleen C. Keough
- Fauna Bio, Inc., Emeryville, CA 94608, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Bogdan Kirilenko
- Faculty of Biosciences, Goethe-University, 60438 Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
| | - Amanda Kowalczyk
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Colleen Lawless
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Abigail L. Lind
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Jennifer R. S. Meadows
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Lucas R. Moreira
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Ruby W. Redlich
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Louise Ryan
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ross Swofford
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Alejandro Valenzuela
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Franziska Wagner
- Museum of Zoology, Senckenberg Natural History Collections Dresden, 01109 Dresden, Germany
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Ashley R. Brown
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Joana Damas
- The Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Kaili Fan
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Jenna Grimshaw
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Sergey V. Kozyrev
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Alyssa J. Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Voichita D. Marinescu
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Kathleen M. Morrill
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Austin Osmanski
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Nicole S. Paulat
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - BaDoi N. Phan
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Steven K. Reilly
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Daniel E. Schäffer
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Cynthia Steiner
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Megan A. Supple
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Aryn P. Wilder
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Morgan E. Wirthlin
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - James R. Xue
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Bruce W. Birren
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Steven Gazal
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | | | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC 20008, USA
- Computer Technologies Laboratory, ITMO University, St. Petersburg 197101, Russia
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA
| | - Tomas Marques-Bonet
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08036 Barcelona, Spain
- Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Wynn K. Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Martin Nweeia
- Department of Comprehensive Care, School of Dental Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Vertebrate Zoology, Canadian Museum of Nature, Ottawa, Ontario K2P 2R1, Canada
- Department of Vertebrate Zoology, Smithsonian Institution, Washington, DC 20002, USA
- Narwhal Genome Initiative, Department of Restorative Dentistry and Biomaterials Sciences, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Mark S. Springer
- Department of Evolution, Ecology and Organismal Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Michael Hiller
- Faculty of Biosciences, Goethe-University, 60438 Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
| | | | - Harris A. Lewin
- The Genome Center, University of California Davis, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA
- John Muir Institute for the Environment, University of California Davis, Davis, CA 95616, USA
| | - William J. Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Arcadi Navarro
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, 08005 Barcelona, Spain
- CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Benedict Paten
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Katherine S. Pollard
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Irina Ruf
- Division of Messel Research and Mammalogy, Senckenberg Research Institute and Natural History Museum Frankfurt, 60325 Frankfurt am Main, Germany
| | - Oliver A. Ryder
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
- Department of Evolution, Behavior and Ecology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92039, USA
| | - Andreas R. Pfenning
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Elinor K. Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605, USA
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Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wang C, Wallerman O, Xue J, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler A, Keough KC, Zheng Z, Zeng J, Wray NR, Li Y, Johnson J, Chen J, Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K. Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science 2023; 380:eabn2937. [PMID: 37104612 PMCID: PMC10259825 DOI: 10.1126/science.abn2937] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/09/2023] [Indexed: 04/29/2023]
Abstract
Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.
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Affiliation(s)
- Patrick F. Sullivan
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Jennifer R. S. Meadows
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Steven Gazal
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - BaDoi N. Phan
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Xue Li
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Diane P. Genereux
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Michael X. Dong
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Matteo Bianchi
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Gregory Andrews
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sharadha Sakthikumar
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Jessika Nordin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Ananya Roy
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Matthew J. Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Voichita D. Marinescu
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Chao Wang
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
| | - James Xue
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Center for System Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Shuyang Yao
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Quan Sun
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | - Jin Szatkiewicz
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | - Laura M. Huckins
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alyssa Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kathleen C. Keough
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA
| | - Zhili Zheng
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Naomi R. Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Yun Li
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | - Jessica Johnson
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
| | | | - Benedict Paten
- UC Santa Cruz Genomics Institute, Santa Cruz, CA 95064, USA
| | - Steven K. Reilly
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Andreas R. Pfenning
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75185 Uppsala, Sweden
- Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Elinor K. Karlsson
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 75132 Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
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Abbott J, Näthke IS. The adenomatous polyposis coli protein 30 years on. Semin Cell Dev Biol 2023:S1084-9521(23)00093-9. [PMID: 37095033 DOI: 10.1016/j.semcdb.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 04/11/2023] [Accepted: 04/16/2023] [Indexed: 04/26/2023]
Abstract
Mutations in the gene encoding the Adenomatous polyposis coli protein (APC) were discovered as driver mutations in colorectal cancers almost 30 years ago. Since then, the importance of APC in normal tissue homeostasis has been confirmed in a plethora of other (model) organisms spanning a large evolutionary space. APC is a multifunctional protein, with roles as a key scaffold protein in complexes involved in diverse signalling pathways, most prominently the Wnt signalling pathway. APC is also a cytoskeletal regulator with direct and indirect links to and impacts on all three major cytoskeletal networks. Correspondingly, a wide range of APC binding partners have been identified. Mutations in APC are extremely strongly associated with colorectal cancers, particularly those that result in the production of truncated proteins and the loss of significant regions from the remaining protein. Understanding the complement of its role in health and disease requires knowing the relationship between and regulation of its diverse functions and interactions. This in turn requires understanding its structural and biochemical features. Here we set out to provide a brief overview of the roles and function of APC and then explore its conservation and structure using the extensive sequence data, which is now available, and spans a broad range of taxonomy. This revealed conservation of APC across taxonomy and new relationships between different APC protein families.
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Affiliation(s)
- James Abbott
- Division of Computational Biology & D'Arcy Thompson Unit, University of Dundee, Dow Street, Dundee, DD2 1 EH, United Kingdom.
| | - Inke S Näthke
- Division of Molecular Cell and Developmental Biology, University of Dundee, Dow Street, Dundee DD2 1EH, United Kingdom.
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Dembech E, Malatesta M, De Rito C, Mori G, Cavazzini D, Secchi A, Morandin F, Percudani R. Identification of hidden associations among eukaryotic genes through statistical analysis of coevolutionary transitions. Proc Natl Acad Sci U S A 2023; 120:e2218329120. [PMID: 37043529 PMCID: PMC10120013 DOI: 10.1073/pnas.2218329120] [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: 10/28/2022] [Accepted: 03/10/2023] [Indexed: 04/13/2023] Open
Abstract
Coevolution at the gene level, as reflected by correlated events of gene loss or gain, can be revealed by phylogenetic profile analysis. The optimal method and metric for comparing phylogenetic profiles, especially in eukaryotic genomes, are not yet established. Here, we describe a procedure suitable for large-scale analysis, which can reveal coevolution based on the assessment of the statistical significance of correlated presence/absence transitions between gene pairs. This metric can identify coevolution in profiles with low overall similarities and is not affected by similarities lacking coevolutionary information. We applied the procedure to a large collection of 60,912 orthologous gene groups (orthogroups) in 1,264 eukaryotic genomes extracted from OrthoDB. We found significant cotransition scores for 7,825 orthogroups associated in 2,401 coevolving modules linking known and unknown genes in protein complexes and biological pathways. To demonstrate the ability of the method to predict hidden gene associations, we validated through experiments the involvement of vertebrate malate synthase-like genes in the conversion of (S)-ureidoglycolate into glyoxylate and urea, the last step of purine catabolism. This identification explains the presence of glyoxylate cycle genes in metazoa and suggests an anaplerotic role of purine degradation in early eukaryotes.
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Affiliation(s)
- Elena Dembech
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Marco Malatesta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Carlo De Rito
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Giulia Mori
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Davide Cavazzini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Andrea Secchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
| | - Francesco Morandin
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma43124, Italy
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma43124, Italy
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Wolf M, Zapf K, Gupta DK, Hiller M, Árnason Ú, Janke A. The genome of the pygmy right whale illuminates the evolution of rorquals. BMC Biol 2023; 21:79. [PMID: 37041515 PMCID: PMC10091562 DOI: 10.1186/s12915-023-01579-1] [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: 07/12/2022] [Accepted: 03/27/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND Baleen whales are a clade of gigantic and highly specialized marine mammals. Their genomes have been used to investigate their complex evolutionary history and to decipher the molecular mechanisms that allowed them to reach these dimensions. However, many unanswered questions remain, especially about the early radiation of rorquals and how cancer resistance interplays with their huge number of cells. The pygmy right whale is the smallest and most elusive among the baleen whales. It reaches only a fraction of the body length compared to its relatives and it is the only living member of an otherwise extinct family. This placement makes the pygmy right whale genome an interesting target to update the complex phylogenetic past of baleen whales, because it splits up an otherwise long branch that leads to the radiation of rorquals. Apart from that, genomic data of this species might help to investigate cancer resistance in large whales, since these mechanisms are not as important for the pygmy right whale as in other giant rorquals and right whales. RESULTS Here, we present a first de novo genome of the species and test its potential in phylogenomics and cancer research. To do so, we constructed a multi-species coalescent tree from fragments of a whole-genome alignment and quantified the amount of introgression in the early evolution of rorquals. Furthermore, a genome-wide comparison of selection rates between large and small-bodied baleen whales revealed a small set of conserved candidate genes with potential connections to cancer resistance. CONCLUSIONS Our results suggest that the evolution of rorquals is best described as a hard polytomy with a rapid radiation and high levels of introgression. The lack of shared positive selected genes between different large-bodied whale species supports a previously proposed convergent evolution of gigantism and hence cancer resistance in baleen whales.
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Affiliation(s)
- Magnus Wolf
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt Am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Strasse. 9, Frankfurt Am Main, Germany
| | - Konstantin Zapf
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt Am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Strasse. 9, Frankfurt Am Main, Germany
| | - Deepak Kumar Gupta
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt Am Main, Germany
| | - Michael Hiller
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt Am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt Am Main, Germany
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-Von-Laue-Str. 9, Frankfurt Am Main, Germany
| | - Úlfur Árnason
- Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Neurosurgery, Skane University Hospital in Lund, Lund, Sweden
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt Am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Strasse. 9, Frankfurt Am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt Am Main, Germany
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Saini JS, Manni M, Hassler C, Cable RN, Duhaime MB, Zdobnov EM. Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno. THE ISME JOURNAL 2023; 17:903-915. [PMID: 37031343 DOI: 10.1038/s41396-023-01396-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 04/10/2023]
Abstract
Meromictic Lake Cadagno is a permanently stratified system with a persistent microbial bloom within the oxic-anoxic boundary called the chemocline. The association between oxygenic and anoxygenic photosynthesis within the chemocline has been known for at least two decades. Although anoxygenic purple and green sulfur bacteria have been well studied, reports on oxygenic phytoplankton have remained sparse since their discovery in the 1920s. Nearly a century later, this study presents the first near-complete genome of a photosynthetic microbial eukaryote from the chemocline of Lake Cadagno, provisionally named Chlorella-like MAG. The 18.9 Mbp nuclear genome displays a high GC content (71.5%), and the phylogenetic placement suggests that it is a novel species of the genus Chlorella of Chlorophytes. Functional annotation of the Chlorella-like metagenome-assembled genome predicted 10,732 protein-coding genes, with an approximate 0.6% proportion potentially involved in carbon, sulfur, and nitrogen (C, N, and S) metabolism. In addition to C4 photosynthesis, this study detected genes for heat shock proteins (HSPs) in the Chlorella-like algae, consistent with the other Chlorella species. Altogether, the genomic insights in this study suggest the cooperation of photosynthetic algae with phototrophic sulfur bacteria via C, N, and S metabolism, which may aid their collective persistence in the Lake Cadagno chemocline. Furthermore, this work additionally presents the chloroplast genome of Cryptomonas-like species, which was likely to be presumed as cyanobacteria in previous studies because of the presence of phycobilisomes.
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Affiliation(s)
- Jaspreet S Saini
- Department F.-A Forel for Environmental and Aquatic Sciences, Earth and Environmental Sciences, University of Geneva, Geneva, Switzerland.
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Mosè Manni
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christel Hassler
- Department F.-A Forel for Environmental and Aquatic Sciences, Earth and Environmental Sciences, University of Geneva, Geneva, Switzerland
- Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | - Rachel N Cable
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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Li J, Kong Y, Sun L, Tang Y, Sun X, Qin S, Li M. Overexpression of Ultrabithorax Changes the Development of Silk Gland and the Expression of Fibroin Genes in Bombyx mori. Int J Mol Sci 2023; 24:ijms24076670. [PMID: 37047645 PMCID: PMC10095271 DOI: 10.3390/ijms24076670] [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: 02/16/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/14/2023] Open
Abstract
Ultrabithorax (Ubx) is a member of the Hox gene group involved in cell fate decisions, cell proliferation and organ identity. Its function has been extensively researched in Drosophila melanogaster but little is known about it in Lepidoptera. To uncover the function of Ubx in the development of lepidopterans, we constructed the Ubx overexpression (UbxOE) strain based on the Nistari strain of Bombyx mori. The UbxOE strain showed a small body size, transparent intersegmental membrane and abnormal posterior silk gland (PSG). In the current study, we focused on the effect of Ubx overexpression on the posterior silk gland. As the major protein product of PSG, the mRNA expression of fibroin heavy chain (Fib-H) and fibroin light chain (Fib-L) was upregulated three times in UbxOE, but the protein expression of Fib-H and Fib-L was not significantly different. We speculated that the overexpression of Ubx downregulated the expression of Myc and further caused abnormal synthesis of the spliceosome and ribosome. Abnormalities of the spliceosome and ribosome affected the synthesis of protein in the PSG and changed its morphology.
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Affiliation(s)
- Jiashuang Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China
| | - Yunhui Kong
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China
| | - Lingling Sun
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China
| | - Yaling Tang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China
| | - Xia Sun
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang 212018, China
| | - Sheng Qin
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang 212018, China
| | - Muwang Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang 212018, China
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40
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Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wallerman O, Xue JR, Li Y, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler AJ, Keough KC, Zheng Z, Zeng J, Wray NR, Johnson J, Chen J, Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K. Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.10.531987. [PMID: 36945512 PMCID: PMC10028973 DOI: 10.1101/2023.03.10.531987] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
Although thousands of genomic regions have been associated with heritable human diseases, attempts to elucidate biological mechanisms are impeded by a general inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function that is agnostic to cell type or disease mechanism. Here, single base phyloP scores from the whole genome alignment of 240 placental mammals identified 3.5% of the human genome as significantly constrained, and likely functional. We compared these scores to large-scale genome annotation, genome-wide association studies (GWAS), copy number variation, clinical genetics findings, and cancer data sets. Evolutionarily constrained positions are enriched for variants explaining common disease heritability (more than any other functional annotation). Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.
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Affiliation(s)
- Patrick F. Sullivan
- Department of Genetics, University of North Carolina Medical School; Chapel Hill, NC 27599, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet; Stockholm, Sweden
| | - Jennifer R. S. Meadows
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - Steven Gazal
- Keck School of Medicine, University of Southern California; Los Angeles, CA 90033, USA
| | - BaDoi N. Phan
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine; Pittsburgh, PA 15261, USA
- Neuroscience Institute, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Xue Li
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School; Worcester, MA 01605, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School; Worcester, MA 01605, USA
| | | | - Michael X. Dong
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - Matteo Bianchi
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - Gregory Andrews
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School; Worcester, MA 01605, USA
| | - Sharadha Sakthikumar
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
| | - Jessika Nordin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University; Uppsala, 751 85, Sweden
| | - Ananya Roy
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University; Uppsala, 751 85, Sweden
| | - Matthew J. Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - Voichita D. Marinescu
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
| | - James R. Xue
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Department of Organismic and Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
| | - Yun Li
- Department of Genetics, University of North Carolina Medical School; Chapel Hill, NC 27599, USA
| | - Shuyang Yao
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet; Stockholm, Sweden
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Jin Szatkiewicz
- Department of Genetics, University of North Carolina Medical School; Chapel Hill, NC 27599, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina Medical School; Chapel Hill, NC 27599, USA
| | - Laura M. Huckins
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Alyssa J. Lawler
- Neuroscience Institute, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Kathleen C. Keough
- Department of Epidemiology & Biostatistics, University of California San Francisco; San Francisco, CA 94158, USA
- Fauna Bio Incorporated; Emeryville, CA 94608, USA
- Gladstone Institutes; San Francisco, CA 94158, USA
| | - Zhili Zheng
- Institute for Molecular Bioscience, University of Queensland; Brisbane, Queensland, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, University of Queensland; Brisbane, Queensland, Australia
| | - Naomi R. Wray
- Institute for Molecular Bioscience, University of Queensland; Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland; Brisbane, Queensland, Australia
| | - Jessica Johnson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | | | - Benedict Paten
- Genomics Institute, University of California Santa Cruz; Santa Cruz, CA 95064, USA
| | - Steven K. Reilly
- Department of Genetics, Yale School of Medicine; New Haven, CT 06510, USA
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin; Belfield, Dublin 4, Ireland
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School; Worcester, MA 01605, USA
| | - Katherine S. Pollard
- Department of Epidemiology & Biostatistics, University of California San Francisco; San Francisco, CA 94158, USA
- Gladstone Institutes; San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub; San Francisco, CA 94158, USA
| | - Andreas R. Pfenning
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University; Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University; Pittsburgh, PA 15213, USA
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University; Uppsala, 751 85, Sweden
- Biodiscovery Institute, University of Nottingham; Nottingham, UK
| | - Elinor K. Karlsson
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School; Worcester, MA 01605, USA
- Program in Molecular Medicine, UMass Chan Medical School; Worcester, MA 01605, USA
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University; Uppsala, 751 32, Sweden
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
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Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom. Nat Ecol Evol 2023; 7:355-366. [PMID: 36646945 PMCID: PMC9998269 DOI: 10.1038/s41559-022-01956-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 11/22/2022] [Indexed: 01/18/2023]
Abstract
Ancestral sequence reconstruction is a fundamental aspect of molecular evolution studies and can trace small-scale sequence modifications through the evolution of genomes and species. In contrast, fine-grained reconstructions of ancestral genome organizations are still in their infancy, limiting our ability to draw comprehensive views of genome and karyotype evolution. Here we reconstruct the detailed gene contents and organizations of 624 ancestral vertebrate, plant, fungi, metazoan and protist genomes, 183 of which are near-complete chromosomal gene order reconstructions. Reconstructed ancestral genomes are similar to their descendants in terms of gene content as expected and agree precisely with reference cytogenetic and in silico reconstructions when available. By comparing successive ancestral genomes along the phylogenetic tree, we estimate the intra- and interchromosomal rearrangement history of all major vertebrate clades at high resolution. This freely available resource introduces the possibility to follow evolutionary processes at genomic scales in chronological order, across multiple clades and without relying on a single extant species as reference.
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Nawae W, Naktang C, Charoensri S, U-thoomporn S, Narong N, Chusri O, Tangphatsornruang S, Pootakham W. Resequencing of durian genomes reveals large genetic variations among different cultivars. FRONTIERS IN PLANT SCIENCE 2023; 14:1137077. [PMID: 36875624 PMCID: PMC9978785 DOI: 10.3389/fpls.2023.1137077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Durian (Durio zibethinus), which yields the fruit known as the "King of Fruits," is an important economic crop in Southeast Asia. Several durian cultivars have been developed in this region. In this study, we resequenced the genomes of three popular durian cultivars in Thailand, including Kradumthong (KD), Monthong (MT), and Puangmanee (PM) to investigate genetic diversities of cultivated durians. KD, MT, and PM genome assemblies were 832.7, 762.6, and 821.6 Mb, and their annotations covered 95.7, 92.4, and 92.7% of the embryophyta core proteins, respectively. We constructed the draft durian pangenome and analyzed comparative genomes with related species in Malvales. Long terminal repeat (LTR) sequences and protein families in durian genomes had slower evolution rates than that in cotton genomes. However, protein families with transcriptional regulation function and protein phosphorylation function involved in abiotic and biotic stress responses appeared to evolve faster in durians. The analyses of phylogenetic relationships, copy number variations (CNVs), and presence/absence variations (PAVs) suggested that the genome evolution of Thai durians was different from that of the Malaysian durian, Musang King (MK). Among the three newly sequenced genomes, the PAV and CNV profiles of disease resistance genes and the expressions of methylesterase inhibitor domain containing genes involved in flowering and fruit maturation in MT were different from those in KD and PM. These genome assemblies and their analyses provide valuable resources to gain a better understanding of the genetic diversity of cultivated durians, which may be useful for the future development of new durian cultivars.
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Affiliation(s)
- Wanapinun Nawae
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Salisa Charoensri
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Sonicha U-thoomporn
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Nattapol Narong
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Orwintinee Chusri
- Chantaburi Horticulture Research Center, Horticulture Research Institute, Department of Agriculture, Chantaburi, Thailand
| | - Sithichoke Tangphatsornruang
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Wirulda Pootakham
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
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Carrera-Salinas A, González-Díaz A, Ehrlich RL, Berbel D, Tubau F, Pomares X, Garmendia J, Domínguez MÁ, Ardanuy C, Huertas D, Marín A, Montón C, Mell JC, Santos S, Marti S. Genetic Adaptation and Acquisition of Macrolide Resistance in Haemophilus spp. during Persistent Respiratory Tract Colonization in Chronic Obstructive Pulmonary Disease (COPD) Patients Receiving Long-Term Azithromycin Treatment. Microbiol Spectr 2023; 11:e0386022. [PMID: 36475849 PMCID: PMC9927455 DOI: 10.1128/spectrum.03860-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Patients with chronic obstructive pulmonary disease (COPD) benefit from the immunomodulatory effect of azithromycin, but long-term administration may alter colonizing bacteria. Our goal was to identify changes in Haemophilus influenzae and Haemophilus parainfluenzae during azithromycin treatment. Fifteen patients were followed while receiving prolonged azithromycin treatment (Hospital Universitari de Bellvitge, Spain). Four patients (P02, P08, P11, and P13) were persistently colonized by H. influenzae for at least 3 months and two (P04 and P11) by H. parainfluenzae. Isolates from these patients (53 H. influenzae and 18 H. parainfluenzae) were included to identify, by whole-genome sequencing, antimicrobial resistance changes and genetic variation accumulated during persistent colonization. All persistent lineages isolated before treatment were azithromycin-susceptible but developed resistance within the first months, apart from those belonging to P02, who discontinued the treatment. H. influenzae isolates from P08-ST107 acquired mutations in 23S rRNA, and those from P11-ST2480 and P13-ST165 had changes in L4 and L22. In H. parainfluenzae, P04 persistent isolates acquired changes in rlmC, and P11 carried genes encoding MefE/MsrD efflux pumps in an integrative conjugative element, which was also identified in H. influenzae P11-ST147. Other genetic variation occurred in genes associated with cell wall and inorganic ion metabolism. Persistent H. influenzae strains all showed changes in licA and hgpB genes. Other genes (lex1, lic3A, hgpC, and fadL) had variation in multiple lineages. Furthermore, persistent strains showed loss, acquisition, or genetic changes in prophage-associated regions. Long-term azithromycin therapy results in macrolide resistance, as well as genetic changes that likely favor bacterial adaptation during persistent respiratory colonization. IMPORTANCE The immunomodulatory properties of azithromycin reduce the frequency of exacerbations and improve the quality of life of COPD patients. However, long-term administration may alter the respiratory microbiota, such as Haemophilus influenzae, an opportunistic respiratory colonizing bacteria that play an important role in exacerbations. This study contributes to a better understanding of COPD progression by characterizing the clinical evolution of H. influenzae in a cohort of patients with prolonged azithromycin treatment. The emergence of macrolide resistance during the first months, combined with the role of Haemophilus parainfluenzae as a reservoir and source of resistance dissemination, is a cause for concern that may lead to therapeutic failure. Furthermore, genetic variations in cell wall and inorganic ion metabolism coding genes likely favor bacterial adaptation to host selective pressures. Therefore, the bacterial pathoadaptive evolution in these severe COPD patients raise our awareness of the possible spread of macrolide resistance and selection of host-adapted clones.
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Affiliation(s)
- Anna Carrera-Salinas
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
| | - Aida González-Díaz
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - Rachel L. Ehrlich
- Department of Microbiology and Immunology, Center for Genomic Sciences, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Dàmaris Berbel
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - Fe Tubau
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - Xavier Pomares
- Department of Respiratory Medicine, Hospital de Sabadell, Hospital Universitari Parc Taulí, Institut d’Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Junkal Garmendia
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
- Instituto de Agrobiotecnología, CSIC-Gobierno de Navarra, Mutilva, Spain
| | - M. Ángeles Domínguez
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
- Research Network for Infectious Diseases (CIBERINFEC), ISCIII, Madrid, Spain
- Department of Pathology and Experimental Therapeutics, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Carmen Ardanuy
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
- Department of Pathology and Experimental Therapeutics, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Daniel Huertas
- Department of Respiratory Medicine, Hospital Residència Sant Camil, Consorci Sanitari Alt Penedès-Garraf, Barcelona, Spain
| | - Alicia Marín
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
- Department of Respiratory Medicine, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Conchita Montón
- Department of Respiratory Medicine, Hospital de Sabadell, Hospital Universitari Parc Taulí, Institut d’Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Joshua Chang Mell
- Department of Microbiology and Immunology, Center for Genomic Sciences, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Salud Santos
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
- Department of Respiratory Medicine, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
- Department of Medicine, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Sara Marti
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
- Department of Medicine, School of Medicine, University of Barcelona, Barcelona, Spain
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Liu K, Chen Q, Huang GH. An Efficient Feature Selection Algorithm for Gene Families Using NMF and ReliefF. Genes (Basel) 2023; 14:421. [PMID: 36833348 PMCID: PMC9957060 DOI: 10.3390/genes14020421] [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: 12/13/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/10/2023] Open
Abstract
Gene families, which are parts of a genome's information storage hierarchy, play a significant role in the development and diversity of multicellular organisms. Several studies have focused on the characteristics of gene families, such as function, homology, or phenotype. However, statistical and correlation analyses on the distribution of gene family members in the genome have yet to be conducted. Here, a novel framework incorporating gene family analysis and genome selection based on NMF-ReliefF is reported. Specifically, the proposed method starts by obtaining gene families from the TreeFam database and determining the number of gene families within the feature matrix. Then, NMF-ReliefF is used to select features from the gene feature matrix, which is a new feature selection algorithm that overcomes the inefficiencies of traditional methods. Finally, a support vector machine is utilized to classify the acquired features. The results show that the framework achieved an accuracy of 89.1% and an AUC of 0.919 on the insect genome test set. We also employed four microarray gene data sets to evaluate the performance of the NMF-ReliefF algorithm. The outcomes show that the proposed method may strike a delicate balance between robustness and discrimination. Additionally, the proposed method's categorization is superior to state-of-the-art feature selection approaches.
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Affiliation(s)
- Kai Liu
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road, Furong District, Changsha 410128, China
- College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China
| | - Qi Chen
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road, Furong District, Changsha 410128, China
| | - Guo-Hua Huang
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road, Furong District, Changsha 410128, China
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45
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Gradistics: An underappreciated dimension in evolutionary space. Biosystems 2023; 224:104844. [PMID: 36736879 DOI: 10.1016/j.biosystems.2023.104844] [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: 09/08/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023]
Abstract
The growth of complexity is an unsolved and underappreciated problem. We consider possible causes of this growth, hypotheses testing, molecular mechanisms, complexity measures, cases of simplification, and significance for biomedicine. We focus on a general ability of regulation, which is based on the growing information storage and processing capacities, as the main proxy of complexity. Natural selection is indifferent to complexity. However, complexification can be inferred from the same first principle, on which natural selection is founded. Natural selection depends on potentially unlimited reproduction under limited environmental conditions. Because of the demographic pressure, the simple ecological niches become fulfilled and diversified (due to species splitting and divergence). Diversification increases complexity of biocenoses. After the filling and diversification of simple niches, the more complex niches can arise. This is the 'atomic orbitals' (AO) model. Complexity has many shortcomings but it has an advantage. This advantage is ability to regulatory adaptation, including behavioral, formed in the evolution by means of genetic adaptation. Regulatory adaptation is much faster than genetic one because it is based on the information previously accumulated via genetic adaptation and learning. Regulatory adaptation further increases complexity of biocenoses. This is the 'regulatory advantage' (RA) model. The comparison of both models allows testable predictions. We focus on the animal evolution because of the appearance of higher regulatory level (nervous system), which is absent in other lineages, and relevance to humans (including biomedical aspects).
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46
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Yang Y, Cao C, Gu N. Identifying magnetosome-associated genes in the extended CtrA regulon in Magnetospirillum magneticum AMB-1 using a combinational approach. Brief Funct Genomics 2023; 22:61-74. [PMID: 36424838 DOI: 10.1093/bfgp/elac039] [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: 06/12/2022] [Revised: 10/01/2022] [Accepted: 10/14/2022] [Indexed: 11/26/2022] Open
Abstract
Magnetotactic bacteria (MTB) are worth studying because of magnetosome biomineralization. Magnetosome biogenesis in MTB is controlled by multiple genes known as magnetosome-associated genes. Recent advances in bioinformatics provide a unique opportunity for studying functions of magnetosome-associated genes and networks that they are involved in. Furthermore, various types of bioinformatics analyses can also help identify genes associated with magnetosome biogenesis. To predict novel magnetosome-associated genes in the extended CtrA regulon, we analyzed expression data of Magnetospirillum magneticum AMB-1 in the GSE35625 dataset in NCBI GEO. We identified 10 potential magnetosome-associated genes using a combinational approach of differential expression analysis, Gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analysis, protein-protein interaction network analysis and weighted gene co-expression network analysis. Meanwhile, we also discovered and compared two co-expression modules that most known magnetosome-associated genes belong to. Our comparison indicated the importance of energy on regulating co-expression module structures for magnetosome biogenesis. At the last stage of our research, we predicted at least four real magnetosome-associated genes out of 10 potential genes, based on a comparison of evolutionary trees between known and potential magnetosome-associated genes. Because of the discovery of common subtrees that the stressed species are enriched in, we proposed a hypothesis that multiple types of environmental stress can trigger magnetosome evolution in different waters, and therefore its evolution can recur at different times in various locations on earth. Overall, our research provides useful information for identifying new MTB species and understanding magnetosome biogenesis.
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Affiliation(s)
- Yizi Yang
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Chen Cao
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Ning Gu
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
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47
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Balamurugan C, Steenwyk JL, Goldman GH, Rokas A. The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.17.524442. [PMID: 36711793 PMCID: PMC9882216 DOI: 10.1101/2023.01.17.524442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Fungi biosynthesize a diversity of secondary metabolites, small organic bioactive molecules that play diverse roles in fungal ecology. Fungal secondary metabolites are often encoded by physically clustered sets of genes known as biosynthetic gene clusters (BGCs). Fungi in the genus Penicillium produce diverse secondary metabolites that have been both useful (e.g., the antibiotic penicillin and the cholesterol-lowering drug mevastatin) and harmful (e.g., the mycotoxin patulin and the immunosuppressant gliotoxin) to human affairs. BGCs often also encode resistance genes that confer self-protection to the secondary metabolite-producing fungus. Some Penicillium species, such as Penicillium lilacinoechinulatum and Penicillium decumbens, are known to produce gliotoxin, a secondary metabolite with known immunosuppressant activity; however, an evolutionary characterization of the BGC responsible for gliotoxin biosynthesis among Penicillium species is lacking. Here, we examine the conservation of genes involved in gliotoxin biosynthesis and resistance in 35 Penicillium genomes from 23 species. We found homologous, less fragmented gliotoxin BGCs in 12 genomes, mostly fragmented remnants of the gliotoxin BGC in 21 genomes, whereas the remaining two Penicillium genomes lacked the gliotoxin BGC altogether. In contrast, we observed broad conservation of homologs of resistance genes that reside outside the BGC across Penicillium genomes. Evolutionary rate analysis revealed that BGCs with higher numbers of genes evolve slower than BGCs with few genes. Even though the gliotoxin BGC is fragmented to varying degrees in nearly all genomes examined, ancestral state reconstruction suggests that the ancestor of Penicillium species possessed the gliotoxin BGC. Our analyses suggest that genes that are part of BGCs can be retained in genomes long after the loss of secondary metabolite biosynthesis.
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Affiliation(s)
- Charu Balamurugan
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| | - Jacob L. Steenwyk
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gustavo H. Goldman
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Antonis Rokas
- Vanderbilt University, Department of Biological Sciences, VU Station B #35-1634, Nashville, TN 37235, United States of America
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
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48
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Ge D, Wen Z, Feijó A, Lissovsky A, Zhang W, Cheng J, Yan C, She H, Zhang D, Cheng Y, Lu L, Wu X, Mu D, Zhang Y, Xia L, Qu Y, Vogler AP, Yang Q. Genomic Consequences of and Demographic Response to Pervasive Hybridization Over Time in Climate-Sensitive Pikas. Mol Biol Evol 2022; 40:6958644. [PMID: 36562771 PMCID: PMC9847633 DOI: 10.1093/molbev/msac274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/13/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Rare and geographically restricted species may be vulnerable to genetic effects from inbreeding depression in small populations or from genetic swamping through hybridization with common species, but a third possibility is that selective gene flow can restore fitness (genetic rescue). Climate-sensitive pikas (Ochotona spp.) of the Qinghai-Tibetan Plateau (QHTP) and its vicinity have been reduced to residual populations through the movement of climatic zones during the Pleistocene and recent anthropogenic disturbance, whereas the plateau pika (O. curzoniae) remains common. Population-level whole-genome sequencing (n = 142) of six closely related species in the subgenus Ochotona revealed several phases of ancient introgression, lineage replacement, and bidirectional introgression. The strength of gene flow was the greatest from the dominant O. curzoniae to ecologically distinct species in areas peripheral to the QHTP. Genetic analyses were consistent with environmental reconstructions of past population movements. Recurrent periods of introgression throughout the Pleistocene revealed an increase in genetic variation at first but subsequent loss of genetic variation in later phases. Enhanced dispersion of introgressed genomic regions apparently contributed to demographic recovery in three peripheral species that underwent range shifts following climate oscillations on the QHTP, although it failed to drive recovery of northeastern O. dauurica and geographically isolated O. sikimaria. Our findings highlight differences in timescale and environmental background to determine the consequence of hybridization and the unique role of the QHTP in conserving key evolutionary processes of sky island species.
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Affiliation(s)
| | | | | | | | | | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chaochao Yan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liang Lu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xinlai Wu
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Danping Mu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Yubo Zhang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing, 100871, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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Kesel E, Hudson AO, Osier MV. Whole-Genome Sequence, Assembly and Annotation of an Invasive Plant, Lonicera maackii (Amur Honeysuckle). PLANTS (BASEL, SWITZERLAND) 2022; 11:3253. [PMID: 36501292 PMCID: PMC9740181 DOI: 10.3390/plants11233253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
The invasive species Lonicera maackii (Amur Honeysuckle) is an increasing problem sweeping from the eastern United States toward the west, impacting normal forest development and animal survival across multiple taxa. Little is known about the genomics of this species, although a related invasive, Lonicera japonica, has been sequenced. Understanding the genomic foundation of the Lonicera maackii species could help us understand the biochemistry and life history that are the underpinnings of invasive success, as well as potential vulnerabilities and strengths which could guide research and development to control its spread. Here we present a draft, but high-quality, short-read whole-genome sequence, assembly, and annotation of Lonicera maackii, demonstrating that inexpensive and rapid short-read technologies can be successfully used in invasive species research. Despite being a short-read assembly, the genome length (7.93 × 108) and completeness (estimated as 90.2-92.1% by BUSCO and Merqury) are close to the previously published chromosome-level sequencing of L. japonica. No bias, by means of a Gene Ontology analysis, was identified among missing BUSCOs. A duplication of the 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase gene in both Lonicera species is identified, and the potential impact on controlling these invasive species is discussed. Future prospects for a diversity analysis of invasive species is also discussed.
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Armeev GA, Gribkova AK, Shaytan AK. Nucleosomes and their complexes in the cryoEM era: Trends and limitations. Front Mol Biosci 2022; 9:1070489. [PMID: 36504712 PMCID: PMC9730872 DOI: 10.3389/fmolb.2022.1070489] [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: 10/14/2022] [Accepted: 11/09/2022] [Indexed: 11/25/2022] Open
Abstract
Twenty-five years have passed since the appearance of the first atomistic model of the nucleosome structure, and since then the number of new structures has gradually increased. With the advent of cryo-microscopy, the rate of accumulation of models has increased significantly. New structures are emerging with different histone variants and a variety of proteins that bind to nucleosomes. At the moment, there are more than four hundred structures containing nucleosomes in the Protein Data Bank. Many of these structures represent similar complexes, others differ in composition, conformation and quality. In this perspective, we investigate the diversity of known nucleosome structures, analyze data and model quality, variations in histone/DNA content of nucleosomes and spectrum of their interactors. We outline those parts of the nucleosome "structurome" that are already explored and those awaiting further exploration.
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Affiliation(s)
- Grigoriy A. Armeev
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia,*Correspondence: Grigoriy A. Armeev, ; Alexey K. Shaytan,
| | - Anna K. Gribkova
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexey K. Shaytan
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia,Department of Computer Science, HSE University, Moscow, Russia,*Correspondence: Grigoriy A. Armeev, ; Alexey K. Shaytan,
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