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Pokrovac I, Rohner N, Pezer Ž. The prevalence of copy number increase at multiallelic copy number variants associated with cave colonization. Mol Ecol 2024; 33:e17339. [PMID: 38556927 DOI: 10.1111/mec.17339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/16/2024] [Accepted: 03/22/2024] [Indexed: 04/02/2024]
Abstract
Copy number variation is a common contributor to phenotypic diversity, yet its involvement in ecological adaptation is not easily discerned. Instances of parallelly evolving populations of the same species in a similar environment marked by strong selective pressures present opportunities to study the role of copy number variants (CNVs) in adaptation. By identifying CNVs that repeatedly occur in multiple populations of the derived ecotype and are not (or are rarely) present in the populations of the ancestral ecotype, the association of such CNVs with adaptation to the novel environment can be inferred. We used this paradigm to identify CNVs associated with recurrent adaptation of the Mexican tetra (Astyanax mexicanus) to cave environment. Using a read-depth approach, we detected CNVs from previously re-sequenced genomes of 44 individuals belonging to two ancestral surfaces and three derived cave populations. We identified 102 genes and 292 genomic regions that repeatedly diverge in copy number between the two ecotypes and occupy 0.8% of the reference genome. Functional analysis revealed their association with processes previously recognized to be relevant for adaptation, such as vision, immunity, oxygen consumption, metabolism, and neural function and we propose that these variants have been selected for in the cave or surface waters. The majority of the ecotype-divergent CNVs are multiallelic and display copy number increases in cavefish compared to surface fish. Our findings suggest that multiallelic CNVs - including gene duplications - and divergence in copy number provide a fast route to produce novel phenotypes associated with adaptation to subterranean life.
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Affiliation(s)
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
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Thomas SK, Hoek KV, Ogoti T, Duong H, Angelovici R, Pires JC, Mendoza-Cozatl D, Washburn J, Schenck CA. Halophytes and heavy metals: A multi-omics approach to understand the role of gene and genome duplication in the abiotic stress tolerance of Cakile maritima. Am J Bot 2024:e16310. [PMID: 38600732 DOI: 10.1002/ajb2.16310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 04/12/2024]
Abstract
PREMISE The origin of diversity is a fundamental biological question. Gene duplications are one mechanism that provides raw material for the emergence of novel traits, but evolutionary outcomes depend on which genes are retained and how they become functionalized. Yet, following different duplication types (polyploidy and tandem duplication), the events driving gene retention and functionalization remain poorly understood. Here we used Cakile maritima, a species that is tolerant to salt and heavy metals and shares an ancient whole-genome triplication with closely related salt-sensitive mustard crops (Brassica), as a model to explore the evolution of abiotic stress tolerance following polyploidy. METHODS Using a combination of ionomics, free amino acid profiling, and comparative genomics, we characterize aspects of salt stress response in C. maritima and identify retained duplicate genes that have likely enabled adaptation to salt and mild levels of cadmium. RESULTS Cakile maritima is tolerant to both cadmium and salt treatments through uptake of cadmium in the roots. Proline constitutes greater than 30% of the free amino acid pool in C. maritima and likely contributes to abiotic stress tolerance. We find duplicated gene families are enriched in metabolic and transport processes and identify key transport genes that may be involved in C. maritima abiotic stress tolerance. CONCLUSIONS These findings identify pathways and genes that could be used to enhance plant resilience and provide a putative understanding of the roles of duplication types and retention on the evolution of abiotic stress response.
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Affiliation(s)
- Shawn K Thomas
- Division of Biological Sciences, University of Missouri, Columbia, 65211, MO, USA
- Bioinformatics and Analytics Core, University of Missouri, Columbia, 65211, MO, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
| | - Kathryn Vanden Hoek
- Department of Biochemistry, University of Missouri, Columbia, 65211, MO, USA
| | - Tasha Ogoti
- Department of Computer Science, University of Missouri, Columbia, 65211, MO, USA
| | - Ha Duong
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Department of Biochemistry, University of Missouri, Columbia, 65211, MO, USA
| | - Ruthie Angelovici
- Division of Biological Sciences, University of Missouri, Columbia, 65211, MO, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
| | - J Chris Pires
- Soil and Crop Sciences, Colorado State University, Fort Collins, 80523-1170, CO, USA
| | - David Mendoza-Cozatl
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Division of Plant Sciences and Technology, University of Missouri, Columbia, 65211, MO, USA
| | - Jacob Washburn
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Plant Genetics Research Unit, USDA-ARS, Columbia, 65211, MO, USA
| | - Craig A Schenck
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Department of Biochemistry, University of Missouri, Columbia, 65211, MO, USA
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Cao J, Zhu H, Gao Y, Hu Y, Li X, Shi J, Chen L, Kang H, Ru D, Ren B, Liu B. Chromosome-level genome assembly and characterization of the Calophaca sinica genome. DNA Res 2024:dsae011. [PMID: 38590243 DOI: 10.1093/dnares/dsae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Indexed: 04/10/2024] Open
Abstract
Calophaca sinica is a rare plant endemic to northern China which belongs to the Fabaceae family and possesses rich nutritional value. To support the preservation of the genetic resources of this plant, we have successfully generated a high-quality genome of C. sinica (1.06 Gb). Notably, transposable elements (TEs) constituted ~73% of the genome, with long terminal repeat retrotransposons (LTR-RTs) dominating this group of elements (~54% of the genome). The average intron length of the C. sinica genome was noticeably longer than what has been observed for closely-related species. The expansion of LTR-RTs and elongated introns emerged had the largest influence on the enlarged genome size of C. sinica in comparison to other Fabaceae species. The proliferation of TEs could be explained by certain modes of gene duplication, namely, whole genome duplication (WGD) and dispersed duplication (DSD). Gene family expansion, which was found to enhance genes associated with metabolism, genetic maintenance, and environmental stress resistance, was a result of transposed duplicated genes (TRD) and WGD. The presented genomic analysis sheds light on the genetic architecture of C. sinica, as well as provides a starting point for future evolutionary biology, ecology, and functional genomics studies centered around C. sinica and closely-related species.
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Affiliation(s)
| | - Hui Zhu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yingqi Gao
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Yue Hu
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Xuejiao Li
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Jianwei Shi
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Luqin Chen
- Taiyuan Botanical Garden, Taiyuan, China
| | - Hao Kang
- Taiyuan Botanical Garden, Taiyuan, China
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | | | - Bingbing Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
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Xu Y, Cheng J, Hu H, Yan L, Jia J, Wu B. Genome-Wide Identification of NAC Family Genes in Oat and Functional Characterization of AsNAC109 in Abiotic Stress Tolerance. Plants (Basel) 2024; 13:1017. [PMID: 38611546 PMCID: PMC11013824 DOI: 10.3390/plants13071017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024]
Abstract
The plant-specific NAC gene family is one of the largest transcription factor families, participating in plant growth regulation and stress response. Despite extensive characterization in various plants, our knowledge of the NAC family in oat is lacking. Herein, we identified 333 NAC genes from the latest release of the common oat genome. We provide a comprehensive overview of the oat NAC gene family, covering gene structure, chromosomal localization, phylogenetic characteristics, conserved motif compositions, and gene duplications. AsNAC gene expression in different tissues and the response to various abiotic stresses were characterized using RT-qPCR. The main driver of oat NAC gene family expansion was identified as segmental duplication using collinearity analysis. In addition, the functions of AsNAC109 in regulating abiotic stress tolerance in Arabidopsis were clarified. This is the first genome-wide investigation of the NAC gene family in cultivated oat, which provided a unique resource for subsequent research to elucidate the mechanisms responsible for oat stress tolerance and provides valuable clues for the improvement of stress resistance in cultivated oat.
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Affiliation(s)
- Yahui Xu
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (Y.X.); (J.C.)
| | - Jialong Cheng
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (Y.X.); (J.C.)
| | - Haibin Hu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- State Key Laboratory of Crop Gene Resources and Breeding, Beijing 100081, China
| | - Lin Yan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- State Key Laboratory of Crop Gene Resources and Breeding, Beijing 100081, China
| | - Juqing Jia
- College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (Y.X.); (J.C.)
| | - Bin Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- State Key Laboratory of Crop Gene Resources and Breeding, Beijing 100081, China
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Zhu XG, Hutang GR, Gao LZ. Ancient Duplication and Lineage-Specific Transposition Determine Evolutionary Trajectory of ERF Subfamily across Angiosperms. Int J Mol Sci 2024; 25:3941. [PMID: 38612750 PMCID: PMC11011629 DOI: 10.3390/ijms25073941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/16/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
AP2/ERF transcription factor family plays an important role in plant development and stress responses. Previous studies have shed light on the evolutionary trajectory of the AP2 and DREB subfamilies. However, knowledge about the evolutionary history of the ERF subfamily in angiosperms still remains limited. In this study, we performed a comprehensive analysis of the ERF subfamily from 107 representative angiosperm species by combining phylogenomic and synteny network approaches. We observed that the expansion of the ERF subfamily was driven not only by whole-genome duplication (WGD) but also by tandem duplication (TD) and transposition duplication events. We also found multiple transposition events in Poaceae, Brassicaceae, Poales, Brassicales, and Commelinids. These events may have had notable impacts on copy number variation and subsequent functional divergence of the ERF subfamily. Moreover, we observed a number of ancient tandem duplications occurred in the ERF subfamily across angiosperms, e.g., in Subgroup IX, IXb originated from ancient tandem duplication events within IXa. These findings together provide novel insights into the evolution of this important transcription factor family.
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Affiliation(s)
- Xun-Ge Zhu
- Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming 650201, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ge-Ran Hutang
- Institute of Forest Industry, Yunnan Academy of Forestry and Grassland Science, Kunming 650201, China;
| | - Li-Zhi Gao
- Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming 650201, China;
- Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education, Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou 570228, China
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Stieb SM, Cortesi F, Mitchell L, Jardim de Queiroz L, Marshall NJ, Seehausen O. Short-wavelength-sensitive 1 ( SWS1) opsin gene duplications and parallel visual pigment tuning support ultraviolet communication in damselfishes (Pomacentridae). Ecol Evol 2024; 14:e11186. [PMID: 38628922 PMCID: PMC11019301 DOI: 10.1002/ece3.11186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/05/2024] [Accepted: 03/12/2024] [Indexed: 04/19/2024] Open
Abstract
Damselfishes (Pomacentridae) are one of the most behaviourally diverse, colourful and species-rich reef fish families. One remarkable characteristic of damselfishes is their communication in ultraviolet (UV) light. Not only are they sensitive to UV, they are also prone to have UV-reflective colours and patterns enabling social signalling. Using more than 50 species, we aimed to uncover the evolutionary history of UV colour and UV vision in damselfishes. All damselfishes had UV-transmitting lenses, expressed the UV-sensitive SWS1 opsin gene, and most displayed UV-reflective patterns and colours. We find evidence for several tuning events across the radiation, and while SWS1 gene duplications are generally very rare among teleosts, our phylogenetic reconstructions uncovered two independent duplication events: one close to the base of the most species-rich clade in the subfamily Pomacentrinae, and one in a single Chromis species. Using amino acid comparisons, we found that known spectral tuning sites were altered several times in parallel across the damselfish radiation (through sequence change and duplication followed by sequence change), causing repeated shifts in peak spectral absorbance of around 10 nm. Pomacentrinae damselfishes expressed either one or both copies of SWS1, likely to further finetune UV-signal detection and differentiation. This highly advanced and modified UV vision among damselfishes, in particular the duplication of SWS1 among Pomacentrinae, might be seen as a key evolutionary innovation that facilitated the evolution of the exuberant variety of UV-reflectance traits and the diversification of this coral reef fish lineage.
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Affiliation(s)
- Sara M. Stieb
- Center for Ecology, Evolution and BiogeochemistryEAWAG Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
- Institute for Ecology and EvolutionUniversity of BernBernSwitzerland
- Queensland Brain InstituteThe University of QueenslandBrisbaneQueenslandAustralia
| | - Fabio Cortesi
- Queensland Brain InstituteThe University of QueenslandBrisbaneQueenslandAustralia
- School of the EnvironmentThe University of QueenslandBrisbaneAustralia
| | - Laurie Mitchell
- Queensland Brain InstituteThe University of QueenslandBrisbaneQueenslandAustralia
- Marine Eco‐Evo‐Devo UnitOkinawa Institute of Science and TechnologyOnna sonOkinawaJapan
| | - Luiz Jardim de Queiroz
- Center for Ecology, Evolution and BiogeochemistryEAWAG Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
- Institute for Ecology and EvolutionUniversity of BernBernSwitzerland
| | - N. Justin Marshall
- Queensland Brain InstituteThe University of QueenslandBrisbaneQueenslandAustralia
| | - Ole Seehausen
- Center for Ecology, Evolution and BiogeochemistryEAWAG Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
- Institute for Ecology and EvolutionUniversity of BernBernSwitzerland
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7
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Dibyachintan S, Dube AK, Bradley D, Lemieux P, Dionne U, Landry CR. Cryptic genetic variation shapes the fate of gene duplicates in a protein interaction network. bioRxiv 2024:2024.02.23.581840. [PMID: 38464075 PMCID: PMC10925128 DOI: 10.1101/2024.02.23.581840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Paralogous genes are often redundant for long periods of time before they diverge in function. While their functions are preserved, paralogous proteins can accumulate mutations that, through epistasis, could impact their fate in the future. By quantifying the impact of all single-amino acid substitutions on the binding of two myosin proteins to their interaction partners, we find that the future evolution of these proteins is highly contingent on their regulatory divergence and the mutations that have silently accumulated in their protein binding domains. Differences in the promoter strength of the two paralogs amplify the impact of mutations on binding in the lowly expressed one. While some mutations would be sufficient to non-functionalize one paralog, they would have minimal impact on the other. Our results reveal how functionally equivalent protein domains could be destined to specific fates by regulatory and cryptic coding sequence changes that currently have little to no functional impact.
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Affiliation(s)
- Soham Dibyachintan
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
| | - Alexandre K Dube
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
| | - David Bradley
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
| | - Pascale Lemieux
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
| | - Ugo Dionne
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Current affiliation: Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Christian R Landry
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
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Nunes WVB, Oliveira DS, Dias GDR, Carvalho AB, Caruso ÍP, Biselli JM, Guegen N, Akkouche A, Burlet N, Vieira C, Carareto CMA. A comprehensive evolutionary scenario for the origin and neofunctionalization of the Drosophila speciation gene Odysseus (OdsH). G3 (Bethesda) 2024; 14:jkad299. [PMID: 38156703 PMCID: PMC10917504 DOI: 10.1093/g3journal/jkad299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 11/22/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Odysseus (OdsH) was the first speciation gene described in Drosophila related to hybrid sterility in offspring of mating between Drosophila mauritiana and Drosophila simulans. Its origin is attributed to the duplication of the gene unc-4 in the subgenus Sophophora. By using a much larger sample of Drosophilidae species, we showed that contrary to what has been previously proposed, OdsH origin occurred 62 MYA. Evolutionary rates, expression, and transcription factor-binding sites of OdsH evidence that it may have rapidly experienced neofunctionalization in male sexual functions. Furthermore, the analysis of the OdsH peptide allowed the identification of mutations of D. mauritiana that could result in incompatibility in hybrids. In order to find if OdsH could be related to hybrid sterility, beyond Sophophora, we explored the expression of OdsH in Drosophila arizonae and Drosophila mojavensis, a pair of sister species with incomplete reproductive isolation. Our data indicated that OdsH expression is not atypical in their male-sterile hybrids. In conclusion, we have proposed that the origin of OdsH occurred earlier than previously proposed, followed by neofunctionalization. Our results also suggested that its role as a speciation gene might be restricted to D. mauritiana and D. simulans.
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Affiliation(s)
- William Vilas Boas Nunes
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Daniel Siqueira Oliveira
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Guilherme de Rezende Dias
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS sl A2-075, 373 Carlos Chagas Filho Avenue, 21941-971 Rio de Janeiro, Brazil
| | - Antonio Bernardo Carvalho
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS sl A2-075, 373 Carlos Chagas Filho Avenue, 21941-971 Rio de Janeiro, Brazil
| | - Ícaro Putinhon Caruso
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
| | - Joice Matos Biselli
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
| | - Nathalie Guegen
- Faculté de Médecine, iGReD, Université Clermont Auvergne, CNRS, INSERM, 4 Bd Claude Bernard, 63000 Clermont-Ferrande, France
| | - Abdou Akkouche
- Faculté de Médecine, iGReD, Université Clermont Auvergne, CNRS, INSERM, 4 Bd Claude Bernard, 63000 Clermont-Ferrande, France
| | - Nelly Burlet
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Claudia M A Carareto
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
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Sobkowiak A, Scherff N, Schuler F, Bletz S, Mellmann A, Schwierzeck V, van Almsick V. Plasmid-encoded gene duplications of extended-spectrum β-lactamases in clinical bacterial isolates. Front Cell Infect Microbiol 2024; 14:1343858. [PMID: 38469349 PMCID: PMC10925753 DOI: 10.3389/fcimb.2024.1343858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/02/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction The emergence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is an urgent and alarming One Health problem. This study aimed to investigate duplications of plasmid-encoded ESBL genes and their impact on antimicrobial resistance (AMR) phenotypes in clinical and screening isolates. Methods Multi-drug-resistant bacteria from hospitalized patients were collected during routine clinical surveillance from January 2022 to June 2023, and their antimicrobial susceptibility patterns were determined. Genotypes were extracted from long-read whole-genome sequencing data. Furthermore, plasmids and other mobile genetic elements associated with ESBL genes were characterized, and the ESBL genes were correlated to ceftazidime minimal inhibitory concentration (MIC). Results In total, we identified four cases of plasmid-encoded ESBL gene duplications that match four genetically similar plasmids during the 18-month surveillance period: five Escherichia coli and three Klebsiella pneumoniae isolates. As the ESBL genes were part of transposable elements, the surrounding sequence regions were duplicated as well. In-depth analysis revealed insertion sequence (IS)-mediated transposition mechanisms. Isolates with duplicated ESBL genes exhibited a higher MIC for ceftazidime in comparison to isolates with a single gene copy (3-256 vs. 1.5-32 mg/L, respectively). Conclusion ESBL gene duplications led to an increased phenotypic resistance against ceftazidime. Our data suggest that ESBL gene duplications by an IS-mediated transposition are a relevant mechanism for how AMR develops in the clinical setting and is part of the microevolution of plasmids.
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Affiliation(s)
- Annika Sobkowiak
- Institute of Hygiene, University Hospital Münster, Münster, Germany
- Department of Cardiology I – Coronary and Peripheral Vascular Disease, Heart Failure, University Hospital Münster, Münster, Germany
| | - Natalie Scherff
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | - Franziska Schuler
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Stefan Bletz
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | | | - Vera Schwierzeck
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | - Vincent van Almsick
- Institute of Hygiene, University Hospital Münster, Münster, Germany
- Department of Cardiology I – Coronary and Peripheral Vascular Disease, Heart Failure, University Hospital Münster, Münster, Germany
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Friedrich M. Cave beetle lineages gained genes before going down under: An example of repeated genomic exaptation? J Exp Zool B Mol Dev Evol 2024. [PMID: 38369877 DOI: 10.1002/jez.b.23245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/08/2024] [Accepted: 01/29/2024] [Indexed: 02/20/2024]
Abstract
The adaptation of animals to subterranean habitats like caves and aquifers stereotypically leads to dramatic trait-loss consequences like the lack of eyes and body pigmentation. These body plan regression trends are expected to be tied to gene loss as well. Indeed, previous studies documented the degeneration of vision genes in obligate cave dwellers. Contradicting this picture, the first broad-scale comparative transcriptome-wide study of gene content evolution in separate subterranean Australian and Mediterranean beetle clades unearthed evidence of global gene gain and retention. This suggests that the transition to cave life may be more contingent on gene repertoire expansion than contraction. Future studies, however, will need to examine how much the observed patterns of gene content evolution reflect subfunctionalization and fitness-securing genetic redundancy outcomes following gene duplication as opposed to adaptive trajectories.
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Affiliation(s)
- Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
- Department of Ophthalmological, Visual, and Anatomical Sciences, Wayne State University, Detroit, Michigan, USA
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11
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Thirulogachandar V, Govind G, Hensel G, Kale SM, Kuhlmann M, Eschen-Lippold L, Rutten T, Koppolu R, Rajaraman J, Palakolanu SR, Seiler C, Sakuma S, Jayakodi M, Lee J, Kumlehn J, Komatsuda T, Schnurbusch T, Sreenivasulu N. HOMEOBOX2, the paralog of SIX-ROWED SPIKE1/HOMEOBOX1, is dispensable for barley spikelet development. J Exp Bot 2024:erae044. [PMID: 38366171 DOI: 10.1093/jxb/erae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Indexed: 02/18/2024]
Abstract
The HD-ZIP class I transcription factor, HvHOX1 (Homeobox 1) or VRS1 (Vulgare Row-type Spike 1 or Six-rowed Spike 1), regulates lateral spikelet fertility in barley (Hordeum vulgare L.). It was shown that HvHOX1 has a high expression only in lateral spikelets, while its paralog HvHOX2 was found to be expressed in different plant organs. Yet, the mechanistic function of HvHOX1 and HvHOX2 during spikelet development is still fragmentary. Here, we show that compared to HvHOX1, HvHOX2 is more highly conserved across different barley genotypes and Hordeum species, hinting at a possibly vital but still unclarified biological role. Using bimolecular fluorescence complementation, DNA-binding, and transactivation assays, we validate that HvHOX1 and HvHOX2 are bona fide transcriptional activators that may potentially heterodimerize. Accordingly, both genes exhibit similar spatiotemporal expression patterns during spike development and growth, albeit their mRNA levels differ quantitatively. We show that HvHOX1 delays the lateral spikelet meristem differentiation and affects fertility by aborting the reproductive organs. Interestingly, the ancestral relationship of these genes inferred from their co-expressed gene networks suggested that HvHOX1 and HvHOX2 might play a similar role during barley spikelet development. However, CRISPR-derived mutants of HvHOX1 and HvHOX2 demonstrated the suppressive role of HvHOX1 on lateral spikelets, while the loss of HvHOX2 does not influence spikelet development. Collectively, our study shows that through the suppression of reproductive organs, lateral spikelet fertility is regulated by HvHOX1, whereas HvHOX2 is dispensable for spikelet development in barley.
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Affiliation(s)
- Venkatasubbu Thirulogachandar
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
| | - Geetha Govind
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Sandip M Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Markus Kuhlmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
| | | | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Ravi Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Jeyaraman Rajaraman
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Sudhakar Reddy Palakolanu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Christiane Seiler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Shun Sakuma
- National Institute of Agrobiological Sciences (NIAS), Plant Genome Research Unit, Tsukuba 3058602, Japan
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Justin Lee
- Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, D-06120 Halle, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences (NIAS), Plant Genome Research Unit, Tsukuba 3058602, Japan
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Nese Sreenivasulu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
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12
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Pajic P, Landau L, Gokcumen O, Ruhl S. Emergence of saliva protein genes in the secretory calcium-binding phosphoprotein (SCPP) locus and accelerated evolution in primates. bioRxiv 2024:2024.02.14.580359. [PMID: 38405690 PMCID: PMC10888740 DOI: 10.1101/2024.02.14.580359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Genes within the secretory calcium-binding phosphoprotein (SCPP) family evolved in conjunction with major evolutionary milestones: the formation of a calcified skeleton in vertebrates, the emergence of tooth enamel in fish, and the introduction of lactation in mammals. The SCPP gene family also contains genes expressed primarily and abundantly in human saliva. Here, we explored the evolution of the saliva-related SCPP genes by harnessing currently available genomic and transcriptomic resources. Our findings provide insights into the expansion and diversification of SCPP genes, notably identifying previously undocumented convergent gene duplications. In primate genomes, we found additional duplication and diversification events that affected genes coding for proteins secreted in saliva. These saliva-related SCPP genes exhibit signatures of positive selection in the primate lineage while the other genes in the same locus remain conserved. We found that regulatory shifts and gene turnover events facilitated the accelerated gain of salivary expression. Collectively, our results position the SCPP gene family as a hotbed of evolutionary innovation, suggesting the potential role of dietary and pathogenic pressures in the adaptive diversification of the saliva composition in primates, including humans.
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Affiliation(s)
- Petar Pajic
- Department of Biological Sciences, University at Buffalo, The State University of New York, NY 14260, USA
| | - Luane Landau
- Department of Biological Sciences, University at Buffalo, The State University of New York, NY 14260, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, The State University of New York, NY 14260, USA
| | - Stefan Ruhl
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, NY 14214, USA
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13
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Abstract
Gene content in genomes changes through several different processes, with gene duplication being an important contributor to such changes. Gene duplication occurs over a range of scales from individual genes to whole genomes, and the dynamics of this process can be context dependent. Still, there are rules by which genes are retained or lost from genomes after duplication, and probabilistic modeling has enabled characterization of these rules, including their context-dependence. Here, we describe the biology and corresponding mathematical models that are used to understand duplicate gene retention and its contribution to the set of biochemical functions encoded in a genome.
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Affiliation(s)
- Raquel Assis
- Florida Atlantic University, Boca Raton, Florida, USA
| | - Gavin Conant
- North Carolina State University, Raleigh, North Carolina, USA
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14
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Li Q, Chan YB, Galtier N, Scornavacca C. The Effect of Copy Number Hemiplasy on Gene Family Evolution. Syst Biol 2024:syae007. [PMID: 38330161 DOI: 10.1093/sysbio/syae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Indexed: 02/10/2024] Open
Abstract
The evolution of gene families is complex, involving gene-level evolutionary events such as gene duplication, horizontal gene transfer, and gene loss (DTL), and other processes such as incomplete lineage sorting (ILS). Because of this, topological differences often exist between gene trees and species trees. A number of models have been recently developed to explain these discrepancies, the most realistic of which attempt to consider both gene-level events and ILS. When unified in a single model, the interaction between ILS and gene-level events can cause polymorphism in gene copy number, which we refer to as copy number hemiplasy (CNH). In this paper we extend the Wright-Fisher process to include duplications and losses over several species, and show that the probability of CNH for this process can be significant. We study how well two unified models - MLMSC (MultiLocus MultiSpecies Coalescent), which models CNH, and DLCoal (Duplication, Loss, and Coalescence), which does not - approximate the Wright-Fisher process with duplication and loss. We then study the effect of CNH on gene family evolution by comparing MLMSC and DLCoal. We generate comparable gene trees under both models, showing significant differences in various summary statistics; most importantly, CNH reduces the number of gene copies greatly. If this is not taken into account, the traditional method of estimating duplication rates (by counting the number of gene copies) becomes inaccurate. The simulated gene trees are also used for species tree inference with the summary methods ASTRAL and ASTRAL-Pro, demonstrating that their accuracy, based on CNH-unaware simulations calibrated on real data, may have been overestimated.
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Affiliation(s)
- Qiuyi Li
- School of Mathematics and Statistics / Melbourne Integrative Genomics, The University of Melbourne, Melbourne, 3010, Australia
- Alibaba Cloud, Hangzhou, China
| | - Yao-Ban Chan
- School of Mathematics and Statistics / Melbourne Integrative Genomics, The University of Melbourne, Melbourne, 3010, Australia
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, Universit´e Montpellier, CNRS, IRD, EPHE, Montpellier, 34095, France
| | - Celine Scornavacca
- Institut des Sciences de l'Evolution, Universit´e Montpellier, CNRS, IRD, EPHE, Montpellier, 34095, France
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15
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Zhou Y, Huang C, Fu G, Tang R, Yang N, Liu W, Qian W, Wan F. Molecular and Functional Characterization of Three General Odorant-Binding Protein 2 Genes in Cydia pomonella (Lepidoptera: Tortricidae). Int J Mol Sci 2024; 25:1746. [PMID: 38339028 PMCID: PMC10855334 DOI: 10.3390/ijms25031746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
General odorant-binding proteins (GOBPs) play a crucial role in the detection of host plant volatiles and pheromones by lepidopterans. Previous studies identified two duplications in the GOBP2 gene in Cydia pomonella. In this study, we employed qRT-PCR, protein purification, and fluorescence competitive binding assays to investigate the functions of three GOBP2 genes in C. pomonella. Our findings reveal that CpomGOBP2a and CpomGOBP2b are specifically highly expressed in antennae, while CpomGOBP2c exhibits high specific expression in wings, suggesting a potential divergence in their functions. Recombinant proteins of CpomGOBP2a, CpomGOBP2b, and CpomGOBP2c were successfully expressed and purified, enabling an in-depth exploration of their functions. Competitive binding assays with 20 host plant volatiles and the sex pheromone (codlemone) demonstrated that CpomGOBP2a exhibits strong binding to four compounds, namely butyl octanoate, ethyl (2E,4Z)-deca-2,4-dienoate (pear ester), codlemone, and geranylacetone, with corresponding dissolution constants (Ki) of 8.59993 μM, 9.14704 μM, 22.66298 μM, and 22.86923 μM, respectively. CpomGOBP2b showed specific binding to pear ester (Ki = 17.37481 μM), while CpomGOBP2c did not exhibit binding to any tested compounds. In conclusion, our results indicate a functional divergence among CpomGOBP2a, CpomGOBP2b, and CpomGOBP2c. These findings contribute valuable insights for the development of novel prevention and control technologies and enhance our understanding of the evolutionary mechanisms of olfactory genes in C. pomonella.
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Affiliation(s)
- Yanan Zhou
- College of Plant Health & Medicine, Qingdao Agricultural University, Qingdao 266109, China
- 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 518120, China
| | - Cong 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 518120, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guanjun Fu
- College of Plant Health & Medicine, Qingdao Agricultural University, Qingdao 266109, China
- 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 518120, China
| | - Rui Tang
- Centre for Resource Insects and Biotechnology, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510220, China
| | - Nianwan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wanxue Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wanqiang Qian
- 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 518120, China
| | - Fanghao Wan
- College of Plant Health & Medicine, Qingdao Agricultural University, Qingdao 266109, China
- 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 518120, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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16
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Dunivant TS, Singh V, Livingston KE, Ross JD, Hileman LC. CYCLOIDEA paralogs function partially redundantly to specify dorsal flower development in Mimulus lewisii. Am J Bot 2024; 111:e16271. [PMID: 38265745 DOI: 10.1002/ajb2.16271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 01/25/2024]
Abstract
PREMISE Duplicated genes (paralogs) are abundant in plant genomes, and their retention may influence the function of genetic programs and contribute to evolutionary novelty. How gene duplication affects genetic modules and what forces contribute to paralog retention are outstanding questions. The CYCLOIDEA(CYC)-dependent flower symmetry program is a model for understanding the evolution of gene duplication, providing multiple examples of paralog partitioning and novelty. However, a novel CYC gene lineage duplication event near the origin of higher core Lamiales (HCL) has received little attention. METHODS To understand the evolutionary fate of duplicated HCL CYC2 genes, we determined the effects on flower symmetry by suppressing MlCYC2A and MlCYC2B expression using RNA interference (RNAi). We determined the phenotypic effects on flower symmetry in single- and double-silenced backgrounds and coupled our functional analyses with expression surveys of MlCYC2A, MlCYC2B, and a putative downstream RADIALIS (MlRAD5) ortholog. RESULTS MlCYC2A and MlCYC2B jointly contribute to bilateral flower symmetry. MlCYC2B exhibits a clear dorsal flower identity function and may additionally function in carpel development. MlCYC2A functions in establishing dorsal petal shape. Further, our results suggest an MlCYC2A-MlCYC2B regulatory interaction, which may affect pathway homeostasis. CONCLUSIONS Our results suggest that CYC paralogs specific to higher core Lamiales may be selectively retained for their joint contribution to bilateral flower symmetry, similar to the independently derived CYC paralogs in the Lamiales model for bilateral flower symmetry research, Antirrhinum majus (snapdragon).
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Affiliation(s)
- Taryn S Dunivant
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
| | - Vibhuti Singh
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
| | - Kaylee E Livingston
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
| | - Jack D Ross
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
| | - Lena C Hileman
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
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17
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Sahajpal N, Ziats C, Chaubey A, DuPont BR, Abidi F, Schwartz CE, Stevenson RE. Clinical findings in individuals with duplication of genes associated with X-linked intellectual disability. Clin Genet 2024; 105:173-184. [PMID: 37899624 DOI: 10.1111/cge.14445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/25/2023] [Accepted: 10/13/2023] [Indexed: 10/31/2023]
Abstract
Duplication of all genes associated with X-linked intellectual disability (XLID) have been reported but the majority of the duplications include more than one XLID gene. It is exceptional for whole XLID gene duplications to cause the same phenotype as sequence variants or deletions of the same gene. Duplication of PLP1, the gene associated with Pelizaeus-Merzbacher syndrome, is the most notable duplication of this type. More commonly, duplication of XLID genes results in very different phenotypes than sequence alterations or deletions. Duplication of MECP2 is widely recognized as a duplication of this type, but a number of others exist. The phenotypes associated with gene duplications are often milder than those caused by deletions and sequence variants. Among some duplications that are clinically significant, marked skewing of X-inactivation in female carriers has been observed. This report describes the phenotypic consequences of duplication of 22 individual XLID genes, of which 10 are described for the first time.
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Affiliation(s)
- Nikhil Sahajpal
- Diagnostic Laboratories, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Catherine Ziats
- Genetics Department, Shodair Children's Hospital, Helena, Montana, USA
| | - Alka Chaubey
- Clinical and Scientific Affairs, Bionano Genomics, San Diego, California, USA
| | - Barbara R DuPont
- Diagnostic Laboratories, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Fatima Abidi
- Diagnostic Laboratories, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Charles E Schwartz
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan, USA
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18
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Lu JB, Ren PP, Li Q, He F, Xu ZT, Wang SN, Chen JP, Li JM, Zhang CX. The evolution and functional divergence of 10 Apolipoprotein D-like genes in Nilaparvata lugens. Insect Sci 2024; 31:91-105. [PMID: 37334667 DOI: 10.1111/1744-7917.13216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 04/16/2023] [Accepted: 04/22/2023] [Indexed: 06/20/2023]
Abstract
Apolipoprotein D (ApoD), a member of the lipocalin superfamily of proteins, is involved in lipid transport and stress resistance. Whereas only a single copy of the ApoD gene is found in humans and some other vertebrates, there are typically several ApoD-like genes in insects. To date, there have been relatively few studies that have examined the evolution and functional differentiation of ApoD-like genes in insects, particularly hemi-metabolous insects. In this study, we identified 10 ApoD-like genes (NlApoD1-10) with distinct spatiotemporal expression patterns in Nilaparvata lugens (BPH), which is an important pest of rice. NlApoD1-10 were found to be distributed on 3 chromosomes in a tandem array of NlApoD1/2, NlApoD3-5, and NlApoD7/8, and show sequence and gene structural divergence in the coding regions, indicating that multiple gene duplication events occurred during evolution. Phylogenetic analysis revealed that NlApoD1-10 can be clustered into 5 clades, with NlApoD3-5 and NlApoD7/8 potentially evolving exclusively in the Delphacidae family. Functional screening using an RNA interference approach revealed that only NlApoD2 was essential for BPH development and survival, whereas NlApoD4/5 are highly expressed in testes, and might play roles in reproduction. Moreover, stress response analysis revealed that NlApoD3-5/9, NlApoD3-5, and NlApoD9 were up-regulated after treatment with lipopolysaccharide, H2 O2 , and ultraviolet-C, respectively, indicating their potential roles in stress resistance.
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Affiliation(s)
- Jia-Bao Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, Zhejiang Province, China
| | - Peng-Peng Ren
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, Zhejiang Province, China
| | - Qiao Li
- Technology Center of Wuhan Customs District, Hubei, China
- Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - Fang He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, Zhejiang Province, China
| | - Zhong-Tian Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, Zhejiang Province, China
| | - Sai-Nan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, Zhejiang Province, China
| | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, Zhejiang Province, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, Zhejiang Province, China
| | - Chuan-Xi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, Zhejiang Province, China
- Institute of Insect Science, Zhejiang University, Hangzhou, China
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19
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Lee WK, Chan BKK, Kim JY, Ju SJ, Kim SJ. Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep-sea hydrothermal vents. Mol Ecol Resour 2024; 24:e13895. [PMID: 37955198 DOI: 10.1111/1755-0998.13895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 10/16/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023]
Abstract
Thoracican barnacles are a diverse group of marine organisms for which the availability of genome assemblies is currently limited. In this study, we sequenced the genomes of two neolepadoid species (Ashinkailepas kermadecensis, Imbricaverruca yamaguchii) from hydrothermal vents, in addition to two intertidal species. Genome sizes ranged from 481 to 1054 Mb, with repetitive sequence contents of 21.2% to 50.7%. Concordance rates of orthologs and heterozygosity rates were between 82.4% and 91.7% and between 1.0% and 2.1%, respectively, indicating high genetic diversity and heterozygosity. Based on phylogenomic analyses, we revised the nomenclature of cement genes encoding cement proteins that are not homologous to any known proteins. The major cement gene, CP100A, was found in all thoracican species, including vent-associated neolepadoids, and was hypothesised to be essential for thoracican settlement. Duplicated genes, CP100B and CP100C, were found only in balanids, suggesting potential functional redundancy or acquisition of new functions associated with the calcareous base. An ancestor of CP52 genes was duplicated dynamically among lepadids, pollicipedids with multiple copies on a single scaffold, and balanids with multiple sequential repeats of the conserved regions, but no CP52 genes were found in neolepadoids, providing insights into cement gene evolution among thoracican lineages. This study enhances our understanding of the adhesion mechanisms of thoracicans in underwater environments. The newly sequenced genomes provide opportunities for studying their evolution and ecology, shedding light on their adaptation to diverse marine environments, and contributing to our knowledge of barnacle biology with valuable genomic resources for further studies in this field.
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Affiliation(s)
- Won-Kyung Lee
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Division of EcoScience, Ewha Womans University, Seoul, Korea
| | - Benny K K Chan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jae-Yoon Kim
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Se-Jong Ju
- Marine Resources & Environment Research Division, Korea Institute of Ocean Science and Technology, Busan, Korea
| | - Se-Joo Kim
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
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20
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Wei W, Zielewicz L, Zhang L. Duplication of a chromosome 2 segment in production CHO cell lines correlates with age-related growth improvement. Biotechnol J 2024; 19:e2300407. [PMID: 38403434 DOI: 10.1002/biot.202300407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/04/2023] [Accepted: 01/02/2024] [Indexed: 02/27/2024]
Abstract
Monitoring the stability of recombinant Chinese Hamster Ovary (CHO) cell lines is essential to ensure the selection of production cell lines suitable for biomanufacturing. It has been frequently observed that recombinant CHO cell lines develop phenotypic changes upon aging, such as accelerated cell growth in late generation cultures. However, the mechanism responsible for age-correlated changes is poorly understood. In this study, we investigated the molecular mechanisms underlying the age-correlated cell growth improvement in Pfizer's platform fed-batch production process, by examining multiple cell lines derived from different CHO expression systems, expressing a variety of monoclonal antibodies (mAbs). Comprehensive whole-genome resequencing analysis revealed duplication of a continuous 50.2 Mbp segment in chromosome 2 (Chr2) specific to clones that showed age-correlated growth change as compared to clones that did not exhibit age-correlated growth change. Moreover, such age- and growth-related Chr2 duplication was independent of the presence or type of recombinant monoclonal antibody expression. When we compared transcriptome profiles from low-growth and high-growth cell lines, we found that >95% of the genes overexpressed in high-growth cell lines were in the duplicated Chr2 segment. To the best of our knowledge, this is the first report of large genomic duplication, specific to Chr2, being associated with age-correlated growth change. Investigation of the cause-and-effect relationship between the genes identified in the duplicated regions and age-correlated growth change is underway. We are confident that this effort will lead to improved cell line screening and targeted rational cell line engineering efforts to develop cell lines with improved stability performance.
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Affiliation(s)
- Wei Wei
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc, Andover, Massachusetts, USA
| | - Laura Zielewicz
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc, Andover, Massachusetts, USA
| | - Lin Zhang
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc, Andover, Massachusetts, USA
- Bioprocess Research and Development, Merck & Co. Inc., Kenilworth, New Jersey, USA
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21
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Ryu T, Okamoto K, Ansai S, Nakao M, Kumar A, Iguchi T, Ogino Y. Gene Duplication of Androgen Receptor As An Evolutionary Driving Force Underlying the Diversity of Sexual Characteristics in Teleost Fishes. Zoolog Sci 2024; 41:68-76. [PMID: 38587519 DOI: 10.2108/zs230098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/15/2024] [Indexed: 04/09/2024]
Abstract
Sexual dimorphism allows species to meet their fitness optima based on the physiological availability of each sex. Although intralocus sexual conflict appears to be a genetic constraint for the evolution of sex-specific traits, sex-linked genes and the regulation of sex steroid hormones contribute to resolving this conflict by allowing sex-specific developments. Androgens and their receptor, androgen receptor (Ar), regulate male-biased phenotypes. In teleost fish, ar ohnologs have emerged as a result of teleost-specific whole genome duplication (TSGD). Recent studies have highlighted the evolutionary differentiation of ar ohnologs responsible for the development of sexual characteristics, which sheds light on the need for comparative studies on androgen regulation among different species. In this review, we discuss the importance of ar signaling as a regulator of male-specific traits in teleost species because teleost species are suitable experimental models for comparative studies owing to their great diversity in male-biased morphological and physiological traits. To date, both in vivo and in vitro studies on teleost ar ohnologs have shown a substantial influence of ars as a regulator of male-specific reproductive traits such as fin elongation, courtship behavior, and nuptial coloration. In addition to these sexual characteristics, ar substantially influences immunity, inducing a sex-biased immune response. This review aims to provide a comprehensive understanding of the current state of teleost ar studies and emphasizes the potential of teleost fishes, given their availability, to find molecular evidence about what gives rise to the spectacular diversity among fish species.
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Affiliation(s)
- Tsukasa Ryu
- Laboratory of Marine Biochemistry, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Keigo Okamoto
- Laboratory of Aquatic Molecular Developmental Biology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Satoshi Ansai
- Laboratory of Genome Editing Breeding, Graduate School of Agriculture, Kyoto University, Kyoto 606-8507, Japan
| | - Miki Nakao
- Laboratory of Marine Biochemistry, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
- Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Anu Kumar
- Commonwealth Scientific and Industrial Research Organization, CSIRO Environment, PMB2, Glen Osmond, 5064 South Australia, Australia
| | - Taisen Iguchi
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa 236-0027, Japan
- Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Ishikawa 927-0553, Japan
| | - Yukiko Ogino
- Laboratory of Aquatic Molecular Developmental Biology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan,
- Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
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22
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Peng Z, Zhang W, Fu H, Li Y, Zhang C, Li J, Chan J, Zhang L. Genome-Wide Comparative Analysis of SRCR Gene Superfamily in Invertebrates Reveals Massive and Independent Gene Expansions in the Sponge and Sea Urchin. Int J Mol Sci 2024; 25:1515. [PMID: 38338794 PMCID: PMC10855680 DOI: 10.3390/ijms25031515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Without general adaptative immunity, invertebrates evolved a vast number of heterogeneous non-self recognition strategies. One of those well-known adaptations is the expansion of the immune receptor gene superfamily coding for scavenger receptor cysteine-rich domain containing proteins (SRCR) in a few invertebrates. Here, we investigated the evolutionary history of the SRCR gene superfamily (SRCR-SF) across 29 metazoan species with an emphasis on invertebrates. We analyzed their domain architectures, genome locations and phylogenetic distribution. Our analysis shows extensive genome-wide duplications of the SRCR-SFs in Amphimedon queenslandica and Strongylocentrotus purpuratus. Further molecular evolution study reveals various patterns of conserved cysteines in the sponge and sea urchin SRCR-SFs, indicating independent and convergent evolution of SRCR-SF expansion during invertebrate evolution. In the case of the sponge SRCR-SFs, a novel motif with seven conserved cysteines was identified. Exon-intron structure analysis suggests the rapid evolution of SRCR-SFs during gene duplications in both the sponge and the sea urchin. Our findings across nine representative metazoans also underscore a heightened expression of SRCR-SFs in immune-related tissues, notably the digestive glands. This observation indicates the potential role of SRCR-SFs in reinforcing distinct immune functions in these invertebrates. Collectively, our results reveal that gene duplication, motif structure variation, and exon-intron divergence might lead to the convergent evolution of SRCR-SF expansions in the genomes of the sponge and sea urchin. Our study also suggests that the utilization of SRCR-SF receptor duplication may be a general and basal strategy to increase immune diversity and tissue specificity for the invertebrates.
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Affiliation(s)
- Zhangjie Peng
- College of Life Sciences, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Z.P.); (H.F.); (Y.L.); (C.Z.)
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Wei Zhang
- College of Life Sciences, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Z.P.); (H.F.); (Y.L.); (C.Z.)
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Hailun Fu
- College of Life Sciences, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Z.P.); (H.F.); (Y.L.); (C.Z.)
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yuzhu Li
- College of Life Sciences, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Z.P.); (H.F.); (Y.L.); (C.Z.)
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Chunyu Zhang
- College of Life Sciences, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Z.P.); (H.F.); (Y.L.); (C.Z.)
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jie Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jiulin Chan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266071, China
| | - Linlin Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266071, China
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23
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Ma F, Lau CY, Zheng C. Young duplicate genes show developmental stage- and cell type-specific expression and function in Caenorhabditis elegans. Cell Genom 2024; 4:100467. [PMID: 38190105 PMCID: PMC10794840 DOI: 10.1016/j.xgen.2023.100467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/06/2023] [Accepted: 11/23/2023] [Indexed: 01/09/2024]
Abstract
Gene duplication produces the material that fuels evolutionary innovation. The "out-of-testis" hypothesis suggests that sperm competition creates selective pressure encouraging the emergence of new genes in male germline, but the somatic expression and function of the newly evolved genes are not well understood. We systematically mapped the expression of young duplicate genes throughout development in Caenorhabditis elegans using both whole-organism and single-cell transcriptomic data. Based on the expression dynamics across developmental stages, young duplicate genes fall into three clusters that are preferentially expressed in early embryos, mid-stage embryos, and late-stage larvae. Early embryonic genes are involved in protein degradation and develop essentiality comparable to the genomic average. In mid-to-late embryos and L4-stage larvae, young genes are enriched in intestine, epidermal cells, coelomocytes, and amphid chemosensory neurons. Their molecular functions and inducible expression indicate potential roles in innate immune response and chemosensory perceptions, which may contribute to adaptation outside of the sperm.
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Affiliation(s)
- Fuqiang Ma
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Chun Yin Lau
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Chaogu Zheng
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
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24
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Takeuchi N, Fullmer MS, Maddock DJ, Poole AM. The Constructive Black Queen hypothesis: new functions can evolve under conditions favouring gene loss. ISME J 2024; 18:wrae011. [PMID: 38366199 PMCID: PMC10942775 DOI: 10.1093/ismejo/wrae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/18/2024]
Abstract
Duplication is a major route for the emergence of new gene functions. However, the emergence of new gene functions via this route may be reduced in prokaryotes, as redundant genes are often rapidly purged. In lineages with compact, streamlined genomes, it thus appears challenging for novel function to emerge via duplication and divergence. A further pressure contributing to gene loss occurs under Black Queen dynamics, as cheaters that lose the capacity to produce a public good can instead acquire it from neighbouring producers. We propose that Black Queen dynamics can favour the emergence of new function because, under an emerging Black Queen dynamic, there is high gene redundancy spread across a community of interacting cells. Using computational modelling, we demonstrate that new gene functions can emerge under Black Queen dynamics. This result holds even if there is deletion bias due to low duplication rates and selection against redundant gene copies resulting from the high cost associated with carrying a locus. However, when the public good production costs are high, Black Queen dynamics impede the fixation of new functions. Our results expand the mechanisms by which new gene functions can emerge in prokaryotic systems.
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Affiliation(s)
- Nobuto Takeuchi
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Universal Biology Institute, University of Tokyo, Tokyo 113-0033, Japan
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Matthew S Fullmer
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Danielle J Maddock
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Anthony M Poole
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
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25
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Gikonyo MW, Ahn SJ, Biondi M, Fritzlar F, Okamura Y, Vogel H, Köllner TG, Şen İ, Hernández-Teixidor D, Lee CF, Letsch H, Beran F. A radiation of Psylliodes flea beetles on Brassicaceae is associated with the evolution of specific detoxification enzymes. Evolution 2024; 78:127-145. [PMID: 37919254 DOI: 10.1093/evolut/qpad197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 10/08/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023]
Abstract
Flea beetles of the genus Psylliodes have evolved specialized interactions with plant species belonging to several distantly related families, mainly Brassicaceae, Solanaceae, and Fagaceae. This diverse host use indicates that Psylliodes flea beetles are able to cope with different chemical defense metabolites, including glucosinolates, the characteristic defense metabolites of Brassicaceae. Here we investigated the evolution of host use and the emergence of a glucosinolate-specific detoxification mechanism in Psylliodes flea beetles. In phylogenetic analyses, Psylliodes species clustered into four major clades, three of which contained mainly species specialized on either Brassicaceae, Solanaceae, or Fagaceae. Most members of the fourth clade have broader host use, including Brassicaceae and Poaceae as major host plant families. Ancestral state reconstructions suggest that Psylliodes flea beetles were initially associated with Brassicaceae and then either shifted to Solanaceae or Fagaceae, or expanded their host repertoire to Poaceae. Despite a putative ancestral association with Brassicaceae, we found evidence that the evolution of glucosinolate-specific detoxification enzymes coincides with the radiation of Psylliodes on Brassicaceae, suggesting that these are not required for using Brassicaceae as hosts but could improve the efficiency of host use by specialized Psylliodes species.
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Affiliation(s)
- Matilda W Gikonyo
- Research Group Sequestration and Detoxification in Insects, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Seung-Joon Ahn
- Research Group Sequestration and Detoxification in Insects, Max Planck Institute for Chemical Ecology, Jena, Germany
- Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology, Mississippi State University, Starkville, MS, US
| | - Maurizio Biondi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Frank Fritzlar
- Thüringer Landesamt für Umwelt, Bergbau und Naturschutz, Weimar, Germany
| | - Yu Okamura
- Department of Entomology, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Heiko Vogel
- Department of Entomology, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Tobias G Köllner
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - İsmail Şen
- Faculty of Technology, Isparta University of Applied Sciences, Isparta, Turkey
| | - David Hernández-Teixidor
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
| | - Chi-Feng Lee
- Applied Zoology Division, Taiwan Agricultural Research Institute, Taichung, Taiwan
| | - Harald Letsch
- Department of Botany and Biodiversity Research, Division of Tropical Ecology and Animal Biodiversity, University of Vienna, Vienna, Austria
| | - Franziska Beran
- Research Group Sequestration and Detoxification in Insects, Max Planck Institute for Chemical Ecology, Jena, Germany
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26
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Lemieux P, Bradley D, Dubé AK, Dionne U, Landry CR. Dissection of the role of a Src homology 3 domain in the evolution of binding preference of paralogous proteins. Genetics 2024; 226:iyad175. [PMID: 37793087 PMCID: PMC10763533 DOI: 10.1093/genetics/iyad175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/07/2023] [Accepted: 08/07/2023] [Indexed: 10/06/2023] Open
Abstract
Protein-protein interactions (PPIs) drive many cellular processes. Some interactions are directed by Src homology 3 (SH3) domains that bind proline-rich motifs on other proteins. The evolution of the binding specificity of SH3 domains is not completely understood, particularly following gene duplication. Paralogous genes accumulate mutations that can modify protein functions and, for SH3 domains, their binding preferences. Here, we examined how the binding of the SH3 domains of 2 paralogous yeast type I myosins, Myo3 and Myo5, evolved following duplication. We found that the paralogs have subtly different SH3-dependent interaction profiles. However, by swapping SH3 domains between the paralogs and characterizing the SH3 domains freed from their protein context, we find that very few of the differences in interactions, if any, depend on the SH3 domains themselves. We used ancestral sequence reconstruction to resurrect the preduplication SH3 domains and examined, moving back in time, how the binding preference changed. Although the most recent ancestor of the 2 domains had a very similar binding preference as the extant ones, older ancestral domains displayed a gradual loss of interaction with the modern interaction partners when inserted in the extant paralogs. Molecular docking and experimental characterization of the free ancestral domains showed that their affinity with the proline motifs is likely not the cause for this loss of binding. Taken together, our results suggest that a SH3 and its host protein could create intramolecular or allosteric interactions essential for the SH3-dependent PPIs, making domains not functionally equivalent even when they have the same binding specificity.
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Affiliation(s)
- Pascale Lemieux
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
| | - David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biologie, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biologie, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
| | - Ugo Dionne
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de Recherche du Centre Hospitalier Universitaire (CHU) de Québec, Université Laval, Québec, QC, Canada G1R 2J6
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada M5G 1X5
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biologie, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
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27
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Schäfer L, Jehle JA, Kleespies RG, Wennmann JT. A practical guide and Galaxy workflow to avoid inter-plasmidic repeat collapse and false gene loss in Unicycler's hybrid assemblies. Microb Genom 2024; 10:001173. [PMID: 38197876 PMCID: PMC10868617 DOI: 10.1099/mgen.0.001173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024] Open
Abstract
Generating complete, high-quality genome assemblies is key for any downstream analysis, such as comparative genomics. For bacterial genome assembly, various algorithms and fully automated pipelines exist, which are free-of-charge and easily accessible. However, these assembly tools often cannot unambiguously resolve a bacterial genome, for example due to the presence of sequence repeat structures on the chromosome or on plasmids. Then, a more sophisticated approach and/or manual curation is needed. Such modifications can be challenging, especially for non-bioinformaticians, because they are generally not considered as a straightforward process. In this study, we propose a standardized approach for manual genome completion focusing on the popular hybrid assembly pipeline Unicycler. The provided Galaxy workflow addresses two weaknesses in Unicycler's hybrid assemblies: (i) collapse of inter-plasmidic repeats and (ii) false loss of single-copy sequences. To demonstrate and validate how to detect and resolve these assembly errors, we use two genomes from the Bacillus cereus group. By applying the proposed pipeline following an automated assembly, the genome sequence quality can be significantly improved.
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Affiliation(s)
- Lea Schäfer
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Johannes A. Jehle
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Regina G. Kleespies
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Jörg T. Wennmann
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
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28
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McKinnie LJ, Cummins SF, Zhao M. Identification of Incomplete Annotations of Biosynthesis Pathways in Rhodophytes Using a Multi-Omics Approach. Mar Drugs 2023; 22:3. [PMID: 38276641 PMCID: PMC10817344 DOI: 10.3390/md22010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Rhodophytes (red algae) are an important source of natural products and are, therefore, a current research focus in terms of metabolite production. The recent increase in publicly available Rhodophyte whole genome and transcriptome assemblies provides the resources needed for in silico metabolic pathway analysis. Thus, this study aimed to create a Rhodophyte multi-omics resource, utilising both genomes and transcriptome assemblies with functional annotations to explore Rhodophyte metabolism. The genomes and transcriptomes of 72 Rhodophytes were functionally annotated and integrated with metabolic reconstruction and phylogenetic inference, orthology prediction, and gene duplication analysis to analyse their metabolic pathways. This resource was utilised via two main investigations: the identification of bioactive sterol biosynthesis pathways and the evolutionary analysis of gene duplications for known enzymes. We report that sterol pathways, including campesterol, β-sitosterol, ergocalciferol and cholesterol biosynthesis pathways, all showed incomplete annotated pathways across all Rhodophytes despite prior in vivo studies showing otherwise. Gene duplication analysis revealed high rates of duplication of halide-associated haem peroxidases in Florideophyte algae, which are involved in the biosynthesis of drug-related halogenated secondary metabolites. In summary, this research revealed trends in Rhodophyte metabolic pathways that have been under-researched and require further functional analysis. Furthermore, the high duplication of haem peroxidases and other peroxidase enzymes offers insight into the potential drug development of Rhodophyte halogenated secondary metabolites.
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Affiliation(s)
- Lachlan J. McKinnie
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia; (L.J.M.); (S.F.C.)
- School of Science, Technology, and Engineering, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia
| | - Scott F. Cummins
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia; (L.J.M.); (S.F.C.)
- School of Science, Technology, and Engineering, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia
| | - Min Zhao
- Seaweed Research Group, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia; (L.J.M.); (S.F.C.)
- School of Science, Technology, and Engineering, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia
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Flipphi M, Márton A, Bíró V, Ág N, Sándor E, Fekete E, Karaffa L. Generation, Transfer, and Loss of Alternative Oxidase Paralogues in the Aspergillaceae Family. J Fungi (Basel) 2023; 9:1195. [PMID: 38132795 PMCID: PMC10744626 DOI: 10.3390/jof9121195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Alternative oxidase (Aox) is a terminal oxidase operating in branched electron transport. The activity correlates positively with overflow metabolisms in certain Aspergilli, converting intracellular glucose by the shortest possible path into organic acids, like citrate or itaconate. Aox is nearly ubiquitous in fungi, but aox gene multiplicity is rare. Nevertheless, within the family of the Aspergillaceae and among its various species of industrial relevance-Aspergillus niger, A. oryzae, A. terreus, Penicillium rubens-paralogous aox genes coexist. Paralogous genes generally arise from duplication and are inherited vertically. Here, we provide evidence of four independent duplication events along the lineage that resulted in aox paralogues (aoxB) in contemporary Aspergillus and Penicillium taxa. In some species, three aox genes are co-expressed. The origin of the A. niger paralogue is different than that of the A. terreus paralogue, but all paralogous clades ultimately arise from ubiquitous aoxA parent genes. We found different patterns of uncorrelated gene losses reflected in the Aspergillus pedigree, albeit the original aoxA orthologues persist everywhere and are never replaced. The loss of acquired paralogues co-determines the contemporary aox gene content of individual species. In Aspergillus calidoustus, the two more ancient paralogues have, in effect, been replaced by two aoxB genes of distinct origins.
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Affiliation(s)
- Michel Flipphi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary; (M.F.); (A.M.); (V.B.); (N.Á.); (L.K.)
| | - Alexandra Márton
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary; (M.F.); (A.M.); (V.B.); (N.Á.); (L.K.)
- Juhász-Nagy Pál Doctoral School of Biology and Environmental Sciences, University of Debrecen, H-4032 Debrecen, Hungary
| | - Vivien Bíró
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary; (M.F.); (A.M.); (V.B.); (N.Á.); (L.K.)
- Juhász-Nagy Pál Doctoral School of Biology and Environmental Sciences, University of Debrecen, H-4032 Debrecen, Hungary
| | - Norbert Ág
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary; (M.F.); (A.M.); (V.B.); (N.Á.); (L.K.)
| | - Erzsébet Sándor
- Institute of Food Science, Faculty of Agricultural and Food Science and Environmental Management, University of Debrecen, H-4032 Debrecen, Hungary;
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary; (M.F.); (A.M.); (V.B.); (N.Á.); (L.K.)
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary; (M.F.); (A.M.); (V.B.); (N.Á.); (L.K.)
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Lu M, Cao M, Yang J, Swenson NG. Comparative transcriptomics reveals divergence in pathogen response gene families amongst 20 forest tree species. G3 (Bethesda) 2023; 13:jkad233. [PMID: 37812763 DOI: 10.1093/g3journal/jkad233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023]
Abstract
Forest trees provide critical ecosystem services for humanity that are under threat due to ongoing global change. Measuring and characterizing genetic diversity are key to understanding adaptive potential and developing strategies to mitigate negative consequences arising from climate change. In the area of forest genetic diversity, genetic divergence caused by large-scale changes at the chromosomal level has been largely understudied. In this study, we used the RNA-seq data of 20 co-occurring forest trees species from genera including Acer, Alnus, Amelanchier, Betula, Cornus, Corylus, Dirca, Fraxinus, Ostrya, Populus, Prunus, Quercus, Ribes, Tilia, and Ulmus sampled from Upper Peninsula of Michigan. These data were used to infer the origin and maintenance of gene family variation, species divergence time, as well as gene family expansion and contraction. We identified a signal of common whole genome duplication events shared by core eudicots. We also found rapid evolution, namely fast expansion or fast contraction of gene families, in plant-pathogen interaction genes amongst the studied diploid species. Finally, the results lay the foundation for further research on the genetic diversity and adaptive capacity of forest trees, which will inform forest management and conservation policies.
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Affiliation(s)
- Mengmeng Lu
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA
| | - Min Cao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
| | - Jie Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
| | - Nathan G Swenson
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA
- University of Notre Dame Environmental Research Center (UNDERC), 736 Flanner Hall, Notre Dame, IN 46556, USA
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Park S, Park S. Intrageneric structural variation in organelle genomes from the genus Dystaenia (Apiaceae): genome rearrangement and mitochondrion-to-plastid DNA transfer. Front Plant Sci 2023; 14:1283292. [PMID: 38116150 PMCID: PMC10728875 DOI: 10.3389/fpls.2023.1283292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023]
Abstract
Introduction During plant evolution, intracellular DNA transfer (IDT) occurs not only from organelles to the nucleus but also between organelles. To further comprehend these events, both organelle genomes and transcriptomes are needed. Methods In this study, we constructed organelle genomes and transcriptomes for two Dystaenia species and described their dynamic IDTs between their nuclear and mitochondrial genomes, or plastid and mitochondrial genomes (plastome and mitogenome). Results and Discussion We identified the putative functional transfers of the mitochondrial genes 5' rpl2, rps10, rps14, rps19, and sdh3 to the nucleus in both Dystaenia species and detected two transcripts for the rpl2 and sdh3 genes. Additional transcriptomes from the Apicaceae species also provided evidence for the transfers and duplications of these mitochondrial genes, showing lineage-specific patterns. Intrageneric variations of the IDT were found between the Dystaenia organelle genomes. Recurrent plastid-to-mitochondrion DNA transfer events were only identified in the D. takeshimana mitogenome, and a pair of mitochondrial DNAs of plastid origin (MIPTs) may generate minor alternative isoforms. We only found a mitochondrion-to-plastid DNA transfer event in the D. ibukiensis plastome. This event may be linked to inverted repeat boundary shifts in its plastome. We inferred that the insertion region involved an MIPT that had already acquired a plastid sequence in its mitogenome via IDT. We propose that the MIPT acts as a homologous region pairing between the donor and recipient sequences. Our results provide insight into the evolution of organelle genomes across the family Apiaceae.
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Affiliation(s)
- Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan, Republic of Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Republic of Korea
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Clark JW. Genome evolution in plants and the origins of innovation. New Phytol 2023; 240:2204-2209. [PMID: 37658677 DOI: 10.1111/nph.19242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/03/2023] [Indexed: 09/03/2023]
Abstract
Plant evolution has been characterised by a series of major novelties in their vegetative and reproductive traits that have led to greater complexity. Underpinning this diversification has been the evolution of the genome. When viewed at the scale of the plant kingdom, plant genome evolution has been punctuated by conspicuous instances of gene and whole-genome duplication, horizontal gene transfer and extensive gene loss. The periods of dynamic genome evolution often coincide with the evolution of key traits, demonstrating the coevolution of plant genomes and phenotypes at a macroevolutionary scale. Conventionally, plant complexity and diversity have been considered through the lens of gene duplication and the role of gene loss in plant evolution remains comparatively unexplored. However, in light of reductive evolution across multiple plant lineages, the association between gene loss and plant phenotypic diversity warrants greater attention.
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Affiliation(s)
- James W Clark
- School of Biological Sciences, University of Bristol, Tyndall Ave, Bristol, BS8 1TQ, UK
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Gnanagobal H, Cao T, Hossain A, Vasquez I, Chakraborty S, Chukwu-Osazuwa J, Boyce D, Espinoza MJ, García-Angulo VA, Santander J. Role of riboflavin biosynthesis gene duplication and transporter in Aeromonas salmonicida virulence in marine teleost fish. Virulence 2023; 14:2187025. [PMID: 36895132 PMCID: PMC10012899 DOI: 10.1080/21505594.2023.2187025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
Active flavins derived from riboflavin (vitamin B2) are essential for life. Bacteria biosynthesize riboflavin or scavenge it through uptake systems, and both mechanisms may be present. Because of riboflavin's critical importance, the redundancy of riboflavin biosynthetic pathway (RBP) genes might be present. Aeromonas salmonicida, the aetiological agent of furunculosis, is a pathogen of freshwater and marine fish, and its riboflavin pathways have not been studied. This study characterized the A. salmonicida riboflavin provision pathways. Homology search and transcriptional orchestration analysis showed that A. salmonicida has a main riboflavin biosynthetic operon that includes ribD, ribE1, ribBA, and ribH genes. Outside the main operon, putative duplicated genes ribA, ribB and ribE, and a ribN riboflavin importer encoding gene, were found. Monocistronic mRNA ribA, ribB and ribE2 encode for their corresponding functional riboflavin biosynthetic enzyme. While the product of ribBA conserved the RibB function, it lacked the RibA function. Likewise, ribN encodes a functional riboflavin importer. Transcriptomics analysis indicated that external riboflavin affected the expression of a relatively small number of genes, including a few involved in iron metabolism. ribB was downregulated in response to external riboflavin, suggesting negative feedback. Deletion of ribA, ribB and ribE1 showed that these genes are required for A. salmonicida riboflavin biosynthesis and virulence in Atlantic lumpfish (Cyclopterus lumpus). A. salmonicida riboflavin auxotrophic attenuated mutants conferred low protection to lumpfish against virulent A. salmonicida. Overall, A. salmonicida has multiple riboflavin endowment forms, and duplicated riboflavin provision genes are critical for A. salmonicida infection.
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Affiliation(s)
- Hajarooba Gnanagobal
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St John's, Canada
| | - Trung Cao
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St John's, Canada
| | - Ahmed Hossain
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St John's, Canada
| | - Ignacio Vasquez
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St John's, Canada
| | - Setu Chakraborty
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St John's, Canada
| | - Joy Chukwu-Osazuwa
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St John's, Canada
| | - Danny Boyce
- The Dr. Joe Brown Aquatic Research Building (JBARB), Ocean Sciences Centre, Memorial University of Newfoundland, St John's, Canada
| | - María Jesus Espinoza
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Víctor Antonio García-Angulo
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Javier Santander
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St John's, Canada
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Selifanova M, Demianchenko O, Noskova E, Pitikov E, Skvortsov D, Drozd J, Vatolkina N, Apel P, Kolodyazhnaya E, Ezhova MA, Tzetlin AB, Neretina TV, Knorre DA. ORFans in Mitochondrial Genomes of Marine Polychaete Polydora. Genome Biol Evol 2023; 15:evad219. [PMID: 38019573 PMCID: PMC10721130 DOI: 10.1093/gbe/evad219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 11/18/2023] [Accepted: 11/24/2023] [Indexed: 11/30/2023] Open
Abstract
Most characterized metazoan mitochondrial genomes are compact and encode a small set of proteins that are essential for oxidative phosphorylation, as well as rRNA and tRNA for their expression. However, in rare cases, invertebrate taxa have additional open reading frames (ORFs) in their mtDNA sequences. Here, we sequenced and analyzed the mitochondrial genome of a polychaete worm, Polydora cf. ciliata, part of whose life cycle takes place in low-oxygen conditions. In the mitogenome, we found three "ORFan" regions (544, 1,060, and 427 bp) that have no resemblance to any standard metazoan mtDNA gene but lack stop codons in one of the reading frames. Similar regions are found in the mitochondrial genomes of three other Polydora species and Bocardiella hamata. All five species share the same gene order in their mitogenomes, which differ from that of other known Spionidae mitogenomes. By analyzing the ORFan sequences, we found that they are under purifying selection pressure and contain conservative regions. The codon adaptation indices (CAIs) of the ORFan genes were in the same range of values as the CAI of conventional protein-coding genes in corresponding mitochondrial genomes. The analysis of the P. cf. ciliata mitochondrial transcriptome showed that ORFan-544, ORFan-427, and a portion of the ORFan-1060 are transcribed. Together, this suggests that ORFan-544 and ORFan-427 encode functional proteins. It is likely that the ORFans originated when the Polydora/Bocardiella species complex separated from the rest of the Spionidae, and this event coincided with massive gene rearrangements in their mitochondrial genomes and tRNA-Met duplication.
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Affiliation(s)
- Maria Selifanova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Oleg Demianchenko
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Elizaveta Noskova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Egor Pitikov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Denis Skvortsov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Jana Drozd
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Nika Vatolkina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Polina Apel
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina Kolodyazhnaya
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Margarita A Ezhova
- Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexander B Tzetlin
- Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana V Neretina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Science, Moscow, Russia
| | - Dmitry A Knorre
- Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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Bryłka K, Pinseel E, Roberts WR, Ruck EC, Conley DJ, Alverson AJ. Gene Duplication, Shifting Selection, and Dosage Balance of Silicon Transporter Proteins in Marine and Freshwater Diatoms. Genome Biol Evol 2023; 15:evad212. [PMID: 37996067 PMCID: PMC10700740 DOI: 10.1093/gbe/evad212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/15/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023] Open
Abstract
Numerous factors shape the evolution of protein-coding genes, including shifts in the strength or type of selection following gene duplications or changes in the environment. Diatoms and other silicifying organisms use a family of silicon transporters (SITs) to import dissolved silicon from the environment. Freshwaters contain higher silicon levels than oceans, and marine diatoms have more efficient uptake kinetics and less silicon in their cell walls, making them better competitors for a scarce resource. We compiled SITs from 37 diatom genomes to characterize shifts in selection following gene duplications and marine-freshwater transitions. A deep gene duplication, which coincided with a whole-genome duplication, gave rise to two gene lineages. One of them (SIT1-2) is present in multiple copies in most species and is known to actively import silicon. These SITs have evolved under strong purifying selection that was relaxed in freshwater taxa. Episodic diversifying selection was detected but not associated with gene duplications or habitat shifts. In contrast, genes in the second SIT lineage (SIT3) were present in just half the species, the result of multiple losses. Despite conservation of SIT3 in some lineages for the past 90-100 million years, repeated losses, relaxed selection, and low expression highlighted the dispensability of SIT3, consistent with a model of deterioration and eventual loss due to relaxed selection on SIT3 expression. The extensive but relatively balanced history of duplications and losses, together with paralog-specific expression patterns, suggest diatoms continuously balance gene dosage and expression dynamics to optimize silicon transport across major environmental gradients.
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Affiliation(s)
| | - Eveline Pinseel
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Wade R Roberts
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Elizabeth C Ruck
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | | | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
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Long H, Johri P, Gout JF, Ni J, Hao Y, Licknack T, Wang Y, Pan J, Jiménez-Marín B, Lynch M. Paramecium Genetics, Genomics, and Evolution. Annu Rev Genet 2023; 57:391-410. [PMID: 38012024 DOI: 10.1146/annurev-genet-071819-104035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The ciliate genus Paramecium served as one of the first model systems in microbial eukaryotic genetics, contributing much to the early understanding of phenomena as diverse as genome rearrangement, cryptic speciation, cytoplasmic inheritance, and endosymbiosis, as well as more recently to the evolution of mating types, introns, and roles of small RNAs in DNA processing. Substantial progress has recently been made in the area of comparative and population genomics. Paramecium species combine some of the lowest known mutation rates with some of the largest known effective populations, along with likely very high recombination rates, thereby harboring a population-genetic environment that promotes an exceptionally efficient capacity for selection. As a consequence, the genomes are extraordinarily streamlined, with very small intergenic regions combined with small numbers of tiny introns. The subject of the bulk of Paramecium research, the ancient Paramecium aurelia species complex, is descended from two whole-genome duplication events that retain high degrees of synteny, thereby providing an exceptional platform for studying the fates of duplicate genes. Despite having a common ancestor dating to several hundred million years ago, the known descendant species are morphologically indistinguishable, raising significant questions about the common view that gene duplications lead to the origins of evolutionary novelties.
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Affiliation(s)
- Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China;
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, Shandong Province, China
| | - Parul Johri
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jean-Francois Gout
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, USA
| | - Jiahao Ni
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China;
| | - Yue Hao
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA;
| | - Timothy Licknack
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA;
| | - Yaohai Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China;
| | - Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China;
| | - Berenice Jiménez-Marín
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA;
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA;
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Takeda T, Ezoe A, Hanada K. Expression profiles in knock-down transgenic plants of high and low diversified duplicate genes in Arabidopsis thaliana. Genes Genet Syst 2023; 98:283-286. [PMID: 37779055 DOI: 10.1266/ggs.23-00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023] Open
Abstract
Duplicated genes show various degrees of functional diversification in plants. We previously identified 1,052 pairs of high diversified duplicates (HDDs) and 600 pairs of low diversified duplicates (LDDs) in Arabidopsis thaliana. Single knock-down of HDDs induced abnormal phenotypic changes because the other gene copy could not compensate for the knock-down effect, while single knock-down of LDDs did not induce abnormal phenotypic changes because of functional compensation by the copy gene. Here, focusing on one pair each of HDDs and LDDs, we performed transcriptome analyses in single-knock-down transgenic plants. The numbers of differentially expressed genes in single-knock-down transgenic plants were not different between HDDs and LDDs. Thus, functional compensation inferred by transcriptomics was similar between HDDs and LDDs. However, the trend of differentially expressed genes was similar in the pair of LDDs, while expression profiles were dissimilar in the pair of HDDs. This result indicates that a pair of LDDs tends to share similar functions but a pair of HDDs tends to have undergone functional divergence. Taking these findings together, as the reason for no phenotypic changes in single knock-down of LDDs but phenotypic changes in double knock-down of LDDs, we concluded that phenotypic changes of LDDs were induced by decreasing gene dosage.
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Affiliation(s)
- Tomoyuki Takeda
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology
| | | | - Kousuke Hanada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology
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Li H, Li Y, Wang X, Jiao Z, Zhang W, Long Y. Characterization of Glycosyltransferase Family 1 (GT1) and Their Potential Roles in Anthocyanin Biosynthesis in Maize. Genes (Basel) 2023; 14:2099. [PMID: 38003042 PMCID: PMC10671782 DOI: 10.3390/genes14112099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Glycosyltransferase family 1 (GT1) is a large group of proteins that play critical roles in secondary metabolite biosynthesis in plants. However, the GT1 family is not well studied in maize. In this study, 107 GT1 unigenes were identified in the maize reference genome and classified into 16 groups according to their phylogenetic relationship. GT1s are unevenly distributed across all ten maize chromosomes, occurring as gene clusters in some chromosomes. Collinearity analysis revealed that gene duplication events, whole-genome or segmental duplication, and tandem duplication occurred at a similar frequency, indicating that both types of gene duplication play notable roles in the expansion of the GT1 gene family. Expression analysis showed GT1s expressing in all tissues with specific expression patterns of each GT1, suggesting that they might participate in multiple biological processes during the whole growth and development stages. Furthermore, 16 GT1s were identified to have similar expression patterns to those of anthocyanidin synthase (ANS), the critical enzyme in anthocyanin biosynthesis. Molecular docking was carried out to examine the affinity of GT1s with substrates in anthocyanin biosynthesis. This study provides valuable information on the GT1s of maize and will promote the development of research on their biological functions in the biosynthesis of other secondary metabolites.
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Affiliation(s)
- Huangai Li
- Research Institute of Biology and Agriculture, Shunde Innovation School, University of Science and Technology Beijing, Beijing 100083, China; (H.L.); (Y.L.); (X.W.)
| | - Yiping Li
- Research Institute of Biology and Agriculture, Shunde Innovation School, University of Science and Technology Beijing, Beijing 100083, China; (H.L.); (Y.L.); (X.W.)
| | - Xiaofang Wang
- Research Institute of Biology and Agriculture, Shunde Innovation School, University of Science and Technology Beijing, Beijing 100083, China; (H.L.); (Y.L.); (X.W.)
| | - Ziwei Jiao
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; (Z.J.); (W.Z.)
| | - Wei Zhang
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; (Z.J.); (W.Z.)
| | - Yan Long
- Research Institute of Biology and Agriculture, Shunde Innovation School, University of Science and Technology Beijing, Beijing 100083, China; (H.L.); (Y.L.); (X.W.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
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Yamada T, Maeda M, Nagai H, Salamin K, Chang YT, Guenova E, Feuermann M, Monod M. Two different types of tandem sequences mediate the overexpression of TinCYP51B in azole-resistant Trichophyton indotineae. Antimicrob Agents Chemother 2023; 67:e0093323. [PMID: 37823662 PMCID: PMC10648874 DOI: 10.1128/aac.00933-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/03/2023] [Indexed: 10/13/2023] Open
Abstract
Trichophyton indotineae is an emerging dermatophyte that causes severe tinea corporis and tinea cruris. Numerous cases of terbinafine- and azole-recalcitrant T. indotineae-related dermatophytosis have been observed in India over the past decade, and cases are now being recorded worldwide. Whole genome sequencing of three azole-resistant strains revealed a variable number of repeats of a 2,404 base pair (bp) sequence encoding TinCYP51B in tandem specifically at the CYP51B locus position. However, many other resistant strains (itraconazole MIC ≥0.25 µg/mL; voriconazole MIC ≥0.25 µg/mL) did not contain such duplications. Whole-genome sequencing of three of these strains revealed a variable number of 7,374 bp tandem repeat blocks harboring TinCYP51B. Consequently, two types of T. indotineae azole-resistant strains were found to host TinCYP51B in tandem sequences (type I with 2,404 bp TinCYP51B blocks and type II with 7,374 bp TinCYP51B blocks). Using the CRISPR/Cas9 genome-editing tool, the copy number of TinCYP51B within the genome of types I and II strains was brought back to a single copy. The azole susceptibility of these modified strains was similar to that of strains without TinCYP51B duplication, showing that azole resistance in T. indotineae strains is mediated by one of two types of TinCYP51B amplification. Type II strains were prevalent among 32 resistant strains analyzed using a rapid and reliable PCR test.
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Affiliation(s)
- Tsuyoshi Yamada
- Teikyo University Institute of Medical Mycology, Tokyo, Japan
- Asia International Institute of Infectious Disease Control, Teikyo University, Tokyo, Japan
| | - Mari Maeda
- Teikyo University Institute of Medical Mycology, Tokyo, Japan
| | | | - Karine Salamin
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Yun-Tsan Chang
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Emmanuella Guenova
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Marc Feuermann
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Michel Monod
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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40
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Sonoda GG, Tobaruela EDC, Norenburg J, Fabi JP, Andrade SCS. Venomous Noodles: The Evolution of Toxins in Nemertea through Positive Selection and Gene Duplication. Toxins (Basel) 2023; 15:650. [PMID: 37999513 PMCID: PMC10674772 DOI: 10.3390/toxins15110650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 11/25/2023] Open
Abstract
Some, probably most and perhaps all, members of the phylum Nemertea are poisonous, documented so far from marine and benthic specimens. Although the toxicity of these animals has been long known, systematic studies on the characterization of toxins, mechanisms of toxicity, and toxin evolution for this group are scarce. Here, we present the first investigation of the molecular evolution of toxins in Nemertea. Using a proteo-transcriptomic approach, we described toxins in the body and poisonous mucus of the pilidiophoran Lineus sanguineus and the hoplonemertean Nemertopsis pamelaroeae. Using these new and publicly available transcriptomes, we investigated the molecular evolution of six selected toxin gene families. In addition, we also characterized in silico the toxin genes found in the interstitial hoplonemertean, Ototyphlonemertes erneba, a meiofaunal taxa. We successfully identified over 200 toxin transcripts in each of these species. Evidence of positive selection and gene duplication was observed in all investigated toxin genes. We hypothesized that the increased rates of gene duplications observed for Pilidiophora could be involved with the expansion of toxin genes. Studies concerning the natural history of Nemertea are still needed to understand the evolution of their toxins. Nevertheless, our results show evolutionary mechanisms similar to other venomous groups.
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Affiliation(s)
- Gabriel Gonzalez Sonoda
- Departamento de Genética e Biologia Evolutiva, IB-Universidade de São Paulo, São Paulo 05508-090, Brazil;
- Instituto Butantan, São Paulo 05503-900, Brazil
| | - Eric de Castro Tobaruela
- Faculdade de Ciências Farmacêuticas, Food Research Center (FoRC), Universidade de São Paulo, São Paulo 05508-080, Brazil; (E.d.C.T.); (J.P.F.)
| | | | - João Paulo Fabi
- Faculdade de Ciências Farmacêuticas, Food Research Center (FoRC), Universidade de São Paulo, São Paulo 05508-080, Brazil; (E.d.C.T.); (J.P.F.)
| | - Sónia C. S. Andrade
- Departamento de Genética e Biologia Evolutiva, IB-Universidade de São Paulo, São Paulo 05508-090, Brazil;
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41
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Mulhair PO, Crowley L, Boyes DH, Lewis OT, Holland PWH. Opsin Gene Duplication in Lepidoptera: Retrotransposition, Sex Linkage, and Gene Expression. Mol Biol Evol 2023; 40:msad241. [PMID: 37935057 PMCID: PMC10642689 DOI: 10.1093/molbev/msad241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Color vision in insects is determined by signaling cascades, central to which are opsin proteins, resulting in sensitivity to light at different wavelengths. In certain insect groups, lineage-specific evolution of opsin genes, in terms of copy number, shifts in expression patterns, and functional amino acid substitutions, has resulted in changes in color vision with subsequent behavioral and niche adaptations. Lepidoptera are a fascinating model to address whether evolutionary change in opsin content and sequence evolution are associated with changes in vision phenotype. Until recently, the lack of high-quality genome data representing broad sampling across the lepidopteran phylogeny has greatly limited our ability to accurately address this question. Here, we annotate opsin genes in 219 lepidopteran genomes representing 33 families, reconstruct their evolutionary history, and analyze shifts in selective pressures and expression between genes and species. We discover 44 duplication events in opsin genes across ∼300 million years of lepidopteran evolution. While many duplication events are species or family specific, we find retention of an ancient long-wavelength-sensitive (LW) opsin duplication derived by retrotransposition within the speciose superfamily Noctuoidea (in the families Nolidae, Erebidae, and Noctuidae). This conserved LW retrogene shows life stage-specific expression suggesting visual sensitivities or other sensory functions specific to the early larval stage. This study provides a comprehensive order-wide view of opsin evolution across Lepidoptera, showcasing high rates of opsin duplications and changes in expression patterns.
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Affiliation(s)
- Peter O Mulhair
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Liam Crowley
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | | | - Owen T Lewis
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
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42
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Eshak MIY, Rubbenstroth D, Beer M, Pfaff F. Diving deep into fish bornaviruses: Uncovering hidden diversity and transcriptional strategies through comprehensive data mining. Virus Evol 2023; 9:vead062. [PMID: 38028148 PMCID: PMC10645145 DOI: 10.1093/ve/vead062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Recently, we discovered two novel orthobornaviruses in colubrid and viperid snakes using an in silico data-mining approach. Here, we present the results of a screening of more than 100,000 nucleic acid sequence datasets of fish samples from the Sequence Read Archive (SRA) for potential bornaviral sequences. We discovered the potentially complete genomes of seven bornavirids in datasets from osteichthyans and chondrichthyans. Four of these are likely to represent novel species within the genus Cultervirus, and we propose that one genome represents a novel genus within the family of Bornaviridae. Specifically, we identified sequences of Wǔhàn sharpbelly bornavirus in sequence data from the widely used grass carp liver and kidney cell lines L8824 and CIK, respectively. A complete genome of Murray-Darling carp bornavirus was identified in sequence data from a goldfish (Carassius auratus). The newly discovered little skate bornavirus, identified in the little skate (Leucoraja erinacea) dataset, contained a novel and unusual genomic architecture (N-Vp1-Vp2-X-P-G-M-L), as compared to other bornavirids. Its genome is thought to encode two additional open reading frames (tentatively named Vp1 and Vp2), which appear to represent ancient duplications of the gene encoding the viral glycoprotein (G). The datasets also provided insights into the possible transcriptional gradients of these bornavirids and revealed previously unknown splicing mechanisms.
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Affiliation(s)
- Mirette I Y Eshak
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Südufer 10, Greifswald—Insel Riems 17493, Germany
| | - Dennis Rubbenstroth
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Südufer 10, Greifswald—Insel Riems 17493, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Südufer 10, Greifswald—Insel Riems 17493, Germany
| | - Florian Pfaff
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Südufer 10, Greifswald—Insel Riems 17493, Germany
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43
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Al Mamun MA, Reza MA, Islam MS. Identification of novel proteins regulating lipid droplet biogenesis in filamentous fungi. Mol Microbiol 2023; 120:702-722. [PMID: 37748926 DOI: 10.1111/mmi.15170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/27/2023]
Abstract
Lipid droplets (LDs) are storage organelles for neutral lipids which are critical for lipid homeostasis. Current knowledge of fungal LD biogenesis is largely limited to budding yeast, while LD regulation in multinucleated filamentous fungi which exhibit considerable metabolic activity remains unexplored. In this study, 19 LD-associated proteins were identified in the multinucleated species Aspergillus oryzae using a colocalization screening of a previously established enhanced green fluorescent protein (EGFP) fusion library. Functional screening identified 12 lipid droplet-regulating (LDR) proteins whose loss of function resulted in irregular LD biogenesis, particularly in terms of LD number and size. Bioinformatics analysis, targeted mutagenesis, and microscopy revealed four LDR proteins that localize to LD via the putative amphipathic helices (AHs). Further analysis revealed that LdrA with an Opi1 domain is essential for cytoplasmic and nuclear LD biogenesis involving a novel AH. Phylogenetic analysis demonstrated that the patterns of gene evolution were predominantly based on gene duplication. Our study identified a set of novel proteins involved in the regulation of LD biogenesis, providing unique molecular and evolutionary insights into fungal lipid storage.
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Affiliation(s)
- Md Abdulla Al Mamun
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - M Abu Reza
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
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44
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Iohannes SD, Jackson D. Tackling redundancy: genetic mechanisms underlying paralog compensation in plants. New Phytol 2023; 240:1381-1389. [PMID: 37724752 DOI: 10.1111/nph.19267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023]
Abstract
Gene duplication is a powerful source of biological innovation giving rise to paralogous genes that undergo diverse fates. Redundancy between paralogous genes is an intriguing outcome of duplicate gene evolution, and its maintenance over evolutionary time has long been considered a paradox. Redundancy can also be dubbed 'a geneticist's nightmare': It hinders the predictability of genome editing outcomes and limits our ability to link genotypes to phenotypes. Genetic studies in yeast and plants have suggested that the ability of ancient redundant duplicates to compensate for dosage perturbations resulting from a loss of function depends on the reprogramming of gene expression, a phenomenon known as active compensation. Starting from considerations on the stoichiometric constraints that drive the evolutionary stability of redundancy, this review aims to provide insights into the mechanisms of active compensation between duplicates that could be targeted for breaking paralog dependencies - the next frontier in plant functional studies.
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Affiliation(s)
- Sessen Daniel Iohannes
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
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45
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Michel F, Romero‐Romero S, Höcker B. Retracing the evolution of a modern periplasmic binding protein. Protein Sci 2023; 32:e4793. [PMID: 37788980 PMCID: PMC10601554 DOI: 10.1002/pro.4793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/05/2023]
Abstract
Investigating the evolution of structural features in modern multidomain proteins helps to understand their immense diversity and functional versatility. The class of periplasmic binding proteins (PBPs) offers an opportunity to interrogate one of the main processes driving diversification: the duplication and fusion of protein sequences to generate new architectures. The symmetry of their two-lobed topology, their mechanism of binding, and the organization of their operon structure led to the hypothesis that PBPs arose through a duplication and fusion event of a single common ancestor. To investigate this claim, we set out to reverse the evolutionary process and recreate the structural equivalent of a single-lobed progenitor using ribose-binding protein (RBP) as our model. We found that this modern PBP can be deconstructed into its lobes, producing two proteins that represent possible progenitor halves. The isolated halves of RBP are well folded and monomeric proteins, albeit with a lower thermostability, and do not retain the original binding function. However, the two entities readily form a heterodimer in vitro and in-cell. The x-ray structure of the heterodimer closely resembles the parental protein. Moreover, the binding function is fully regained upon formation of the heterodimer with a ligand affinity similar to that observed in the modern RBP. This highlights how a duplication event could have given rise to a stable and functional PBP-like fold and provides insights into how more complex functional structures can evolve from simpler molecular components.
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Affiliation(s)
- Florian Michel
- Department of BiochemistryUniversity of BayreuthBayreuthGermany
| | | | - Birte Höcker
- Department of BiochemistryUniversity of BayreuthBayreuthGermany
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46
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Fang C, Yang M, Tang Y, Zhang L, Zhao H, Ni H, Chen Q, Meng F, Jiang J. Dynamics of cis-regulatory sequences and transcriptional divergence of duplicated genes in soybean. Proc Natl Acad Sci U S A 2023; 120:e2303836120. [PMID: 37871213 PMCID: PMC10622917 DOI: 10.1073/pnas.2303836120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/19/2023] [Indexed: 10/25/2023] Open
Abstract
Transcriptional divergence of duplicated genes after whole genome duplication (WGD) has been described in many plant lineages and is often associated with subgenome dominance, a genome-wide mechanism. However, it is unknown what underlies the transcriptional divergence of duplicated genes in polyploid species that lack subgenome dominance. Soybean is a paleotetraploid with a WGD that occurred 5 to 13 Mya. Approximately 50% of the duplicated genes retained from this WGD exhibit transcriptional divergence. We developed accessible chromatin region (ACR) datasets from leaf, flower, and seed tissues using MNase-hypersensitivity sequencing. We validated enhancer function of several ACRs associated with known genes using CRISPR/Cas9-mediated genome editing. The ACR datasets were used to examine and correlate the transcriptional patterns of 17,111 pairs of duplicated genes in different tissues. We demonstrate that ACR dynamics are correlated with divergence of both expression level and tissue specificity of individual gene pairs. Gain or loss of flanking ACRs and mutation of cis-regulatory elements (CREs) within the ACRs can change the balance of the expression level and/or tissue specificity of the duplicated genes. Analysis of DNA sequences associated with ACRs revealed that the extensive sequence rearrangement after the WGD reshaped the CRE landscape, which appears to play a key role in the transcriptional divergence of duplicated genes in soybean. This may represent a general mechanism for transcriptional divergence of duplicated genes in polyploids that lack subgenome dominance.
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Affiliation(s)
- Chao Fang
- Department of Plant Biology, Michigan State University, East Lansing, MI48824
| | - Mingyu Yang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin150081, China
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin150030, China
| | - Yuecheng Tang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin150081, China
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin150030, China
| | - Ling Zhang
- Agro-Biotechnology Research Institute, Jilin Academy of Agricultural Sciences, Changchun130033, China
| | - Hainan Zhao
- Department of Plant Biology, Michigan State University, East Lansing, MI48824
| | - Hejia Ni
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin150030, China
| | - Qingshan Chen
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin150030, China
| | - Fanli Meng
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin150081, China
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI48824
- Department of Horticulture, Michigan State University, East Lansing, MI48824
- Michigan State University AgBioResearch, East Lansing, MI48824
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47
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Pajuste FD, Remm M. GeneToCN: an alignment-free method for gene copy number estimation directly from next-generation sequencing reads. Sci Rep 2023; 13:17765. [PMID: 37853040 PMCID: PMC10584998 DOI: 10.1038/s41598-023-44636-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
Genomes exhibit large regions with segmental copy number variation, many of which include entire genes and are multiallelic. We have developed a computational method GeneToCN that counts the frequencies of gene-specific k-mers in FASTQ files and uses this information to infer copy number of the gene. We validated the copy number predictions for amylase genes (AMY1, AMY2A, AMY2B) using experimental data from digital droplet PCR (ddPCR) on 39 individuals and observed a strong correlation (R = 0.99) between GeneToCN predictions and experimentally determined copy numbers. An additional validation on FCGR3 genes showed a higher concordance for FCGR3A compared to two other methods, but reduced accuracy for FCGR3B. We further tested the method on three different genomic regions (SMN, NPY4R, and LPA Kringle IV-2 domain). Predicted copy number distributions of these genes in a set of 500 individuals from the Estonian Biobank were in good agreement with the previously published studies. In addition, we investigated the possibility to use GeneToCN on sequencing data generated by different technologies by comparing copy number predictions from Illumina, PacBio, and Oxford Nanopore data of the same sample. Despite the differences in variability of k-mer frequencies, all three sequencing technologies give similar predictions with GeneToCN.
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Affiliation(s)
- Fanny-Dhelia Pajuste
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Str., 51010, Tartu, Estonia.
| | - Maido Remm
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Str., 51010, Tartu, Estonia
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48
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Huang Z, Jiang C, Gu J, Uvizl M, Power S, Douglas D, Kacprzyk J. Duplications of Human Longevity-Associated Genes Across Placental Mammals. Genome Biol Evol 2023; 15:evad186. [PMID: 37831410 PMCID: PMC10588791 DOI: 10.1093/gbe/evad186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/31/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023] Open
Abstract
Natural selection has shaped a wide range of lifespans across mammals, with a few long-lived species showing negligible signs of ageing. Approaches used to elucidate the genetic mechanisms underlying mammalian longevity usually involve phylogenetic selection tests on candidate genes, detections of convergent amino acid changes in long-lived lineages, analyses of differential gene expression between age cohorts or species, and measurements of age-related epigenetic changes. However, the link between gene duplication and evolution of mammalian longevity has not been widely investigated. Here, we explored the association between gene duplication and mammalian lifespan by analyzing 287 human longevity-associated genes across 37 placental mammals. We estimated that the expansion rate of these genes is eight times higher than their contraction rate across these 37 species. Using phylogenetic approaches, we identified 43 genes whose duplication levels are significantly correlated with longevity quotients (False Discovery Rate (FDR) < 0.05). In particular, the strong correlation observed for four genes (CREBBP, PIK3R1, HELLS, FOXM1) appears to be driven mainly by their high duplication levels in two ageing extremists, the naked mole rat (Heterocephalus glaber) and the greater mouse-eared bat (Myotis myotis). Further sequence and expression analyses suggest that the gene PIK3R1 may have undergone a convergent duplication event, whereby the similar region of its coding sequence was independently duplicated multiple times in both of these long-lived species. Collectively, this study identified several candidate genes whose duplications may underlie the extreme longevity in mammals, and highlighted the potential role of gene duplication in the evolution of mammalian long lifespans.
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Affiliation(s)
- Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Chongyi Jiang
- Institute of Ecology and Evolution, Friedrich Schiller University, Jena, Germany
| | - Jiayun Gu
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Marek Uvizl
- Department of Zoology, National Museum, Prague, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Sarahjane Power
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Declan Douglas
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Joanna Kacprzyk
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
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49
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Vance Z, McLysaght A. Ohnologs and SSD Paralogs Differ in Genomic and Expression Features Related to Dosage Constraints. Genome Biol Evol 2023; 15:evad174. [PMID: 37776514 PMCID: PMC10563793 DOI: 10.1093/gbe/evad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/02/2023] Open
Abstract
Gene duplication is recognized as a critical process in genome evolution; however, many questions about this process remain unanswered. Although gene duplicability has been observed to differ by duplication mechanism and evolutionary rate, there is so far no broad characterization of its determinants. Many features correlate with this difference in duplicability; however, our ability to exploit these observations to advance our understanding of the role of duplication in evolution is hampered by limitations within existing work. In particular, the existence of methodological differences across studies impedes meaningful comparison. Here, we use consistent definitions of duplicability in the human lineage to explore these associations, allow resolution of the impact of confounding factors, and define the overall relevance of individual features. Using a classifier approach and controlling for the confounding effect of duplicate longevity, we find a subset of gene features important in differentiating genes duplicable by small-scale duplication from those duplicable by whole-genome duplication, revealing critical roles for gene dosage and expression costs in duplicability. We further delve into patterns of functional enrichment and find a lack of constraint on duplicate retention in any context for genes duplicable by small-scale duplication.
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Affiliation(s)
- Zoe Vance
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
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Carscadden KA, Batstone RT, Hauser FE. Origins and evolution of biological novelty. Biol Rev Camb Philos Soc 2023; 98:1472-1491. [PMID: 37056155 DOI: 10.1111/brv.12963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
Understanding the origins and impacts of novel traits has been a perennial interest in many realms of ecology and evolutionary biology. Here, we build on previous evolutionary and philosophical treatments of this subject to encompass novelties across biological scales and eco-evolutionary perspectives. By defining novelties as new features at one biological scale that have emergent effects at other biological scales, we incorporate many forms of novelty that have previously been treated in isolation (such as novelty from genetic mutations, new developmental pathways, new morphological features, and new species). Our perspective is based on the fundamental idea that the emergence of a novelty, at any biological scale, depends on its environmental and genetic context. Through this lens, we outline a broad array of generative mechanisms underlying novelty and highlight how genomic tools are transforming our understanding of the origins of novelty. Lastly, we present several case studies to illustrate how novelties across biological scales and systems can be understood based on common mechanisms of change and their environmental and genetic contexts. Specifically, we highlight how gene duplication contributes to the evolution of new complex structures in visual systems; how genetic exchange in symbiosis alters functions of both host and symbiont, resulting in a novel organism; and how hybridisation between species can generate new species with new niches.
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Affiliation(s)
- Kelly A Carscadden
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant St, Boulder, CO, 80309, USA
| | - Rebecca T Batstone
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Frances E Hauser
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
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