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Aggarwal M, Periwal V. Dory: Computation of persistence diagrams up to dimension two for Vietoris-Rips filtrations of large data sets. J Comput Sci 2024; 79:102290. [PMID: 38774487 PMCID: PMC11105796 DOI: 10.1016/j.jocs.2024.102290] [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] [Indexed: 05/24/2024]
Abstract
Persistent homology (PH) is an approach to topological data analysis (TDA) that computes multi-scale topologically invariant properties of high-dimensional data that are robust to noise. While PH has revealed useful patterns across various applications, computational requirements have limited applications to small data sets of a few thousand points. We present Dory, an efficient and scalable algorithm that can compute the persistent homology of sparse Vietoris-Rips complexes on larger data sets, up to and including dimension two and over the field Z 2 . As an application, we compute the PH of the human genome at high resolution as revealed by a genome-wide Hi-C data set containing approximately three million points. Extant algorithms were unable to process it, whereas Dory processed it within five minutes, using less than five GB of memory. Results show that the topology of the human genome changes significantly upon treatment with auxin, a molecule that degrades cohesin, corroborating the hypothesis that cohesin plays a crucial role in loop formation in DNA.
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Affiliation(s)
- Manu Aggarwal
- Laboratory of Biological Modeling, NIDDK, National Institutes of Health, 31 Center Dr, Bethesda, 20892, MD, United States
| | - Vipul Periwal
- Laboratory of Biological Modeling, NIDDK, National Institutes of Health, 31 Center Dr, Bethesda, 20892, MD, United States
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2
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Roman-Reyna V, Sharma A, Toth H, Konkel Z, Omiotek N, Murthy S, Faith S, Slot J, Peduto Hand F, Goss EM, Jacobs JM. Live tracking of a plant pathogen outbreak reveals rapid and successive, multidecade plasmid reduction. mSystems 2024; 9:e0079523. [PMID: 38275768 PMCID: PMC10878067 DOI: 10.1128/msystems.00795-23] [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: 07/27/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Quickly understanding the genomic changes that lead to pathogen emergence is necessary to launch mitigation efforts and reduce harm. In this study, we tracked in real time a 2022 bacterial plant disease outbreak in U.S. geraniums (Pelargonium × hortorum) caused by Xhp2022, a novel lineage of Xanthomonas hortorum. Genomes from 31 Xhp2022 isolates from seven states showed limited chromosomal variation and all contained a single plasmid (p93). Time tree and single nucleotide polymorphism whole-genome analysis estimated that Xhp2022 emerged within the last decade. The phylogenomic analysis determined that p93 resulted from the cointegration of three plasmids (p31, p45, and p66) found sporadically across isolates from previous outbreaks. Although p93 had a 49 kb nucleotide reduction, it retained putative fitness genes, which became predominant in the 2022 outbreak. Overall, we demonstrated, through rapid whole-genome sequencing and analysis, a recent, traceable event of genome reduction for niche adaptation typically observed over millennia in obligate and fastidious pathogens.IMPORTANCEThe geranium industry, valued at $4 million annually, faces an ongoing Xanthomonas hortorum pv. pelargonii (Xhp) pathogen outbreak. To track and describe the outbreak, we compared the genome structure across historical and globally distributed isolates. Our research revealed Xhp population has not had chromosome rearrangements since 1974 and has three distinct plasmids. In 2012, we found all three plasmids in individual Xhp isolates. However, in 2022, the three plasmids co-integrated into one plasmid named p93. p93 retained putative fitness genes but lost extraneous genomic material. Our findings show that the 2022 strain group of the bacterial plant pathogen Xanthomonas hortorum underwent a plasmid reduction. We also observed several Xanthomonas species from different years, hosts, and continents have similar plasmids to p93, possibly due to shared agricultural settings. We noticed parallels between genome efficiency and reduction that we see across millennia with obligate parasites with increased niche specificity.
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Affiliation(s)
- Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Anuj Sharma
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Hannah Toth
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Zachary Konkel
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Nicolle Omiotek
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Shashanka Murthy
- Applied Microbiology Services Laboratory, The Ohio State University, Columbus, Ohio, USA
| | - Seth Faith
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Applied Microbiology Services Laboratory, The Ohio State University, Columbus, Ohio, USA
| | - Jason Slot
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
| | | | - Erica M. Goss
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Jonathan M. Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
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Wang H, Zhang Y, Zhang L, Wang J, Guo H, Zong J, Chen J, Li D, Li L, Liu J, Li J. Molecular Characterization and Phylogenetic Analysis of Centipedegrass [ Eremochloa ophiuroides (Munro) Hack.] Based on the Complete Chloroplast Genome Sequence. Curr Issues Mol Biol 2024; 46:1635-1650. [PMID: 38392224 PMCID: PMC10888139 DOI: 10.3390/cimb46020106] [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: 01/08/2024] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024] Open
Abstract
Centipedegrass (Eremochloa ophiuroides) is an important warm-season grass plant used as a turfgrass as well as pasture grass in tropical and subtropical regions, with wide application in land surface greening and soil conservation in South China and southern United States. In this study, the complete cp genome of E. ophiuroides was assembled using high-throughput Illumina sequencing technology. The circle pseudomolecule for E. ophiuroides cp genome is 139,107 bp in length, with a quadripartite structure consisting of a large single copyregion of 82,081 bp and a small single copy region of 12,566 bp separated by a pair of inverted repeat regions of 22,230 bp each. The overall A + T content of the whole genome is 61.60%, showing an asymmetric nucleotide composition. The genome encodes a total of 131 gene species, composed of 20 duplicated genes within the IR regions and 111 unique genes comprising 77 protein-coding genes, 30 transfer RNA genes, and 4 ribosome RNA genes. The complete cp genome sequence contains 51 long repeats and 197 simple sequence repeats, and a high degree of collinearity among E. ophiuroide and other Gramineae plants was disclosed. Phylogenetic analysis showed E. ophiuroides, together with the other two Eremochloa species, is closely related to Mnesithea helferi within the subtribe Rottboelliinae. These findings will be beneficial for the classification and identification of the Eremochloa taxa, phylogenetic resolution, novel gene discovery, and functional genomic studies for the genus Eremochloa.
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Affiliation(s)
- Haoran Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Yuan Zhang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Ling Zhang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jingjing Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Hailin Guo
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Junqin Zong
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jingbo Chen
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Dandan Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Ling Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jianxiu Liu
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jianjian Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
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Xu KL, Zhang ZM, Fang WL, Wang YD, Jin HY, Wei F, Ma SC. Comparative analyses of complete chloroplast genomes reveal interspecific difference and intraspecific variation of Tripterygium genus. Front Plant Sci 2024; 14:1288943. [PMID: 38264022 PMCID: PMC10803662 DOI: 10.3389/fpls.2023.1288943] [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: 09/05/2023] [Accepted: 12/14/2023] [Indexed: 01/25/2024]
Abstract
The genus Tripterygium was of great medicinal value and attracted much attention on the taxonomic study using morphological and molecular methods. In this study, we assembled 12 chloroplast genomes of Tripterygium to reveal interspecific difference and intraspecific variation. The sequence length (156,692-157,061 bp) and structure of Tripterygium were conserved. Comparative analyses presented abundant variable regions for further study. Meanwhile, we determined the ndhB gene under positive selection through adaptive evolution analysis. And the phylogenetic analyses based on 15 chloroplast genomes supported the monophyly of Tripterygium hypoglaucum and the potential sister relationship between Tripterygium wilfordii and Tripterygium regelii. Molecular dating analysis indicated that the divergence time within Tripterygium was approximately 5.99 Ma (95% HPD = 3.11-8.68 Ma). The results in our study provided new insights into the taxonomy, evolution process, and phylogenetic construction of Tripterygium using complete plastid genomes.
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Affiliation(s)
- Kai-Ling Xu
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Zhong-Mou Zhang
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Wen-Liang Fang
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Ya-Dan Wang
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Hong-Yu Jin
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Feng Wei
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Shuang-Cheng Ma
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
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Xiang KL, Mao W, Peng HW, Erst AS, Yang YX, He WC, Wu ZQ. Corrigendum: Organization, phylogenetic marker exploitation, and gene evolution in the plastome of Thalictrum (Ranunculaceae). Front Plant Sci 2023; 14:1303516. [PMID: 37920717 PMCID: PMC10619843 DOI: 10.3389/fpls.2023.1303516] [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: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 11/04/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2022.897843.].
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Affiliation(s)
- Kun-Li Xiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wei Mao
- College of Ecology and Environment, Hainan University, Haikou, China
| | - Huan-Wen Peng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Andrey S. Erst
- Central Siberian Botanical Garden, Russian Academy of Sciences, Novosibirsk, Russia
- Laboratory Herbarium (TK), Tomsk State University, Tomsk, Russia
| | - Ying-Xue Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wen-Chuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhi-Qiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan, China
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Díez Menéndez C, Poczai P, Williams B, Myllys L, Amiryousefi A. IRplus: An Augmented Tool to Detect Inverted Repeats in Plastid Genomes. Genome Biol Evol 2023; 15:evad177. [PMID: 37793175 PMCID: PMC10581538 DOI: 10.1093/gbe/evad177] [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: 02/28/2023] [Revised: 09/20/2023] [Accepted: 09/28/2023] [Indexed: 10/06/2023] Open
Abstract
High-throughput sequencing methods have increased the accessibility of plastid genomes, which are crucial for clarifying phylogenetic relationships. Current large sequencing efforts require software tools for routine display of their distinctive quadripartite structure, which is denoted by four junction sites. By concentrating on these junctions and their close vicinity, IRscope has emerged as the standard tool for detection of this structure and creating simplified comparative graphical maps of plastid genomes. Here, we provide an augmented version (IRplus) that encompasses a novel set of functions such as integrated error detection, flexible color schemes, and an upgraded method to detect inverted repeats in genomic sequences. Spanning across the plant tree of life, IRplus allows the quick visualization of various sets of plastid genomes and features, next to smooth interoperability with other widely used annotation file formats and platforms. The IRplus can be accessed at https://irscope.shinyapps.io/IRplus/, and source codes are freely available at https://github.com/AmiryousefiLab/IRplus.
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Affiliation(s)
| | - Peter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Museomics Research Group, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Bernardo Williams
- Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Leena Myllys
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Ali Amiryousefi
- Systems Oncology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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Vlasova NN, Chernykh OY, Krivonos RA, Verkhovsky OA, Aliper TI, Anoyatbekova AM, Zhukova EV, Kucheruk OD, Yuzhakov AG, Gulyukin MI, Gulyukin AM. [Adaptation of african swine fever virus (Asfarviridae: Asfivirus)to growth in the continuous culture PPK-66b cells by the method of accelerated passaging]. Vopr Virusol 2023; 68:334-342. [PMID: 38156590 DOI: 10.36233/0507-4088-186] [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: 07/25/2023] [Indexed: 12/30/2023]
Abstract
INTRODUCTION African swine fever virus (ASF) is a large, enveloped virus with an icosahedral capsid morphology and a double-stranded DNA genome ranging in size from 170 to 190 kb. The replication cycle proceeds in two phases, the early phase lasting 4-6 hours and the late 8-20 hours after infection. The adaptation of the ASF virus to growth in continuous cell lines makes efficient and reliable genetic analysis and more accurate interpretation of its results. OBJECTIVE Adaptation of a new isolate of the ASF virus to growth in a continuous cell line by the method of accelerated passages and preliminary genetic analysis of the resulting strain. MATERIALS AND METHODS For virus isolation and passaging of the ASF virus, a porcine leukocyte cell culture (PL) and continuous cell cultures of porcine origin (ST, PK, PPK-66b) were used with Eagle MEM and HLA essential media with 10% porcine or fetal serum. RESULTS The article presents data on the isolation and analysis of the changes in the reproductive properties of a new African swine fever (ASF) virus isolate in the process of adaptation to growth in a continuous piglet kidney cell culture clone b (PPK-66b). The current state of the problem of cultivation of the ASF virus, the features of its reproduction, and the basis of the genetic differentiation of its isolates are described in detail. Understanding the uniqueness of the nature of the ASF virus determined the approaches to the processes of its cultivation and adaptation. In this regard, the results of studies of cultural properties, and analysis of the nucleotide sequence of 6 genes of the new isolate, as well as phylogenetic analysis of these genes with already known strains and isolates of the ASF virus are presented. CONCLUSION A new strain obtained in the process of cell adaptation of ASVF/Znaury/PPK-23 ASF virus by the accelerated passaging method reaches a high level of reproduction in 72 hours with an accumulation titer of 7.07 lg HAdE50/cm3. Primary genetic analysis allowed to establish the main phylogenetic relationships of the newly isolated strain with previously known variants of the current ASF panzootic.
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Affiliation(s)
- N N Vlasova
- Federal Scientific Center - All-Russian Research Institute of Experimental Veterinary Medicine named after V.I. K.I. Scriabin and Ya.R. Kovalenko of the Russian Academy of Sciences
| | - O Y Chernykh
- Department of Veterinary Medicine of the Krasnodar Territory
| | - R A Krivonos
- Department of Veterinary Medicine of the Krasnodar Territory
| | - O A Verkhovsky
- Research Institute for Diagnosis and Prevention of Human and Animal Diseases
| | - T I Aliper
- Federal Scientific Center - All-Russian Research Institute of Experimental Veterinary Medicine named after V.I. K.I. Scriabin and Ya.R. Kovalenko of the Russian Academy of Sciences
| | - A M Anoyatbekova
- Federal Scientific Center - All-Russian Research Institute of Experimental Veterinary Medicine named after V.I. K.I. Scriabin and Ya.R. Kovalenko of the Russian Academy of Sciences
| | - E V Zhukova
- Federal Scientific Center - All-Russian Research Institute of Experimental Veterinary Medicine named after V.I. K.I. Scriabin and Ya.R. Kovalenko of the Russian Academy of Sciences
| | - O D Kucheruk
- Federal Scientific Center - All-Russian Research Institute of Experimental Veterinary Medicine named after V.I. K.I. Scriabin and Ya.R. Kovalenko of the Russian Academy of Sciences
| | - A G Yuzhakov
- Federal Scientific Center - All-Russian Research Institute of Experimental Veterinary Medicine named after V.I. K.I. Scriabin and Ya.R. Kovalenko of the Russian Academy of Sciences
| | - M I Gulyukin
- Federal Scientific Center - All-Russian Research Institute of Experimental Veterinary Medicine named after V.I. K.I. Scriabin and Ya.R. Kovalenko of the Russian Academy of Sciences
| | - A M Gulyukin
- Federal Scientific Center - All-Russian Research Institute of Experimental Veterinary Medicine named after V.I. K.I. Scriabin and Ya.R. Kovalenko of the Russian Academy of Sciences
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Mattick JS. A Kuhnian revolution in molecular biology: Most genes in complex organisms express regulatory RNAs. Bioessays 2023; 45:e2300080. [PMID: 37318305 DOI: 10.1002/bies.202300080] [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: 05/08/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023]
Abstract
Thomas Kuhn described the progress of science as comprising occasional paradigm shifts separated by interludes of 'normal science'. The paradigm that has held sway since the inception of molecular biology is that genes (mainly) encode proteins. In parallel, theoreticians posited that mutation is random, inferred that most of the genome in complex organisms is non-functional, and asserted that somatic information is not communicated to the germline. However, many anomalies appeared, particularly in plants and animals: the strange genetic phenomena of paramutation and transvection; introns; repetitive sequences; a complex epigenome; lack of scaling of (protein-coding) genes and increase in 'noncoding' sequences with developmental complexity; genetic loci termed 'enhancers' that control spatiotemporal gene expression patterns during development; and a plethora of 'intergenic', overlapping, antisense and intronic transcripts. These observations suggest that the original conception of genetic information was deficient and that most genes in complex organisms specify regulatory RNAs, some of which convey intergenerational information. Also see the video abstract here: https://youtu.be/qxeGwahBANw.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, New South Wales, Australia
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Xu XM, Wei Z, Sun JZ, Zhao QF, Lu Y, Wang ZL, Zhu SX. Phylogeny of Leontopodium (Asteraceae) in China-with a reference to plastid genome and nuclear ribosomal DNA. Front Plant Sci 2023; 14:1163065. [PMID: 37583593 PMCID: PMC10425225 DOI: 10.3389/fpls.2023.1163065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023]
Abstract
The infrageneric taxonomy system, species delimitation, and interspecies systematic relationships of Leontopodium remain controversial and complex. However, only a few studies have focused on the molecular phylogeny of this genus. In this study, the characteristics of 43 chloroplast genomes of Leontopodium and its closely related genera were analyzed. Phylogenetic relationships were inferred based on chloroplast genomes and nuclear ribosomal DNA (nrDNA). Finally, together with the morphological characteristics, the relationships within Leontopodium were identified and discussed. The results showed that the chloroplast genomes of Filago, Gamochaeta, and Leontopodium were well-conserved in terms of gene number, gene order, and GC content. The most remarkable differences among the three genera were the length of the complete chloroplast genome, large single-copy region, small single-copy region, and inverted repeat region. In addition, the chloroplast genome structure of Leontopodium exhibited high consistency and was obviously different from that of Filago and Gamochaeta in some regions, such as matk, trnK (UUU)-rps16, petN-psbM, and trnE (UUC)-rpoB. All the phylogenetic trees indicated that Leontopodium was monophyletic. Except for the subgeneric level, our molecular phylogenetic results were inconsistent with the previous taxonomic system, which was based on morphological characteristics. Nevertheless, we found that the characteristics of the leaf base, stem types, and carpopodium base were phylogenetically correlated and may have potential value in the taxonomic study of Leontopodium. In the phylogenetic trees inferred using complete chloroplast genomes, the subgen. Leontopodium was divided into two clades (Clades 1 and 2), with most species in Clade 1 having herbaceous stems, amplexicaul, or sheathed leaves, and constricted carpopodium; most species in Clade 2 had woody stems, not amplexicaul and sheathed leaves, and not constricted carpopodium.
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Affiliation(s)
| | | | | | | | | | | | - Shi-Xin Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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10
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Cheng CHC, Rivera-Colón AG, Minhas BF, Wilson L, Rayamajhi N, Vargas-Chacoff L, Catchen JM. Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus-The Closest Ancestral Proxy of Antarctic Cryonotothenioids. Genes (Basel) 2023; 14:1196. [PMID: 37372376 DOI: 10.3390/genes14061196] [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: 04/18/2023] [Revised: 05/26/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
The basal South American notothenioid Eleginops maclovinus (Patagonia blennie or róbalo) occupies a uniquely important phylogenetic position in Notothenioidei as the singular closest sister species to the Antarctic cryonotothenioid fishes. Its genome and the traits encoded therein would be the nearest representatives of the temperate ancestor from which the Antarctic clade arose, providing an ancestral reference for deducing polar derived changes. In this study, we generated a gene- and chromosome-complete assembly of the E. maclovinus genome using long read sequencing and HiC scaffolding. We compared its genome architecture with the more basally divergent Cottoperca gobio and the derived genomes of nine cryonotothenioids representing all five Antarctic families. We also reconstructed a notothenioid phylogeny using 2918 proteins of single-copy orthologous genes from these genomes that reaffirmed E. maclovinus' phylogenetic position. We additionally curated E. maclovinus' repertoire of circadian rhythm genes, ascertained their functionality by transcriptome sequencing, and compared its pattern of gene retention with C. gobio and the derived cryonotothenioids. Through reconstructing circadian gene trees, we also assessed the potential role of the retained genes in cryonotothenioids by referencing to the functions of the human orthologs. Our results found E. maclovinus to share greater conservation with the Antarctic clade, solidifying its evolutionary status as the direct sister and best suited ancestral proxy of cryonotothenioids. The high-quality genome of E. maclovinus will facilitate inquiries into cold derived traits in temperate to polar evolution, and conversely on the paths of readaptation to non-freezing habitats in various secondarily temperate cryonotothenioids through comparative genomic analyses.
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Affiliation(s)
- Chi-Hing Christina Cheng
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Angel G Rivera-Colón
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Bushra Fazal Minhas
- Informatics Program, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Loralee Wilson
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Niraj Rayamajhi
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Luis Vargas-Chacoff
- Laboratorio de Fisiología de Peces, Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia 5090000, Chile
- Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia 5090000, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Universidad Austral de Chile, Valdivia 5090000, Chile
| | - Julian M Catchen
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
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11
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Bakkas J, Hanine M, Chekry A, Gounane S, de la Torre Díez I, Lipari V, López NMM, Ashraf I. SARSMutOnto: An Ontology for SARS-CoV-2 Lineages and Mutations. Viruses 2023; 15:v15020505. [PMID: 36851719 PMCID: PMC9967353 DOI: 10.3390/v15020505] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
Mutations allow viruses to continuously evolve by changing their genetic code to adapt to the hosts they infect. It is an adaptive and evolutionary mechanism that helps viruses acquire characteristics favoring their survival and propagation. The COVID-19 pandemic declared by the WHO in March 2020 is caused by the SARS-CoV-2 virus. The non-stop adaptive mutations of this virus and the emergence of several variants over time with characteristics favoring their spread constitute one of the biggest obstacles that researchers face in controlling this pandemic. Understanding the mutation mechanism allows for the adoption of anticipatory measures and the proposal of strategies to control its propagation. In this study, we focus on the mutations of this virus, and we propose the SARSMutOnto ontology to model SARS-CoV-2 mutations reported by Pango researchers. A detailed description is given for each mutation. The genes where the mutations occur and the genomic structure of this virus are also included. The sub-lineages and the recombinant sub-lineages resulting from these mutations are additionally represented while maintaining their hierarchy. We developed a Python-based tool to automatically generate this ontology from various published Pango source files. At the end of this paper, we provide some examples of SPARQL queries that can be used to exploit this ontology. SARSMutOnto might become a 'wet bench' machine learning tool for predicting likely future mutations based on previous mutations.
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Affiliation(s)
- Jamal Bakkas
- LAPSSII Laboratory, Graduate School of Technology, Cadi Ayyad University, Safi 46000, Morocco
| | - Mohamed Hanine
- Department of Telecommunications, Networks, and Informatics, LTI Laboratory, ENSA, Chouaib Doukkali University, Eljadida 24000, Morocco
| | - Abderrahman Chekry
- LAPSSII Laboratory, Graduate School of Technology, Cadi Ayyad University, Safi 46000, Morocco
| | - Said Gounane
- MIMSC Laboratory, Graduate School of Technology, Cadi Ayyad University, Essaouira 44000, Morocco
| | - Isabel de la Torre Díez
- Department of Signal Theory and Communications and Telematic Engineering, University of Valladolid, Paseo de Belén, 15, 47011 Valladolid, Spain
| | - Vivian Lipari
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, Isabel Torres 21, 39011 Santander, Spain
- Department of Project Management, Universidad Internacional Iberoamericana Campeche, Mexico City 24560, Mexico
- Fundación Universitaria Internacional de Colombia Bogotá, Bogotá 11001, Colombia
| | - Nohora Milena Martínez López
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, Isabel Torres 21, 39011 Santander, Spain
- Research Group on Foods, Nutritional Biochemistry and Health Universidad Internacional Iberoamericana, Arecibo, PR 00613, USA
- Research Group on Foods, Nutritional Biochemistry and Health Universidade Internacional do Cuanza, Cuito EN250, Angola
| | - Imran Ashraf
- Department of Information and Communication Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
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12
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Ruan C, Morton BR. Evidence for Strand Asymmetry in Different Plastid Genomes. Genes (Basel) 2023; 14. [PMID: 36833247 DOI: 10.3390/genes14020320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/28/2023] Open
Abstract
A common genome composition pattern in eubacteria is an asymmetry between the leading and lagging strands resulting in opposite skew patterns in the two replichores that lie between the origin and terminus of replication. Although this pattern has been reported for a couple of isolated plastid genomes, it is not clear how widespread it is overall in this chromosome. Using a random walk approach, we examine plastid genomes outside of the land plants, which are excluded since they are known not to initiate replication at a single site, for such a pattern of asymmetry. Although it is not a common feature, we find that it is detectable in the plastid genome of species from several diverse lineages. The euglenozoa in particular show a strong skew pattern as do several rhodophytes. There is a weaker pattern in some chlorophytes but it is not apparent in other lineages. The ramifications of this for analyses of plastid evolution are discussed.
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13
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Tarkington J, Zhang H, Azevedo RBR, Zufall RA. Sex, amitosis, and evolvability in the ciliate Tetrahymena thermophila. Evolution 2023; 77:36-48. [PMID: 36622280 DOI: 10.1093/evolut/qpac031] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 09/07/2022] [Accepted: 11/17/2022] [Indexed: 01/10/2023]
Abstract
Understanding the mechanisms that generate genetic variation, and thus contribute to the process of adaptation, is a major goal of evolutionary biology. Mutation and genetic exchange have been well studied as mechanisms to generate genetic variation. However, there are additional factors, such as genome architecture, that may also impact the amount of genetic variation in some populations, and the extent to which these variation generating mechanisms are themselves shaped by natural selection is still an open question. To test the effect of genome architecture on the generation of genetic variation, and hence evolvability, we studied Tetrahymena thermophila, a ciliate with an unusual genome structure and mechanism of nuclear division, called amitosis, whereby homologous chromosomes are randomly distributed to daughter cells. Amitosis leads to genetic variation among the asexual descendants of a newly produced sexual progeny because different progeny cells will contain different combinations of parental alleles. We hypothesize that amitosis thus increases the evolvability of newly produced sexual progeny relative to their unmated parents and species that undergo mitosis. To test this hypothesis, we used experimental evolution and simulations to compare the rate of adaptation in T. thermophila populations founded by a single sexual progeny to parental populations that had not had sex in many generations. The populations founded by a sexual progeny adapted more quickly than parental populations in both laboratory populations and simulated populations. This suggests that the additional genetic variation generated by amitosis of a heterozygote can increase the rate of adaptation following sex and may help explain the evolutionary success of the unusual genetic architecture of Tetrahymena and ciliates more generally.
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Affiliation(s)
- Jason Tarkington
- Department of Genetics, Stanford University, Stanford, CA, United States
| | - Hao Zhang
- Department of Genetics, Stanford University, Stanford, CA, United States
| | | | - Rebecca A Zufall
- Department of Genetics, Stanford University, Stanford, CA, United States
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14
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Wei L, Wang HX, Chen DJ, Ke XR, Zhu ZX, Wang HF. The complete plastome sequence of Artocarpus altilis (Parkinson ex F.A. Zorn) Fosberg, (Moraceae). Mitochondrial DNA B Resour 2023; 8:154-156. [PMID: 36685647 PMCID: PMC9848291 DOI: 10.1080/23802359.2022.2163595] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Artocarpus altilis (Parkinson ex F.A. Zorn) Fosberg is native to the Pacific Islands, India, and the Philippines. It is also cultivated in Taiwan and Hainan. The complete plastome of the species was assembled and annotated in this study. The circular genome was 160,184 bp in size, presenting a typical quadripartite structure including two inverted repeats (IRs) of 25,734 bp, a large single-copy (LSC) of 88,791 bp, and a small single-copy (SSC) of 19,925 bp. The genome contained 132 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The total G/C content of complete plastome was 36.0%, with the corresponding values of the LSC, SSC, and IR being 33.7%, 28.8%, and 42.7%, respectively. The complete plastome sequence of A. altilis (Parkinson ex F.A. Zorn) Fosberg will make contributions to the conservation genetics of this species as well as to phylogenetic studies of Moraceae.
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Affiliation(s)
- Lv Wei
- College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Hong-Xin Wang
- College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China,Zhai Mingguo Academician Work Station, Sanya University, Sanya, China
| | - Da-Juan Chen
- College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Xiu-Rong Ke
- College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Zhi-Xin Zhu
- College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Hua-Feng Wang
- College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China,Sanya Nanfan Research Institute of Hainan University, Sanya, Hainan, China,CONTACT Hua-Feng Wang College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
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15
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Liu J, Yang Y, Yan Z, Wang H, Bai M, Shi C, Li J. Analysis of the Mitogenomes of Two Helotid Species Provides New Insights into the Phylogenetic Relationship of the Basal Cucujoidea (Insecta: Coleoptera). Biology (Basel) 2023; 12:biology12010135. [PMID: 36671827 PMCID: PMC9855730 DOI: 10.3390/biology12010135] [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: 12/14/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023]
Abstract
Helotid beetles are commonly found in places where sap flows from tree trunks and in crevices in bark. The Helotidae family is a rare and primitive group of Cucujoidea. To date, no complete mitochondrial (mt) genome has been sequenced for this family. To better understand the characteristics of the mt genome and the evolution of Cucujoidea, we sequenced and annotated the complete mt genomes of Helota thoracica (Ritsema, 1895) and Helota yehi Lee, 2017 using next-generation sequencing. These are the first record of Helotidae mt genomes. The RNA secondary structures of both species were also predicted in this study. The mt genomes of H. thoracica and H. yehi are circular, with total lengths of 16,112 bp and 16,401 bp, respectively. After comparing the mt genomes of H. thoracica and H. yehi, we observed the gene arrangement, codon usage patterns, base content, and RNA secondary structures of both species to be similar, which has also been noted in other Coleoptera insects. The nucleotide sequence of the coding regions and the control region has small differences. The phylogenetic analysis indicated that Helotidae and Protocucujidae are sister groups and revealed the relationship between seven families; however, the validity of the two series (Erotylid series and Nitidulid series) as larger groups in the superfamily was not supported. The mt phylogenomic relationships have strong statistical support. Therefore, the division of Cucujoidea into series should be re-examined. Our results will provide a better understanding of the mt genome and phylogeny of Helotidae and Cucujoidea and will provide valuable molecular markers for further genetic studies.
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Affiliation(s)
- Jing Liu
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Yuhang Yang
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Zihan Yan
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Haishan Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Ming Bai
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (M.B.); (J.L.)
| | - Chengmin Shi
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Jing Li
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
- Correspondence: (M.B.); (J.L.)
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16
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Roy SW, Gozashti L, Bowser BA, Weinstein BN, Larue GE, Corbett-Detig R. Intron-rich dinoflagellate genomes driven by Introner transposable elements of unprecedented diversity. Curr Biol 2023; 33:189-196.e4. [PMID: 36543167 DOI: 10.1016/j.cub.2022.11.046] [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: 10/14/2020] [Revised: 06/18/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022]
Abstract
Spliceosomal introns, which interrupt nuclear genes, are ubiquitous features of eukaryotic nuclear genes.1 Spliceosomal intron evolution is complex, with different lineages ranging from virtually zero to thousands of newly created introns.2,3,4,5 This punctate phylogenetic distribution could be explained if intron creation is driven by specialized transposable elements ("Introners"), with Introner-containing lineages undergoing frequent intron gain.6,7,8,9,10 Fragmentation of nuclear genes by spliceosomal introns reaches its apex in dinoflagellates, which have some twenty introns per gene11,12; however, little is known about dinoflagellate intron evolution. We reconstructed intron evolution in five dinoflagellate genomes, revealing a dynamic history of intron gain. We find evidence for historical creation of introns in all five species and identify recently active Introners in 4/5 studied species. In one species, Polarella glacialis, we find an unprecedented diversity of Introners, with recent Introner insertion leading to creation of some 12,253 introns, and with 15 separate families of Introners accounting for at least 100 introns each. These Introner families show diverse mechanisms of moblization and intron creation. Comparison within and between Introner families provides evidence that biases in the so-called intron phase, intron position relative to codon periodicity, could be driven by Introner insertion site requirements.9,13,14 Finally, we report additional transformations of the spliceosomal system in dinoflagellates, including widespread loss of ancestral introns, and novelties of tolerated and favored donor sequence motifs. These results reveal unappreciated diversity of intron-creating elements and spliceosomal evolutionary capacity and highlight the complex evolutionary dependencies shaping genome structures.
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Affiliation(s)
- Scott William Roy
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA; Department of Molecular and Cell Biology, University of California, Merced, 5200 North Lake Road, Merced, CA 95343, USA.
| | - Landen Gozashti
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bradley A Bowser
- Department of Molecular and Cell Biology, University of California, Merced, 5200 North Lake Road, Merced, CA 95343, USA
| | - Brooke N Weinstein
- Department of Molecular and Cell Biology, University of California, Merced, 5200 North Lake Road, Merced, CA 95343, USA
| | - Graham E Larue
- Department of Molecular and Cell Biology, University of California, Merced, 5200 North Lake Road, Merced, CA 95343, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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17
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Jeong DM, Kim HJ, Jeon MS, Yoo SJ, Moon HY, Jeon EJ, Jeon CO, Eyun SI, Kang HA. Genomic and functional features of yeast species in Korean traditional fermented alcoholic beverage and soybean products. FEMS Yeast Res 2023; 23:6958799. [PMID: 36564017 DOI: 10.1093/femsyr/foac066] [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: 09/26/2022] [Revised: 12/10/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022] Open
Abstract
In this review, we describe the genomic and physiological features of the yeast species predominantly isolated from Nuruk, a starter for traditional Korean rice wines, and Jang, a traditional Korean fermented soy product. Nuruk and Jang have several prevalent yeast species, including Saccharomycopsis fibuligera, Hyphopichia burtonii, and Debaryomyces hansenii complex, which belong to the CUG clade showing high osmotic tolerance. Comparative genomics revealed that the interspecies hybridization within yeast species for generating heterozygous diploid genomes occurs frequently as an evolutional strategy in the fermentation environment of Nuruk and Jang. Through gene inventory analysis based on the high-quality reference genome of S. fibuligera, new genes involved in cellulose degradation and volatile aroma biosynthesis and applicable to the production of novel valuable enzymes and chemicals can be discovered. The integrated genomic and transcriptomic analysis of Hyphopichia yeasts, which exhibit strong halotolerance, provides insights into the novel mechanisms of salt and osmo-stress tolerance for survival in fermentation environments with a low-water activity and high-concentration salts. In addition, Jang yeast isolates, such as D. hansenii, show probiotic potential for the industrial application of yeast species beyond fermentation starters to diverse human health sectors.
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Affiliation(s)
- Da Min Jeong
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
| | - Hyeon Jin Kim
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
| | - Min-Seung Jeon
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
| | - Su Jin Yoo
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
| | - Hye Yun Moon
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
| | - Eun-Joo Jeon
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
| | - Che Ok Jeon
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
| | - Seong-Il Eyun
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
| | - Hyun Ah Kang
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
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18
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Gozashti L, Roy SW, Thornlow B, Kramer A, Ares M, Corbett-Detig R. Transposable elements drive intron gain in diverse eukaryotes. Proc Natl Acad Sci U S A 2022; 119:e2209766119. [PMID: 36417430 PMCID: PMC9860276 DOI: 10.1073/pnas.2209766119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/19/2022] [Indexed: 11/24/2022] Open
Abstract
There is massive variation in intron numbers across eukaryotic genomes, yet the major drivers of intron content during evolution remain elusive. Rapid intron loss and gain in some lineages contrast with long-term evolutionary stasis in others. Episodic intron gain could be explained by recently discovered specialized transposons called Introners, but so far Introners are only known from a handful of species. Here, we performed a systematic search across 3,325 eukaryotic genomes and identified 27,563 Introner-derived introns in 175 genomes (5.2%). Species with Introners span remarkable phylogenetic diversity, from animals to basal protists, representing lineages whose last common ancestor dates to over 1.7 billion years ago. Aquatic organisms were 6.5 times more likely to contain Introners than terrestrial organisms. Introners exhibit mechanistic diversity but most are consistent with DNA transposition, indicating that Introners have evolved convergently hundreds of times from nonautonomous transposable elements. Transposable elements and aquatic taxa are associated with high rates of horizontal gene transfer, suggesting that this combination of factors may explain the punctuated and biased diversity of species containing Introners. More generally, our data suggest that Introners may explain the episodic nature of intron gain across the eukaryotic tree of life. These results illuminate the major source of ongoing intron creation in eukaryotic genomes.
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Affiliation(s)
- Landen Gozashti
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA95064
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA95064
| | - Scott W. Roy
- Department of Biology, San Francisco State University, San Francisco, CA94117
| | - Bryan Thornlow
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA95064
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA95064
| | - Alexander Kramer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA95064
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA95064
| | - Manuel Ares
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA95064
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA95064
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA95064
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19
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Li SF, She HB, Yang LL, Lan LN, Zhang XY, Wang LY, Zhang YL, Li N, Deng CL, Qian W, Gao WJ. Impact of LTR-Retrotransposons on Genome Structure, Evolution, and Function in Curcurbitaceae Species. Int J Mol Sci 2022; 23:ijms231710158. [PMID: 36077556 PMCID: PMC9456015 DOI: 10.3390/ijms231710158] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Long terminal repeat (LTR)-retrotransposons (LTR-RTs) comprise a major portion of many plant genomes and may exert a profound impact on genome structure, function, and evolution. Although many studies have focused on these elements in an individual species, their dynamics on a family level remains elusive. Here, we investigated the abundance, evolutionary dynamics, and impact on associated genes of LTR-RTs in 16 species in an economically important plant family, Cucurbitaceae. Results showed that full-length LTR-RT numbers and LTR-RT content varied greatly among different species, and they were highly correlated with genome size. Most of the full-length LTR-RTs were amplified after the speciation event, reflecting the ongoing rapid evolution of these genomes. LTR-RTs highly contributed to genome size variation via species-specific distinct proliferations. The Angela and Tekay lineages with a greater evolutionary age were amplified in Trichosanthes anguina, whereas a recent activity burst of Reina and another ancient round of Tekay activity burst were examined in Sechium edule. In addition, Tekay and Retand lineages belonging to the Gypsy superfamily underwent a recent burst in Gynostemma pentaphyllum. Detailed investigation of genes with intronic and promoter LTR-RT insertion showed diverse functions, but the term of metabolism was enriched in most species. Further gene expression analysis in G.pentaphyllum revealed that the LTR-RTs within introns suppress the corresponding gene expression, whereas the LTR-RTs within promoters exert a complex influence on the downstream gene expression, with the main function of promoting gene expression. This study provides novel insights into the organization, evolution, and function of LTR-RTs in Cucurbitaceae genomes.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Hong-Bing She
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Long-Long Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Li-Na Lan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Xin-Yu Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Li-Ying Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Yu-Lan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Wei Qian
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (W.Q.); (W.-J.G.)
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Correspondence: (W.Q.); (W.-J.G.)
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Munke A, Kimura K, Tomaru Y, Wang H, Yoshida K, Mito S, Hongo Y, Okamoto K. Primordial Capsid and Spooled ssDNA Genome Structures Unravel Ancestral Events of Eukaryotic Viruses. mBio 2022;:e0015622. [PMID: 35856561 DOI: 10.1128/mbio.00156-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Marine algae viruses are important for controlling microorganism communities in the marine ecosystem and played fundamental roles during the early events of viral evolution. Here, we have focused on one major group of marine algae viruses, the single-stranded DNA (ssDNA) viruses from the Bacilladnaviridae family. We present the capsid structure of the bacilladnavirus Chaetoceros tenuissimus DNA virus type II (CtenDNAV-II), determined at 2.4-Å resolution. A structure-based phylogenetic analysis supported the previous theory that bacilladnaviruses have acquired their capsid protein via horizontal gene transfer from a ssRNA virus. The capsid protein contains the widespread virus jelly-roll fold but has additional unique features; a third β-sheet and a long C-terminal tail. Furthermore, a low-resolution reconstruction of the CtenDNAV-II genome revealed a partially spooled structure, an arrangement previously only described for dsRNA and dsDNA viruses. Together, these results exemplify the importance of genetic recombination for the emergence and evolution of ssDNA viruses and provide important insights into the underlying mechanisms that dictate genome organization. IMPORTANCE Single-stranded DNA (ssDNA) viruses are an extremely widespread group of viruses that infect diverse hosts from all three domains of life, consequently having great economic, medical, and ecological importance. In particular, bacilladnaviruses are highly abundant in marine sediments and greatly influence the dynamic appearance and disappearance of certain algae species. Despite the importance of ssDNA viruses and the last couple of years' advancements in cryo-electron microscopy, structural information on the genomes of ssDNA viruses remains limited. This paper describes two important achievements: (i) the first atomic structure of a bacilladnavirus capsid, which revealed that the capsid protein gene presumably was acquired from a ssRNA virus in early evolutionary events; and (ii) the structural organization of a ssDNA genome, which retains a spooled arrangement that previously only been observed for double-stranded viruses.
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21
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Popay TM, Dixon JR. Coming full circle: on the origin and evolution of the looping model for enhancer-promoter communication. J Biol Chem 2022; 298:102117. [PMID: 35691341 PMCID: PMC9283939 DOI: 10.1016/j.jbc.2022.102117] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/05/2022] Open
Abstract
In mammalian organisms, enhancers can regulate transcription from great genomic distances. How enhancers affect distal gene expression has been a major question in the field of gene regulation. One model to explain how enhancers communicate with their target promoters, the chromatin looping model, posits that enhancers and promoters come in close spatial proximity to mediate communication. Chromatin looping has been broadly accepted as a means for enhancer–promoter communication, driven by accumulating in vitro and in vivo evidence. The genome is now known to be folded into a complex 3D arrangement, created and maintained in part by the interplay of the Cohesin complex and the DNA-binding protein CTCF. In the last few years, however, doubt over the relationship between looping and transcriptional activation has emerged, driven by studies finding that only a modest number of genes are perturbed with acute degradation of looping machinery components. In parallel, newer models describing distal enhancer action have also come to prominence. In this article, we explore the emergence and development of the looping model as a means for enhancer–promoter communication and review the contrasting evidence between historical gene-specific and current global data for the role of chromatin looping in transcriptional regulation. We also discuss evidence for alternative models to chromatin looping and their support in the literature. We suggest that, while there is abundant evidence for chromatin looping as a major mechanism for enhancer function, enhancer–promoter communication is likely mediated by more than one mechanism in an enhancer- and context-dependent manner.
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Affiliation(s)
- Tessa M Popay
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jesse R Dixon
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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22
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Xiang KL, Mao W, Peng HW, Erst AS, Yang YX, He WC, Wu ZQ. Organization, Phylogenetic Marker Exploitation, and Gene Evolution in the Plastome of Thalictrum (Ranunculaceae). Front Plant Sci 2022; 13:897843. [PMID: 35668810 PMCID: PMC9166237 DOI: 10.3389/fpls.2022.897843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/11/2022] [Indexed: 05/31/2023]
Abstract
Thalictrum is a phylogenetically and economically important genus in the family Ranunculaceae, but is also regarded as one of the most challengingly difficult in plants for resolving the taxonomical and phylogenetical relationships of constituent taxa within this genus. Here, we sequenced the complete plastid genomes of two Thalictrum species using Illumina sequencing technology via de novo assembly. The two Thalictrum plastomes exhibited circular and typical quadripartite structure that was rather conserved in overall structure and the synteny of gene order. By updating the previously reported plastome annotation of other nine Thalictrum species, we found that the expansion or contraction of the inverted repeat region affect the boundary of the single-copy regions in Thalictrum plastome. We identified eight highly variable noncoding regions-infA-rps8, ccsA-ndhD, trnSUGA-psbZ, trnHGUG-psbA, rpl16-rps3, ndhG-ndhI, ndhD-psaC, and ndhJ-ndhK-that can be further used for molecular identification, phylogenetic, and phylogeographic in different species. Selective pressure and codon usage bias of all the plastid coding genes were also analyzed for the 11 species. Phylogenetic relationships showed Thalictrum is monophyly and divided into two major clades based on 11 Thalictrum plastomes. The availability of these plastomes offers valuable genetic information for accurate identification of species and taxonomy, phylogenetic resolution, and evolutionary studies of Thalictrum, and should assist with exploration and utilization of Thalictrum plants.
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Affiliation(s)
- Kun-Li Xiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wei Mao
- College of Ecology and Environment, Hainan University, Haikou, China
| | - Huan-Wen Peng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Andrey S. Erst
- Central Siberian Botanical Garden, Russian Academy of Sciences, Novosibirsk, Russia
- Laboratory Herbarium (TK), Tomsk State University, Tomsk, Russia
| | - Ying-Xue Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wen-Chuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhi-Qiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan, China
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Rajpal VR, Sharma S, Sehgal D, Singh A, Kumar A, Vaishnavi S, Tiwari M, Bhalla H, Goel S, Raina SN. A comprehensive account of SARS-CoV-2 genome structure, incurred mutations, lineages and COVID-19 vaccination program. Future Virol 2022. [PMID: 35747328 PMCID: PMC9203033 DOI: 10.2217/fvl-2021-0277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 05/26/2022] [Indexed: 12/23/2022]
Abstract
This review collates information on the onset of COVID-19, SARS-CoV-2 genome architecture, emergence of novel viral lineages that drove multiple waves of infection around the world and standard and fast track development of vaccines. With the passage of time, the continuously evolving SARS-CoV-2 has acquired an expanded mutational landscape. The functional characterization of spike protein mutations, the primary target of diagnostics, therapeutics and vaccines has revealed increased transmission, pathogenesis and immune escape potential in the variant lineages of the virus. The incurred mutations have also resulted in substantial viral neutralization escape to vaccines, monoclonal, polyclonal and convalescent antibodies presently in use. The present situation suggests the need for development of precise next-generation vaccines and therapeutics by targeting the more conservative genomic viral regions for providing adequate protection.
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Affiliation(s)
| | - Shashi Sharma
- Virology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - Deepmala Sehgal
- International Maize & Wheat Improvement Center (CIMMYT) Carretera México-Veracruz Km. 45, El Batán, Texcoco, 56237, México
| | - Apekshita Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, Uttar Pradesh, India
| | - Avinash Kumar
- Department of Botany, Vinoba Bhave University, Hazaribag, Jharkhand, 825319, India
| | - Samantha Vaishnavi
- Department of Botany, Central University of Jammu, Rahya Suchani (Bagla), Distt. Samba, Jammu and Kashmir, 181143, India
| | - Mugdha Tiwari
- ICMR-National Institute of Occupational Health (ICMR-NIOH), Meghaninagar, Ahmedabad, 380016, India
| | - Hemal Bhalla
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Shailendra Goel
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, Uttar Pradesh, India
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24
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Yu L, Majerciak V, Zheng ZM. HPV16 and HPV18 Genome Structure, Expression, and Post-Transcriptional Regulation. Int J Mol Sci 2022; 23:ijms23094943. [PMID: 35563334 PMCID: PMC9105396 DOI: 10.3390/ijms23094943] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 12/18/2022] Open
Abstract
Human papillomaviruses (HPV) are a group of small non-enveloped DNA viruses whose infection causes benign tumors or cancers. HPV16 and HPV18, the two most common high-risk HPVs, are responsible for ~70% of all HPV-related cervical cancers and head and neck cancers. The expression of the HPV genome is highly dependent on cell differentiation and is strictly regulated at the transcriptional and post-transcriptional levels. Both HPV early and late transcripts differentially expressed in the infected cells are intron-containing bicistronic or polycistronic RNAs bearing more than one open reading frame (ORF), because of usage of alternative viral promoters and two alternative viral RNA polyadenylation signals. Papillomaviruses proficiently engage alternative RNA splicing to express individual ORFs from the bicistronic or polycistronic RNA transcripts. In this review, we discuss the genome structures and the updated transcription maps of HPV16 and HPV18, and the latest research advances in understanding RNA cis-elements, intron branch point sequences, and RNA-binding proteins in the regulation of viral RNA processing. Moreover, we briefly discuss the epigenetic modifications, including DNA methylation and possible APOBEC-mediated genome editing in HPV infections and carcinogenesis.
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25
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Bahng S, Kumar R, Marians KJ. Inter- and intra-Subunit interactions driving the MukBEF ATPase. J Biol Chem 2022;:101964. [PMID: 35452680 DOI: 10.1016/j.jbc.2022.101964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/15/2022] [Accepted: 04/16/2022] [Indexed: 11/23/2022] Open
Abstract
MukBEF, a structural maintenance of chromosome-like protein complex consisting of an ATPase, MukB, and two interacting subunits, MukE and MukF, functions as the bacterial condensin. It is likely that MukBEF compacts DNA via an ATP hydrolysis-dependent DNA loop-extrusion reaction similar to that demonstrated for the yeast structural maintenance of chromosome proteins condensin and cohesin. MukB also interacts with the ParC subunit of the cellular chromosomal decatenase topoisomerase IV, an interaction that is required for proper chromosome condensation and segregation in Escherichia coli, although it suppresses the MukB ATPase activity. Other structural determinants and interactions that regulate the ATPase activity of MukBEF are not clear. Here, we have investigated the MukBEF ATPase activity, identifying intersubunit and intrasubunit interactions by protein-protein crosslinking and site-specific mutagenesis. We show that interactions between the hinge of MukB and its neck region are essential for the ATPase activity, that the ParC subunit of topoisomerase IV inhibits the MukB ATPase by preventing this interaction, that MukE interaction with DNA is likely essential for viability, and that interactions between MukF and the MukB neck region are necessary for ATPase activity and viability.
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26
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Abrahams JS, Weigand MR, Ring N, MacArthur I, Etty J, Peng S, Williams MM, Bready B, Catalano AP, Davis JR, Kaiser MD, Oliver JS, Sage JM, Bagby S, Tondella ML, Gorringe AR, Preston A. Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications in Bordetella pertussis and Mycobacterium tuberculosis. Microb Genom 2022; 8:000761. [PMID: 35143385 PMCID: PMC8942028 DOI: 10.1099/mgen.0.000761] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 12/11/2021] [Indexed: 11/18/2022] Open
Abstract
Bacterial genetic diversity is often described solely using base-pair changes despite a wide variety of other mutation types likely being major contributors. Tandem duplication/amplifications are thought to be widespread among bacteria but due to their often-intractable size and instability, comprehensive studies of these mutations are rare. We define a methodology to investigate amplifications in bacterial genomes based on read depth of genome sequence data as a proxy for copy number. We demonstrate the approach with Bordetella pertussis, whose insertion sequence element-rich genome provides extensive scope for amplifications to occur. Analysis of data for 2430 B. pertussis isolates identified 272 putative amplifications, of which 94 % were located at 11 hotspot loci. We demonstrate limited phylogenetic connection for the occurrence of amplifications, suggesting unstable and sporadic characteristics. Genome instability was further described in vitro using long-read sequencing via the Nanopore platform, which revealed that clonally derived laboratory cultures produced heterogenous populations rapidly. We extended this research to analyse a population of 1000 isolates of another important pathogen, Mycobacterium tuberculosis. We found 590 amplifications in M. tuberculosis, and like B. pertussis, these occurred primarily at hotspots. Genes amplified in B. pertussis include those involved in motility and respiration, whilst in M. tuberuclosis, functions included intracellular growth and regulation of virulence. Using publicly available short-read data we predicted previously unrecognized, large amplifications in B. pertussis and M. tuberculosis. This reveals the unrecognized and dynamic genetic diversity of B. pertussis and M. tuberculosis, highlighting the need for a more holistic understanding of bacterial genetics.
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Affiliation(s)
- Jonathan S. Abrahams
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - Michael R. Weigand
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Natalie Ring
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - Iain MacArthur
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - Joss Etty
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - Scott Peng
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Margaret M. Williams
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | | | | | | | | | | | - Stefan Bagby
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - M. Lucia Tondella
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Andrew Preston
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
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27
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Frontiers Production Office. Erratum: Comparative Chloroplast Genomes of Zosteraceae Species Provide Adaptive Evolution Insights Into Seagrass. Front Plant Sci 2021; 12:811304. [PMID: 34899818 PMCID: PMC8663023 DOI: 10.3389/fpls.2021.811304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2021.741152.].
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28
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Cliff ER, Kirkpatrick RL, Cunningham-Bryant D, Fernandez B, Harman JL, Zalatan JG. CRISPR-Cas-Mediated Tethering Recruits the Yeast HMR Mating-Type Locus to the Nuclear Periphery but Fails to Silence Gene Expression. ACS Synth Biol 2021; 10:2870-2877. [PMID: 34723510 DOI: 10.1021/acssynbio.1c00306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To investigate the relationship between genome structure and function, we have developed a programmable CRISPR-Cas system for nuclear peripheral recruitment in yeast. We benchmarked this system at the HMR and GAL2 loci, both of which are well-characterized model systems for localization to the nuclear periphery. Using microscopy and gene silencing assays, we demonstrate that CRISPR-Cas-mediated tethering can recruit the HMR locus but does not detectably silence reporter gene expression. A previously reported Gal4-mediated tethering system does silence gene expression, and we demonstrate that the silencing effect has an unexpected dependence on the properties of the protein tether. The CRISPR-Cas system was unable to recruit GAL2 to the nuclear periphery. Our results reveal potential challenges for synthetic genome structure perturbations and suggest that distinct functional effects can arise from subtle structural differences in how genes are recruited to the periphery.
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29
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Fitzgerald SF, Lupolova N, Shaaban S, Dallman TJ, Greig D, Allison L, Tongue SC, Evans J, Henry MK, McNeilly TN, Bono JL, Gally DL. Genome structural variation in Escherichia coli O157:H7. Microb Genom 2021; 7. [PMID: 34751643 PMCID: PMC8743559 DOI: 10.1099/mgen.0.000682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human zoonotic pathogen Escherichia coli O157:H7 is defined by its extensive prophage repertoire including those that encode Shiga toxin, the factor responsible for inducing life-threatening pathology in humans. As well as introducing genes that can contribute to the virulence of a strain, prophage can enable the generation of large-chromosomal rearrangements (LCRs) by homologous recombination. This work examines the types and frequencies of LCRs across the major lineages of the O157:H7 serotype. We demonstrate that LCRs are a major source of genomic variation across all lineages of E. coli O157:H7 and by using both optical mapping and Oxford Nanopore long-read sequencing prove that LCRs are generated in laboratory cultures started from a single colony and that these variants can be recovered from colonized cattle. LCRs are biased towards the terminus region of the genome and are bounded by specific prophages that share large regions of sequence homology associated with the recombinational activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that important virulence phenotypes such as Shiga-toxin production, type-3 secretion and motility can be affected by LCRs. In summary, E. coli O157:H7 has acquired multiple prophage regions over time that act to continually produce structural variants of the genome. These findings raise important questions about the significance of this prophage-mediated genome contingency to enhance adaptability between environments.
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Affiliation(s)
- Stephen F Fitzgerald
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Nadejda Lupolova
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Sharif Shaaban
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Timothy J Dallman
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - David Greig
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - Lesley Allison
- Scottish E. coli O157/VTEC Reference Laboratory, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - Sue C Tongue
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Judith Evans
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Madeleine K Henry
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Tom N McNeilly
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 OPZ, UK
| | - James L Bono
- United States Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, Nebraska, USA
| | - David L Gally
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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30
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Chen J, Zang Y, Shang S, Liang S, Zhu M, Wang Y, Tang X. Comparative Chloroplast Genomes of Zosteraceae Species Provide Adaptive Evolution Insights Into Seagrass. Front Plant Sci 2021; 12:741152. [PMID: 34630493 PMCID: PMC8495015 DOI: 10.3389/fpls.2021.741152] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/23/2021] [Indexed: 05/29/2023]
Abstract
Seagrasses are marine flowering plants found in tropical and sub-tropical areas that live in coastal regions between the sea and land. All seagrass species evolved from terrestrial monocotyledons, providing the opportunity to study plant adaptation to sea environments. Here, we sequenced the chloroplast genomes (cpGenomes) of three Zostera species, then analyzed and compared their cpGenome structures and sequence variations. We also performed a phylogenetic analysis using published seagrass chloroplasts and calculated the selection pressure of 17 species within seagrasses and nine terrestrial monocotyledons, as well as estimated the number of shared genes of eight seagrasses. The cpGenomes of Zosteraceae species ranged in size from 143,877 bp (Zostera marina) to 152,726 bp (Phyllospadix iwatensis), which were conserved and displayed similar structures and gene orders. Additionally, we found 17 variable hotspot regions as candidate DNA barcodes for Zosteraceae species, which will be helpful for studying the phylogenetic relationships and interspecies differences between seagrass species. Interestingly, nine genes had positive selection sites, including two ATP subunit genes (atpA and atpF), two ribosome subunit genes (rps4 and rpl20), two DNA-dependent RNA polymerase genes (rpoC1 and rpoC2), as well as accD, clpP, and ycf2. These gene regions may have played key roles in the seagrass adaptation to diverse environments. The Branch model analysis showed that seagrasses had a higher rate of evolution than terrestrial monocotyledons, suggesting that seagrasses experienced greater environmental pressure. Moreover, a branch-site model identified positively selected sites (PSSs) in ccsA, suggesting their involvement in the adaptation to sea environments. These findings are valuable for further investigations on Zosteraceae cpGenomes and will serve as an excellent resource for future studies on seagrass adaptation to sea environments.
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Affiliation(s)
- Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yu Zang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Shuai Shang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Shuo Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Meiling Zhu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ying Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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31
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Ren Y, Lu H, Chen L, Sabatelli S, Wang C, Xie G, Wang P, Liu M, Wang W, Audisio P. Comparative Mitogenomic Analysis of Two Longhorn Beetles (Coleoptera: Cerambycidae: Lamiinae) with Preliminary Investigation into Phylogenetic Relationships of Tribes of Lamiinae. Insects 2021; 12:820. [PMID: 34564260 PMCID: PMC8471637 DOI: 10.3390/insects12090820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022]
Abstract
The subfamily Lamiinae is the most taxonomically diverse subfamily of Cerambycidae, but relationships between tribes of Lamiinae are still unresolved. In order to study the characteristics of the mitogenomes of Lamiinae and the tribal-level phylogenetic relationships, we sequenced the mitogenomes of two species representing two tribes, Agapanthia amurensis (Agapanthiini) and Moechotypa diphysis (Ceroplesini), with a total length of 15,512 bp and 15,493 bp, respectively. The gene arrangements of these two new mitogenomes were consistent with the inferred ancestral insect mitogenomes. Each species contained 37 typical mitochondrial genes and a control region (A + T-rich region), including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs). All PCGs initiated with the standard start codon ATN, and terminated with the complete stop codons of TAA and TAG, or incomplete stop codon T. All tRNAs could be folded into a clover-leaf secondary structure except for trnS1, in which the dihydrouridine (DHU) arm was reduced. Moreover, we studied the phylogenetic relationships between some tribes of Lamiinae based in mitochondrial PCGs in nucleotides; our results show that the relationships were as follows: (Onciderini + ((Apomecynini + Acanthocinini) + ((Ceroplesini + Agapanthiini) + ((Mesosini + Pteropliini) + ((Dorcaschematini + (Saperdini 1 + (Phytoeciini + Saperdini 2))) + (Batocerini + Lamiini)))))).
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Affiliation(s)
- Yifang Ren
- Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.R.); (L.C.); (C.W.); (G.X.); (P.W.)
| | - Huanhuan Lu
- Chongqing Key Laboratory of Vector Insects, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China;
| | - Longyan Chen
- Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.R.); (L.C.); (C.W.); (G.X.); (P.W.)
| | - Simone Sabatelli
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Viale dell’Università 32, I-00185 Rome, Italy; (S.S.); (P.A.)
| | - Chaojie Wang
- Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.R.); (L.C.); (C.W.); (G.X.); (P.W.)
| | - Guanglin Xie
- Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.R.); (L.C.); (C.W.); (G.X.); (P.W.)
| | - Ping Wang
- Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.R.); (L.C.); (C.W.); (G.X.); (P.W.)
| | - Meike Liu
- Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.R.); (L.C.); (C.W.); (G.X.); (P.W.)
| | - Wenkai Wang
- Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.R.); (L.C.); (C.W.); (G.X.); (P.W.)
| | - Paolo Audisio
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Viale dell’Università 32, I-00185 Rome, Italy; (S.S.); (P.A.)
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Vozárová R, Macková E, Vlk D, Řepková J. Variation in Ribosomal DNA in the Genus Trifolium (Fabaceae). Plants (Basel) 2021; 10:1771. [PMID: 34579303 DOI: 10.3390/plants10091771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/23/2021] [Indexed: 01/13/2023]
Abstract
The genus Trifolium L. is characterized by basic chromosome numbers 8, 7, 6, and 5. We conducted a genus-wide study of ribosomal DNA (rDNA) structure variability in diploids and polyploids to gain insight into evolutionary history. We used fluorescent in situ hybridization to newly investigate rDNA variation by number and position in 30 Trifolium species. Evolutionary history among species was examined using 85 available sequences of internal transcribed spacer 1 (ITS1) of 35S rDNA. In diploid species with ancestral basic chromosome number (x = 8), one pair of 5S and 26S rDNA in separate or adjacent positions on a pair of chromosomes was prevalent. Genomes of species with reduced basic chromosome numbers were characterized by increased number of signals determined on one pair of chromosomes or all chromosomes. Increased number of signals was observed also in diploids Trifolium alpestre and Trifolium microcephalum and in polyploids. Sequence alignment revealed ITS1 sequences with mostly single nucleotide polymorphisms, and ITS1 diversity was greater in diploids with reduced basic chromosome numbers compared to diploids with ancestral basic chromosome number (x = 8) and polyploids. Our results suggest the presence of one 5S rDNA site and one 26S rDNA site as an ancestral state.
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Chen Y, Ke XR, Zhang XF, Zhu ZX, Wang HF. Complete plastome sequence of Bridelia tomentosa Blume (Phyllanthaceae): a medicinal shrub species in South Asia. Mitochondrial DNA B Resour 2021; 6:2330-2331. [PMID: 34345687 PMCID: PMC8284139 DOI: 10.1080/23802359.2021.1951134] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Bridelia tomentosa is a deciduous shrub in the family of Phyllanthaceae. It grows in the evergreen primary or secondary thickets or forests in the sea level from 1000 to 1500 m. It distributed in.south China (e.g., Fujian, Guangdong, Guangxi, Hainan etc) and other south Asian countries (e.g. Bangladesh, Bhutan, Cambodia etc). Here, we report and characterize the complete plastome of B. tomentosa. The complete plastome is of 149,958 bp in length with a typical structure and gene content of angiosperm plastome, including two inverted repeat (IRs) regions of 26,354 bp, a large single-copy (LSC) region of 81,355 bp and a small single-copy (SSC) region of 15,895 bp. The plastome contains 129 genes, consisting of 84 protein-coding genes, 37 tRNA genes, eight rRNA genes. The overall G/C content in the plastome of B. tomentosa is 36.0%. The complete plastome sequence of B. tomentosa will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Phyllanthaceae.
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Affiliation(s)
- Yan Chen
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Xiu-Rong Ke
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Xiao-Feng Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Zhi-Xin Zhu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Hua-Feng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
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Shah SMA, Khojasteh M, Wang Q, Taghavi SM, Xu Z, Khodaygan P, Zou L, Mohammadikhah S, Chen G, Osdaghi E. Genomics-Enabled Novel Insight Into the Pathovar-Specific Population Structure of the Bacterial Leaf Streak Pathogen Xanthomonas translucens in Small Grain Cereals. Front Microbiol 2021; 12:674952. [PMID: 34122388 PMCID: PMC8195340 DOI: 10.3389/fmicb.2021.674952] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/27/2021] [Indexed: 11/30/2022] Open
Abstract
The Gram-negative bacterium Xanthomonas translucens infects a wide range of gramineous plants with a notable impact on small grain cereals. However, genomics-informed intra-species population structure and virulence repertories of the pathogen have rarely been investigated. In this study, the complete genome sequences of seven X. translucens strains representing an entire set of genetic diversity of two pathovars X. translucens pv. undulosa and X. translucens pv. translucens is provided and compared with those of seven publicly available complete genomes of the pathogen. Organization of the 25 type III secretion system genes in all the 14 X. translucens strains was exactly the same, while TAL effector genes localized singly or in clusters across four loci in X. translucens pv. translucens and five to six loci in X. translucens pv. undulosa. Beside two previously unreported endogenous plasmids in X. translucens pv. undulosa, and variations in repeat variable diresidue (RVD) of the 14 strains, tal1a of X. translucens pv. translucens strain XtKm8 encode the new RVDs HE and YI which have not previously been reported in xanthomonads. Further, a number of truncated tal genes were predicted among the 14 genomes lacking conserved BamHI site at N-terminus and SphI site at C-terminus. Our data have doubled the number of complete genomes of X. translucens clarifying the population structure and genomics of the pathogen to pave the way in the small grain cereals industry for disease resistance breeding in the 21st century's agriculture.
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Affiliation(s)
- Syed Mashab Ali Shah
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Moein Khojasteh
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
- Department of Plant Protection, University of Tehran, Karaj, Iran
| | - Qi Wang
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - S. Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Zhengyin Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Pejman Khodaygan
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Lifang Zou
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Sedighe Mohammadikhah
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Ebrahim Osdaghi
- Department of Plant Protection, University of Tehran, Karaj, Iran
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Zhang M, Li Q, Wu F, Ou Z, Li Y, You F, Chen Q. Epidemiology, Genetic Characterization, and Evolution of Hunnivirus Carried by Rattus norvegicus and Rattus tanezumi: The First Epidemiological Evidence from Southern China. Pathogens 2021; 10:661. [PMID: 34071186 DOI: 10.3390/pathogens10060661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 11/17/2022] Open
Abstract
Hunnivirus is a novel member of the family Picornaviridae. A single species, Hunnivirus A, is currently described. However, there is limited information on the identification of Hunnivirus to date, and thereby the circulation of Hunnivirus is not fully understood. Thus, the objective of this study was to investigate the prevalence, genomic characteristics, and evolution of rat hunnivirus in southern China. A total of 404 fecal samples were subjected to detection of Hunnivirus from urban rats (Rattus norvegicus and Rattus tanezumi) using PCR assay based on specific primers targeted to partial 3D regions, with the prevalence of 17.8% in Rattus norvegicus and 15.6% in Rattus tanezumi. An almost full-length rat hunnivirus sequence (RatHuV/YY12/CHN) and the genome structure were acquired in the present study. Phylogenetic analysis of the P1 coding regions suggested the RatHuV/YY12/CHN sequence was found to be within the genotype of Hunnivirus A4. The negative selection was further identified based on analysis of non-synonymous to synonymous substitution rates. The present findings suggest that hunniviruses are common in urban rats. Further research is needed for increased surveillance and awareness of potential risks to human health.
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Devenish LP, Mhlanga MM, Negishi Y. Immune Regulation in Time and Space: The Role of Local- and Long-Range Genomic Interactions in Regulating Immune Responses. Front Immunol 2021; 12:662565. [PMID: 34046034 PMCID: PMC8144502 DOI: 10.3389/fimmu.2021.662565] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 12/27/2022] Open
Abstract
Mammals face and overcome an onslaught of endogenous and exogenous challenges in order to survive. Typical immune cells and barrier cells, such as epithelia, must respond rapidly and effectively to encountered pathogens and aberrant cells to prevent invasion and eliminate pathogenic species before they become overgrown and cause harm. On the other hand, inappropriate initiation and failed termination of immune cell effector function in the absence of pathogens or aberrant tissue gives rise to a number of chronic, auto-immune, and neoplastic diseases. Therefore, the fine control of immune effector functions to provide for a rapid, robust response to challenge is essential. Importantly, immune cells are heterogeneous due to various factors relating to cytokine exposure and cell-cell interaction. For instance, tissue-resident macrophages and T cells are phenotypically, transcriptionally, and functionally distinct from their circulating counterparts. Indeed, even the same cell types in the same environment show distinct transcription patterns at the single cell level due to cellular noise, despite being robust in concert. Additionally, immune cells must remain quiescent in a naive state to avoid autoimmunity or chronic inflammatory states but must respond robustly upon activation regardless of their microenvironment or cellular noise. In recent years, accruing evidence from next-generation sequencing, chromatin capture techniques, and high-resolution imaging has shown that local- and long-range genome architecture plays an important role in coordinating rapid and robust transcriptional responses. Here, we discuss the local- and long-range genome architecture of immune cells and the resultant changes upon pathogen or antigen exposure. Furthermore, we argue that genome structures contribute functionally to rapid and robust responses under noisy and distinct cellular environments and propose a model to explain this phenomenon.
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Affiliation(s)
- Liam P Devenish
- Division of Chemical, Systems, and Synthetic Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Musa M Mhlanga
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Yutaka Negishi
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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Wu WP, Zhang XF, Zhu ZX, Wang HF. Complete plastome sequence of Mallotus japonicus (Linn. f.) Müll. Arg. (Euphorbiaceae): a medicinal plant species endemic in East Asia. Mitochondrial DNA B Resour 2021; 6:1409-1410. [PMID: 33969189 PMCID: PMC8079058 DOI: 10.1080/23802359.2021.1911707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Mallotus japonicus is a shrub species in the family of Euphorbiaceae. The study of plastome would be helpful for its phylogenetic study and species identification. The total length of complete plastome for Mallotus japonicus is of 164,912 bp, with typical part-four structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 27,829 bp, a large single-copy (LSC) region of 90,319 bp, and a small single-copy (SSC) region of 18,935 bp. The plastome contains 125 genes, consisting of 80 unique protein-coding genes, 31 unique tRNA gene, four unique rRNA genes (5S rRNA, 4.5S rRNA, 16S rRNA, and 23S rRNA), and five pseudogenes. The overall G/C content in the plastome of Mallotus japonicus is 40.2%. The phylogenetic analysis indicates that M. japonicus is closer to M. peltatus than other species in this study. The complete plastome sequence is conducive to the exploitation and utilization of Euphorbiaceae resources and the phylogenetic study in future.
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Affiliation(s)
- Wan-Ping Wu
- College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Xiao-Feng Zhang
- College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Zhi-Xin Zhu
- College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Hua-Feng Wang
- College of Tropical Crops, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
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Hovenga V, Oluwadare O. CBCR: A Curriculum Based Strategy For Chromosome Reconstruction. Int J Mol Sci 2021; 22:ijms22084140. [PMID: 33923653 PMCID: PMC8073114 DOI: 10.3390/ijms22084140] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/30/2022] Open
Abstract
In this paper, we introduce a novel algorithm that aims to estimate chromosomes’ structure from their Hi-C contact data, called Curriculum Based Chromosome Reconstruction (CBCR). Specifically, our method performs this three dimensional reconstruction using cis-chromosomal interactions from Hi-C data. CBCR takes intra-chromosomal Hi-C interaction frequencies as an input and outputs a set of xyz coordinates that estimate the chromosome’s three dimensional structure in the form of a .pdb file. The algorithm relies on progressively training a distance-restraint-based algorithm with a strategy we refer to as curriculum learning. Curriculum learning divides the Hi-C data into classes based on contact frequency and progressively re-trains the distance-restraint algorithm based on the assumed importance of each curriculum in predicting the underlying chromosome structure. The distance-restraint algorithm relies on a modification of a Gaussian maximum likelihood function that scales probabilities based on the importance of features. We evaluate the performance of CBCR on both simulated and actual Hi-C data and perform validation on FISH, HiChIP, and ChIA-PET data as well. We also compare the performance of CBCR to several current methods. Our analysis shows that the use of curricula affects the rate of convergence of the optimization while decreasing the computational cost of our distance-restraint algorithm. Also, CBCR is more robust to increases in data resolution and therefore yields superior reconstruction accuracy of higher resolution data than all other methods in our comparison.
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Affiliation(s)
- Van Hovenga
- Department of Mathematics, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA;
| | - Oluwatosin Oluwadare
- Department of Computer Science, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
- Correspondence:
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Li XD, Pan H, Lu XJ, Wei XY, Shi M, Lu P. Complete chloroplast genome sequencing of Job's tears ( Coix L.): genome structure, comparative analysis, and phylogenetic relationships. Mitochondrial DNA B Resour 2021; 6:1399-1405. [PMID: 33948493 PMCID: PMC8057079 DOI: 10.1080/23802359.2021.1911704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/25/2021] [Indexed: 12/30/2022] Open
Abstract
Job's tears, also known as adlay, is a valuable plant that has commonly been used in traditional Chinese medicine, as well as an edible food. Due to the lack of knowledge of its genetics and gaps in its evolutionary analysis, breeding of adlay has been hindered. Here, we report five complete chloroplast genomes of various species and varieties in the genus by Illumina sequencing, while their genome structure, comparative analysis, and phylogenetic relationships were conducted. Genome sizes ranged from 140,860 to 140,864 bp in length, GC contents were 38.43%, and genome architecture was of a typical quadripartite structure. We annotated 82~83 protein-coding genes and 46~47 non-coding RNA genes in each genome and they functionally associated with self-replication, photosynthesis, cytochrome synthesis and other unknown functions. Three codons that encoded tryptophan, arginine and leucine were used frequently at rates of 41.42, 37.98, and 32.28% respectively. The preferred codons consistently ended with A or T. A total of 146 simple sequence repeats (SSR), 9 insertions and deletions (InDels) and 143 single nucleotide polymorphisms (SNPs) were observed among genomes. The InDel and SNP variations were mostly distributed in intergenic regions. It confirmed that Coix, Sorghum, Saccharum, Zea, Tripsacum and Saccharum were closely genera and the genetic distance of Sorghum to Coix was closer than Zea to Coix. These results give us more insight into the evolution of Coix in a wide range of evolutionary studies.
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Affiliation(s)
- Xiang-Dong Li
- Southwest Guizhou Institute of Karst Regional Development, Xingyi, Guizhou, China
- Adlay of Engineering Technical Research Centre in Guizhou, Xingyi, Guizhou, China
| | - Hong Pan
- Southwest Guizhou Institute of Karst Regional Development, Xingyi, Guizhou, China
- Adlay of Engineering Technical Research Centre in Guizhou, Xingyi, Guizhou, China
| | - Xiu-Juan Lu
- Southwest Guizhou Institute of Karst Regional Development, Xingyi, Guizhou, China
- Adlay of Engineering Technical Research Centre in Guizhou, Xingyi, Guizhou, China
| | - Xin-Yuan Wei
- Southwest Guizhou Institute of Karst Regional Development, Xingyi, Guizhou, China
- Adlay of Engineering Technical Research Centre in Guizhou, Xingyi, Guizhou, China
| | - Ming Shi
- Adlay of Engineering Technical Research Centre in Guizhou, Xingyi, Guizhou, China
| | - Ping Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Mohamadian M, Chiti H, Shoghli A, Biglari S, Parsamanesh N, Esmaeilzadeh A. COVID-19: Virology, biology and novel laboratory diagnosis. J Gene Med 2021; 23:e3303. [PMID: 33305456 PMCID: PMC7883242 DOI: 10.1002/jgm.3303] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/15/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND At the end of December 2019, a novel coronavirus tentatively named SARS-CoV-2 in Wuhan, a central city in China, was announced by the World Health Organization. SARS-CoV-2 is an RNA virus that has become a major public health concern after the outbreak of the Middle East Respiratory Syndrome-CoV (MERS-CoV) and Severe Acute Respiratory Syndrome-CoV (SARS-CoV) in 2002 and 2012, respectively. As of 29 October 2020, the total number of COVID-19 cases had reached over 44 million worldwide, with more than 1.17 million confirmed deaths. DISCUSSION SARS-CoV-2 infected patients usually present with severe viral pneumonia. Similar to SARS-CoV, the virus enters respiratory tract cells via the angiotensin-converting enzyme receptor 2. The structural proteins play an essential role in budding the virus particles released from different host cells. To date, an approved vaccine or treatment option of a preventive character to avoid severe courses of COVID-19 is still not available. CONCLUSIONS In the present study, we provide a brief review of the general biological features of CoVs and explain the pathogenesis, clinical symptoms and diagnostic approaches regarding monitoring future infectivity and prevent emerging COVID-19 infections.
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Affiliation(s)
- Malihe Mohamadian
- Department of Molecular MedicineBirjand University of Medical SciencesBirjandIran
- Cellular and Molecular Research CenterBirjand University of Medical SciencesBirjandIran
| | - Hossein Chiti
- Zanjan Metabolic Diseases Research CenterZanjan University of Medical SciencesZanjanIran
| | - Alireza Shoghli
- Social Determinants of Health Research CenterZanjan University of Medical SciencesZanjanIran
| | - Sajjad Biglari
- School of MedicineZanjan University of Medical SciencesZanjanIran
| | - Negin Parsamanesh
- Zanjan Metabolic Diseases Research CenterZanjan University of Medical SciencesZanjanIran
| | - Abdolreza Esmaeilzadeh
- Department of ImmunologyZanjan University of Medical ScienceZanjanIran
- Cancer Gene Therapy Research CenterZanjan University of Medical ScienceZanjanIran
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Lu H, He B, Hao Y, Zhou Z, Su C, Huang D. Comparative Mitogenomic Analysis of Two Cuckoo Bees (Apoidea: Anthophila: Megachilidae) with Phylogenetic Implications. Insects 2021; 12:29. [PMID: 33466344 DOI: 10.3390/insects12010029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/03/2021] [Accepted: 01/03/2021] [Indexed: 11/17/2022]
Abstract
Bees (Hymenoptera, Apoidea and Anthophila) are distributed worldwide and considered the primary pollinators of angiosperm. Megachilidae is one of the largest families of Anthophila. In this study, two complete mitogenomes of cuckoo bees in Megachilidae, namely Coelioxys fenestrata and Euaspis polynesia, were amplified and sequenced, with a length of 17,004 bp (C. fenestrata) and 17,682 bp (E. polynesia). The obtained results show that 37 mitogenomic genes and one putative control region were conserved within Hymenoptera. Truncated stop codon T was found in the cox3 gene of E. polynesia. The secondary structure of small (rrnS) and large (rrnL) rRNA subunits contained three domains (28 helices) and five domains (44 helices) conserved within Hymenoptera, respectively. Compared with ancestral gene order, gene rearrangement events included local inversion and gene shuffling. In order to reveal the phylogenetic position of cuckoo bees, we performed phylogenetic analysis. The results supported that all families of Anthophila were monophyletic, the tribe-level relationship of Megachilidae was Osmiini + (Anthidiini + Megachilini) and Coelioxys fenestrata was clustered to the Megachile genus, which was more closely related to Megachile sculpturalis and Megachile strupigera than Euaspis polynesia.
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He X, Kim JS, Diaz-Martinez LA, Han C, Lane WS, Budnik B, Waldman T. USP13 interacts with cohesin and regulates its ubiquitination in human cells. J Biol Chem 2021; 296:100194. [PMID: 33334891 PMCID: PMC7948425 DOI: 10.1074/jbc.ra120.015762] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 01/26/2023] Open
Abstract
Cohesin is a multiprotein ring complex that regulates 3D genome organization, sister chromatid cohesion, gene expression, and DNA repair. Cohesin is known to be ubiquitinated, although the mechanism, regulation, and effects of cohesin ubiquitination remain poorly defined. We previously used gene editing to introduce a dual epitope tag into the endogenous allele of each of 11 known components of cohesin in human HCT116 cells. Here we report that mass spectrometry analysis of dual-affinity purifications identified the USP13 deubiquitinase as a novel cohesin-interacting protein. Subsequent immunoprecipitation/Western blots confirmed the endogenous interaction in HCT116, 293T, HeLa, and RPE-hTERT cells; demonstrated that the interaction occurs specifically in the soluble nuclear fraction (not in the chromatin); requires the ubiquitin-binding domains (UBA1/2) of USP13; and occurs preferentially during DNA replication. Reciprocal dual-affinity purification of endogenous USP13 followed by mass spectrometry demonstrated that cohesin is its primary interactor in the nucleus. Ectopic expression and CRISPR knockout of USP13 showed that USP13 is paradoxically required for both deubiquitination and ubiquitination of cohesin subunits in human cells. USP13 was dispensable for sister chromatid cohesion in HCT116 and HeLa cells, whereas it was required for the dissociation of cohesin from chromatin as cells transit through mitosis. Together these results identify USP13 as a new cohesin-interacting protein that regulates the ubiquitination of cohesin and its cell cycle regulated interaction with chromatin.
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Affiliation(s)
- Xiaoyuan He
- Departments of Oncology, Biochemistry & Molecular Biology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia, USA
| | - Jung-Sik Kim
- Departments of Oncology, Biochemistry & Molecular Biology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia, USA
| | | | - Cecil Han
- Departments of Oncology, Biochemistry & Molecular Biology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia, USA
| | - William S Lane
- Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts, USA
| | - Bogdan Budnik
- Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts, USA
| | - Todd Waldman
- Departments of Oncology, Biochemistry & Molecular Biology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia, USA.
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Lin CH, Yang CY, Wang M, Ou SC, Lo CY, Tsai TL, Wu HY. Effects of Coronavirus Persistence on the Genome Structure and Subsequent Gene Expression, Pathogenicity and Adaptation Capability. Cells 2020; 9:E2322. [PMID: 33086697 PMCID: PMC7589090 DOI: 10.3390/cells9102322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/04/2020] [Accepted: 10/15/2020] [Indexed: 12/16/2022] Open
Abstract
Coronaviruses are able to establish persistence. However, how coronaviruses react to persistence and whether the selected viruses have altered their characteristics remain unclear. In this study, we found that the persistent infection of bovine coronavirus (BCoV), which is in the same genus as SARS-COV-2, led to alterations of genome structure, attenuation of gene expression, and the synthesis of subgenomic mRNA (sgmRNA) with a previously unidentified pattern. Subsequent analyses revealed that the altered genome structures were associated with the attenuation of gene expression. In addition, the genome structure at the 5' terminus and the cellular environment during the persistence were responsible for the sgmRNA synthesis, solving the previously unanswered question regarding the selection of transcription regulatory sequence for synthesis of BCoV sgmRNA 12.7. Although the BCoV variants (BCoV-p95) selected under the persistence replicated efficiently in cells without persistent infection, its pathogenicity was still lower than that of wild-type (wt) BCoV. Furthermore, in comparison with wt BCoV, the variant BCoV-p95 was not able to efficiently adapt to the challenges of alternative environments, suggesting wt BCoV is genetically robust. We anticipate that the findings derived from this fundamental research can contribute to the disease control and treatments against coronavirus infection including SARS-CoV-2.
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Affiliation(s)
- Ching-Hung Lin
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
| | - Cheng-Yao Yang
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
| | - Meilin Wang
- Department of Microbiology and Immunology, School of Medicine, Chung-Shan Medical University, Taichung 40201, Taiwan;
| | - Shan-Chia Ou
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan;
| | - Chen-Yu Lo
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
| | - Tsung-Lin Tsai
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
| | - Hung-Yi Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
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44
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Han R, Tian M, Zhang G, Shao D, Ren Y. Complete chloroplast genome sequence of turnip (Brassica rapa. ssp. rapa): genome structure and phylogenetic analysis. Mitochondrial DNA B Resour 2020; 5:3555-3557. [PMID: 33458239 PMCID: PMC7782280 DOI: 10.1080/23802359.2020.1829124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Turnip (Brassica rapa. ssp. rapa) is considered worldwide to be one of the most important leaf and root vegetable crops in the Brassicaceae family. However, to date, few chloroplast (cp) genomic resources have been reported for this genus. Here, we determined the complete cp genome sequences of Brassica rapa ssp. rapa. A 153,621 bp quadripartite cycle without any gap was obtained with a large single-copy region (LSC) of 83,512 bp, a small single-copy region (SSC) of 17,683 bp, and two inverted repeat (IR), IRa and IRb of 26,213 bp. A total of 132 genes were identified, including 87 protein-coding genes (PCG), 37 transfer RNA (tRNA), and 8 ribosomal RNA (rRNA). The phylogenetic analysis of ten other crops selected showed that the turnip was most closely related to the Brassica rapa.
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Affiliation(s)
- Rui Han
- Academy of Agriculture and Forestry Sciences of Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Xining, P. R. China
| | - Minyu Tian
- Academy of Agriculture and Forestry Sciences of Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Xining, P. R. China
| | - Guangnan Zhang
- Academy of Agriculture and Forestry Sciences of Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Xining, P. R. China.,Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining, P. R. China
| | - Dengkui Shao
- Academy of Agriculture and Forestry Sciences of Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Xining, P. R. China.,Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining, P. R. China
| | - Yanjing Ren
- Academy of Agriculture and Forestry Sciences of Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Xining, P. R. China.,Qinghai Key Laboratory of Vegetable Genetics and Physiology, Xining, P. R. China
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45
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Lin CH, Yang CY, Ou SC, Wang M, Lo CY, Tsai TL, Wu HY. The Impacts of Antivirals on the Coronavirus Genome Structure and Subsequent Pathogenicity, Virus Fitness and Antiviral Design. Biomedicines 2020; 8:E376. [PMID: 32987828 PMCID: PMC7601523 DOI: 10.3390/biomedicines8100376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 08/28/2020] [Revised: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 01/29/2023] Open
Abstract
With the global threat of SARS-CoV-2, much effort has been focused on treatment and disease control. However, how coronaviruses react to the treatments and whether the surviving viruses have altered their characteristics are also unanswered questions with medical importance. To this end, bovine coronavirus (BCoV), which is in the same genus as SARS-CoV-2, was used as a test model and the findings were as follows. With the treatment of antiviral remdesivir, the selected BCoV variant with an altered genome structure developed resistance, but its pathogenicity was not increased in comparison to that of wild type (wt) BCoV. Under the selection pressure of innate immunity, the genome structure was also altered; however, neither resistance developed nor pathogenicity increased for the selected BCoV variant. Furthermore, both selected BCoV variants showed a better efficiency in adapting to alternative host cells than wt BCoV. In addition, the previously unidentified feature that the spike protein was a common target for mutations under different antiviral treatments might pose a problem for vaccine development because spike protein is a common target for antibody and vaccine designs. The findings derived from this fundamental research may contribute to the disease control and treatments against coronaviruses, including SARS-CoV-2.
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Affiliation(s)
- Ching-Hung Lin
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
| | - Cheng-Yao Yang
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
| | - Shan-Chia Ou
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan;
| | - Meilin Wang
- Department of Microbiology and Immunology, Chung Shan Medical University, Taichung 40201, Taiwan;
| | - Chen-Yu Lo
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
| | - Tsung-Lin Tsai
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
| | - Hung-Yi Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
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Asghari A, Naseri M, Safari H, Saboory E, Parsamanesh N. The Novel Insight of SARS-CoV-2 Molecular Biology and Pathogenesis and Therapeutic Options. DNA Cell Biol 2020; 39:1741-1753. [PMID: 32716648 DOI: 10.1089/dna.2020.5703] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 12/15/2022] Open
Abstract
On December 31, 2019, a novel coronavirus, being the third highly infective CoV and named as coronavirus disease 2019 (COVID-19) in the city of Wuhan, was announced by the World Health Organization. COVID-19 has a 2% mortality rate, is known as the third extremely infective CoV infection, and has a mortality rate less than MERS-CoV and SARS-CoV. The CoV family comprises a chief number of positive single-stranded ss (+) RNA viruses that are recognized in mammals. The 2019-nCoV patients showed that the angiotensin-converting enzyme II (ACE2) was the same for SARS-CoV. Structural proteins have an essential role in virus released and budding to various host cells. Notably, evidence indicated human-to-human transmission, along with several exported patients of virus infection worldwide. Nowadays, no licensed antivirals drugs or vaccines for being utilized against these coronavirus infections are recognized. There is an urgent requirement for an extensive research of CoV infections to disclose the route of extension, pathogenesis, and diagnosis and then to recognize the therapeutic targets to facilitate disease control and surveillance. In this article, we present an overview of the common biological criteria of CoVs and explain pathogenesis with a focus on the therapeutic approach to suggest potential goals for treating and monitoring this emerging zoonotic disease.
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Affiliation(s)
- Arghavan Asghari
- Student Research Committee and Birjand University of Medical Sciences, Birjand, Iran
| | - Mohsen Naseri
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Hamidreza Safari
- Department of Immunology, Torbat Jam Faculty of Medical Sciences, Torbat Jam, Iran
| | - Ehsan Saboory
- Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Negin Parsamanesh
- Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
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Abstract
Rearrangements of large genome fragments occur in bacteria between repeat sequences and can impact on growth and gene expression. Homologous recombination resulting in inversion between indirect repeats and excision/translocation between direct repeats enables these structural changes. One form of rearrangement occurs around ribosomal operons, found in multiple copies across many bacteria, but identification of these rearrangements by sequencing requires reads of several thousand bases to span the ribosomal operons. With long-read sequencing aiding the routine generation of complete bacterial assemblies, we have developed socru, a typing method for the order and orientation of genome fragments between ribosomal operons. It allows for a single identifier to convey the order and orientation of genome-level structure and we have successfully applied this typing to 433 of the most common bacterial species. In a focused analysis, we observed the presence of multiple structural genotypes in nine bacterial pathogens, underscoring the importance of routinely assessing this form of variation alongside traditional single-nucleotide polymorphism (SNP) typing.
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Affiliation(s)
- Andrew J Page
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Emma V Ainsworth
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Gemma C Langridge
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
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Abstract
In this study, we assembled the chloroplast genome of Osmanthus didymopetalus (Oleaceae), a rare evergreen tree native to Hainan, China. The genome of O. didymopetalus was 155,155 bp in length and contained a pair of inverted repeats (IR, 25,697-25,704 bp) regions, which were separated by the small single copy (SSC, 17,591 bp) and the large single copy (LSC, 86,225 bp) regions. The cp genome encoded 133 genes including 88 protein-coding genes, 37 tRNA genes, and eight rRNA ribosomal genes. The overall GC content of O. didymopetalus chloroplast genome is 37.8%. Phylogenetic results showed that O. didymopetalus was more closely to O. yunnanensis, O. fragrans and O. insularis. This study will be beneficial for the evolutionary study and phylogenetic reconstruction of Osmanthus.
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Affiliation(s)
- Changheng Zhao
- College of Life and Environment Science, Huangshan University, Anhui, Huangshan, China.,Anhui Runyi Ecological Construction Co. Ltd, Anhui, Huangshan, China
| | - Qinghua Yang
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Jiangsu, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, Nanjing, China
| | - Min Zhang
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Jiangsu, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, Nanjing, China
| | - Cheng Zhang
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Jiangsu, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, Nanjing, China
| | - Xiaofei Wang
- Department of Bioengineering, Huangshan Vocational and Technical College, Anhui, Huangshan, China
| | - Xianrong Wang
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Jiangsu, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, Nanjing, China
| | - Yongfu Li
- International Cultivar Registration Center for Osmanthus, College of Biology and the Environment, Nanjing Forestry University, Jiangsu, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, Nanjing, China
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Kyalo CM, Li ZZ, Mkala EM, Malombe I, Hu GW, Wang QF. The First Glimpse of Streptocarpus ionanthus (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies' Chloroplast Genomes. Plants (Basel) 2020; 9:E456. [PMID: 32260377 PMCID: PMC7238178 DOI: 10.3390/plants9040456] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/29/2020] [Accepted: 04/02/2020] [Indexed: 02/05/2023]
Abstract
Streptocarpus ionanthus (Gesneriaceae) comprise nine herbaceous subspecies, endemic to Kenya and Tanzania. The evolution of Str. ionanthus is perceived as complex due to morphological heterogeneity and unresolved phylogenetic relationships. Our study seeks to understand the molecular variation within Str. ionanthus using a phylogenomic approach. We sequence the chloroplast genomes of five subspecies of Str. ionanthus, compare their structural features and identify divergent regions. The five genomes are identical, with a conserved structure, a narrow size range (170 base pairs (bp)) and 115 unique genes (80 protein-coding, 31 tRNAs and 4 rRNAs). Genome alignment exhibits high synteny while the number of Simple Sequence Repeats (SSRs) are observed to be low (varying from 37 to 41), indicating high similarity. We identify ten divergent regions, including five variable regions (psbM, rps3, atpF-atpH, psbC-psbZ and psaA-ycf3) and five genes with a high number of polymorphic sites (rps16, rpoC2, rpoB, ycf1 and ndhA) which could be investigated further for phylogenetic utility in Str. ionanthus. Phylogenomic analyses here exhibit low polymorphism within Str. ionanthus and poor phylogenetic separation, which might be attributed to recent divergence. The complete chloroplast genome sequence data concerning the five subspecies provides genomic resources which can be expanded for future elucidation of Str. ionanthus phylogenetic relationships.
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Affiliation(s)
- Cornelius M. Kyalo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (C.M.K.); (E.M.M.); (Q.-F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China;
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Zhi-Zhong Li
- University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Elijah M. Mkala
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (C.M.K.); (E.M.M.); (Q.-F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China;
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Itambo Malombe
- East African Herbarium, National Museums of Kenya, P.O. Box 45166-00100 Nairobi, Kenya;
| | - Guang-Wan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (C.M.K.); (E.M.M.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (C.M.K.); (E.M.M.); (Q.-F.W.)
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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50
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Ke XR, Zhang XF, Wang HX, Zhu ZX, Li JL, Wang HF. Complete plastome sequence of Mallotus peltatus (Geiseler) Müll. Arg. (Euphorbiaceae): A beverage and medicinal plant in Hainan, China. Mitochondrial DNA B Resour 2020; 5:953-954. [PMID: 33366823 PMCID: PMC7748731 DOI: 10.1080/23802359.2020.1719935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Mallotus peltatus is a tropical plant of the Euphorbiaceae family, which could be used as a beverage and medicine in Hainan, China. Here, we report and characterize the complete plastome of M. peltatus. The complete plastome is 163,304 bp in length and contains a typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 27,112 bp, a large single-copy (LSC) region of 89,886 bp and a small single-copy (SSC) region of 18,840 bp. The plastome contains 131 genes, consisting of 78 unique protein-coding genes, 30 unique tRNA gene, four unique rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA and 16S rRNA), and eight pseudogenes. The overall A/T content in the plastome of M. peltatus is 64.02%. The complete plastome sequence of M. peltatus will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Euphorbiaceae.
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Affiliation(s)
- Xiu-Rong Ke
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Xiao-Feng Zhang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Hong-Xin Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Zhi-Xin Zhu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Juan-Ling Li
- College of Forestry, Hainan University, Haikou, China
| | - Hua-Feng Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
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