1
|
Xu S, Man Y, Yu Z, Xu X, Ji J, Kan Y, Bi Y, Xie Q, Yao L. Molecular analysis of Gyrovirus galga1 variants identified from the sera of dogs and cats in China. Vet Q 2024; 44:1-8. [PMID: 38595267 PMCID: PMC11008310 DOI: 10.1080/01652176.2024.2338381] [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: 12/11/2023] [Accepted: 03/29/2024] [Indexed: 04/11/2024] Open
Abstract
Gyrovirus galga1 (GyVg1), a member of the Anelloviridae family and Gyrovirus genus, has been detected in chicken and human tissue samples. In this study, the DNA of GyVg1-related gyroviruses in the sera of six dogs and three cats from Central and Eastern China was identified using PCR. Alignment analysis between the nine obtained and reference GyVg1 strains revealed that the genome identity ranged from 99.20% (DOG03 and DOG04 strains) to 96.17% (DOG01 and DOG06 strains). Six recombination events were predicted in multiple strains, including DOG01, DOG05, DOG06, CAT01, CAT02, and CAT03. The predicted major and minor parents of DOG05 came from Brazil. The DOG06 strain is potentially recombined from strains originating from humans and cats, whereas DOG01 is potentially recombined from G17 (ferret-originated) and Ave3 (chicken-originated), indicating that transmissions across species and regions may occur. Sixteen representative amino acid mutation sites were identified: nine in VP1 (12 R/H, 114S/N, 123I/M, 167 L/P, 231 P/S, 237 P/L, 243 R/W, 335 T/A, and 444S/N), four in VP2 (81 A/P, 103 R/H, 223 R/G, and 228 A/T), and three in VP3 (38 M/I, 61 A/T, and 65 V/A). These mutations were only harbored in strains identified in dogs and cats in this study. Whether this is related to host tropism needs further investigation. In this study, GyVg1 was identified in the sera of dogs and cats, and the molecular characteristics prompted the attention of public health.
Collapse
Affiliation(s)
- Shuqi Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, PR China
| | - Yuanzhuo Man
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, PR China
| | - Zhengli Yu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, PR China
| | - Xin Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, PR China
| | - Jun Ji
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, PR China
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, PR China
| | - Yingzuo Bi
- College of Animal Science, South China Agricultural University, Guangzhou, PR China
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University, Guangzhou, PR China
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, PR China
| |
Collapse
|
2
|
Lan C, Zhu B, Zhuo H, Shi Y, Sun Z, Zhang L, Jia L, Li H, Liu Y, Wang X, Li J, Zhang B, Han J, Jiang J, Li L. Near Full-Length Genome Characterization of Two Novel Unique Recombinants (CRF01_AE/CRF07_BC) in Beijing, China. AIDS Res Hum Retroviruses 2024. [PMID: 38517080 DOI: 10.1089/aid.2023.0149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024] Open
Abstract
With the prevalence of human immunodeficiency virus type 1 (HIV-1) CRF01_AE and CRF07_BC subtypes in China, the co-circulation of multiple subtypes in the HIV-1-positive population may result in dual infection or superinfection in the population, leading to the emergence of unique recombinant forms (URFs) of the HIV-1 virus. In this study, two second-generation unique recombinant strains, BI0114 and BI0116, were identified, and their near full-length genome sequences were obtained. Recombination analysis showed that both sequences were isoforms of URF_0107, and they were second-generation unique recombinant strains formed by the recombination of CRF01_AE and CRF07_BC, with the isoforms being CRF01_AE and CRF0107_BC, respectively. The continued emergence of novel CRF01_AE/CRF07_BC recombinant strains suggests that the epidemiological, preventive, and control situation of HIV-1 is complex and that the relevant health authorities urgently need to establish responses to the challenges posed by changes in the pattern of strain recombination.
Collapse
Affiliation(s)
- Chunlin Lan
- Department of Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bo Zhu
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hailong Zhuo
- Department of Transfusion Medicine, the Fifth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Yuting Shi
- Department of Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zixuan Sun
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lixuan Zhang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bohan Zhang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Junjun Jiang
- Department of Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| |
Collapse
|
3
|
Gao Y, Yin S. The complete chloroplast genome assembly of Amorphophallus kiusianus makino 1913 (araceae) from Southern China. Mitochondrial DNA B Resour 2024; 9:522-526. [PMID: 38634040 PMCID: PMC11022911 DOI: 10.1080/23802359.2024.2342934] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
The mountainous region of southern China has been characterized by its complicated environment and topography. Amorphophallus kiusianus Makino 1913 is a representative species of extreme habitat preference that resides mainly in this region. To help study the genetic differentiation mechanisms of A. kiusianus populations, we sequenced the first chloroplast genome of this species using next-generation sequencing. The chloroplast genome was 166,269 bp in length with an average GC content of 36% (GenBank accession number: PP072243). The lengths of the large single-copy region (LSC), small single-copy region (SSC), and two inverted repeats (IRs) were 90,701 bp, 14,802 bp, 31,383 bp, and 31,383 bp, respectively. One hundred and twenty-nine genes were annotated in the chloroplast genome, including 84 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The phylogenetic tree suggested a close relationship among A. kiusianus, A. yunnanensis, and A. coaetaneus. The chloroplast genome reported in this study provides valuable genomic resources for the future phylogeographic research of A. kiusianus.
Collapse
Affiliation(s)
- Yong Gao
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, China
| | - Si Yin
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, China
| |
Collapse
|
4
|
Maeda H, Kakiuchi N. Clonal expansion in normal tissues. Cancer Sci 2024. [PMID: 38623936 DOI: 10.1111/cas.16183] [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: 02/07/2024] [Revised: 03/24/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Cancer originates from a single ancestral cell that acquires a driver mutation, which confers a growth or survival advantage, followed by the acquisition of additional driver mutations by descendant cells. Recently, it has become evident that somatic cell mutations accumulate in normal tissues with aging and exposure to environmental factors, such as alcohol, smoking, and UV rays, increases the mutation rate. Clones harboring driver mutations expand with age, leading to tissue remodeling. Lineage analysis of myeloproliferative neoplasms and der(1;16)-positive breast cancer revealed that driver mutations were acquired early in our lives and that the development of cancer takes decades, unveiling the previously unknown early process of cancer development. Evidence that clonal hematopoiesis affects various diseases, including nonneoplastic diseases, highlights the potential role of the identification and functional analysis of mutated clones in unraveling unknown pathologies. In this review, we summarize the recent updates on clonal expansion in normal tissues and the natural history of cancer revealed through lineage analysis of noncancerous and cancerous tissues.
Collapse
Affiliation(s)
- Hirona Maeda
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- The Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| |
Collapse
|
5
|
Zhang B, Liu W, Ding X, Zhang W, Zhu J, Wang X. Characterization of the complete chloroplast genome sequence of Lycium qingshuiheense (Solanaceae). Mitochondrial DNA B Resour 2024; 9:517-521. [PMID: 38628907 PMCID: PMC11020591 DOI: 10.1080/23802359.2024.2341113] [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] [Received: 10/19/2023] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
Lycium qingshuiheense is a typical drought and salt-alkali-tolerant plant, which has been added to the new species of Lycium in recent years. Here, we first sequenced the complete chloroplast genome of L. qingshuiheense to investigate its evolutionary relationship within the family Solanaceae. Results suggested that the circular complete chloroplast genome of L. qingshuiheense was 154,945 bp in length, including a large single-copy (LSC) of 85,930 bp, a small single-copy (SSC) of 18,203 bp, and two inverted repeats (IRs) of 25,406 bp. The GC content accounts for 37.90% and annotated 131 genes, including 86 protein-coding genes, eight rRNA genes, and 37 tRNA genes. A neighbor-joining phylogenetic tree revealed that L. qingshuiheense was a sister species to L. ruthenicum. Our study provides a new insight into the systematic evolution of Lycium in the Solanaceae family.
Collapse
Affiliation(s)
- Bo Zhang
- Ningxia Technical College of Wine and Desertification Prevention, Yinchuan, China
| | - Wangsuo Liu
- Department of Chemical and Environmental Engineering, Hetao College, Bayannur, China
| | - Xueli Ding
- Ningxia Technical College of Wine and Desertification Prevention, Yinchuan, China
| | - Wei Zhang
- Qixin Wolfberry Seedling Professional Cooperative of Zhongning County, Zhongwei, China
| | - Jinzhong Zhu
- Qixin Wolfberry Seedling Professional Cooperative of Zhongning County, Zhongwei, China
| | - Xuejun Wang
- Qixin Wolfberry Seedling Professional Cooperative of Zhongning County, Zhongwei, China
| |
Collapse
|
6
|
Yin S, Gao Y. The complete chloroplast genome assembly of Castanopsis orthacantha Franch. 1899 (Fagaceae) in Southwestern China. Mitochondrial DNA B Resour 2024; 9:527-531. [PMID: 38628906 PMCID: PMC11020572 DOI: 10.1080/23802359.2024.2342940] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
Castanopsis orthacantha Franch. 1899 is one representative tree species distributed in the evergreen broad-leaved forests of southwestern China. This species is an important source of timber for manufacturing furniture, floors, and paper. It also plays a significant role in maintaining ecological balance and stability. To help with the genetic diversity assessment of C. orthacantha, we sequenced and assembled the first complete chloroplast genome. The length of the chloroplast genome was 160,588 bp, with a typical quadripartite structure (GenBank accession no. OR900101). The large single-copy (LSC), small single-copy (SSC), and two inverted repeats (IRs) were 90,237 bp, 18,953 bp, and 25,699 bp in length, respectively. We annotated one hundred and thirty genes across the chloroplast genome, including 86 protein-coding genes (79 are unique), 37 tRNA genes (29 are unique), and eight rRNA genes (four are unique). Seventeen genes had one intron, and four were detected with two introns. The maximum likelihood phylogeny suggested that C. orthacantha, C. lamontii, C. sclerophylla, and C. hainanensis formed a clade with a high bootstrap value. This newly sequenced chloroplast genome assembly will aid in the population genetic and phylogenetic studies of Castanopsis species in the future.
Collapse
Affiliation(s)
- Si Yin
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, China
| | - Yong Gao
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, China
| |
Collapse
|
7
|
Gao Y, Hu Y, Xu S, Liang H, Lin H, Yin TH, Zhao K. Characterisation of the mitochondrial genome and phylogenetic analysis of Toxocara apodemi (Nematoda: Ascarididae). J Helminthol 2024; 98:e33. [PMID: 38618902 DOI: 10.1017/s0022149x24000221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
We first sequenced and characterised the complete mitochondrial genome of Toxocara apodeme, then studied the evolutionary relationship of the species within Toxocaridae. The complete mitochondrial genome was amplified using PCR with 14 specific primers. The mitogenome length was 14303 bp in size, including 12 PCGs (encoding 3,423 amino acids), 22 tRNAs, 2 rRNAs, and 2 NCRs, with 68.38% A+T contents. The mt genomes of T. apodemi had relatively compact structures with 11 intergenic spacers and 5 overlaps. Comparative analyses of the nucleotide sequences of complete mt genomes showed that T. apodemi had higher identities with T. canis than other congeners. A sliding window analysis of 12 PCGs among 5 Toxocara species indicated that nad4 had the highest sequence divergence, and cox1 was the least variable gene. Relative synonymous codon usage showed that UUG, ACU, CCU, CGU, and UCU most frequently occurred in the complete genomes of T. apodemi. The Ka/Ks ratio showed that all Toxocara mt genes were subject to purification selection. The largest genetic distance between T. apodemi and the other 4 congeneric species was found in nad2, and the smallest was found in cox2. Phylogenetic analyses based on the concatenated amino acid sequences of 12 PCGs demonstrated that T. apodemi formed a distinct branch and was always a sister taxon to other congeneric species. The present study determined the complete mt genome sequences of T. apodemi, which provide novel genetic markers for further studies of the taxonomy, population genetics, and systematics of the Toxocaridae nematodes.
Collapse
Affiliation(s)
- Y Gao
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou Key Laboratory of Biomedicine and Advanced Dosage Forms, School of Life Sciences, Taizhou University, Zhejiang Taizhou318000, China
- Zhejiang-Malaysia Joint Laboratory for Bioactive Materials and Applied Microbiology, School of Life Sciences, Taizhou University, Zhejiang Taizhou318000, China
| | - Y Hu
- Taizhou City Center for Disease Control and Prevention, Zhejiang Taizhou318000, China
| | - S Xu
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou Key Laboratory of Biomedicine and Advanced Dosage Forms, School of Life Sciences, Taizhou University, Zhejiang Taizhou318000, China
- Zhejiang-Malaysia Joint Laboratory for Bioactive Materials and Applied Microbiology, School of Life Sciences, Taizhou University, Zhejiang Taizhou318000, China
| | - H Liang
- Taizhou City Center for Disease Control and Prevention, Zhejiang Taizhou318000, China
| | - H Lin
- Taizhou City Center for Disease Control and Prevention, Zhejiang Taizhou318000, China
| | - T H Yin
- Zhejiang-Malaysia Joint Laboratory for Bioactive Materials and Applied Microbiology, School of Life Sciences, Taizhou University, Zhejiang Taizhou318000, China
- Tunku Abdul Rahman University of Management and Technology, Jalan Genting Kelang, Kuala Lumpur 53300, Malaysia
| | - K Zhao
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou Key Laboratory of Biomedicine and Advanced Dosage Forms, School of Life Sciences, Taizhou University, Zhejiang Taizhou318000, China
- Zhejiang-Malaysia Joint Laboratory for Bioactive Materials and Applied Microbiology, School of Life Sciences, Taizhou University, Zhejiang Taizhou318000, China
| |
Collapse
|
8
|
Zhan Q, Gai Y, Zhao Y. Characterization of the complete mitochondrial genome of the Libelloides sibiricus (Neuroptera, Ascalaphidae). Mitochondrial DNA B Resour 2024; 9:493-499. [PMID: 38623174 PMCID: PMC11018059 DOI: 10.1080/23802359.2024.2339486] [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] [Received: 11/06/2023] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Libelloides sibiricus (Eversmann, 1850) is widely distributed in China, Korea and eastern Russia. To date, few studies have been conducted on this species, with the exception of morphological taxonomy studies. In this study, we sequenced the complete mitochondrial genome (mitogenome) of Libelloides sibiricus, which is 15,811 bp in length, with an overall A + T content of 74.8%, encoding 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes, and a control region. The gene arrangement and components of L. sibiricus are identical to those of most other Neuropteran species. TAA is utilized as the termination codon for most PCGs and TAG for nd1, however, nd6 and atp6 used the incomplete termination codon TA- and cox1, cox2, nd5, cytb had termination codons consisting of only T-. In addition, we selected all known 59 species of Neuroptera from NCBI, and used Sialis hamata, Sialis melania, Sialis longidens and Sialis jiyuni (Megaloptera: Sialidae) as the outgroup. Phylogenetic analysis suggested that the mitogenome of L. sibiricus was the most closely related to L. macaronius and all the owlflies formed the monophyletic group within the superfamily Myrmeleontoidea.
Collapse
Affiliation(s)
- Qingbin Zhan
- Department of Criminal Science and Technology, Nanjing Police University, Nanjing, Jiangsu, China
- Key Laboratory of State Forestry and Grassland Administration on Wildlife Evidence Technology, Nanjing, Jiangsu, China
| | - Yunpeng Gai
- School of Grassland Science, Beijing Forestry University, Nanjing, JiangsuChina
| | - Yang Zhao
- Research Institute of Pomology, Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, Nanjing, Jiangsu, China
| |
Collapse
|
9
|
Wang Q, Wu Y, Merchant A, Li E, Wei M, Zhang Y, Zhou X. The mitochondrial genome and life history of Tomostethus sinofraxini (Hymenoptera: Tenthredinidae), an emerging pest of Fraxinus chinensis. J Econ Entomol 2024; 117:564-577. [PMID: 38289982 DOI: 10.1093/jee/toae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/27/2023] [Accepted: 01/11/2024] [Indexed: 02/01/2024]
Abstract
Tomostethus sinofraxini Wang & Wei (a new name is proposed for Tomostethus fraxini Niu & Wei, 2022: Tomostethus sinofraxini Wang & Wei, nom. nov.), an emerging sawfly pest of the Chinese ash, Fraxinus chinensis, is now endemic to Beijing, Tianjin, Hebei, and Shandong provinces. Given the severity of its infestation and the speed of its range expansion, we studied the phylogenetic relationship of T. sinofraxini with other sawfly species and its life history to be better informed for the management strategies. The nearly complete T. sinofraxini mitogenome is 16,169 bp in length and encodes 2 ribosomal RNAs (rrnL and rrnS), 22 transfer RNAs (tRNAs), and 13 protein-coding genes. The nucleotide composition is biased toward adenine and thymine (A + T = 81.7%). In comparison to the architecture of the ancestral insect mitogenome, 2 transposition events occur on the IQM tRNA cluster, rearranging it from IQM to MQI. Our phylogenetic analysis suggests that T. sinofraxini belongs to a group composed of paraphyletic subfamilies Blennocampinae and Heterarthrinae. In addition, to document its life history, we observed T. sinofraxini development at 2 geographical locations in Beijing, China, with different altitudes. At Jiulong Mountain, with a higher altitude and a lower average temperature, the developmental time of egg, larval, and adult stages was 19%-31% longer than that observed at the Chinese Academy of Forestry. A basic understanding of biological traits and molecular signatures is the critical first step to develop an integrated pest management framework for this emerging pest of the Chinese ash.
Collapse
Affiliation(s)
- Qinghua Wang
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Beijing 100091, China
- Department of Entomology, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546, USA
| | - Yunfei Wu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Austin Merchant
- Department of Entomology, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546, USA
| | - Enjie Li
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Beijing 102300, China
| | - Meicai Wei
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Yongan Zhang
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Beijing 100091, China
| | - Xuguo Zhou
- Department of Entomology, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546, USA
- Department of Entomology, School of Integrative Biology, College of Liberal Arts & Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
10
|
Wang G, An J, Si J. The complete chloroplast genome sequence of Rhamnella wilsonii Schneid (Rhamnaceae). Mitochondrial DNA B Resour 2024; 9:488-492. [PMID: 38623175 PMCID: PMC11018004 DOI: 10.1080/23802359.2024.2339492] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Rhamnella wilsonii Schneid 1914 is a member of the Rhamnaceae and endemic to China. In this study, the complete chloroplast genome of R. wilsonii was sequenced and assembled. The complete chloroplast genome was 160,049 bp in length, including a pair of inverted repeats (IRs) of 26,502 bp, one large single copy (LSC) region of 88,274 bp and one small single copy (SSC) region of 18,771 bp. The genome contained 129 genes, including 8 rRNA genes, 37 tRNA genes and 84 protein-coding genes. The overall GC content of the complete chloroplast genome was 37.15%. The phylogenetic analysis demonstrated that R. wilsonii is closely related to R. martinni. This study provides basic information for further studies on the identification and evolution of R. wilsonii and Rhamnella from genomic perspective.
Collapse
Affiliation(s)
- Gaini Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Jilong An
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Jianping Si
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| |
Collapse
|
11
|
Liang YN, Cui N, Liang XB, Huang XY, Zhang W, Li H. The complete chloroplast genome sequence of Zanthoxylum ailanthoides Sieb. et. Zucc (Rutaceae): an important medicinal plant. Mitochondrial DNA B Resour 2024; 9:506-511. [PMID: 38623176 PMCID: PMC11018064 DOI: 10.1080/23802359.2024.2338260] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 03/28/2024] [Indexed: 04/17/2024] Open
Abstract
Zanthoxylum ailanthoides is a deciduous tree, with important medicinal and economic values. The complete chloroplast genome sequence of Z. ailanthoides was assembled and the phylogenetic relationship to other species was inferred in this study. The chloroplast genome is 157,209 bp in length, including two inverted repeats of 26,408 bp, a large single-copy of 86,099 bp and a small single copy of 18,294 bp. Moreover, the chloroplast genome contains 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the chloroplast genome is 38.4%. The phylogenetic analysis indicated that Z. ailanthoides was grouped with a clade containing the species of Z. multijugum, Z. calcicola, Z. oxyphyllum, Z. stenophyllum, and the genus was closely related to Phellodendron. This study contributes to a better understanding of the phylogenetic relationships among Zanthoxylum species.
Collapse
Affiliation(s)
- Yan-Ni Liang
- Modern Industry College of Liupao Tea, Wuzhou University, Wuzhou, China
| | - Nan Cui
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Xiao-Bin Liang
- Guangxi Zhongheng Chinese Medicinal Crops Industry Development Co., Ltd., Wuzhou, China
| | - Xi-Yang Huang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Wei Zhang
- Modern Industry College of Liupao Tea, Wuzhou University, Wuzhou, China
| | - Hong Li
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| |
Collapse
|
12
|
Tomida J, Miyoshi-Akiyama T, Kutsuna R, Tsutsuki H, Sawa T, Cnockaert M, Vandamme P, Kawamura Y. Proposal of Helicobacter higonensis sp. nov. isolated from a human clinical specimen, and emended description of Helicobacter valdiviensis Collado, 2014. Microbiol Immunol 2024. [PMID: 38599769 DOI: 10.1111/1348-0421.13127] [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: 09/14/2023] [Revised: 11/25/2023] [Accepted: 04/01/2024] [Indexed: 04/12/2024]
Abstract
We have previously isolated a gram-negative microaerophilic strain, PAGU2000T from a patient presenting with a fever in Kumamoto Prefecture, Japan. The present study aimed to comprehensively analyze the taxonomy of the isolated strain using a polyphasic approach. The 16S rRNA gene sequence analysis indicated that the strain was a member of enterohepatic Helicobacter. The strain PAGU2000T shared a 97.5% 16S rRNA gene nucleotide identity with Helicobacter valdiviensis, and this taxonomic position was confirmed by phylogenetic analysis of the GyrA amino acid sequences. The proposed strain PAGU2000T has a 1.482 Mbp chromosome with a DNA G + C content of 31.3 mol% and encodes 1520 predicted coding sequences. The average nucleotide identity between the strain PAGU2000T and type strain of H. valdiviensis was 70.3%, which was lower than the recommended threshold of 95% for species delineation. The strain PAGU2000T was a motile, non-spore-forming, and spiral-shaped bacterium, exhibiting catalase and oxidase activities but not urease and nitrate reduction. This study demonstrates that the isolate represents a novel species within enterohepatic Helicobacter, for which the name Helicobacter higonensis is proposed (type strain: PAGU2000T = GTC 16811T = LMG 33095T). In this study, we describe the phenotypic and morphological features of this strain and propose an emended description of some biochemical traits of H. valdiviensis.
Collapse
Affiliation(s)
- Junko Tomida
- Department of Microbiology, School of Pharmacy, Aichi Gakuin University, Nagoya, Japan
| | - Tohru Miyoshi-Akiyama
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan
| | - Ryo Kutsuna
- Department of Microbiology, School of Pharmacy, Aichi Gakuin University, Nagoya, Japan
| | - Hiroyasu Tsutsuki
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Tomohiro Sawa
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Margo Cnockaert
- Department of Biochemistry and Microbiology, Laboratory of Microbiology, Ghent University, Gent, Belgium
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Laboratory of Microbiology, Ghent University, Gent, Belgium
| | - Yoshiaki Kawamura
- Department of Microbiology, School of Pharmacy, Aichi Gakuin University, Nagoya, Japan
| |
Collapse
|
13
|
Miliotis G, Sengupta P, Hameed A, Chuvochina M, McDonagh F, Simpson AC, Parker CW, Singh NK, Rekha PD, Morris D, Raman K, Kyrpides NC, Hugenholtz P, Venkateswaran K. Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov. mBio 2024; 15:e0018124. [PMID: 38477597 PMCID: PMC11005411 DOI: 10.1128/mbio.00181-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 03/14/2024] Open
Abstract
A comprehensive microbial surveillance was conducted at NASA's Mars 2020 spacecraft assembly facility (SAF), where whole-genome sequencing (WGS) of 110 bacterial strains was performed. One isolate, designated 179-BFC-A-HST, exhibited less than 80% average nucleotide identity (ANI) to known species, suggesting a novel organism. This strain demonstrated high-level resistance [minimum inhibitory concentration (MIC) >256 mg/L] to third-generation cephalosporins, including ceftazidime, cefpodoxime, combination ceftazidime/avibactam, and the fourth-generation cephalosporin cefepime. The results of a comparative genomic analysis revealed that 179-BFC-A-HST is most closely related to Virgibacillus halophilus 5B73CT, sharing an ANI of 78.7% and a digital DNA-DNA hybridization (dDDH) value of 23.5%, while their 16S rRNA gene sequences shared 97.7% nucleotide identity. Based on these results and the recent recognition that the genus Virgibacillus is polyphyletic, strain 179-BFC-A-HST is proposed as a novel species of a novel genus, Tigheibacillus jepli gen. nov., sp. nov (type strain 179-BFC-A-HST = DSM 115946T = NRRL B-65666T), and its closest neighbor, V. halophilus, is proposed to be reassigned to this genus as Tigheibacillus halophilus comb. nov. (type strain 5B73CT = DSM 21623T = JCM 21758T = KCTC 13935T). It was also necessary to reclassify its second closest neighbor Virgibacillus soli, as a member of a novel genus Paracerasibacillus, reflecting its phylogenetic position relative to the genus Cerasibacillus, for which we propose Paracerasibacillus soli comb. nov. (type strain CC-YMP-6T = DSM 22952T = CCM 7714T). Within Amphibacillaceae (n = 64), P. soli exhibited 11 antibiotic resistance genes (ARG), while T. jepli encoded for 3, lacking any known β-lactamases, suggesting resistance from variant penicillin-binding proteins, disrupting cephalosporin efficacy. P. soli was highly resistant to azithromycin (MIC >64 mg/L) yet susceptible to cephalosporins and penicillins. IMPORTANCE The significance of this research extends to understanding microbial survival and adaptation in oligotrophic environments, such as those found in SAF. Whole-genome sequencing of several strains isolated from Mars 2020 mission assembly cleanroom facilities, including the discovery of the novel species Tigheibacillus jepli, highlights the resilience and antimicrobial resistance (AMR) in clinically relevant antibiotic classes of microbes in nutrient-scarce settings. The study also redefines the taxonomic classifications within the Amphibacillaceae family, aligning genetic identities with phylogenetic data. Investigating ARG and virulence factors (VF) across these strains illuminates the microbial capability for resistance under resource-limited conditions while emphasizing the role of human-associated VF in microbial survival, informing sterilization practices and microbial management in similar oligotrophic settings beyond spacecraft assembly cleanrooms such as pharmaceutical and medical industry cleanrooms.
Collapse
Affiliation(s)
- Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Asif Hameed
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Australia
| | - Francesca McDonagh
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Anna C. Simpson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Ceth W. Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Punchappady D. Rekha
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Nikos C. Kyrpides
- US Department of Energy Joint Genome Institute, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Australia
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| |
Collapse
|
14
|
Choi JH, Shin HD, Choi YJ. First Report of Anthracnose Caused by Colletotrichum spaethianum on Hosta longipes in Korea. Plant Dis 2024. [PMID: 38595059 DOI: 10.1094/pdis-02-24-0340-pdn] [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: 04/11/2024]
Abstract
Hosta longipes (Franch. & Sav.) Matsum. (Asparagaceae) is a perennial, herbaceous plant, native to Japan and Korea (Lee et al. 2021). In Korea, the plant is used as an edible vegetable and ornamental (Kang and Ju 2015). During 2021-2022, anthracnose symptoms were observed on leaves of H. longipes with over 70% disease incidence in Wanju-gun (35°38'47''N; 127°31'16''E) and Jangsu-gun (35°35'31''N; 127°30'03''E) in Jeollabuk-do, Korea. The disease initially appeared on old leaves, gradually spreading to young ones. The symptoms were characterized as yellow to white discoloration on the upper leaf surface with black necrotic tissue in the center of the lesion. Three H. longipes samples with anthracnose symptoms were collected. From each, a monoconidial isolate was obtained and then deposited in the Korea Agricultural Culture Collection (accession Nos. KACC 410038, 410391, and 410443). The dried specimens were housed at the herbarium of Jeonbuk National University (JBNU0129, 0137) and Korea University (KUS-F33379). Conidiomata was acervular, 65 to 80 × 56 to 70 µm in diam. Setae were dark brown, 2 to 4-septate, 63 to 161 µm long, being formed on a pale brown cushion. Conidia were hyaline, smooth-walled, aseptate, slightly curved, base truncate, 3.9 to 5.1 × 17 to 23 µm. The appressoria were solitary, olivaceous-brown, ovoid or irregularly shaped. Two-week-old colonies grown on PDA at 25 ℃ were 20-25 mm in diameter, initially white, then turned gray with age, with cottony aerial mycelium. The morphological and cultural characteristics of the fungus were consistent with those of Colletotrichum spaethianum (Allesch.) Damm, P.F. Cannon & Crous (Damm et al. 2012). To confirm morphology-based identification, the nucleotide sequences of the internal transcribed spacer (ITS) rDNA region, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), actin (actA), chitin synthase (CHS1), histone (HIS3) and tubulin (TUB2) genes were determined for KACC410443, as outlined by Cannon et al. (2012) and Damm et al. (2009). The resulting sequences were submitted into GenBank (PP000829 for ITS, PP133094 for GAPDH, PP083418 for actA, PP133091 for CHS1, PP133097 for HIS3, and PP133099 for TUB2) and compared with reference sequences in GenBank using BLASTn search tool. The results showed a 100% match with C. spaethianum (MT611068), C. incanum (MN880260) and C. truncatum (EF016303) for ITS, and 100% with C. spaethianum for GAPDH (MH370513), actA (MH045677), CHS1 (MH370520), HIS3 (MH985161), and TUB (MH456884). Pathogenicity was tested by inoculating conidial suspension (1 ×104 cfu/ml) of three-week-old fungal colonies of the isolate KACC410443 onto leaves of three healthy potted plants. Prior to inoculation, leaves were deliberately wounded by pinpricking with a sterilized needle. Two wounded but non-inoculated plants served as controls. Plants were maintained in a greenhouse at 25 to 30 °C. Inoculated plants developed anthracnose symptoms after eight days, while the control plants remained symptomless. The fungus isolated from the inoculated plants was morphologically identical to that observed initially, fulfilling Koch's postulates. To our knowledge, there is no previous record of C. spaethianum on H. longipes, although C. spaethianum has been reported to infect another species, H. plantaginea (Cheon and Jeon 2016). This is the first report of this fungus on H. longipes in Korea (KSPP 2024) and globally (Farr and Rossman 2024). The anthracnose on this ornamental plant can be considered a new severe threat to planting strategies in gardens.
Collapse
Affiliation(s)
- Joon-Ho Choi
- Jeonbuk National University, 26714, Agricultural Biology, 백제대로 567, Jeonju, Korea (the Republic of), 54896;
| | - Hyeon-Dong Shin
- Korea University, Environmental Science & Ecological Engineering, Seoul, Seoul, Korea (the Republic of), 02841;
| | - Young-Joon Choi
- College of Natural Sciences, Kunsan National University, Department of Biology, 558 Daehak-ro, Gunsan, Korea (the Republic of), 54150;
| |
Collapse
|
15
|
Cafardi JM, Lin HT, Lange L, Kelley L, Lemon K, Odegard EA, Meeds HL, Blackard JT, Feinberg J. Vertical Transmission of Hepatitis C Virus Among Women with a History of Injection Opioid Use. Clin Infect Dis 2024:ciae177. [PMID: 38576379 DOI: 10.1093/cid/ciae177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/13/2024] [Accepted: 03/27/2024] [Indexed: 04/06/2024] Open
Abstract
We evaluated vertical transmission and linkage to care in women with HCV and history of injection drug use employing co-localized testing and treatment. Transmission occurred in 1 of 23 infants, with mother-infant genetic distance of 1.26%. Rates for infant testing, maternal linkage and cure were 77%, 52%, and 100%, respectively.
Collapse
Affiliation(s)
- John M Cafardi
- Division of Infectious Diseases, Department of Medicine, The Christ Hospital and the Lindner Research Institute, Cincinnati, OH USA
| | - Hong T Lin
- Division of Digestive Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Lana Lange
- Department of Gynecology and Obstetrics, The Christ Hospital, Cincinnati, OH USA
| | - Lacey Kelley
- Department of Behavioral Medicine and Psychiatry, West Virginia University School of Medicine, Morgantown, WV USA
| | - Kelly Lemon
- Department of Gynecology and Obstetrics, West Virginia University School of Medicine, Morgantown, WV USA
| | - Elizabeth A Odegard
- Division of Digestive Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Heidi L Meeds
- Division of Digestive Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Jason T Blackard
- Division of Digestive Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Judith Feinberg
- Departments of Behavioral Medicine and Psychiatry & Medicine/Infectious Diseases, West Virginia University School of Medicine, Morgantown, WV USA
| |
Collapse
|
16
|
Yi L, Wang Y, Li Y, Zhang D, Tong W. Characterization of the complete chloroplast genome sequence of Camellia tetracocca (Theaceae). Mitochondrial DNA B Resour 2024; 9:461-464. [PMID: 38591053 PMCID: PMC11000617 DOI: 10.1080/23802359.2024.2316067] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 02/04/2024] [Indexed: 04/10/2024] Open
Abstract
Camellia tetracocca H.T. Chang 1981 is an important wild relative of cultivated tea plants. Its leaves are widely used by local people to make tea, showing great economic and breeding values. We here report the complete chloroplast genome of C. tetracocca using Illumina sequencing technology. The complete chloroplast genome of C. tetracocca is 157,026 bp in length, and structurally contains a pair of inverted repeat regions (IRa and IRb, 26,052 bp) separated by a large single-copy region (LSC, 86,669 bp) and a small single-copy region (SSC, 18,253 bp). It is composed of 131 predicted genes, including 86 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. The overall GC content is 37.31%. Phylogenetic analysis among four Camellia species and 11 other close species reveals a close relationship between C. tetracocca and C. gymnogyna.
Collapse
Affiliation(s)
- Lianghui Yi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Yanli Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Yunze Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Dandan Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| |
Collapse
|
17
|
Gao Y, Yin S. Assembly and analysis of the chloroplast genome of Amorphophallus kachinensis Engler & Gehrmann (Araceae) from Southwestern China: implications for conservation and utilization. Mitochondrial DNA B Resour 2024; 9:452-456. [PMID: 38586510 PMCID: PMC10993747 DOI: 10.1080/23802359.2024.2338550] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/31/2024] [Indexed: 04/09/2024] Open
Abstract
Konjac glucomannan consists of D-mannose and D-glucose units and is a hydrocolloid obtained from the corm of Amorphophallus species. Due to its bioactive properties, biodegradability, and hydrophilic ability, glucomannan is widely used in the fields of food, medicine, and industry. Amorphophallus species have been cultivated as cash crops in many Asian countries. Amorphophallus kachinensis Engler & Gehrmann 1911 is naturally distributed in southwestern China, Laos, and northern Thailand. To help the genetic assessment and conservation of this species, the first chloroplast genome of A. kachinensis was sequenced on the Illumina sequencing platform. We assembled the chloroplast genome using the software GetOrganelle and annotated the genome by Geseq and Cpgavas 2. The assembled chloroplast genome was 173,330 bp long, and the average GC content was 35% (GenBank accession number: PP072244). The chloroplast genome of A. kachinensis contained one large single copy, one small single copy, and two inverted repeats, with lengths of 92,030 bp, 15,118 bp, 33,091 bp, and 33,091 bp, respectively. We successfully annotated 132 genes across the genome, which was consistent with other Amorphophallus species. The phylogenetic tree indicates a sub-divergence in the Amorphophallus genus with two main genetic groups detected among eight species. The two genetic groups should be treated as distinct evolutionarily significant units when making conservation strategies. Our study enriched the chloroplast genome resources of the Amorphophallus genus and could help future phylogeographic studies, protection, and utilization of wild resources.
Collapse
Affiliation(s)
- Yong Gao
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| | - Si Yin
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| |
Collapse
|
18
|
Jang JE, Jeong HJ, Kim AL, Choi YR, Lazkov GA, Jang CG, Choi HJ, Gil HY. The complete chloroplast genome of Eremurus zoae Vved. (Asphodelaceae), an endemic species of Kyrgyz Republic. Mitochondrial DNA B Resour 2024; 9:437-441. [PMID: 38586509 PMCID: PMC10993749 DOI: 10.1080/23802359.2024.2336003] [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] [Received: 12/01/2023] [Accepted: 03/23/2024] [Indexed: 04/09/2024] Open
Abstract
Eremurus zoae Vved. 1971 is a perennial herbaceous plant in the family Asphodelaceae and an endemic species of the Kyrgyz Republic; however, its complete chloroplast genome sequence has not been reported. Here, we investigated the complete chloroplast (cp) genome of E. zoae using next-generation sequencing. The cp genome was 153,744 bp long, with a large single copy (84,020 bp), a small single copy (16,766 bp), and a pair of inverted repeats (26,479 bp). The genome encodes 132 genes, including 86 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis revealed that the genus Eremurus forms a monophyletic group and E. zoae is closely related to E. chinensis. This study provides a molecular foundation for future phylogenetic studies of Eremurus.
Collapse
Affiliation(s)
- Ju Eun Jang
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
| | - Hyeon Jin Jeong
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
| | - Aleksey L. Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
| | - Ye-Rim Choi
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
| | - Georgii A. Lazkov
- Institute for Biology, National Academy of Sciences, Bishkek, Kyrgyzstan
| | - Chang-Gee Jang
- Department of Biology Education, Kongju University, Gongju, South Korea
| | - Hyeok Jae Choi
- Department of Biology & Chemistry, Changwon National University, Changwon, South Korea
| | - Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, South Korea
| |
Collapse
|
19
|
Zhou H, Zhang H. The complete chloroplast genome of the medicinally important plant Plumbago zeylanica L. (plumbaginaceae) and phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:428-431. [PMID: 38586506 PMCID: PMC10993748 DOI: 10.1080/23802359.2024.2333574] [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] [Received: 11/22/2023] [Accepted: 03/15/2024] [Indexed: 04/09/2024] Open
Abstract
Plumbago zeylanica L. 1753 is a medicinally-important herb in family Plumbaginaceae. In this study, we assembled and reported the complete chloroplast genome of P. zeylanica. The plastome of P. zeylanica was 169,178 bp, including a large single-copy region of 92,135 bp, a small single-copy region (SSC) of 13,455 bp and a pair of inverted repeat regions (IRs) of 31,794 bp. It contained 124 genes, including 79 protein-coding genes, 37 tRNA genes and eight rRNA genes. Phylogenetic analysis showed that P. zeylanica formed a close relationship with P. auriculata in Plumbago. The first complete chloroplast genome report of P. zeylanica providing an opportunity to explore the genetic diversity, and would be also helpful in the species identification and conservation.
Collapse
Affiliation(s)
- Hao Zhou
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
20
|
Zeng Q, Chen YJ, Liu M, Wang C. Characteristics of the complete mitochondrial genome of Gerres limbatus (Cuvier, 1830) (Perciformes: Gerreidae). Mitochondrial DNA B Resour 2024; 9:419-422. [PMID: 38586512 PMCID: PMC10993760 DOI: 10.1080/23802359.2024.2333571] [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] [Received: 10/17/2023] [Accepted: 03/15/2024] [Indexed: 04/09/2024] Open
Abstract
The saddleback silver-biddy Gerres limbatus (Cuvier 1830) is distributed in Indo-West Pacific Oceans and associated with shallow coastal marine waters and estuaries. In this study, the complete mitochondrial genome of G. limbatus was firstly documented, which is 16,730 bp in length, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The overall base composition of the mitochondrial genome is 26.42% A, 28.68% C, 27.32% T, and 17.58% G. The Maximum Likelihood phylogenetic tree was constructed based on COI gene of the 31 species from the family Gerreidae, with Heteroclinus puellarum and Hypopterus macropterus as outgroups. It revealed that G. erythrourus was placed as the sister group to G. limbatus.
Collapse
Affiliation(s)
- Qi Zeng
- College of Ocean and Earth Sciences, Xiamen University, Xiamen City, Fujian Province, China
| | - Yu-jia Chen
- College of Ocean and Earth Sciences, Xiamen University, Xiamen City, Fujian Province, China
| | - Min Liu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen City, Fujian Province, China
| | - Chen Wang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen City, Fujian Province, China
| |
Collapse
|
21
|
Hou WJ, Men WX, Xing YP, Yang YY, Xu L, Kang TG, Song YY. The complete chloroplast genome of Lagochilus ilicifolius Bunge ex Bentham, Labiat. Gen. 1834 (Lamiaceae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:423-427. [PMID: 38586511 PMCID: PMC10993758 DOI: 10.1080/23802359.2024.2334013] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
Lagochilus ilicifolius Bunge ex Bentham, Labiat. Gen is a perennial herb with much-branched stems native to Nei Mongol, Ningxia, Gansu, N Shaanxi. It can be used clinically as a hemostatic agent. The chloroplast genome length is 151,466 bp. It contained two inverted repeat regions of 25,660 bp each, a large single-copy region of length 82,504 bp, and a small single-copy region of length 17,642 bp. Also, the GC content is 38.6%. There were 133 genes annotated, including 88 known protein-coding genes, 37 tRNAs, and eight rRNAs. The phylogenetic tree was constructed using Bayesian method for plastome data of 29 species. The entire chloroplast genome of L. ilicifolius within the Lamiaceae is the first to reveal genetic taxonomy at the molecular level, and the new phylogenetic tree data can be used for future evolutionary studies.
Collapse
Affiliation(s)
- Wen-Juan Hou
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Wen-Xiao Men
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yan-Ping Xing
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yan-yun Yang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Liang Xu
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Ting-Guo Kang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yue-Yue Song
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| |
Collapse
|
22
|
Luo J, Li J, Wang C, Li M, Hu S, Lu K, Wang G. Rubellicoccus peritrichatus gen. nov., sp. nov., isolated from crustose coralline algae in a coral aquarium. Int J Syst Evol Microbiol 2024; 74. [PMID: 38568201 DOI: 10.1099/ijsem.0.006325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
A Gram-stain-negative, motile, aerobic, non-spore-forming coccus, designated strain CR14T, was isolated from crustose coralline algae. Cells grew at 20-30 °C (optimum, 25 °C), at pH 6-9 (optimum, pH 7.6) and with NaCl concentrations of 0.5-9 % (w/v; optimum, 2-4 %). Global alignment based on 16S rRNA gene sequences indicated strain CR14T is closest to Ruficoccus amylovorans JCM 31066T with an identity of 92 %. The average nucleotide identity and average amino acid identity values between CR14T and R. amylovorans JCM 31066T were 68.4 and 59.9 %, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CR14T forms an independent branch within the family Cerasicoccaeae, which was consistent with the phylogenomic results. The sole isoprenoid quinone was MK-7. The major fatty acids were C14 : 0, C18 : 1 ω9c, C19 : 0 cyc 9,10 DMA, C16 : 0, and C18 : 2 ω6c. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and two unidentified lipids. The genome DNA G+C content was 48.7 mol%. Based on morphological, physiological and chemotaxonomic characteristics, strain CR14T is suggested to represent a novel species in a new genus, for which the name Rubellicoccus peritrichatus gen. nov., sp. nov. is proposed. The type strain is CR14T (=MCCC 1K03845T=KCTC 72139T).
Collapse
Affiliation(s)
- Jixin Luo
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Jin Li
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Chenyan Wang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Mi Li
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Siyu Hu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Kun Lu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Guanghua Wang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| |
Collapse
|
23
|
Ribeiro I, Correia S, Blümel M, Albuquerque P, Gorb SN, Mendes MV, Tasdemir D, Mucha AP, Carvalho MF. Streptomyces profundus sp. nov., a novel marine actinobacterium isolated from deep-sea sediment of Madeira Archipelago, Portugal. Int J Syst Evol Microbiol 2024; 74. [PMID: 38639738 DOI: 10.1099/ijsem.0.006341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
A novel strain, MA3_2.13T, was isolated from deep-sea sediment of Madeira Archipelago, Portugal, and characterized using a polyphasic approach. This strain produced dark brown soluble pigments, bronwish black substrate mycelia and an aerial mycelium with yellowish white spores, when grown on GYM 50SW agar. The main respiratory quinones were MK-10(H4), MK-10(H6) and MK-10(H8). Diphosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids and two glycophospholipids were identified as the main phospholipids. The major cellular fatty acids were iso-C16 : 1, iso-C16 : 0, anteiso-C17 : 1 and anteiso-C17 : 0. Phylogenetic analyses based on 16S rRNA gene showed that strain MA3_2.13T is a member of the genus Streptomyces and was most closely related to Streptomyces triticirhizae NEAU-YY642T (NR_180032.1; 16S rRNA gene similarity 97.9 %), Streptomyces sedi YIM 65188T (NR_044582.1; 16S rRNA gene similarity 97.4 %), Streptomyces mimosae 3MP-10T (NR_170412.1; 16S rRNA gene similarity 97.3 %) and Streptomyces zhaozhouensis NEAU-LZS-5T (NR_133874.1; 16S rRNA gene similarity 97.0 %). Genome pairwise comparisons with closest related type strains retrieved values below the threshold for species delineation suggesting that strain MA3_2.13T represents a new branch within the genus Streptomyces. Based on these results, strain MA3_2.13T (=DSM 115980T=LMG 33094T) is proposed as the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces profundus sp. nov. is proposed.
Collapse
Affiliation(s)
- Inês Ribeiro
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research,University of Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal
- ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | - Sofia Correia
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research,University of Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal
- ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- FCUP - Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Pedro Albuquerque
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
- IBMC - Institute for Molecular and Cell Biology, University of Porto, Porto, Portugal
| | - Stanislav N Gorb
- Functional Morphology and Biomechanics, Zoological Institute, Kiel University, Kiel, Germany
| | - Marta V Mendes
- ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
- IBMC - Institute for Molecular and Cell Biology, University of Porto, Porto, Portugal
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Kiel University, Kiel, Germany
| | - Ana P Mucha
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research,University of Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal
- FCUP - Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Maria F Carvalho
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research,University of Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal
- ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| |
Collapse
|
24
|
Cardinali I, Ceccarelli M. Molecular and cytogenetic analyses in Geranium macrorrhizum L. wild Italian plants. R Soc Open Sci 2024; 11:240035. [PMID: 38601032 PMCID: PMC11004676 DOI: 10.1098/rsos.240035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 04/12/2024]
Abstract
Geranium macrorrhizum L. is a herbaceous species native to southern Europe and was introduced in central Europe and North America. It is also widely distributed in Italy. In this study, molecular and cytogenetic analyses were carried out on 22 wild plants, collected in central and southern Italy, compared with five cultivated plants, with the main purpose to identify those living near the Marmore waterfalls in central Italy, recently described as the new species Geranium lucarinii. Four barcoding markers (rbcL, matK, trnH-psbA intergenic spacer and internal transcribed spacer region) were sequenced and their variability among the plants was evaluated. Chromosome numbers were determined and 45S rDNA was physically mapped by fluorescence in situ hybridization. Moreover, genomic affinity between wild and cultivated plants was evaluated by genomic in situ hybridization. The results of this study supported that all the plants belong to G. macrorrhizum, including the Marmore population. Barcoding analyses showed a close similarity among the wild plants, and a differentiation, although not significant, between the wild plants on one hand and the cultivated plants on the other. Integrated studies focusing on morphological, genetic and ecological characterization of a larger number of wild populations would allow us to know the extent of the variability within the species.
Collapse
Affiliation(s)
- Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia06123, Italy
| | - Marilena Ceccarelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia06123, Italy
| |
Collapse
|
25
|
Wajid A, Maqsood Q, Ben Said M, Sherzada S, Nooruzzaman M, Batool A, Yin R, Sabra M, Hanif A, Azam Kakar M, Hussain T, Ahmed N. Geographic distribution and genetic diversity of Newcastle disease virus in pigeons from Pakistan. Avian Pathol 2024; 53:134-145. [PMID: 38037737 DOI: 10.1080/03079457.2023.2291107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/29/2023] [Indexed: 12/02/2023]
Abstract
RESEARCH HIGHLIGHTS Virulent NDV genotypes were repeatedly isolated from pigeons.Evidence of epidemiological links among viruses isolated from various locations.Distinct phylogenetic branches suggest separate, simultaneous evolution of NDVs.Study information could be helpful in the development of an effective vaccine.
Collapse
Affiliation(s)
- Abdul Wajid
- Department of Biotechnology, FLS&I, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Quratulain Maqsood
- Centre for Applied Molecular Biology, University of the Punjab Quaid-I-Azam Campus, Lahore, Pakistan
| | - Mourad Ben Said
- Department of Basic Sciences, Higher Institute of Biotechnology of Sidi Thabet, University of Manouba, Manouba, Tunisia
- Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, University of Manouba, Manouba, Tunisia
| | - Shahid Sherzada
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Mohammed Nooruzzaman
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Andleeb Batool
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Renfu Yin
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Mahmoud Sabra
- Department of Poultry Diseases, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Atif Hanif
- Department of Botany and Microbiology, King Saud University, Riyadh, Saudi Arabia
| | | | - Tanveer Hussain
- Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Nazeer Ahmed
- Department of Biotechnology, FLS&I, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| |
Collapse
|
26
|
Lo Presti A, Rubino S, Ibba G, Ambrosio L, Di Martino A, Ferraro F, Rapiti A, Maraglino F, Frisicale EM, Rezza G, Angioj F, Uzzau S, Contini ML, Manca S, Coghe F, Orrù G, Palamara AT, Stefanelli P. An outbreak of COVID-19 after a pilgrimage to Medjugorje due to Delta sub-lineages. J Infect Dev Ctries 2024; 18:332-336. [PMID: 38635610 DOI: 10.3855/jidc.18652] [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: 06/01/2023] [Accepted: 10/18/2023] [Indexed: 04/20/2024] Open
Abstract
INTRODUCTION A COVID-19 outbreak occurred at the end of October 2021 among pilgrims returning from Medjugorje (Bosnia and Herzegovina). METHODOLOGY Whole genome sequencing (WGS) of SARS-CoV-2, epidemiological data, and phylogenetic analysis were used to reconstruct outbreak dynamics. RESULTS The results suggest that only in one case, associated with the SARS-CoV-2 sub-lineage AY.9.2, it is possible to trace back the place of contagion to Medjugorje, while the other cases were likely to be acquired in the country of origin. CONCLUSIONS The combined use of phylogenetic data derived from WGS, and epidemiological data allowed us to study epidemic dynamics and to formulate a possible hypothesis on the place of exposure to SARS-CoV-2. The identification of different sub-lineages of the SARS-CoV-2 Delta variant also suggested that different chains of transmission contributed to the outbreak.
Collapse
Affiliation(s)
| | - Salvatore Rubino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Gabriele Ibba
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Luigina Ambrosio
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Angela Di Martino
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Federica Ferraro
- Ministry of Health, Directorate-General for Health Prevention, Rome, Italy
| | - Alessia Rapiti
- Ministry of Health, Directorate-General for Health Prevention, Rome, Italy
| | | | | | - Giovanni Rezza
- Ministry of Health, Directorate-General for Health Prevention, Rome, Italy
| | - Flavia Angioj
- Microbiology and Virology Unit, Azienda Ospedaliera Universitaria, Sassari, Italy
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Maria Luciana Contini
- Servizio igiene e sanità pubblica, Azienda Ospedaliera Universitaria, Sassari, Italy
| | - Stefania Manca
- Servizio igiene e sanità pubblica, Azienda Ospedaliera Universitaria, Sassari, Italy
| | - Ferdinando Coghe
- Laboratorio Analisi Chimico Cliniche e Microbiologia, Azienda Ospedaliera Universitaria di Cagliari, Cagliari, Italy
| | - Germano Orrù
- Molecular Biology, Department of Surgical Sciences, University of Cagliari, Cagliari, Italy
| | | | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| |
Collapse
|
27
|
Zheng W, Liu J, Zhao W, Zhao Z, Lan Z, Wen J. The complete chloroplast genomes of three Alismataceae species, including the medicinally important Alisma orientale. Mitochondrial DNA B Resour 2024; 9:385-389. [PMID: 38562439 PMCID: PMC10984228 DOI: 10.1080/23802359.2024.2320419] [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] [Received: 12/06/2023] [Accepted: 02/13/2024] [Indexed: 04/04/2024] Open
Abstract
Alismataceae is one of the early diverged families of monocotyledonous plants. We report the complete chloroplast genomes of three Alisma species, including Alisma orientale (Sam.) Juzep. 1934, A. subcordatum Raf. 1908, and A. triviale Pursh 1813, of which A. orientale is a traditional Chinese medical plant used widely to treat diuretics, diabetes, hepatitis, and inflammation. We sequenced the complete chloroplast genomes with the Illumina Nova-Seq 6000 platform using herbarium collections. The chloroplast genomes of A. orientale, A. subcordatum and A. triviale are 159,861 bp, 160,180 bp, and 159,727 bp in length, respectively. The three chloroplast genomes each contain 113 genes, including four rRNAs, 30 tRNAs genes, and 79 protein-coding genes, and the average GC content is 36.0%. Based on the whole chloroplast genomes of 19 species of Alismataceae and the close allies, the medicinally important A. orientale was found to be closely related to another medicinal plant Alisma plantago-aquatica L. 1753 in the phylogenetic analysis. The genus Alisma was supported to be monophyletic.
Collapse
Affiliation(s)
- Wen Zheng
- School of Pharmacy/College of Modern Chinese Medicine Industry, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jing Liu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Wenqi Zhao
- School of Pharmacy/College of Modern Chinese Medicine Industry, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zongyi Zhao
- School of Pharmacy/College of Modern Chinese Medicine Industry, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhiqiong Lan
- School of Pharmacy/College of Modern Chinese Medicine Industry, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC, USA
| |
Collapse
|
28
|
Huang G, Hu Y, Li F, Zuo X, Wang X, Li F, Li R. Genome-wide characterization of heavy metal-associated isoprenylated plant protein gene family from Citrus sinensis in response to huanglongbing. Front Plant Sci 2024; 15:1369883. [PMID: 38601304 PMCID: PMC11004388 DOI: 10.3389/fpls.2024.1369883] [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: 01/13/2024] [Accepted: 03/12/2024] [Indexed: 04/12/2024]
Abstract
Introduction Heavy metal-associated isoprenylated plant proteins (HIPPs) play vital roles in maintaining heavy metal balance and responding to both biotic and abiotic stresses in vascular plants. However, the role of HIPPs in the response to Huanglongbing (HLB), a harmful disease of citrus caused by the phloem-colonizing bacterium Candidatus Liberibacter asiaticus (CLas), has not been examined. Methods and results In this study, a total of 26 HIPP genes were identified in Citrus sinensis, and they were grouped into 5 clades. The CsHIPP genes are distributed on 8 chromosomes and exhibited considerable synteny with HIPPs found in Arabidopsis thaliana. Additionally, we analyzed the gene structure, conserved motifs and domains of the CsHIPPs. Various cis-acting elements related to plant hormones and stress responses were identified in the promoters of CsHIPPs. Public transcriptome data and RT-qPCR analysis showed that the expression level of CsHIPP03 was significantly reduced in samples infected by CLas and Xanthomonas citri ssp. citri (Xcc). Furthermore, silencing the homologous gene of CsHIPP03 in Nicotiana benthamiana increased the disease resistance of plants to bacteria. Discussion Our results provide a basis for functional studies of HIPP gene family in C. sinensis, highlighting their functions in bacterial resistance, and improve our understanding to the susceptibility mechanism of HLB.
Collapse
Affiliation(s)
- Guiyan Huang
- College of Life Sciences, Gannan Normal University, Ganzhou, China
- China-USA Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Yanan Hu
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Fuxuan Li
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Xiru Zuo
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Xinyou Wang
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Fengyao Li
- College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Ruimin Li
- College of Life Sciences, Gannan Normal University, Ganzhou, China
- China-USA Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, Jiangxi, China
| |
Collapse
|
29
|
Li T, Li H, Zhu C, Yang K, Lin Z, Wang J, Gao Z. Unveiling the Biological Function of Phyllostachys edulis FBA6 ( PeFBA6) through the Identification of the Fructose-1,6-Bisphosphate Aldolase Gene. Plants (Basel) 2024; 13:968. [PMID: 38611497 PMCID: PMC11013174 DOI: 10.3390/plants13070968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024]
Abstract
Fructose-1,6-bisphosphate aldolase (FBA) is a pivotal enzyme in various metabolic pathways, including glycolysis, gluconeogenesis, and the Calvin cycle. It plays a critical role in CO2 fixation. Building on previous studies on the FBA gene family in Moso bamboo, our study revealed the biological function of PeFBA6. To identify CSN5 candidate genes, this study conducted a yeast two-hybrid library screening experiment. Subsequently, the interaction between CSN5 and PeFBA6 was verified using yeast two-hybrid and LCI experiments. This investigation uncovered evidence that FBA may undergo deubiquitination to maintain glycolytic stability. To further assess the function of PeFBA6, it was overexpressed in rice. Various parameters were determined, including the light response curve, CO2 response curve, and the levels of glucose, fructose, sucrose, and starch in the leaves of overexpressing rice. The results demonstrated that overexpressed rice exhibited a higher saturation light intensity, net photosynthetic rate, maximum carboxylation rate, respiration rate, and increased levels of glucose, fructose, and starch than wild-type rice. These findings indicated that PeFBA6 not only enhanced the photoprotection ability of rice but also improved the photosynthetic carbon metabolism. Overall, this study enhanced our understanding of the function of FBA and revealed the biological function of PeFBA6, thereby providing a foundation for the development of excellent carbon fixation bamboo varieties through breeding.
Collapse
Affiliation(s)
- Tiankuo Li
- Key Laboratory of State Forestry and Grassland Administration/Beijing on Bamboo and Rattan Science and Technology, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Hui Li
- Key Laboratory of State Forestry and Grassland Administration/Beijing on Bamboo and Rattan Science and Technology, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Chenglei Zhu
- Key Laboratory of State Forestry and Grassland Administration/Beijing on Bamboo and Rattan Science and Technology, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Kebin Yang
- Key Laboratory of State Forestry and Grassland Administration/Beijing on Bamboo and Rattan Science and Technology, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Zeming Lin
- Key Laboratory of State Forestry and Grassland Administration/Beijing on Bamboo and Rattan Science and Technology, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Jiangfei Wang
- Key Laboratory of State Forestry and Grassland Administration/Beijing on Bamboo and Rattan Science and Technology, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Zhimin Gao
- Key Laboratory of State Forestry and Grassland Administration/Beijing on Bamboo and Rattan Science and Technology, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| |
Collapse
|
30
|
Ali M, Shafiq M, Haider MZ, Sami A, Alam P, Albalawi T, Kamran Z, Sadiq S, Hussain M, Shahid MA, Jeridi M, Ashraf GA, Manzoor MA, Sabir IA. Genome-wide analysis of NPR1-like genes in citrus species and expression analysis in response to citrus canker ( Xanthomonas axonopodis pv. citri). Front Plant Sci 2024; 15:1333286. [PMID: 38606070 PMCID: PMC11007782 DOI: 10.3389/fpls.2024.1333286] [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: 11/05/2023] [Accepted: 02/08/2024] [Indexed: 04/13/2024]
Abstract
Citrus fruits, revered for their nutritional value, face significant threats from diseases like citrus canker, particularly impacting global citrus cultivation, notably in Pakistan. This study delves into the critical role of NPR1-like genes, the true receptors for salicylic acid (SA), in the defense mechanisms of citrus against Xanthomonas axonopodis pv. citri (Xcc). By conducting a comprehensive genome-wide analysis and phylogenetic study, the evolutionary dynamics of Citrus limon genes across diverse citrus cultivars are elucidated. Structural predictions unveil conserved domains, such as the BTB domain and ankyrin repeat domains, crucial for the defense mechanism. Motif analysis reveals essential conserved patterns, while cis-regulatory elements indicate their involvement in transcription, growth, response to phytohormones, and stress. The predominantly cytoplasmic and nuclear localization of NPR1-like genes underscores their pivotal role in conferring resistance to various citrus species. Analysis of the Ks/Ka ratio indicates a purifying selection of NPR1-like genes, emphasizing their importance in different species. Synteny and chromosomal mapping provide insights into duplication events and orthologous links among citrus species. Notably, Xac infection stimulates the expression of NPR1-like genes, revealing their responsiveness to pathogenic challenges. Interestingly, qRT-PCR profiling post-Xac infection reveals cultivar-specific alterations in expression within susceptible and resistant citrus varieties. Beyond genetic factors, physiological parameters like peroxidase, total soluble protein, and secondary metabolites respond to SA-dependent PR genes, influencing plant characteristics. Examining the impact of defense genes (NPR1) and plant characteristics on disease resistance in citrus, this study marks the inaugural investigation into the correlation between NPR1-associated genes and various plant traits in both susceptible and resistant citrus varieties to citrus bacterial canker.
Collapse
Affiliation(s)
- Mobeen Ali
- Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Shafiq
- Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Zeshan Haider
- Department of Plant Breeding & Genetics, Faculty of Agriculture Sciences, University of the Punjab, Lahore, Pakistan
| | - Adnan Sami
- Department of Plant Breeding & Genetics, Faculty of Agriculture Sciences, University of the Punjab, Lahore, Pakistan
| | - Pravej Alam
- Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Thamir Albalawi
- Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Zuha Kamran
- Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Saleh Sadiq
- Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Mujahid Hussain
- Horticultural Science Department University of Florida-Institute of Food and Agricultural Sciences (IFAS) North Florida Research and Education Center, Gainesville FL, United States
| | - Muhammad Adnan Shahid
- Horticultural Science Department University of Florida-Institute of Food and Agricultural Sciences (IFAS) North Florida Research and Education Center, Gainesville FL, United States
| | - Mouna Jeridi
- Biology Department, College of Science, King Khalid University, Abha, Saudi Arabia
| | | | | | - Irfan Ali Sabir
- College of Horticulture, South China Agricultural University, Guangzhou, China
| |
Collapse
|
31
|
Ushijima H, Hoque SA, Akari Y, Pham NTK, Phan T, Nishimura S, Kobayashi M, Sugita K, Okitsu S, Komoto S, Thongprachum A, Khamrin P, Maneekarn N, Hayakawa S. Molecular Evolution of GII.P31/GII.4_Sydney_2012 Norovirus over a Decade in a Clinic in Japan. Int J Mol Sci 2024; 25:3619. [PMID: 38612429 PMCID: PMC11011564 DOI: 10.3390/ijms25073619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Norovirus (NoV) genogroup II, polymerase type P31, capsid genotype 4, Sydney_2012 variant (GII.P31/GII.4_Sydney_2012) has been circulating at high levels for over a decade, raising the question of whether this strain is undergoing molecular alterations without demonstrating a substantial phylogenetic difference. Here, we applied next-generation sequencing to learn more about the genetic diversity of 14 GII.P31/GII.4_Sydney_2012 strains that caused epidemics in a specific region of Japan, with 12 from Kyoto and 2 from Shizuoka, between 2012 and 2022, with an emphasis on amino acid (aa) differences in all three ORFs. We found numerous notable aa alterations in antigenic locations in the capsid region (ORF2) as well as in other ORFs. In all three ORFs, earlier strains (2013-2016) remained phylogenetically distinct from later strains (2019-2022). This research is expected to shed light on the evolutionary properties of dominating GII.P31/GII.4_Sydney_2012 strains, which could provide useful information for viral diarrhea prevention and treatment.
Collapse
Affiliation(s)
- Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Itabashi, Tokyo 173-8610, Japan
| | - Sheikh Ariful Hoque
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Itabashi, Tokyo 173-8610, Japan
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka 1000, Bangladesh
| | - Yuki Akari
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Ngan Thi Kim Pham
- College of Industrial Technology, Nihon University, Narashino, Chiba 275-8575, Japan;
| | - Tung Phan
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | | | | | - Kumiko Sugita
- Sugita Children Clinic, Ibaraki, Osaka 567-0035, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Itabashi, Tokyo 173-8610, Japan
| | - Satoshi Komoto
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
- Center for Infectious Disease Research, Research Promotion Headquarters, Fujita Health University, Toyoake, Aichi 470-1192, Japan
- Division of One Health, Research Center for GLOBAL and LOCAL Infectious Diseases, Oita University, Yufu, Oita 879-5593, Japan
| | | | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine and Emerging and Re-Emerging Diarrheal Viruses Research Center, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine and Emerging and Re-Emerging Diarrheal Viruses Research Center, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Itabashi, Tokyo 173-8610, Japan
| |
Collapse
|
32
|
Matiz-González JM, Ballesteros-Ballesteros JA, Hernández M, Mejorano-Fonseca JA, Cuervo C, Faccini-Martínez ÁA, Hidalgo M, Pérez-Torres J, Silva-Ramos CR. Genetic diversity of P1/pathogenic Leptospira species hosted by bats worldwide. Zoonoses Public Health 2024. [PMID: 38509439 DOI: 10.1111/zph.13126] [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: 11/07/2023] [Revised: 03/04/2024] [Accepted: 03/12/2024] [Indexed: 03/22/2024]
Abstract
INTRODUCTION Bats are a diverse group of mammals that have unique features allowing them to act as reservoir hosts for several zoonotic pathogens such as Leptospira. Leptospires have been classified into pathogenic, intermediate, and saprophytic groups and more recently into clades P1, P2, S1, and S2, being all the most important pathogenic species related to leptospirosis included within the P1/pathogenic clade. Leptospira has been detected from bats in several regions worldwide; however, the diversity of leptospires harboured by bats is still unknown. AIM The aim of the present study was to determine the genetic diversity of Leptospira spp. harboured by bats worldwide. METHODS A systematic review was conducted on four databases to retrieve studies in which Leptospira was detected from bats. All studies were screened to retrieve all available Leptospira spp. 16S rRNA sequences from the GenBank database and data regarding their origin. Sequences obtained were compared with each other and reference sequences of Leptospira species and analysed through phylogenetic analysis. RESULTS A total of 418 Leptospira spp. 16S rRNA sequences isolated from 55 bat species from 14 countries were retrieved from 15 selected manuscripts. From these, 417 sequences clustered within the P1/pathogenic group, and only one sequence clustered within the P2/intermediate group. Six major clades of P1/pathogenic Leptospira spp. were identified, three of them composed exclusively of sequences obtained from bats. CONCLUSION We identified that bats harbour a great genetic diversity of Leptospira spp. that form part of the P1/pathogenic clade, some of which are closely related to leptospirosis-associated species. This finding contributes to the knowledge of the diversity of leptospires hosted by bats worldwide and reinforces the role of bats as reservoirs of P1/pathogenic Leptospira spp.
Collapse
Affiliation(s)
- J Manuel Matiz-González
- Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá, Colombia
| | - Jesús A Ballesteros-Ballesteros
- Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - María Hernández
- Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Julián A Mejorano-Fonseca
- Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Claudia Cuervo
- Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Álvaro A Faccini-Martínez
- Servicio de Infectología, Hospital Militar Central, Bogotá, Colombia
- Servicios y Asesorías en Infectología - SAI, Bogotá, Colombia
- Facultad de Medicina, Universidad Militar Nueva Granada, Bogotá, Colombia
| | - Marylin Hidalgo
- Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Jairo Pérez-Torres
- Unidad de Ecología y Sistemática (UNESIS), Laboratorio de Ecología Funcional, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Carlos Ramiro Silva-Ramos
- Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| |
Collapse
|
33
|
Wang M, Xu F, Hu X, Chen J, Song X, Song T. The complete mitochondrial genome of Hericium erinaceus (Bull.:Fr.) Pers., 1797 (Russulales, Basidiomycota): an edible and medicinal fungus. Mitochondrial DNA B Resour 2024; 9:357-360. [PMID: 38516230 PMCID: PMC10956905 DOI: 10.1080/23802359.2024.2324923] [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] [Received: 09/27/2023] [Accepted: 02/23/2024] [Indexed: 03/23/2024] Open
Abstract
Hericium erinaceus (Bull.:Fr.) Pers., 1797, is an edible and medicinal fungus found in China. In this study, specimens of H. erinaceus HE0021 were collected from southeastern China (Yunhe County, Lishui City, Zhejiang Province, 28°7'12″N, 119°34'12″E). The whole mitochondrial genome of H. erinaceus HE0021 was sequenced using next-generation sequencing (NGS) technology, which comprised 15 protein-coding genes (PCGs), 27 transfer RNAs (tRNAs), two ribosomal RNAs, with a total length of 83,518 base pairs (bp). The results of the phylogenetic analysis show that H. erinaceus and H. coralloides were clustered in the same clade. The complete mitogenome sequence provides essential data for the subsequent investigation of Hericium and Russulales.
Collapse
Affiliation(s)
- Mei Wang
- College of Life Science, Northeast Agricultural University, Harbin, People’s Republic of China
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Fei Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Xiaomei Hu
- College of Life Science, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Jianfei Chen
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Xiaoya Song
- Lishui Academy of Agricultural and Forestry Sciences, Lishui, People’s Republic of China
| | - Tingting Song
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| |
Collapse
|
34
|
Zhang G, Xu T, Chen Y, Xu W, Wang Y, Li Y, Zhu F, Liu H, Ruan H. Complete Mitochondrial Genomes of Nedyopus patrioticus: New Insights into the Color Polymorphism of Millipedes. Curr Issues Mol Biol 2024; 46:2514-2527. [PMID: 38534775 DOI: 10.3390/cimb46030159] [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: 02/19/2024] [Revised: 03/04/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024] Open
Abstract
There has been debate about whether individuals with different color phenotypes should have different taxonomic status. In order to determine whether the different color phenotypes of Nedyopus patrioticus require separate taxonomic status or are simply synonyms, here, the complete mitochondrial genomes (mitogenomes) of two different colored N. patrioticus, i.e., red N. patrioticus and white N. patrioticus, are presented. The two mitogenomes were 15,781 bp and 15,798 bp in length, respectively. Each mitogenome contained 13 PCGs, 19 tRNAs, 2 rRNAs, and 1 CR, with a lack of trnI, trnL2, and trnV compared to other Polydesmida species. All genes were located on a single strand in two mitogenomes. Mitochondrial DNA analyses revealed that red N. patrioticus and white N. patrioticus did not show clear evolutionary differences. Furthermore, no significant divergence was discovered by means of base composition analysis. As a result, we suggest that white N. patrioticus might be regarded as a synonym for red N. patrioticus. The current findings confirmed the existence of color polymorphism in N. patrioticus, which provides exciting possibilities for future research. It is necessary to apply a combination of molecular and morphological methods in the taxonomy of millipedes.
Collapse
Affiliation(s)
- Gaoji Zhang
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Tangjun Xu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Yukun Chen
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Xu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Yinuo Wang
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Yuanyuan Li
- College of Ecology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Fuyuan Zhu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Hongyi Liu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
- College of Ecology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Honghua Ruan
- College of Ecology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| |
Collapse
|
35
|
Singh A, Maurya A, Rajkumar S, Singh AK, Bhardwaj R, Kaushik SK, Kumar S, Singh K, Singh GP, Singh R. Genome-Wide Comparative Analysis of Five Amaranthaceae Species Reveals a Large Amount of Repeat Content. Plants (Basel) 2024; 13:824. [PMID: 38592842 PMCID: PMC10975975 DOI: 10.3390/plants13060824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 04/11/2024]
Abstract
Amaranthus is a genus of C4 dicotyledonous herbaceous plant species that are widely distributed in Asia, Africa, Australia, and Europe and are used as grain, vegetables, forages, and ornamental plants. Amaranth species have gained significant attention nowadays as potential sources of nutritious food and industrial products. In this study, we performed a comparative genome analysis of five amaranth species, namely, Amaranthus hypochondriacus, Amaranthus tuberculatus, Amaranthus hybridus, Amaranthus palmeri, and Amaranthus cruentus. The estimated repeat content ranged from 54.49% to 63.26% and was not correlated with the genome sizes. Out of the predicted repeat classes, the majority of repetitive sequences were Long Terminal Repeat (LTR) elements, which account for about 13.91% to 24.89% of all amaranth genomes. Phylogenetic analysis based on 406 single-copy orthologous genes revealed that A. hypochondriacus is most closely linked to A. hybridus and distantly related to A. cruentus. However, dioecious amaranth species, such as A. tuberculatus and A. palmeri, which belong to the subgenera Amaranthus Acnida, have formed their distinct clade. The comparative analysis of genomic data of amaranth species will be useful to identify and characterize agronomically important genes and their mechanisms of action. This will facilitate genomics-based, evolutionary studies, and breeding strategies to design faster, more precise, and predictable crop improvement programs.
Collapse
Affiliation(s)
- Akshay Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India; (A.S.); (A.M.); (S.R.); (A.K.S.)
| | - Avantika Maurya
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India; (A.S.); (A.M.); (S.R.); (A.K.S.)
| | - Subramani Rajkumar
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India; (A.S.); (A.M.); (S.R.); (A.K.S.)
| | - Amit Kumar Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India; (A.S.); (A.M.); (S.R.); (A.K.S.)
| | - Rakesh Bhardwaj
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India; (R.B.); (S.K.K.); (S.K.)
| | - Surinder Kumar Kaushik
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India; (R.B.); (S.K.K.); (S.K.)
| | - Sandeep Kumar
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India; (R.B.); (S.K.K.); (S.K.)
| | - Kuldeep Singh
- International Crop Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India;
| | | | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India; (A.S.); (A.M.); (S.R.); (A.K.S.)
| |
Collapse
|
36
|
Huang Y, Cao J, Zhao M, Guo J, Li J, Wang R. The complete chloroplast genome sequence of an invasive plant, Tragopogon dubius Scopoli (asteraceae). Mitochondrial DNA B Resour 2024; 9:352-356. [PMID: 38487811 PMCID: PMC10939102 DOI: 10.1080/23802359.2024.2329668] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/07/2024] [Indexed: 03/17/2024] Open
Abstract
Tragopogon dubius Scopoli is native to Europe and western Asia and is considered an invasive plant in China. In this study, the complete chloroplast genome of T. dubius was obtained using high-throughput next-generation sequencing technology. The whole chloroplast genome was 153,017 bp long with a GC content of 38% and comprised 130 genes (86 protein-coding genes, 36 tRNA genes, and 8 rRNA genes). Phylogenetic analysis based on the concatenated chloroplast protein-coding sequences showed that T. dubius is most closely related to Tragopogon pratensis. This study provides valuable genetic data for further phylogenetic analysis and molecular identification of species in the genus Tragopogon.
Collapse
Affiliation(s)
- Yue Huang
- College of Life Science, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingjing Cao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengxin Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianying Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiamei Li
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Rui Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
37
|
Wang H, Zeng S, Zhang Z, Yang D. The complete mitochondrial genome of Rhynchocinetes brucei Okuno 1994 (Decapoda: Rhynchocinetidae). Mitochondrial DNA B Resour 2024; 9:347-351. [PMID: 38476839 PMCID: PMC10930117 DOI: 10.1080/23802359.2023.2261636] [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] [Received: 07/10/2023] [Accepted: 09/17/2023] [Indexed: 03/14/2024] Open
Abstract
We report the complete mitochondrial genome of Rhynchocinetes brucei Okuno 1994. The mitogenome was found to contain 16158 bp with 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), 2 rRNA genes (rRNAs), and 1 putative control region. Phylogenetic analysis indicated that R. brucei was sister to Rhynchocinetes durbanensis (PP= 1), of the same family Rhynchocinetidae. These results are helpful for research on the phylogenetic and evolutionary studies of this group.
Collapse
Affiliation(s)
- Hangjun Wang
- Wenzhou Marine Center, Ministry of Natural Resources of the People’s Republic of China, Beijing, China
- Marine Ecosystem Observation and Research Station on the Yangtze River Estuary, Wenzhou, China
| | - Sheng Zeng
- College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zhao Zhang
- Wenzhou Marine Center, Ministry of Natural Resources of the People’s Republic of China, Beijing, China
- Marine Ecosystem Observation and Research Station on the Yangtze River Estuary, Wenzhou, China
| | - Deyuan Yang
- College of the Environment and Ecology, Xiamen University, Xiamen, China
- National Taiwan Ocean University, Keelung, Taiwan, China
| |
Collapse
|
38
|
Li Y, Luo J, Shang J, Zhang F, Deng C, Feng Y, Meng G, Jiang W, Yu X, Liu H. Epidemiological investigation and pathogenicity analysis of waterfowl astroviruses in some areas of China. Front Microbiol 2024; 15:1375826. [PMID: 38529177 PMCID: PMC10961457 DOI: 10.3389/fmicb.2024.1375826] [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] [Received: 01/24/2024] [Accepted: 02/26/2024] [Indexed: 03/27/2024] Open
Abstract
Waterfowl astroviruses are mainly duck astroviruses and goose astroviruses, of which duck astroviruses (DAstV-3, -4), goose astroviruses (GoAstV-1, -2) are the four new waterfowl 21 astroviruses in recent years, which can lead to enteritis, viral hepatitis, gout and reduce the growth performance of waterfowl, affecting the healthy development of the waterfowl farming industry. Since no targeted drugs or vaccines on the market, studies on the epidemiology of the virus are necessary for vaccine development. In this study, we collected 1546 waterfowl samples from 13 provinces in China for epidemiological investigation. The results showed that 260 samples (16.8%) were positive. Four species of astrovirus were detected in 13 provinces except Fujian province. Among the four sites tested, the highest positive rates were found in farms and slaughterhouses. Cross-host and mixed infection were observed in four species of waterfowl astroviruses. The whole genome of 17 isolates was sequenced and compared with published sequences. Genetic evolution and homology analysis showed that the isolated strains had high similarity to their reference sequences. To assess the pathogenicity of GoAstV, 7-day-old goslings were inoculated with GoAstV-1 and GoAstV-2 by the intramuscular route, and infected geese showed similar clinical signs, such as anorexia, depression, and weight loss. Organ damage was seen after infection, with histopathological changes in the heart, liver, spleen, kidney, and intestine, and higher viral loads in throat and anal swabs. These findings increase our understanding of the pathogenicity of GoAstV-1 and GoAstV-2 in goslings and provide more references for future research.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Hualei Liu
- China Animal Health and Epidemiology Center, Qingdao, China
| |
Collapse
|
39
|
Huang YB, Qi ZC, Feng JY, Ge BJ, Huang CZ, Feng YQ, Wu J, Wei PR, Ito T, Kokubugata G, Li P, Wei YK. Salvia guidongensis sp. nov.: unraveling a critical evolutionary link in East Asian Salvia from Central China integrating morphology, phylogeny, and plastid genomics. Front Plant Sci 2024; 15:1332443. [PMID: 38504896 PMCID: PMC10948445 DOI: 10.3389/fpls.2024.1332443] [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: 11/02/2023] [Accepted: 02/12/2024] [Indexed: 03/21/2024]
Abstract
Introduction Salvia L., representing the largest genus within the mint family, is noted for its global distribution of approximately 1000 species, with East Asia, and particularly China, recognized as a critical center of diversity for the genus. Methods Our research was conducted through extensive fieldwork in Guidong County, Hunan Province, China, where we identified a previously undescribed species of Salvia. The identification process involved detailed morphological observations, phylogenetic analyses, and plastid genomics. Results The newly discovered species, Salvia guidongensis, exhibits unique characteristics not commonly observed in the East Asian lineage of Salvia, including dual floral colors within natural populations-either pale purple or pale yellow. Morphologically, while it shares similarities with members of sect. Glutinaria, S. guidongensis is distinct in its floral morphology, stature, and specific foliar traits. Phylogenetic analysis places S. guidongensis in a unique clade within the East Asian lineage of Salvia, suggesting it may serve as an important evolutionary link. Additionally, we explored the plastome features of S. guidongensis, comparing them with those of closely related species. Discussion The discovery of S. guidongensis not only entriches the taxonomic tapestry of Salvia but also provides critical insights into the biogeography and evolutionary pathways of the genus in East Asia. By integrating morphological and molecular data, we validate the novel status of S. guidongensis and highlight its significance in bridging taxonomic and evolutionary gaps within Sect. Glutinaria of Salvia.
Collapse
Affiliation(s)
- Yan-Bo Huang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Zhe-Chen Qi
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jie-Ying Feng
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Bin-Jie Ge
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | | | - Yu-Qing Feng
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jing Wu
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Pu-Rui Wei
- East China Survey and Planning Institute of the National Forestry and Grassland Administration, Hangzhou, China
| | - Takuro Ito
- Tohoku University Botanical Gardens, 12-2 Kawauchi, Aoba-ku, Sendai-shi, Miyagi, Japan
| | - Goro Kokubugata
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yu-Kun Wei
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Shanghai Engineering Research Centre of Sustainable Plant Innovation, Shanghai Botanical Garden, Shanghai, China
| |
Collapse
|
40
|
Li JJ, Qiu XY, Dai YJ, Nyonga TM, Li CC. Genome-Wide Identification and Co-Expression Networks of WOX Gene Family in Nelumbo nucifera. Plants (Basel) 2024; 13:720. [PMID: 38475567 DOI: 10.3390/plants13050720] [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: 01/15/2024] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
WUSCHEL-related homeobox (WOX) genes are a class of plant-specific transcription factors, regulating the development of multiple tissues. However, the genomic characterizations and expression patterns of WOX genes have not been analyzed in lotus. In this study, 15 NnWOX genes were identified based on the well-annotated reference genome of lotus. According to the phylogenetic analysis, the NnWOX genes were clustered into three clades, i.e., ancient clade, intermediate clade, and WUS clade. Except for the conserved homeobox motif, we further found specific motifs of NnWOX genes in different clades and divergence gene structures, suggesting their distinct functions. In addition, two NnWOX genes in the ancient clade have conserved expression patterns and other NnWOX genes exhibit different expression patterns in lotus tissues, suggesting a low level of functional redundancy in lotus WOX genes. Furthermore, we constructed the gene co-expression networks for each NnWOX gene. Based on weighted gene co-expression network analysis (WGCNA), ten NnWOX genes and their co-expressed genes were assigned to the modules that were significantly related to the cotyledon and seed coat. We further performed RT-qPCR experiments, validating the expression levels of ten NnWOX genes in the co-expression networks. Our study reveals comprehensive genomic features of NnWOX genes in lotus, providing a solid basis for further function studies.
Collapse
Affiliation(s)
- Juan-Juan Li
- Hubei Province Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Xiao-Yan Qiu
- Hubei Province Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Yu-Jun Dai
- Hubei Province Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Tonny M Nyonga
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Chang-Chun Li
- Hubei Province Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| |
Collapse
|
41
|
Tian H, Zhu X, Qiu J, Zhang H, Shi X. The complete chloroplast genome sequence of Ammodendron bifolium (Fabaceae), an endangered desert shrub from China. Mitochondrial DNA B Resour 2024; 9:309-313. [PMID: 38450410 PMCID: PMC10913713 DOI: 10.1080/23802359.2024.2324922] [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] [Received: 12/06/2023] [Accepted: 02/23/2024] [Indexed: 03/08/2024] Open
Abstract
Ammodendron bifolium, a rare deciduous shrub, is the only species of Ammodendron (Fabaceae) in China, which distributes in Huocheng county, Xinjiang. This study employed high-throughput sequencing technology to assemble the complete chloroplast genome sequence of A. bifolium. The entire length of chloroplast genome is 154,426 bp. It comprises 128 genes, which include 85 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. The A. bifolium chloroplast genome has a GC content of 36.41%. Phylogenetic analysis strongly supported that A. bifolium is sister to the members of the Sophora genus. This study will provide the genetic information data for further phylogenetic studies of Ammodendron.
Collapse
Affiliation(s)
- Haowen Tian
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
| | - Xinyu Zhu
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
| | - Juan Qiu
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
| | - Hongxiang Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Xiaojun Shi
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
| |
Collapse
|
42
|
Naqvi SAH, Abbas A, Farhan M, Kiran R, Hassan Z, Mehmood Y, Ali A, Ahmed N, Hassan MZ, Alrefaei AF, Ölmez F, Yang SH, Baloch FS. Unveiling the Genetic Tapestry: Exploring Rhizoctonia solani AG-3 Anastomosis Groups in Potato Crops across Borders. Plants (Basel) 2024; 13:715. [PMID: 38475561 DOI: 10.3390/plants13050715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
The current study was carried out to screen 10 isolates (ARS-01-ARS-10) of Rhizoctonia. solani from potato tubers cv. Kuroda, which were collected from various potato fields in Multan, Pakistan. The isolates were found to be morphologically identical, as the hyphae exhibit the production of branches at right angles and acute angles often accompanied by septum near the emerging branches. Anastomosis grouping showed that these isolates belonged to AG-3. A pathogenicity test was performed against the susceptible Kuroda variety and among the isolates, ARS-05 exhibited the highest mean severity score of approximately 5.43, followed by ARS-09, which showed a mean severity score of about 3.67, indicating a moderate level of severity. On the lower end of the severity scale, isolates ARS-06 and ARS-07 displayed mean severity scores of approximately 0.53 and 0.57, respectively, suggesting minimal symptom severity. These mean severity scores offer insights into the varying degrees of symptom expression among the different isolates of R. solani under examination. PCoA indicates that the severe isolate causing black scurf on the Kuroda variety was AG-3. A comprehensive analysis of the distribution, genetic variability, and phylogenetic relationships of R. solani anastomosis groups (AGs) related to potato crops across diverse geographic regions was also performed to examine AG prevalence in various countries. AG-3 was identified as the most widespread group, prevalent in Sweden, China, and the USA. AG-5 showed prominence in Sweden and the USA, while AG-2-1 exhibited prevalence in China and Japan. The phylogenetic analysis unveiled two different clades: Clade I comprising AG-3 and Clade II encompassing AG-2, AG-4, and AG-5, further subdivided into three subclades. Although AGs clustered together regardless of origin, their genetic diversity revealed complex evolutionary patterns. The findings pave the way for region-specific disease management strategies to combat R. solani's impact on potato crops.
Collapse
Affiliation(s)
- Syed Atif Hasan Naqvi
- Department of Plant Pathology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Aqleem Abbas
- Department of Agriculture and Food Technology, Karakoram International University, Gilgit Baltistan, Gilgit 15100, Pakistan
| | - Muhammad Farhan
- Department of Plant Pathology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Rafia Kiran
- Department of Plant Pathology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Zeshan Hassan
- College of Agriculture, University of Layyah, Layyah 31200, Pakistan
| | - Yasir Mehmood
- Department of Plant Pathology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Amjad Ali
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye
| | - Niaz Ahmed
- Department of Soil Science, Bahauddin Zakariya University, Multan 60800, Pakistan
| | | | - Abdulwahed Fahad Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Fatih Ölmez
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye
| | - Seung-Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu 59626, Republic of Korea
| | - Faheem Shehzad Baloch
- Department of Biotechnology, Faculty of Science, Mersin University, Yenişehir, Mersin 33343, Türkiye
| |
Collapse
|
43
|
Han ZZ, Li JC, Xiao JB, Hong M, Lu HH, Song Y, Liu Y, Wang R, Fu HH, Wang FM, Zhu SL, Yan DM, Ji TJ, Zhao LQ, Zhang Y. Identification and genetic characterization of a recently identified enterovirus C116 in China. J Med Virol 2024; 96:e29503. [PMID: 38445750 DOI: 10.1002/jmv.29503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/08/2024] [Accepted: 02/23/2024] [Indexed: 03/07/2024]
Abstract
Enterovirus C116 (EV-C116) is a new member of the enterovirus C group which is closely associated with several infectious diseases. Although sporadic studies have detected EV-C116 in clinical samples worldwide, there is currently limited information available. In this study, two EV-C-positive fecal specimens were detected in apparently healthy children, which harbored low abundance, through meta-transcriptome sequencing. Based on the prototypes of several EV-Cs, two lineages were observed. Lineage 1 included many types that could not cause EV-like cytopathic effect in cell culture. Three genogroups of EV-C116 were divided in the maximum likelihood tree, and the two strains in this study (XZ2 and XZ113) formed two different lineages, suggesting that EV-C116 still diffuses worldwide. Obvious inter-type recombination events were observed in the XZ2 strain, with CVA22 identified as a minor donor. However, another strain (XZ113) underwent different recombination situations, highlighting the importance of recombination in the formation of EV-Cs biodiversity. The EV-C116 strains could propagate in rhabdomyosarcoma cell cultures at low titer; however, EV-like cytopathic effects were not observed. HEp-2, L20B, VERO, and 293T cell lines did not provide an appropriate environment for EV-C116 growth. These results challenge the traditional recognition of the uncultured nature of EV-C116 strains and explain the difficulty of clinical detection.
Collapse
Affiliation(s)
- Zhen-Zhi Han
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ji-Chen Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jin-Bo Xiao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mei Hong
- Tibet Center for Disease Control and Prevention, Lhasa City, Tibet Autonomous Region, China
| | - Huan-Huan Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ying Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Rui Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Han-Haoyu Fu
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China
| | - Fang-Ming Wang
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China
| | - Shuang-Li Zhu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dong-Mei Yan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Tian-Jiao Ji
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lin-Qing Zhao
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China
| | - Yong Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| |
Collapse
|
44
|
Iller M, Lipczyńska-Ilczuk K, Sokół R, Borsuk G, Bancerz-Kisiel A. Phylogenetic analysis of the trypanosomatid parasite Lotmaria passim in honey bees ( Apis mellifera) in Poland. J Vet Res 2024; 68:123-127. [PMID: 38525230 PMCID: PMC10960264 DOI: 10.2478/jvetres-2024-0018] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 03/13/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction Lotmaria passim (L. passim) is a single-celled flagellate which colonises the bee gastrointestinal tract and is highly prevalent in honey bees. This parasite is associated with colony losses. Honey bee (Apis mellifera) colonies were sampled from five apiaries in the north-eastern part of Poland for the phylogenetic analysis of L. passim. Material and Methods Each apiary consisted of approximately 60 bee colonies, of which 20 were randomly selected. Samples of 60 differently aged worker bees were collected from each colony and pooled. A total of 100 bee colonies from five apiaries were examined. Protozoa of the Trypanosomatidae family were identified by PCR. L. passim was detected in 47 (47%) of the samples. The 18S ribosomal (r) RNA amplicons of L. passim were sequenced by a commercial service. Their sequences were analysed with BLASTN and noted to be compatible with the GenBank sequences of this region of the organism's genome. A sequence analysis was performed using the BioEdit Sequence Alignment Editor and Clustal W software. Results The amplicon sequences of L. passim were 100% homologous with the sequences deposited in GenBank under accession numbers KM066243.1., KJ684964.1 and KM980181.1. Conclusion This is the first study to perform a phylogenetic analysis of L. passim in Polish honey bees. The analysis demonstrated high levels of genetic similarity between isolates of L. passim colonising apiaries in the north-eastern region of Poland.
Collapse
Affiliation(s)
- Maria Iller
- Department of Parasitology and Invasive Diseases, Faculty of Veterinary Medicine, University of Warmia and Mazury, 10-719Olsztyn, Poland
| | - Karolina Lipczyńska-Ilczuk
- Department of Epizootiology, Faculty of Veterinary Medicine, University of Warmia and Mazury, 10-719Olsztyn, Poland
| | - Rajmund Sokół
- Department of Parasitology and Invasive Diseases, Faculty of Veterinary Medicine, University of Warmia and Mazury, 10-719Olsztyn, Poland
| | - Grzegorz Borsuk
- Department of Apidology, Faculty of Animal Sciences and Bioeconomy, Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, 20-950Lublin, Poland
| | - Agata Bancerz-Kisiel
- Department of Epizootiology, Faculty of Veterinary Medicine, University of Warmia and Mazury, 10-719Olsztyn, Poland
| |
Collapse
|
45
|
Akanwari J, Yu Q, Sultana T. Redetection and description of the European dagger nematode Xiphinema diversicaudatum on peach ( Prunus persica L.) in Canada. J Nematol 2024; 56:20240010. [PMID: 38516362 PMCID: PMC10956561 DOI: 10.2478/jofnem-2024-0010] [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] [Received: 01/10/2024] [Indexed: 03/23/2024] Open
Abstract
The study reports the detection of Xiphinema diversicaudatum in a peach field in Ontario, Canada. Comprehensive population characterization involved morphological and molecular analyses using 18S and 28S rDNA sequences. Morphological and molecular analysis demonstrated a close relationship between the Ontario population and those from Central Europe. This is the first report of X. diversicaudatum from peaches (Prunus persica) in Canada and in North America.
Collapse
Affiliation(s)
- Jerry Akanwari
- London Research and Development Center, Vineland Station, Agriculture and Agri-Food, Canada, ON, Canada
- Department of Biological Sciences, Brock University, ON, Canada
| | - Qing Yu
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Tahera Sultana
- London Research and Development Center, Vineland Station, Agriculture and Agri-Food, Canada, ON, Canada
| |
Collapse
|
46
|
Dunowska M, Lal R, Dissanayake SD, Bond SD, Burrows E, Moffat J, Howe L. Bovine viral diarrhoea viruses from New Zealand belong predominantly to the BVDV-1a genotype. N Z Vet J 2024; 72:66-78. [PMID: 38212951 DOI: 10.1080/00480169.2023.2291039] [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: 07/28/2023] [Accepted: 11/22/2023] [Indexed: 01/13/2024]
Abstract
AIM To determine which genotypes of bovine viral diarrhoea virus (BVDV) circulate among cattle in New Zealand. METHODS Samples comprised BVDV-1-positive sera sourced from submissions to veterinary diagnostic laboratories in 2019 (n = 25), 2020 (n = 59) and 2022 (n = 74) from both beef and dairy herds, as well as archival BVDV-1 isolates (n = 5). Fragments of the 5' untranslated region (5' UTR) and glycoprotein E2 coding sequence of the BVDV genome were amplified and sequenced. The sequences were aligned to each other and to international BVDV-1 sequences to determine their similarities and phylogenetic relationships. The 5' UTR sequences were also used to create genetic haplotype networks to determine if they were correlated with selected traits (location, type of farm, and year of collection). RESULTS The 5' UTR sequences from New Zealand BVDV were closely related to each other, with pairwise identities between 89% and 100%. All clustered together and were designated as BVDV-1a (n = 144) or BVDV-1c (n = 5). There was no evidence of a correlation between the 5' UTR sequence and the geographical origin within the country, year of collection or the type of farm. Partial E2 sequences from New Zealand BVDV (n = 76) showed 74-100% identity to each other and clustered in two main groups. The subtype assignment based on the E2 sequence was the same as based on the 5' UTR analysis. This is the first comprehensive analysis of genomic variability of contemporary New Zealand BVDV based on the analysis of the non-coding (5' UTR) and coding (E2) sequences. CONCLUSIONS AND CLINICAL RELEVANCE Knowledge of the diversity of the viruses circulating in the country is a prerequisite for the development of effective control strategies, including a selection of suitable vaccines. The data presented suggest that New Zealand BVDV are relatively homogeneous, which should facilitate eradication efforts including selection or development of the most suitable vaccines.
Collapse
Affiliation(s)
- M Dunowska
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - R Lal
- College of Health, Massey University, Palmerston North, New Zealand
| | - S D Dissanayake
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - S D Bond
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - E Burrows
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - J Moffat
- Scipharma Ltd., Upper Moutere, New Zealand
| | - L Howe
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
| |
Collapse
|
47
|
Sha L, Liang X, Zhang X, Gao S, Zhang Y, Zhou Y, Fan X. Roegneria yenchiana: A new species in the Triticeae (Poaceae) from the Hengduan Mountain region. Ecol Evol 2024; 14:e11171. [PMID: 38495436 PMCID: PMC10944672 DOI: 10.1002/ece3.11171] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 03/19/2024] Open
Abstract
Roegneria yenchiana sp. nov. (Triticeae) is a new species collected from Shangri-la of Yunnan Province in China based on morphological, cytological, and molecular data. It is morphologically characterized by one spikelet per node, rectangular glums, awns flanked by two short mucros in lemmas, distinguished from other species of Roegneria. The genomic in situ hybridization results indicate that R. yenchiana is an allotetraploid, and its genomic constitution is StY. Phylogenetic analyses based on multiple loci suggested that R. yenchiana is closely related to Pseudoroegneria and Roegneria, and the Pseudoroegneria served as the maternal donors during its polyploid speciation.
Collapse
Affiliation(s)
- Li‐Na Sha
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduSichuanChina
| | - Xiao Liang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Xin‐Yi Zhang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Shan Gao
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Yue Zhang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Yong‐Hong Zhou
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Xing Fan
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| |
Collapse
|
48
|
de Araújo AC, Silva LMN, Cho AY, Repenning M, Amgarten D, de Moraes AP, Malta F, Miller M, Dorlass EG, Palameta S, Oliveira DBL, de Araújo J, Arns CW, Durigon EL, Pinho JRR, Lee DH, Ferreira HL. Incursion of Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus, Brazil, 2023. Emerg Infect Dis 2024; 30:619-621. [PMID: 38290826 PMCID: PMC10902554 DOI: 10.3201/eid3003.231157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024] Open
Abstract
We report 4 highly pathogenic avian influenza A(H5N1) clade 2.3.4.4.b viruses in samples collected during June 2023 from Royal terns and Cabot's terns in Brazil. Phylodynamic analysis revealed viral movement from Peru to Brazil, indicating a concerning spread of this clade along the Atlantic Americas migratory bird flyway.
Collapse
|
49
|
Nie RE, Zhang SK, Xue HJ. Diversity, adaptation, and evolution II: Preface. Arch Insect Biochem Physiol 2024; 115:e22097. [PMID: 38533905 DOI: 10.1002/arch.22097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024]
Affiliation(s)
- Rui-E Nie
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Shou-Ke Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Huai-Jun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| |
Collapse
|
50
|
Tian X, Guo J, Song Y, Yu Q, Liu C, Fu Z, Shi Y, Shao Y, Yuan Z. Intraspecific differentiation of Lindera obtusiloba as revealed by comparative plastomic and evolutionary analyses. Ecol Evol 2024; 14:e11119. [PMID: 38469045 PMCID: PMC10927362 DOI: 10.1002/ece3.11119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 01/08/2024] [Accepted: 02/23/2024] [Indexed: 03/13/2024] Open
Abstract
Lindera obtusiloba Blume is the northernmost tree species in the family Lauraceae, and it is a key species in understanding the evolutionary history of this family. The species of L. obtusiloba in East Asia has diverged into the Northern and Southern populations, which are geographically separated by an arid belt. Though the morphological differences between populations have been observed and well documented, intraspecific variations at the plastomic level have not been systematically investigated to date. Here, ten chloroplast genomes of L. obtusiloba individuals were sequenced and analyzed along with three publicly available plastomes. Comparative plastomic analysis suggests that both the Northern and the Southern populations share similar overall structure, gene order, and GC content in their plastomes although the size of the plasome and the level of intraspecific variability do vary between the two populations. The Northern have relatively larger plastomes while the Southern population possesses higher intraspecific variability, which could be attributed to the complexity of the geological environments in the South. Phylogenomic analyses also support the split of the Northern and Southern clades among L. obtusiloba individuals. However, there is no obvious species boundary between var. obtusiloba and var. heterophylla in the Southern population, indicating that gene flow could still occur between these two varieties, and this could be used as a good example of reticulate evolution. It is also found that a few photosynthesis-related genes are under positive selection, which is mainly related to the geological and environmental differences between the Northern and the Southern regions. Our results provide a reference for phylogenetic analysis within species and suggest that phylogenomic analyses with a sufficient number of nuclear and chloroplast genomic target loci from widely distributed individuals could provide a deeper understanding of the population evolution of the widespread species.
Collapse
Affiliation(s)
- Xiangyu Tian
- College of Life SciencesHenan Agricultural UniversityZhengzhouHenanChina
| | - Jia Guo
- School of Life SciencesZhengzhou UniversityZhengzhouHenanChina
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education)Guangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinGuangxiChina
| | - Qunfei Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaYunnanChina
| | - Chao Liu
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Zhixi Fu
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Yuhua Shi
- School of Life SciencesZhengzhou UniversityZhengzhouHenanChina
| | - Yizhen Shao
- College of Life SciencesHenan Agricultural UniversityZhengzhouHenanChina
| | - Zhiliang Yuan
- College of Life SciencesHenan Agricultural UniversityZhengzhouHenanChina
| |
Collapse
|