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Jusic A, Erpapazoglou Z, Dalgaard LT, Lakkisto P, de Gonzalo-Calvo D, Benczik B, Ágg B, Ferdinandy P, Fiedorowicz K, Schroen B, Lazou A, Devaux Y. Guidelines for mitochondrial RNA analysis. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102262. [PMID: 39091381 PMCID: PMC11292373 DOI: 10.1016/j.omtn.2024.102262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Mitochondria are the energy-producing organelles of mammalian cells with critical involvement in metabolism and signaling. Studying their regulation in pathological conditions may lead to the discovery of novel drugs to treat, for instance, cardiovascular or neurological diseases, which affect high-energy-consuming cells such as cardiomyocytes, hepatocytes, or neurons. Mitochondria possess both protein-coding and noncoding RNAs, such as microRNAs, long noncoding RNAs, circular RNAs, and piwi-interacting RNAs, encoded by the mitochondria or the nuclear genome. Mitochondrial RNAs are involved in anterograde-retrograde communication between the nucleus and mitochondria and play an important role in physiological and pathological conditions. Despite accumulating evidence on the presence and biogenesis of mitochondrial RNAs, their study continues to pose significant challenges. Currently, there are no standardized protocols and guidelines to conduct deep functional characterization and expression profiling of mitochondrial RNAs. To overcome major obstacles in this emerging field, the EU-CardioRNA and AtheroNET COST Action networks summarize currently available techniques and emphasize critical points that may constitute sources of variability and explain discrepancies between published results. Standardized methods and adherence to guidelines to quantify and study mitochondrial RNAs in normal and disease states will improve research outputs, their reproducibility, and translation potential to clinical application.
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Affiliation(s)
- Amela Jusic
- HAYA Therapeutics SA, Route De La Corniche 6, SuperLab Suisse - Batiment Serine, 1066 Epalinges, Switzerland
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
| | - Zoi Erpapazoglou
- Ιnstitute for Fundamental Biomedical Research, B.S.R.C. “Alexander Fleming”, Vari, 16672 Athens, Greece
| | - Louise Torp Dalgaard
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Päivi Lakkisto
- Minerva Foundation Institute for Medical Research, 00290 Helsinki, Finland
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Bettina Benczik
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
| | - Bence Ágg
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
| | - Péter Ferdinandy
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
| | | | - Blanche Schroen
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University, ER 6229 Maastricht, the Netherlands
| | - Antigone Lazou
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
| | - on behalf of EU-CardioRNA COST Action CA17129
- HAYA Therapeutics SA, Route De La Corniche 6, SuperLab Suisse - Batiment Serine, 1066 Epalinges, Switzerland
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
- Ιnstitute for Fundamental Biomedical Research, B.S.R.C. “Alexander Fleming”, Vari, 16672 Athens, Greece
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
- Minerva Foundation Institute for Medical Research, 00290 Helsinki, Finland
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
- NanoBioMedical Centre, Adam Mickiewicz University in Poznan, 61614 Poznan, Poland
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University, ER 6229 Maastricht, the Netherlands
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - AtheroNET COST Action CA21153
- HAYA Therapeutics SA, Route De La Corniche 6, SuperLab Suisse - Batiment Serine, 1066 Epalinges, Switzerland
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
- Ιnstitute for Fundamental Biomedical Research, B.S.R.C. “Alexander Fleming”, Vari, 16672 Athens, Greece
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
- Minerva Foundation Institute for Medical Research, 00290 Helsinki, Finland
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
- NanoBioMedical Centre, Adam Mickiewicz University in Poznan, 61614 Poznan, Poland
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University, ER 6229 Maastricht, the Netherlands
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Ahmad F, Muhmood T. Clinical translation of nanomedicine with integrated digital medicine and machine learning interventions. Colloids Surf B Biointerfaces 2024; 241:114041. [PMID: 38897022 DOI: 10.1016/j.colsurfb.2024.114041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024]
Abstract
Nanomaterials based therapeutics transform the ways of disease prevention, diagnosis and treatment with increasing sophistications in nanotechnology at a breakneck pace, but very few could reach to the clinic due to inconsistencies in preclinical studies followed by regulatory hinderances. To tackle this, integrating the nanomedicine discovery with digital medicine provide technologies as tools of specific biological activity measurement. Hence, overcome the redundancies in nanomedicine discovery by the on-site data acquisition and analytics through integrating intelligent sensors and artificial intelligence (AI) or machine learning (ML). Integrated AI/ML wearable sensors directly gather clinically relevant biochemical information from the subject's body and process data for physicians to make right clinical decision(s) in a time and cost-effective way. This review summarizes insights and recommend the infusion of actionable big data computation enabled sensors in burgeoning field of nanomedicine at academia, research institutes, and pharmaceutical industries, with a potential of clinical translation. Furthermore, many blind spots are present in modern clinically relevant computation, one of which could prevent ML-guided low-cost new nanomedicine development from being successfully translated into the clinic was also discussed.
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Affiliation(s)
- Farooq Ahmad
- State Key Laboratory of Chemistry and Utilization of Carbon Based Energy Resources, College of Chemistry, Xinjiang University, Urumqi 830017, China.
| | - Tahir Muhmood
- International Iberian Nanotechnology Laboratory (INL), Avenida Mestre José Veiga, Braga 4715-330, Portugal.
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3
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Feng R, Wang H, Zhang X, Li T, Huang C, Zhang S, Sun M, Shi C, Hu J, Gou J. Characteristics of Corynespora cassiicola, the causal agent of tobacco Corynespora leaf spot, revealed by genomic and metabolic phenomic analysis. Sci Rep 2024; 14:18326. [PMID: 39112526 PMCID: PMC11306238 DOI: 10.1038/s41598-024-67510-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Corynespora cassiicola is a highly diverse fungal pathogen that commonly occurs in tropical, subtropical, and greenhouse environments worldwide. In this study, the isolates were identified as C. cassiicola, and the optimum growth and sporulation were studied. The phenotypic characteristics of C. cassiicola, concerning 950 different growth conditions, were tested using Biolog PM plates 1-10. In addition, the strain of C. cassiicola DWZ from tobacco hosts was sequenced for the using Illumina PE150 and Pacbio technologies. The host resistance of tobacco Yunyan 87 with different maturity levels was investigated. In addition, the resistance evaluation of 10 common tobacco varieties was investigated. The results showed that C. cassiicola metabolized 89.47% of the tested carbon source, 100% of the nitrogen source, 100% of the phosphorus source, and 97.14% of the sulfur source. It can adapt to a variety of different osmotic pressure and pH environments, and has good decarboxylase and deaminase activities. The optimum conditions for pathogen growth and sporulation were 25-30 °C, and the growth was better on AEA and OA medium. The total length of the genome was 45.9 Mbp, the GC content was 51.23%, and a total of 13,061 protein-coding genes, 202 non-coding RNAs and 2801 and repeat sequences were predicted. Mature leaves were more susceptible than proper mature and immature leaves, and the average diameter of diseased spots reached 17.74 mm at 12 days. None of the tested ten cultivars exhibited obvious resistance to Corynespora leaf spot of tobacco, whereby all disease spot diameters reached > 10 mm and > 30 mm when at 5 and 10 days after inoculation, respectively. The phenotypic characteristics, genomic analysis of C. cassiicola and the cultivar resistance assessment of this pathogen have increased our understanding of Corynespora leaf spot of tobacco.
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Affiliation(s)
- Ruichao Feng
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, 550081, People's Republic of China
- Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou, 434025, People's Republic of China
| | - Hancheng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, 550081, People's Republic of China.
| | - Xinghong Zhang
- College of Agricultural Sciences, Guizhou University, Guiyang, 550081, People's Republic of China
| | - Tong Li
- Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou, 434025, People's Republic of China
| | - Chunyang Huang
- Zunyi Branch of Guizhou Tobacco Company, Zunyi Guizhou, 564200, People's Republic of China
| | - Songbai Zhang
- Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou, 434025, People's Republic of China.
| | - Meili Sun
- Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou, 434025, People's Republic of China
| | - Caihua Shi
- Institute of Advanced Agricultural Science, Hubei University of Arts and Science, Xiangyang, Hubei Province, 441053, People's Republic of China
| | - Jingrong Hu
- Institute of Advanced Agricultural Science, Hubei University of Arts and Science, Xiangyang, Hubei Province, 441053, People's Republic of China
| | - Jianyu Gou
- Zunyi Branch of Guizhou Tobacco Company, Zunyi Guizhou, 564200, People's Republic of China.
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4
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Toga K, Sakamoto T, Kanda M, Tamura K, Okuhara K, Tabunoki H, Bono H. Long-read genome assembly of the Japanese parasitic wasp Copidosoma floridanum (Hymenoptera: Encyrtidae). G3 (BETHESDA, MD.) 2024; 14:jkae127. [PMID: 38860489 PMCID: PMC11304982 DOI: 10.1093/g3journal/jkae127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/07/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
Copidosoma floridanum is a cosmopolitan species and an egg-larval parasitoid of the Plusiine moth. C. floridanum has a unique development mode called polyembryony, in which over two thousand genetically identical embryos are produced from a single egg. Some embryos develop into sterile soldier larvae precociously, and their emergence period and aggressive behavior differ between the US and Japanese C. floridanum strains. Genome sequencing expects to contribute to our understanding of the molecular bases underlying the progression of polyembryony. However, only the genome sequence of the US strain generated by the short-read assembly has been reported. In the present study, we determined the genome sequence of the Japanese strain using Pacific Biosciences high-fidelity reads and generating a highly contiguous assembly (552.7 Mb, N50: 17.9 Mb). Gene prediction and annotation identified 13,886 transcripts derived from 10,786 gene models. We searched the genomic differences between US and Japanese strains. Among gene models predicted in this study, 100 gene loci in the Japanese strain had extremely different gene structures from those in the US strain. This was accomplished through functional annotation (GGSEARCH) and long-read sequencing. Genomic differences between strains were also reflected in amino acid sequences of vasa that play a central role in caste determination in this species. The genome assemblies constructed in this study will facilitate the genomic comparisons between Japanese and US strains, leading to our understanding of detailed genomic regions responsible for the ecological and physiological characteristics of C. floridanum.
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Affiliation(s)
- Kouhei Toga
- Laboratory of BioDX, PtBio Co-Creation Research Center, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima city, Hiroshima 739-0046, Japan
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima city, Hiroshima 739-0046, Japan
| | - Takuma Sakamoto
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Miyuki Kanda
- Laboratory of BioDX, PtBio Co-Creation Research Center, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima city, Hiroshima 739-0046, Japan
- Research and Development Department, PtBio Inc., 3-10-23 Kagamiyama, Higashi-Hiroshima city, Hiroshima 739-0046, Japan
| | - Keita Tamura
- Laboratory of BioDX, PtBio Co-Creation Research Center, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima city, Hiroshima 739-0046, Japan
| | - Keisuke Okuhara
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima city, Hiroshima 739-0046, Japan
- Research and Development Department, PtBio Inc., 3-10-23 Kagamiyama, Higashi-Hiroshima city, Hiroshima 739-0046, Japan
| | - Hiroko Tabunoki
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
- Cooperative Major in Advanced Health Science, Graduate School of Bio-Applications and System Engineering, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Hidemasa Bono
- Laboratory of BioDX, PtBio Co-Creation Research Center, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima city, Hiroshima 739-0046, Japan
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima city, Hiroshima 739-0046, Japan
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5
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Padigepati SR, Stafford DA, Tan CA, Silvis MR, Jamieson K, Keyser A, Nunez PAC, Nicoludis JM, Manders T, Fresard L, Kobayashi Y, Araya CL, Aradhya S, Johnson B, Nykamp K, Reuter JA. Scalable approaches for generating, validating and incorporating data from high-throughput functional assays to improve clinical variant classification. Hum Genet 2024; 143:995-1004. [PMID: 39085601 PMCID: PMC11303574 DOI: 10.1007/s00439-024-02691-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/12/2024] [Indexed: 08/02/2024]
Abstract
As the adoption and scope of genetic testing continue to expand, interpreting the clinical significance of DNA sequence variants at scale remains a formidable challenge, with a high proportion classified as variants of uncertain significance (VUSs). Genetic testing laboratories have historically relied, in part, on functional data from academic literature to support variant classification. High-throughput functional assays or multiplex assays of variant effect (MAVEs), designed to assess the effects of DNA variants on protein stability and function, represent an important and increasingly available source of evidence for variant classification, but their potential is just beginning to be realized in clinical lab settings. Here, we describe a framework for generating, validating and incorporating data from MAVEs into a semi-quantitative variant classification method applied to clinical genetic testing. Using single-cell gene expression measurements, cellular evidence models were built to assess the effects of DNA variation in 44 genes of clinical interest. This framework was also applied to models for an additional 22 genes with previously published MAVE datasets. In total, modeling data was incorporated from 24 genes into our variant classification method. These data contributed evidence for classifying 4043 observed variants in over 57,000 individuals. Genetic testing laboratories are uniquely positioned to generate, analyze, validate, and incorporate evidence from high-throughput functional data and ultimately enable the use of these data to provide definitive clinical variant classifications for more patients.
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Affiliation(s)
| | | | | | - Melanie R Silvis
- Invitae Corporation, San Francisco, CA, 94103, USA
- Epic Bio, South San Francisco, CA, 94080, USA
| | - Kirsty Jamieson
- Invitae Corporation, San Francisco, CA, 94103, USA
- Epic Bio, South San Francisco, CA, 94080, USA
| | - Andrew Keyser
- Invitae Corporation, San Francisco, CA, 94103, USA
- Calico Life Sciences, South San Francisco, CA, 94080, USA
| | | | - John M Nicoludis
- Invitae Corporation, San Francisco, CA, 94103, USA
- Department of Structural Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Toby Manders
- Invitae Corporation, San Francisco, CA, 94103, USA
| | | | | | - Carlos L Araya
- Invitae Corporation, San Francisco, CA, 94103, USA
- Tapanti.org, Santa Barbara, CA, 93108, USA
| | | | - Britt Johnson
- Invitae Corporation, San Francisco, CA, 94103, USA
- GeneDx, Stamford, CT, 06902, USA
| | - Keith Nykamp
- Invitae Corporation, San Francisco, CA, 94103, USA.
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6
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Lysenkova Wiklander M, Arvidsson G, Bunikis I, Lundmark A, Raine A, Marincevic-Zuniga Y, Gezelius H, Bremer A, Feuk L, Ameur A, Nordlund J. A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing. Life Sci Alliance 2024; 7:e202302481. [PMID: 38777370 PMCID: PMC11111970 DOI: 10.26508/lsa.202302481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
The B-cell acute lymphoblastic leukemia (ALL) cell line REH, with the t(12;21) ETV6::RUNX1 translocation, is known to have a complex karyotype defined by a series of large-scale chromosomal rearrangements. Taken from a 15-yr-old at relapse, the cell line offers a practical model for the study of pediatric B-ALL. In recent years, short- and long-read DNA and RNA sequencing have emerged as a complement to karyotyping techniques in the resolution of structural variants in an oncological context. Here, we explore the integration of long-read PacBio and Oxford Nanopore whole-genome sequencing, IsoSeq RNA sequencing, and short-read Illumina sequencing to create a detailed genomic and transcriptomic characterization of the REH cell line. Whole-genome sequencing clarified the molecular traits of disrupted ALL-associated genes including CDKN2A, PAX5, BTG1, VPREB1, and TBL1XR1, as well as the glucocorticoid receptor NR3C1 Meanwhile, transcriptome sequencing identified seven fusion genes within the genomic breakpoints. Together, our extensive whole-genome investigation makes high-quality open-source data available to the leukemia genomics community.
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Affiliation(s)
- Mariya Lysenkova Wiklander
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Gustav Arvidsson
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Anders Lundmark
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Yanara Marincevic-Zuniga
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Henrik Gezelius
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Anna Bremer
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/01apvbh93 Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Lars Feuk
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Adam Ameur
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
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Sund KL, Liu J, Lee J, Garbe J, Abdelhamed Z, Maag C, Hallinan B, Wu SW, Sperry E, Deshpande A, Stottmann R, Smolarek TA, Dyer LM, Hestand MS. Long-read sequencing and optical genome mapping identify causative gene disruptions in noncoding sequence in two patients with neurologic disease and known chromosome abnormalities. Am J Med Genet A 2024:e63818. [PMID: 39041659 DOI: 10.1002/ajmg.a.63818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/12/2024] [Accepted: 07/07/2024] [Indexed: 07/24/2024]
Abstract
Despite advances in next generation sequencing (NGS), genetic diagnoses remain elusive for many patients with neurologic syndromes. Long-read sequencing (LRS) and optical genome mapping (OGM) technologies improve upon existing capabilities in the detection and interpretation of structural variation in repetitive DNA, on a single haplotype, while also providing enhanced breakpoint resolution. We performed LRS and OGM on two patients with known chromosomal rearrangements and inconclusive Sanger or NGS. The first patient, who had epilepsy and developmental delay, had a complex translocation between two chromosomes that included insertion and inversion events. The second patient, who had a movement disorder, had an inversion on a single chromosome disrupted by multiple smaller inversions and insertions. Sequence level resolution of the rearrangements identified pathogenic breaks in noncoding sequence in or near known disease-causing genes with relevant neurologic phenotypes (MBD5, NKX2-1). These specific variants have not been reported previously, but expected molecular consequences are consistent with previously reported cases. As the use of LRS and OGM technologies for clinical testing increases and data analyses become more standardized, these methods along with multiomic data to validate noncoding variation effects will improve diagnostic yield and increase the proportion of probands with detectable pathogenic variants for known genes implicated in neurogenetic disease.
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Affiliation(s)
- Kristen L Sund
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jie Liu
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Joyce Lee
- Bionano Genomics, San Diego, California, USA
| | - John Garbe
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Zakia Abdelhamed
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Chelsey Maag
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Barbara Hallinan
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Steven W Wu
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Ethan Sperry
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Archana Deshpande
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Rolf Stottmann
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Teresa A Smolarek
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Lisa M Dyer
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Matthew S Hestand
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
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8
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Jiang F, Huang S, Liu T, Wang J, Zhou J, Zuo L, Li J, Li R, Liao C, Li D. Identification of a Novel 16.8Kb Deletion of the α-Globin Gene Cluster by Third-Generation Sequencing. Hemoglobin 2024:1-6. [PMID: 39007770 DOI: 10.1080/03630269.2024.2378078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/22/2024] [Indexed: 07/16/2024]
Abstract
α-thalassemia major (α-TM) often causes Hb Bart's (c4) hydrops fetalis and severe obstetric complications in the mother. Step-wise screening for couples at risk of having offspring(s) affected by α-TM is the efficient prevention method but some rare genotypes of thalassemia cannot be detected. A 32-year-old male with low HbA2 (2.4%) and mild anemia was performed real-time PCR-based multicolor melting curve analysis (MMCA) because his wife was -SEA deletion carrier. The result of multiplex ligation-dependent probe amplification (MLPA) suggested the existence of -SEA deletion in the proband. A novel deletion of the α-globin gene cluster was found using self-designed MLPA probes combined with longer PCR, which was further accurately described to be 16.8Kb (hg38, Chr16:1,65,236-1,82,113) deletion by the third-generation sequencing. A fragment ranging from 1,53,226 to 1,54,538(GRch38/hg38) was identified which suggested the existence of the homologous recombination event. The third-generation sequencing is accurate and efficient in obtaining accurate information for complex structural variations.
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Affiliation(s)
- Fan Jiang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated with Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Shuang Huang
- Department of Laboratory Medicine, He Xian Memorial Hospital, Southern Medical University, Guangzhou, China
| | - Tuoen Liu
- Department of Biomedical Sciences West VA School of Osteopathic Medicine, Lewisburg, WV, USA
| | - Jieyu Wang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated with Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Jianying Zhou
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated with Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Liandong Zuo
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated with Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Jian Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated with Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Ru Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated with Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Can Liao
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated with Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Dongzhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated with Guangzhou Medical University, Guangzhou, Guangdong Province, China
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9
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Sadurski J, Polak-Berecka M, Staniszewski A, Waśko A. Step-by-Step Metagenomics for Food Microbiome Analysis: A Detailed Review. Foods 2024; 13:2216. [PMID: 39063300 PMCID: PMC11276190 DOI: 10.3390/foods13142216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
This review article offers a comprehensive overview of the current understanding of using metagenomic tools in food microbiome research. It covers the scientific foundation and practical application of genetic analysis techniques for microbial material from food, including bioinformatic analysis and data interpretation. The method discussed in the article for analyzing microorganisms in food without traditional culture methods is known as food metagenomics. This approach, along with other omics technologies such as nutrigenomics, proteomics, metabolomics, and transcriptomics, collectively forms the field of foodomics. Food metagenomics allows swift and thorough examination of bacteria and potential metabolic pathways by utilizing foodomic databases. Despite its established scientific basis and available bioinformatics resources, the research approach of food metagenomics outlined in the article is not yet widely implemented in industry. The authors believe that the integration of next-generation sequencing (NGS) with rapidly advancing digital technologies such as artificial intelligence (AI), the Internet of Things (IoT), and big data will facilitate the widespread adoption of this research strategy in microbial analysis for the food industry. This adoption is expected to enhance food safety and product quality in the near future.
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Affiliation(s)
- Jan Sadurski
- Department of Biotechnology, Microbiology and Human Nutrition, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, 20-704 Lublin, Poland; (M.P.-B.); (A.S.); (A.W.)
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10
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Lee SI, Bae S, Kim YS, Lee S. Complete genome sequencing of three methicillin-resistant Staphylococcus aureus isolated from the blood of patients with persistent bacteremia. Microbiol Resour Announc 2024:e0117723. [PMID: 38990024 DOI: 10.1128/mra.01177-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
We report the complete genome sequences of three molecular types of methicillin-resistant Staphylococcus aureus (MRSA) clinical strains isolated from the blood of three patients diagnosed with persistent MRSA bacteremia: KNIH_5618 (ST5-t5076-SCCmecII), KNIH_5844 (ST72-t664-SCCmecIV), and KNIH_6268 (ST89-t375-SCCmecII). These genome sequences contribute to an enhanced understanding of the underlying causes of persistent MRSA infection.
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Affiliation(s)
- Soo In Lee
- Department of Bacterial Disease Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Seongman Bae
- Division of Infectious Diseases, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yang Soo Kim
- Division of Infectious Diseases, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sungkyoung Lee
- Department of Bacterial Disease Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
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11
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Xie NB, Wang M, Ji TT, Guo X, Gang FY, Hao Y, Zeng L, Wang YF, Feng YQ, Yuan BF. Simultaneous detection of 5-methylcytosine and 5-hydroxymethylcytosine at specific genomic loci by engineered deaminase-assisted sequencing. Chem Sci 2024; 15:10073-10083. [PMID: 38966352 PMCID: PMC11220598 DOI: 10.1039/d4sc00930d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/17/2024] [Indexed: 07/06/2024] Open
Abstract
Cytosine modifications, particularly 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), play crucial roles in numerous biological processes. Current analytical methods are often constrained to the separate detection of either 5mC or 5hmC, or the combination of both modifications. The ability to simultaneously detect C, 5mC, and 5hmC at the same genomic locations with precise stoichiometry is highly desirable. Herein, we introduce a method termed engineered deaminase-assisted sequencing (EDA-seq) for the simultaneous quantification of C, 5mC, and 5hmC at the same genomic sites. EDA-seq utilizes a specially engineered protein, derived from human APOBEC3A (A3A), known as eA3A-M5. eA3A-M5 exhibits distinct deamination capabilities for C, 5mC, and 5hmC. In EDA-seq, C undergoes complete deamination and is sequenced as T. 5mC is partially deaminated resulting in a mixed readout of T and C, and 5hmC remains undeaminated and is read as C. Consequently, the proportion of T readouts (P T) reflects the collective occurrences of C and 5mC, regulated by the deamination rate of 5mC (R 5mC). By determining R 5mC and P T values, we can deduce the precise levels of C, 5mC, and 5hmC at particular genomic locations. We successfully used EDA-seq to simultaneously measure C, 5mC, and 5hmC at specific loci within human lung cancer tissue and their normal counterpart. The results from EDA-seq demonstrated a strong concordance with those obtained from the combined application of BS-seq and ACE-seq methods. EDA-seq eliminates the need for bisulfite treatment, DNA oxidation or glycosylation and uniquely enables simultaneous quantification of C, 5mC and 5hmC at the same genomic locations.
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Affiliation(s)
- Neng-Bin Xie
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University Wuhan 430071 China
- Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University Wuhan 430060 China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences Wuhan 430071 China
| | - Min Wang
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 China
- College of Chemical Engineering and Environmental Chemistry, Weifang University Weifang 261061 China
| | - Tong-Tong Ji
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 China
| | - Xia Guo
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 China
| | - Fang-Yin Gang
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University Wuhan 430071 China
| | - Ying Hao
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 China
| | - Li Zeng
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 China
| | - Ya-Fen Wang
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University Wuhan 430071 China
| | - Yu-Qi Feng
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University Wuhan 430071 China
| | - Bi-Feng Yuan
- Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University Wuhan 430071 China
- Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University Wuhan 430060 China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences Wuhan 430071 China
- College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 China
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12
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Yano N, Chong PF, Kojima KK, Miyoshi T, Luqmen-Fatah A, Kimura Y, Kora K, Kayaki T, Maizuru K, Hayashi T, Yokoyama A, Ajiro M, Hagiwara M, Kondo T, Kira R, Takita J, Yoshida T. Long-read sequencing identifies an SVA_D retrotransposon insertion deep within the intron of ATP7A as a novel cause of occipital horn syndrome. J Med Genet 2024:jmg-2024-110056. [PMID: 38960580 DOI: 10.1136/jmg-2024-110056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND SINE-VNTR-Alu (SVA) retrotransposons move from one genomic location to another in a 'copy-and-paste' manner. They continue to move actively and cause monogenic diseases through various mechanisms. Currently, disease-causing SVA retrotransposons are classified into human-specific young SVA_E or SVA_F subfamilies. In this study, we identified an evolutionarily old SVA_D retrotransposon as a novel cause of occipital horn syndrome (OHS). OHS is an X-linked, copper metabolism disorder caused by dysfunction of the copper transporter, ATP7A. METHODS We investigated a 16-year-old boy with OHS whose pathogenic variant could not be detected via routine molecular genetic analyses. RESULTS A 2.8 kb insertion was detected deep within the intron of the patient's ATP7A gene. This insertion caused aberrant mRNA splicing activated by a new donor splice site located within it. Long-read circular consensus sequencing enabled us to accurately read the entire insertion sequence, which contained highly repetitive and GC-rich segments. Consequently, the insertion was identified as an SVA_D retrotransposon. Antisense oligonucleotides (AOs) targeting the new splice site restored the expression of normal transcripts and functional ATP7A proteins. AO treatment alleviated excessive accumulation of copper in patient fibroblasts in a dose-dependent manner. Pedigree analysis revealed that the retrotransposon had moved into the OHS-causing position two generations ago. CONCLUSION This is the first report of a human monogenic disease caused by the SVA_D retrotransposon. The fact that the evolutionarily old SVA_D is still actively transposed, leading to increased copy numbers may make a notable impact on rare genetic disease research.
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Affiliation(s)
- Naoko Yano
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Pin Fee Chong
- Department of Pediatric Neurology, Fukuoka Children's Hospital, Fukuoka, Japan
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kenji K Kojima
- Genetic Information Research Institute, Cupertino, CA, USA
| | - Tomoichiro Miyoshi
- Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Gene Mechanisms, Kyoto University Graduate School of Biostudies, Kyoto, Japan
| | - Ahmad Luqmen-Fatah
- Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yu Kimura
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kengo Kora
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Taisei Kayaki
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kanako Maizuru
- Department of Pediatrics, Tenri Yorozu Hospital, Tenri, Japan
| | - Takahiro Hayashi
- Department of Pediatrics, Kurashiki Central Hospital, Kurashiki, Japan
| | - Atsushi Yokoyama
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masahiko Ajiro
- Division of Cancer RNA Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Masatoshi Hagiwara
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Teruyuki Kondo
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Ryutaro Kira
- Department of Pediatric Neurology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Junko Takita
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takeshi Yoshida
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
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13
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Ji Z, Xing Y, Li J, Feng X, Yang F, Zhu B, Yan J. Male-specific age prediction based on Y-chromosome DNA methylation with blood using pyrosequencing. Forensic Sci Int Genet 2024; 71:103050. [PMID: 38703560 DOI: 10.1016/j.fsigen.2024.103050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/14/2024] [Accepted: 04/19/2024] [Indexed: 05/06/2024]
Abstract
Age prediction is an important aspect of forensic science that offers valuable insight into identification. In recent years, extensive studies have been conducted on age prediction based on DNA methylation, and numerous studies have demonstrated that DNA methylation is a reliable biomarker for age prediction. However, almost all studies on age prediction based on DNA methylation have focused on age-related CpG sites in autosomes, which are concentrated on single-source DNA samples. Mixed samples, especially male-female mixed samples, are common in forensic casework. The application of Y-STRs and Y-SNPs can provide clues for the genetic typing of male individuals in male-female mixtures, but they cannot provide the age information of male individuals. Studies on Y-chromosome DNA methylation can address this issue. In this study, we identified five age-related CpG sites on the Y chromosome (Y-CpGs) and developed a male-specific age prediction model using pyrosequencing combined with a support vector machine algorithm. The mean absolute deviation of the model was 5.50 years in the training set and 6.74 years in the testing set. When we used a male blood sample to predict age, the deviation between the predicted and chronological age was 1.18 years. Then, we mixed the genomic DNA of the male and a female at ratios of 1:1, 1:5, 1:10, and 1:50, the range of deviation between the predicted and chronological age of the male in the mixture was 1.16-1.74 years. In addition, there was no significant difference between the methylation values of bloodstains and blood in the same sample, which indicates that our model is also suitable for bloodstain samples. Overall, our results show that age prediction using DNA methylation of the Y chromosome has potential applications in forensic science and can be of great help in predicting the age of males in male-female mixtures. Furthermore, this work lays the foundation for future research on age-related applications of Y-CpGs.
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Affiliation(s)
- Zhimin Ji
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030009, PR China
| | - Yangfeng Xing
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030009, PR China
| | - Junli Li
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030009, PR China
| | - Xiaoxiao Feng
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030009, PR China
| | - Fenglong Yang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030009, PR China.
| | - Bofeng Zhu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030009, PR China; Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, PR China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030009, PR China.
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14
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Huang R, Liu Y, Xu J, Lin D, Mao A, Yang L, Zhong G, Wang H, Xu R, Chen Y, Zhou Q. Back-to-Back Comparison of Third-Generation Sequencing and Next-Generation Sequencing in Carrier Screening of Thalassemia. Arch Pathol Lab Med 2024; 148:797-804. [PMID: 36630651 DOI: 10.5858/arpa.2022-0168-oa] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2022] [Indexed: 01/13/2023]
Abstract
CONTEXT.— Recently, new technologies, such as next-generation sequencing and third-generation sequencing, have been used in carrier screening of thalassemia. However, there is no direct comparison between the 2 methods in carrier screening of thalassemia. OBJECTIVE.— To compare the clinical performance of third-generation sequencing with next-generation sequencing in carrier screening of thalassemia. DESIGN.— Next-generation sequencing and third-generation sequencing were simultaneously conducted for 1122 individuals in Hainan Province. RESULTS.— Among 1122 genetic results, 1105 (98.48%) were concordant and 17 (1.52%) were discordant between the 2 methods. Among the 17 discordant results, 4 were common thalassemia variants, 9 were rare thalassemia variants, and 4 were variations with unknown pathogenicity. Sanger sequencing and polymerase chain reaction for discordant samples confirmed all the results of third-generation sequencing. Among the 685 individuals with common and rare thalassemia variants detected by third-generation sequencing, 512 (74.74%) were carriers of α-thalassemia, 110 (16.06%) were carriers of β-thalassemia, and 63 (9.20%) had coinheritance of α-thalassemia and β-thalassemia. Three thalassemia variants were reported for the first time in Hainan Province, including -THAI, -α2.4, and ααααanti3.7. Eleven variants with potential pathogenicity were identified in 36 patients with positive hemoglobin test results. Among 52 individuals with negative hemoglobin test results, 17 were identified with thalassemia variants. In total, third-generation sequencing and next-generation sequencing correctly detected 763 and 746 individuals with variants, respectively. Third-generation sequencing yielded a 2.28% (17 of 746) increment compared with next-generation sequencing. CONCLUSIONS.— Third-generation sequencing was demonstrated to be a more accurate and reliable approach in carrier screening of thalassemia compared with next-generation sequencing.
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Affiliation(s)
- Renliang Huang
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Yinyin Liu
- Berry Genomics Corporation, Beijing, 102200, China (Liu, Mao, R. Xu, Chen)
| | - Jing Xu
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Dan Lin
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Aiping Mao
- Berry Genomics Corporation, Beijing, 102200, China (Liu, Mao, R. Xu, Chen)
| | - Liuqing Yang
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Gaobu Zhong
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Huoniao Wang
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Ruofan Xu
- Berry Genomics Corporation, Beijing, 102200, China (Liu, Mao, R. Xu, Chen)
| | - Yiwei Chen
- Berry Genomics Corporation, Beijing, 102200, China (Liu, Mao, R. Xu, Chen)
| | - Qiaomiao Zhou
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
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15
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Liu G, Chen C, Jiang Z, Liu Y, Wang X, Qiao L, Liu K, Han X. Characterization and the first complete genome sequence of a novel strain of Bergeyella porcorum isolated from pigs in China. BMC Microbiol 2024; 24:214. [PMID: 38886642 PMCID: PMC11181579 DOI: 10.1186/s12866-024-03366-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Bergeyella porcorum is a newly identified bacterium that has an ambiguous relationship with pneumonia in pigs. However, few studies have adequately characterized this species. RESULTS In this study, we analyzed the morphological, physiological, and genomic characteristics of the newly identified B. porcorum sp. nov. strain QD2021 isolated from pigs. The complete genome sequence of the B. porcorum QD2021 strain consists of a single circular chromosome (2,271,736 bp, 38.51% G + C content), which encodes 2,578 genes. One plasmid with a size of 70,040 bp was detected. A total of 121 scattered repeat sequences, 319 tandem repeat sequences, 4 genomic islands, 5 prophages, 3 CRISPR sequences, and 51 ncRNAs were predicted. The coding genes of the B. porcorum genome were successfully annotated across eight databases (NR, GO, KEGG, COG, TCDB, Pfam, Swiss-Prot and CAZy) and four pathogenicity-related databases (PHI, CARD, VFDB and ARDB). In addition, a comparative genome analysis was performed to explore the evolutionary relationships of B. porcorum QD2021. CONCLUSIONS To our knowledge, this is the first study to provide fundamental phenotypic and whole-genome sequences for B. porcorum. Our results extensively expand the current knowledge and could serve as a valuable genomic resource for future research on B. porcorum.
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Affiliation(s)
- Gang Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Chao Chen
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Zhikang Jiang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Yu Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xianwen Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Lei Qiao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Kang Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xianjie Han
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, Shandong, China.
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16
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Shelton WJ, Zandpazandi S, Nix JS, Gokden M, Bauer M, Ryan KR, Wardell CP, Vaske OM, Rodriguez A. Long-read sequencing for brain tumors. Front Oncol 2024; 14:1395985. [PMID: 38915364 PMCID: PMC11194609 DOI: 10.3389/fonc.2024.1395985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/27/2024] [Indexed: 06/26/2024] Open
Abstract
Brain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in the advanced molecular characterization of brain tumors for diagnosis, prognosis, and treatment. Since the implementation of molecular biomarkers by the WHO CNS in 2016, the genomics of brain tumors has been integrated into diagnostic criteria. Long-read sequencing, also known as third generation sequencing, is an emerging technique that allows for the sequencing of longer DNA segments leading to improved detection of structural variants and epigenetics. These capabilities are opening a way for better characterization of brain tumors. Here, we present a comprehensive summary of the state of the art of third-generation sequencing in the application for brain tumor diagnosis, prognosis, and treatment. We discuss the advantages and potential new implementations of long-read sequencing into clinical paradigms for neuro-oncology patients.
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Affiliation(s)
- William J. Shelton
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Sara Zandpazandi
- Department of Neurosurgery, Medical University of South Carolina, Charleston, SC, United States
| | - J Stephen Nix
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Murat Gokden
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Michael Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Katie Rose Ryan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Christopher P. Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Olena Morozova Vaske
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Analiz Rodriguez
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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17
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Traisrisilp K, Zheng Y, Choy KW, Chareonkwan P. Thalassemia screening by third-generation sequencing: Pilot study in a Thai population. Obstet Med 2024; 17:101-107. [PMID: 38784187 PMCID: PMC11110746 DOI: 10.1177/1753495x231207676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 09/27/2023] [Indexed: 05/25/2024] Open
Abstract
Background Conventional thalassemia screening takes a stepwise approach and has limitations in comprehensively identifying all spectrums of mutations. This study aimed to investigate the performance of third-generation sequencing (TGS) compared to conventional molecular testing. Methods TGS was applied to validate all known variants detected by conventional testing and to detect missing variants in undiagnosed cases. The study was conducted at Maharaj Nakorn Chiang Mai Hospital between December 2021 and April 2022. Results In total, 19 cases were included in this study, among which 52.6% (10/19) had known thalassemia variants, while 47.7% (9/19) cases were undiagnosed by conventional methods. All 16 variants previously detected were validated by TGS, and TGS additionally detected 43.8% (7/16) thalassemia variants for 36.8% (7/19) cases. Conclusion TGS could provide additional genetic diagnoses compared with conventional methods. Further cost-effectiveness studies with a larger sample size are needed to explore the role of TGS in clinical practices.
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Affiliation(s)
- Kuntharee Traisrisilp
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Yu Zheng
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Pimlak Chareonkwan
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
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Sun K, Fu K, Hu T, Shentu X, Yu X. Leveraging insect viruses and genetic manipulation for sustainable agricultural pest control. PEST MANAGEMENT SCIENCE 2024; 80:2515-2527. [PMID: 37948321 DOI: 10.1002/ps.7878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/16/2023] [Accepted: 11/11/2023] [Indexed: 11/12/2023]
Abstract
The potential of insect viruses in the biological control of agricultural pests is well-recognized, yet their practical application faces obstacles such as host specificity, variable virulence, and resource scarcity. High-throughput sequencing (HTS) technologies have significantly advanced our capabilities in discovering and identifying new insect viruses, thereby enriching the arsenal for pest management. Concurrently, progress in reverse genetics has facilitated the development of versatile viral expression vectors. These vectors have enhanced the specificity and effectiveness of insect viruses in targeting specific pests, offering a more precise approach to pest control. This review provides a comprehensive examination of the methodologies employed in the identification of insect viruses using HTS. Additionally, it explores the domain of genetically modified insect viruses and their associated challenges in pest management. The adoption of these cutting-edge approaches holds great promise for developing environmentally sustainable and effective pest control solutions. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Kai Sun
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Kang Fu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Tao Hu
- Zhejinag Seed Industry Group Xinchuang Bio-breeding Co., Ltd., Hangzhou, China
| | - Xuping Shentu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
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Thingujam D, Pajerowska-Mukhtar KM, Mukhtar MS. Duckweed: Beyond an Efficient Plant Model System. Biomolecules 2024; 14:628. [PMID: 38927032 PMCID: PMC11201744 DOI: 10.3390/biom14060628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Duckweed (Lemnaceae) rises as a crucial model system due to its unique characteristics and wide-ranging utility. The significance of physiological research and phytoremediation highlights the intricate potential of duckweed in the current era of plant biology. Special attention to duckweed has been brought due to its distinctive features of nutrient uptake, ion transport dynamics, detoxification, intricate signaling, and stress tolerance. In addition, duckweed can alleviate environmental pollutants and enhance sustainability by participating in bioremediation processes and wastewater treatment. Furthermore, insights into the genomic complexity of Lemnaceae species and the flourishing field of transgenic development highlight the opportunities for genetic manipulation and biotechnological innovations. Novel methods for the germplasm conservation of duckweed can be adopted to preserve genetic diversity for future research endeavors and breeding programs. This review centers around prospects in duckweed research promoting interdisciplinary collaborations and technological advancements to drive its full potential as a model organism.
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Affiliation(s)
- Doni Thingujam
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA;
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC 29634, USA
| | - Karolina M. Pajerowska-Mukhtar
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA;
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC 29634, USA
| | - M. Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA;
- Department of Genetics & Biochemistry, Clemson University, 105 Collings St. Biosystems Research Complex, Clemson, SC 29634, USA
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20
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Domrazek K, Jurka P. Application of Next-Generation Sequencing (NGS) Techniques for Selected Companion Animals. Animals (Basel) 2024; 14:1578. [PMID: 38891625 PMCID: PMC11171117 DOI: 10.3390/ani14111578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Next-Generation Sequencing (NGS) techniques have revolutionized veterinary medicine for cats and dogs, offering insights across various domains. In veterinary parasitology, NGS enables comprehensive profiling of parasite populations, aiding in understanding transmission dynamics and drug resistance mechanisms. In infectious diseases, NGS facilitates rapid pathogen identification, characterization of virulence factors, and tracking of outbreaks. Moreover, NGS sheds light on metabolic processes by elucidating gene expression patterns and metabolic pathways, essential for diagnosing metabolic disorders and designing tailored treatments. In autoimmune diseases, NGS helps identify genetic predispositions and molecular mechanisms underlying immune dysregulation. Veterinary oncology benefits from NGS through personalized tumor profiling, mutation analysis, and identification of therapeutic targets, fostering precision medicine approaches. Additionally, NGS plays a pivotal role in veterinary genetics, unraveling the genetic basis of inherited diseases and facilitating breeding programs for healthier animals. Physiological investigations leverage NGS to explore complex biological systems, unraveling gene-environment interactions and molecular pathways governing health and disease. Application of NGS in treatment planning enhances precision and efficacy by enabling personalized therapeutic strategies tailored to individual animals and their diseases, ultimately advancing veterinary care for companion animals.
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Affiliation(s)
- Kinga Domrazek
- Institute of Veterinary Medicine, Warsaw University of Life Sciences—SGGW, Nowoursynowska 159c, 02-776 Warsaw, Poland;
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21
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Xing K, Li H, Wang X, Sun Y, Zhang J. A Full-Length Transcriptome and Analysis of the NHL-1 Gene Family in Neocaridina denticulata sinensis. BIOLOGY 2024; 13:366. [PMID: 38927246 PMCID: PMC11200715 DOI: 10.3390/biology13060366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024]
Abstract
Neocaridina denticulata sinensis has emerged as a promising model organism for basic studies in Decapod. However, the current transcriptome information on this species is based on next-generation sequencing technologies, which are limited by a short read length. Therefore, the present study aimed to generate a full-length transcriptome assembly of N. denticulata sinensis utilizing the PacBio Sequel Ⅱ platform. The resulting transcriptome assembly comprised 5831 transcripts with an N50 value of 3697 bp. Remarkably, 90.5% of these transcripts represented novel isoforms of known genes. The transcripts were further searched against the NR, SwissProt, KEGG, KOG, GO, NT, and Pfam databases. A total of 24.8% of the transcripts can be annotated across all seven databases. Additionally, 1236 alternative splicing events, 344 transcription factors, and 124 long non-coding RNAs (LncRNAs) were predicted. Based on the alternative splicing annotation results, a RING finger protein NHL-1 gene from N. denticulata sinensis (NdNHL-1) was identified. There are 15 transcripts in NdNHL-1. The longest transcript is 4995 bp in length and encodes a putative protein of 1665 amino acids. A phylogenetic analysis showed its close relationship with NHL-1 from other crustacean species. This report represents the full-length transcriptome of N. denticulata sinensis and will facilitate research on functional genomics and environmental adaptation in this species.
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Affiliation(s)
- Kefan Xing
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, China; (K.X.); (H.L.); (X.W.)
| | - Huimin Li
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, China; (K.X.); (H.L.); (X.W.)
| | - Xiongfei Wang
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, China; (K.X.); (H.L.); (X.W.)
| | - Yuying Sun
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, China; (K.X.); (H.L.); (X.W.)
- Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Jiquan Zhang
- School of Life Sciences/Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, China; (K.X.); (H.L.); (X.W.)
- Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
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22
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Ruan Z, Jiao J, Zhao J, Liu J, Liang C, Yang X, Sun Y, Tang G, Li P. Genome sequencing and comparative genomics reveal insights into pathogenicity and evolution of Fusarium zanthoxyli, the causal agent of stem canker in prickly ash. BMC Genomics 2024; 25:502. [PMID: 38773367 PMCID: PMC11110190 DOI: 10.1186/s12864-024-10424-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Fusarium zanthoxyli is a destructive pathogen causing stem canker in prickly ash, an ecologically and economically important forest tree. However, the genome lack of F. zanthoxyli has hindered research on its interaction with prickly ash and the development of precise control strategies for stem canker. RESULTS In this study, we sequenced and annotated a relatively high-quality genome of F. zanthoxyli with a size of 43.39 Mb, encoding 11,316 putative genes. Pathogenicity-related factors are predicted, comprising 495 CAZymes, 217 effectors, 156 CYP450s, and 202 enzymes associated with secondary metabolism. Besides, a comparative genomics analysis revealed Fusarium and Colletotrichum diverged from a shared ancestor approximately 141.1 ~ 88.4 million years ago (MYA). Additionally, a phylogenomic investigation of 12 different phytopathogens within Fusarium indicated that F. zanthoxyli originated approximately 34.6 ~ 26.9 MYA, and events of gene expansion and contraction within them were also unveiled. Finally, utilizing conserved domain prediction, the results revealed that among the 59 unique genes, the most enriched domains were PnbA and ULP1. Among the 783 expanded genes, the most enriched domains were PKc_like kinases and those belonging to the APH_ChoK_Like family. CONCLUSION This study sheds light on the genetic basis of F. zanthoxyli's pathogenicity and evolution which provides valuable information for future research on its molecular interactions with prickly ash and the development of effective strategies to combat stem canker.
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Affiliation(s)
- Zhao Ruan
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jiahui Jiao
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Junchi Zhao
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jiaxue Liu
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chaoqiong Liang
- Shaanxi Academy of Forestry, Xi'an, Shaanxi, 710082, People's Republic of China
| | - Xia Yang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yan Sun
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Guanghui Tang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Peiqin Li
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Szakállas N, Barták BK, Valcz G, Nagy ZB, Takács I, Molnár B. Can long-read sequencing tackle the barriers, which the next-generation could not? A review. Pathol Oncol Res 2024; 30:1611676. [PMID: 38818014 PMCID: PMC11137202 DOI: 10.3389/pore.2024.1611676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/30/2024] [Indexed: 06/01/2024]
Abstract
The large-scale heterogeneity of genetic diseases necessitated the deeper examination of nucleotide sequence alterations enhancing the discovery of new targeted drug attack points. The appearance of new sequencing techniques was essential to get more interpretable genomic data. In contrast to the previous short-reads, longer lengths can provide a better insight into the potential health threatening genetic abnormalities. Long-reads offer more accurate variant identification and genome assembly methods, indicating advances in nucleotide deflect-related studies. In this review, we introduce the historical background of sequencing technologies and show their benefits and limits, as well. Furthermore, we highlight the differences between short- and long-read approaches, including their unique advances and difficulties in methodologies and evaluation. Additionally, we provide a detailed description of the corresponding bioinformatics and the current applications.
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Affiliation(s)
- Nikolett Szakállas
- Department of Biological Physics, Faculty of Science, Eötvös Loránd University, Budapest, Hungary
| | - Barbara K. Barták
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Gábor Valcz
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- HUN-REN-SU Translational Extracellular Vesicle Research Group, Budapest, Hungary
| | - Zsófia B. Nagy
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - István Takács
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Béla Molnár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
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24
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Scarano C, Veneruso I, De Simone RR, Di Bonito G, Secondino A, D’Argenio V. The Third-Generation Sequencing Challenge: Novel Insights for the Omic Sciences. Biomolecules 2024; 14:568. [PMID: 38785975 PMCID: PMC11117673 DOI: 10.3390/biom14050568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/05/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The understanding of the human genome has been greatly improved by the advent of next-generation sequencing technologies (NGS). Despite the undeniable advantages responsible for their widespread diffusion, these methods have some constraints, mainly related to short read length and the need for PCR amplification. As a consequence, long-read sequencers, called third-generation sequencing (TGS), have been developed, promising to overcome NGS. Starting from the first prototype, TGS has progressively ameliorated its chemistries by improving both read length and base-calling accuracy, as well as simultaneously reducing the costs/base. Based on these premises, TGS is showing its potential in many fields, including the analysis of difficult-to-sequence genomic regions, structural variations detection, RNA expression profiling, DNA methylation study, and metagenomic analyses. Protocol standardization and the development of easy-to-use pipelines for data analysis will enhance TGS use, also opening the way for their routine applications in diagnostic contexts.
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Affiliation(s)
- Carmela Scarano
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Iolanda Veneruso
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Rosa Redenta De Simone
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Gennaro Di Bonito
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Angela Secondino
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Valeria D’Argenio
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Via di Val Cannuta 247, 00166 Roma, Italy
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Yan Q, Zhang G, Zhang X, Huang L. A Review of Transcriptomics and Metabolomics in Plant Quality and Environmental Response: From Bibliometric Analysis to Science Mapping and Future Trends. Metabolites 2024; 14:272. [PMID: 38786749 PMCID: PMC11123105 DOI: 10.3390/metabo14050272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Transcriptomics and metabolomics offer distinct advantages in investigating the differentially expressed genes and cellular entities that have the greatest influence on end-phenotype, making them crucial techniques for studying plant quality and environmental responses. While numerous relevant articles have been published, a comprehensive summary is currently lacking. This review aimed to understand the global and longitudinal research trends of transcriptomics and metabolomics in plant quality and environmental response (TMPQE). Utilizing bibliometric methods, we presented a comprehensive science mapping of the social structure, conceptual framework, and intellectual foundation of TMPQE. We uncovered that TMPQE research has been categorized into three distinct stages since 2020. A citation analysis of the 29 most cited articles, coupled with a content analysis of recent works (2020-2023), highlight five potential research streams in plant quality and environmental responses: (1) biosynthetic pathways, (2) abiotic stress, (3) biotic stress, (4) development and ripening, and (5) methodologies and tools. Current trends and future directions are shaped by technological advancements, species diversity, evolving research themes, and an environmental ecology focus. Overall, this review provides a novel and comprehensive perspective to understand the longitudinal trend on TMPQE.
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Affiliation(s)
| | | | | | - Linfang Huang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, HaiDian District, Beijing 100193, China; (Q.Y.); (G.Z.); (X.Z.)
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26
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Ahmad T, Erum Ishaq S, Liang L, Hou J, Xie R, Dong Y, Yu T, Wang F. Description of the first cultured representative of "Candidatus Synoicihabitans" genus, isolated from deep-sea sediment of South China Sea. Syst Appl Microbiol 2024; 47:126490. [PMID: 38330528 DOI: 10.1016/j.syapm.2024.126490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
In this study we describe the first cultured representative of Candidatus Synoicihabitans genus, a novel strain designated as LMO-M01T, isolated from deep-sea sediment of South China Sea. This bacterium is a facultative aerobe, Gram-negative, non-motile, and has a globular-shaped morphology, with light greenish, small, and circular colonies. Analysis of the 16S rRNA gene sequences of strain LMO-M01T showed less than 93% similarity to its closest cultured members. Furthermore, employing advanced phylogenomic methods such as comparative genome analysis, average nucleotide identity (ANI), average amino acids identity (AAI), and digital DNA-DNA hybridization (dDDH), placed this novel species within the candidatus genus Synoicihabitans of the family Opitutaceae, Phylum Verrucomicrobiota. The genomic analysis of strain LMO-M01T revealed 175 genes, encoding putative carbohydrate-active enzymes. This suggests its metabolic potential to degrade and utilize complex polysaccharides, indicating a significant role in carbon cycling and nutrient turnover in deep-sea sediment. In addition, the strain's physiological capacity to utilize diverse biopolymers such as lignin, xylan, starch, and agar as sole carbon source opens up possibilities for sustainable energy production and environmental remediation. Moreover, the genome sequence of this newly isolated strain has been identified across diverse ecosystems, including marine sediment, fresh water, coral, soil, plants, and activated sludge highlighting its ecological significance and adaptability to various environments. The recovery of strain LMO-M01T holds promise for taxonomical, ecological and biotechnological applications. Based on the polyphasic data, we propose that this ecologically important strain LMO-M01T represents a novel genus (previously Candidatus) within the family Opitutaceae of phylum Verrucomicrobiota, for which the name Synoicihabitans lomoniglobus gen. nov., sp. nov. was proposed. The type of strain is LMO-M01T (= CGMCC 1.61593T = KCTC 92913T).
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Affiliation(s)
- Tariq Ahmad
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Sidra Erum Ishaq
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Lewen Liang
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Jialin Hou
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Ruize Xie
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yijing Dong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Tiantian Yu
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China; Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China.
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27
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Kumar KR, Cowley MJ, Davis RL. Next-Generation Sequencing and Emerging Technologies. Semin Thromb Hemost 2024. [PMID: 38692283 DOI: 10.1055/s-0044-1786397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Genetic sequencing technologies are evolving at a rapid pace with major implications for research and clinical practice. In this review, the authors provide an updated overview of next-generation sequencing (NGS) and emerging methodologies. NGS has tremendously improved sequencing output while being more time and cost-efficient in comparison to Sanger sequencing. The authors describe short-read sequencing approaches, such as sequencing by synthesis, ion semiconductor sequencing, and nanoball sequencing. Third-generation long-read sequencing now promises to overcome many of the limitations of short-read sequencing, such as the ability to reliably resolve repeat sequences and large genomic rearrangements. By combining complementary methods with massively parallel DNA sequencing, a greater insight into the biological context of disease mechanisms is now possible. Emerging methodologies, such as advances in nanopore technology, in situ nucleic acid sequencing, and microscopy-based sequencing, will continue the rapid evolution of this area. These new technologies hold many potential applications for hematological disorders, with the promise of precision and personalized medical care in the future.
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Affiliation(s)
- Kishore R Kumar
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Molecular Medicine Laboratory, Concord Hospital, Sydney, Australia
| | - Mark J Cowley
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Computational Biology Group, Children's Cancer Institute, University of New South Wales, Randwick, New South Wales, Australia
| | - Ryan L Davis
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, New South Wales, Australia
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28
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Filius M, van Wee R, de Lannoy C, Westerlaken I, Li Z, Kim SH, de Agrela Pinto C, Wu Y, Boons GJ, Pabst M, de Ridder D, Joo C. Full-length single-molecule protein fingerprinting. NATURE NANOTECHNOLOGY 2024; 19:652-659. [PMID: 38351230 DOI: 10.1038/s41565-023-01598-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/22/2023] [Indexed: 03/21/2024]
Abstract
Proteins are the primary functional actors of the cell. While proteoform diversity is known to be highly biologically relevant, current protein analysis methods are of limited use for distinguishing proteoforms. Mass spectrometric methods, in particular, often provide only ambiguous information on post-translational modification sites, and sequences of co-existing modifications may not be resolved. Here we demonstrate fluorescence resonance energy transfer (FRET)-based single-molecule protein fingerprinting to map the location of individual amino acids and post-translational modifications within single full-length protein molecules. Our data show that both intrinsically disordered proteins and folded globular proteins can be fingerprinted with a subnanometer resolution, achieved by probing the amino acids one by one using single-molecule FRET via DNA exchange. This capability was demonstrated through the analysis of alpha-synuclein, an intrinsically disordered protein, by accurately quantifying isoforms in mixtures using a machine learning classifier, and by determining the locations of two O-GlcNAc moieties. Furthermore, we demonstrate fingerprinting of the globular proteins Bcl-2-like protein 1, procalcitonin and S100A9. We anticipate that our ability to perform proteoform identification with the ultimate sensitivity may unlock exciting new venues in proteomics research and biomarker-based diagnosis.
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Affiliation(s)
- Mike Filius
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Raman van Wee
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Carlos de Lannoy
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Ilja Westerlaken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Zeshi Li
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Sung Hyun Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Department of Physics, Ewha Womans University, Seoul, Republic of Korea
| | - Cecilia de Agrela Pinto
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Yunfei Wu
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Geert-Jan Boons
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Chirlmin Joo
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.
- Department of Physics, Ewha Womans University, Seoul, Republic of Korea.
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Gulati P, Singh A, Patra S, Bhat S, Verma A. Restriction modification systems in archaea: A panoramic outlook. Heliyon 2024; 10:e27382. [PMID: 38644887 PMCID: PMC11033074 DOI: 10.1016/j.heliyon.2024.e27382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 04/23/2024] Open
Abstract
Restriction modification (RM) systems are one of the ubiquitous yet primitive defense responses employed by bacteria and archaea with the primary role of safeguarding themselves against invading bacteriophages. Protection of the host occurs by the cleavage of the invading foreign DNA via restriction endonucleases with concomitant methylation of host DNA with the aid of a methyltransferase counterpart. RM systems have been extensively studied in bacteria, however, in the case of archaea there are limited reports of RM enzymes that are investigated to date owing to their inhospitable growth demands. This review aims to broaden the knowledge about what is known about the diversity of RM systems in archaea and encapsulate the current knowledge on restriction and modification enzymes characterized in archaea so far and the role of RM systems in the milieu of archaeal biology.
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Affiliation(s)
- Pallavi Gulati
- Department of Microbiology, Ram Lal Anand College, University of Delhi South Campus, New Delhi 110021, India
| | - Ashish Singh
- Department of Microbiology, University of Delhi South Campus, New Delhi 110021, India
| | - Sandeep Patra
- Department of Microbiology, Ram Lal Anand College, University of Delhi South Campus, New Delhi 110021, India
| | - Shreyas Bhat
- Department of Microbiology, Ram Lal Anand College, University of Delhi South Campus, New Delhi 110021, India
| | - Anil Verma
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA-15213, USA
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Pan X, Liu H, Feng L, Zong Y, Cao Z, Guo L, Yang G. Full-length transcriptome analysis of a bloom-forming dinoflagellate Prorocentrum shikokuense (Dinophyceae). Sci Data 2024; 11:430. [PMID: 38664437 PMCID: PMC11045741 DOI: 10.1038/s41597-024-03269-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Prorocentrum shikokuense (formerly P. donghaiense) is a pivotal dinoflagellate species associating with the HABs in the East China Sea. The complexity of its large nuclear genome hindered us from understanding its genomic characteristics. Full-length transcriptome sequencing offers a practical solution to decipher the physiological mechanisms of a species without the reference genome. In this study, we employed single-molecule real-time (SMRT) sequencing technology to sequence the full-length transcriptome of Prorocentrum shikokuense. We successfully generated 41.73 Gb of clean SMRT sequencing reads and isolated 105,249 non-redundant full-length non-chimeric reads. Our trial has led to the identification of 11,917 long non-coding RNA transcripts, 514 alternative splicing events, 437 putative transcription factor genes from 17 TF gene families, and 34,723 simple sequence repeats. Additionally, a total of 78,265 open reading frames were identified, of them 15,501 were the protein coding sequences. This dataset is valuable for annotating P. shikokuense genome, and will contribute significantly to the in-depth studies on the molecular mechanisms underlining the dinoflagellate bloom formation.
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Affiliation(s)
- Xiaohui Pan
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, P. R. China
| | - Hang Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, P. R. China
| | - Leili Feng
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, P. R. China
| | - Yanan Zong
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, P. R. China
| | - Zihao Cao
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, P. R. China
| | - Li Guo
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, P. R. China.
| | - Guanpin Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, P. R. China.
- Key Laboratory of Evolution and Marine Biodiversity of Ministry of Education, Ocean University of China (OUC), Qingdao, 266003, P. R. China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, P. R. China.
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31
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Bromfield ESP, Cloutier S. Bradyrhizobium ontarionense sp. nov., a novel bacterial symbiont isolated from Aeschynomene indica (Indian jointvetch), harbours photosynthesis, nitrogen fixation and nitrous oxide (N 2O) reductase genes. Antonie Van Leeuwenhoek 2024; 117:69. [PMID: 38647727 PMCID: PMC11035471 DOI: 10.1007/s10482-024-01940-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/02/2024] [Indexed: 04/25/2024]
Abstract
A novel bacterial symbiont, strain A19T, was previously isolated from a root-nodule of Aeschynomene indica and assigned to a new lineage in the photosynthetic clade of the genus Bradyrhizobium. Here data are presented for the detailed genomic and taxonomic analyses of novel strain A19T. Emphasis is placed on the analysis of genes of practical or ecological significance (photosynthesis, nitrous oxide reductase and nitrogen fixation genes). Phylogenomic analysis of whole genome sequences as well as 50 single-copy core gene sequences placed A19T in a highly supported lineage distinct from described Bradyrhizobium species with B. oligotrophicum as the closest relative. The digital DNA-DNA hybridization and average nucleotide identity values for A19T in pair-wise comparisons with close relatives were far lower than the respective threshold values of 70% and ~ 96% for definition of species boundaries. The complete genome of A19T consists of a single 8.44 Mbp chromosome and contains a photosynthesis gene cluster, nitrogen-fixation genes and genes encoding a complete denitrifying enzyme system including nitrous oxide reductase implicated in the reduction of N2O, a potent greenhouse gas, to inert dinitrogen. Nodulation and type III secretion system genes, needed for nodulation by most rhizobia, were not detected. Data for multiple phenotypic tests complemented the sequence-based analyses. Strain A19T elicits nitrogen-fixing nodules on stems and roots of A. indica plants but not on soybeans or Macroptilium atropurpureum. Based on the data presented, a new species named Bradyrhizobium ontarionense sp. nov. is proposed with strain A19T (= LMG 32638T = HAMBI 3761T) as the type strain.
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Affiliation(s)
- Eden S P Bromfield
- Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, K1A 0C6, Canada.
| | - Sylvie Cloutier
- Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, K1A 0C6, Canada
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32
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Xin R, Zhang F, Zheng J, Zhang Y, Yu C, Feng X. SDBA: Score Domain-Based Attention for DNA N4-Methylcytosine Site Prediction from Multiperspectives. J Chem Inf Model 2024; 64:2839-2853. [PMID: 37646411 DOI: 10.1021/acs.jcim.3c00688] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
In tasks related to DNA sequence classification, choosing the appropriate encoding methods is challenging. Some of the methods encode sequences based on prior knowledge that limits the ability of the model to obtain multiperspective information from the sequences. We introduced a new trainable ensemble method based on the attention mechanism SDBA, which stands for Score Domain-Based Attention. Unlike other methods, we fed the task-independent encoding results into the models and dynamically ensembled features from different perspectives using the SDBA mechanism. This approach allows the model to acquire and weight sequence features voluntarily. SDBA is conceptually general and empirically powerful. It has achieved new state-of-the-art results on the benchmark data sets associated with DNA N4-methylcytosine site prediction.
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Affiliation(s)
- Ruihao Xin
- College of Information and Control Engineering, Jilin Institute of Chemical Technology, Jilin 130000, P.R. China
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, P.R. China
| | - Fan Zhang
- College of Information and Control Engineering, Jilin Institute of Chemical Technology, Jilin 130000, P.R. China
| | - Jiaxin Zheng
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, P.R. China
| | - Yangyi Zhang
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Cuinan Yu
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, P.R. China
| | - Xin Feng
- School of Science, Jilin Institute of Chemical Technology, Jilin 130000, P.R. China
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, P.R. China
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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] [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).
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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
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Zhang S, Liu Y, Wang H, Xu Z, Peng J, Xu Q, Li K, Wang H, Guo Y. Achromobacter seleniivolatilans sp. nov. and Buttiauxella selenatireducens sp. nov., isolated from the rhizosphere of selenium hyperaccumulator Cardamine hupingshanesis. Int J Syst Evol Microbiol 2024; 74. [PMID: 38619980 DOI: 10.1099/ijsem.0.006334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024] Open
Abstract
Two Gram-stain-negative bacterial strains, R39T and R73T, were isolated from the rhizosphere soil of the selenium hyperaccumulator Cardamine hupingshanesis in China. Strain R39T transformed selenite into elemental and volatile selenium, whereas strain R73T transformed both selenate and selenite into elemental selenium. Phylogenetic and phylogenomic analyses indicated that strain R39T belonged to the genus Achromobacter, while strain R73T belonged to the genus Buttiauxella. Strain R39T (genome size, 6.68 Mb; G+C content, 61.6 mol%) showed the closest relationship to Achromobacter marplatensis LMG 26219T and Achromobacter kerstersii LMG 3441T, with average nucleotide identity (ANI) values of 83.6 and 83.4 %, respectively. Strain R73T (genome size, 5.22 Mb; G+C content, 50.3 mol%) was most closely related to Buttiauxella ferragutiae ATCC 51602T with an ANI value of 86.4 %. Furthermore, strain A111 from the GenBank database was found to cluster with strain R73T within the genus Buttiauxella through phylogenomic analyses. The ANI and digital DNA-DNA hybridization values between strains R73T and A111 were 97.5 and 80.0% respectively, indicating that they belong to the same species. Phenotypic characteristics also differentiated strain R39T and strain R73T from their closely related species. Based on the polyphasic analyses, strain R39T and strain R73T represent novel species of the genera Achromobacter and Buttiauxella, respectively, for which the names Achromobacter seleniivolatilans sp. nov. (type strain R39T=GDMCC 1.3843T=JCM 36009T) and Buttiauxella selenatireducens sp. nov. (type strain R73T=GDMCC 1.3636T=JCM 35850T) are proposed.
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Affiliation(s)
- Sasa Zhang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, PR China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, PR China
| | - Yi Liu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, PR China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, PR China
| | - Hao Wang
- Division of Biology and Biological Engineering, California Institute of Technology, California, 91125, USA
| | - Zhongnan Xu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, PR China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, PR China
| | - Jing Peng
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, PR China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, PR China
| | - Qiaolin Xu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, PR China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, PR China
| | - Kui Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, PR China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, PR China
| | - Haoyang Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, PR China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, PR China
| | - Yanbin Guo
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, PR China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, PR China
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Wang F, Jin Z, Wang S, Yang L, Fan Z, Yao Y. ASAPA: a bioinformatic pipeline based on Iso-Seq that identifies the links among alternative splicing, alternative transcription initiation and alternative polyadenylation. Funct Integr Genomics 2024; 24:67. [PMID: 38528184 DOI: 10.1007/s10142-024-01332-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 02/29/2024] [Accepted: 03/02/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND Although the events associated with alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI) can be identified by many approaches based on isoform sequencing (Iso-Seq), these analyses are generally independent of each other and the links between these events are still rarely mentioned. However, an interdependency analysis can be achieved because the transcriptional start site, splice sites and polyA site could be simultaneously included in a long, full-length read from Iso-Seq. RESULTS We create ASAPA pipeline that enables streamlined analysis for a robust detection of potential links among AS, ATI and APA using Iso-Seq data. We tested this pipeline using Arabidopsis data and found some interesting results: some adjacent introns tend to be simultaneously spliced or retained; coupling between AS and ATI or APA is limited to the initial or terminal intron; and ATI and APA are potentially linked in some special cases. CONCLUSION Our pipeline enables streamlined analysis for a robust detection of potential links among AS, ATI and APA using Iso-Seq data, which is conducive to a better understanding of transcription landscape generation.
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Grants
- 32072537,31872068 This work is supported by the National Natural Science Foundation of China (32072537,31872068), fruit industry technology system of Shandong Province (SDAIT-06-03), and Agriculture Improved Variety Project of Shandong Province (2020LZGC008).
- 32072537,31872068 This work is supported by the National Natural Science Foundation of China (32072537,31872068), fruit industry technology system of Shandong Province (SDAIT-06-03), and Agriculture Improved Variety Project of Shandong Province (2020LZGC008).
- 32072537,31872068 This work is supported by the National Natural Science Foundation of China (32072537,31872068), fruit industry technology system of Shandong Province (SDAIT-06-03), and Agriculture Improved Variety Project of Shandong Province (2020LZGC008).
- 32072537,31872068 This work is supported by the National Natural Science Foundation of China (32072537,31872068), fruit industry technology system of Shandong Province (SDAIT-06-03), and Agriculture Improved Variety Project of Shandong Province (2020LZGC008).
- 32072537,31872068 This work is supported by the National Natural Science Foundation of China (32072537,31872068), fruit industry technology system of Shandong Province (SDAIT-06-03), and Agriculture Improved Variety Project of Shandong Province (2020LZGC008).
- 32072537,31872068 This work is supported by the National Natural Science Foundation of China (32072537,31872068), fruit industry technology system of Shandong Province (SDAIT-06-03), and Agriculture Improved Variety Project of Shandong Province (2020LZGC008).
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Affiliation(s)
- Fei Wang
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Zhongxin Jin
- National Key Laboratory of Tropical Crop Breeding, Tropical Bioscience and Biotechnology Institute, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shengnan Wang
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Longcheng Yang
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Zongbao Fan
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Yuxin Yao
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
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Wang L, Chen M, Zheng X, Li X. Comparative genomics of fungal mutants provides a systemic view of extreme cadmium tolerance in eukaryotic microbes. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133354. [PMID: 38154183 DOI: 10.1016/j.jhazmat.2023.133354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/09/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023]
Abstract
Whether eukaryotic organisms can evolve for higher heavy metal resistance in laboratory conditions remains unknown. In this study, we challenged a macrofungi, Pleurotus ostreatus, in a designed microbial evolution and growth arena (MEGA)-plate with an extreme Cd gradient. Within months, the wild-type strain developed 10 mutants, exhibiting a maximum three-fold increase in Cd tolerance and slower growth rates. Genomic sequencing and re-sequencing of the wild-type and ten mutant strains generated about 51 GB data, allowing a comprehensive comparative genomics analysis. As a result, a total of 2512 common single nucleotide polymorphisms, 70 inserts and deletes, 39 copy number variations and 21 structural variations were found in the 10 mutants. The mutant genes were primarily involved in substrate transport. In combination with transcriptome analysis, we discovered that the ten mutants had a distinct Cd-resistant mechanism compared to the wild-type strain. Genes involved in oxidation-reduction, ion transmembrane transport, and metal compartment/efflux are primarily responsible for the extreme Cd tolerance in the P. ostreatus mutants. Our findings contribute to the understanding of eukaryotic Cd resistance at the genome level and establish a foundation for developing bioremediation tools utilizing highly tolerant macrofungi.
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Affiliation(s)
- Likun Wang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | | | - Xin Zheng
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Xiaofang Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China.
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Westfall DH, Deng W, Pankow A, Murrell H, Chen L, Zhao H, Williamson C, Rolland M, Murrell B, Mullins JI. Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations-Application to HIV-1 quasispecies. Virus Evol 2024; 10:veae019. [PMID: 38765465 PMCID: PMC11099545 DOI: 10.1093/ve/veae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 12/19/2023] [Accepted: 02/20/2024] [Indexed: 05/22/2024] Open
Abstract
Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing, which can require extensive optimizations to overcome. We present complete laboratory and bioinformatics workflows to overcome many of these hurdles. The Pacific Biosciences single molecule real-time platform was used to sequence polymerase-chain reaction (PCR) amplicons derived from cDNA templates tagged with unique molecular identifiers (SMRT-UMI). Optimized laboratory protocols were developed through extensive testing of different sample preparation conditions to minimize between-template recombination during PCR. The use of UMI allowed accurate template quantitation as well as removal of point mutations introduced during PCR and sequencing to produce a highly accurate consensus sequence from each template. Production of highly accurate sequences from the large datasets produced from SMRT-UMI sequencing is facilitated by a novel bioinformatic pipeline, Probabilistic Offspring Resolver for Primer IDs (PORPIDpipeline). PORPIDpipeline automatically filters and parses circular consensus reads by sample, identifies and discards reads with UMIs likely created from PCR and sequencing errors, generates consensus sequences, checks for contamination within the dataset, and removes any sequence with evidence of PCR recombination, heteroduplex formation, or early cycle PCR errors. The optimized SMRT-UMI sequencing and PORPIDpipeline methods presented here represent a highly adaptable and established starting point for accurate sequencing of diverse pathogens. These methods are illustrated through characterization of human immunodeficiency virus quasispecies in a virus transmitter-recipient pair of individuals.
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Affiliation(s)
- Dylan H Westfall
- Department of Microbiology, University of Washington School of Medicine, 960 Republican Street, Seattle, WA 98195-8070, USA
| | - Wenjie Deng
- Department of Microbiology, University of Washington School of Medicine, 960 Republican Street, Seattle, WA 98195-8070, USA
| | - Alec Pankow
- Department of Microbiology, University of Washington School of Medicine, 960 Republican Street, Seattle, WA 98195-8070, USA
| | - Hugh Murrell
- Department of Pathology, Division of Medical Virology, University of Cape Town and National Health Laboratory Services, Observatory, Cape Town 7925, South Africa
| | - Lennie Chen
- Department of Microbiology, University of Washington School of Medicine, 960 Republican Street, Seattle, WA 98195-8070, USA
| | - Hong Zhao
- Department of Microbiology, University of Washington School of Medicine, 960 Republican Street, Seattle, WA 98195-8070, USA
| | - Carolyn Williamson
- Department of Pathology, Division of Medical Virology, University of Cape Town and National Health Laboratory Services, Observatory, Cape Town 7925, South Africa
| | - Morgane Rolland
- US Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda, MD 20817, USA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, Stockholm 171 65, Sweden
| | - James I Mullins
- Department of Microbiology, University of Washington School of Medicine, 960 Republican Street, Seattle, WA 98195-8070, USA
- Department of Medicine, University of Washington School of Medicine, 960 Republican Street, Seattle, WA 98195-8070, USA
- Department of Global Health, University of Washington Schools of Medicine and Public Health, 960 Republican Street, Seattle, WA 98195-8070, USA
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Sahın Vural G, Bolat H. Nanopore sequencing method for CTG18.1 expansion in TCF4 in late-onset Fuchs endothelial corneal dystrophy and a comparison of the structural features of cornea with first-degree relatives. Graefes Arch Clin Exp Ophthalmol 2024; 262:903-911. [PMID: 37747538 DOI: 10.1007/s00417-023-06243-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/26/2023] Open
Abstract
BACKGROUND To evaluate the relationship between the number of trinucleotide repeats (TNR) in late-onset Fuchs corneal endothelial dystrophy (FCED) and to compare the endothelial properties of FCED, first-degree relatives, and controls. METHODS Blood samples were collected from FCEDs to determine TNR number. The FCED patients, first-degree relatives, and controls were examined with specular microscopy for central corneal thickness (CCT), endothelial cell density (ECD), pleomorphism and polymegatism, and with corneal topography for specific indicators such as (i) displacement of thinnest point of cornea, (ii) loss of isopachs, (iii) focal posterior surface depression towards anterior chamber. RESULTS This study included 92 patients with FCED, 92 first-degree relatives, and 96 controls. CCT was thickest in FCEDs (558.0 μm) (p < 0.05) while there was no difference between relatives (533.0 μm) and controls (530.4 μm) (p = 0.845). ECD was decreased in both FCED (2069.2 mm2) and relatives (2171.4 mm2) than controls (2822.9 mm2) (p < 0.05 in both). The presence of pleomorphism and polymegatism was significant in patients with FCED (93.4% and 93.4%, respectively), relatives (86.9% and 86.04%, respectively), and controls (8.33% and 1.04%, respectively) (p < 0.05). Specific topographic indicators differed among the groups (p < 0.05). The mean repeat number of the FCED patients was 17.48 ± 4.54 (12-25) times. The TNR number of FCED cases correlated with the relative CCT (p < 0.05, R = 0.615) and cell density (p = 0.009, R = -0.499). CONCLUSIONS A strong association between the corneal endothelium in relatives and TNR number of FCEDs was defined. Relatives tended to have fewer corneal endothelial cells, even though they did not have clinical findings.
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Affiliation(s)
- Gozde Sahın Vural
- Department of Ophthalmology, Balıkesir University Medicine Faculty, Balıkesir, Turkey.
- Department of Ophthalmology, Balıkesir University Medicine Faculty Hospital, Balıkesir, Turkey.
| | - Hilmi Bolat
- Department of Genetics, Balıkesir University Medicine Faculty, Balıkesir, Turkey
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Li Y, Sun Z. Phenotypic and genomic insights into the pathogenicity and antimicrobial resistance of an Enterobacter roggenkampii strain isolated from diseased silver arowana (Osteoglossum bicirrhosum). JOURNAL OF FISH DISEASES 2024; 47:e13898. [PMID: 38014710 DOI: 10.1111/jfd.13898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023]
Abstract
Enterobacter roggenkampii is an opportunistic pathogen that causes infections in a wide range of hosts. A bacterial strain named EOBSR_19 was isolated from diseased silver arowana, Osteoglossum bicirrhosum. This bacterium was identified as E. roggenkampii based on the phenotypic characteristics and sequence analysis of the16S rDNA and gyrB genes. Average nucleotide identity and phylogenetic analysis based on the whole genome sequence further confirmed the bacterial taxonomy of EOBSR_19. Artificial experimental infection indicated that EOBSR_19 was pathogenic to fish. Antimicrobial susceptibility test showed it was multi-drug resistant. The EOBSR_19 was found to be resistant to 18 antibiotics belonging to quinolones, macrolides, sulfonamides, aminoglycosides, and β-lactams classes. The whole genome sequencing analysis showed that EOBSR_19 carried 730 virulence genes that were annotated for different functional modules, such as adhesion and invasion, secretion system, siderophore transport system and bacterial toxin. Among them, the virulence genes related to adhesion and invasion were the most abundant. In addition, drug resistance genes involved in multiple mechanisms of antimicrobial resistance were identified in its genomics, including multidrug resistance efflux pumps, antibiotic inactivating enzymes, and antibiotic binding site mutations. Its genomic analysis via whole-genome sequencing provided insights into the pathogenicity and antimicrobial resistance.
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Affiliation(s)
- Yuerui Li
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Zhongshi Sun
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
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Xu Z, Hu L, Liu Y, Peng C, Zeng G, Zeng L, Yang M, Linpeng S, Bu X, Jiang X, Xie T, Chen L, Zhou S, He J. Comparison of Third-Generation Sequencing and Routine Polymerase Chain Reaction in Genetic Analysis of Thalassemia. Arch Pathol Lab Med 2024; 148:336-344. [PMID: 37270807 DOI: 10.5858/arpa.2022-0299-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2023] [Indexed: 06/06/2023]
Abstract
CONTEXT.— Thalassemia is the most widely distributed monogenic autosomal recessive disorder in the world. Accurate genetic analysis of thalassemia is crucial for thalassemia prevention. OBJECTIVE.— To compare the clinical utility of a third-generation sequencing-based approach termed comprehensive analysis of thalassemia alleles with routine polymerase chain reaction (PCR) in genetic analysis of thalassemia and explore the molecular spectrum of thalassemia in Hunan Province. DESIGN.— Subjects in Hunan Province were recruited, and hematologic testing was performed. Five hundred four subjects positive on hemoglobin testing were then used as the cohort, and third-generation sequencing and routine PCR were used for genetic analysis. RESULTS.— Of the 504 subjects, 462 (91.67%) had the same results, whereas 42 (8.33%) exhibited discordant results between the 2 methods. Sanger sequencing and PCR testing confirmed the results of third-generation sequencing. In total, third-generation sequencing correctly detected 247 subjects with variants, whereas PCR identified 205, which showed an increase in detection of 20.49%. Moreover, α triplications were identified in 1.98% (10 of 504) hemoglobin testing-positive subjects in Hunan Province. Seven hemoglobin variants with potential pathogenicity were detected in 9 hemoglobin testing-positive subjects. CONCLUSIONS.— Third-generation sequencing is a more comprehensive, reliable, and efficient approach for genetic analysis of thalassemia than PCR, and allowed for a characterization of the thalassemia spectrum in Hunan Province.
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Affiliation(s)
- Zhen Xu
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Lanping Hu
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Yinyin Liu
- Berry Genomics Corporation, Beijing, China (Liu, Xie, Chen)
| | - Can Peng
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Guo Zeng
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Li Zeng
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Mengyue Yang
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Siyuan Linpeng
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Xiufen Bu
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Xuanyu Jiang
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Tiantian Xie
- Berry Genomics Corporation, Beijing, China (Liu, Xie, Chen)
| | - Libao Chen
- Berry Genomics Corporation, Beijing, China (Liu, Xie, Chen)
| | - Shihao Zhou
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Jun He
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
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Xu L, Ren Y, Wu J, Cui T, Dong R, Huang C, Feng Z, Zhang T, Yang P, Yuan J, Xu X, Liu J, Wang J, Chen W, Mi D, Irwin DM, Yan Y, Xu L, Yu X, Li G. Evolution and expression patterns of the neo-sex chromosomes of the crested ibis. Nat Commun 2024; 15:1670. [PMID: 38395916 PMCID: PMC10891136 DOI: 10.1038/s41467-024-46052-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Bird sex chromosomes play a unique role in sex-determination, and affect the sexual morphology and behavior of bird species. Core waterbirds, a major clade of birds, share the common characteristics of being sexually monomorphic and having lower levels of inter-sexual conflict, yet their sex chromosome evolution remains poorly understood. Here, by we analyse of a chromosome-level assembly of a female crested ibis (Nipponia nippon), a typical core waterbird. We identify neo-sex chromosomes resulting from fusion of microchromosomes with ancient sex chromosomes. These fusion events likely occurred following the divergence of Threskiornithidae and Ardeidae. The neo-W chromosome of the crested ibis exhibits the characteristics of slow degradation, which is reflected in its retention of abundant gametologous genes. Neo-W chromosome genes display an apparent ovary-biased gene expression, which is largely driven by genes that are retained on the crested ibis W chromosome but lost in other bird species. These results provide new insights into the evolutionary history and expression patterns for the sex chromosomes of bird species.
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Affiliation(s)
- Lulu Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yandong Ren
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jiahong Wu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing, China
| | - Tingting Cui
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Rong Dong
- Research Center for Qinling Giant Panda, Shaanxi Academy of Forestry, Xi'an, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Zhe Feng
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Tianmin Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Peng Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiao Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jiao Liu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Wu Chen
- Guangzhou Wildlife Research Center, Guangzhou Zoo, Guangzhou, China
| | - Da Mi
- Xi'an Haorui Genomics Technology Co., LTD, Xi'an, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Yaping Yan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Luohao Xu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing, China.
| | - Xiaoping Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
- Guangzhou Wildlife Research Center, Guangzhou Zoo, Guangzhou, China.
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Garg D, Patel N, Rawat A, Rosado AS. Cutting edge tools in the field of soil microbiology. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100226. [PMID: 38425506 PMCID: PMC10904168 DOI: 10.1016/j.crmicr.2024.100226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
The study of the whole of the genetic material contained within the microbial populations found in a certain environment is made possible by metagenomics. This technique enables a thorough knowledge of the variety, function, and interactions of microbial communities that are notoriously difficult to research. Due to the limitations of conventional techniques such as culturing and PCR-based methodologies, soil microbiology is a particularly challenging field. Metagenomics has emerged as an effective technique for overcoming these obstacles and shedding light on the dynamic nature of the microbial communities in soil. This review focuses on the principle of metagenomics techniques, their potential applications and limitations in soil microbial diversity analysis. The effectiveness of target-based metagenomics in determining the function of individual genes and microorganisms in soil ecosystems is also highlighted. Targeted metagenomics, including high-throughput sequencing and stable-isotope probing, is essential for studying microbial taxa and genes in complex ecosystems. Shotgun metagenomics may reveal the diversity of soil bacteria, composition, and function impacted by land use and soil management. Sanger, Next Generation Sequencing, Illumina, and Ion Torrent sequencing revolutionise soil microbiome research. Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)'s third and fourth generation sequencing systems revolutionise long-read technology. GeoChip, clone libraries, metagenomics, and metabarcoding help comprehend soil microbial communities. The article indicates that metagenomics may improve environmental management and agriculture despite existing limitations.Metagenomics has revolutionised soil microbiology research by revealing the complete diversity, function, and interactions of microorganisms in soil. Metagenomics is anticipated to continue defining the future of soil microbiology research despite some limitations, such as the difficulty of locating the appropriate sequencing method for specific genes.
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Affiliation(s)
- Diksha Garg
- Department of Microbiology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Niketan Patel
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
- Computational Bioscience Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
| | - Anamika Rawat
- Center of Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
| | - Alexandre Soares Rosado
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
- Computational Bioscience Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
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Adachi E, Nakagawa R, Tsuji-Hosokawa A, Gau M, Kirino S, Yogi A, Nakatani H, Takasawa K, Yamaguchi T, Kosho T, Murakami M, Tajima T, Hasegawa T, Yamada T, Morio T, Ohara O, Kashimada K. A MinION-based Long-Read Sequencing Application With One-Step PCR for the Genetic Diagnosis of 21-Hydroxylase Deficiency. J Clin Endocrinol Metab 2024; 109:750-760. [PMID: 37804107 DOI: 10.1210/clinem/dgad577] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/13/2023] [Accepted: 09/26/2023] [Indexed: 10/08/2023]
Abstract
CONTEXT Recently developed long-read sequencing (LRS) technology has been considered an option for CYP21A2 analysis. However, the clinical use of LRS for CYP21A2 analysis is limited. OBJECTIVE This study's objective is to develop an efficient and low-cost LRS system for CYP21A2 screening. METHODS A DNA fragment library was prepared in a single polymerase chain reaction (PCR) that covers the entire CYP21A2 gene and all known junctions caused by TNXB gene structural rearrangements, yielding a single 8-kb product of CYP21A2 or CYP21A1P/CYP21A2 chimera. After barcoding, the PCR products were sequenced on a MinION-based platform with Flongle Flow Cell R9.4.1 and R10.4.1. RESULTS The reference genotypes of 55 patients with 21-hydroxylase deficiency (21OHD) were established using the conventional method with multiplex ligation-dependent probe amplification (MLPA) and nested PCR. LRS using Flongle Flow Cell R9.4.1 yielded consistent results. Additionally, the recently updated LRS "duplex" analysis with Flongle flow cell R10.4.1 was tested to reveal an advantage of accurately sequencing a variant located on the homopolymer region. By introducing a barcode system, the cost was reduced to be comparable to that of conventional analysis. A novel single-nucleotide variation was discovered at the acceptor site of intron 7, c.940-1G > C. We also identified a subtype of the classical chimeric junction CH2, "CH2a," in the region from the latter part of intron 5 to exon 6. CONCLUSION We successfully established a novel low-cost and highly accurate LRS system for 21OHD genetic analysis. Our study provides insight into the feasibility of LRS for diagnosing 21OHD and other genetic diseases caused by structural rearrangements.
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Affiliation(s)
- Eriko Adachi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
| | - Ryuichi Nakagawa
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
| | - Atsumi Tsuji-Hosokawa
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Maki Gau
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
| | - Shizuka Kirino
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
| | - Analia Yogi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
| | - Hisae Nakatani
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
| | - Kei Takasawa
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
| | - Tomomi Yamaguchi
- Center for Medical Genetics, Shinshu University Hospital, Nagano 390-8621, Japan
- Department of Medical Genetics, Shinshu University School of Medicine, Nagano 390-8621, Japan
- Division of Clinical Sequencing, Shinshu University School of Medicine, Nagano 390-8621, Japan
| | - Tomoki Kosho
- Center for Medical Genetics, Shinshu University Hospital, Nagano 390-8621, Japan
- Department of Medical Genetics, Shinshu University School of Medicine, Nagano 390-8621, Japan
- Division of Clinical Sequencing, Shinshu University School of Medicine, Nagano 390-8621, Japan
- Research Center for Supports to Advanced Science, Shinshu University, Nagano 390-8621, Japan
| | - Masanori Murakami
- Department of Molecular Endocrinology and Metabolism, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
| | - Toshihiro Tajima
- Department of Pediatrics, Jichi Medical University, Tochigi 329-0498, Japan
| | - Tomonobu Hasegawa
- Department of Pediatrics, Keio University, School of Medicine, Tokyo 160-8582, Japan
| | - Tetsuya Yamada
- Department of Molecular Endocrinology and Metabolism, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | - Kenichi Kashimada
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8519, Japan
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Nadeem S, Riaz Ahmed S, Luqman T, Tan DKY, Maryum Z, Akhtar KP, Muhy Ud Din Khan S, Tariq MS, Muhammad N, Khan MKR, Liu Y. A comprehensive review on Gossypium hirsutum resistance against cotton leaf curl virus. Front Genet 2024; 15:1306469. [PMID: 38440193 PMCID: PMC10909863 DOI: 10.3389/fgene.2024.1306469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/01/2024] [Indexed: 03/06/2024] Open
Abstract
Cotton (Gossypium hirsutum L.) is a significant fiber crop. Being a major contributor to the textile industry requires continuous care and attention. Cotton is subjected to various biotic and abiotic constraints. Among these, biotic factors including cotton leaf curl virus (CLCuV) are dominant. CLCuV is a notorious disease of cotton and is acquired, carried, and transmitted by the whitefly (Bemisia tabaci). A cotton plant affected with CLCuV may show a wide range of symptoms such as yellowing of leaves, thickening of veins, upward or downward curling, formation of enations, and stunted growth. Though there are many efforts to protect the crop from CLCuV, long-term results are not yet obtained as CLCuV strains are capable of mutating and overcoming plant resistance. However, systemic-induced resistance using a gene-based approach remained effective until new virulent strains of CLCuV (like Cotton Leaf Curl Burewala Virus and others) came into existence. Disease control by biological means and the development of CLCuV-resistant cotton varieties are in progress. In this review, we first discussed in detail the evolution of cotton and CLCuV strains, the transmission mechanism of CLCuV, the genetic architecture of CLCuV vectors, and the use of pathogen and nonpathogen-based approaches to control CLCuD. Next, we delineate the uses of cutting-edge technologies like genome editing (with a special focus on CRISPR-Cas), next-generation technologies, and their application in cotton genomics and speed breeding to develop CLCuD resistant cotton germplasm in a short time. Finally, we delve into the current obstacles related to cotton genome editing and explore forthcoming pathways for enhancing precision in genome editing through the utilization of advanced genome editing technologies. These endeavors aim to enhance cotton's resilience against CLCuD.
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Affiliation(s)
- Sahar Nadeem
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Syed Riaz Ahmed
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
- Pakistan Agriculture Research Council (PARC), Horticulture Research Institute Khuzdar Baghbana, Khuzdar, Pakistan
| | - Tahira Luqman
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Daniel K. Y. Tan
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Zahra Maryum
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Khalid Pervaiz Akhtar
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Sana Muhy Ud Din Khan
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Sayyam Tariq
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Nazar Muhammad
- Agriculture and Cooperative Department, Quetta, Pakistan
| | - Muhammad Kashif Riaz Khan
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
- Plant Breeding and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Yongming Liu
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
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Singh G, Alser M, Denolf K, Firtina C, Khodamoradi A, Cavlak MB, Corporaal H, Mutlu O. RUBICON: a framework for designing efficient deep learning-based genomic basecallers. Genome Biol 2024; 25:49. [PMID: 38365730 PMCID: PMC10870431 DOI: 10.1186/s13059-024-03181-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
Nanopore sequencing generates noisy electrical signals that need to be converted into a standard string of DNA nucleotide bases using a computational step called basecalling. The performance of basecalling has critical implications for all later steps in genome analysis. Therefore, there is a need to reduce the computation and memory cost of basecalling while maintaining accuracy. We present RUBICON, a framework to develop efficient hardware-optimized basecallers. We demonstrate the effectiveness of RUBICON by developing RUBICALL, the first hardware-optimized mixed-precision basecaller that performs efficient basecalling, outperforming the state-of-the-art basecallers. We believe RUBICON offers a promising path to develop future hardware-optimized basecallers.
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Affiliation(s)
- Gagandeep Singh
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zürich, Switzerland
- Research and Advanced Development, AMD, Longmont, USA
| | - Mohammed Alser
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zürich, Switzerland
| | | | - Can Firtina
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zürich, Switzerland.
| | | | - Meryem Banu Cavlak
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zürich, Switzerland
| | - Henk Corporaal
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Onur Mutlu
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zürich, Switzerland.
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Sheng Q, Xu Q, Lan Z, Wu Z. Comparative Genome Analysis of Two Streptococcus suis Serotype 8 Strains Identifies Two New Virulence-Associated Genes. Animals (Basel) 2024; 14:572. [PMID: 38396540 PMCID: PMC10886379 DOI: 10.3390/ani14040572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Streptococcus suis is an important zoonotic pathogen that can cause meningitis and septicemia in swine and humans. Among numerous pathogenic serotypes, S. suis serotype 8 has distinctive characteristics such as a high detection rate and causing multi-host infection. There is no complete genome of serotype 8 strains so far. In this study, the complete genome of two S. suis serotype 8 strains, virulent strain 2018WUSS151 and non-virulent strain WUSS030, were sequenced. Comparative genomic analysis showed that the homology of the two genomes reaches 99.68%, and the main difference is the distinctive prophages. There are 83 genes unique to virulent strain 2018WUSS151, including three putative virulence-associated genes (PVGs). Two PVGs, padR and marR, are passenger genes in ISSsu2 family transposons that are able to form circular DNA intermediates during transposition, indicating the possibility of horizontal transmission among S. suis strains. The deletion mutant of PVGs marR or atpase attenuated the virulence of serotype 2 virulent SC070731 in a mouse infection model, confirming their role in S. suis virulence. These findings contribute to clarifying the genomic characterization of S. suis serotype 8 and S. suis pathogenesis.
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Affiliation(s)
- Qi Sheng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; (Q.S.); (Q.X.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210014, China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing 210014, China
| | - Qiuhua Xu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; (Q.S.); (Q.X.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210014, China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing 210014, China
| | - Zouran Lan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; (Q.S.); (Q.X.)
- Shandong Provincial Center for Animal Disease Control, Jinan 250100, China
| | - Zongfu Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210014, China; (Q.S.); (Q.X.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210014, China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing 210014, China
- Guangdong Provincial Key Laboratory of Research on the Technology of Pig-Breeding and Pig-Disease Prevention, Guangzhou 511400, China
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47
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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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48
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Kim C, Pongpanich M, Porntaveetus T. Unraveling metagenomics through long-read sequencing: a comprehensive review. J Transl Med 2024; 22:111. [PMID: 38282030 PMCID: PMC10823668 DOI: 10.1186/s12967-024-04917-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 01/21/2024] [Indexed: 01/30/2024] Open
Abstract
The study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of shotgun metagenomics. However, a new era has emerged with the advent of long-read sequencing (LRS), which offers substantial improvements over its predecessor, short-read sequencing (SRS). LRS produces reads that are several kilobases long, enabling researchers to obtain more complete and contiguous genomic information, characterize structural variations, and study epigenetic modifications. The current leaders in LRS technologies are Pacific Biotechnologies (PacBio) and Oxford Nanopore Technologies (ONT), each offering a distinct set of advantages. This review covers the workflow of long-read metagenomics sequencing, including sample preparation (sample collection, sample extraction, and library preparation), sequencing, processing (quality control, assembly, and binning), and analysis (taxonomic annotation and functional annotation). Each section provides a concise outline of the key concept of the methodology, presenting the original concept as well as how it is challenged or modified in the context of LRS. Additionally, the section introduces a range of tools that are compatible with LRS and can be utilized to execute the LRS process. This review aims to present the workflow of metagenomics, highlight the transformative impact of LRS, and provide researchers with a selection of tools suitable for this task.
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Affiliation(s)
- Chankyung Kim
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
- Graduate Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence for Cancer and Inflammation, Chulalongkorn University, Bangkok, Thailand
| | - Thantrira Porntaveetus
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
- Graduate Program in Geriatric and Special Patients Care, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
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Jia J, Deng Y, Yi M, Zhu Y. 4mCPred-GSIMP: Predicting DNA N4-methylcytosine sites in the mouse genome with multi-Scale adaptive features extraction and fusion. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2024; 21:253-271. [PMID: 38303422 DOI: 10.3934/mbe.2024012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
The epigenetic modification of DNA N4-methylcytosine (4mC) is vital for controlling DNA replication and expression. It is crucial to pinpoint 4mC's location to comprehend its role in physiological and pathological processes. However, accurate 4mC detection is difficult to achieve due to technical constraints. In this paper, we propose a deep learning-based approach 4mCPred-GSIMP for predicting 4mC sites in the mouse genome. The approach encodes DNA sequences using four feature encoding methods and combines multi-scale convolution and improved selective kernel convolution to adaptively extract and fuse features from different scales, thereby improving feature representation and optimization effect. In addition, we also use convolutional residual connections, global response normalization and pointwise convolution techniques to optimize the model. On the independent test dataset, 4mCPred-GSIMP shows high sensitivity, specificity, accuracy, Matthews correlation coefficient and area under the curve, which are 0.7812, 0.9312, 0.8562, 0.7207 and 0.9233, respectively. Various experiments demonstrate that 4mCPred-GSIMP outperforms existing prediction tools.
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Affiliation(s)
- Jianhua Jia
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333403, China
| | - Yu Deng
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333403, China
| | - Mengyue Yi
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333403, China
| | - Yuhui Zhu
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333403, China
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50
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Yi X, Lu H, Liu X, He J, Li B, Wang Z, Zhao Y, Zhang X, Yu X. Unravelling the enigma of the human microbiome: Evolution and selection of sequencing technologies. Microb Biotechnol 2024; 17:e14364. [PMID: 37929823 PMCID: PMC10832515 DOI: 10.1111/1751-7915.14364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/18/2023] [Indexed: 11/07/2023] Open
Abstract
The human microbiome plays a crucial role in maintaining health, with advances in high-throughput sequencing technology and reduced sequencing costs triggering a surge in microbiome research. Microbiome studies generally incorporate five key phases: design, sampling, sequencing, analysis, and reporting, with sequencing strategy being a crucial step offering numerous options. Present mainstream sequencing strategies include Amplicon sequencing, Metagenomic Next-Generation Sequencing (mNGS), and Targeted Next-Generation Sequencing (tNGS). Two innovative technologies recently emerged, namely MobiMicrobe high-throughput microbial single-cell genome sequencing technology and 2bRAD-M simplified metagenomic sequencing technology, compensate for the limitations of mainstream technologies, each boasting unique core strengths. This paper reviews the basic principles and processes of these three mainstream and two novel microbiological technologies, aiding readers in understanding the benefits and drawbacks of different technologies, thereby guiding the selection of the most suitable method for their research endeavours.
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Affiliation(s)
- Xin Yi
- Department of PharmacyShanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Hong Lu
- Department of Clinical laboratoryThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Xiang Liu
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Junyi He
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Bing Li
- Department of Public HealthShanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Zhelong Wang
- Department of PharmacyGuangdong Pharmaceutical UniversityGuangzhouPeople's Republic of China
| | - Yujing Zhao
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Xinri Zhang
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Xiao Yu
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
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