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Sahu TK, Verma SK, Gayacharan, Singh NP, Joshi DC, Wankhede DP, Singh M, Bhardwaj R, Singh B, Parida SK, Chattopadhyay D, Singh GP, Singh AK. Transcriptome-wide association mapping provides insights into the genetic basis and candidate genes governing flowering, maturity and seed weight in rice bean (Vigna umbellata). BMC PLANT BIOLOGY 2024; 24:379. [PMID: 38720284 PMCID: PMC11077894 DOI: 10.1186/s12870-024-04976-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 04/02/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Rice bean (Vigna umbellata), an underrated legume, adapts to diverse climatic conditions with the potential to support food and nutritional security worldwide. It is used as a vegetable, minor food crop and a fodder crop, being a rich source of proteins, minerals, and essential fatty acids. However, little effort has been made to decipher the genetic and molecular basis of various useful traits in this crop. Therefore, we considered three economically important traits i.e., flowering, maturity and seed weight of rice bean and identified the associated candidate genes employing an associative transcriptomics approach on 100 diverse genotypes out of 1800 evaluated rice bean accessions from the Indian National Genebank. RESULTS The transcriptomics-based genotyping of one-hundred diverse rice bean cultivars followed by pre-processing of genotypic data resulted in 49,271 filtered markers. The STRUCTURE, PCA and Neighbor-Joining clustering of 100 genotypes revealed three putative sub-populations. The marker-trait association analysis involving various genome-wide association study (GWAS) models revealed significant association of 82 markers on 48 transcripts for flowering, 26 markers on 22 transcripts for maturity and 22 markers on 21 transcripts for seed weight. The transcript annotation provided information on the putative candidate genes for the considered traits. The candidate genes identified for flowering include HSC80, P-II PsbX, phospholipid-transporting-ATPase-9, pectin-acetylesterase-8 and E3-ubiquitin-protein-ligase-RHG1A. Further, the WRKY1 and DEAD-box-RH27 were found to be associated with seed weight. Furthermore, the associations of PIF3 and pentatricopeptide-repeat-containing-gene with maturity and seed weight, and aldo-keto-reductase with flowering and maturity were revealed. CONCLUSION This study offers insights into the genetic basis of key agronomic traits in rice bean, including flowering, maturity, and seed weight. The identified markers and associated candidate genes provide valuable resources for future exploration and targeted breeding, aiming to enhance the agronomic performance of rice bean cultivars. Notably, this research represents the first transcriptome-wide association study in pulse crop, uncovering the candidate genes for agronomically useful traits.
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Affiliation(s)
- Tanmaya Kumar Sahu
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, Uttar Pradesh, India
| | - Sachin Kumar Verma
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Gayacharan
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | | | - Dinesh Chandra Joshi
- ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, India
| | - D P Wankhede
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Mohar Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Rakesh Bhardwaj
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Badal Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Swarup Kumar Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | | | | | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India.
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Podgorica M, Drivet E, Viken JK, Richman A, Vestbøstad J, Szodoray P, Kvam AK, Wik HS, Tjønnfjord GE, Munthe LA, Frietze S, Schjerven H. Transcriptome analysis of primary adult B-cell lineage acute lymphoblastic leukemia identifies pathogenic variants and gene fusions, and predicts subtypes for in depth molecular diagnosis. Eur J Haematol 2024; 112:731-742. [PMID: 38192186 PMCID: PMC10990798 DOI: 10.1111/ejh.14164] [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: 07/25/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND B-cell acute lymphoblastic leukemia (B-ALL) is classified into subgroups based on known driver oncogenes and molecular lesions, including translocations and recurrent mutations. However, the current diagnostic tests do not identify subtypes or oncogenic lesions for all B-ALL samples, creating a heterogeneous B-ALL group of unknown subtypes. METHODS We sorted primary adult B-ALL cells and performed transcriptome analysis by bulk RNA sequencing (RNA-seq). RESULTS Transcriptomic analysis of an adult B-ALL cohort allowed the classification of four patient samples with subtypes that were not previously revealed by standard gene panels. The leukemia of two patients were of the DUX4 subtype and two were CRLF2+ Ph-like B-ALL. Furthermore, single nucleotide variant analysis detected the oncogenic NRAS-G12D, KRAS-G12D, and KRAS-G13D mutations in three of the patient samples, presenting targetable mutations. Additional oncogenic variants and gene fusions were uncovered, as well as multiple variants in the PDE4DIP gene across five of the patient samples. CONCLUSION We demonstrate that RNA-seq is an effective tool for precision medicine in B-ALL by providing comprehensive molecular profiling of leukemia cells, identifying subtype and oncogenic lesions, and stratifying patients for appropriate therapy.
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Affiliation(s)
- Mirjam Podgorica
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Elsa Drivet
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jonas Krag Viken
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Laboratory Medicine, University of California San Francisco, CA, USA
| | - Alyssa Richman
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, USA
| | - Johanne Vestbøstad
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Peter Szodoray
- B Cell Receptor Signaling Group (BCRSG), Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Ann Kristin Kvam
- Department of Haematology, Oslo University Hospital, Oslo, Norway
| | | | - Geir E. Tjønnfjord
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Haematology, Oslo University Hospital, Oslo, Norway
| | - Ludvig A. Munthe
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, USA
| | - Hilde Schjerven
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Center for B-cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Laboratory Medicine, University of California San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
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Razi A, Lo CC, Wang S, Leek JT, Hansen KD. Genotype prediction of 336,463 samples from public expression data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.21.562237. [PMID: 38559266 PMCID: PMC10979922 DOI: 10.1101/2023.10.21.562237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Tens of thousands of RNA-sequencing experiments comprising hundreds of thousands of individual samples have now been performed. These data represent a broad range of experimental conditions, sequencing technologies, and hypotheses under study. The Recount project has aggregated and uniformly processed hundreds of thousands of publicly available RNA-seq samples. Most of these samples only include RNA expression measurements; genotype data for these same samples would enable a wide range of analyses including variant prioritization, eQTL analysis, and studies of allele specific expression. Here, we developed a statistical model based on the existing reference and alternative read counts from the RNA-seq experiments available through Recount3 to predict genotypes at autosomal biallelic loci in coding regions. We demonstrate the accuracy of our model using large-scale studies that measured both gene expression and genotype genome-wide. We show that our predictive model is highly accurate with 99.5% overall accuracy, 99.6% major allele accuracy, and 90.4% minor allele accuracy. Our model is robust to tissue and study effects, provided the coverage is high enough. We applied this model to genotype all the samples in Recount 3 and provide the largest ready-to-use expression repository containing genotype information. We illustrate that the predicted genotype from RNA-seq data is sufficient to unravel the underlying population structure of samples in Recount3 using Principal Component Analysis.
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Affiliation(s)
- Afrooz Razi
- Department of Genetic Medicine, Johns Hopkins University School of Medicine
| | - Christopher C. Lo
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
| | - Siruo Wang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
| | - Jeffrey T. Leek
- Biostatistics Program, Division of Public Health Sciences, Fred Hutchinson Cancer Center
| | - Kasper D. Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine
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Sathapondecha P, Suksri P, Nuanpirom J, Nakkanong K, Nualsri C, Whankaew S. Development of Gene-Based InDel Markers on Putative Drought Stress-Responsive Genes and Genetic Diversity of Durian (Durio zibethinus). Biochem Genet 2024:10.1007/s10528-023-10638-9. [PMID: 38306004 DOI: 10.1007/s10528-023-10638-9] [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: 07/22/2023] [Accepted: 12/12/2023] [Indexed: 02/03/2024]
Abstract
Insertion-deletion (InDel) markers are co-dominant, relatively abundant and practical for agarose gel genotyping. InDel polymorphism usually affects gene functions. Nucleotide sequences of durian (Durio zibethinus) are available, but InDel makers have not been well established. This study aimed to develop drought-related gene-based InDel markers for durian through bioinformatic analysis of RNA-Seq datasets. The polymorphism of the markers was verified in 24 durian genotypes local to Thailand. Bioinformatic analysis indicated 496 InDel loci having lengths more than 9 bp. To evaluate these InDel markers, 15 InDel loci were selected. Nine markers were successfully amplified a clear polymorphic band pattern on 2% agarose gel. The polymorphic information content (PIC) of these nine markers ranged from 0.1103 to 0.5808. The genetic distance between the 24 genotypes ranged from 0.222 to 0.889. The phylogeny based on the nine InDel loci distinguished the 24 genotypes and divided samples into four groups. This set of gene-based InDel markers on putative drought-responsive genes will be useful for genetic studies.
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Affiliation(s)
- Ponsit Sathapondecha
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Phassorn Suksri
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Jiratchaya Nuanpirom
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Korakot Nakkanong
- Department of Plant Science, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand
| | - Charassri Nualsri
- Department of Plant Science, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand
| | - Sukhuman Whankaew
- Department of Plant Science, Faculty of Technology and Community Development, Thaksin University, Phatthalung Campus, Phatthalung, 93210, Thailand.
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5
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Ousmael K, Whetten RW, Xu J, Nielsen UB, Lamour K, Hansen OK. Identification and high-throughput genotyping of single nucleotide polymorphism markers in a non-model conifer (Abies nordmanniana (Steven) Spach). Sci Rep 2023; 13:22488. [PMID: 38110478 PMCID: PMC10728141 DOI: 10.1038/s41598-023-49462-x] [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: 05/01/2023] [Accepted: 12/08/2023] [Indexed: 12/20/2023] Open
Abstract
Single nucleotide polymorphism (SNP) markers are powerful tools for investigating population structures, linkage analysis, and genome-wide association studies, as well as for breeding and population management. The availability of SNP markers has been limited to the most commercially important timber species, primarily due to the cost of genome sequencing required for SNP discovery. In this study, a combination of reference-based and reference-free approaches were used to identify SNPs in Nordmann fir (Abies nordmanniana), a species previously lacking genomic sequence information. Using a combination of a genome assembly of the closely related Silver fir (Abies alba) species and a de novo assembly of low-copy regions of the Nordmann fir genome, we identified a high density of reliable SNPs. Reference-based approaches identified two million SNPs in common between the Silver fir genome and low-copy regions of Nordmann fir. A combination of one reference-free and two reference-based approaches identified 250 shared SNPs. A subset of 200 SNPs were used to genotype 342 individuals and thereby tested and validated in the context of identity analysis and/or clone identification. The tested SNPs successfully identified all ramets per clone and five mislabeled individuals via identity and genomic relatedness analysis. The identified SNPs will be used in ad hoc breeding of Nordmann fir in Denmark.
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Affiliation(s)
- Kedra Ousmael
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark.
| | - Ross W Whetten
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27606, USA
| | - Jing Xu
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
| | - Ulrik B Nielsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Ole K Hansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
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Arlt C, Wachtmeister T, Köhrer K, Stich B. Affordable, accurate and unbiased RNA sequencing by manual library miniaturization: A case study in barley. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2241-2253. [PMID: 37593840 PMCID: PMC10579711 DOI: 10.1111/pbi.14126] [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: 11/16/2022] [Revised: 05/12/2023] [Accepted: 07/01/2023] [Indexed: 08/19/2023]
Abstract
We present an easy-to-reproduce manual miniaturized full-length RNA sequencing (RNAseq) library preparation workflow that does not require the upfront investment in expensive lab equipment or long setup times. With minimal adjustments to an established commercial protocol, we were able to manually miniaturize the RNAseq library preparation by a factor of up to 1:8. This led to cost savings for miniaturized library preparation of up to 86.1% compared to the gold standard. The resulting data were the basis of a rigorous quality control analysis that inspected: sequencing quality metrics, gene body coverage, raw read duplications, alignment statistics, read pair duplications, detected transcripts and sequence variants. We also included a deep dive data analysis identifying rRNA contamination and suggested ways to circumvent these. In the end, we could not find any indication of biases or inaccuracies caused by the RNAseq library miniaturization. The variance in detected transcripts was minimal and not influenced by the miniaturization level. Our results suggest that the workflow is highly reproducible and the sequence data suitable for downstream analyses such as differential gene expression analysis or variant calling.
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Affiliation(s)
- Christopher Arlt
- Institute of Quantitative Genetics and Genomics of PlantsHeinrich Heine University DuesseldorfDuesseldorfGermany
| | - Thorsten Wachtmeister
- Genomics & Transcriptomics Laboratory, Biological and Medical Research Centre (BMFZ)Heinrich Heine University DuesseldorfDuesseldorfGermany
| | - Karl Köhrer
- Genomics & Transcriptomics Laboratory, Biological and Medical Research Centre (BMFZ)Heinrich Heine University DuesseldorfDuesseldorfGermany
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of PlantsHeinrich Heine University DuesseldorfDuesseldorfGermany
- Cluster of Excellence on Plant Sciences (CEPLAS)DuesseldorfGermany
- Max Planck Institute for Plant Breeding ResearchCologneGermany
- Present address:
Institute for Breeding Research on Agricultural CropsJulius Kühn Institute (JKI) ‐ Federal Research Centre for Cultivated PlantsSanitzGermany
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7
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Liu S, Jiang Y, Wang Y, Huo H, Cilkiz M, Chen P, Han Y, Li L, Wang K, Zhao M, Zhu L, Lei J, Wang Y, Zhang M. Genetic and molecular dissection of ginseng ( Panax ginseng Mey.) germplasm using high-density genic SNP markers, secondary metabolites, and gene expressions. FRONTIERS IN PLANT SCIENCE 2023; 14:1165349. [PMID: 37575919 PMCID: PMC10416250 DOI: 10.3389/fpls.2023.1165349] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/27/2023] [Indexed: 08/15/2023]
Abstract
Genetic and molecular knowledge of a species is crucial to its gene discovery and enhanced breeding. Here, we report the genetic and molecular dissection of ginseng, an important herb for healthy food and medicine. A mini-core collection consisting of 344 cultivars and landraces was developed for ginseng that represents the genetic variation of ginseng existing in its origin and diversity center. We sequenced the transcriptomes of all 344 cultivars and landraces; identified over 1.5 million genic SNPs, thereby revealing the genic diversity of ginseng; and analyzed them with 26,600 high-quality genic SNPs or a selection of them. Ginseng had a wide molecular diversity and was clustered into three subpopulations. Analysis of 16 ginsenosides, the major bioactive components for healthy food and medicine, showed that ginseng had a wide variation in the contents of all 16 ginsenosides and an extensive correlation of their contents, suggesting that they are synthesized through a single or multiple correlated pathways. Furthermore, we pair-wisely examined the relationships between the cultivars and landraces, revealing their relationships in gene expression, gene variation, and ginsenoside biosynthesis. These results provide new knowledge and new genetic and genic resources for advanced research and breeding of ginseng and related species.
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Affiliation(s)
- Sizhang Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yue Jiang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yanfang Wang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, Jilin, China
| | - Huimin Huo
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Mustafa Cilkiz
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Ping Chen
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, China
| | - Yilai Han
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Li Li
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, China
| | - Lei Zhu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Jun Lei
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, China
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, China
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, China
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Vigorito E, Barton A, Pitzalis C, Lewis MJ, Wallace C. BBmix: a Bayesian beta-binomial mixture model for accurate genotyping from RNA-sequencing. Bioinformatics 2023; 39:btad393. [PMID: 37338536 PMCID: PMC10318392 DOI: 10.1093/bioinformatics/btad393] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 05/15/2023] [Accepted: 06/19/2023] [Indexed: 06/21/2023] Open
Abstract
MOTIVATION While many pipelines have been developed for calling genotypes using RNA-sequencing (RNA-Seq) data, they all have adapted DNA genotype callers that do not model biases specific to RNA-Seq such as allele-specific expression (ASE). RESULTS Here, we present Bayesian beta-binomial mixture model (BBmix), a Bayesian beta-binomial mixture model that first learns the expected distribution of read counts for each genotype, and then deploys those learned parameters to call genotypes probabilistically. We benchmarked our model on a wide variety of datasets and showed that our method generally performed better than competitors, mainly due to an increase of up to 1.4% in the accuracy of heterozygous calls, which may have a big impact in reducing false positive rate in applications sensitive to genotyping error such as ASE. Moreover, BBmix can be easily incorporated into standard pipelines for calling genotypes. We further show that parameters are generally transferable within datasets, such that a single learning run of less than 1 h is sufficient to call genotypes in a large number of samples. AVAILABILITY AND IMPLEMENTATION We implemented BBmix as an R package that is available for free under a GPL-2 licence at https://gitlab.com/evigorito/bbmix and https://cran.r-project.org/package=bbmix with accompanying pipeline at https://gitlab.com/evigorito/bbmix_pipeline.
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Affiliation(s)
- Elena Vigorito
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, United Kingdom
| | - Anne Barton
- Division of Musculoskeletal and Dermatological Sciences, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Costantino Pitzalis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Myles J Lewis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Chris Wallace
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, United Kingdom
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9
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Dar MA, Bhat B, Nazir J, Saleem A, Manzoor T, Khan M, Haq Z, Bhat SS, Ahmad SM. Identification of SNPs Related to Salmonella Resistance in Chickens Using RNA-Seq and Integrated Bioinformatics Approach. Genes (Basel) 2023; 14:1283. [PMID: 37372463 DOI: 10.3390/genes14061283] [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: 05/11/2023] [Revised: 06/09/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Potential single nucleotide polymorphisms (SNPs) were detected between two chicken breeds (Kashmir favorella and broiler) using deep RNA sequencing. This was carried out to comprehend the coding area alterations, which cause variances in the immunological response to Salmonella infection. In the present study, we identified high impact SNPs from both chicken breeds in order to delineate different pathways that mediate disease resistant/susceptibility traits. Samples (liver and spleen) were collected from Salmonella resistant (K. favorella) and susceptible (broiler) chicken breeds. Salmonella resistance and susceptibility were checked by different pathological parameters post infection. To explore possible polymorphisms in genes linked with disease resistance, SNP identification analysis was performed utilizing RNA seq data from nine K. favorella and ten broiler chickens. A total of 1778 (1070 SNPs and 708 INDELs) and 1459 (859 SNPs and 600 INDELs) were found to be specific to K. favorella and broiler, respectively. Based on our results, we conclude that in broiler chickens the enriched pathways mostly included metabolic pathways like fatty acid metabolism, carbon metabolism and amino acid metabolism (Arginine and proline metabolism), while as in K. favorella genes with high impact SNPs were enriched in most of the immune-related pathways like MAPK signaling pathway, Wnt signaling pathway, NOD-like receptor signaling pathway, etc., which could be a possible resistance mechanism against salmonella infection. In K. favorella, protein-protein interaction analysis also shows some important hub nodes, which are important in providing defense against different infectious diseases. Phylogenomic analysis revealed that indigenous poultry breeds (resistant) are clearly separated from commercial breeds (susceptible). These findings will offer fresh perspectives on the genetic diversity in chicken breeds and will aid in the genomic selection of poultry birds.
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Affiliation(s)
- Mashooq Ahmad Dar
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-Kashmir, Srinagar 190006, India
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology of Polish Academy of Sciences 3, 02-093 Warsaw, Poland
| | - Basharat Bhat
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-Kashmir, Srinagar 190006, India
| | - Junaid Nazir
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-Kashmir, Srinagar 190006, India
- Department of Clinical Biochemistry, Lovely Professional University, Phagwara 144402, India
| | - Afnan Saleem
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-Kashmir, Srinagar 190006, India
| | - Tasaduq Manzoor
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-Kashmir, Srinagar 190006, India
| | - Mahak Khan
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-Kashmir, Srinagar 190006, India
| | - Zulfqarul Haq
- Indian Council of Medical Research Project, Division of Livestock Production and Management, F.V.Sc & AH, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India
| | - Sahar Saleem Bhat
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-Kashmir, Srinagar 190006, India
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10
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Cook DE, Venkat A, Yelizarov D, Pouliot Y, Chang PC, Carroll A, De La Vega FM. A deep-learning-based RNA-seq germline variant caller. BIOINFORMATICS ADVANCES 2023; 3:vbad062. [PMID: 37416509 PMCID: PMC10320079 DOI: 10.1093/bioadv/vbad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/31/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023]
Abstract
Summary RNA sequencing (RNA-seq) can be applied to diverse tasks including quantifying gene expression, discovering quantitative trait loci and identifying gene fusion events. Although RNA-seq can detect germline variants, the complexities of variable transcript abundance, target capture and amplification introduce challenging sources of error. Here, we extend DeepVariant, a deep-learning-based variant caller, to learn and account for the unique challenges presented by RNA-seq data. Our DeepVariant RNA-seq model produces highly accurate variant calls from RNA-sequencing data, and outperforms existing approaches such as Platypus and GATK. We examine factors that influence accuracy, how our model addresses RNA editing events and how additional thresholding can be used to facilitate our models' use in a production pipeline. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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11
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Iqbal MA, Hadlich F, Reyer H, Oster M, Trakooljul N, Murani E, Perdomo‐Sabogal A, Wimmers K, Ponsuksili S. RNA-Seq-based discovery of genetic variants and allele-specific expression of two layer lines and broiler chicken. Evol Appl 2023; 16:1135-1153. [PMID: 37360029 PMCID: PMC10286233 DOI: 10.1111/eva.13557] [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: 12/21/2022] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 06/28/2023] Open
Abstract
Recent advances in the selective breeding of broilers and layers have made poultry production one of the fastest-growing industries. In this study, a transcriptome variant calling approach from RNA-seq data was used to determine population diversity between broilers and layers. In total, 200 individuals were analyzed from three different chicken populations (Lohmann Brown (LB), n = 90), Lohmann Selected Leghorn (LSL, n = 89), and Broiler (BR, n = 21). The raw RNA-sequencing reads were pre-processed, quality control checked, mapped to the reference genome, and made compatible with Genome Analysis ToolKit for variant detection. Subsequently, pairwise fixation index (F ST) analysis was performed between broilers and layers. Numerous candidate genes were identified, that were associated with growth, development, metabolism, immunity, and other economically significant traits. Finally, allele-specific expression (ASE) analysis was performed in the gut mucosa of LB and LSL strains at 10, 16, 24, 30, and 60 weeks of age. At different ages, the two-layer strains showed significantly different allele-specific expressions in the gut mucosa, and changes in allelic imbalance were observed across the entire lifespan. Most ASE genes are involved in energy metabolism, including sirtuin signaling pathways, oxidative phosphorylation, and mitochondrial dysfunction. A high number of ASE genes were found during the peak of laying, which were particularly enriched in cholesterol biosynthesis. These findings indicate that genetic architecture as well as biological processes driving particular demands relate to metabolic and nutritional requirements during the laying period shape allelic heterogeneity. These processes are considerably affected by breeding and management, whereby elucidating allele-specific gene regulation is an essential step towards deciphering the genotype to phenotype map or functional diversity between the chicken populations. Additionally, we observed that several genes showing significant allelic imbalance also colocalized with the top 1% of genes identified by the FST approach, suggesting a fixation of genes in cis-regulatory elements.
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Affiliation(s)
| | - Frieder Hadlich
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
| | - Henry Reyer
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
| | - Michael Oster
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
| | - Nares Trakooljul
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
| | - Eduard Murani
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
| | | | - Klaus Wimmers
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
- Faculty of Agricultural and Environmental SciencesUniversity RostockRostockGermany
| | - Siriluck Ponsuksili
- Research Institute for Farm Animal BiologyInstitute of Genome BiologyDummerstorfGermany
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12
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Marrella MA, Biase FH. Robust identification of regulatory variants (eQTLs) using a differential expression framework developed for RNA-sequencing. J Anim Sci Biotechnol 2023; 14:62. [PMID: 37143150 PMCID: PMC10161580 DOI: 10.1186/s40104-023-00861-0] [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: 11/17/2022] [Accepted: 03/05/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND A gap currently exists between genetic variants and the underlying cell and tissue biology of a trait, and expression quantitative trait loci (eQTL) studies provide important information to help close that gap. However, two concerns that arise with eQTL analyses using RNA-sequencing data are normalization of data across samples and the data not following a normal distribution. Multiple pipelines have been suggested to address this. For instance, the most recent analysis of the human and farm Genotype-Tissue Expression (GTEx) project proposes using trimmed means of M-values (TMM) to normalize the data followed by an inverse normal transformation. RESULTS In this study, we reasoned that eQTL analysis could be carried out using the same framework used for differential gene expression (DGE), which uses a negative binomial model, a statistical test feasible for count data. Using the GTEx framework, we identified 35 significant eQTLs (P < 5 × 10-8) following the ANOVA model and 39 significant eQTLs (P < 5 × 10-8) following the additive model. Using a differential gene expression framework, we identified 930 and six significant eQTLs (P < 5 × 10-8) following an analytical framework equivalent to the ANOVA and additive model, respectively. When we compared the two approaches, there was no overlap of significant eQTLs between the two frameworks. Because we defined specific contrasts, we identified trans eQTLs that more closely resembled what we expect from genetic variants showing complete dominance between alleles. Yet, these were not identified by the GTEx framework. CONCLUSIONS Our results show that transforming RNA-sequencing data to fit a normal distribution prior to eQTL analysis is not required when the DGE framework is employed. Our proposed approach detected biologically relevant variants that otherwise would not have been identified due to data transformation to fit a normal distribution.
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Affiliation(s)
- Mackenzie A Marrella
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Fernando H Biase
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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13
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Nagi SC, Oruni A, Weetman D, Donnelly MJ. RNA-Seq-Pop: Exploiting the sequence in RNA sequencing-A Snakemake workflow reveals patterns of insecticide resistance in the malaria vector Anopheles gambiae. Mol Ecol Resour 2023; 23:946-961. [PMID: 36695302 PMCID: PMC10568660 DOI: 10.1111/1755-0998.13759] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/12/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023]
Abstract
We provide a reproducible and scalable Snakemake workflow, called RNA-Seq-Pop, which provides end-to-end analysis of RNA sequencing data sets. The workflow allows the user to perform quality control, perform differential expression analyses and call genomic variants. Additional options include the calculation of allele frequencies of variants of interest, summaries of genetic variation and population structure, and genome-wide selection scans, together with clear visualizations. RNA-Seq-Pop is applicable to any organism, and we demonstrate the utility of the workflow by investigating pyrethroid resistance in selected strains of the major malaria mosquito, Anopheles gambiae. The workflow provides additional modules specifically for An. gambiae, including estimating recent ancestry and determining the karyotype of common chromosomal inversions. The Busia laboratory colony used for selections was collected in Busia, Uganda, in November 2018. We performed a comparative analysis of three groups: a parental G24 Busia strain; its deltamethrin-selected G28 offspring; and the susceptible reference strain Kisumu. Measures of genetic diversity reveal patterns consistent with that of laboratory colonization and selection, with the parental Busia strain exhibiting the highest nucleotide diversity, followed by the selected Busia offspring, and finally, Kisumu. Differential expression and variant analyses reveal that the selected Busia colony exhibits a number of distinct mechanisms of pyrethroid resistance, including the Vgsc-995S target-site mutation, upregulation of SAP genes, P450s and a cluster of carboxylesterases. During deltamethrin selections, the 2La chromosomal inversion rose in frequency (from 33% to 86%), supporting a previous link with pyrethroid resistance. RNA-Seq-Pop is hosted at: github.com/sanjaynagi/rna-seq-pop. We anticipate that the workflow will provide a useful tool to facilitate reproducible, transcriptomic studies in An. gambiae and other taxa.
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Affiliation(s)
- Sanjay C. Nagi
- Department of Vector BiologyLiverpool School of Tropical MedicineLiverpoolUK
| | | | - David Weetman
- Department of Vector BiologyLiverpool School of Tropical MedicineLiverpoolUK
| | - Martin J. Donnelly
- Department of Vector BiologyLiverpool School of Tropical MedicineLiverpoolUK
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14
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Sasaki K, Takahashi S, Ouchi K, Otsuki Y, Wakayama S, Ishioka C. Different impacts of TP53 mutations on cell cycle-related gene expression among cancer types. Sci Rep 2023; 13:4868. [PMID: 36964217 PMCID: PMC10039000 DOI: 10.1038/s41598-023-32092-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/22/2023] [Indexed: 03/26/2023] Open
Abstract
Functional properties caused by TP53 mutations are involved in cancer development and progression. Although most of the mutations lose normal p53 functions, some of them, gain-of-function (GOF) mutations, exhibiting novel oncogenic functions. No reports have analyzed the impact of TP53 mutations on the gene expression profile of the p53 signaling pathway across cancer types. This study is a cross-cancer type analysis of the effects of TP53 mutations on gene expression. A hierarchical cluster analysis of the expression profile of the p53 signaling pathway classified 21 cancer types into two clusters (A1 and A2). Changes in the expression of cell cycle-related genes and MKI67 by TP53 mutations were greater in cluster A1 than in cluster A2. There was no distinct difference in the effects between GOF and non-GOF mutations on the gene expression profile of the p53 signaling pathway.
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Affiliation(s)
- Keiju Sasaki
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
- Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Shin Takahashi
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Kota Ouchi
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
- Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Yasufumi Otsuki
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
- Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Shonosuke Wakayama
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
- Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Chikashi Ishioka
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan.
- Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi, Japan.
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, Japan.
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15
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Comparison of allele-specific expression in Sistani cattle and its crossbreed with Holstein, Simmental, and Montbeliarde breeds. Trop Anim Health Prod 2023; 55:7. [DOI: 10.1007/s11250-022-03422-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
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16
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Karam A, El-Assal SEDS, Hussein BA, Atia MAM. Transcriptome data mining towards characterization of single nucleotide polymorphisms (SNPs) controlling salinity tolerance in bread wheat. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2081516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Ahmed Karam
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | | | | | - Mohamed Atia Mohamed Atia
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
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17
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Li B, Gschwend AR, Hovick SM, Gutek A, McHale L, Harrison SK, Regnier EE. Evolution of weedy giant ragweed ( Ambrosia trifida): Multiple origins and gene expression variability facilitates weediness. Ecol Evol 2022; 12:e9590. [PMID: 36514541 PMCID: PMC9731915 DOI: 10.1002/ece3.9590] [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: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
Agricultural weeds may originate from wild populations, but the origination patterns and genetics underlying this transition remain largely unknown. Analysis of weedy-wild paired populations from independent locations may provide evidence to identify key genetic variation contributing to this adaptive shift. We performed genetic variation and expression analyses on transcriptome data from 67 giant ragweed samples collected from different locations in Ohio, Iowa, and Minnesota and found geographically separated weedy populations likely originated independently from their adjacent wild populations, but subsequent spreading of weedy populations also occurred locally. By using eight closely related weedy-wild paired populations, we identified thousands of unique transcripts in weedy populations that reflect shared or specific functions corresponding, respectively, to both convergently evolved and population-specific weediness processes. In addition, differential expression of specific groups of genes was detected between weedy and wild giant ragweed populations using gene expression diversity and gene co-expression network analyses. Our study suggests an integrated route of weedy giant ragweed origination, consisting of independent origination combined with the subsequent spreading of certain weedy populations, and provides several lines of evidence to support the hypothesis that gene expression variability plays a key role in the evolution of weedy species.
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Affiliation(s)
- Bo Li
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Andrea R. Gschwend
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Stephen M. Hovick
- Department of Evolution, Ecology and Organismal BiologyThe Ohio State UniversityColumbusOhioUSA
| | - Amanda Gutek
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Leah McHale
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - S. Kent Harrison
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Emilie E. Regnier
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
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18
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Zhao X, Zhang J, Wang H, Li H, Qu C, Wen J, Zhang X, Zhu T, Nie C, Li X, Muhatai G, Wang L, Lv X, Yang W, Zhao C, Bao H, Li J, Zhu B, Cao G, Xiong W, Ning Z, Qu L. Genomic and transcriptomic analyses reveal genetic adaptation to cold conditions in the chickens. Genomics 2022; 114:110485. [PMID: 36126832 DOI: 10.1016/j.ygeno.2022.110485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/27/2022] [Accepted: 09/16/2022] [Indexed: 01/14/2023]
Abstract
Under the pressure of natural and artificial selection, domestic animals, including chickens, have evolved unique mechanisms of genetic adaptations such as high-altitude adaptation, hot and arid climate adaptation, and desert adaptation. Here, we investigated the genetic basis of cold tolerance in chicken by integrating whole-genome and transcriptome sequencing technologies. Genome-wide comparative analyses of 118 chickens living in different latitudes showed 46 genes and several pathways that may be involved in cold adaptation. The results of the functional enrichment analysis of differentially expressed genes proved the important role of metabolic pathways and immune-related pathways in cold tolerance in chickens. The subsequent integration of whole genome and transcriptome sequencing technology further identified six genes - dnah5 (dynein axonemal heavy chain 5), ptgs2 (prostaglandin-endoperoxide synthase 2), inhba (inhibin beta A subunit), irx2 (iroquois homeobox 2), ensgalg00000054917, and ensgalg00000046652 - requiring more detailed studies. In addition, we also discovered different allele frequency distributions of five SNPs (single nucleotide polymorphisms) within ptgs2 and nine SNPs within dnah5 in chickens in different latitudes, suggesting strong selective pressure of these two genes in chickens. We provide a novel insight into the genetic adaptation in chickens to cold environments, and provide a reference for evaluating and developing adaptive chicken breeds in cold environments.
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Affiliation(s)
- Xiurong Zhao
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Jinxin Zhang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Huie Wang
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar, Xinjiang 843300, China.
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830000, China.
| | - Changqing Qu
- Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine of Anhui Province, Fuyang Normal University, Fuyang, Anhui 236037, China.
| | - Junhui Wen
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Xinye Zhang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Tao Zhu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Changsheng Nie
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Xinghua Li
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Gemingguli Muhatai
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar, Xinjiang 843300, China.
| | - Liang Wang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China.
| | - XueZe Lv
- Beijing Municipal General Station of Animal Science, Beijing 100107, China.
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China.
| | - Chunjiang Zhao
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Haigang Bao
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Junying Li
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Bo Zhu
- Animal Health Supervision Institute of Zhuozhou, Hebei Province 072750, China.
| | - Guomin Cao
- Animal husbandry station of Fangchenggang, Guangxi Province 538001, China.
| | - Wenjie Xiong
- Animal Disease Prevention and Control Center of Fangchenggang, Guangxi Province 538001, China.
| | - Zhonghua Ning
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Lujiang Qu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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19
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Torrens-Mas M, Perelló-Reus CM, Trias-Ferrer N, Ibargüen-González L, Crespí C, Galmes-Panades AM, Navas-Enamorado C, Sanchez-Polo A, Piérola-Lopetegui J, Masmiquel L, Crespi LS, Barcelo C, Gonzalez-Freire M. GDF15 and ACE2 stratify COVID-19 patients according to severity while ACE2 mutations increase infection susceptibility. Front Cell Infect Microbiol 2022; 12:942951. [PMID: 35937703 PMCID: PMC9355674 DOI: 10.3389/fcimb.2022.942951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/27/2022] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 19 (COVID-19) is a persistent global pandemic with a very heterogeneous disease presentation ranging from a mild disease to dismal prognosis. Early detection of sensitivity and severity of COVID-19 is essential for the development of new treatments. In the present study, we measured the levels of circulating growth differentiation factor 15 (GDF15) and angiotensin-converting enzyme 2 (ACE2) in plasma of severity-stratified COVID-19 patients and uninfected control patients and characterized the in vitro effects and cohort frequency of ACE2 SNPs. Our results show that while circulating GDF15 and ACE2 stratify COVID-19 patients according to disease severity, ACE2 missense SNPs constitute a risk factor linked to infection susceptibility.
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Affiliation(s)
- Margalida Torrens-Mas
- Translational Research in Aging and Longevity Group (TRIAL group), Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain
| | - Catalina M. Perelló-Reus
- Translational Pancreatic Cancer Oncogenesis Group, Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain
| | - Neus Trias-Ferrer
- Translational Research in Aging and Longevity Group (TRIAL group), Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain
| | - Lesly Ibargüen-González
- Translational Pancreatic Cancer Oncogenesis Group, Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain
| | - Catalina Crespí
- Cell Culture and Flow Cytometry Facility, Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain
| | - Aina Maria Galmes-Panades
- Translational Research in Aging and Longevity Group (TRIAL group), Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain
- Physical Activity and Sport Sciences Research Group (GICAFE), Institute for Educational Research and Innovation (IRIE), University of the Balearic Islands, Palma de Mallorca, Spain
| | - Cayetano Navas-Enamorado
- Translational Research in Aging and Longevity Group (TRIAL group), Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain
| | - Andres Sanchez-Polo
- Translational Research in Aging and Longevity Group (TRIAL group), Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain
| | - Javier Piérola-Lopetegui
- Microscopy Facility, Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain
| | - Luis Masmiquel
- Vascular and Metabolic Pathologies Group, Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain
| | - Lorenzo Socias Crespi
- Intensive Care Unit, Health Research Institute of the Balearic Islands (IdISBa), Son Llatzer University Hospital, Palma de Mallorca, Spain
| | - Carles Barcelo
- Translational Pancreatic Cancer Oncogenesis Group, Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain
- *Correspondence: Marta Gonzalez-Freire, ; Carles Barcelo,
| | - Marta Gonzalez-Freire
- Translational Research in Aging and Longevity Group (TRIAL group), Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain
- *Correspondence: Marta Gonzalez-Freire, ; Carles Barcelo,
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20
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Jiang Y, Peng Z, Man Q, Wang S, Huang X, Meng L, Wang H, Zhu G. H3K27ac chromatin acetylation and gene expression analysis reveal sex- and situs-related differences in developing chicken gonads. Biol Sex Differ 2022; 13:6. [PMID: 35135592 PMCID: PMC8822763 DOI: 10.1186/s13293-022-00415-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 01/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Birds exhibit a unique asymmetry in terms of gonad development. The female left gonad generates a functional ovary, whereas the right gonad regresses. In males, both left and right gonads would develop into testes. How is this left/right asymmetry established only in females but not in males remains unknown. The epigenetic regulation of gonadal developmental genes may contribute to this sex disparity. The modification of histone tails such as H3K27ac is tightly coupled to chromatin activation and gene expression. To explore whether H3K27ac marked chromatin activation is involved in the asymmetric development of avian gonads, we probed genome-wide H3K27ac occupancy in left and right gonads from both sexes and related chromatin activity profile to the expression of gonadal genes. Furthermore, we validated the effect of chromatin activity on asymmetric gonadal development by manipulating the chromatin histone acetylation levels. METHODS The undifferentiated gonads from both sides of each sex were collected and subjected to RNA-Seq and H3K27ac ChIP-Seq experiments. Integrated analysis of gene expression and active chromatin regions were performed to identify the sex- and situs-specific regulation and expression of gonadal genes. The histone deacetylase inhibitor trichostatin A (TSA) was applied to the undifferentiated female right gonads to assess the effect of chromatin activation on gonadal gene expression and cell proliferation. RESULTS Even before sex differentiation, the gonads already show divergent gene expression between different sexes and between left/right sides in females. The sex-specific H3K27ac chromatin distributions coincide with the higher expression of male/female specification genes in each sex. Unexpectedly, the H3K27ac marked chromatin activation show a dramatic difference between left and right gonads in both sexes, although the left/right asymmetric gonadal development was observed only in females but not in males. In females, the side-specific H3K27ac occupancy instructs the differential expression of developmental genes between the pair of gonads and contributes to the development of left but not right gonad. However, in males, the left/right discrepancy of H3K27ac chromatin distribution does not drive the side-biased gene expression or gonad development. The TSA-induced retention of chromatin acetylation causes up-regulation of ovarian developmental genes and increases cell proliferation in the female right gonad. CONCLUSIONS We revealed that left/right asymmetry in H3K27ac marked chromatin activation exists in both sexes, but this discrepancy gives rise to asymmetric gonadal development only in females. Other mechanisms overriding the chromatin activation would control the symmetric development of male gonads in chicken.
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Affiliation(s)
- Yunqi Jiang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Shandong Agricultural University, Taian, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhelun Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qiu Man
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sheng Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaochen Huang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lu Meng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Heng Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China.
| | - Guiyu Zhu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Shandong Agricultural University, Taian, China. .,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China.
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21
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Degalez F, Jehl F, Muret K, Bernard M, Lecerf F, Lagoutte L, Désert C, Pitel F, Klopp C, Lagarrigue S. Watch Out for a Second SNP: Focus on Multi-Nucleotide Variants in Coding Regions and Rescued Stop-Gained. Front Genet 2021; 12:659287. [PMID: 34306009 PMCID: PMC8293744 DOI: 10.3389/fgene.2021.659287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/27/2021] [Indexed: 12/30/2022] Open
Abstract
Most single-nucleotide polymorphisms (SNPs) are located in non-coding regions, but the fraction usually studied is harbored in protein-coding regions because potential impacts on proteins are relatively easy to predict by popular tools such as the Variant Effect Predictor. These tools annotate variants independently without considering the potential effect of grouped or haplotypic variations, often called "multi-nucleotide variants" (MNVs). Here, we used a large RNA-seq dataset to survey MNVs, comprising 382 chicken samples originating from 11 populations analyzed in the companion paper in which 9.5M SNPs- including 3.3M SNPs with reliable genotypes-were detected. We focused our study on in-codon MNVs and evaluate their potential mis-annotation. Using GATK HaplotypeCaller read-based phasing results, we identified 2,965 MNVs observed in at least five individuals located in 1,792 genes. We found 41.1% of them showing a novel impact when compared to the effect of their constituent SNPs analyzed separately. The biggest impact variation flux concerns the originally annotated stop-gained consequences, for which around 95% were rescued; this flux is followed by the missense consequences for which 37% were reannotated with a different amino acid. We then present in more depth the rescued stop-gained MNVs and give an illustration in the SLC27A4 gene. As previously shown in human datasets, our results in chicken demonstrate the value of haplotype-aware variant annotation, and the interest to consider MNVs in the coding region, particularly when searching for severe functional consequence such as stop-gained variants.
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Affiliation(s)
- Fabien Degalez
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, Saint-Gilles, France
| | - Frédéric Jehl
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, Saint-Gilles, France
| | - Kévin Muret
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, Saint-Gilles, France
| | - Maria Bernard
- INRAE, SIGENAE, Genotoul Bioinfo MIAT, Castanet-Tolosan, France.,INRAE, AgroParisTech, Université Paris-Saclay, GABI UMR 1313, Jouy-en-Josas, France
| | | | | | - Colette Désert
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, Saint-Gilles, France
| | - Frédérique Pitel
- INRAE, INPT, ENVT, Université de Toulouse, GenPhySE UMR 1388, Castanet-Tolosan, France
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