1
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Wenz BM, He Y, Chen NC, Pickrell JK, Li JH, Dudek MF, Li T, Keener R, Voight BF, Brown CD, Battle A. Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.610850. [PMID: 39282458 PMCID: PMC11398312 DOI: 10.1101/2024.09.04.610850] [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: 09/21/2024]
Abstract
Background Understanding the genetic causes for variability in chromatin accessibility can shed light on the molecular mechanisms through which genetic variants may affect complex traits. Thousands of ATAC-seq samples have been collected that hold information about chromatin accessibility across diverse cell types and contexts, but most of these are not paired with genetic information and come from diverse distinct projects and laboratories. Results We report here joint genotyping, chromatin accessibility peak calling, and discovery of quantitative trait loci which influence chromatin accessibility (caQTLs), demonstrating the capability of performing caQTL analysis on a large scale in a diverse sample set without pre-existing genotype information. Using 10,293 profiling samples representing 1,454 unique donor individuals across 653 studies from public databases, we catalog 23,381 caQTLs in total. After joint discovery analysis, we cluster samples based on accessible chromatin profiles to identify context-specific caQTLs. We find that caQTLs are strongly enriched for annotations of gene regulatory elements across diverse cell types and tissues and are often strongly linked with genetic variation associated with changes in expression (eQTLs), indicating that caQTLs can mediate genetic effects on gene expression. We demonstrate sharing of causal variants for chromatin accessibility and diverse complex human traits, enabling a more complete picture of the genetic mechanisms underlying complex human phenotypes. Conclusions Our work provides a proof of principle for caQTL calling from previously ungenotyped samples, and represents one of the largest, most diverse caQTL resources currently available, informing mechanisms of genetic regulation of gene expression and contribution to disease.
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Affiliation(s)
- Brandon M Wenz
- Genetics and Epigenetics Program, Cell and Molecular Biology Graduate Group, Biomedical Graduate Studies, University of Pennsylvania - Perelman School of Medicine, Philadelphia PA 19104
| | - Yuan He
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, 21218
| | - Nae-Chyun Chen
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, 21218
| | | | | | - Max F Dudek
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Taibo Li
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, 21218
| | - Rebecca Keener
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, 21218
| | - Benjamin F Voight
- Department of Genetics, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, 19104
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania - Perelman School of Medicine, Philadelphia PA, 19104
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, 19104
| | - Christopher D Brown
- Department of Genetics, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, 19104
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, 21218
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, 21218
- Department of Genetic Medicine, Johns Hopkins University; Baltimore, MD, 21218
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, 21218
- Data Science and AI Institute, Johns Hopkins University, Baltimore, MD, 21218
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2
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Huo D, Hu Y, Li L, Gao H, Wang M, Guan H, Zhang Q, Yu B. Complete genome sequence of Rhodococcus sp. strain PD04, a pyridine-degrading bacterium under hypersaline condition. Microbiol Resour Announc 2024; 13:e0010324. [PMID: 38860809 PMCID: PMC11256795 DOI: 10.1128/mra.00103-24] [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: 02/02/2024] [Accepted: 05/17/2024] [Indexed: 06/12/2024] Open
Abstract
We report the complete genome sequence of a pyridine-degrading Rhodococcus sp. strain PD04 under 4% salinity environment, isolated from wastewater of coking plant. The genome is 6.07 Mb with 5,767 annotated gene coding sequences.
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Affiliation(s)
- Donghui Huo
- SINOPEC (Dalian) Research Institute of Petroleum and Petro-Chemicals Co., Ltd., Dalian, China
| | - Yangfan Hu
- Department of Microbial Physiological & Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lanpeng Li
- SINOPEC (Dalian) Research Institute of Petroleum and Petro-Chemicals Co., Ltd., Dalian, China
| | - Huipeng Gao
- SINOPEC (Dalian) Research Institute of Petroleum and Petro-Chemicals Co., Ltd., Dalian, China
| | - Meng Wang
- SINOPEC (Dalian) Research Institute of Petroleum and Petro-Chemicals Co., Ltd., Dalian, China
| | - Hao Guan
- SINOPEC (Dalian) Research Institute of Petroleum and Petro-Chemicals Co., Ltd., Dalian, China
| | - Quan Zhang
- SINOPEC (Dalian) Research Institute of Petroleum and Petro-Chemicals Co., Ltd., Dalian, China
| | - Bo Yu
- Department of Microbial Physiological & Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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3
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Phillips AR. Variant calling in polyploids for population and quantitative genetics. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11607. [PMID: 39184203 PMCID: PMC11342233 DOI: 10.1002/aps3.11607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/03/2024] [Accepted: 04/10/2024] [Indexed: 08/27/2024]
Abstract
Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid species. Compared to popular reduced-representation sequencing approaches, the genome-wide coverage and greater marker density provided by WGS data can greatly improve our understanding of polyploid species and polyploid biology. However, biological features that make polyploid species interesting also pose challenges in read mapping, variant identification, and genotype estimation. Accounting for characteristics in variant calling like allelic dosage uncertainty, homology between subgenomes, and variance in chromosome inheritance mode can reduce errors. Here, I discuss the challenges of variant calling in polyploid WGS data and discuss where potential solutions can be integrated into a standard variant calling pipeline.
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Affiliation(s)
- Alyssa R. Phillips
- Department of Evolution and EcologyUniversity of California, DavisDavis95616CaliforniaUSA
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4
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Zheng H, Liu J, Cheng Q, Zhang Q, Zhang Y, Jiang L, Huang Y, Li W, Zhao Y, Chen G, Yu F, Liu L, Li Y, Liao X, Xu L, Xiao Y, Zheng Z, Li M, Wang H, Hu G, Du L, Chen Q. Targeted activation of ferroptosis in colorectal cancer via LGR4 targeting overcomes acquired drug resistance. NATURE CANCER 2024; 5:572-589. [PMID: 38291304 DOI: 10.1038/s43018-023-00715-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/14/2023] [Indexed: 02/01/2024]
Abstract
Acquired drug resistance is a major challenge for cancer therapy and is the leading cause of cancer mortality; however, the mechanisms of drug resistance are diverse and the strategy to specifically target drug-resistant cancer cells remains an unmet clinical issue. Here, we established a colorectal cancer-derived organoid biobank and induced acquired drug resistance by repeated low-level exposures of chemo-agents. Chemosensitivity profiling and transcriptomic analysis studies revealed that chemoresistant cancer-derived organoids exhibited elevated expression of LGR4 and activation of the Wnt signaling pathway. Further, we generated a monoclonal antibody (LGR4-mAb) that potently inhibited LGR4-Wnt signaling and found that treatment with LGR4-mAb notably sensitized drug-induced ferroptosis. Mechanistically, LGR4-dependent Wnt signaling transcriptionally upregulated SLC7A11, a key inhibitor of ferroptosis, to confer acquired drug resistance. Our findings reveal that targeting of Wnt signaling by LGR4-mAb augments ferroptosis when co-administrated with chemotherapeutic agents, demonstrating a potential opportunity to fight refractory and recurrent cancers.
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Affiliation(s)
- Hao Zheng
- The Frontier Center for Cell Response, State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Jinming Liu
- The Frontier Center for Cell Response, State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Qi Cheng
- The State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qianping Zhang
- The Frontier Center for Cell Response, State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Yaoyao Zhang
- The Frontier Center for Cell Response, State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Lingyu Jiang
- The Frontier Center for Cell Response, State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Yan Huang
- The Frontier Center for Cell Response, State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenlei Li
- The Frontier Center for Cell Response, State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Yanping Zhao
- School of Statistics and Data Science, LPMC and KLMDASR, Nankai University, Tianjin, China
| | - Guo Chen
- The Frontier Center for Cell Response, State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Fan Yu
- The Frontier Center for Cell Response, State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Lei Liu
- The State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Yanjun Li
- The Frontier Center for Cell Response, State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
- CNBG-Nankai University Joint Research and Development Center, Tianjin, China
| | - Xudong Liao
- The Frontier Center for Cell Response, State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Lai Xu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi Xiao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhibo Zheng
- Department of International Medical Services, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Ming Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Hongyi Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Gang Hu
- School of Statistics and Data Science, LPMC and KLMDASR, Nankai University, Tianjin, China.
| | - Lei Du
- The State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- CNBG-Nankai University Joint Research and Development Center, Tianjin, China.
| | - Quan Chen
- The Frontier Center for Cell Response, State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China.
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5
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Zoullas S, Morel D, Zafeer F, Borjas-Mendoza P, Angeli S, Zhou Y, Bademci G, Tekin M. Two novel heterozygous exonic deletions lead to Chanarin-Dorfman syndrome in a patient with congenital ichthyosis, sensorineural hearing loss, and liver dysfunction. Am J Med Genet A 2024; 194:e63481. [PMID: 37984424 DOI: 10.1002/ajmg.a.63481] [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: 08/18/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023]
Abstract
Chanarin-Dorfman syndrome is an autosomal recessively inherited disorder characterized by ichthyosis, sensorineural hearing loss, and hepatic dysfunction. We report on a 60-year-old female of Venezuelan descent who presented with congenital ichthyosis, progressive sensorineural hearing loss, and liver cirrhosis. We identify a heterozygous copy number deletion involving exon 1 and another heterozygous deletion involving exon 3 of the ABHD5 gene. Exon 2 is preserved. Both deletions were confirmed with RT-PCR. RNAseq from peripheral blood shows a reduction of ABHD5 expression overall and an absence of exon 3 expression, confirming the deleterious effects of the identified deletions. We present exonic deletions as a potentially common type of ABHD5 variation.
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Affiliation(s)
- Sofia Zoullas
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Dayna Morel
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Faraz Zafeer
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Paulo Borjas-Mendoza
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Simon Angeli
- Department of Otolaryngology, University of Miami, Miami, Florida, USA
| | - Yi Zhou
- Department of Pathology, University of Miami, Miami, Florida, USA
| | - Guney Bademci
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Mustafa Tekin
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA
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6
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Zhang L, Li H, Shi M, Ren K, Zhang W, Cheng Y, Wang Y, Xia XQ. FishSNP: a high quality cross-species SNP database of fishes. Sci Data 2024; 11:286. [PMID: 38461307 PMCID: PMC10924876 DOI: 10.1038/s41597-024-03111-8] [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: 09/20/2023] [Accepted: 03/04/2024] [Indexed: 03/11/2024] Open
Abstract
The progress of aquaculture heavily depends on the efficient utilization of diverse genetic resources to enhance production efficiency and maximize profitability. Single nucleotide polymorphisms (SNPs) have been widely used in the study of aquaculture genomics, genetics, and breeding research since they are the most prevalent molecular markers on the genome. Currently, a large number of SNP markers from cultured fish species are scattered in individual studies, making querying complicated and data reuse problematic. We compiled relevant SNP data from literature and public databases to create a fish SNP database, FishSNP ( http://bioinfo.ihb.ac.cn/fishsnp ), and also used a unified analysis pipeline to process raw data that the author of the literature did not perform SNP calling on to obtain SNPs with high reliability. This database presently contains 45,690,243 (45 million) nonredundant SNP data for 13 fish species, with 30,288,958 (30 million) of those being high-quality SNPs. The main function of FishSNP is to search, browse, annotate and download SNPs, which provide researchers various and comprehensive associated information.
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heng Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mijuan Shi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Keyi Ren
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Wanting Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yingyin Cheng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yaping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Qin Xia
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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7
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Guo J, Han X, Wu T, Wang R, Zhao J, Wang R, Tan D, Yan S, Gao J, Huang W, Zhang H, Zhang C. Potential locus W and candidate gene McPRR2 associated with pericarp pigment accumulation in bitter gourd (Momordica charantia L.) revealed via BSA-seq analysis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108515. [PMID: 38484681 DOI: 10.1016/j.plaphy.2024.108515] [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: 11/09/2023] [Revised: 02/17/2024] [Accepted: 03/07/2024] [Indexed: 04/02/2024]
Abstract
Pericarp color is a prominent agronomic trait that exerts a significant impact on consumer and breeder preferences. Genetic analysis has revealed that the pericarp color of bitter gourd is a quantitative trait. However, the underlying mechanism for this trait in bitter gourd remains largely unknown. In the present study, we employed bulked segregant analysis (BSA) to identify the candidate genes responsible for bitter gourd pericarp color (specifically, dark green versus white) within F2 segregation populations resulting from the crossing of B07 (dark green pericarp) and A06 (white pericarp). Through genomic variation, genetic mapping, and expression analysis, we identified a candidate gene named McPRR2, which was a homolog of Arabidopsis pseudo response regulator 2 (APRR2) encoded by LOC111023472. Sequence alignment of the candidate gene between the two parental lines revealed a 15-bp nucleotide insertion in the coding region of LOC111023472, leading to a premature stop codon and potentially causing a loss-of-function mutation. qRT-PCR analysis demonstrated that the expression of McPRR2 was significantly higher in B07 compared to A06, and it was primarily expressed in the immature fruit pericarp. Moreover, overexpression of McPRR2 in tomato could enhance the green color of immature fruit pericarp by increasing the chlorophyll content. Consequently, McPRR2 emerged as a strong candidate gene regulating the bitter gourd pericarp color by influencing chlorophyll accumulation. Finally, we developed a molecular marker linked to pericarp color, enabling the identification of genotypes in breeding populations. These findings provided valuable insights into the genetic improvement of bitter gourd pericarp color.
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Affiliation(s)
- Jinju Guo
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Xin Han
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Tingquan Wu
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Rui Wang
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Junhong Zhao
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Rufang Wang
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Delong Tan
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Shijuan Yan
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Jie Gao
- Environment Horticulture Research Institute/Guangdong Provincial Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Wenjie Huang
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Huiyao Zhang
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Changyuan Zhang
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China.
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8
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Bhérer C, Eveleigh R, Trajanoska K, St-Cyr J, Paccard A, Nadukkalam Ravindran P, Caron E, Bader Asbah N, McClelland P, Wei C, Baumgartner I, Schindewolf M, Döring Y, Perley D, Lefebvre F, Lepage P, Bourgey M, Bourque G, Ragoussis J, Mooser V, Taliun D. A cost-effective sequencing method for genetic studies combining high-depth whole exome and low-depth whole genome. NPJ Genom Med 2024; 9:8. [PMID: 38326393 PMCID: PMC10850497 DOI: 10.1038/s41525-024-00390-3] [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: 05/12/2023] [Accepted: 12/07/2023] [Indexed: 02/09/2024] Open
Abstract
Whole genome sequencing (WGS) at high-depth (30X) allows the accurate discovery of variants in the coding and non-coding DNA regions and helps elucidate the genetic underpinnings of human health and diseases. Yet, due to the prohibitive cost of high-depth WGS, most large-scale genetic association studies use genotyping arrays or high-depth whole exome sequencing (WES). Here we propose a cost-effective method which we call "Whole Exome Genome Sequencing" (WEGS), that combines low-depth WGS and high-depth WES with up to 8 samples pooled and sequenced simultaneously (multiplexed). We experimentally assess the performance of WEGS with four different depth of coverage and sample multiplexing configurations. We show that the optimal WEGS configurations are 1.7-2.0 times cheaper than standard WES (no-plexing), 1.8-2.1 times cheaper than high-depth WGS, reach similar recall and precision rates in detecting coding variants as WES, and capture more population-specific variants in the rest of the genome that are difficult to recover when using genotype imputation methods. We apply WEGS to 862 patients with peripheral artery disease and show that it directly assesses more known disease-associated variants than a typical genotyping array and thousands of non-imputable variants per disease-associated locus.
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Affiliation(s)
- Claude Bhérer
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Robert Eveleigh
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - Katerina Trajanoska
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Janick St-Cyr
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | - Antoine Paccard
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | - Praveen Nadukkalam Ravindran
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Elizabeth Caron
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | - Nimara Bader Asbah
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | - Peyton McClelland
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Clare Wei
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Iris Baumgartner
- Division of Angiology, Swiss Cardiovascular Center, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Marc Schindewolf
- Division of Angiology, Swiss Cardiovascular Center, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Yvonne Döring
- Division of Angiology, Swiss Cardiovascular Center, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians University Munich, Pettenkoferstr 9, 80336, Munich, Germany
| | - Danielle Perley
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - François Lefebvre
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - Pierre Lepage
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | | | - Guillaume Bourque
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
| | - Vincent Mooser
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - Daniel Taliun
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada.
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec, Canada.
- Canada Excellence Research Chair in Genomic Medicine, McGill University, Montréal, Québec, Canada.
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9
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Yang S, Ning C, Yang C, Li W, Zhang Q, Wang D, Tang H. Identify Candidate Genes Associated with the Weight and Egg Quality Traits in Wenshui Green Shell-Laying Chickens by the Copy Number Variation-Based Genome-Wide Association Study. Vet Sci 2024; 11:76. [PMID: 38393094 PMCID: PMC10892766 DOI: 10.3390/vetsci11020076] [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: 12/18/2023] [Revised: 02/03/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Copy number variation (CNV), as an essential source of genetic variation, can have an impact on gene expression, genetic diversity, disease susceptibility, and species evolution in animals. To better understand the weight and egg quality traits of chickens, this paper aimed to detect CNVs in Wenshui green shell-laying chickens and conduct a copy number variation regions (CNVRs)-based genome-wide association study (GWAS) to identify variants and candidate genes associated with their weight and egg quality traits to support related breeding efforts. In our paper, we identified 11,035 CNVRs in Wenshui green shell-laying chickens, which collectively spanned a length of 13.1 Mb, representing approximately 1.4% of its autosomal genome. Out of these CNVRs, there were 10,446 loss types, 491 gain types, and 98 mixed types. Notably, two CNVRs showed significant correlations with egg quality, while four CNVRs exhibited significant associations with body weight. These significant CNVRs are located on chromosome 4. Further analysis identified potential candidate genes that influence weight and egg quality traits, including FAM184B, MED28, LAP3, ATOH8, ST3GAL5, LDB2, and SORCS2. In this paper, the CNV map of the Wenshui green shell-laying chicken genome was constructed for the first time through population genotyping. Additionally, CNVRs can be employed as molecular markers to genetically improve chickens' weight and egg quality traits.
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Affiliation(s)
- Suozhou Yang
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
| | - Chao Ning
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
| | - Cheng Yang
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
| | - Wenqiang Li
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
- College of Animal Science and Technology, China Agricultural University, Beijing 100083, China
| | - Dan Wang
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
| | - Hui Tang
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
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10
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Contreras Yametti GP, Robbins G, Chowdhury A, Narang S, Ostrow TH, Kilberg H, Greenberg J, Kramer L, Raetz E, Tsirigos A, Evensen NA, Carroll WL. SETD2 mutations do not contribute to clonal fitness in response to chemotherapy in childhood B cell acute lymphoblastic leukemia. Leuk Lymphoma 2024; 65:78-90. [PMID: 37874744 DOI: 10.1080/10428194.2023.2273752] [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: 06/19/2023] [Revised: 10/12/2023] [Accepted: 10/14/2023] [Indexed: 10/26/2023]
Abstract
Mutations in genes encoding epigenetic regulators are commonly observed at relapse in B cell acute lymphoblastic leukemia (B-ALL). Loss-of-function mutations in SETD2, an H3K36 methyltransferase, have been observed in B-ALL and other cancers. Previous studies on mutated SETD2 in solid tumors and acute myelogenous leukemia support a role in promoting resistance to DNA damaging agents. We did not observe chemoresistance, an impaired DNA damage response, nor increased mutation frequency in response to thiopurines using CRISPR-mediated knockout in wild-type B-ALL cell lines. Likewise, restoration of SETD2 in cell lines with hemizygous mutations did not increase sensitivity. SETD2 mutations affected the chromatin landscape and transcriptional output that was unique to each cell line. Collectively our data does not support a role for SETD2 mutations in driving clonal evolution and relapse in B-ALL, which is consistent with the lack of enrichment of SETD2 mutations at relapse in most studies.
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Affiliation(s)
- Gloria P Contreras Yametti
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Gabriel Robbins
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Ashfiyah Chowdhury
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Sonali Narang
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Talia H Ostrow
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Harrison Kilberg
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Joshua Greenberg
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Lindsay Kramer
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Elizabeth Raetz
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Aristotelis Tsirigos
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Nikki A Evensen
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - William L Carroll
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Langone Health, New York, NY, USA
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11
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Sun F, Yang Y, Wang P, Ma J, Du X. Quantitative trait loci and candidate genes for yield-related traits of upland cotton revealed by genome-wide association analysis under drought conditions. BMC Genomics 2023; 24:531. [PMID: 37679709 PMCID: PMC10485960 DOI: 10.1186/s12864-023-09640-7] [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: 05/18/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Due to the influence of extreme weather, the environment in China's main cotton-producing areas is prone to drought stress conditions, which affect the growth and development of cotton and lead to a decrease in cotton yield. RESULTS In this study, 188 upland cotton germplasm resources were phenotyped for data of 8 traits (including 3 major yield traits) under drought conditions in three environments for two consecutive years. Correlation analysis revealed significant positive correlations between the three yield traits. Genetic analysis showed that the estimated heritability of the seed cotton index (SC) under drought conditions was the highest (80.81%), followed by that of boll weight (BW) (80.64%) and the lint cotton index (LC) (70.49%) With genome-wide association study (GWAS) analysis, a total of 75 quantitative trait loci (QTLs) were identified, including two highly credible new QTL hotspots. Three candidate genes (Gh_D09G064400, Gh_D10G261000 and Gh_D10G254000) located in the two new QTL hotspots, QTL51 and QTL55, were highly expressed in the early stage of fiber development and showed significant correlations with SC, LC and BW. The expression of three candidate genes in two extreme materials after drought stress was analyzed by qRT-PCR, and the expression of these two materials in fibers at 15, 20 and 25 DPA. The expression of these three candidate genes was significantly upregulated after drought stress and was significantly higher in drought-tolerant materials than in drought-sensitive materials. In addition, the expression levels of the three candidate genes were higher in the early stage of fiber development (15 DPA), and the expression levels in drought-tolerant germplasm were higher than those in drought-sensitive germplasm. These three candidate genes may play an important role in determining cotton yield under drought conditions. CONCLUSIONS This study is helpful for understanding the regulatory genes affecting cotton yield under drought conditions and provides germplasm and candidate gene resources for breeding high-yield cotton varieties under these conditions.
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Affiliation(s)
- Fenglei Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572000, China
| | - Yanlong Yang
- Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China.
| | - Penglong Wang
- Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Jun Ma
- Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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12
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Wang L, Ho AT, Hurst LD, Yang S. Re-evaluating evidence for adaptive mutation rate variation. Nature 2023; 619:E52-E56. [PMID: 37495884 PMCID: PMC10371861 DOI: 10.1038/s41586-023-06314-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 06/12/2023] [Indexed: 07/28/2023]
Affiliation(s)
- Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Alexander T Ho
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.
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13
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Chen B, Bai Y, Wang J, Ke Q, Zhou Z, Zhou T, Pan Y, Wu R, Wu X, Zheng W, Xu P. Population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:141-154. [PMID: 37275538 PMCID: PMC10232709 DOI: 10.1007/s42995-023-00165-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 01/25/2023] [Indexed: 06/07/2023]
Abstract
The large yellow croaker (Larimichthys crocea) is one of the most economically valuable marine fish in China and is a notable species in ecological studies owing to a serious collapse of wild germplasm in the past few decades. The stock division and species distribution, which have important implications for ecological protection, germplasm recovery, and fishery resource management, have been debated since the 1960s. However, it is still uncertain even how many stocks exist in this species. To address this, we evaluated the fine-scale genetic structure of large yellow croaker populations distributed along the eastern and southern Chinese coastline based on 7.64 million SNP markers. Compared with the widely accepted stock boundaries proposed in the 1960s, our results revealed that a climate-driven habitat change probably occurred between the Naozhou (Nanhai) Stock and the Ming-Yuedong (Mindong) Stock. The boundary between these two stocks might have shifted northwards from the Pearl River Estuary to the northern area of the Taiwan Strait, accompanied by highly asymmetric introgression. In addition, we found divergent landscapes of natural selection between the stocks inhabiting northern and southern areas. The northern population exhibited highly agminated signatures of strong natural selection in genes related to developmental processes, whereas moderate and interspersed selective signatures were detected in many immune-related genes in the southern populations. These findings establish the stock status and genome-wide evolutionary landscapes of large yellow croaker, providing a basis for conservation, fisheries management and further evolutionary biology studies. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00165-2.
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Affiliation(s)
- Baohua Chen
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
- National Key Laboratory of Mariculture Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352000 China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102 China
| | - Yulin Bai
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
| | - Jiaying Wang
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
| | - Qiaozhen Ke
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
- National Key Laboratory of Mariculture Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352000 China
| | - Zhixiong Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
| | - Ying Pan
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, 350000 China
| | - Renxie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088 China
| | - Xiongfei Wu
- Ningbo Academy of Oceanology and Fishery, Ningbo, 315012 China
| | - Weiqiang Zheng
- National Key Laboratory of Mariculture Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352000 China
| | - Peng Xu
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102 China
- National Key Laboratory of Mariculture Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352000 China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102 China
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14
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Wang W, Liu H, Xie Y, King GJ, White PJ, Zou J, Xu F, Shi L. Rapid identification of a major locus qPRL-C06 affecting primary root length in Brassica napus by QTL-seq. ANNALS OF BOTANY 2023; 131:569-583. [PMID: 36181516 PMCID: PMC10147330 DOI: 10.1093/aob/mcac123] [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: 08/21/2022] [Accepted: 09/30/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Brassica napus is one of the most important oilseed crops worldwide. Seed yield of B. napus significantly correlates with the primary root length (PRL). The aims of this study were to identify quantitative trait loci (QTLs) for PRL in B. napus. METHODS QTL-seq and conventional QTL mapping were jointly used to detect QTLs associated with PRL in a B. napus double haploid (DH) population derived from a cross between 'Tapidor' and 'Ningyou 7'. The identified major locus was confirmed and resolved by an association panel of B. napus and an advanced backcross population. RNA-seq analysis of two long-PRL lines (Tapidor and TN20) and two short-PRL lines (Ningyou 7 and TN77) was performed to identify differentially expressed genes in the primary root underlying the target QTLs. KEY RESULTS A total of 20 QTLs impacting PRL in B. napus grown at a low phosphorus (P) supply were found by QTL-seq. Eight out of ten QTLs affecting PRL at a low P supply discovered by conventional QTL mapping could be detected by QTL-seq. The locus qPRL-C06 identified by QTL-seq was repeatedly detected at both an optimal P supply and a low P supply by conventional QTL mapping. This major constitutive QTL was further confirmed by regional association mapping. qPRL-C06 was delimited to a 0.77 Mb genomic region on chromosome C06 using an advanced backcross population. A total of 36 candidate genes within qPRL-C06 were identified that showed variations in coding sequences and/or exhibited significant differences in mRNA abundances in primary root between the long-PRL and short-PRL lines, including five genes involved in phytohormone biosynthesis and signaling. CONCLUSIONS These results both demonstrate the power of the QTL-seq in rapid QTL detection for root traits and will contribute to marker-assisted selective breeding of B. napus cultivars with increased PRL.
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Affiliation(s)
- Wei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Haijiang Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiwen Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Graham John King
- Southern Cross Plant Science, Southern Cross University, Lismore NSW 2480, Australia
| | - Philip John White
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
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15
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Li W, Huang L, Liu N, Chen Y, Guo J, Yu B, Luo H, Zhou X, Huai D, Chen W, Yan L, Wang X, Lei Y, Liao B, Jiang H. Identification of a stable major sucrose-related QTL and diagnostic marker for flavor improvement in peanut. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:78. [PMID: 36952020 DOI: 10.1007/s00122-023-04306-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
An InDel marker closely linked with a major and stable quantitative trait locus (QTL) on chromosome A08, qSUCA08.2, controlling sucrose content will benefit peanut flavor improvement. Sucrose is the main soluble sugar in mature peanut kernel, and its content is a key determinant of flavor. However, the genetic basis of sucrose content in peanut remains poorly understood, which limits the progress of flavor improvement. In the present study, two genomic regions (qSUCA08a and qSUCB06a) for sucrose content on chromosomes A08 and B06 were identified by QTL-seq in a RIL population derived from a cross between Zhonghua 10 and ICG 12625. In the interval of qSUCB06a, QTL qSUCB06.2 was detected through QTL mapping in a single environment. The qSUCA08a was further dissected into 3 adjacent genomic regions using linkage analysis including a major QTL qSUCA08.2 explaining 5.43-17.84% phenotypic variation across five environments. A 61-bp insertion at position 35,099,320 in the higher sucrose parent ICG 12625 was found in qSUCA08.2. An InDel marker SUC.InDel.A08 based on the insertion/deletion polymorphism was developed and validated within a natural population containing 172 peanut cultivars in two environments. The mean sucrose content of 93 cultivars with ICG 12625 allele was significantly higher than that of 79 cultivars with Zhonghua 10 allele. The qSUCA08.2 corresponding to a 2.11 Mb interval harbored 110 genes. Among these genes, a total of 19 genes were considered as candidate genes including 5 non-synonymous mutation genes and 14 differentially expressed genes during seed development. These results provide new insights into the genetic basis of sucrose regulation in peanut and benefit the breeding program for developing new varieties with excellent flavor.
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Affiliation(s)
- Weitao Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Jianbin Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Bolun Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Xin Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China.
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16
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Zhang G, Zhang X, Yu S, Sun H. Novel insights on genes and pathways involved in Pinus elliottii response to resinosis. TREE PHYSIOLOGY 2023; 43:351-362. [PMID: 36209440 DOI: 10.1093/treephys/tpac118] [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: 06/06/2022] [Accepted: 08/17/2022] [Indexed: 06/16/2023]
Abstract
Pinus elliottii, an important coniferous timber species, has recently become one of the most popular sources of resin in China. Resinosis is a common disease that may negatively affect pine tree growth and production. In this study, we used single-molecule real-time sequencing and Illumina RNA sequencing to generate an accurate transcriptome for P. elliottii. The transcriptome included 90,026 transcripts, 5160 long non-coding RNAs and 7710 transcription factors. We then analyzed RNA-sequencing, small RNA-sequencing and degradome data to identify genes, miRNAs and key miRNA-target pairs involved in response to resinosis in P. elliottii. We identified 1305 genes and 1151 miRNAs exhibiting significant differential expression in response to resinosis. According to the degradome sequencing analysis, 318 differentially expressed transcripts were targets of 14 differentially expressed miRNAs. Our study has provided resources for further functional characterization of genes and miRNAs involved in resinosis in P. elliottii, which should aid the future disease-resistance breeding of this species.
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Affiliation(s)
- Guoyun Zhang
- Research Institute of Forestry, Chinese Academy of Forestry, Haidian, Beijing 100091, China
| | - Xu Zhang
- Research Institute of Subtropical Forestry of Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Sujun Yu
- Fengshushan Forestry Farm, Jingdezhen, Jiangxi 333000, China
| | - Honggang Sun
- Research Institute of Subtropical Forestry of Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
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17
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Mao J, Wang Y, Wang B, Li J, Zhang C, Zhang W, Li X, Li J, Zhang J, Li H, Zhang Z. High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry. HORTICULTURE RESEARCH 2023; 10:uhad002. [PMID: 37077373 PMCID: PMC10108017 DOI: 10.1093/hr/uhad002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/03/2023] [Indexed: 05/03/2023]
Abstract
Cultivated strawberry (Fragaria × ananassa), a perennial herb belonging to the family Rosaceae, is a complex octoploid with high heterozygosity at most loci. However, there is no research on the haplotype of the octoploid strawberry genome. Here we aimed to obtain a high-quality genome of the cultivated strawberry cultivar, "Yanli", using single molecule real-time sequencing and high-throughput chromosome conformation capture technology. The "Yanli" genome was 823 Mb in size, with a long terminal repeat assembly index of 14.99. The genome was phased into two haplotypes, Hap1 (825 Mb with contig N50 of 26.70 Mb) and Hap2 (808 Mb with contig N50 of 27.51 Mb). Using the combination of Hap1 and Hap2, we obtained for the first time a haplotype-resolved genome with 56 chromosomes for the cultivated octoploid strawberry. We identified a ~ 10 Mb inversion and translocation on chromosome 2-1. 104 957 and 102 356 protein-coding genes were annotated in Hap1 and Hap2, respectively. Analysis of the genes related to the anthocyanin biosynthesis pathway revealed the structural diversity and complexity in the expression of the alleles in the octoploid F. × ananassa genome. In summary, we obtained a high-quality haplotype-resolved genome assembly of F. × ananassa, which will provide the foundation for investigating gene function and evolution of the genome of cultivated octoploid strawberry.
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Affiliation(s)
| | | | - Baotian Wang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Jiqi Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Chao Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Wenshuo Zhang
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Xue Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Jie Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Junxiang Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
- Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang 110866, China
| | - He Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
- Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang 110866, China
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Huang K, Li W, Yang B, Wang D, He S, Shen Y, Ao J, Li Y, Cui Y, Kong Y, Li W, Li N, Dunn DW, Li B. vcfpop: Performing population genetics analyses for autopolyploids and aneuploids based on next-generation sequencing data sets. Mol Ecol Resour 2022. [PMID: 36458971 DOI: 10.1111/1755-0998.13744] [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: 04/09/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
Polyploids are cells or organisms with a genome consisting of more than two sets of homologous chromosomes. Polyploid plants have important traits that facilitate speciation and are thus often model systems for evolutionary, molecular ecology and agricultural studies. However, due to their unusual mode of inheritance and double-reduction, diploid models of population genetic analysis cannot properly be applied to autopolyploids. To overcome this problem, we developed a software package entitled vcfpop to perform a variety of population genetic analyses for autopolyploids, such as parentage analysis, analysis of molecular variance, principal coordinates analysis, hierarchical clustering analysis and Bayesian clustering. We used three data sets to evaluate the capability of vcfpop to analyse large data sets on a desktop computer. This software is freely available at http://github.com/huangkang1987/vcfpop.
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Affiliation(s)
- Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wenkai Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Bing Yang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Dan Wang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Shujun He
- Shaanxi Key Laboratory for Animal Conservation, Institute of Zoology, Shaanxi Academy of Sciences, Xi'an, China
| | - Yujia Shen
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Jincuo Ao
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Yuhang Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Yunxia Cui
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Yuchen Kong
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Wei Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Nianlong Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Derek W Dunn
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
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Liu X, Huang X, Chu C, Xu H, Wang L, Xue Y, Arifeen Muhammad ZU, Inagaki F, Liu C. Genome, genetic evolution, and environmental adaptation mechanisms of Schizophyllum commune in deep subseafloor coal-bearing sediments. iScience 2022; 25:104417. [PMID: 35663011 PMCID: PMC9156946 DOI: 10.1016/j.isci.2022.104417] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/30/2022] [Accepted: 05/12/2022] [Indexed: 12/15/2022] Open
Abstract
To understand the genomic evolution and adaptation strategies of fungi to subseafloor sedimentary environments, we de novo assembled the genome of Schizophyllum commune strain 20R-7-F01 isolated from ∼2.0 km-deep, ∼20-millionyearsago (Mya) coal-bearing sediments. Phylogenomics study revealed a differentiation time of 28-73 Mya between this strain and the terrestrial type-strain H4-8, in line with sediment age records. Comparative genome analyses showed that FunK1 protein kinase, NmrA family, and transposons in this strain are significantly expanded, possibly linking to the environmental adaptation and persistence in sediment for over millions of years. Re-sequencing study of 14 S. commune strains sampled from different habitats revealed that subseafloor strains have much lower nucleotide diversity, substitution rate, and homologous recombination rate than other strains, reflecting that the growth and/or reproduction of subseafloor strains are extremely slow. Our data provide new insights into the adaptation and long-term survival of the fungi in the subseafloor sedimentary biosphere.
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Affiliation(s)
- Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Xin Huang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Chen Chu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Hui Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Yarong Xue
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | | | - Fumio Inagaki
- Mantle Drilling Promotion Office, Institute for Marine-Earth Exploration and Engineering (MarE3), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama 236-0001, Japan
- Department of Earth Sciences, Graduate School of Science, Tohoku University, Sendai 980-8574, Japan
| | - Changhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
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Deng L, Xie B, Wang Y, Zhang X, Xu S. A protocol for applying a population-specific reference genome assembly to population genetics and medical studies. STAR Protoc 2022; 3:101440. [PMID: 35664259 PMCID: PMC9157554 DOI: 10.1016/j.xpro.2022.101440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
With a growing number of available de novo sequenced genomes, protocols for their applications to population genetics will benefit our understanding of the human genome. Here we detail analytic steps to apply an example de novo reference genome to map and detect variants of short-read sequences from corresponding populations and to discover variants of disease-relevant genes. Using this protocol, we can improve variant discovery, better investigate population-specific genome properties, and evaluate the potential of sequenced genomes in medical studies. For complete details on the use and execution of this protocol, please refer to Lou et al. (2022). Protocol for mapping and variants detection of short-read sequences Advantages of using a population-specific reference genome in population genomic studies Analytic steps to discover potential variants of disease-relevant genes
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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Affiliation(s)
- Lian Deng
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Bo Xie
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yimin Wang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaoxi Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Corresponding author
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Swargam S, Kumari I, Kumar A, Pradhan D, Alam A, Singh H, Jain A, Devi KR, Trivedi V, Sarma J, Hanif M, Narain K, Ehtesham NZ, Hasnain SE, Ahmad S. MycoVarP: Mycobacterium Variant and Drug Resistance Prediction Pipeline for Whole-Genome Sequence Data Analysis. FRONTIERS IN BIOINFORMATICS 2022; 1:805338. [PMID: 36303799 PMCID: PMC9580932 DOI: 10.3389/fbinf.2021.805338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
Whole-genome sequencing (WGS) provides a comprehensive tool to analyze the bacterial genomes for genotype–phenotype correlations, diversity of single-nucleotide variant (SNV), and their evolution and transmission. Several online pipelines and standalone tools are available for WGS analysis of Mycobacterium tuberculosis (Mtb) complex (MTBC). While they facilitate the processing of WGS data with minimal user expertise, they are either too general, providing little insights into bacterium-specific issues such as gene variations, INDEL/synonymous/PE-PPE (IDP family), and drug resistance from sample data, or are limited to specific objectives, such as drug resistance. It is understood that drug resistance and lineage-specific issues require an elaborate prioritization of identified variants to choose the best target for subsequent therapeutic intervention. Mycobacterium variant pipeline (MycoVarP) addresses these specific issues with a flexible battery of user-defined and default filters. It provides an end-to-end solution for WGS analysis of Mtb variants from the raw reads and performs two quality checks, viz, before trimming and after alignments of reads to the reference genome. MycoVarP maps the annotated variants to the drug-susceptible (DS) database and removes the false-positive variants, provides lineage identification, and predicts potential drug resistance. We have re-analyzed the WGS data reported by Advani et al. (2019) using MycoVarP and identified some additional variants not reported so far. We conclude that MycoVarP will help in identifying nonsynonymous, true-positive, drug resistance–associated variants more effectively and comprehensively, including those within the IDP of the PE-PPE/PGRS family, than possible from the currently available pipelines.
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Affiliation(s)
- Sandeep Swargam
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, India
- Department of Molecular Medicine, School of Interdisciplinary Sciences, Jamia Hamdard, New Delhi, India
| | - Indu Kumari
- Inflammation Biology and Cell Signalling Lab, Safdarjung Hospital Campus, ICMR National Institute of Pathology, New Delhi, India
| | - Amit Kumar
- ICMR Computational Genomics Centre, Informatics Systems and Research Management (ISRM) Division, Indian Council of Medical Research (ICMR), New Delhi, India
| | - Dibyabhaba Pradhan
- ICMR Computational Genomics Centre, Informatics Systems and Research Management (ISRM) Division, Indian Council of Medical Research (ICMR), New Delhi, India
| | - Anwar Alam
- Inflammation Biology and Cell Signalling Lab, Safdarjung Hospital Campus, ICMR National Institute of Pathology, New Delhi, India
| | - Harpreet Singh
- ICMR Computational Genomics Centre, Informatics Systems and Research Management (ISRM) Division, Indian Council of Medical Research (ICMR), New Delhi, India
| | - Anuja Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Vishal Trivedi
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Guwahati, Guwahati, India
| | - Jogesh Sarma
- Department of Pulmonary Medicine, Guwahati, India
| | | | - Kanwar Narain
- ICMR-Regional Medical Research Centre, Dibrugarh, India
| | - Nasreen Zafar Ehtesham
- Inflammation Biology and Cell Signalling Lab, Safdarjung Hospital Campus, ICMR National Institute of Pathology, New Delhi, India
| | - Seyed Ehtesham Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, India
- Department of Life Sciences, Sharda University, Greater NOIDA, India
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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22
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Han W, Zhao J, Deng X, Gu A, Li D, Wang Y, Lu X, Zu Q, Chen Q, Chen Q, Zhang J, Qu Y. Quantitative Trait Locus Mapping and Identification of Candidate Genes for Resistance to Fusarium Wilt Race 7 Using a Resequencing-Based High Density Genetic Bin Map in a Recombinant Inbred Line Population of Gossypium barbadense. FRONTIERS IN PLANT SCIENCE 2022; 13:815643. [PMID: 35371113 PMCID: PMC8965654 DOI: 10.3389/fpls.2022.815643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/10/2022] [Indexed: 05/16/2023]
Abstract
Fusarium wilt caused by Fusarium oxysporum f. sp. vasinfectum (FOV) is one of the most destructive diseases in cotton (Gossypium spp.) production, and use of resistant cultivars is the most cost-effective method managing the disease. To understand the genetic basis of cotton resistance to FOV race 7 (FOV7), this study evaluated a recombinant inbred line (RIL) population of 110 lines of G. barbadense from a cross between susceptible Xinhai 14 and resistant 06-146 in eight tests and constructed a high-density genetic linkage map with resequencing-based 933,845 single-nucleotide polymorphism (SNP) markers covering a total genetic distance of 2483.17 cM. Nine quantitative trait loci (QTLs) for FOV7 resistance were identified, including qFOV7-D03-1 on chromosome D03 in two tests. Through a comparative analysis of gene expression and DNA sequence for predicted genes within the QTL region between the two parents and selected lines inoculated with FOV7, GB_D03G0217 encoding for a calmodulin (CaM)-like (CML) protein was identified as a candidate gene. A further analysis confirmed that the expression of GB_D03G0217 was suppressed, leading to increased disease severity in plants of the resistant parent with virus induced gene silencing (VIGS).
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Affiliation(s)
- Wanli Han
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Jieyin Zhao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Xiaojuan Deng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Aixing Gu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Duolu Li
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Yuxiang Wang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Xiaoshuang Lu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Qianli Zu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Qin Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
| | - Yanying Qu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
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Liu J, Shen Q, Bao H. Comparison of seven SNP calling pipelines for the next-generation sequencing data of chickens. PLoS One 2022; 17:e0262574. [PMID: 35100292 PMCID: PMC8803190 DOI: 10.1371/journal.pone.0262574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 12/29/2021] [Indexed: 11/18/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are widely used in genome-wide association studies and population genetics analyses. Next-generation sequencing (NGS) has become convenient, and many SNP-calling pipelines have been developed for human NGS data. We took advantage of a gap knowledge in selecting the appropriated SNP calling pipeline to handle with high-throughput NGS data. To fill this gap, we studied and compared seven SNP calling pipelines, which include 16GT, genome analysis toolkit (GATK), Bcftools-single (Bcftools single sample mode), Bcftools-multiple (Bcftools multiple sample mode), VarScan2-single (VarScan2 single sample mode), VarScan2-multiple (VarScan2 multiple sample mode) and Freebayes pipelines, using 96 NGS data with the different depth gradients of approximately 5X, 10X, 20X, 30X, 40X, and 50X coverage from 16 Rhode Island Red chickens. The sixteen chickens were also genotyped with a 50K SNP array, and the sensitivity and specificity of each pipeline were assessed by comparison to the results of SNP arrays. For each pipeline, except Freebayes, the number of detected SNPs increased as the input read depth increased. In comparison with other pipelines, 16GT, followed by Bcftools-multiple, obtained the most SNPs when the input coverage exceeded 10X, and Bcftools-multiple obtained the most when the input was 5X and 10X. The sensitivity and specificity of each pipeline increased with increasing input. Bcftools-multiple had the highest sensitivity numerically when the input ranged from 5X to 30X, and 16GT showed the highest sensitivity when the input was 40X and 50X. Bcftools-multiple also had the highest specificity, followed by GATK, at almost all input levels. For most calling pipelines, there were no obvious changes in SNP numbers, sensitivities or specificities beyond 20X. In conclusion, (1) if only SNPs were detected, the sequencing depth did not need to exceed 20X; (2) the Bcftools-multiple may be the best choice for detecting SNPs from chicken NGS data, but for a single sample or sequencing depth greater than 20X, 16GT was recommended. Our findings provide a reference for researchers to select suitable pipelines to obtain SNPs from the NGS data of chickens or nonhuman animals.
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Affiliation(s)
- Jing Liu
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qingmiao Shen
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haigang Bao
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
- * E-mail:
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Clonal and subclonal TP53 molecular impairment is associated with prognosis and progression in multiple myeloma. Blood Cancer J 2022; 12:15. [PMID: 35082295 PMCID: PMC8791929 DOI: 10.1038/s41408-022-00610-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/14/2021] [Accepted: 11/11/2021] [Indexed: 02/06/2023] Open
Abstract
Aberrations on TP53, either as deletions of chromosome 17p (del17p) or mutations, are associated with poor outcome in multiple myeloma (MM), but conventional detection methods currently in use underestimate their incidence, hindering an optimal risk assessment and prognostication of MM patients. We have investigated the altered status of TP53 gene by SNPs array and sequencing techniques in a homogenous cohort of 143 newly diagnosed MM patients, evaluated both at diagnosis and at first relapse: single-hit on TP53 gene, either deletion or mutation, detected both at clonal and sub-clonal level, had a minor effect on outcomes. Conversely, the coexistence of both TP53 deletion and mutation, which defined the so-called double-hit patients, was associated with the worst clinical outcome (PFS: HR 3.34 [95% CI: 1.37–8.12] p = 0.008; OS: HR 3.47 [95% CI: 1.18–10.24] p = 0.02). Moreover, the analysis of longitudinal samples pointed out that TP53 allelic status might increase during the disease course. Notably, the acquisition of TP53 alterations at relapse dramatically worsened the clinical course of patients. Overall, our analyses showed these techniques to be highly sensitive to identify TP53 aberrations at sub-clonal level, emphasizing the poor prognosis associated with double-hit MM patients.
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Population Genomics of Megalobrama Provides Insights into Evolutionary History and Dietary Adaptation. BIOLOGY 2022; 11:biology11020186. [PMID: 35205053 PMCID: PMC8869164 DOI: 10.3390/biology11020186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 11/21/2022]
Abstract
Simple Summary Megalobrama is the economically most important freshwater fish genus in China. In recent years, germplasm resources of Megalobrama have been depleting as a result of environmental degradation and artificial factors. In this study, we established the whole genome database of Megalobrama populations using the whole genome re-sequencing technology, explored population genetic structure, and inferred comprehensive evolutionary relationships using principal component analysis and population structure analysis. Furthermore, employing selective sweep analysis, we identified candidate genes related to variations in feeding habits, revealing the molecular mechanisms of environmental adaptability in Megalobrama populations. Taken together, this study describes the population history and genetic diversity of Megalobrama populations and also the molecular mechanisms likely involved their environmental adaptability. These findings will make a substantial contribution to conservation and utilization of Megalobrama germplasm resources. Abstract Megalobrama, a genus of cyprinid fish, is an economically important freshwater fish widely distributed in major waters of China. Here, we report the genome resequencing of 180 Megalobrama fish including M. amblycephala, M. skolkovii, M. hoffmanni, and M. pellegrini. Population structure indicated that geographically divergent Megalobrama populations were separated into six subgroups. A phylogenetic tree showed that M. skolkovii was more closely related to M. pellegrini than other species and M. hoffmanni was clustered apart from other Megalobrama species, showing a high nucleotide diversity in geographic groups. Treemix validated gene flow from M. amblycephala to M. skolkovii, suggesting that introgression may provide an important source of genetic variation in the M. skolkovii populations. According to the demographic history analysis, it is speculated that Megalobrama might have been originally distributed in the Pearl River with some spread to Hainan Island and northern China due to lower sea levels during the glacial period. Whole-genome selective sweeps analysis demonstrated that M. amblycephala likely developed an enhanced energy metabolism mostly through fatty acid degradation pathways whereas M. hoffmanni possibly regulate lipid absorption via the cholesterol metabolism pathway. Taken together, this study provides a valuable genomic resource for future genetic investigations aiming to improve genome-assisted breeding of Megalobrama species.
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Yuan M, Guo Y, Xia H, Xu H, Deng H, Yuan L. Novel SCN5A and GPD1L Variants Identified in Two Unrelated Han-Chinese Patients With Clinically Suspected Brugada Syndrome. Front Cardiovasc Med 2021; 8:758903. [PMID: 34957250 PMCID: PMC8692717 DOI: 10.3389/fcvm.2021.758903] [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: 08/15/2021] [Accepted: 10/29/2021] [Indexed: 12/25/2022] Open
Abstract
Brugada syndrome (BrS) is a complexly genetically patterned, rare, malignant, life-threatening arrhythmia disorder. It is autosomal dominant in most cases and characterized by identifiable electrocardiographic patterns, recurrent syncope, nocturnal agonal respiration, and other symptoms, including sudden cardiac death. Over the last 2 decades, a great number of variants have been identified in more than 36 pathogenic or susceptibility genes associated with BrS. The present study used the combined method of whole exome sequencing and Sanger sequencing to identify pathogenic variants in two unrelated Han-Chinese patients with clinically suspected BrS. Minigene splicing assay was used to evaluate the effects of the splicing variant. A novel heterozygous splicing variant c.2437-2A>C in the sodium voltage-gated channel alpha subunit 5 gene (SCN5A) and a novel heterozygous missense variant c.161A>T [p.(Asp54Val)] in the glycerol-3-phosphate dehydrogenase 1 like gene (GPD1L) were identified in these two patients with BrS-1 and possible BrS-2, respectively. Minigene splicing assay indicated the deletion of 15 and 141 nucleotides in exon 16, resulting in critical amino acid deletions. These findings expand the variant spectrum of SCN5A and GPD1L, which can be beneficial to genetic counseling and prenatal diagnosis.
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Affiliation(s)
- Meng Yuan
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yi Guo
- Department of Medical Information, School of Life Sciences, Central South University, Changsha, China
| | - Hong Xia
- Department of Emergency, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hongbo Xu
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hao Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China.,Disease Genome Research Center, Central South University, Changsha, China
| | - Lamei Yuan
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China.,Disease Genome Research Center, Central South University, Changsha, China
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27
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Bathke J, Lühken G. OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow. BMC Bioinformatics 2021; 22:402. [PMID: 34388963 PMCID: PMC8361789 DOI: 10.1186/s12859-021-04317-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/04/2021] [Indexed: 12/30/2022] Open
Abstract
Background The advent of next generation sequencing has opened new avenues for basic and applied research. One application is the discovery of sequence variants causative of a phenotypic trait or a disease pathology. The computational task of detecting and annotating sequence differences of a target dataset between a reference genome is known as "variant calling". Typically, this task is computationally involved, often combining a complex chain of linked software tools. A major player in this field is the Genome Analysis Toolkit (GATK). The "GATK Best Practices" is a commonly referred recipe for variant calling. However, current computational recommendations on variant calling predominantly focus on human sequencing data and ignore ever-changing demands of high-throughput sequencing developments. Furthermore, frequent updates to such recommendations are counterintuitive to the goal of offering a standard workflow and hamper reproducibility over time. Results A workflow for automated detection of single nucleotide polymorphisms and insertion-deletions offers a wide range of applications in sequence annotation of model and non-model organisms. The introduced workflow builds on the GATK Best Practices, while enabling reproducibility over time and offering an open, generalized computational architecture. The workflow achieves parallelized data evaluation and maximizes performance of individual computational tasks. Optimized Java garbage collection and heap size settings for the GATK applications SortSam, MarkDuplicates, HaplotypeCaller, and GatherVcfs effectively cut the overall analysis time in half. Conclusions The demand for variant calling, efficient computational processing, and standardized workflows is growing. The Open source Variant calling workFlow (OVarFlow) offers automation and reproducibility for a computationally optimized variant calling task. By reducing usage of computational resources, the workflow removes prior existing entry barriers to the variant calling field and enables standardized variant calling.
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Affiliation(s)
- Jochen Bathke
- Institute of Animal Breeding and Genetics, Justus Liebig University Gießen, Ludwigstraße 21, 35390, Gießen, Germany.
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University Gießen, Ludwigstraße 21, 35390, Gießen, Germany
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28
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Abstract
Minimizing false positives is a critical issue when variant calling as no method is without error. It is common practice to post-process a variant-call file (VCF) using hard filter criteria intended to discriminate true-positive (TP) from false-positive (FP) calls. These are applied on the simple principle that certain characteristics are disproportionately represented among the set of FP calls and that a user-chosen threshold can maximize the number detected. To provide guidance on this issue, this study empirically characterized all false SNP and indel calls made using real Illumina sequencing data from six disparate species and 166 variant-calling pipelines (the combination of 14 read aligners with up to 13 different variant callers, plus four ‘all-in-one’ pipelines). We did not seek to optimize filter thresholds but instead to draw attention to those filters of greatest efficacy and the pipelines to which they may most usefully be applied. In this respect, this study acts as a coda to our previous benchmarking evaluation of bacterial variant callers, and provides general recommendations for effective practice. The results suggest that, of the pipelines analysed in this study, the most straightforward way of minimizing false positives would simply be to use Snippy. We also find that a disproportionate number of false calls, irrespective of the variant-calling pipeline, are located in the vicinity of indels, and highlight this as an issue for future development.
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Affiliation(s)
- Stephen J Bush
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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29
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Drljaca T, Zukic B, Kovacevic V, Gemovic B, Klaassen-Ljubicic K, Perovic V, Lazarevic M, Pavlovic S, Veljkovic N. The first insight into the genetic structure of the population of modern Serbia. Sci Rep 2021; 11:13995. [PMID: 34234178 PMCID: PMC8263702 DOI: 10.1038/s41598-021-93129-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 06/18/2021] [Indexed: 11/16/2022] Open
Abstract
The complete understanding of the genomic contribution to complex traits, diseases, and response to treatments, as well as genomic medicine application to the well-being of all humans will be achieved through the global variome that encompasses fine-scale genetic diversity. Despite significant efforts in recent years, uneven representation still characterizes genomic resources and among the underrepresented European populations are the Western Balkans including the Serbian population. Our research addresses this gap and presents the first ever targeted sequencing dataset of variants in clinically relevant genes. By measuring population differentiation and applying the Principal Component and Admixture analysis we demonstrated that the Serbian population differs little from other European populations, yet we identified several novel and more frequent variants that appear as its unique genetic determinants. We explored thoroughly the functional impact of frequent variants and its correlation with the health burden of the population of Serbia based on a sample of 144 individuals. Our variants catalogue improves the understanding of genetics of modern Serbia, contributes to research on ancestry, and aids in improvements of well-being and health equity. In addition, this resource may also be applicable in neighboring regions and valuable in worldwide functional analyses of genetic variants in individuals of European descent.
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Affiliation(s)
- Tamara Drljaca
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Branka Zukic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | | | - Branislava Gemovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | | | - Vladimir Perovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | | | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.
| | - Nevena Veljkovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia.
- Heliant Ltd, Belgrade, Serbia.
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30
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Roy NS, Ban YW, Yoo H, Ramekar RV, Cheong EJ, Park NI, Na JK, Park KC, Choi IY. Analysis of genome variants in dwarf soybean lines obtained in F6 derived from cross of normal parents (cultivated and wild soybean). Genomics Inform 2021; 19:e19. [PMID: 34261303 PMCID: PMC8261272 DOI: 10.5808/gi.21024] [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: 04/08/2021] [Accepted: 04/21/2021] [Indexed: 11/20/2022] Open
Abstract
Plant height is an important component of plant architecture and significantly affects crop breeding practices and yield. We studied DNA variations derived from F5 recombinant inbred lines (RILs) with 96.8% homozygous genotypes. Here, we report DNA variations between the normal and dwarf members of four lines harvested from a single seed parent in an F6 RIL population derived from a cross between Glycine max var. Peking and Glycine soja IT182936. Whole genome sequencing was carried out, and the DNA variations in the whole genome were compared between the normal and dwarf samples. We found a large number of DNA variations in both the dwarf and semi-dwarf lines, with one single nucleotide polymorphism (SNP) per at least 3.68 kb in the dwarf lines and 1 SNP per 11.13 kb of the whole genome. This value is 2.18 times higher than the expected DNA variation in the F6 population. A total of 186 SNPs and 241 SNPs were discovered in the coding regions of the dwarf lines 1282 and 1303, respectively, and we discovered 33 homogeneous nonsynonymous SNPs that occurred at the same loci in each set of dwarf and normal soybean. Of them, five SNPs were in the same positions between lines 1282 and 1303. Our results provide important information for improving our understanding of the genetics of soybean plant height and crop breeding. These polymorphisms could be useful genetic resources for plant breeders, geneticists, and biologists for future molecular biology and breeding projects.
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Affiliation(s)
- Neha Samir Roy
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
| | - Yong-Wook Ban
- Department of Forest Environmental System, Kangwon National University, Chuncheon 24341, Korea
| | - Hana Yoo
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
| | - Rahul Vasudeo Ramekar
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
| | - Eun Ju Cheong
- Department of Forest Environmental System, Kangwon National University, Chuncheon 24341, Korea
| | - Nam-Il Park
- Department of Plant Science, Gangneung-Wonju National University, Gangneung 25457, Korea
| | - Jong Kuk Na
- Department of Controlled Agriculture, Kangwon National University, Chuncheon 24341, Korea
| | - Kyong-Cheul Park
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
| | - Ik-Young Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
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31
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Wang X, Yue Z, Xu F, Wang S, Hu X, Dai J, Zhao G. Coevolution of ribosomal RNA expansion segment 7L and assembly factor Noc2p specializes the ribosome biogenesis pathway between Saccharomyces cerevisiae and Candida albicans. Nucleic Acids Res 2021; 49:4655-4667. [PMID: 33823547 PMCID: PMC8096215 DOI: 10.1093/nar/gkab218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 03/01/2021] [Accepted: 03/20/2021] [Indexed: 01/20/2023] Open
Abstract
Ribosomes of different species share an evolutionarily conserved core, exhibiting flexible shells formed partially by the addition of species-specific ribosomal RNAs (rRNAs) with largely unexplored functions. In this study, we showed that by swapping the Saccharomyces cerevisiae 25S rRNA genes with non-S. cerevisiae homologs, species-specific rRNA variations caused moderate to severe pre-rRNA processing defects. Specifically, rRNA substitution by the Candida albicans caused severe growth defects and deficient pre-rRNA processing. We observed that such defects could be attributed primarily to variations in expansion segment 7L (ES7L) and could be restored by an assembly factor Noc2p mutant (Noc2p-K384R). We showed that swapping ES7L attenuated the incorporation of Noc2p and other proteins (Erb1p, Rrp1p, Rpl6p and Rpl7p) into pre-ribosomes, and this effect could be compensated for by Noc2p-K384R. Furthermore, replacement of Noc2p with ortholog from C. albicans could also enhance the incorporation of Noc2p and the above proteins into pre-ribosomes and consequently restore normal growth. Taken together, our findings help to elucidate the roles played by the species-specific rRNA variations in ribosomal biogenesis and further provide evidence that coevolution of rRNA expansion segments and cognate assembly factors specialized the ribosome biogenesis pathway, providing further insights into the function and evolution of ribosome.
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Affiliation(s)
- Xiangxiang Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China
| | - Zhiyong Yue
- School of Medicine, Xi'an International University, Xi'an 710077, China
| | - Feifei Xu
- Department of Anesthesiology and Perioperative Medicine, Xijing Hospital, the Fourth Military Medical University, Xi'an 710032, China
| | - Sufang Wang
- School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xin Hu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guanghou Zhao
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China
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32
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Serrão de Andrade AA, Soares AER, Paula de Almeida LG, Ciapina LP, Pestana CP, Aquino CL, Medeiros MA, Ribeiro de Vasconcelos AT. Testing the genomic stability of the Brazilian yellow fever vaccine strain using next-generation sequencing data. Interface Focus 2021; 11:20200063. [PMID: 34123353 PMCID: PMC8193464 DOI: 10.1098/rsfs.2020.0063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 01/06/2023] Open
Abstract
The live attenuated yellow fever (YF) vaccine was developed in the 1930s. Currently, the 17D and 17DD attenuated substrains are used for vaccine production. The 17D strain is used for vaccine production by several countries, while the 17DD strain is used exclusively in Brazil. The cell passages carried out through the seed-lot system of vaccine production influence the presence of quasispecies causing changes in the stability and immunogenicity of attenuated genotypes by increasing attenuation or virulence. Using next-generation sequencing, we carried out genomic characterization and genetic diversity analysis between vaccine lots of the Brazilian YF vaccine, produced by BioManguinhos–Fiocruz, and used during 11 years of vaccination in Brazil. We present 20 assembled and annotated genomes from the Brazilian 17DD vaccine strain, eight single nucleotide polymorphisms and the quasispecies spectrum reconstruction for the 17DD vaccine, through a pipeline here introduced. The V2IDA pipeline provided a relationship between low genetic diversity, maintained through the seed lot system, and the confirmation of genetic stability of lots of the Brazilian vaccine against YF. Our study sets precedents for use of V2IDA in genetic diversity analysis and in silico stability investigation of attenuated viral vaccines, facilitating genetic surveillance during the vaccine production process.
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Affiliation(s)
- Amanda Araújo Serrão de Andrade
- National Laboratory for Scientific Computing, Bioinformatics Laboratory (LABINFO), Avenida Getúlio Vargas, 333, Quitandinha 25651-075, Petrópolis, Rio de Janeiro, Brazil
| | - André E R Soares
- National Laboratory for Scientific Computing, Bioinformatics Laboratory (LABINFO), Avenida Getúlio Vargas, 333, Quitandinha 25651-075, Petrópolis, Rio de Janeiro, Brazil
| | - Luiz Gonzaga Paula de Almeida
- National Laboratory for Scientific Computing, Bioinformatics Laboratory (LABINFO), Avenida Getúlio Vargas, 333, Quitandinha 25651-075, Petrópolis, Rio de Janeiro, Brazil
| | - Luciane Prioli Ciapina
- National Laboratory for Scientific Computing, Bioinformatics Laboratory (LABINFO), Avenida Getúlio Vargas, 333, Quitandinha 25651-075, Petrópolis, Rio de Janeiro, Brazil
| | - Cristiane Pinheiro Pestana
- Fiocruz, Bio-Manguinhos, Recombinant Technology Laboratory (LATER), Brazilian Ministry of Health, Rio de Janeiro, Brazil
| | - Carolina Lessa Aquino
- Fiocruz, Bio-Manguinhos, Recombinant Technology Laboratory (LATER), Brazilian Ministry of Health, Rio de Janeiro, Brazil
| | - Marco Alberto Medeiros
- Fiocruz, Bio-Manguinhos, Recombinant Technology Laboratory (LATER), Brazilian Ministry of Health, Rio de Janeiro, Brazil
| | - Ana Tereza Ribeiro de Vasconcelos
- National Laboratory for Scientific Computing, Bioinformatics Laboratory (LABINFO), Avenida Getúlio Vargas, 333, Quitandinha 25651-075, Petrópolis, Rio de Janeiro, Brazil
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33
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Meng X, Liu X, Li Y, Guo T, Yang L. Correlation between Genotype and Phenotype in 69 Chinese Patients with USH2A Mutations: A comparative study of the patients with Usher Syndrome and Nonsyndromic Retinitis Pigmentosa. Acta Ophthalmol 2021; 99:e447-e460. [PMID: 33124170 DOI: 10.1111/aos.14626] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/16/2020] [Accepted: 08/18/2020] [Indexed: 12/18/2022]
Abstract
PURPOSE The aim of this study was to analyse 69 Chinese patients with USH2A mutations and to assess the genotype-phenotype correlation. METHODS All 36 Usher syndrome type IIA patients and 33 nonsyndromic RP (retinitis pigmentosa) patients underwent clinical examinations. Eye examinations included best-corrected visual acuity, slit-lamp biomicroscopy, fundus examination with dilated pupils, fundus fluorescent angiography, visual field test, full-field electroretinography and optic coherence tomography; audiological assessment included pure tone audiometry and hearing thresholds. The molecular diagnosis of genotype combined the single-gene Sanger sequencing and next-generation sequencing. This study is a retrospective study. RESULTS The mean age of first symptoms with Usher syndrome type IIa and nonsyndromic RP patients was 13.7 versus 29.8 years (ocular phenotypes, p < 0.001); 17.7 versus 29.9 years (nyctalopia, p < 0.001); 44.7 versus 54.8 years (low vision based on VF, p < 0.001); 41.7 versus 54.7 years (low vision based on VA, p < 0.001); and 46.0 versus 56.7 years (legal blindness based on VF, p < 0.001). There was significant difference in variants in the two groups (p < 0.05). Among patients with mutation c.2802T > G (p.Cys934Trp), more (66.7%) presented with normal hearing. All patients (3/3, 100%) with the variant c.8232G > C (p.Trp2744Cys) had hearing loss. Furthermore, we identified 23 novel variants in USH2A. CONCLUSIONS Patients with Usher syndrome type IIa had an earlier onset of the disease, inferior visual function and presented with more truncating variants, compared with the nonsyndromic RP patients.
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Affiliation(s)
- Xiang Meng
- Department of Ophthalmology Peking University Third Hospital Beijing Key Laboratory of Restoration of Damaged Ocular Nerve Beijing China
| | - XiaoZhen Liu
- Department of Ophthalmology Peking University Third Hospital Beijing Key Laboratory of Restoration of Damaged Ocular Nerve Beijing China
| | - YingYing Li
- Department of Ophthalmology Peking University Third Hospital Beijing Key Laboratory of Restoration of Damaged Ocular Nerve Beijing China
| | - Tong Guo
- Department of Ophthalmology Peking University Third Hospital Beijing Key Laboratory of Restoration of Damaged Ocular Nerve Beijing China
| | - Liping Yang
- Department of Ophthalmology Peking University Third Hospital Beijing Key Laboratory of Restoration of Damaged Ocular Nerve Beijing China
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34
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Karimzadeh MR, Omidi F, Sahebalzamani A, Saeidi K. A Novel VPS13B Mutation Identified by Whole-Exome Sequencing in Iranian Patients with Cohen Syndrome. J Mol Neurosci 2021; 71:2566-2574. [PMID: 34041686 DOI: 10.1007/s12031-021-01852-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/26/2021] [Indexed: 11/27/2022]
Abstract
Cohen syndrome is caused by homozygous mutation in the vacuolar protein sorting 13 homolog B (VPS13B, also referred to as COH1) gene on chromosome 8q22.2. The VPS13B protein is involved in transmembrane transport, Golgi integrity, and neuritogenesis. Clinical manifestations of Cohen syndrome are mainly intellectual disability, developmental delay, facial abnormalities, and eye disorders. This study aimed to identify the causative variant in two unrelated families with Cohen syndrome. To this end, whole-exome sequencing (WES) was performed to identify the pathogenic variants. A homozygous nonsense variant (NM_017890:c.10369C > T; NP_060360.3: p.Q3457X) in the VPS13B gene was identified and co-segregated with all affected individuals in both families. In silico analysis highly suggested this variant as damaging for protein function. The present study increases the mutation spectrum of the VPS13B gene and could be useful in genetic diagnosis and genetic counseling in Cohen syndrome patients.
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Affiliation(s)
- Mohammad Reza Karimzadeh
- Department of Medical Genetics, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Fatemeh Omidi
- Department of Medical Genetics, Afzalipour Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | | | - Kolsoum Saeidi
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran.
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35
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Arora D, Srikanth K, Lee J, Lee D, Park N, Wy S, Kim H, Park JE, Chai HH, Lim D, Cho IC, Kim J, Park W. Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon. Sci Rep 2021; 11:7219. [PMID: 33785872 PMCID: PMC8009959 DOI: 10.1038/s41598-021-86683-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/12/2021] [Indexed: 02/01/2023] Open
Abstract
Pig as a food source serves daily dietary demand to a wide population around the world. Preference of meat depends on various factors with muscle play the central role. In this regards, selective breeding abled us to develop "Nanchukmacdon" a pig breeds with an enhanced variety of meat and high fertility rate. To identify genomic regions under selection we performed whole-genome resequencing, transcriptome, and whole-genome bisulfite sequencing from Nanchukmacdon muscles samples and used published data for three other breeds such as Landrace, Duroc, Jeju native pig and analyzed the functional characterization of candidate genes. In this study, we present a comprehensive approach to identify candidate genes by using multi-omics approaches. We performed two different methods XP-EHH, XP-CLR to identify traces of artificial selection for traits of economic importance. Moreover, RNAseq analysis was done to identify differentially expressed genes in the crossed breed population. Several genes (UGT8, ZGRF1, NDUFA10, EBF3, ELN, UBE2L6, NCALD, MELK, SERP2, GDPD5, and FHL2) were identified as selective sweep and differentially expressed in muscles related pathways. Furthermore, nucleotide diversity analysis revealed low genetic diversity in Nanchukmacdon for identified genes in comparison to related breeds and whole-genome bisulfite sequencing data shows the critical role of DNA methylation pattern in identified genes that leads to enhanced variety of meat. This work demonstrates a way to identify the molecular signature and lays a foundation for future genomic enabled pig breeding.
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Affiliation(s)
- Devender Arora
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - Krishnamoorthy Srikanth
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea ,grid.5386.8000000041936877XDepartment of Animal Science, Cornell University, Ithaca, NY 14853 USA
| | - Jongin Lee
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Daehwan Lee
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Nayoung Park
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Suyeon Wy
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Hyeonji Kim
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Jong-Eun Park
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - Han-Ha Chai
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - Dajeong Lim
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - In-Cheol Cho
- grid.484502.f0000 0004 5935 1171Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju, 63242 Korea
| | - Jaebum Kim
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Woncheoul Park
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
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36
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Arora I, Tollefsbol TO. Computational methods and next-generation sequencing approaches to analyze epigenetics data: Profiling of methods and applications. Methods 2021; 187:92-103. [PMID: 32941995 PMCID: PMC7914156 DOI: 10.1016/j.ymeth.2020.09.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/20/2022] Open
Abstract
Epigenetics is mainly comprised of features that regulate genomic interactions thereby playing a crucial role in a vast array of biological processes. Epigenetic mechanisms such as DNA methylation and histone modifications influence gene expression by modulating the packaging of DNA in the nucleus. A plethora of studies have emphasized the importance of analyzing epigenetics data through genome-wide studies and high-throughput approaches, thereby providing key insights towards epigenetics-based diseases such as cancer. Recent advancements have been made towards translating epigenetics research into a high throughput approach such as genome-scale profiling. Amongst all, bioinformatics plays a pivotal role in achieving epigenetics-related computational studies. Despite significant advancements towards epigenomic profiling, it is challenging to understand how various epigenetic modifications such as chromatin modifications and DNA methylation regulate gene expression. Next-generation sequencing (NGS) provides accurate and parallel sequencing thereby allowing researchers to comprehend epigenomic profiling. In this review, we summarize different computational methods such as machine learning and other bioinformatics tools, publicly available databases and resources to identify key modifications associated with epigenetic machinery. Additionally, the review also focuses on understanding recent methodologies related to epigenome profiling using NGS methods ranging from library preparation, different sequencing platforms and analytical techniques to evaluate various epigenetic modifications such as DNA methylation and histone modifications. We also provide detailed information on bioinformatics tools and computational strategies responsible for analyzing large scale data in epigenetics.
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Affiliation(s)
- Itika Arora
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA; Comprehensive Center for Healthy Aging, University of Alabama Birmingham, 1530 3rd Avenue South, Birmingham, AL 35294, USA; Comprehensive Cancer Center, University of Alabama Birmingham, 1802 6th Avenue South, Birmingham, AL 35294, USA; Nutrition Obesity Research Center, University of Alabama Birmingham, 1675 University Boulevard, Birmingham, AL 35294, USA; Comprehensive Diabetes Center, University of Alabama Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA.
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Quinodoz M, Peter VG, Bedoni N, Royer Bertrand B, Cisarova K, Salmaninejad A, Sepahi N, Rodrigues R, Piran M, Mojarrad M, Pasdar A, Ghanbari Asad A, Sousa AB, Coutinho Santos L, Superti-Furga A, Rivolta C. AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data. Nat Commun 2021; 12:518. [PMID: 33483490 PMCID: PMC7822856 DOI: 10.1038/s41467-020-20584-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
Homozygosity mapping is a powerful method for identifying mutations in patients with recessive conditions, especially in consanguineous families or isolated populations. Historically, it has been used in conjunction with genotypes from highly polymorphic markers, such as DNA microsatellites or common SNPs. Traditional software performs rather poorly with data from Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS), which are now extensively used in medical genetics. We develop AutoMap, a tool that is both web-based or downloadable, to allow performing homozygosity mapping directly on VCF (Variant Call Format) calls from WES or WGS projects. Following a training step on WES data from 26 consanguineous families and a validation procedure on a matched cohort, our method shows higher overall performances when compared with eight existing tools. Most importantly, when tested on real cases with negative molecular diagnosis from an internal set, AutoMap detects three gene-disease and multiple variant-disease associations that were previously unrecognized, projecting clear benefits for both molecular diagnosis and research activities in medical genetics. Homozygosity mapping is a useful tool for identifying candidate mutations in recessive conditions, however application to next generation sequencing data has been sub-optimal. Here, the authors present AutoMap, which efficiently identifies runs of homozygosity in whole exome/genome sequencing data.
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Affiliation(s)
- Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Experimental Pathology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Nicola Bedoni
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Béryl Royer Bertrand
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Katarina Cisarova
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Arash Salmaninejad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Neda Sepahi
- Noncommunicable Diseases Research Center, Fasa University of Sciences, Fasa, Iran
| | - Raquel Rodrigues
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon Academic Medical Center (CAML), Lisbon, Portugal
| | - Mehran Piran
- Noncommunicable Diseases Research Center, Fasa University of Sciences, Fasa, Iran.,Bioinformatics and Computational Biology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Majid Mojarrad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Pasdar
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine, Medical School, University of Aberdeen, Aberdeen, UK
| | - Ali Ghanbari Asad
- Noncommunicable Diseases Research Center, Fasa University of Sciences, Fasa, Iran
| | - Ana Berta Sousa
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon Academic Medical Center (CAML), Lisbon, Portugal.,Medical Faculty, Lisbon University, Lisbon, Portugal
| | | | - Andrea Superti-Furga
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland. .,Department of Ophthalmology, University of Basel, Basel, Switzerland. .,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
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Genome-Wide Characterization of RNA Editing Sites in Primary Gastric Adenocarcinoma through RNA-seq Data Analysis. Int J Genomics 2020; 2020:6493963. [PMID: 33415135 PMCID: PMC7768588 DOI: 10.1155/2020/6493963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/28/2020] [Accepted: 12/07/2020] [Indexed: 12/15/2022] Open
Abstract
RNA editing is a posttranscriptional nucleotide modification in humans. Of the various types of RNA editing, the adenosine to inosine substitution is the most widespread in higher eukaryotes, which is mediated by the ADAR family enzymes. Inosine is recognized by the biological machinery as guanosine; therefore, editing could have substantial functional effects throughout the genome. RNA editing could contribute to cancer either by exclusive editing of tumor suppressor/promoting genes or by introducing transcriptomic diversity to promote cancer progression. Here, we provided a comprehensive overview of the RNA editing sites in gastric adenocarcinoma and highlighted some of their possible contributions to gastric cancer. RNA-seq data corresponding to 8 gastric adenocarcinoma and their paired nontumor counterparts were retrieved from the GEO database. After preprocessing and variant calling steps, a stringent filtering pipeline was employed to distinguish potential RNA editing sites from SNPs. The identified potential editing sites were annotated and compared with those in the DARNED database. Totally, 12362 high-confidence adenosine to inosine RNA editing sites were detected across all samples. Of these, 12105 and 257 were known and novel editing events, respectively. These editing sites were unevenly distributed across genomic regions, and nearly half of them were located in 3′UTR. Our results revealed that 4868 editing sites were common in both normal and cancer tissues. From the remaining sites, 3985 and 3509 were exclusive to normal and cancer tissues, respectively. Further analysis revealed a significant number of differentially edited events among these sites, which were located in protein coding genes and microRNAs. Given the distinct pattern of RNA editing in gastric adenocarcinoma and adjacent normal tissue, edited sites have the potential to serve as the diagnostic biomarkers and therapeutic targets in gastric cancer.
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Liu X, Tao T, Zhao L, Li G, Yang L. Molecular diagnosis based on comprehensive genetic testing in 800 Chinese families with non-syndromic inherited retinal dystrophies. Clin Exp Ophthalmol 2020; 49:46-59. [PMID: 33090715 DOI: 10.1111/ceo.13875] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 09/23/2020] [Accepted: 10/05/2020] [Indexed: 12/16/2022]
Abstract
IMPORTANCE Inherited retinal dystrophies (IRDs) are a group of monogenic diseases, one of the leading causes of blindness. BACKGROUND Introducing a comprehensive genetic testing strategy by combining single gene Sanger sequencing, next-generation sequencing (NGS) including whole exome sequencing (WES), and a specific hereditary eye disease enrichment panel (HEDEP) sequencing, to identify the disease-causing variants of 800 Chinese probands affected with non-syndromic IRDs. DESIGN Retrospective analysis. PARTICIPANTS Eight hundred Chinese non-syndromic IRDs probands and their families. METHODS A total of 149 patients were subjected to Sanger sequencing. Of the 651 patients subjected to NGS, 86 patients underwent WES and 565 underwent HEDEP. Patients that likely carried copy number variations (CNVs) detected by HEDEP were further validated by multiplex ligation-dependent probe amplification (MLPA) or quantitative fluorescence PCR (QF-PCR). MAIN OUTCOME MEASURES The diagnostic rate. RESULTS (Likely) pathogenic variants were determined in 481 cases (60.13% detection rate). The detection rates of single gene Sanger sequencing, WES and HEDEP were 86.58%, 31.40% and 56.99%, respectively. Approximately 11.64% of 481 cases carried autosomal dominant variants, 72.97% carried AR variants and 15.39% were found to be X-linked. CNVs were confirmed by MLPA or QF-PCR in 17 families. Fourteen genes that each caused disease in 1% or more of the cohort were detected, and these genes were collectively responsible for disease in almost one half (46.38%) of the families. CONCLUSIONS AND RELEVANCE Sanger sequencing is ideal to detect pathogenic variants of clinical homogeneous diseases, whereas NGS is more appropriate for patients without an explicit clinical diagnosis.
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Affiliation(s)
- Xiaozhen Liu
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Tianchang Tao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Lin Zhao
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Genlin Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Liping Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
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40
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Hamdi-Rozé H, Ware M, Guyodo H, Rizzo A, Ratié L, Rupin M, Carré W, Kim A, Odent S, Dubourg C, David V, de Tayrac M, Dupé V. Disrupted Hypothalamo-Pituitary Axis in Association With Reduced SHH Underlies the Pathogenesis of NOTCH-Deficiency. J Clin Endocrinol Metab 2020; 105:5836893. [PMID: 32403133 DOI: 10.1210/clinem/dgaa249] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/10/2020] [Indexed: 12/16/2022]
Abstract
CONTEXT In human, Sonic hedgehog (SHH) haploinsufficiency is the predominant cause of holoprosencephaly, a structural malformation of the forebrain midline characterized by phenotypic heterogeneity and incomplete penetrance. The NOTCH signaling pathway has recently been associated with holoprosencephaly in humans, but the precise mechanism involving NOTCH signaling during early brain development remains unknown. OBJECTIVE The aim of this study was to evaluate the relationship between SHH and NOTCH signaling to determine the mechanism by which NOTCH dysfunction could cause midline malformations of the forebrain. DESIGN In this study, we have used a chemical inhibition approach in the chick model and a genetic approach in the mouse model. We also reported results obtained from the clinical diagnosis of a cohort composed of 141 holoprosencephaly patients. RESULTS We demonstrated that inhibition of NOTCH signaling in chick embryos as well as in mouse embryos induced a specific downregulation of SHH in the anterior hypothalamus. Our data in the mouse also revealed that the pituitary gland was the most sensitive tissue to Shh insufficiency and that haploinsufficiency of the SHH and NOTCH signaling pathways synergized to produce a malformed pituitary gland. Analysis of a large holoprosencephaly cohort revealed that some patients possessed multiple heterozygous mutations in several regulators of both pathways. CONCLUSIONS These results provided new insights into molecular mechanisms underlying the extreme phenotypic variability observed in human holoprosencephaly. They showed how haploinsufficiency of the SHH and NOTCH activity could contribute to specific congenital hypopituitarism that was associated with a sella turcica defect.
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Affiliation(s)
- Houda Hamdi-Rozé
- Univ Rennes, CNRS, IGDR - Institut de Génétique et Développement de Rennes - UMR6290, Rennes, France
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
| | - Michelle Ware
- Univ Rennes, CNRS, IGDR - Institut de Génétique et Développement de Rennes - UMR6290, Rennes, France
| | - Hélène Guyodo
- Univ Rennes, CNRS, IGDR - Institut de Génétique et Développement de Rennes - UMR6290, Rennes, France
| | - Aurélie Rizzo
- Univ Rennes, CNRS, IGDR - Institut de Génétique et Développement de Rennes - UMR6290, Rennes, France
| | - Leslie Ratié
- Univ Rennes, CNRS, IGDR - Institut de Génétique et Développement de Rennes - UMR6290, Rennes, France
| | - Maïlys Rupin
- Univ Rennes, CNRS, IGDR - Institut de Génétique et Développement de Rennes - UMR6290, Rennes, France
| | - Wilfrid Carré
- Univ Rennes, CNRS, IGDR - Institut de Génétique et Développement de Rennes - UMR6290, Rennes, France
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
| | - Artem Kim
- Univ Rennes, CNRS, IGDR - Institut de Génétique et Développement de Rennes - UMR6290, Rennes, France
| | - Sylvie Odent
- Univ Rennes, CNRS, IGDR - Institut de Génétique et Développement de Rennes - UMR6290, Rennes, France
- Service de Génétique Clinique, CHU, Rennes, France
| | - Christèle Dubourg
- Univ Rennes, CNRS, IGDR - Institut de Génétique et Développement de Rennes - UMR6290, Rennes, France
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
| | - Véronique David
- Univ Rennes, CNRS, IGDR - Institut de Génétique et Développement de Rennes - UMR6290, Rennes, France
| | - Marie de Tayrac
- Univ Rennes, CNRS, IGDR - Institut de Génétique et Développement de Rennes - UMR6290, Rennes, France
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
| | - Valérie Dupé
- Univ Rennes, CNRS, IGDR - Institut de Génétique et Développement de Rennes - UMR6290, Rennes, France
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Gao Y, Han Z, Wu X, Lan R, Zhang X, Shen W, Liu Y, Liu X, Lan X, Xu B, Xu W. Next-generation sequencing identifies a novel heterozygous I229T mutation on LMNA associated with familial cardiac conduction disease. Medicine (Baltimore) 2020; 99:e21797. [PMID: 32846814 PMCID: PMC7447464 DOI: 10.1097/md.0000000000021797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
LMNA gene encodes Lamin A and C (Lamin A/C), which are intermediate filament protein implicating in DNA replication and transcription. Mutations in LMNA are validated to cause cardiac conduction disease (CCD) and cardiomyopathy.In a Chinese family, we identified 5 members harboring the identical heterozygous LMNA (c.686T>C, I229T) disease-causing mutation, which was not found in the 535 healthy controls. In silico analysis, we revealed structural alteration in Lamin A/C I229T mutant. Furthermore, molecular docking identified human polycomb repressive complex 2 and Lamin A/C interact with higher affinity in the presence of I229T, thus may downregulate Nav1.5 channel expression.Our findings expanded the spectrum of mutations associated with CCD and were valuable in the genetic diagnosis and clinical screening for CCD. Molecular docking analysis provided useful information of increased binding affinity between mutant Lamin A/C and polycomb repressive complex 2. However, the concrete mechanism of LMNA mutation (I229T) remains undetermined in our study, future genetics and molecular studies are still needed.
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Affiliation(s)
- Yuan Gao
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School
- Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Zhonglin Han
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School
| | - Xiang Wu
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School
| | - Rongfang Lan
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School
| | - Xinlin Zhang
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School
| | - Wenzhi Shen
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School
| | - Yu Liu
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School
| | - Xuehua Liu
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School
| | - Xi Lan
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School
| | - Biao Xu
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School
| | - Wei Xu
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School
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Yang X, Ye Y, Fan D, Lin S, Li M, Hou H, Zhang J, Yang X. Non‑invasive prenatal diagnosis of thalassemia through multiplex PCR, target capture and next‑generation sequencing. Mol Med Rep 2020; 22:1547-1557. [PMID: 32627040 PMCID: PMC7339645 DOI: 10.3892/mmr.2020.11234] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 05/14/2020] [Indexed: 11/14/2022] Open
Abstract
Prenatal clinical detection of thalassemia involves gap-PCR and reverse dot blot (RDB) analysis of fetal DNA acquired through invasive methods. The present study aimed to develop a non-invasive prenatal diagnostic method for thalassemia based on next-generation sequencing (NGS). A total of eight families with proband children with thalassemia were recruited for the study during a subsequent pregnancy. The sequence of the thalassemia genes of the parents and proband were determined using NGS, based on a thalassemia AmpliSeq panel. Cell-free plasma DNA from pregnant women related to the aforementioned proband was analyzed using an NGS panel, based on thalassemia-associated capture probes. Heterozygous single nucleotide polymorphisms within the 10 kb regions flanking exons of the targeted thalassemia genes were acquired using probes or AmpliSeq and employed for parental haplotype construction using Trio-based panel sequencing. The fetal haplotype was deduced from the parental haplotypes and relative haplotype dosage, and subsequently validated using gap-PCR and RDB, based on invasively sampled amniotic fluid. A non-invasive prenatal diagnosis procedure from maternal plasma fetal DNA was successfully developed based on haplotype analysis. The deduced haplotypes of eight fetuses were identical to the results of invasive prenatal diagnosis procedures, with an accuracy rate of 100%. Taken together, the present study demonstrated the potential for non-invasive prenatal diagnosis of α- and β-thalassemia using NGS and haplotype-assisted analysis.
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Affiliation(s)
- Xu Yang
- nstitute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Yanchou Ye
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Dongmei Fan
- nstitute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Sheng Lin
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, Guangdong 510507, P.R. China
| | - Ming Li
- nstitute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Hongying Hou
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Jun Zhang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Xuexi Yang
- nstitute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
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Perucca P, Anderson A, Jazayeri D, Hitchcock A, Graham J, Todaro M, Tomson T, Battino D, Perucca E, Ferri MM, Rochtus A, Lagae L, Canevini MP, Zambrelli E, Campbell E, Koeleman BPC, Scheffer IE, Berkovic SF, Kwan P, Sisodiya SM, Goldstein DB, Petrovski S, Craig J, Vajda FJE, O'Brien TJ. Antiepileptic Drug Teratogenicity and De Novo Genetic Variation Load. Ann Neurol 2020; 87:897-906. [PMID: 32215971 DOI: 10.1002/ana.25724] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 03/13/2020] [Accepted: 03/20/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The mechanisms by which antiepileptic drugs (AEDs) cause birth defects (BDs) are unknown. Data suggest that AED-induced BDs may result from a genome-wide increase of de novo variants in the embryo, a mechanism that we investigated. METHODS Whole exome sequencing data from child-parent trios were interrogated for de novo single-nucleotide variants/indels (dnSNVs/indels) and de novo copy number variants (dnCNVs). Generalized linear models were applied to assess de novo variant burdens in children exposed prenatally to AEDs (AED-exposed children) versus children without BDs not exposed prenatally to AEDs (AED-unexposed unaffected children), and AED-exposed children with BDs versus those without BDs, adjusting for confounders. Fisher exact test was used to compare categorical data. RESULTS Sixty-seven child-parent trios were included: 10 with AED-exposed children with BDs, 46 with AED-exposed unaffected children, and 11 with AED-unexposed unaffected children. The dnSNV/indel burden did not differ between AED-exposed children and AED-unexposed unaffected children (median dnSNV/indel number/child [range] = 3 [0-7] vs 3 [1-5], p = 0.50). Among AED-exposed children, there were no significant differences between those with BDs and those unaffected. Likely deleterious dnSNVs/indels were detected in 9 of 67 (13%) children, none of whom had BDs. The proportion of cases harboring likely deleterious dnSNVs/indels did not differ significantly between AED-unexposed and AED-exposed children. The dnCNV burden was not associated with AED exposure or birth outcome. INTERPRETATION Our study indicates that prenatal AED exposure does not increase the burden of de novo variants, and that this mechanism is not a major contributor to AED-induced BDs. These results can be incorporated in routine patient counseling. ANN NEUROL 2020;87:897-906.
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Affiliation(s)
- Piero Perucca
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Neurology, Alfred Health, Melbourne, Victoria, Australia
| | - Alison Anderson
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Dana Jazayeri
- Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Alison Hitchcock
- Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Janet Graham
- Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Marian Todaro
- Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Torbjörn Tomson
- Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Dina Battino
- Epilepsy Center, Department of Neurophysiology and Experimental Epileptology, IRCCS Neurological Institute "Carlo Besta" Foundation, Milan, Italy
| | - Emilio Perucca
- Department of Internal Medicine and Therapeutics, University of Pavia, and Clinical Trial Center, IRCCS Mondino Foundation, Pavia, Italy
| | | | - Anne Rochtus
- Department of Development and Regeneration, Section of Pediatric Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Lieven Lagae
- Department of Development and Regeneration, Section of Pediatric Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Maria Paola Canevini
- Child Neuropsychiatry Unit-Epilepsy Center, San Paolo Hospital, Milan, Italy.,Department of Health Sciences, University of Milan, Milan, Italy
| | - Elena Zambrelli
- Child Neuropsychiatry Unit-Epilepsy Center, San Paolo Hospital, Milan, Italy
| | - Ellen Campbell
- Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Bobby P C Koeleman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Florey and Murdoch Children's Research Institutes, Melbourne, Victoria, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Patrick Kwan
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Neurology, Alfred Health, Melbourne, Victoria, Australia
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, University College London Queen Square Institute of Neurology, London, United Kingdom.,Chalfont Centre for Epilepsy, Chalfont-St-Peter, United Kingdom
| | - David B Goldstein
- Institute of Genomic Medicine, Columbia University, New York, NY, USA
| | - Slavé Petrovski
- Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Centre for Genomic Research, AstraZeneca, Cambridge, United Kingdom
| | - John Craig
- Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Frank J E Vajda
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Terence J O'Brien
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Departments of Medicine and Neurology, University of Melbourne, Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Neurology, Alfred Health, Melbourne, Victoria, Australia
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Zhang J, Yang J, Zhang L, Luo J, Zhao H, Zhang J, Wen C. A new SNP genotyping technology Target SNP-seq and its application in genetic analysis of cucumber varieties. Sci Rep 2020; 10:5623. [PMID: 32221398 PMCID: PMC7101363 DOI: 10.1038/s41598-020-62518-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 03/11/2020] [Indexed: 01/18/2023] Open
Abstract
To facilitate the utility of SNP-based genotyping, we developed a new method called target SNP-seq which combines the advantages of multiplex PCR amplification and high throughput sequencing. Compared with KASP, Microarrays, GBS and other SNP genotyping methods, target SNP-seq is flexible both in SNPs and samples, yields high accuracy, especially when genotyping genome wide perfect SNPs with high polymorphism and conserved flanking sequences, and is cost-effective, requiring 3 days and $7 for per DNA sample to genotype hundreds of SNP loci. The present study established a DNA fingerprint of 261 cucumber varieties by target SNP-seq with 163 perfect SNPs from 4,612,350 SNPs based on 182 cucumber resequencing datasets. Four distinct subpopulations were found in 261 Chinese cucumber varieties: the north China type, the south China type, the Europe type, and the Xishuangbanna type. The north China type and Xishuangbanna type harbored lower genetic diversity, indicating greater risk of genetic erosion in these two subpopulations. Furthermore, a core set of 24 SNPs was able to distinguish 99% of the 261 cucumber varieties. 29 core cucumber backbone varieties in China were identified. Therefore, target SNP-seq provides a new way to screen out core SNP loci from the whole genome for DNA fingerprinting of crop varieties. The high efficiency and low cost of target SNP-seq is more competitive than the current SNP genotyping methods, and it has excellent application prospects in genetic research, as well as in promoting plant breeding processes in the near future.
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Affiliation(s)
- Jian Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Jingjing Yang
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Like Zhang
- National Agricultural Technology Extension and Service Center, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jiang Luo
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Hong Zhao
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Jianan Zhang
- Molbreeding Biotechnology Company, Shijiazhuang, 050000, China
| | - Changlong Wen
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China.
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Li Q, Ding G, Yang N, White PJ, Ye X, Cai H, Lu J, Shi L, Xu F. Comparative genome and transcriptome analysis unravels key factors of nitrogen use efficiency in Brassica napus L. PLANT, CELL & ENVIRONMENT 2020; 43:712-731. [PMID: 31759338 DOI: 10.1111/pce.13689] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
Considerable genetic variation in agronomic nitrogen (N) use efficiency (NUE) has been reported among genotypes of Brassica napus. However, the physiological and molecular mechanisms underpinning these differences remain poorly understood. In this study, physiological and genetic factors impacting NUE were identified in field trials and hydroponic experiments using two B. napus genotypes with contrasting NUE. The results showed that the N-efficient genotype (D4-15) had greater N uptake and utilization efficiencies, more root tips, larger root surface and root volume, and higher N assimilation and photosynthesis capacity than the N-inefficient genotype (D2-1). Genomic analysis revealed that D4-15 had a greater genome diversity related to NUE than D2-1. By combining genomic and transcriptomic analysis, genes involved in photosynthesis and C/N metabolism were implicated in conferring NUE. Co-expression network analysis of genes that differed between the two genotypes suggested gene clusters impacting NUE. A nitrate transporter gene BnaA06g04560D (NRT2.1) and two vacuole nitrate transporter CLC genes (BnaA02g11800D and BnaA02g28670D) were up-regulated by N starvation in D4-15 but not in D2-1. The study revealed that high N uptake and utilization efficiencies, maintained photosynthesis and coordinated C/N metabolism confer high NUE in B. napus, and identified candidate genes that could facilitate breeding for enhanced NUE in B. napus.
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Affiliation(s)
- Quan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Ningmei Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Philip John White
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- The James Hutton Institute, Invergowrie, Dundee, UK
| | - Xiangsheng Ye
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongmei Cai
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianwei Lu
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
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46
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Gu L, Wang F, Lin Z, Xu T, Lin D, Xing M, Yang S, Chao Z, Ye B, Lin P, Hui C, Lu L, Hou S. Genetic characteristics of Jiaji Duck by whole genome re-sequencing. PLoS One 2020; 15:e0228964. [PMID: 32049997 PMCID: PMC7015413 DOI: 10.1371/journal.pone.0228964] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 01/27/2020] [Indexed: 12/30/2022] Open
Abstract
Jiaji Duck (JJ) is a Muscovy duck species that possesses many superior characteristics, and it has become an important genetic resource in China. However, to date, its genetic characteristics and genetic relationship with other duck breeds have not been explored yet, which greatly limits the utilization of JJ. In the present study, we investigated the genome sequences of 15 individual ducks representing five different duck populations, including JJ, French Muscovy duck (FF), mallard (YD), hong duck (HD) and Beijing duck (BD). Moreover, we investigated the characteristics of JJ-specific single nucleotide polymorphisms (SNPs) and compared the genome sequences of JJ vs. YD and JJ vs. BD using integrated strategies, including mutation detection, selective screening, and Gene Ontology (GO) analysis. More than 40 Gb of clean data were obtained for each population (mean coverage of 13.46 Gb per individual). A total number of 22,481,367 SNPs and 4,156,829 small insertion-deletions (Indels) were identified for the five duck populations, which could be used as molecular markers in breeding and utilization of JJ. Moreover, we identified 1,447,932 JJ-specific SNPs, and found that genes covering at least one JJ-specific SNP mainly involved in protein phosphorylation and dephosphorylation, as well as DNA modification. Phylogenetic tree and principal components analysis (PCA) revealed that the genetic relationship of JJ was closest to FF, while it was farthest to BD. A total of 120 and 111 genes were identified as positive selection genes for JJ vs. BD and JJ vs. YD, respectively. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the positive selection genes for JJ vs. BD ducks mainly involved in pigmentation, muscle contraction and stretch, gland secretion, and immunology, while the positive selection genes obtained from JJ vs. YD ducks mainly involved in embryo development, muscle contraction and stretch, and gland secretion. Taken together, our findings enabled us to better understand the characteristics of JJ and provided a molecular basis for the breeding and hybrid utilization of JJ in the future.
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Affiliation(s)
- Lihong Gu
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Feng Wang
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Zhemin Lin
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Tieshan Xu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, P. R. China
| | - Dajie Lin
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Manping Xing
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Shaoxiong Yang
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Zhe Chao
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Baoguo Ye
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Peng Lin
- Hainan Chuanwei Muscovy Duck Breeding Co., Ltd, Wenchang, P. R. China
| | - Chunhui Hui
- Institute of Animal Science & Veterinary, Hainan Academy of Agricultural Sciences, Haikou, P. R. China
| | - Lizhi Lu
- Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Shuisheng Hou
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
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47
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Rodríguez-López ML, Martínez-Magaña JJ, Cabrera-Mendoza B, Genis-Mendoza AD, García-Dolores F, López-Armenta M, Flores G, Vázquez-Roque RA, Nicolini H. Exploratory analysis of genetic variants influencing molecular traits in cerebral cortex of suicide completers. Am J Med Genet B Neuropsychiatr Genet 2020; 183:26-37. [PMID: 31418530 DOI: 10.1002/ajmg.b.32752] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/13/2019] [Accepted: 07/09/2019] [Indexed: 12/28/2022]
Abstract
Genetic factors have been implicated in suicidal behavior. It has been suggested that one of the roles of genetic factors in suicide could be represented by the effect of genetic variants on gene expression regulation. Alteration in the expression of genes participating in multiple biological systems in the suicidal brain has been demonstrated, so it is imperative to identify genetic variants that could influence gene expression or its regulatory mechanisms. In this study, we integrated DNA methylation, gene expression, and genotype data from the prefrontal cortex of suicides to identify genetic variants that could be factors in the regulation of gene expression, generally called quantitative trait locus (xQTLs). We identify 6,224 methylation quantitative trait loci and 2,239 expression quantitative trait loci (eQTLs) in the prefrontal cortex of suicide completers. The xQTLs identified influence the expression of genes involved in neurodevelopment and cell organization. Two of the eQTLs identified (rs8065311 and rs1019238) were previously associated with cannabis dependence, highlighting a candidate genetic variant for the increased suicide risk in subjects with substance use disorders. Our findings suggest that genetic variants may regulate gene expression in the prefrontal cortex of suicides through the modulation of promoter and enhancer activity, and to a lesser extent, binding transcription factors.
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Affiliation(s)
- Mariana L Rodríguez-López
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | - José J Martínez-Magaña
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | - Brenda Cabrera-Mendoza
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | - Alma D Genis-Mendoza
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico.,Psychiatric Care Services, Child Psychiatric Hospital Dr. Juan N Navarro, CDMX, Mexico
| | | | | | - Gonzalo Flores
- Neuropsychiatry Laboratory, Institute of Physiology, Meritorious Autonomous University of Puebla, Puebla, Mexico
| | - Rubén A Vázquez-Roque
- Neuropsychiatry Laboratory, Institute of Physiology, Meritorious Autonomous University of Puebla, Puebla, Mexico
| | - Humberto Nicolini
- Genomics of Psychiatric and Neurodegenerative Diseases Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico.,Carracci Medical Group, CDMX, Mexico
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48
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Gampawar P, Saba Y, Werner U, Schmidt R, Müller-Myhsok B, Schmidt H. Evaluation of the Performance of AmpliSeq and SureSelect Exome Sequencing Libraries for Ion Proton. Front Genet 2019; 10:856. [PMID: 31608108 PMCID: PMC6774276 DOI: 10.3389/fgene.2019.00856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/16/2019] [Indexed: 12/14/2022] Open
Abstract
Library preparation for whole-exome sequencing is a critical step serving the enrichment of the regions of interest. For Ion Proton, there are only two exome library preparation methods available, AmpliSeq and SureSelect. Although of major interest, a comparison of the two methods is hitherto missing in the literature. Here, we systematically evaluate the performance of AmpliSeq and SureSelect and present an improved variant calling pipeline. We used 12 in-house DNA samples with genome-wide and exome microarray data and a commercially available reference DNA (NA12878) for evaluation. Both methods had a high concordance (>97%) with microarray genotypes and, when validating against NA12878, a sensitivity and positive predictive values of >93% and >80%, respectively. Application of our variant calling pipeline decreased the number of false positive variants dramatically by 90% and resulted in positive predictive value of 97%. This improvement is highly relevant in research as well as clinical setting.
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Affiliation(s)
- Piyush Gampawar
- Research Unit-Genetic Epidemiology, Gottfried Schatz Research Centre for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University Graz, Graz, Austria
| | - Yasaman Saba
- Research Unit-Genetic Epidemiology, Gottfried Schatz Research Centre for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University Graz, Graz, Austria
| | - Ulrike Werner
- Research Unit-Genetic Epidemiology, Gottfried Schatz Research Centre for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University Graz, Graz, Austria
| | - Reinhold Schmidt
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University Graz, Graz, Austria
| | - Bertram Müller-Myhsok
- Max Planck Institute of Psychiatry, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Helena Schmidt
- Research Unit-Genetic Epidemiology, Gottfried Schatz Research Centre for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University Graz, Graz, Austria
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49
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Wu X, Heffelfinger C, Zhao H, Dellaporta SL. Benchmarking variant identification tools for plant diversity discovery. BMC Genomics 2019; 20:701. [PMID: 31500583 PMCID: PMC6734213 DOI: 10.1186/s12864-019-6057-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/22/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ability to accurately and comprehensively identify genomic variations is critical for plant studies utilizing high-throughput sequencing. Most bioinformatics tools for processing next-generation sequencing data were originally developed and tested in human studies, raising questions as to their efficacy for plant research. A detailed evaluation of the entire variant calling pipeline, including alignment, variant calling, variant filtering, and imputation was performed on different programs using both simulated and real plant genomic datasets. RESULTS A comparison of SOAP2, Bowtie2, and BWA-MEM found that BWA-MEM was consistently able to align the most reads with high accuracy, whereas Bowtie2 had the highest overall accuracy. Comparative results of GATK HaplotypCaller versus SAMtools mpileup indicated that the choice of variant caller affected precision and recall differentially depending on the levels of diversity, sequence coverage and genome complexity. A cross-reference experiment of S. lycopersicum and S. pennellii reference genomes revealed the inadequacy of single reference genome for variant discovery that includes distantly-related plant individuals. Machine-learning-based variant filtering strategy outperformed the traditional hard-cutoff strategy resulting in higher number of true positive variants and fewer false positive variants. A 2-step imputation method, which utilized a set of high-confidence SNPs as the reference panel, showed up to 60% higher accuracy than direct LD-based imputation. CONCLUSIONS Programs in the variant discovery pipeline have different performance on plant genomic dataset. Choice of the programs is subjected to the goal of the study and available resources. This study serves as an important guiding information for plant biologists utilizing next-generation sequencing data for diversity characterization and crop improvement.
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Affiliation(s)
- Xing Wu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8104, USA
| | - Christopher Heffelfinger
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8104, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, 06520-8034, USA
| | - Stephen L Dellaporta
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8104, USA.
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50
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Naj AC, Lin H, Vardarajan BN, White S, Lancour D, Ma Y, Schmidt M, Sun F, Butkiewicz M, Bush WS, Kunkle BW, Malamon J, Amin N, Choi SH, Hamilton-Nelson KL, van der Lee SJ, Gupta N, Koboldt DC, Saad M, Wang B, Nato AQ, Sohi HK, Kuzma A, Wang LS, Cupples LA, van Duijn C, Seshadri S, Schellenberg GD, Boerwinkle E, Bis JC, Dupuis J, Salerno WJ, Wijsman EM, Martin ER, DeStefano AL. Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project. Genomics 2019; 111:808-818. [PMID: 29857119 PMCID: PMC6397097 DOI: 10.1016/j.ygeno.2018.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/03/2018] [Accepted: 05/06/2018] [Indexed: 12/30/2022]
Abstract
The Alzheimer's Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants (indels) was performed centrally using GATK-HaplotypeCaller and Atlas V2. The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each pipeline, and developed and implemented a novel protocol, termed "consensus calling," to combine genotype calls from both pipelines into a single high-quality set. QC was applied to autosomal bi-allelic SNVs and indels, and included pipeline-recommended QC filters, variant-level QC, and sample-level QC. Low-quality variants or genotypes were excluded, and sample outliers were noted. Quality was assessed by examining Mendelian inconsistencies (MIs) among 67 parent-offspring pairs, and MIs were used to establish additional genotype-specific filters for GATK calls. After QC, 578 subjects remained. Pipeline-specific QC excluded ~12.0% of GATK and 14.5% of Atlas SNVs. Between pipelines, ~91% of SNV genotypes across all QCed variants were concordant; 4.23% and 4.56% of genotypes were exclusive to Atlas or GATK, respectively; the remaining ~0.01% of discordant genotypes were excluded. For indels, variant-level QC excluded ~36.8% of GATK and 35.3% of Atlas indels. Between pipelines, ~55.6% of indel genotypes were concordant; while 10.3% and 28.3% were exclusive to Atlas or GATK, respectively; and ~0.29% of discordant genotypes were. The final WGS consensus dataset contains 27,896,774 SNVs and 3,133,926 indels and is publicly available.
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Affiliation(s)
- Adam C Naj
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Honghuang Lin
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Badri N Vardarajan
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Simon White
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Daniel Lancour
- Department of Biomedical Genetics, Boston University School of Medicine, Boston, MA, USA
| | - Yiyi Ma
- Department of Biomedical Genetics, Boston University School of Medicine, Boston, MA, USA
| | - Michael Schmidt
- John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Fangui Sun
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Mariusz Butkiewicz
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
| | - William S Bush
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
| | - Brian W Kunkle
- John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - John Malamon
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Seung Hoan Choi
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sven J van der Lee
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Namrata Gupta
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
| | - Daniel C Koboldt
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Mohamad Saad
- Department of Biostatistics, University of Washington, Seattle, WA, USA; Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Bowen Wang
- Department of Statistics, University of Washington, Seattle, WA, USA
| | - Alejandro Q Nato
- Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Harkirat K Sohi
- Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Amanda Kuzma
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA; The Framingham Heart Study, Framingham, MA, USA
| | - Cornelia van Duijn
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Sudha Seshadri
- The Framingham Heart Study, Framingham, MA, USA; Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Human Genetics Center, University of Texas Health Science Center, Houston, TX, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA; The Framingham Heart Study, Framingham, MA, USA
| | - William J Salerno
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ellen M Wijsman
- Department of Biostatistics, University of Washington, Seattle, WA, USA; Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Anita L DeStefano
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA; The Framingham Heart Study, Framingham, MA, USA; Department of Neurology, Boston University School of Medicine, Boston, MA, USA
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