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Gao Z, Lu Y, Chong Y, Li M, Hong J, Wu J, Wu D, Xi D, Deng W. Beef Cattle Genome Project: Advances in Genome Sequencing, Assembly, and Functional Genes Discovery. Int J Mol Sci 2024; 25:7147. [PMID: 39000250 PMCID: PMC11240973 DOI: 10.3390/ijms25137147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/23/2024] [Accepted: 06/26/2024] [Indexed: 07/16/2024] Open
Abstract
Beef is a major global source of protein, playing an essential role in the human diet. The worldwide production and consumption of beef continue to rise, reflecting a significant trend. However, despite the critical importance of beef cattle resources in agriculture, the diversity of cattle breeds faces severe challenges, with many breeds at risk of extinction. The initiation of the Beef Cattle Genome Project is crucial. By constructing a high-precision functional annotation map of their genome, it becomes possible to analyze the genetic mechanisms underlying important traits in beef cattle, laying a solid foundation for breeding more efficient and productive cattle breeds. This review details advances in genome sequencing and assembly technologies, iterative upgrades of the beef cattle reference genome, and its application in pan-genome research. Additionally, it summarizes relevant studies on the discovery of functional genes associated with key traits in beef cattle, such as growth, meat quality, reproduction, polled traits, disease resistance, and environmental adaptability. Finally, the review explores the potential of telomere-to-telomere (T2T) genome assembly, structural variations (SVs), and multi-omics techniques in future beef cattle genetic breeding. These advancements collectively offer promising avenues for enhancing beef cattle breeding and improving genetic traits.
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Affiliation(s)
- Zhendong Gao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Ying Lu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Yuqing Chong
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Mengfei Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jieyun Hong
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jiao Wu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Dongwang Wu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Dongmei Xi
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Weidong Deng
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Kunming 650201, China
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Zhang X, Sun J, Zhang Y, Li J, Liu M, Li L, Li S, Wang T, Shaw RK, Jiang F, Fan X. Hotspot Regions of Quantitative Trait Loci and Candidate Genes for Ear-Related Traits in Maize: A Literature Review. Genes (Basel) 2023; 15:15. [PMID: 38275597 PMCID: PMC10815758 DOI: 10.3390/genes15010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/12/2023] [Accepted: 12/16/2023] [Indexed: 01/27/2024] Open
Abstract
In this study, hotspot regions, QTL clusters, and candidate genes for eight ear-related traits of maize (ear length, ear diameter, kernel row number, kernel number per row, kernel length, kernel width, kernel thickness, and 100-kernel weight) were summarized and analyzed over the past three decades. This review aims to (1) comprehensively summarize and analyze previous studies on QTLs associated with these eight ear-related traits and identify hotspot bin regions located on maize chromosomes and key candidate genes associated with the ear-related traits and (2) compile major and stable QTLs and QTL clusters from various mapping populations and mapping methods and techniques providing valuable insights for fine mapping, gene cloning, and breeding for high-yield and high-quality maize. Previous research has demonstrated that QTLs for ear-related traits are distributed across all ten chromosomes in maize, and the phenotypic variation explained by a single QTL ranged from 0.40% to 36.76%. In total, 23 QTL hotspot bins for ear-related traits were identified across all ten chromosomes. The most prominent hotspot region is bin 4.08 on chromosome 4 with 15 QTLs related to eight ear-related traits. Additionally, this study identified 48 candidate genes associated with ear-related traits. Out of these, five have been cloned and validated, while twenty-eight candidate genes located in the QTL hotspots were defined by this study. This review offers a deeper understanding of the advancements in QTL mapping and the identification of key candidates associated with eight ear-related traits. These insights will undoubtedly assist maize breeders in formulating strategies to develop higher-yield maize varieties, contributing to global food security.
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Affiliation(s)
- Xingjie Zhang
- School of Agriculture, Yunnan University, Kunming 650500, China; (X.Z.); (J.L.); (M.L.); (L.L.); (S.L.)
| | - Jiachen Sun
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (J.S.); (T.W.)
| | - Yudong Zhang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (F.J.)
| | - Jinfeng Li
- School of Agriculture, Yunnan University, Kunming 650500, China; (X.Z.); (J.L.); (M.L.); (L.L.); (S.L.)
| | - Meichen Liu
- School of Agriculture, Yunnan University, Kunming 650500, China; (X.Z.); (J.L.); (M.L.); (L.L.); (S.L.)
| | - Linzhuo Li
- School of Agriculture, Yunnan University, Kunming 650500, China; (X.Z.); (J.L.); (M.L.); (L.L.); (S.L.)
| | - Shaoxiong Li
- School of Agriculture, Yunnan University, Kunming 650500, China; (X.Z.); (J.L.); (M.L.); (L.L.); (S.L.)
| | - Tingzhao Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (J.S.); (T.W.)
| | - Ranjan Kumar Shaw
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (F.J.)
| | - Fuyan Jiang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (F.J.)
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (F.J.)
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Hwang HY, Wang J. Effect of recombination on genetic diversity of Caenorhabditis elegans. Sci Rep 2023; 13:16425. [PMID: 37777524 PMCID: PMC10542817 DOI: 10.1038/s41598-023-42600-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/12/2023] [Indexed: 10/02/2023] Open
Abstract
Greater molecular divergence and genetic diversity are present in regions of high recombination in many species. Studies describing the correlation between variant abundance and recombination rate have long focused on recombination in the context of linked selection models, whereby interference between linked sites under positive or negative selection reduces genetic diversity in regions of low recombination. Here, we show that indels, especially those of intermediate sizes, are enriched relative to single nucleotide polymorphisms in regions of high recombination in C. elegans. To explain this phenomenon, we reintroduce an alternative model that emphasizes the mutagenic effect of recombination. To extend the analysis, we examine the variants with a phylogenetic context and discuss how different models could be examined together. The number of variants generated by recombination in natural populations could be substantial including possibly the majority of some indel subtypes. Our work highlights the potential importance of a mutagenic effect of recombination, which could have a significant role in the shaping of natural genetic diversity.
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Affiliation(s)
- Ho-Yon Hwang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
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Guo D, Huang X, Xiong T, Wang X, Zhang J, Wang Y, Liang J. Molecular mechanisms of programmed cell death in methamphetamine-induced neuronal damage. Front Pharmacol 2022; 13:980340. [PMID: 36059947 PMCID: PMC9428134 DOI: 10.3389/fphar.2022.980340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/28/2022] [Indexed: 12/02/2022] Open
Abstract
Methamphetamine, commonly referred to as METH, is a highly addictive psychostimulant and one of the most commonly misused drugs on the planet. Using METH continuously can increase your risk for drug addiction, along with other health complications like attention deficit disorder, memory loss, and cognitive decline. Neurotoxicity caused by METH is thought to play a significant role in the onset of these neurological complications. The molecular mechanisms responsible for METH-caused neuronal damage are discussed in this review. According to our analysis, METH is closely associated with programmed cell death (PCD) in the process that causes neuronal impairment, such as apoptosis, autophagy, necroptosis, pyroptosis, and ferroptosis. In reviewing this article, some insights are gained into how METH addiction is accompanied by cell death and may help to identify potential therapeutic targets for the neurological impairment caused by METH abuse.
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Affiliation(s)
- Dongming Guo
- Institute of Translational Medicine, Medical, Yangzhou University, Yangzhou, China
| | - Xinlei Huang
- Institute of Translational Medicine, Medical, Yangzhou University, Yangzhou, China
| | - Tianqing Xiong
- Institute of Translational Medicine, Medical, Yangzhou University, Yangzhou, China
| | - Xingyi Wang
- Institute of Translational Medicine, Medical, Yangzhou University, Yangzhou, China
| | - Jingwen Zhang
- Institute of Translational Medicine, Medical, Yangzhou University, Yangzhou, China
| | - Yingge Wang
- Department of Neurology, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Jingyan Liang
- Institute of Translational Medicine, Medical, Yangzhou University, Yangzhou, China
- *Correspondence: Jingyan Liang,
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Abstract
Over the past 50 years, the nematode worm Caenorhabditis elegans has become established as one of the most powerful and widely used model organisms. This article explores the origins and subsequent history of a generally accepted system for gene naming and genetic nomenclature in C. elegans.
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Affiliation(s)
- Jonathan Hodgkin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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6
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The great small organisms of developmental genetics: Caenorhabditis elegans and Drosophila melanogaster. Dev Biol 2022; 485:93-122. [PMID: 35247454 PMCID: PMC9092520 DOI: 10.1016/j.ydbio.2022.02.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 12/30/2022]
Abstract
Experimental embryologists working at the turn of the 19th century suggested fundamental mechanisms of development, such as localized cytoplasmic determinants and tissue induction. However, the molecular basis underlying these processes proved intractable for a long time, despite concerted efforts in many developmental systems to isolate factors with a biological role. That road block was overcome by combining developmental biology with genetics. This powerful approach used unbiased genome-wide screens to isolate mutants with developmental defects and to thereby identify genes encoding key determinants and regulatory pathways that govern development. Two small invertebrates were the pioneers: the fruit fly Drosophila melanogaster and the nematode Caenorhabditis elegans. Their modes of development differ in many ways, but the two together led the way to unraveling the molecular mechanisms of many fundamental developmental processes. The discovery of the grand homologies between key players in development throughout the animal kingdom underscored the usefulness of studying these small invertebrate models for animal development and even human disease. We describe developmental genetics in Drosophila and C. elegans up to the rise of genomics at the beginning of the 21st Century. Finally, we discuss themes that emerge from the histories of such distinct organisms and prospects of this approach for the future.
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Waterston RH, Moerman DG. John Sulston (1942-2018): a personal perspective. J Neurogenet 2021; 34:238-246. [PMID: 33446017 DOI: 10.1080/01677063.2020.1833008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
John Sulston changed the way we do science, not once, but three times - initially with the complete cell lineage of the nematode Caenorhabditis elegans, next with completion of the genome sequences of the worm and human genomes and finally with his strong and active advocacy for open data sharing. His contributions were widely recognized and in 2002 he received the Nobel Prize in Physiology and Medicine.
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Affiliation(s)
- Robert H Waterston
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Donald G Moerman
- Department of Zoology, University of British Columbia, Vancouver, BC, USA
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Yu L, Nie Y, Jiao J, Jian L, Zhao J. The Sequencing-Based Mapping Method for Effectively Cloning Plant Mutated Genes. Int J Mol Sci 2021; 22:ijms22126224. [PMID: 34207582 PMCID: PMC8226582 DOI: 10.3390/ijms22126224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/03/2021] [Accepted: 06/05/2021] [Indexed: 11/23/2022] Open
Abstract
A forward genetic approach is a powerful tool for identifying the genes underlying the phenotypes of interest. However, the conventional map-based cloning method is lengthy, requires a large mapping population and confirmation of many candidate genes in a broad genetic region to clone the causal variant. The whole-genome sequencing method clones the variants with a certain failure probability for multiple reasons, especially for heterozygotes, and could not be used to clone the mutation of epigenetic modifications. Here, we applied the highly complementary characteristics of these two methods and developed a sequencing-based mapping method (SBM) for identifying the location of plant variants effectively with a small population and low cost, which is very user-friendly for most popular laboratories. This method used the whole-genome sequencing data of two pooled populations to screen out enough markers. These markers were used to identify and narrow the candidate region by analyzing the marker-indexes and recombinants. Finally, the possible mutational sites were identified using the whole-genome sequencing data and verified in individual mutants. To elaborate the new method, we displayed the cloned processes in one Arabidopsis heterozygous mutant and two rice homozygous mutants. Thus, the sequencing-based mapping method could clone effectively different types of plant mutations and was a powerful tool for studying the functions of plant genes in the species with known genomic sequences.
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Harnessing the power of genetics: fast forward genetics in Caenorhabditis elegans. Mol Genet Genomics 2020; 296:1-20. [PMID: 32888055 DOI: 10.1007/s00438-020-01721-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 08/27/2020] [Indexed: 12/23/2022]
Abstract
Forward genetics is a powerful tool to unravel molecular mechanisms of diverse biological processes. The success of genetic screens primarily relies on the ease of genetic manipulation of an organism and the availability of a plethora of genetic tools. The roundworm Caenorhabditis elegans has been one of the favorite models for genetic studies due to its hermaphroditic lifestyle, ease of maintenance, and availability of various genetic manipulation tools. The strength of C. elegans genetics is highlighted by the leading role of this organism in the discovery of several conserved biological processes. In this review, the principles and strategies for forward genetics in C. elegans are discussed. Further, the recent advancements that have drastically accelerated the otherwise time-consuming process of mutation identification, making forward genetic screens a method of choice for understanding biological functions, are discussed. The emphasis of the review has been on providing practical and conceptual pointers for designing genetic screens that will identify mutations, specifically disrupting the biological processes of interest.
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Abstract
This review article highlights our efforts to decode the role of the nervous system in regulating intestinal lipid metabolism in Caenorhabditis elegans. Capitalizing on the prescient and pioneering work of Sydney Brenner and John Sulston in establishing C. elegans as an immensely valuable model system, we have uncovered critical roles for oxygen sensing, population density sensing and food sensing in orchestrating the balance between storing lipids and utilizing them for energy in the intestine, the major organ for lipid metabolism in this model system. Our long-term goal is to reveal the integrative mechanisms and regulatory logic that underlies the complex relationship between genes, environment and internal state in the regulation of energy and whole-body physiology.
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Affiliation(s)
- Supriya Srinivasan
- Department of Neuroscience and Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA
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11
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Liang Y, Yan C, Qin X, Nan W, Zhang H. Construction of three half-sib SSR linkage maps derived from overwintering cultivated rice and segregation distortion loci mapping. Genome 2020; 63:239-251. [PMID: 32053407 DOI: 10.1139/gen-2019-0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Segregation distortion is a common phenomenon that has been observed in genetics and plant breeding; however, the mechanism of segregation distortion is unknown. In the present study, three half-sib F2 populations derived from three japonica overwinter (perennial) rice varieties (W1, W2, and W3) crossed to the indica rice variety Minghui725 (MH725) were developed to construct three half-sib linkage maps. We established linkage map lengths of 2032.8, 2317.4, and 2108.7 cM with average intervals of 20.1, 20.5, and 19.7 cM using 101, 113, and 107 SSR markers in W1/MH725, W2/MH725, and W3/MH725, respectively. Discrepancies in marker order and genetic linkage distance occurred in the three half-sib linkage maps due to segregation distortion. A total of 88 markers exhibited segregation distortion across the three linkage maps at P < 0.01 level, 42 segregation distortion loci (SDLs) were detected across the three half-sib populations and exhibited variable LOD value that ranged from 3.2 (SDL2f) to 30.1 (SDL5d), and 13 of the 42 SDLs were repeatedly located at the same chromosomal regions of the previously published hybrid sterility quantitative trait loci. Data from this study provide an extensive archive for investigating the genetic characteristic of overwintering cultivated rice and the future exploration and innovation of overwintering rice breeding.
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Affiliation(s)
- Yongshu Liang
- Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China.,Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China
| | - Chao Yan
- Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China.,Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China
| | - Xiaojian Qin
- Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China.,Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China
| | - Wenbin Nan
- Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China.,Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China
| | - Hanma Zhang
- Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China.,Chongqing Key Laboratory of Molecular Biology of Plant Environmental Adaptations, Chongqing Normal University, Chongqing 401331, P.R. China
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Maxson Jones K, Ankeny RA, Cook-Deegan R. The Bermuda Triangle: The Pragmatics, Policies, and Principles for Data Sharing in the History of the Human Genome Project. JOURNAL OF THE HISTORY OF BIOLOGY 2018; 51:693-805. [PMID: 30390178 PMCID: PMC7307446 DOI: 10.1007/s10739-018-9538-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project (HGP). They were adopted by the HGP at a strategy meeting in Bermuda in February of 1996 and implemented in formal policies by early 1998, mandating daily release of HGP-funded DNA sequences into the public domain. The idea of daily sharing, we argue, emanated directly from strategies for large, goal-directed molecular biology projects first tested within the "community" of C. elegans researchers, and were introduced and defended for the HGP by the nematode biologists John Sulston and Robert Waterston. In the C. elegans community, and subsequently in the HGP, daily sharing served the pragmatic goals of quality control and project coordination. Yet in the HGP human genome, we also argue, the Bermuda Principles addressed concerns about gene patents impeding scientific advancement, and were aspirational and flexible in implementation and justification. They endured as an archetype for how rapid data sharing could be realized and rationalized, and permitted adaptation to the needs of various scientific communities. Yet in addition to the support of Sulston and Waterston, their adoption also depended on the clout of administrators at the US National Institutes of Health (NIH) and the UK nonprofit charity the Wellcome Trust, which together funded 90% of the HGP human sequencing effort. The other nations wishing to remain in the HGP consortium had to accommodate to the Bermuda Principles, requiring exceptions from incompatible existing or pending data access policies for publicly funded research in Germany, Japan, and France. We begin this story in 1963, with the biologist Sydney Brenner's proposal for a nematode research program at the Laboratory of Molecular Biology (LMB) at the University of Cambridge. We continue through 2003, with the completion of the HGP human reference genome, and conclude with observations about policy and the historiography of molecular biology.
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Affiliation(s)
- Kathryn Maxson Jones
- Department of History, Princeton University, Princeton, NJ, USA.
- MBL McDonnell Foundation Scholar, Marine Biological Laboratory, Woods Hole, MA, USA.
| | - Rachel A Ankeny
- School of Humanities, The University of Adelaide, Adelaide, Australia
| | - Robert Cook-Deegan
- School for the Future of Innovation in Society, Consortium for Science, Policy & Outcomes, Arizona State University, Barrett & O'Connor Washington Center, Washington, D.C., USA
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Abstract
Abstract
John Sulston, a pioneer in the developmental studies of the nematode C. elegans who went on to spearhead the sequencing of the genome of this organism and ultimately the human genome, died on 6th March 2018, shortly after being diagnosed with stomach cancer. Here, I reflect on John's life and work, with a particular focus on his time working on the developmental genetics and lineage of C. elegans.
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Affiliation(s)
- John White
- Emeritus Professor, Department of Biomedical Engineering, University of Wisconsin-Madison, LOCI, Room 271 Animal Sciences, 1675 Observatory Drive, Madison, WI 53706, USA
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14
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MTOPVIB interacts with AtPRD1 and plays important roles in formation of meiotic DNA double-strand breaks in Arabidopsis. Sci Rep 2017; 7:10007. [PMID: 28855712 PMCID: PMC5577129 DOI: 10.1038/s41598-017-10270-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 07/28/2017] [Indexed: 12/19/2022] Open
Abstract
Meiotic recombination is initiated from the formation of DNA double-strand breaks (DSBs). In Arabidopsis, several proteins, such as AtPRD1, AtPRD2, AtPRD3, AtDFO and topoisomerase (Topo) VI-like complex, have been identified as playing important roles in DSB formation. Topo VI-like complex in Arabidopsis may consist of subunit A (Topo VIA: AtSPO11-1 and AtSPO11-2) and subunit B (Topo VIB: MTOPVIB). Little is known about their roles in Arabidopsis DSB formation. Here, we report on the characterization of the MTOPVIB gene using the Arabidopsis mutant alleles mtopVIB-2 and mtopVIB-3, which were defective in DSB formation. mtopVIB-3 exhibited abortion in embryo sac and pollen development, leading to a significant reduction in fertility. The mtopVIB mutations affected the homologous chromosome synapsis and recombination. MTOPVIB could interact with Topo VIA proteins AtSPO11-1 and AtSPO11-2. AtPRD1 interacted directly with Topo VI–like proteins. AtPRD1 also could interact with AtPRD3 and AtDFO. The results indicated that AtPRD1 may act as a bridge protein to interact with AtPRD3 and AtDFO, and interact directly with the Topo VI-like proteins MTOPVIB, AtSPO11-1 and AtSPO11-2 to take part in DSB formation in Arabidopsis.
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Broadgate S, Yu J, Downes SM, Halford S. Unravelling the genetics of inherited retinal dystrophies: Past, present and future. Prog Retin Eye Res 2017; 59:53-96. [PMID: 28363849 DOI: 10.1016/j.preteyeres.2017.03.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 02/07/2023]
Abstract
The identification of the genes underlying monogenic diseases has been of interest to clinicians and scientists for many years. Using inherited retinal dystrophies as an example of monogenic disease we describe the history of molecular genetic techniques that have been pivotal in the discovery of disease causing genes. The methods that were developed in the 1970's and 80's are still in use today but have been refined and improved. These techniques enabled the concept of the Human Genome Project to be envisaged and ultimately realised. When the successful conclusion of the project was announced in 2003 many new tools and, as importantly, many collaborations had been developed that facilitated a rapid identification of disease genes. In the post-human genome project era advances in computing power and the clever use of the properties of DNA replication has allowed the development of next-generation sequencing technologies. These methods have revolutionised the identification of disease genes because for the first time there is no need to define the position of the gene in the genome. The use of next generation sequencing in a diagnostic setting has allowed many more patients with an inherited retinal dystrophy to obtain a molecular diagnosis for their disease. The identification of novel genes that have a role in the development or maintenance of retinal function is opening up avenues of research which will lead to the development of new pharmacological and gene therapy approaches. Neither of which can be used unless the defective gene and protein is known. The continued development of sequencing technologies also holds great promise for the advent of truly personalised medicine.
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Affiliation(s)
- Suzanne Broadgate
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Jing Yu
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Susan M Downes
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 9DU, UK
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK.
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A Behind-the-Scenes Story of Precision Medicine. GENOMICS, PROTEOMICS & BIOINFORMATICS 2017; 15:3-10. [PMID: 28188874 PMCID: PMC5339399 DOI: 10.1016/j.gpb.2017.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/25/2017] [Indexed: 12/24/2022]
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Zhu Z, Zhang D, Lee H, Jin Y. Caenorhabditis elegans: An important tool for dissecting microRNA functions. ACTA ACUST UNITED AC 2016; 1:34-36. [PMID: 28529981 DOI: 10.15761/bgg.1000106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Caenorhabditis elegans (C. elegans), a member of the phylum Nematoda, carries the evolutionarily conserved genes comparing to mammals. Due to its short lifespan and completely sequenced genome, C. elegans becomes a potentially powerful model for mechanistic studies in human diseases. In this mini review, we will outline the current understandings on C. elegans as a model organism for microRNA (miRNA)-related research in the pathogenesis of human diseases.
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Affiliation(s)
- Ziwen Zhu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, USA
| | - Duo Zhang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, USA
| | - Heedoo Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, USA
| | - Yang Jin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, USA
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Lv Y, Ma D, Liang W, Lv Y, Guo W, Hu Y, Zhang T. Construction of BAC contig maps of homoeologous chromosomes A12 and D12 of Gossypium hirsutum L. acc. TM-1. Mol Cytogenet 2015. [PMID: 26221184 PMCID: PMC4517413 DOI: 10.1186/s13039-015-0158-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background The Gossypium hirsutum homoeologous chromosome 12 encodes important genes that contribute to fiber fuzz, lethality, gland development and male sterility. In this study a physical map of the cotton TM-1 chromosome 12 was constructed. A number of large-insert cotton genome libraries are available, and genome-wide physical mapping using large insert segments combined with bacterial cloning is a thriving area of genome research. However, sequencing of the cotton genome is difficult due to sequence repeats and homoeologous regions. In order to effectively distinguish the homologous segments, a new method for adjusting the parameters of the FPC software was applied for contig map construction. Results All available markers on chromosomes A12 and D12 were used to screen the TM-1 BAC library by PCR. A total of 775 clones (387 for A12, 388 for D12) were obtained using Hind III fingerprinting and used for construction of the contig map. Seven pairs of SSR markers located on A12 and D12 were chosen for contig analysis. Following optimization of the tolerance (10) and cutoff (1e-12) parameters, combining all clones from A12 and D12 produced two separate contigs. Conclusions The BAC contig map of chromosomes A12 and D12 was constructed and FPC software parameters were optimized for analysis. The resulting approach is a powerful platform for genome-wide and evolutionary research on cotton.
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Affiliation(s)
- Yanhui Lv
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Dan Ma
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wenhua Liang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yuanda Lv
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yan Hu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
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von Reuss SH, Schroeder FC. Combinatorial chemistry in nematodes: modular assembly of primary metabolism-derived building blocks. Nat Prod Rep 2015; 32:994-1006. [PMID: 26059053 PMCID: PMC4884655 DOI: 10.1039/c5np00042d] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The nematode Caenorhabditis elegans was the first animal to have its genome fully sequenced and has become an important model organism for biomedical research. However, like many other animal model systems, its metabolome remained largely uncharacterized, until recent investigations demonstrated the importance of small molecule-based signalling cascades for virtually every aspect of nematode biology. These studies have revealed that nematodes are amazingly skilled chemists: using simple building blocks from conserved primary metabolism and a strategy of modular assembly, C. elegans and other nematode species create complex molecular architectures to regulate their development and behaviour. These nematode-derived modular metabolites (NDMMs) are based on the dideoxysugars ascarylose or paratose, which serve as scaffolds for attachment of moieties from lipid, amino acid, carbohydrate, citrate, and nucleoside metabolism. Mutant screens and comparative metabolomics based on NMR spectroscopy and MS have so-far revealed several 100 different ascarylose ("ascarosides") and a few paratose ("paratosides") derivatives, many of which represent potent signalling molecules that can be active at femtomolar levels, regulating development, behaviour, body shape, and many other life history traits. NDMM biosynthesis appears to be carefully regulated as assembly of different modules proceeds with very high specificity. Preliminary biosynthetic studies have confirmed the primary metabolism origin of some NDMM building blocks, whereas the mechanisms that underlie their highly specific assembly are not understood. Considering their functions and biosynthetic origin, NDMMs represent a new class of natural products that cannot easily be classified as "primary" or "secondary". We believe that the identification of new variants of primary metabolism-derived structures that serve important signalling functions in C. elegans and other nematodes provides a strong incentive for a comprehensive re-analysis of metabolism in higher animals, including humans.
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Affiliation(s)
- Stephan H. von Reuss
- Max Planck Institute for Chemical Ecology, Department of Bioorganic Chemistry, Jena, Germany
| | - Frank C. Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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Johnson TE, Lithgow GJ. The Search for the Genetic Basis of Aging: The Identification of Gerontogenes in the NematodeCaenorhabditis elegans. J Am Geriatr Soc 2015; 40:936-45. [PMID: 1355097 DOI: 10.1111/j.1532-5415.1992.tb01993.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Study of C. elegans has provided much information for gerontologists. The influence of the genome on life span is clearly observable, and at least one gerontogene, age-1, has been defined. Data relating to important evolutionary questions has emerged and will continue to be used in testing current hypotheses. We are using an approach unbiased by theoretical constraints to delineate aging processes simultaneously at the molecular and organismal levels. Much remains to be discovered before fundamental questions posed in this article are answered to a satisfactory degree. The immediate agenda is the identification and isolation of gerontogenes which influence life span in invertebrate models. This work is well in hand and will lead to the unraveling of specific life-span-determining processes. At this point we may be able to predict whether analogous processes also limit life in mammals. If we are fortunate and aging processes exhibit evolutionary conservation, many exciting possibilities await. Molecular tools provided by the invertebrate system can then be used to isolate homologous mammalian gerontogenes that could be subsequently utilized in highly targeted attempts to intervene in mammalian aging. This offers the most direct strategy for identifying life-span prolongation genes in humans.
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Affiliation(s)
- T E Johnson
- Institute for Behavioral Genetics, University of Colorado, Boulder 80309
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21
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Abstract
Over a century ago, the zoologist Emile Maupas first identified the nematode, Rhabditis elegans, in the soil in Algiers. Subsequent work and phylogenic studies renamed the species Caenorhabditis elegans or more commonly referred to as C. elegans; (Caeno meaning recent; rhabditis meaning rod; elegans meaning nice). However, it was not until 1963, when Sydney Brenner, already successful from his work on DNA, RNA, and the genetic code, suggested the future of biological research lay in model organisms. Brenner believed that biological research required a model system that could grow in vast quantities in the lab, were cheap to maintain and had a simple body plan, and he chose the nematode C. elegans to fulfill such a role. Since that time, C. elegans has emerged as one of the premiere model systems for aging research. This paper reviews some initial identification of mutants with altered lifespan with a focus on genetics and then discusses advantages and disadvantages for using C. elegans as a model system to understand human aging. This review focuses on molecular genetics aspects of this model organism.
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Affiliation(s)
- Heidi A Tissenbaum
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School , Worcester , MA 01605 , USA
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22
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Sagy O, Shamir R, Rechavi O. Examination of exhaustive cloning attempts reveals that C. elegans piRNAs, transposons, and repeat sequences are efficiently cloned in yeast, but not in bacteria. Front Genet 2014; 5:275. [PMID: 25221566 PMCID: PMC4148067 DOI: 10.3389/fgene.2014.00275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/26/2014] [Indexed: 11/13/2022] Open
Abstract
Genome sequencing requires insertion of random fragments of the sequenced organism’s DNA into a unicellular host, most often Escherichia coli bacteria. This manipulation was found in the past to be analogous to naturally occurring horizontal gene transfer, and moreover has proved valuable to understanding toxicity of foreign genetic elements to E. coli. Sequencing of the Caenorhabditis elegans genome was similarly achieved via DNA transformation into E. coli. However, numerous attempts have proven a significant percentage of the genome unclonable using bacteria, although clonable via yeast. We examined the genomic segments that were not clonable in bacteria but were clonable in yeast, and observed that, in line with previous hypotheses, such sequences are more repetitive on average compared with the entire C. elegans genome. In addition, we found that these gap-sequences encode significantly more for DNA transposons. Surprisingly, we discovered that although the vast majority of the C. elegans genome is clonable in bacteria (77.5%), almost all the thousands of sequences that encode for PIWI-interacting small RNAs, or 21U-RNAs (91.6%) were only clonable in yeast. These results might help understanding why most piRNAs in C. elegans are physically clustered on particular loci on chromosome IV. In worms and in a large number of other organisms, piRNAs serve to distinguish “Self” from “Non-Self” sequences, and thus to protect the integrity of the genome against foreign genetic elements, such as transposons. We discuss the possible implications of these discoveries.
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Affiliation(s)
- Or Sagy
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University Tel Aviv, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University Tel Aviv, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University Tel Aviv, Israel
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23
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Beck CD, Rankin CH. Effects of aging on habituation in the nematode Caenorhabditis elegans. Behav Processes 2014; 28:145-63. [PMID: 24897600 DOI: 10.1016/0376-6357(93)90088-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/1992] [Indexed: 11/16/2022]
Abstract
The effects of aging on spontaneous locomotor behavior and habituation in a mechanosensory reflex were examined in the nematode Caenorhabditis elegans. Worms were tested at 4 days (at the peak of egg laying), at 7 days (when egg laying ends) and at 12 days post-hatching. Both spontaneous and reflexive movements were smaller in older worms than in younger worms. In addition the magnitude of these movements was related to life span; the shorter an animal's life span, the smaller its reversal movements while still young. Worms at all ages expressed habituation and dishabituation at a 10 s interstimulus interval (ISI); thus even aged worms were capable of non-associative learning. However, older worms showed greater habituation than did 4-day-old worms to stimuli delivered at a 60 s ISI. There was also an age-related change in the recovery from habituation. At days 4 and 7, worms had recovered from habituation by 30 min after training; However, responses of day 12 worms were still significantly smaller than baseline at 30 min after training. Further behavioral tests with normal and mutant worms may help elucidate the nature of the age-related changes in the learning and memory processes of C. elegans and the genetic mechanisms which underlie them.
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Affiliation(s)
- C D Beck
- Department of Psychology, University of British Columbia, Vancouver, British Columbia, Canada
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Dohm JC, Lange C, Holtgräwe D, Sörensen TR, Borchardt D, Schulz B, Lehrach H, Weisshaar B, Himmelbauer H. Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene-based physical and genetic mapping of the sugar beet genome (Beta vulgaris). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:528-540. [PMID: 22211633 DOI: 10.1111/j.1365-313x.2011.04898.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Sugar beet (Beta vulgaris) is an important crop plant that accounts for 30% of the world's sugar production annually. The genus Beta is a distant relative of currently sequenced taxa within the core eudicotyledons; the genomic characterization of sugar beet is essential to make its genome accessible to molecular dissection. Here, we present comprehensive genomic information in genetic and physical maps that cover all nine chromosomes. Based on this information we identified the proposed ancestral linkage groups of rosids and asterids within the sugar beet genome. We generated an extended genetic map that comprises 1127 single nucleotide polymorphism markers prepared from expressed sequence tags and bacterial artificial chromosome (BAC) end sequences. To construct a genome-wide physical map, we hybridized gene-derived oligomer probes against two BAC libraries with 9.5-fold cumulative coverage of the 758 Mbp genome. More than 2500 probes and clones were integrated both in genetic maps and the physical data. The final physical map encompasses 535 chromosomally anchored contigs that contains 8361 probes and 22 815 BAC clones. By using the gene order established with the physical map, we detected regions of synteny between sugar beet (order Caryophyllales) and rosid species that involves 1400-2700 genes in the sequenced genomes of Arabidopsis, poplar, grapevine, and cacao. The data suggest that Caryophyllales share the palaeohexaploid ancestor proposed for rosids and asterids. Taken together, we here provide extensive molecular resources for sugar beet and enable future high-resolution trait mapping, gene identification, and cross-referencing to regions sequenced in other plant species.
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Affiliation(s)
- Juliane C Dohm
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
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García-Sancho M. From the genetic to the computer program: the historicity of 'data' and 'computation' in the investigations on the nematode worm C. elegans (1963-1998). STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2012; 43:16-28. [PMID: 22326069 DOI: 10.1016/j.shpsc.2011.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This paper argues that the history of the computer, of the practice of computation and of the notions of 'data' and 'programme' are essential for a critical account of the emergence and implications of data-driven research. In order to show this, I focus on the transition that the investigations on the worm C. elegans experienced in the Laboratory of Molecular Biology of Cambridge (UK). Throughout the 1980s, this research programme evolved from a study of the genetic basis of the worm's development and behaviour to a DNA mapping and sequencing initiative. By examining the changing computing technologies which were used at the Laboratory, I demonstrate that by the time of this transition researchers shifted from modelling the worm's genetic programme on a mainframe apparatus to writing minicomputer programs aimed at providing map and sequence data which was then circulated to other groups working on the genetics of C. elegans. The shift in the worm research should thus not be simply explained in the application of computers which transformed the project from hypothesis-driven to a data-intensive endeavour. The key factor was rather a historically specific technology-in-house and easy programmable minicomputers-which redefined the way of achieving the project's long-standing goal, leading the genetic programme to co-evolve with the practices of data production and distribution.
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Affiliation(s)
- Miguel García-Sancho
- Department of Science, Technology and Society, Spanish National Research Council (CSIC), Calle Albasanz, 26-28, 28037 Madrid, Spain.
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Integration of the Draft Sequence and Physical Map as a Framework for Genomic Research in Soybean (Glycine max (L.) Merr.) and Wild Soybean (Glycine soja Sieb. and Zucc.). G3-GENES GENOMES GENETICS 2012; 2:321-9. [PMID: 22413085 PMCID: PMC3291501 DOI: 10.1534/g3.111.001834] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 12/21/2011] [Indexed: 11/21/2022]
Abstract
Soybean is a model for the legume research community because of its importance as a crop, densely populated genetic maps, and the availability of a genome sequence. Even though a whole-genome shotgun sequence and bacterial artificial chromosome (BAC) libraries are available, a high-resolution, chromosome-based physical map linked to the sequence assemblies is still needed for whole-genome alignments and to facilitate map-based gene cloning. Three independent G. max BAC libraries combined with genetic and gene-based markers were used to construct a minimum tiling path (MTP) of BAC clones. A total of 107,214 clones were assembled into 1355 FPC (FingerPrinted Contigs) contigs, incorporating 4628 markers and aligned to the G. max reference genome sequence using BAC end-sequence information. Four different MTPs were made for G. max that covered from 92.6% to 95.0% of the soybean draft genome sequence (gmax1.01). Because our purpose was to pick the most reliable and complete MTP, and not the MTP with the minimal number of clones, the FPC map and draft sequence were integrated and clones with unpaired BES were added to build a high-quality physical map with the fewest gaps possible (http://soybase.org). A physical map was also constructed for the undomesticated ancestor (G. soja) of soybean to explore genome variation between G. max and G. soja. 66,028 G. soja clones were assembled into 1053 FPC contigs covering approximately 547 Mbp of the G. max genome sequence. These physical maps for G. max and its undomesticated ancestor, G. soja, will serve as a framework for ordering sequence fragments, comparative genomics, cloning genes, and evolutionary analyses of legume genomes.
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Advances in BAC-based physical mapping and map integration strategies in plants. J Biomed Biotechnol 2012; 2012:184854. [PMID: 22500080 PMCID: PMC3303678 DOI: 10.1155/2012/184854] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 10/26/2011] [Accepted: 11/11/2011] [Indexed: 12/29/2022] Open
Abstract
In the advent of next-generation sequencing (NGS) platforms, map-based sequencing strategy has been recently suppressed being too expensive and laborious. The detailed studies on NGS drafts alone indicated these assemblies remain far from gold standard reference quality, especially when applied on complex genomes. In this context the conventional BAC-based physical mapping has been identified as an important intermediate layer in current hybrid sequencing strategy. BAC-based physical map construction and its integration with high-density genetic maps have benefited from NGS and high-throughput array platforms. This paper addresses the current advancements of BAC-based physical mapping and high-throughput map integration strategies to obtain densely anchored well-ordered physical maps. The resulted maps are of immediate utility while providing a template to harness the maximum benefits of the current NGS platforms.
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Avinoam O, Podbilewicz B. Eukaryotic cell-cell fusion families. CURRENT TOPICS IN MEMBRANES 2012; 68:209-34. [PMID: 21771501 DOI: 10.1016/b978-0-12-385891-7.00009-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ori Avinoam
- Department of Biology, Technion, Israel Institute of Technology, Haifa, Israel
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3D multicolor super-resolution imaging offers improved accuracy in neuron tracing. PLoS One 2012; 7:e30826. [PMID: 22292051 PMCID: PMC3265519 DOI: 10.1371/journal.pone.0030826] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 12/29/2011] [Indexed: 11/19/2022] Open
Abstract
The connectivity among neurons holds the key to understanding brain function. Mapping neural connectivity in brain circuits requires imaging techniques with high spatial resolution to facilitate neuron tracing and high molecular specificity to mark different cellular and molecular populations. Here, we tested a three-dimensional (3D), multicolor super-resolution imaging method, stochastic optical reconstruction microscopy (STORM), for tracing neural connectivity using cultured hippocampal neurons obtained from wild-type neonatal rat embryos as a model system. Using a membrane specific labeling approach that improves labeling density compared to cytoplasmic labeling, we imaged neural processes at 44 nm 2D and 116 nm 3D resolution as determined by considering both the localization precision of the fluorescent probes and the Nyquist criterion based on label density. Comparison with confocal images showed that, with the currently achieved resolution, we could distinguish and trace substantially more neuronal processes in the super-resolution images. The accuracy of tracing was further improved by using multicolor super-resolution imaging. The resolution obtained here was largely limited by the label density and not by the localization precision of the fluorescent probes. Therefore, higher image resolution, and thus higher tracing accuracy, can in principle be achieved by further improving the label density.
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Affiliation(s)
- Mark Blaxter
- Institute of Evolutionary Biology, The University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom.
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Frenkel Z, Paux E, Mester D, Feuillet C, Korol A. LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes. BMC Bioinformatics 2010; 11:584. [PMID: 21118513 PMCID: PMC3098104 DOI: 10.1186/1471-2105-11-584] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 11/30/2010] [Indexed: 11/25/2022] Open
Abstract
Background Physical maps are the substrate of genome sequencing and map-based cloning and their construction relies on the accurate assembly of BAC clones into large contigs that are then anchored to genetic maps with molecular markers. High Information Content Fingerprinting has become the method of choice for large and repetitive genomes such as those of maize, barley, and wheat. However, the high level of repeated DNA present in these genomes requires the application of very stringent criteria to ensure a reliable assembly with the FingerPrinted Contig (FPC) software, which often results in short contig lengths (of 3-5 clones before merging) as well as an unreliable assembly in some difficult regions. Difficulties can originate from a non-linear topological structure of clone overlaps, low power of clone ordering algorithms, and the absence of tools to identify sources of gaps in Minimal Tiling Paths (MTPs). Results To address these problems, we propose a novel approach that: (i) reduces the rate of false connections and Q-clones by using a new cutoff calculation method; (ii) obtains reliable clusters robust to the exclusion of single clone or clone overlap; (iii) explores the topological contig structure by considering contigs as networks of clones connected by significant overlaps; (iv) performs iterative clone clustering combined with ordering and order verification using re-sampling methods; and (v) uses global optimization methods for clone ordering and Band Map construction. The elements of this new analytical framework called Linear Topological Contig (LTC) were applied on datasets used previously for the construction of the physical map of wheat chromosome 3B with FPC. The performance of LTC vs. FPC was compared also on the simulated BAC libraries based on the known genome sequences for chromosome 1 of rice and chromosome 1 of maize. Conclusions The results show that compared to other methods, LTC enables the construction of highly reliable and longer contigs (5-12 clones before merging), the detection of "weak" connections in contigs and their "repair", and the elongation of contigs obtained by other assembly methods.
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Affiliation(s)
- Zeev Frenkel
- University of Haifa, Institute of Evolution, Haifa 31905, Israel.
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A first generation BAC-based physical map of the Asian seabass (Lates calcarifer). PLoS One 2010; 5:e11974. [PMID: 20700486 PMCID: PMC2916840 DOI: 10.1371/journal.pone.0011974] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 07/12/2010] [Indexed: 11/19/2022] Open
Abstract
Background The Asian seabass (Lates calcarifer) is an important marine foodfish species in Southeast Asia and Australia. Genetic improvement of this species has been achieved to some extent through selective breeding programs since 1990s. Several genomic tools such as DNA markers, a linkage map, cDNA and BAC libraries have been developed to assist selective breeding. A physical map is still lacking, although it is essential for positional cloning of genes located in quantitative trait loci (QTL) and assembly of whole genome sequences. Methodology/Principal Findings A genome-wide physical map of the Asian seabass was constructed by restriction fingerprinting of 38,208 BAC clones with SNaPshot HICF FPC technique. A total of 30,454 were assembled into 2,865 contigs. The physical length of the assembled contigs summed up to 665 Mb. Analyses of some contigs using different methods demonstrated the reliability of the assembly. Conclusions/Significance The present physical map is the first physical map for Asian seabass. This physical map will facilitate the fine mapping of QTL for economically important traits and the positional cloning of genes located in QTL. It will also be useful for the whole genome sequencing and assembly. Detailed information about BAC-contigs and BAC clones are available upon request.
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Scalabrin S, Troggio M, Moroldo M, Pindo M, Felice N, Coppola G, Prete G, Malacarne G, Marconi R, Faes G, Jurman I, Grando S, Jesse T, Segala C, Valle G, Policriti A, Fontana P, Morgante M, Velasco R. Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar. BMC Genomics 2010; 11:204. [PMID: 20346114 PMCID: PMC2865496 DOI: 10.1186/1471-2164-11-204] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 03/26/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most of the grapevine (Vitis vinifera L.) cultivars grown today are those selected centuries ago, even though grapevine is one of the most important fruit crops in the world. Grapevine has therefore not benefited from the advances in modern plant breeding nor more recently from those in molecular genetics and genomics: genes controlling important agronomic traits are practically unknown. A physical map is essential to positionally clone such genes and instrumental in a genome sequencing project. RESULTS We report on the first whole genome physical map of grapevine built using high information content fingerprinting of 49,104 BAC clones from the cultivar Pinot Noir. Pinot Noir, as most grape varieties, is highly heterozygous at the sequence level. This resulted in the two allelic haplotypes sometimes assembling into separate contigs that had to be accommodated in the map framework or in local expansions of contig maps. We performed computer simulations to assess the effects of increasing levels of sequence heterozygosity on BAC fingerprint assembly and showed that the experimental assembly results are in full agreement with the theoretical expectations, given the heterozygosity levels reported for grape. The map is anchored to a dense linkage map consisting of 994 markers. 436 contigs are anchored to the genetic map, covering 342 of the 475 Mb that make up the grape haploid genome. CONCLUSIONS We have developed a resource that makes it possible to access the grapevine genome, opening the way to a new era both in grape genetics and breeding and in wine making. The effects of heterozygosity on the assembly have been analyzed and characterized by using several complementary approaches which could be easily transferred to the study of other genomes which present the same features.
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Affiliation(s)
- Simone Scalabrin
- Istituto di Genomica Applicata, Parco Scientifico e Tecnologico di Udine Luigi Danieli, Via J Linussio 51, 33100 Udine, Italy
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A neuronal acetylcholine receptor regulates the balance of muscle excitation and inhibition in Caenorhabditis elegans. PLoS Biol 2009; 7:e1000265. [PMID: 20027209 PMCID: PMC2787625 DOI: 10.1371/journal.pbio.1000265] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Accepted: 11/12/2009] [Indexed: 12/29/2022] Open
Abstract
In the nematode Caenorhabditis elegans, cholinergic motor neurons stimulate muscle contraction as well as activate GABAergic motor neurons that inhibit contraction of the contralateral muscles. Here, we describe the composition of an ionotropic acetylcholine receptor that is required to maintain excitation of the cholinergic motor neurons. We identified a gain-of-function mutation that leads to spontaneous muscle convulsions. The mutation is in the pore domain of the ACR-2 acetylcholine receptor subunit and is identical to a hyperactivating mutation in the muscle receptor of patients with myasthenia gravis. Screens for suppressors of the convulsion phenotype led to the identification of other receptor subunits. Cell-specific rescue experiments indicate that these subunits function in the cholinergic motor neurons. Expression of these subunits in Xenopus oocytes demonstrates that the functional receptor is comprised of three alpha-subunits, UNC-38, UNC-63 and ACR-12, and two non-alpha-subunits, ACR-2 and ACR-3. Although this receptor exhibits a partially overlapping subunit composition with the C. elegans muscle acetylcholine receptor, it shows distinct pharmacology. Recordings from intact animals demonstrate that loss-of-function mutations in acr-2 reduce the excitability of the cholinergic motor neurons. By contrast, the acr-2(gf) mutation leads to a hyperactivation of cholinergic motor neurons and an inactivation of downstream GABAergic motor neurons in a calcium dependent manner. Presumably, this imbalance between excitatory and inhibitory input into muscles leads to convulsions. These data indicate that the ACR-2 receptor is important for the coordinated excitation and inhibition of body muscles underlying sinusoidal movement.
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Bozdag S, Close TJ, Lonardi S. A compartmentalized approach to the assembly of physical maps. BMC Bioinformatics 2009; 10:217. [PMID: 19604400 PMCID: PMC2717093 DOI: 10.1186/1471-2105-10-217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Accepted: 07/15/2009] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Physical maps have been historically one of the cornerstones of genome sequencing and map-based cloning strategies. They also support marker assisted breeding and EST mapping. The problem of building a high quality physical map is computationally challenging due to unavoidable noise in the input fingerprint data. RESULTS We propose a novel compartmentalized method for the assembly of high quality physical maps from fingerprinted clones. The knowledge of genetic markers enables us to group clones into clusters so that clones in the same cluster are more likely to overlap. For each cluster of clones, a local physical map is first constructed using FingerPrinted Contigs (FPC). Then, all the individual maps are carefully merged into the final physical map. Experimental results on the genomes of rice and barley demonstrate that the compartmentalized assembly produces significantly more accurate maps, and that it can detect and isolate clones that would induce "chimeric" contigs if used in the final assembly. CONCLUSION The software is available for download at http://www.cs.ucr.edu/~sbozdag/assembler/
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Affiliation(s)
- Serdar Bozdag
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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38
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Genomic organization in Caenorhabditis elegans: deficiency mapping on linkage group V(left). Genet Res (Camb) 2009. [DOI: 10.1017/s0016672300027476] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SummaryIn this study we genetically analyse a large autosomal region (23 map units) in Caenorhabditis elegans. The region comprises the left half of linkage group V [LGV(left)] and is recombinationally balanced by the translocation eT1(III; V). We have used rearrangement breakpoints to subdivide the region from the left end of LGV to daf-11 into a set of 23 major zones. Twenty of these zones are balanced by eT1. To establish the zones we examined a total of 110 recessive lethal mutations derived from a variety of screening protocols. The mutations identified 12 deficiencies, 1 duplication, as well as 98 mutations that fell into 59 complementation groups, significantly increasing the number of available genetic sites on LGV. Twenty-six of the latter had more than 1 mutant allele. Significant differences were observed among the alleles of only 6 genes, 3 of which have at least one ‘visible’ allele. Several deficiencies and 3 alleles of let-336 were demonstrated to affect recombination. The duplication identified in this study is sDp30(V;X). Lethal mutations covered by sDp30 were not suppressed uniformly in hermaphrodites. The basis for this non-uniformity may be related to the mechanism of X chromosome dosage compensation in C. elegans.
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Abstract
Recent advances in both clone fingerprinting and draft sequencing technology have made it increasingly common for species to have a bacterial artificial clone (BAC) fingerprint map, BAC end sequences (BESs) and draft genomic sequence. The FPC (fingerprinted contigs) software package contains three modules that maximize the value of these resources. The BSS (blast some sequence) module provides a way to easily view the results of aligning draft sequence to the BESs, and integrates the results with the following two modules. The MTP (minimal tiling path) module uses sequence and fingerprints to determine a minimal tiling path of clones. The DSI (draft sequence integration) module aligns draft sequences to FPC contigs, displays them alongside the contigs and identifies potential discrepancies; the alignment can be based on either individual BES alignments to the draft, or on the locations of BESs that have been assembled into the draft. FPC also supports high-throughput fingerprint map generation as its time-intensive functions have been parallelized for Unix-based desktops or servers with multiple CPUs. Simulation results are provided for the MTP, DSI and parallelization. These features are in the FPC V9.3 software package, which is freely available.
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Affiliation(s)
- William Nelson
- Arizona Genomics Computational Laboratory, BIO5 Institute, University of Arizona, Tucson, AZ, USA
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Mathewson CA, Schein JE, Marra MA. Large-scale BAC clone restriction digest fingerprinting. ACTA ACUST UNITED AC 2008; Chapter 5:Unit 5.19. [PMID: 18428413 DOI: 10.1002/0471142905.hg0519s53] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Restriction digest fingerprinting is a common method for characterizing large insert genomic clones, e.g., bacterial artificial chromosome (BAC), P1 artificial chromosome (PAC) and Fosmid clones. This clone fingerprinting method has been widely applied in the construction of clone-based physical maps, which have been used as positional cloning resources as well as to support directed and genome-wide sequencing efforts. This unit describes a robust, large-scale procedure for generation of agarose gel-based clone fingerprints from BAC clones.
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Affiliation(s)
- Carrie A Mathewson
- Canada's Michael Smith Genome Sciences Center Vancouver, British Columbia, Canada
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41
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Monaco AP, Larin Z. Generating subclones from large-insert genomic clones. CURRENT PROTOCOLS IN HUMAN GENETICS 2008; Chapter 5:Unit 5.11. [PMID: 18428285 DOI: 10.1002/0471142905.hg0511s03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This unit provides a simple protocol for generating a partial-digest sublibrary of yeast DNA containing a YAC of interest. The starting material is high-molecular-weight chromosomal DNA embedded in agarose plugs. Many genome equivalents of these YAC subclones in bacteriophage or cosmid vectors can be plated and screened by hybridization with total human DNA to identify clones that originate from the human portion of the YAC. The human-positive clones can be picked into 96-well microtiter plates for spotting on membranes. Once stored in ordered arrays, the YAC subclones can be constructed into contigs using an end-probe or Alu-PCR hybridization strategy, or a gel fingerprinting technique. This unit provides a simple protocol for generating a partial-digest sublibrary of yeast DNA containing a YAC of interest.
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Affiliation(s)
- A P Monaco
- John Radcliffe Hospital, Headington, Oxford
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42
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Foote S, Marshall V, Munroe DJ, Segre JA. Constructing contigs from large-insert clones. CURRENT PROTOCOLS IN HUMAN GENETICS 2008; Chapter 5:Unit 5.10. [PMID: 18428284 DOI: 10.1002/0471142905.hg0510s15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This unit describes three approaches that are widely used to define alignments between overlapping clones bearing large-insert genomic DNA and to generate extensive contiguous overlapping sets of clones (contigs). The three approaches are sequence-tagged site (STS) content mapping, repetitive-element hybridization fingerprinting, and Alu-PCR fingerprinting. Methods for isolating the necessary BAC DNA suitable for automated fluorescent sequencing and generating new STS markers are discussed in support protocols. An alternate protocol presents repetitive-element hybridization fingerprinting to detect overlaps and build contigs with full-genomic YAC libraries.
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Affiliation(s)
- S Foote
- Walter and Eliza Hall Institute, Victoria, Australia
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43
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Moerman DG, Barstead RJ. Towards a mutation in every gene in Caenorhabditis elegans. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 7:195-204. [PMID: 18417533 DOI: 10.1093/bfgp/eln016] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The combined efforts of the Caenorhabditis elegans Knockout Consortium and individuals within the worm community are moving us closer to the goal of identifying mutations in every gene in the nematode C. elegans. At present, we count about 7000 deletion alleles that fall within 5500 genes. The principal method used to detect deletion mutations in the nematode utilizes polymerase chain reaction (PCR). More recently, the Moerman group has incorporated array comparative genome hybridization (aCGH) to detect deletions across the entire coding genome. Other methods used to detect mutant alleles in C. elegans include targeting induced local lesion in genomes (TILLING), transposon tagging, using either Tc1 or Mos1 and resequencing. These combined strategies have improved the overall throughput of the gene-knockout labs, and have broadened the types of mutations that we, and others, can identify. In this review, we will discuss these different approaches.
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Affiliation(s)
- Donald G Moerman
- Department of Zoology, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver B.C. V6T 1Z3 Canada.
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44
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Brueckner M, McGrath J, D'Eustachio P, Horwich AL. Establishment of left-right asymmetry in vertebrates: genetically distinct steps are involved. CIBA FOUNDATION SYMPOSIUM 2007; 162:202-12; discussion 212-8. [PMID: 1802643 DOI: 10.1002/9780470514160.ch12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Vertebrates exhibit a characteristic pattern of asymmetrical positioning of the visceral organs along the left-right axis. A remarkable developmental step establishes this pattern--primitive organs migrate from symmetrical midline positions of origin into lateral positions. The first organ to pursue such movement is the cardiac tube, which forms a rightward 'D' loop; other organs follow concordantly. The signals and mechanisms directing such organ migration can be studied by analysis of heritable defects of humans and mice. In general, these defects behave as loss-of-function mutations that lead to random determination of visceral situs: for an affected embryo there is an equal chance of correct situs or situs inversus. Distinct phenotypes and patterns of inheritance of these defects suggest that at least three genes are involved in left-right determination, apparently members of a developmental pathway. These genes should be amenable to molecular analysis. We are studying a recessive allele of the mouse called inversus viscerum (iv). Using linkage analysis with cloned restriction fragment length polymorphism markers, we have genetically mapped the iv gene to the distal portion of mouse chromosome 12. We are now pursuing isolation of the gene using methods of positional cloning. Analysis of the iv gene product and of its site and timing of expression may offer clues to how left-right lateralization occurs.
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Affiliation(s)
- M Brueckner
- Department of Pediatric Cardiology, Yale University School of Medicine, New Haven, CT 06510
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45
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Brenner S. The human genome: the nature of the enterprise. CIBA FOUNDATION SYMPOSIUM 2007; 149:6-12; discussion 12-7. [PMID: 2335125 DOI: 10.1002/9780470513903.ch2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of methods of cloning and sequencing DNA has liberated genetics from the constraints of breeding experiments, and all organisms are now accessible to genetical analysis by the new methods. The analysis of the human genome is likely to produce a revolution in biomedical science, and it is argued that high priority should be given to gene identification. The strategy advocated is one which identifies the expressed genes and pursues mapping in parallel.
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Affiliation(s)
- S Brenner
- MRC Molecular Genetics Unit, Cambridge, UK
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46
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Wendl MC. Algebraic correction methods for computational assessment of clone overlaps in DNA fingerprint mapping. BMC Bioinformatics 2007; 8:127. [PMID: 17442113 PMCID: PMC1868038 DOI: 10.1186/1471-2105-8-127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Accepted: 04/18/2007] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The Sulston score is a well-established, though approximate metric for probabilistically evaluating postulated clone overlaps in DNA fingerprint mapping. It is known to systematically over-predict match probabilities by various orders of magnitude, depending upon project-specific parameters. Although the exact probability distribution is also available for the comparison problem, it is rather difficult to compute and cannot be used directly in most cases. A methodology providing both improved accuracy and computational economy is required. RESULTS We propose a straightforward algebraic correction procedure, which takes the Sulston score as a provisional value and applies a power-law equation to obtain an improved result. Numerical comparisons indicate dramatically increased accuracy over the range of parameters typical of traditional agarose fingerprint mapping. Issues with extrapolating the method into parameter ranges characteristic of newer capillary electrophoresis-based projects are also discussed. CONCLUSION Although only marginally more expensive to compute than the raw Sulston score, the correction provides a vastly improved probabilistic description of hypothesized clone overlaps. This will clearly be important in overlap assessment and perhaps for other tasks as well, for example in using the ranking of overlap probabilities to assist in clone ordering.
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Affiliation(s)
- Michael C Wendl
- Genome Sequencing Center, Washington University, St. Louis, MO 63108, USA.
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47
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García-Sancho M. Mapping and sequencing information: the social context for the genomics revolution. ENDEAVOUR 2007; 31:18-23. [PMID: 17336383 DOI: 10.1016/j.endeavour.2007.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2006] [Revised: 01/25/2007] [Accepted: 01/31/2007] [Indexed: 05/14/2023]
Abstract
In 1983, after devoting some eight years of his life to the description of how a nematode worm develops from an embryo into an adult, molecular biologist John Sulston embarked on a remarkably different project: he decided to map the worm's genome. Sulston's impulsive desire to characterise this creature's DNA from start to finish offers only a partial explanation for this transition. Instead, a close examination of the wider social context for this 'moment' in molecular biology gives a more rewarding explanation of Sulston's intellectual leap. This reveals a world in which biotechnology gradually adapted to and integrated into an 'information society' increasingly dependent on the creation, distribution and manipulation of information. The application of computing to DNA during the first half of the 1980s was crucial for this integration, fostering the emergence of genomics and ultimately the Human Genome Project.
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48
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Han Y, Gasic K, Marron B, Beever JE, Korban SS. A BAC-based physical map of the apple genome. Genomics 2007; 89:630-7. [PMID: 17270394 DOI: 10.1016/j.ygeno.2006.12.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 12/15/2006] [Accepted: 12/20/2006] [Indexed: 11/25/2022]
Abstract
Genome-wide physical mapping is an essential step toward investigating the genetic basis of complex traits as well as pursuing genomics research of virtually all plant and animal species. We have constructed a physical map of the apple genome from a total of 74,281 BAC clones representing approximately 10.5x haploid genome equivalents. The physical map consists of 2702 contigs, and it is estimated to span approximately 927 Mb in physical length. The reliability of contig assembly was evaluated by several methods, including assembling contigs using variable stringencies, assembling contigs using fingerprints from individual libraries, checking consensus maps of contigs, and using DNA markers. Altogether, the results demonstrated that the contigs were properly assembled. The apple genome-wide BAC-based physical map represents the first draft genome sequence not only for any member of the large Rosaceae family, but also for all tree species. This map will play a critical role in advanced genomics research for apple and other tree species, including marker development in targeted chromosome regions, fine-mapping and isolation of genes/QTL, conducting comparative genomics analyses of plant chromosomes, and large-scale genomics sequencing.
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Affiliation(s)
- Yuepeng Han
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA
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49
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Johnson SM, Tan FJ, McCullough HL, Riordan DP, Fire AZ. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res 2006; 16:1505-16. [PMID: 17038564 PMCID: PMC1665634 DOI: 10.1101/gr.5560806] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Nucleosome positions within the chromatin landscape are known to serve as a major determinant of DNA accessibility to transcription factors and other interacting components. To delineate nucleosomal patterns in a model genetic organism, Caenorhabditis elegans, we have carried out a genome-wide analysis in which DNA fragments corresponding to nucleosome cores were liberated using an enzyme (micrococcal nuclease) with a strong preference for cleavage in non-nucleosomal regions. Sequence analysis of 284,091 putative nucleosome cores obtained in this manner from a mixed-stage population of C. elegans reveals a combined picture of flexibility and constraint in nucleosome positioning. As has previously been observed in studies of individual loci in diverse biological systems, we observe areas in the genome where nucleosomes can adopt a wide variety of positions in a given region, areas with little or no nucleosome coverage, and areas where nucleosomes reproducibly adopt a specific positional pattern. In addition to illuminating numerous aspects of chromatin structure for C. elegans, this analysis provides a reference from which to begin an investigation of relationships between the nucleosomal pattern, chromosomal architecture, and lineage-based gene activity on a genome-wide scale.
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Affiliation(s)
- Steven M. Johnson
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305-5324, USA
| | - Frederick J. Tan
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Heather L. McCullough
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5324, USA
| | - Daniel P. Riordan
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5324, USA
| | - Andrew Z. Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305-5324, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5324, USA
- Corresponding author.E-mail ; fax (650) 724-9070
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50
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Abe K, Gomi K, Hasegawa F, Machida M. Impact of Aspergillus oryzae genomics on industrial production of metabolites. Mycopathologia 2006; 162:143-53. [PMID: 16944282 DOI: 10.1007/s11046-006-0049-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Aspergillus oryzae is used extensively for the production of the traditional Japanese fermented foods sake (rice wine), shoyu (soy sauce), and miso (soybean paste). In recent years, recombinant DNA technology has been used to enhance industrial enzyme production by A. oryzae. Recently completed genomic studies using expressed sequence tag (EST) analyses and whole-genome sequencing are quickly expanding the industrial potential of the fungus in biotechnology. Genes that have been newly discovered through genome research can be used for the production of novel valuable enzymes and chemicals, and are important for designing new industrial processes. This article describes recent progress of A . oryzae genomics and its impact on industrial production of enzymes, metabolites, and bioprocesses.
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Affiliation(s)
- Keietsu Abe
- Laboratory of Enzymology, Division of Life Science, Graduate School of Agricultural Science, Tohoku University, Sendai, 981-8555, Japan.
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