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Bernard Dujon is Professor Emeritus at Sorbonne University, France and at the Pasteur Institute in Paris. He is a member of the French Academy of Sciences and his research focuses on eukaryotic genomes.
Georges Pelletier, agronomist and member of the French Academy of Sciences, is currently honorary research director at INRA - the French National Institute for Agriculture. His research focuses on the mechanisms of genetic exchange of cytoplasmic genomes.
Introduction ix
Chapter 1. Following Ariadne's Thread from Genetics to DNA 1
1.1. The birth of genetics 1
1.2. The foundations of a new science 5
1.3. Gene, locus and genetic maps 7
1.4. Mutagenesis: first ideas on the material nature of the gene 10
1.5. First ideas on gene products 13
1.6. The order of things and the elements of disorder 14
1.7. Dissecting the invisible: allelism, cistron and the locus again 16
1.8. The DNA trail 19
1.9. Important ideas to remember 21
1.10. References 21
Chapter 2. The Molecular Nature of Genes and Their Products 25
2.1. DNA and its replication 25
2.2. Permanence and alteration of DNA, mutations 26
2.3. Protein synthesis and the central dogma of molecular biology 28
2.4. The genetic code: how to read the genetic message 35
2.5. First paradigm of gene expression: the bacterial lactose operon 40
2.6. Reverse transcription and retrogenes 43
2.7. Exons, introns and splicing: the first complexity of RNA life 44
2.8. Sequence editing: the second complexity of RNA life 51
2.9. RNA interference and epigenetics 52
2.10. Important ideas to remember 56
2.11. References 57
Chapter 3. Chromosomes and Reproduction 61
3.1. The "true" chromosomes 61
3.2. Sexual reproduction and alternating generations 63
3.3. Meiosis 65
3.4. Genetic determinism of sex 70
3.4.1. From gametes to sex 70
3.4.2. Sex determinism in animals 71
3.4.3. Sex determinism of brown algae 74
3.5. Clonal reproduction and its derivatives 75
3.6. The genetics of organelles 77
3.6.1. In unicellular eukaryotes 78
3.6.2. In humans and animals 78
3.6.3. In plants 79
3.7. Important ideas to remember 80
3.8. References 81
Chapter 4. From Genetic Engineering to Genomics 83
4.1. Restriction of DNA 83
4.2. Recombinant DNA and the birth of genetic engineering 85
4.3. Sequencing of biological macromolecules 87
4.4. The beginnings of genomics: the very first genome sequences 91
4.5. The trigger 92
4.6. The impact of the first real genomes 93
4.7. The human genome 96
4.8. New methods of genome sequencing and the current state of genomics 98
4.9. Important ideas to remember 100
4.10. References 101
Chapter 5. Uniqueness and Polymorphism of Genomes 103
5.1. The immensity of nucleic acid sequences 104
5.2. Components of genomes and their replication 105
5.3. A little perspective on the content of genomes 109
5.4. Traces of the past and driving forces for the future 112
5.5. Genes in genomes 117
5.6. Genes and genetic determinism 120
5.7. Natural populations: pan-, core-genomes and SNP 123
5.8. Population genomics 126
5.9. The genetics of genomes 127
5.10. Important ideas to remember 128
5.11. References 129
Chapter 6. Natural Dynamics and Directed Modifications of Genomes 131
6.1. The dynamics of genomes 131
6.2. Hereditary acquisitions 134
6.2.1. Transformation by DNA and horizontal gene transfer 134
6.2.2. Primary endosymbioses of eukaryotes 136
6.2.3. Viruses and transposable elements 137
6.3. Directed manipulations of genomes: principles and tools 139
6.4. Directed manipulations of genomes: applications 144
6.5. Important ideas to remember 146
6.6. References 147
Chapter 7. Of Genes and Humans 149
7.1. Ancient DNA and human history 150
7.2. Traces of the past in today's human genome 153
7.2.1. Adaptations to the world's regions 154
7.2.2. Adaptations to lifestyles 154
7.2.3. Adaptations to diseases 155
7.2.4. Maladaptation following past selections 156
7.2.5. Conclusion 157
7.3. Traces of past climates in the trees of our forests 157
7.4. The domestication of cultivated plants 159
7.4.1. Characteristics of domestication 160
7.4.2. The mutations that enabled domestication 162
7.5. Selection of livestock 163
7.6. Conclusion 167
7.7. Important ideas to remember 168
7.8. References 169
Chapter 8. Genetics and Human Health 173
8.1. "Mendelian" and multifactorial diseases, a continuum of complexity 174
8.2. Interpretation and use of DNA sequences 175
8.3. Autism 177
8.4. Gene therapy 178
8.5. The multiple genetic causes of cancers 181
8.6. Microbiota 184
8.7. Important ideas to remember 187
8.8. References 188
Chapter 9. Now and Tomorrow 191
9.1. A living world to be further explored 191
9.2. Genome synthesis 197
9.3. New lives 200
9.4. Important ideas to remember 203
9.5. References 203
Conclusion 207
Glossary 213
References 233
Index 235
In order to make natural history a true science, we must focus ourselves to research that can reveal, not the individual and particular aspect of one animal or another, but the general process by which nature reproduces and preserves itself.
So wrote Pierre Louis Moreau de Maupertuis in 1752 (Moreau de Maupertuis 1752) more than a century before the beginning of genetics.
The natural sciences have long been interested in describing the diversity of species before considering the mystery of this commonplace feature of life that makes individuals of one species generate other individuals of the same species. While genetics met the recommendation of P. Maupertuis, the path taken by scientists to develop this science was, as we will see, more like a labyrinth than a Roman road!
In 2016, genetics turned 110 years old (Gayon 2016). This term was first introduced publicly by Bateson at the Third Conference on Plant Hybridization held in London in 19061, exactly 40 years after Mendel's publication (Mendel 1866), which had been poorly distributed and very generally misunderstood because it represented a methodological and conceptual break with everything that had existed before. However, in the century preceding Mendel's work, botanists and horticulturists observed many offspring of plant crosses. Thomas A. Knight, at the end of the 18th Century in England, crossed pea varieties differing in seed and leaf colors and observed their offspring, but without having the idea of counting the different types obtained. In France, by hybridizing melons differing by several characters, Augustin Sageret in the 1820s had the first intuition concerning the discontinuous nature of heredity, in opposition to the vision of heredity by mixing, like two fluids, the dominant idea of the time. He wrote:
It appeared to me that, in general, the similarity of the hybrid to its two ancestors does not consist in an intimate fusion of the various characters specific to each, but rather in an equal or unequal distribution of these same characters.
At the beginning of his memoir, Mendel (see Box 1.1) justifies the literally "monastic" work that he had done during the eight preceding years by the desire "to follow up the developments of hybrid progenies" in ornamental plants. The first part of the memoir on pea hybrids (Pisum sativum) is a real experimental demonstration that ends with a kind of theorem:
Hybrids produce ovular and pollen cells that correspond in equal number to all constant forms resulting from the combination of traits brought together by fertilization [which produced this hybrid].
In other words, the stated rule is simple: a hybrid that has received from one parent the form "A" and from the other the form "a" of a given character, will produce gametes* "A" and "a" in equal numbers, A and a being mutually exclusive in these gametes, hence their name "allelomorphs2". This law is currently known as the "law of purity of gametes" or "Mendel's First Law". He continued:
This proposal provides a sufficient explanation of the diversity of forms in the descendants of hybrids as well as of the numerical relationships we observe between them.
Indeed, this simple equality explains the different types of plants and their proportions in the progeny of the pea hybrids that he had produced either by self-fertilization or by back-crossing with each of their parents3. Mendel systematically found the same proportions for the seven differential traits he followed, for which there are two contrasting states and only two, such as two colors (yellow/green) or two seed shapes (smooth/wrinkled), two pod shapes (uniform/strained), two plant sizes (high/dwarf), etc.
Gregor Johann Mendel was born on July 20, 1822, on the family farm in Heinzendorf in what is now the Czech Republic. He received elementary education in the village school where the teacher encouraged his parents to make him continue his studies in high school, which he did excellently from 1834 to 1840. In 1838, the family situation became more precarious after a serious accident prevented his father from working. However, Mendel continued his studies at the Institute of Philosophy in Olomouc for two years, then entered the monastery of Saint Thomas in Brno (Order of Saint Augustine) as a monk in the hope of becoming a teacher by completing his training at the monastery's expense. He was admitted to the novitiate in 1843, chosing Gregor as a first name, before being ordained priest in 1847, appointed parish priest in 1848 and assistant professor in 1849. In 1851, he went to study mathematics and physics at the Vienna Institute of Physics (Christian Doppler) and deepen his knowledge of entomology, paleontology, botany and plant physiology. Upon his return to Brno in 1854, he began his experiments on plant hybrids while teaching natural sciences and physics. The city of Brno and its monastery, then ruled by Abbot Napp, offered a particularly rich intellectual environment. In particular, the monastery was engaged in reflections on heredity, with objectives of application to sheep breeding and to the orchards of its domains.
Mendel had been interested in gardening and flowers since childhood. For example, he produced a variety of fuchsia that bears his name, and an original variety of peas from his hybridizations. He made crosses of pear, apple and cherry trees for the monastery's orchards and even obtained a medal for his stone fruit varieties. He bred white and gray mice and crossed them to follow the heredity of coat color, a task he could not pursue within the monastery. Throughout his life, he was fascinated by bees, practicing beekeeping and their selection. He had a strong reputation in the country as a meteorologist, taking an interest in sunspots and taking precise and regular measurements until the day before his death. He had the opportunity to travel, going to Paris and London in 1862 (without being able to meet Darwin, absent at the time), to Germany, to the Alps, and to visit the Pope in Rome.
In 1868, he was appointed abbot at the head of the monastery, and recognized as an excellent teacher, an esteemed botanist and a highly valued citizen in the city of Brno. Part of his activity consisted in managing and inspecting the different dependences of the monastery. He had disputes with the government that was trying to tax monastic property. He was a member of many learned societies, curator of the Institut des sourds et muets (an institute for the deaf and mute) and, towards the end of his life, President of the Moravian Mortgage Bank. He died on January 6, 1884, as a result of kidney disease. His funeral was attended by a large crowd, paying tribute to a man highly appreciated by his fellow citizens, but unaware of his scientific contribution to biology. His successor at the head of the monastery burned his archives.
Often cited by other scientists as early as 1867, his demonstrations were generally misunderstood until the early 20th Century.
We now know that this rule corresponds to the mechanism of this particular cell division called meiosis* that halves the number of chromosomes to form gametes (see Chapter 3). In Mendel's time, the existence of chromosomes was unknown. They were described in 1875 by Eduard Strasburger (Strasburger 1875) and named in 1888 by Heinrich-Wilhelm Waldeyer-Hartz (Waldeyer 1888). Walther Flemming (Flemming 1879) described their movement and distribution between the two daughter cells during mitosis* in 1879, but it was Edouard Van Beneden who, in the Parascaris equorum nematode, first described meiosis in 1883 (Van Beneden 1883). The individuality and continuity of chromosomes during development were demonstrated by Theodor Boveri between 1887 and 1902, and it was in 1903 that Walter S. Sutton (Sutton 1903), explicitly linked the distribution of chromosomes during meiosis in a grasshopper (Brachystola magna) to Mendel's rule: chromosomes are distributed in pairs (like pairs of stockings!) before meiosis, and a gamete retrieves one from each pair. For a given pair, there will therefore be as many gametes possessing one member as gametes possessing the other, exactly like Mendel's A and a factors. The gametes, in turn, after fertilization*, will reproduce an organism with the initial number of chromosomes. This is how the chromosomal theory of heredity developed, offering the first materialization on which relied, as it was said at the time, the "power to transmit some particular traits of the parents to the progenies, in addition to the characteristics of the species".
Defined at the time by Wilhelm Johannsen as "the science of the propagation of life", or "the science of the fixed elements that compose organisms", genetics was to be officially born in 1900 after the rediscovery of Mendel's work by three botanists, Hugo de Vries, Carl Correns and Erich Von Tschermak, working independently on different plant species (Campbell 1980). What became known as "Mendelism" was confirmed in mice, for coat characteristics, by Lucien Cuénot as early as 1902 (Cuénot 1902), and in...
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