The Genomic Distribution of L1 Elements: The Role of Insertion Bias and Natural Selection

LINE-1 (L1) retrotransposons constitute the most successful family of retroelements in mammals and account for as much as 20% of mammalian DNA. L1 elements can be found in all genomic regions but they are far more abundant in AT-rich, gene-poor, and low-recombining regions of the genome. In addition, the sex chromosomes and some genes seem disproportionately enriched in L1 elements. Insertion bias and selective processes can both account for this biased distribution of L1 elements. L1 elements do not appear to insert randomly in the genome and this insertion bias can at least partially explain the genomic distribution of L1. The contrasted distribution of L1 and Alu elements suggests that postinsertional processes play a major role in shaping L1 distribution. The most likely mechanism is the loss of recently integrated L1 elements that are deleterious (negative selection) either because of disruption of gene function or their ability to mediate ectopic recombination. By comparison, the retention of L1 elements because of some positive effect is limited to a small fraction of the genome. Understanding the respective importance of insertion bias and selection will require a better knowledge of insertion mechanisms and the dynamics of L1 inserts in populations

The Evolution of LINE-1 in Vertebrates

The abundance and diversity of the LINE-1 (L1) retrotransposon differ greatly among vertebrates. Mammalian genomes contain hundreds of thousands L1s that have accumulated since the origin of mammals. A single group of very similar elements is active at a time in mammals, thus a single lineage of active families has evolved in this group. In contrast, non-mammalian genomes (fish, amphibians, reptiles) harbor a large diversity of concurrently transposing families, which are all represented by very small number of recently inserted copies. Why the pattern of diversity and abundance of L1 is so different among vertebrates remains unknown. To address this issue,we performed a detailed analysis of the evolutionof active L1 in14mammalsand in3non-mammalianvertebrate model species. We examined the evolution of base composition and codon bias, the general structure, and the evolution of the different domains of L1 (50UTR, ORF1, ORF2, 30UTR). L1s differ substantially in length, base composition, and structure among vertebrates. The most variation is found in the 50UTR, which is longer in amniotes, and in the ORF1, which tend to evolve faster in mammals. The highly divergent L1familiesof lizard, frog, and fish share species-specific features suggesting that they are subjected to the same functional constraints imposed by their host. The relative conservation of the 50UTR and ORF1 in non-mammalian vertebrates suggests that the repression of transposition by the host does not act in a sequence-specific manner and did not result in an arms race, as is observed in mammals

Developing a community-based genetic nomenclature for anole lizards

Background: Comparative studies of amniotes have been hindered by a dearth of reptilian molecular sequences. With the genomic assembly of the green anole, Anolis carolinensis available, non-avian reptilian genes can now be compared to mammalian, avian, and amphibian homologs. Furthermore, with more than 350 extant species in the genus Anolis, anoles are an unparalleled example of tetrapod genetic diversity and divergence. As an important ecological, genetic and now genomic reference, it is imperative to develop a standardized Anolis gene nomenclature alongside associated vocabularies and other useful metrics. Results: Here we report the formation of the Anolis Gene Nomenclature Committee (AGNC) and propose a standardized evolutionary characterization code that will help researchers to define gene orthology and paralogy with tetrapod homologs, provide a system for naming novel genes in Anolis and other reptiles, furnish abbreviations to facilitate comparative studies among the Anolis species and related iguanid squamates, and classify the geographical origins of Anolis subpopulations. Conclusions: This report has been generated in close consultation with members of the Anolis and genomic research communities, and using public database resources including NCBI and Ensembl. Updates will continue to be regularly posted to new research community websites such as lizardbase. We anticipate that this standardized gene nomenclature will facilitate the accessibility of reptilian sequences for comparative studies among tetrapods and will further serve as a template for other communities in their sequencing and annotation initiatives.Organismic and Evolutionary BiologyOther Research Uni

The genome of the green anole lizard and a comparative analysis with birds and mammals

The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse—more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.National Science Foundation (U.S.) (NSF grant DEB-0920892)National Science Foundation (U.S.) (NSF grant DEB-0844624)National Human Genome Research Institute (U.S.

The genome of the green anole lizard and a comparative analysis with birds and mammals

The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments1. Among amniotes, genome sequences are available for mammals2 and birds3–5, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes3. Also, A. carolinensis mobile elements are very young and diverse – more so than in any other sequenced amniote genome. This lizard genome’s GC content is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds6. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations

A new species of puddle frog from an unexplored mountain in southwestern Ethiopia (Anura, Phrynobatrachidae, Phrynobatrachus)

A new species of Phrynobatrachus is described from the unexplored and isolated Bibita Mountain, southwestern Ethiopia, based on morphological characters and sequences of the mitochondrial rRNA16s. The new species can be distinguished from all its congeners by a small size (SVL = 16.8 ± 0.1 mm for males, 20.3 ± 0.9 mm for females), a slender body with long legs and elongated fingers and toes, a golden coloration, a completely hidden tympanum, and a marked canthus rostralis. The phylogenetic hypothesis based on 16s sequences places the new species as sister to the species group that includes P. natalensis, although it is morphologically more similar to other dwarf Phrynobatrachus species, such as the Ethiopian P. minutus

L1 (LINE-1) Retrotransposon Diversity Differs Dramatically between Mammals and Fish

L1 retrotransposons replicate (amplify) by copying (reverse transcribing) their RNA transcript into genomic DNA. The evolutionary history of L1 in mammals has been unique. In mice and humans ~80 million years of L1 evolution and replication produced a single evolutionary lineage of L1 elements while generating ~20% of the genomic mass in each species. By contrast, zebrafish contain \u3e30 distinct L1 lineages that have generated approximately one-tenth as much DNA. We contend that, by becoming far more permissive of interspersed repeated DNA than other organisms, mammals are conducive to competition between L1 families for replicative dominance, and that this competition, perhaps for the host factors required for L1 replication, results in a single L1 lineage

Matériaux et joints d’étanchéité pour les hautes pressions (Réédition)

pour le champs 'auteurs', les Directeurs de publications apparaissent en premier puis le Directeur de collection.International audiencePréface / Dominique Leguillon|P. 17|Introduction générale / Patrick Boissinot, Patrick Langlois, Agílio A.H. Pádua|P. 21|Introduction au dimensionnement / Agílio A.H. Pádua|1 — Définition du problème|2 — Dimensionnement|3 — Obturateurs|4 — Conclusion|P. 31|Frettage et autofrettage / Patrick Langlois|1 — Considérations préliminaires au frettage|2 — Frettage d’une enceinte bibloc|3 — Frettage d’une enceinte multibloc|4 — Formulation de l’autofrettage|5 — Modes de réalisation de l’autofrettage|6 — Conclusion|P. 55|Méthodes d’éléments finis en calcul de structures élastiques / Joël Frelat|1 — Introduction|2 — Rappel de la formule théorique|3 — Formulation variationnelle|4 — Formulation numérique|5 — Etapes d’une mise en œuvre pratique|6 — Conclusion – Extension aux problèmes non linéaires|P. 65|Les matériaux sidérurgiques et les hautes pressions / Jean-Paul Dichtel|1 — Caractérisation mécanique des aciers|2 — Métallurgie des aciers et superalliages|3 — Commentaires : la Directive Européenne Appareils à Pression|P. 77|Les métaux non ferreux – Alliage cuivre-béryllium et titane / Jean-Pierre Petitet|1 — Introduction|2 — Le cuivre-béryllium|3 — Le titane|P. 85|Les Carbures cémentés WC-Co / Emmanuel Pauty|1 — Les procédés de fabrication|2 — Les propriétés des carbures cémentés|3 — Conclusions|P. 99|Choix et usinage des carbures de tungstène / Jacques Calzas|1 — Choix des carbures de tungstène|2 — Usinage du carbure de tungstène|P. 111|Céramiques et matériaux pour l’optique / Jean-Claude Chervin|1 — Céramiques|2 — Matériaux pour l’optique|P. 141|Types de joints et de montage / Roger Argoud et Jacques Roux|1 — Introduction|2 — Généralités|3 — Joints à basse pression|4 — Joints cône sur cône|5 — Joints Bridgman Champignon|6 — Joints annulaires auto-serrés|7 — Joints coniques d’Amagat|8 — Autres joints|9 — Conclusion|P. 161|Joints hautes pressions pour la compression de gros volumes solides / Sylvie Le Floch|1 — Joints solides utilisés dans les différents types d’enceintes hautes pressions|2 — Matières premières des joints|3 — Assemblages HP-HT|P. 173|Le matériel standard / Jean-Pierre Petitet|1 — Tubes, conduites et raccords|2 — Les vannes|3 — Quelques types d’enceintes commercialisées|4 — Les générateurs de pression|5 — Le matériel moins standard|P. 187|Assemblages haute pression / Gérard Hamel|1 — Montage des raccords de pressions|2 — Montage de quelques passages électriques|3 — Les passages de thermocouple|4 — Les passages optiques, montage des fenêtres|5 — Montage des joints et des obturateurs sur une cellule haute pression|P. 197|Usinage / Jean-Pierre Michel|1 — Introduction|2 — Les joints de faible épaisseur|3 — Les bagues anti-extrusion à 45°|4 — Les joints à 45°|5 — Les joints « double Bridgman »|6 — Les joints plats en élastomères|7 — Les joints en indium (étanchéité en hélium et azote liquide|8 — Joints métal-métal type Lens ring|9 — Les passages du courant|10 — Usinage de matériaux exotiques|P. 211|Les règles de sécurité / Patrick Boissinot|1 — Dangers présentés par les appareils à pression|2 — Appareils à pression rencontrés dans les laboratoires et facteurs de risques|3 — Principes généraux de prévention et réglementation|4 — Moyens de protection|5 — Conclusio