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Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes

Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes

Carine Genet 1* , Patrice Dehais 2,3 , Yniv Palti 4 , Guangtu Gao 4 , Frederick Gavory 5 , Patrick Wincker 5 , Edwige Quillet 1 and Mekki Boussaha 1 Abstract Background: Rainbow trout (Oncorhynchus mykiss) are cultivated worldwide for aquaculture production and are widely used as a model species to gain knowledge of many aspects of fish biology. The common ancestor of the salmonids experienced a whole genome duplication event, making extant salmonids such as the rainbow trout an excellent model for studying the evolution of tetraploidization and re-diploidization in vertebrates. However, the lack of a reference genome sequence hampers research progress for both academic and applied purposes. In order to enrich the genomic tools already available in this species and provide further insight on the complexity of its genome, we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their contents.
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SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping

SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping

Background Single-Nucleotide Polymorphisms (SNPs) are the most frequent type of variation found in DNA [1]. As EST databases and whole genome sequences grow in avail- ability, SNPs have become the most abundant and powerful polymorphic codominant markers that can be selected all along the genome [2]. SNPs allow the imple- mentation of very dense genetic linkage maps in animals and plants [3-5]. Moreover, SNPs are generally consid- ered to have a high identity by descent rate, and thus, they are very useful for genetic association studies [6,7]. The actual array methodologies for the high throughput genotyping of SNPs are built upon the principle of mea- suring the relative signal strength of two expected alleles [8,9] and require the use of oligonucleotides correspond- ing to the direct flanking regions of the SNPs. This should present some limitations for germplasm genetic studies. The primary limitation is that the revealed genetic organization of the genotyped germplasm is strongly dependent on the discovery panel [10-15]. This ascertainment bias is particularly noted when SNPs are selected from only one sequenced heterozygous geno- type, as proposed in Vitis vitifera L. from the whole gen- ome sequence of the cultivar ‘Pinot Noir’[16]. Moreover, unexpected alleles may exist at any polymorphism. These unknown or ‘null’ alleles can interfere with accu- rate genotyping of the expected alleles, potentially impacting genetic studies in a negative manner [17]. The frequency of these alleles should increase when working with wider genetic distances between the geno- typed samples and the discovery panel. A recent review [18] analyzed the importance of the discovery panel and SNP mining methods for genetic studies on plant and animals.
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Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B

Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B

BES are a valuable source of chromosome-specific markers for repetitive genomes BES were analysed as a source of new molecular markers for genetic, cytogenetic and physical mapping in wheat. The complete set of sequences was first searched for single-se- quence repeats (SSRs) that potentially could be converted into new markers. We identified 1942 perfect repeats of one to four nucleotide motifs, corresponding to a mean density of one SSR per 5.6 kb. Of these, 166 (8.5%) harboured mononucleotide motifs, whereas 324 (16.7%), 943 (48.6%) and 515 (26.5%) had dinucleotide, trinucleotide and tetra- nucleotide motifs, respectively. The most abundant motif (14.8%) was the trinucleotide AAG. Interestingly, previous FISH experiments with SSR had shown that the AAG microsatellite is highly represented on the seven chromo- somes of the B-genome of hexaploid wheat (Cuadrado et al., 2000), supporting the assumption that the sequence data from chromosome 3B are representative of the B-genome. From the 1942 SSRs detected, 176 (41 with mononucleotide; 79 with dinucleotide; 33 with trinucleotide; 23 with tetranu- cleotide motifs), which originated mainly from low copy sequences, were selected for primer design. More than 80% of the primer pairs gave an amplification product on at least one of the five hexaploid wheat varieties that have been used as parents in different mapping populations (Chinese Spring, Courtot, Renan, Synthetic W7984 and Opata 85), and 45% of the products exhibited polymorphism between at least two varieties (data not shown). About one-third (36%) of the SSRs were mapped to a single locus in one of the 3B deletion bins (Endo and Gill, 1996) without ambiguity. These data indicate that BAC-end sequences represent a potential source of new SSR markers for mapping in wheat. However, BES-derived SSRs are not as good, in terms of polymorph- ism, as microsatellites originating from enriched genomic libraries (reviewed by Gupta and Varshney, 2000) or EST
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A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R

A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R

the predicted gene numbers in other plants. Most recent estimate for gene number in A. thaliana genome is 33,000 (TAIR8 release) [38], the current TIGR rice genome anno- tation (Release 5) [39] estimates 41,000 genes in rice genome. Both numbers are close to our prediction for rye. In addition to the analysis of the rye genome composi- tion, we used BAC end sequences for marker develop- ment. There is still a low density of markers available for rye genome and additional markers are urgently needed. Development of a genetic linkage map of rye with 183 markers was reported by Korzun et al. [40]. Bednarek et al. [41] presented a genetic map of rye containing 480 mark- ers including 200 RFLPs, 179 AFLPs, 88 RAPDs and 13 proteins. Khlestkina et al. [42] mapped 99 SSRs derived from EST sequences (SSR-ESTs), nine of which mapped to chromosome 1R. Several attempts were made to transfer SSR and/or EST-SSR markers from wheat and barley into rye [43-45]. Recently Varshney et al. [46] succeeded in transferring and mapping 12 barley SNP markers in rye. Thus, to date the density of markers is quite low and does not allow efficient map based cloning or MAS in rye. This work presents a method for targeted development of molecular markers from specific parts of the rye genome using the 1RS chromosome arm as a case study. Until now, there are only a few markers available for this critical part of the rye genome. This hampers marker assisted breeding not only in rye, but also in wheat where the markers from 1RS would permit selection of lines with introgressions of desired parts of 1RS without the harmful genes. We have developed twelve new ISBPs markers for 1RS and designed almost 200 additional primer pairs for potential ISBP markers that remain to be tested. If needed, generation of additional BAC end sequences from 1RS is possible. In addition to the development of new ISBP markers, BES containing microsatellites were used to develop new 1RS-specific SSR markers. Out of the 63 tested microsatellites that were tested, 21 were specific for 1RS [47]. Thus, in total 33 1RS-specific markers were obtained using our strategy. On the other hand, Badnarek et al. [41] isolated 198 AFLP and RAPD markers from genomic DNA and only 29 markers were specific for 1RS. This clearly demonstrates the efficiency of the targeted approach.
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Improving the assembly of Botrytis cinerea genome using a genetic map and a BAC ends sequences library

Improving the assembly of Botrytis cinerea genome using a genetic map and a BAC ends sequences library

1 INRA, Biologie et Gestion des Risques en Agriculture - Champignons Pathogènes des Plantes, 78850 Thiverval-Grignon, France. 2 CIRAD - INRA - SupAgro, Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France. In the context of the sequencing and assembly of strain T4, a genetic map has been built. A crossing between strain T4 and strain 32 (kindly provided by Caroline Kunz) gave 68 usable progeny. About 134 polymorphic microsatellite markers were selected, mainly at the ends of the scaffolds built during the sequencing project (118 main scaffolds called SuperContigs or SuperSuperContigs), by using the GRAMENE and FONZIE software to find the microsatellites and the minisatellites sequences (1,2). The primers, bounding these markers, were designed with PRIMER3 (3) and the products separated by size directly on agarose gels or by using an adapted M13 fluorescent technology. From a collection of 140 SNPs devoted to Botrytis population studies, about 62 SNPs were found polymorphic in the T4X32 crossing and were also used in the constitution of this map. The genetic linkage groups were constructed by using MAPMAKER (4). The total length of the scaffolds appearing in the genetic map covered 31.8 Mbp, representing about 80% of the T4 sequence assembly (5). The use of an extra BAC end sequences library made in T4 permit to add information in the constitution of bigger scaffolds, often reinforced by linkage groups representing up to 87% of the total sequences produced with strain T4. This reduced the number of groups of sequences to 32 which leads closer to the 16 chromosomes described in this species (6). Only two scaffolds bt4_SupSuperContig_114_320_122_1 and bt4_SuperContig_29_1 seemed to be misassembled as pointed out by the BAC ends and the genetic data. This set of genetic markers has also shown to be useful in localizing fungicide resistance genes (7) or spontaneous mutations like the lack of sclerotia formation in strain T4.
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Regular sequences and synchronized sequences in abstract numeration systems

Regular sequences and synchronized sequences in abstract numeration systems

Regularity can be defined in numeration systems generalizing integer bases. See for instance [1, 10, 11, 15, 23, 27] for work on the matter. The most general setting in this area is given by the so-called abstract numeration systems [22]. An abstract numeration system S is a triple (L, A, <) where L is an infinite regular language over a totally ordered alphabet (A, <). The numeration language L is ordered thanks to the radix (or genealogi- cal) order induced by <. Any non-negative integer n is then represented by the n-th word of the language. This family of numeration systems includes the usual integer bases and more generally, any positional numeration system having a regular numeration language. Maes and Rigo [27] extended (b, K)-regular sequences to abstract numeration systems S by generalizing the notion of b-kernel to that of S-kernel. However, this definition is not satisfying for it does not allow us to generalize most characterizations of (b, K)-regular sequences.
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End-to-End Encrypted Messaging Protocols: An Overview

End-to-End Encrypted Messaging Protocols: An Overview

mainstream IM clients relies on it yet. The website lists 17 clients and 6 servers using Matrix.org. 8 The Signal Protocol, the non-federated protocol developed in 2013 by Open Whisper Systems, provides end-to-end encryption for groups. Moxie Marlinspike, the co-author of Signal, was inspired with some OTR features, such as the idea of ephe- meral key exchange [7], but also added additional security features such as future secrecy, support for asynchronous messaging and group messaging, going above and beyond OTR by allowing also clients to be offline. The Signal Protocol uses the “Axolotl” keyratchet for initial key exchange and the ongoing renewal and mainten- ance of short-lived session keys, so there is not only no long-term key that can be compromised. This provides forward secrecy so that the compromise of a short-term key does not compromise past keys (so that an adversary can decrypt past messages) as well as “backwards secrecy” (also called “future secrecy”) so that the compromise of a key does not endanger future messages. It could be a standard, but is not yet rec- ognized as such. The Signal protocol is said to be widely used in mobile messaging applications such as Signal (formerly TextSecure and RedPhone), WhatsApp 9 , Secure Chat (by GData). Silent Circle uses a version of the Signal Protocol since 2015 in its Silent Phone. Recently Facebook announced the implementation of Signal Protocol for their Messenger 10 . The first step towards “standardization” of the Signal Protocol so far has been the creation of OMEMO.
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VNET: Towards End-to-End Network Cloudification

VNET: Towards End-to-End Network Cloudification

Cloud solutions such as computing and storage services wit- nessed a wide adoption. In fact, the cloud offered highly elastic environments with auto-configuration and auto-adaptability capabilities. However, the cloud is limited actually to the infrastructure, platform, and software as a service models. The natural following step is to ”cloudify” also the networks to provide an end-to-end solution and add the Network as a Service (NaaS) model. In recent years, Software Defined Networks (SDN) started to emerge. The latter concept focuses on virtualizing the control functions of network equipment and has lead to a new research field named ”Network Functions Virtualization” (NFV). NFV promises to make networks work based on the same scale-based, cheap, general purpose hard- ware used in current cloud infrastructure. While these ideas look obvious and appealing, they are far from being easy to realize. Most of the obstacles to make them reality are yet to be understood and solved.
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End-to-End Automation of 5G Networks

End-to-End Automation of 5G Networks

The article “An End-to-End Automation Framework for Mobile Network Testbeds” by A. D. Zayas et al. describes the end-to-end automation framework developed as part of the TRIANGLE project. The TRIANGLE project is devoted to the benchmarking of apps and devices in mobile networks. For that purpose, it is needed to ensure the repeatability in the behaviour of all the components of the mobile network during the execution of the same test. This is why one of the main objectives of the project was to develop an end-to-end automation framework to provide repeatable testing. The paper describes in detail the design and the implementation of the framework.
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Le projet Feedbacks 1er Bac de l’ULiège en perspective

Le projet Feedbacks 1er Bac de l’ULiège en perspective

• axé autour d’un thème porteur : promouvoir et développer les pratiques de feedbacks formatifs adaptées dans des cours de 1er Bac de mêmes filières • inscrit dans une logique d’« Ancrage Facultaire » et de partenariat étroit avec les enseignants sur le terrain

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End-to-End Automatic Speech Translation of Audiobooks

End-to-End Automatic Speech Translation of Audiobooks

(3) contrary to [3], in both BTEC and LibriSpeech settings, best AST performance is observed when a symbolic sequence of symbols in the source language is used as an intermedi- ary representation during the speech translation process (cas- caded system); (4) finally, the AST results presented on Lib- riSpeech demonstrate that our augmented corpus is useful, al- though challenging, to benchmark end-to-end AST systems on real speech at a large scale. We hope that our baseline on Augmented LibriSpeech will be challenged in the future.

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d3 4 sequences

d3 4 sequences

Sequences A geometric progression (G.P.) is a sequence in which each term after the first is formed by multiplying the preceding term by a fixed number, called the common ratio. If a 1 is the first term and r is the common ratio, the nth term is: a n = a 1 r n-1 . Exercise:

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Le bac à sable, un espace pour jouer et apprendre des notions de programmation

Le bac à sable, un espace pour jouer et apprendre des notions de programmation

Cette partie nous amène à décrire assez succinctement les grandes caractéristiques de Minecraft puis de les illustrer avec des copies d’écran. Minecraft est un jeu de type « bac à sable ». Selon un wiki [ 3 ] consacré à ce jeu, il n’y aurait pas de but particulier à atteindre ni une façon de finir une partie. Cependant, à titre d’exemple, il est indiqué au joueur qu’« un jour dans Minecraft ne dure que 10 minutes » et durant le premier jour, il est conseillé de construire un abri pour se protéger des créatures hostiles qui apparaissent durant la nuit.

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Translates of M-sequences

Translates of M-sequences

L’accès à ce site Web et l’utilisation de son contenu sont assujettis aux conditions présentées dans le site LISEZ CES CONDITIONS ATTENTIVEMENT AVANT D’UTILISER CE SITE WEB. Report (Nati[r]

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d3 23 sequences

d3 23 sequences

The minimal number of moves required to solve a Tower of Hanoi puzzle is 2 n  1 , n being the number of disks. 1) Can you find a solution for 3 disks? 2) According to an ancient Indian prophecy, solving a Towers of Hanoi puzzle with 64 disks will lead to the end of the world.

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d3 5 sequences

d3 5 sequences

The first part of this page is a summary that can be useful to do the exercises. Sequences A sequence is called an arithmetic progression where each term (except the first term) is obtained by adding a constant, called the common difference, to the previous term. If the first term is denoted by a and the common difference is d , then the arithmetic progression is a  ( a  d )  ( a  2 d )  ... , the n th term is given by

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End-to-End Probabilistic Ego-Vehicle Localization Framework

End-to-End Probabilistic Ego-Vehicle Localization Framework

3 O VERALL LOCALIZATION ALGORITHM In this work, we present an end-to-end algorithm for ego localization as highlighted on Figure 1 . The algorithm is intentionally divided into three modules: Road-level local- ization (RLL), Ego-lane level localization (ELL) and Lane level localization (LLL). This split allows us to be in phase with the current literature. Moreover, the pipeline of the algorithm allows to have modular algorithms that can be changed in the future without changing the entire algorithm architecture. In the following, we will first introduce our map-matching module based on OSM datasets, then we will use this map as a prior for our ego-lane marking detection in order to locate the vehicle within its lane. Once the ego- lane level localization is performed, we will proceed to the identification of the ego-lane in the road.
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S'ORIENTER EN LICENCE APRÈS UN BAC TECHNOLOGIQUE

S'ORIENTER EN LICENCE APRÈS UN BAC TECHNOLOGIQUE

UNE LICENCE DANS LA CONTINUITÉ DE LA TERMINALE Quasiment tous les lycéens de série technologique de l’académie de Créteil ont utilisé l’ap- plication APB pour s’orienter après le bac (91 %). En cela, leur comportement est très proche de celui des élèves de terminale générale (92 %). En revanche, ils se démarquent quant à leur premier vœu d’orientation : un peu moins de la moitié envisage une orientation en STS (section de technicien supérieur) alors que moins de 10 % des lycéens généraux formulent ce souhait ↘ Tableau 2 . Ils se distinguent également des élèves de terminale de séries pro- fessionnelles, qui d’une part sont moins nombreux à utiliser APB (60 %), et d’autre part sou- haitent plus fréquemment intégrer une STS (les trois quarts). En ce qui concerne l’orientation privilégiée en licence, un peu moins du quart des élèves en terminale technologique l’envi- sagent ; comparativement, ce vœu est placé en tête pour un peu moins de la moitié des élèves de série générale et un élève de série professionnelle sur sept.
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Le plan complexe au bac S

Le plan complexe au bac S

Faire des mathématiques … avec GéoPlan Page 9 /9 Plan complexe 12 Bac S Amérique du Nord 1999 - EXERCICE 2 : candidats n'ayant que l'enseignement obligatoire Le plan orienté est rapporté au repère orthonormal direct (O, , ), l’unité graphique étant 4 cm. On considère les points A0 , A 1 , d'affixes respectives : a 0 = l ; a 1 = .

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trinome bac pro fiche1

trinome bac pro fiche1

Sélectionnez l’objet et avec clic droit sur votre souris une fenêtre apparaît.. En choisissant Propriétés… une autre fenêtre apparaît?[r]

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