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Description of the topic. Geographical distribution, historical occurrences, and human activity are some of the variables that affect the genetic diversity of Pinus species. Understanding these patterns is critical for conservation efforts and for adapting forest management strategies to climate change.Objectives. The contrasting levels of genetic diversity among Pinus species underscore the importance of species-specific approaches in conservation and management programs. DNA barcoding is an effective method for identifying diverse plant species across taxa and ecosystems. Method. In this study, Pinus species were classified, and their geographical distribution was studied in the Al-Jabel Al-Akhdar region, growing at different altitudes in natural forests and afforested. The anatomical composition of the wood was examined, including tracheid wall thicknesses, latewood thickness, ray parenchyma area, number of resin ducts, ray height, and fiber length. Additionally, DNA barcoding was conducted using rbcL primers.Results. The results of the cross-sectional examination of the wood of Pinus species showed significant differences among the species. However, the ray parenchyma area showed no significant differences among the species. Chloroplast rbcL regions were used as barcode markers to identify 10 Pinus plants. The results highlight the need for an advanced DNA barcode reference library with broad species coverage for accurate species identification.Conclusions. This study not only provides insights into the diversity and taxonomy of Pinus but also contributes to the ongoing conservation of Pinus resources and supports sustainable resource management in the region. DNA barcoding technology is critical for taxonomy and biodiversity studies because it allows rapid and accurate species identification in forests. Diversité génétique et anatomie des pins d’Al-Jabal Al-Akhdar, Libye : une approche par code-barres ADNDescription du sujet. La distribution géographique, les occurrences historiques et l’activité humaine font partie des variables qui influencent la diversité génétique des espèces de Pinus. Comprendre ces schémas est essentiel dans les efforts de conservation et pour adapter les stratégies de gestion forestière aux changements climatiques.Objectifs. Les niveaux contrastés de diversité génétique entre les espèces de Pinus soulignent l’importance d’approches spécifiques à chaque espèce dans les programmes de conservation et de gestion. Le code-barres ADN constitue une méthode efficace pour identifier diverses espèces végétales à travers les taxons et les écosystèmes.Méthode. Dans cette étude, les espèces de Pinus ont été classifiées et leur distribution géographique a été étudiée dans la région d’Al-Jabel Al-Akhdar où elles poussent à différentes altitudes dans des forêts naturelles et reboisées. La composition anatomique du bois a été examinée, notamment l’épaisseur des parois des trachéides, l’épaisseur du bois final, la surface du parenchyme des rayons, le nombre de canaux résinifères, la hauteur des rayons et la longueur des fibres. De plus, le code-barres ADN a été réalisé à l’aide des amorces rbcL.Résultats. Les résultats de l’examen en coupe transversale du bois des espèces de Pinus ont montré des différences significatives entre les espèces. Cependant, la surface du parenchyme des rayons ne présentait pas de différences significatives entre elles. Les régions chloroplastiques rbcL ont été utilisées comme marqueurs de code-barres pour identifier 10 plants de Pinus. Les résultats soulignent la nécessité de disposer d’une bibliothèque de référence avancée de codes-barres ADN couvrant un large éventail d’espèces pour une identification précise des espèces.Conclusions. Cette étude ne fournit pas seulement des éclaircissements sur la diversité et la taxonomie du Pinus mais elle contribue également à la conservation continue des ressources en Pinus et soutient la gestion durable des ressources dans la région. La technologie du code-barres ADN est essentielle pour les études de taxonomie et de biodiversité car elle permet une identification rapide et précise des espèces forestières.

Polymorphisms in the mitochondrial DNA polymerase gamma (POLG) have been speculated to be associated with male infertility. The main objective of our study was to assess the possible association of CAG repeat polymorphism in POLG1 gene and male infertility in Algerian population. Genomic DNA from 89 infertile men and 84 controls was extracted using salting-out method . CAG repeat polymorphism was analyzed by the automated direct sequencing protocol. Statistical analysis was performed by Epi-info® (v6.0) software. A significant association with male infertility was found for CAG repeat polymorphism in heterozygous genotypes (10/ ≠ 10 vs 10/10: OR = 2.00 [0.99 - 4.05], p = 0.03; \"infertile vs control groups\"; 10/≠10 vs 10/10: OR = 3.75 [1.20-11.96], p=0.01 \"oligoasthenoteratospermic group\"). Also, the results showed a significant association between the morbid allele (≠10) and male infertility (2.07 [01.07 - 04.02], p = 0.01). Our results showed that POLG1 CAG repeat polymorphism might be a risk factor for male infertility in Algerian population. Investigations with larger sample sizes and representative population-based cases and matched controls are needed to validate our results.(Afr J Reprod Health 2021; 25[1]: 67-75). Les polymorphismes de l'ADN polymérase gamma mitochondriale (POLG) ont été supposés être associés à l'infertilité masculine. L'objectif principal de notre étude était d'évaluer l'association possible du polymorphisme de répétition CAG dans le gène POLG1 et l'infertilité masculine dans la population algérienne. L'ADN génomique de 89 hommes stériles et 84 témoins a été extrait en utilisant la méthode de salting-out. Le polymorphisme de répétition CAG a été analysé par le protocole de séquençage direct automatisé. L'analyse statistique a été réalisée par le logiciel Epi-info® (v6.0). Une association significative avec l'infertilité masculine a été trouvée pour le polymorphisme de répétition CAG dans les génotypes hétérozygotes (10 / ≠ 10 vs 10/10: OR = 2,00 [0,99 -4,05], p = 0,03; «infertiles vs groupes témoins»; 10 / ≠ 10 vs 10/10: OR = 3,75 [1,20-11,96], p = 0,01 «groupe oligoasthénotératospermique»). De plus, les résultats ont montré une association significative entre l'allèle morbide (≠ 10) et l'infertilité masculine (2,07 [1.07-4.02], p = 0.01). Nos résultats ont montré que le polymorphisme répété de POLG1 CAG pourrait être un facteur de risque d'infertilité masculine dans la population algérienne. Des enquêtes avec des échantillons de plus grande taille et des cas représentatifs basés sur la population et des témois appariés sont nécessaires pour valider nos résultats.(Afr J Reprod Health 2021; 25[1]: 67-75).

Background The Fagaceae family comprises about 1,000 woody species worldwide. About half belong to the Quercus family. These oaks are often a source of raw material for biomass wood and fiber. Pedunculate and sessile oaks, are among the most important deciduous forest tree species in Europe. Despite their ecological and economical importance, very few genomic resources have yet been generated for these species. Here, we describe the development of an EST catalogue that will support ecosystem genomics studies, where geneticists, ecophysiologists, molecular biologists and ecologists join their efforts for understanding, monitoring and predicting functional genetic diversity. Results We generated 145,827 sequence reads from 20 cDNA libraries using the Sanger method. Unexploitable chromatograms and quality checking lead us to eliminate 19,941 sequences. Finally a total of 125,925 ESTs were retained from 111,361 cDNA clones. Pyrosequencing was also conducted for 14 libraries, generating 1,948,579 reads, from which 370,566 sequences (19.0%) were eliminated, resulting in 1,578,192 sequences. Following clustering and assembly using TGICL pipeline, 1,704,117 EST sequences collapsed into 69,154 tentative contigs and 153,517 singletons, providing 222,671 non-redundant sequences (including alternative transcripts). We also assembled the sequences using MIRA and PartiGene software and compared the three unigene sets. Gene ontology annotation was then assigned to 29,303 unigene elements. Blast search against the SWISS-PROT database revealed putative homologs for 32,810 (14.7%) unigene elements, but more extensive search with Pfam, Refseq_protein, Refseq_RNA and eight gene indices revealed homology for 67.4% of them. The EST catalogue was examined for putative homologs of candidate genes involved in bud phenology, cuticle formation, phenylpropanoids biosynthesis and cell wall formation. Our results suggest a good coverage of genes involved in these traits. Comparative orthologous sequences (COS) with other plant gene models were identified and allow to unravel the oak paleo-history. Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 52,834 SSRs and 36,411 SNPs. All of these are available through the Oak Contig Browser http://genotoul-contigbrowser.toulouse.inra.fr:9092/Quercus_robur/index.html . Conclusions This genomic resource provides a unique tool to discover genes of interest, study the oak transcriptome, and develop new markers to investigate functional diversity in natural populations.

Legumes are members of the family Fabaceae or Leguminosae and include economically important grain legumes, oilseed crops, forage crops, shrubs, and tropical or subtropical trees. Legumes are a rich source of quality protein for humans and animals. They also enrich the soil by producing their own nitrogen in symbiosis with nitrogen-fixing bacteria. International centers and national institutes collect, maintain, distribute, and produce high-yielding legumes (grain-pulses, oilseeds, forages, nutraceuticals, medicinal shrubs, and trees). Legume breeders are confined within the primary gene pools (GP-1) in their varietal improvement programs and have not exploited secondary gene pools (GP-2), tertiary gene pools (GP-3), or quaternary gene pools (GP-4). Legumes are also an excellent source of timber, medicine, nutraceuticals, tannins, gums, insecticides, resins, varnish, paints, dyes, and eco-friendly by-products such as soy diesel. Three forage crops, Medicago truncatula, Lotus japonicus, and Trifolium pratense, are model legumes for phylogenetic studies and genome sequencing. This paper concludes that a “protein revolution” is needed to meet the protein demands of the world.

Brachypodium is well suited as a model system for temperate grasses because of its compact genome and a range of biological features. In an effort to develop resources for genome research in this emerging model species, we constructed 2 bacterial artificial chromosome (BAC) libraries from an inbred diploid Brachypodium distachyon line, Bd21, using restriction enzymes HindIII and BamHI. A total of 73 728 clones (36 864 per BAC library) were picked and arrayed in 192 384-well plates. The average insert size for the BamHI and HindIII libraries is estimated to be 100 and 105 kb, respectively, and inserts of chloroplast origin account for 4.4% and 2.4%, respectively. The libraries individually represent 9.4- and 9.9-fold haploid genome equivalents with combined 19.3-fold genome coverage, based on a genome size of 355 Mb reported for the diploid Brachypodium, implying a 99.99% probability that any given specific sequence will be present in each library. Hybridization of the libraries with 8 starch biosynthesis genes was used to empirically evaluate this theoretical genome coverage; the frequency at which these genes were present in the library clones gave an estimated coverage of 11.6- and 19.6-fold genome equivalents. To obtain a first view of the sequence composition of the Brachypodium genome, 2185 BAC end sequences (BES) representing 1.3 Mb of random genomic sequence were compared with the NCBI GenBank database and the GIRI repeat database. Using a cutoff expectation value of E < 10(-10), only 3.3% of the BESs showed similarity to repetitive sequences in the existing database, whereas 40.0% had matches to the sequences in the EST database, suggesting that a considerable portion of the Brachypodium genome is likely transcribed. When the BESs were compared with individual EST databases, more matches hit wheat than maize, although their EST collections are of a similar size, further supporting the close relationship between Brachypodium and the Triticeae. Moreover, 122 BESs have significant matches to wheat ESTs mapped to individual chromosome bin positions. These BACs represent colinear regions containing the mapped wheat ESTs and would be useful in identifying additional markers for specific wheat chromosome regions.

Aporocotyle mariachristinae n. sp. and A. ymakara Villalba & Fernández, 1986 were collected from the bulbus arteriosus and ventral aorta of pink cusk-eels, Genypterus blacodes (Forster, 1801) from Patagonia, Argentina. A. mariachristinae n. sp. can be distinguished from all the species of Aporocotyle by the asymmetrical extension of posterior caeca (right posterior caecum longer, terminating at the area between mid-level of ovary and posterior body end; left posterior caecum shorter, terminating at the area between mid-level of cirrus sac and posterior to reproductive organs), the distribution of spines along the ventro-lateral body margins and the number of testes. The new species clearly differs from A. ymakara, from the same host species, in the esophagus / body length ratio, the absence of distal loops at caeca, the anterior caeca / posterior caeca length ratio, and the number of testes. Additionally, in A. ymakara the left posterior caecum may be longer than right posterior caecum, while in the new species left posterior caecum is always shorter. The specimen of A. ymakara collected from Argentina is also described. We also provide observations of the distribution of spines in different species of Aporocotyle, including new specimens of A. argentinensis Smith, 1969 from Merluccius hubbsi Marini, 1933. Molecular sequence data obtained from partial 18S and 28S rDNA regions were compared between the new species and other two species of Aporocotyle (A. argentinensis and A. spinosicanalis Williams, 1958). This is a new locality record for A. ymakara, extending the known geographical distribution for this species from Chile to Argentina, and the first report of two species of Aporocotyle in the same host species and locality. Les espèces Aporocotyle mariachristinae n. sp. et A. ymakara Villalba & Fernández, 1986 ont été prélevées sur le bulbe artériel et l’aorte ventrale d’abèches roses Genypterus blacodes (Forster, 1801) de Patagonie, Argentine. A. mariachristinae n. sp. se distingue de toutes les autres espèces d’Aporocotyle par la prolongation asymétrique de son caecum postérieur (le caecum postérieur droit est plus long et s’achève à un endroit situé à mi-hauteur entre l’ovaire et l’extrémité postérieure du corps ; le caecum postérieur gauche est moins long et s’achève à un endroit situé à mi-hauteur entre le cirrus, le postérieur et les organes reproducteurs), par la distribution des épines qui longent les parties ventro-latérales du corps, et encore par le nombre de testicules. Cette nouvelle espèce se différencie clairement de l’espèce A. ymakara, qui parasite la même espèce, par la proportion entre la longueur de l’oesophage et celle du corps, par l’absence de boucle distale au niveau du caecum, par la proportion entre la longueur du caecum antérieur et celle du caecum postérieur, ainsi que par son nombre de testicules. De plus, on remarque que chez A. ymakara, le caecum postérieur gauche peut être plus long que le caecum postérieur droit, alors que chez la nouvelle espèce, le caecum postérieur gauche est toujours plus court. Le spécimen d’A. ymakara recueilli en Argentine fait aussi l’objet d’une description. Nous faisons aussivpart de nos observations concernant la distribution des épines chez les différentes espèces d’Aporocotyle, y compris chez de nouveaux spécimens d’A. argentinensis Smith, 1969 prélevés sur le Merluccius hubbsi Marini, 1933. Nous avons comparé les séquences moléculaires obtenues à partir de régions particulières d’ADN ribosomique 18S et 28S chez la nouvelle espèce et chez deux autres espèces d’Aporocotyle (A. argentinensis et A. spinosicanalis Williams, 1958). A. ymakara fait donc l’objet d’une nouvelle répartition géographique qui s’étend désormais du Chili à l’Argentine. C’est la première fois que deux espèces d’Aporocotyle sont recensées sur une même espèce-hôte et dans une même zone géographique.

From a who's whoù of pioneers in the field comes a unique resource covering the latest advances in next-generation genome sequencing and assembly. This groundbreaking book includes non-conventional techniques that are paving the way to potential new biomedical applications. You get unparalleled access to state-of-the-art DNA sequencing technologies, new algorithmic sequence assembly techniques, and emerging methods for both resequencing and de novo genome analysis which all together give you the most solid foundation possible for tackling the full range of experimental and computational challenges in the genome sciences today. This first-of-its-kind resource walks you step-by-step through new sequencing technologies involving sequencing by synthesis, nanopore sequencing, polymerase colonies, and single molecule sequencing. It then explores the latest algorithmic techniques for DNA sequence assembly and offers expert insight into assembly packages like Arachne, EULER, CAP, AMASS, and Celera. You also get coverage of emerging biotechnology-oriented approaches to the resequencing and analysis of genomes, with the latest techniques for SNP, genome rearrangement, and comparative sequencing and assembly. Moreover, the book critiques strengths and weaknesses of existing techniques and spotlights possible ways to improve them. The most comprehensive treatment of the field's frontier topics, this definitive volume will prove indispensable in your efforts to achieve more rapid and accurate DNA sequencing and to develop the next generation of high-throughput methods and devices.

No Phlebotomine sandflies had ever been reported in the Comoros Archipelago, including the three islands of the Republic of the Union of Comoros (Grande Comore, Mohéli and Anjouan) and the French oversea department of Mayotte. During three field surveys carried out in 2003, 2007 and 2011, we provided the first record of Phlebotomine sandflies in this area. A total of 85 specimens belonging to three species were caught: a new species S. (Vattieromyia) pessoni n. sp. (two females from Grande Comore), a new subspecies of Sergentomyia (Rondanomyia) goodmani (80 specimens from Grande Comore and one from Anjouan) and Grassomyia sp. (two females from Mohéli). The individualisation of these taxa was inferred both from morphological criteria and sequencing of a part of the cytochrome b of the mitochondrial DNA. These taxa are closely related to Malagasy sandflies. Aucun phlébotome n’avait jamais été rapporté dans l’archipel des Comores, incluant les trois îles de l’Union des Comores (la Grande Comore, Mohéli et Anjouan) et le département français d’outremer, Mayotte. Au cours de trois campagnes d’études sur le terrain en 2003, 2007 et 2011, nous avons fait la première observation de phlébotomes dans cette zone. 85 spécimens appartenant à trois espèces ont été capturés : une nouvelle espèce, S. (Vattieromyia) pessoni n. sp. (deux femelles de la Grande Comore), une nouvelle sous-espèce de Sergentomyia (Rondanomyia) goodmani (80 spécimens de la Grande Comore et une d’Anjouan) et Grassomyia sp. (deux femelles à Mohéli). L’individualisation de ces taxons s’est faite à la fois à partir de critères morphologiques et du séquençage d’une partie du cytochrome b de l’ADN mitochondrial. Ces taxons sont très proches des phlébotomes de Madagascar.

Most forms of congenital heart disease (CHD) result from aberrations in cardiac morphogenesis including errors in septation, valve formation, and proper patterning of the great vessels. Transcription factors are key proteins that dictate mRNA synthesis rate and subsequent protein production in most eukaryotes. NFATC1 belongs to the Rel family of transcription factors. In mice, it is expressed in the embryonic heart and is restricted to the endocardium where it plays a major role in valve formation. To establish a role for NFATC1 in CHD, we started screening for mutations in the exons encoding the DNA-binding domain of NFATC1 in patients enrolled in our study on CHD in Lebanon. DNA was extracted from patients with pulmonary stenosis (PS), tricuspid atresia (TA) and ventricular septal defect (VSD). PCR amplification and DNA sequencing were done on the patients and their parents and (or) siblings. PCR amplification of the exon 7 region showed that 2 bands are obtained in 57% of patients with CHD (32/56) and in 45% of their healthy parents and (or) siblings. Sequencing of the 2 bands revealed that both are amplicons of the exon 7 region, and that the additional band harbors an additional 44 nucleotides segment in the intronic region. The homozygous form of this allele was only present in patients with VSD (2/21). A screen of a pool of 81 healthy, unrelated individuals showed no presence for the homozygous form of this allele, suggesting that NFATC1 is a potential VSD-susceptibility gene.

No detailed description available for \"Combinatorial Libraries\".