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https://www.readbyqxmd.com/read/27922628/a-chromosome-level-genome-assembly-of-the-asian-arowana-scleropages-formosus
#1
Jia Li, Chao Bian, Yinchang Hu, Xidong Mu, Xueyan Shen, Vydianathan Ravi, Inna S Kuznetsova, Ying Sun, Xinxin You, Ying Qiu, Xinhui Zhang, Hui Yu, Yu Huang, Pao Xu, Ruobo Gu, Junmin Xu, László Orbán, Byrappa Venkatesh, Qiong Shi
Asian arowana (Scleropages formosus), an ancient teleost belonging to the Order Osteoglossomorpha, has been a valuable ornamental fish with some varieties. However, its biological studies and breeding germplasm have been remarkably limited by the lack of a reference genome. To solve these problems, here we report high-quality genome sequences of three common varieties of Asian arowana (the golden, red and green arowana). We firstly generated a chromosome-level genome assembly of the golden arowana, on basis of the genetic linkage map constructed with the restriction site-associated DNA sequencing (RAD-seq)...
December 6, 2016: Scientific Data
https://www.readbyqxmd.com/read/27907810/prediction-of-autosomal-str-typing-success-in-ancient-and-second-world-war-bone-samples
#2
Irena Zupanič Pajnič, Tomaž Zupanc, Jože Balažic, Živa Miriam Geršak, Oliver Stojković, Ivan Skadrić, Matija Črešnar
Human-specific quantitative PCR (qPCR) has been developed for forensic use in the last 10 years and is the preferred DNA quantification technique since it is very accurate, sensitive, objective, time-effective and automatable. The amount of information that can be gleaned from a single quantification reaction using commercially available quantification kits has increased from the quantity of nuclear DNA to the amount of male DNA, presence of inhibitors and, most recently, to the degree of DNA degradation. In skeletal remains samples from disaster victims, missing persons and war conflict victims, the DNA is usually degraded...
November 19, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27904152/mitochondrial-dna-diversity-of-present-day-aboriginal-australians-and-implications-for-human-evolution-in-oceania
#3
Nano Nagle, Kaye N Ballantyne, Mannis van Oven, Chris Tyler-Smith, Yali Xue, Stephen Wilcox, Leah Wilcox, Rust Turkalov, Roland A H van Oorschot, Sheila van Holst Pellekaan, Theodore G Schurr, Peter McAllister, Lesley Williams, Manfred Kayser, R John Mitchell
Aboriginal Australians are one of the more poorly studied populations from the standpoint of human evolution and genetic diversity. Thus, to investigate their genetic diversity, the possible date of their ancestors' arrival and their relationships with neighboring populations, we analyzed mitochondrial DNA (mtDNA) diversity in a large sample of Aboriginal Australians. Selected mtDNA single-nucleotide polymorphisms and the hypervariable segment haplotypes were analyzed in 594 Aboriginal Australians drawn from locations across the continent, chiefly from regions not previously sampled...
December 1, 2016: Journal of Human Genetics
https://www.readbyqxmd.com/read/27903241/abundant-rna-editing-sites-of-chloroplast-protein-coding-genes-in-ginkgo-biloba-and-an-evolutionary-pattern-analysis
#4
Peng He, Sheng Huang, Guanghui Xiao, Yuzhou Zhang, Jianing Yu
BACKGROUND: RNA editing is a posttranscriptional modification process that alters the RNA sequence so that it deviates from the genomic DNA sequence. RNA editing mainly occurs in chloroplasts and mitochondrial genomes, and the number of editing sites varies in terrestrial plants. Why and how RNA editing systems evolved remains a mystery. Ginkgo biloba is one of the oldest seed plants and has an important evolutionary position. Determining the patterns and distribution of RNA editing in the ancient plant provides insights into the evolutionary trend of RNA editing, and helping us to further understand their biological significance...
December 1, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27891505/comparative-genomics-of-the-conjugation-region-of-f-like-plasmids-five-shades-of-f
#5
Raul Fernandez-Lopez, Maria de Toro, Gabriel Moncalian, M Pilar Garcillan-Barcia, Fernando de la Cruz
The F plasmid is the foremost representative of a large group of conjugative plasmids, prevalent in Escherichia coli, and widely distributed among the Enterobacteriaceae. These plasmids are of clinical relevance, given their frequent association with virulence determinants, colicins, and antibiotic resistance genes. Originally defined by their sensitivity to certain male-specific phages, IncF plasmids share a conserved conjugative system and regulatory circuits. In order to determine whether the genetic architecture and regulation circuits are preserved among these plasmids, we analyzed the natural diversity of F-like plasmids...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27881876/the-efficacy-of-high-throughput-sequencing-and-target-enrichment-on-charred-archaeobotanical-remains
#6
H M Nistelberger, O Smith, N Wales, B Star, S Boessenkool
The majority of archaeological plant material is preserved in a charred state. Obtaining reliable ancient DNA data from these remains has presented challenges due to high rates of nucleotide damage, short DNA fragment lengths, low endogenous DNA content and the potential for modern contamination. It has been suggested that high-throughput sequencing (HTS) technologies coupled with DNA enrichment techniques may overcome some of these limitations. Here we report the findings of HTS and target enrichment on four important archaeological crops (barley, grape, maize and rice) performed in three different laboratories, presenting the largest HTS assessment of charred archaeobotanical specimens to date...
November 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27881865/bandicoot-fossils-and-dna-elucidate-lineage-antiquity-amongst-xeric-adapted-australasian-marsupials
#7
Benjamin P Kear, Ken P Aplin, Michael Westerman
Bandicoots (Peramelemorphia) are a unique order of Australasian marsupials whose sparse fossil record has been used as prima facie evidence for climate change coincident faunal turnover. In particular, the hypothesized replacement of ancient rainforest-dwelling extinct lineages by antecedents of xeric-tolerant extant taxa during the late Miocene (~10 Ma) has been advocated as a broader pattern evident amongst other marsupial clades. Problematically, however, this is in persistent conflict with DNA phylogenies...
November 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27880868/origin-and-evolution-of-the-metazoan-non-coding-regulatory-genome
#8
REVIEW
Federico Gaiti, Andrew D Calcino, Miloš Tanurdžić, Bernard M Degnan
Animals rely on genomic regulatory systems to direct the dynamic spatiotemporal and cell-type specific gene expression that is essential for the development and maintenance of a multicellular lifestyle. Although it is widely appreciated that these systems ultimately evolved from genomic regulatory mechanisms present in single-celled stem metazoans, it remains unclear how this occurred. Here, we focus on the contribution of the non-coding portion of the genome to the evolution of animal gene regulation, specifically on recent insights from non-bilaterian metazoan lineages, and unicellular and colonial holozoan sister taxa...
November 20, 2016: Developmental Biology
https://www.readbyqxmd.com/read/27869396/-real-time-quantification-to-analyze-historical-colombian-samples-detecting-a-short-fragment-of-hypervariable-region-ii-of-mitochondrial-dna
#9
Luz Adriana Pérez, Freddy Rodríguez, Carl Henrik Langebaek, Helena Groot
Unlike other molecular biology studies, the analysis of ancient DNA (aDNA) requires special infrastructure and methodological conditions to guarantee the quality of the results. One of the main authenticity criteria is DNA quantification, where quantitative real-time PCR is often used given its sensitivity and specificity. Nevertheless, the implementation of these conditions and methodologies to fulfill authenticity criteria imply higher costs. Objective: To develop a simple and less costly method for mitochondrial DNA quantification suitable for highly degraded samples...
September 1, 2016: Biomédica: Revista del Instituto Nacional de Salud
https://www.readbyqxmd.com/read/27863852/the-rag-recombinase-beyond-breaking
#10
Chloé Lescale, Ludovic Deriano
DNA double-strand breaks (DSBs) are commonly seen as lesions that threaten genome integrity and contribute to cancer and aging processes. However, in the context of antigen receptor gene assembly, known as V(D)J recombination, DSBs are obligatory intermediates that allow the establishment of genetic diversity and adaptive immunity. V(D)J recombination is initiated when the lymphoid-restricted recombination-activating genes RAG1 and RAG2 are expressed and form a site-specific endonuclease (the RAG nuclease or RAG recombinase)...
November 15, 2016: Mechanisms of Ageing and Development
https://www.readbyqxmd.com/read/27863491/the-year-of-the-wisent
#11
Johannes A Lenstra, Jianquan Liu
Delving into European prehistory, two recent studies analyze ancient DNA from bison species depicted by our ancestors on the walls of their caves. The DNA tells a story of migrations driven by climate change but leaves some mystery clouding the genetic descent and climate preference of the still-extant wisent, otherwise known as the European bison.See research articles: https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-016-0317-7 http://www.nature.com/articles/ncomms13158.
November 18, 2016: BMC Biology
https://www.readbyqxmd.com/read/27863405/identification-of-evolutionarily-conserved-dna-damage-response-genes-that-alter-sensitivity-to-cisplatin
#12
Anna V Gaponova, Alexander Y Deneka, Tim N Beck, Hanqing Liu, Gregory Andrianov, Anna S Nikonova, Emmanuelle Nicolas, Margret B Einarson, Erica A Golemis, Ilya G Serebriiskii
Ovarian, head and neck, and other cancers are commonly treated with cisplatin and other DNA damaging cytotoxic agents. Altered DNA damage response (DDR) contributes to resistance of these tumors to chemotherapies, some targeted therapies, and radiation. DDR involves multiple protein complexes and signaling pathways, some of which are evolutionarily ancient and involve protein orthologs conserved from yeast to humans. To identify new regulators of cisplatin-resistance in human tumors, we integrated high throughput and curated datasets describing yeast genes that regulate sensitivity to cisplatin and/or ionizing radiation...
November 15, 2016: Oncotarget
https://www.readbyqxmd.com/read/27859602/integrating-archaeology-and-ancient-dna-to-address-invasive-species-colonization-in-the-gulf-of-alaska
#13
Catherine West, Courtney A Hofman, Steve Ebbert, John Martin, Sabrina Shirazi, Samantha Dunning, Jesus E Maldonado
The intentional and unintentional movement of plants and animals by humans has transformed ecosystems and landscapes globally. Assessing when and how a species was introduced are central to managing these transformed landscapes, particularly in island environments. In the Gulf of Alaska, there is considerable interest in the history of mammal introductions and rehabilitating Gulf of Alaska island environments by eradicating those mammals classified as invasive species. The Arctic ground squirrel (Urocitellus parryii) is of concern because of its effect on vegetation and seabirds on Gulf of Alaska islands...
November 17, 2016: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/27855648/genome-and-transcriptome-sequencing-characterises-the-gene-space-of-macadamia-integrifolia-proteaceae
#14
Catherine J Nock, Abdul Baten, Bronwyn J Barkla, Agnelo Furtado, Robert J Henry, Graham J King
BACKGROUND: The large Gondwanan plant family Proteaceae is an early-diverging eudicot lineage renowned for its morphological, taxonomic and ecological diversity. Macadamia is the most economically important Proteaceae crop and represents an ancient rainforest-restricted lineage. The family is a focus for studies of adaptive radiation due to remarkable species diversification in Mediterranean-climate biodiversity hotspots, and numerous evolutionary transitions between biomes. Despite a long history of research, comparative analyses in the Proteaceae and macadamia breeding programs are restricted by a paucity of genetic information...
November 17, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27853601/origin-and-timing-of-new-zealand-s-earliest-domestic-chickens-polynesian-commensals-or-european-introductions
#15
Jamie R Wood, Michael J B Herrera, R Paul Scofield, Janet M Wilmshurst
Human settlers transported chickens (Gallus gallus domesticus) to most East Polynesian archipelagos between AD 1000 and 1300; however, it has long been assumed that New Zealand was an exception. Despite the fact that chicken bones have been recovered from localities of early archaeological middens in New Zealand, their age and genetic relationships have never been critically assessed. Here, we test the assumption that chickens were not introduced to New Zealand during prehistory through ancient DNA and radiocarbon analyses of chicken bones from sites of Māori middens containing prehistoric material...
August 2016: Royal Society Open Science
https://www.readbyqxmd.com/read/27851823/molecular-and-morphological-study-of-leaping-frogs-anura-ranixalidae-with-description-of-two-new-species
#16
Sonali Garg, S D Biju
The monotypic anuran family Ranixalidae is endemic to India, with a predominant distribution in the Western Ghats, a region that is home to several unique amphibian lineages. It is also one of the three ancient anuran families that diversified on the Indian landmass long before several larger radiations of extant frogs in this region. In recent years, ranixalids have been subjected to DNA barcoding and systematic studies. Nearly half of the presently recognized species in this family have been described over the last three years, along with recognition of a new genus to accommodate three previously known members...
2016: PloS One
https://www.readbyqxmd.com/read/27848993/the-caste-and-sex-specific-dna-methylome-of-the-termite-zootermopsis-nevadensis
#17
Karl M Glastad, Kaustubh Gokhale, Jürgen Liebig, Michael A D Goodisman
Epigenetic inheritance plays an important role in mediating alternative phenotype in highly social species. In order to gain a greater understanding of epigenetic effects in societies, we investigated DNA methylation in the termite Zootermopsis nevadensis. Termites are the most ancient social insects, and developmentally distinct from highly-studied, hymenopteran social insects. We used replicated bisulfite-sequencing to investigate patterns of DNA methylation in both sexes and among castes of Z. nevadensis...
November 16, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27848937/reconstructing-druze-population-history
#18
Scarlett Marshall, Ranajit Das, Mehdi Pirooznia, Eran Elhaik
The Druze are an aggregate of communities in the Levant and Near East living almost exclusively in the mountains of Syria, Lebanon and Israel whose ~1000 year old religion formally opposes mixed marriages and conversions. Despite increasing interest in genetics of the population structure of the Druze, their population history remains unknown. We investigated the genetic relationships between Israeli Druze and both modern and ancient populations. We evaluated our findings in light of three hypotheses purporting to explain Druze history that posit Arabian, Persian or mixed Near Eastern-Levantine roots...
November 16, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27846491/going-global-by-adapting-local-a-review-of-recent-human-adaptation
#19
REVIEW
Shaohua Fan, Matthew E B Hansen, Yancy Lo, Sarah A Tishkoff
The spread of modern humans across the globe has led to genetic adaptations to diverse local environments. Recent developments in genomic technologies, statistical analyses, and expanded sampled populations have led to improved identification and fine-mapping of genetic variants associated with adaptations to regional living conditions and dietary practices. Ongoing efforts in sequencing genomes of indigenous populations, accompanied by the growing availability of "-omics" and ancient DNA data, promises a new era in our understanding of recent human evolution and the origins of variable traits and disease risks...
October 7, 2016: Science
https://www.readbyqxmd.com/read/27843712/yangtze-river-an-insignificant-genetic-boundary-in-tufted-deer-elaphodus-cephalophus-the-evidence-from-a-first-population-genetics-study
#20
Zhonglou Sun, Tao Pan, Hui Wang, Mujia Pang, Baowei Zhang
Great rivers were generally looked at as the geographical barrier to gene flow for many taxonomic groups. The Yangtze River is the third largest river in the world, and flows across South China and into the East China Sea. Up until now, few studies have been carried out to evaluate its effect as a geographical barrier. In this study, we attempted to determine the barrier effect of the Yangtze River on the tufted deer (Elaphodus cephalophus) using the molecular ecology approach. Using mitochondrial DNA control region (CR) sequences and 13 nuclear microsatellite loci, we explored the genetic structure and gene flow in two adjacent tufted deer populations (Dabashan and Wulingshan populations), which are separated by the Yangtze River...
2016: PeerJ
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