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https://www.readbyqxmd.com/read/29673316/a-study-on-fast-calling-variants-from-next-generation-sequencing-data-using-decision-tree
#1
Zhentang Li, Yi Wang, Fei Wang
BACKGROUND: The rapid development of next-generation sequencing (NGS) technology has continuously been refreshing the throughput of sequencing data. However, due to the lack of a smart tool that is both fast and accurate, the analysis task for NGS data, especially those with low-coverage, remains challenging. RESULTS: We proposed a decision-tree based variant calling algorithm. Experiments on a set of real data indicate that our algorithm achieves high accuracy and sensitivity for SNVs and indels and shows good adaptability on low-coverage data...
April 19, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29659490/a-comparative-genomic-survey-provides-novel-insights-into-molecular-evolution-of-l-aromatic-amino-acid-decarboxylase-in-vertebrates
#2
Yanping Li, Yunyun Lv, Chao Bian, Xinxin You, Li Deng, Qiong Shi
Melatonin is a pleiotropic molecule with various important physiological roles in vertebrates. l-aromatic amino acid decarboxylase (AAAD) is the second enzyme for melatonin synthesis. By far, a clear-cut gene function of AAAD in the biosynthesis of melatonin has been unclear in vertebrates. Here, we provide novel insights into the evolution of AAAD based on 77 vertebrate genomes. According to our genome-wide alignments, we extracted a total of 151 aaad nucleotide sequences. A phylogenetic tree was constructed on the basis of these sequences and corresponding protein alignments, indicating that tetrapods and diploid bony fish genomes contained one aaad gene and a new aaad -like gene, which formed a novel AAAD family...
April 16, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29572497/use-of-implanted-acoustic-tags-to-assess-platypus-movement-behaviour-across-spatial-and-temporal-scales
#3
Gilad Bino, Richard T Kingsford, Tom Grant, Matthew D Taylor, Larry Vogelnest
The platypus (Ornithorhynchus anatinus) is an evolutionarily distinct mammal, endemic to Australian freshwaters. Many aspects of its ecology and life-history, including detailed understanding of movements, are poorly known, hampered by its cryptic and mainly nocturnal habits and small numbers. We effectively trialled intraperitoneal implanted acoustic transmitters in nine platypuses in the Severn River (NSW), Australia, as a potential approach for studying movements in this challenging species. We tracked platypus movements over six months, at fine and broad spatial scales, using an array of acoustic sensors...
March 23, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29529849/prevalence-and-intensity-of-clonorchis-sinensis-metacercariae-in-freshwater-fish-from-wicheon-stream-in-gunwi-gun-gyeongsangbuk-do-korea
#4
Woon-Mok Sohn, Byoung-Kuk Na, Shin-Hyeong Cho, Jung-Won Ju, Dong-Chul Son
The infection status of Clonorchis sinensis metacercariae (CsMc) was examined in freshwater fish from a highly prevalent site, Wicheon (a branch of Nakdong-gang), which is located in Gunwi-gun, Gyeongsangbuk-do, the Republic of Korea. Total 1,162 fish in 32 species were examined by the artificial digestion method through 6 years. CsMc were detected in 720 (67.5%) out of 1,067 fish (26 spp.) and their density was 610 per fish infected. In the susceptible gobioninid fish group, i.e., Pungtungia herzi, Squalidus gracilis majimae, Squalidus japonicus coreanus, Sarcocheilichthys variegatus wakiyae and Pseudorasbora parva , all of 323 fish were infected with an average of 1,310 CsMc...
February 2018: Korean Journal of Parasitology
https://www.readbyqxmd.com/read/29529033/characterization-of-the-mel1c-melatoninergic-receptor-in-platypus-ornithorhynchus-anatinus
#5
Célia Gautier, Sophie-Penelope Guenin, Isabelle Riest-Fery, Tahlia Jade Perry, Céline Legros, Olivier Nosjean, Valerie Simonneaux, Frank Grützner, Jean A Boutin
Melatonin is a neurohormone produced in both animals and plants. It binds at least three G-protein-coupled receptors: MT1 and MT2, and Mel1cGPR. Mammalian GPR50 evolved from the reptilian/avian Mel1c and lost its capacity to bind melatonin in all the therian mammal species that have been tested. In order to determine if binding is lost in the oldest surviving mammalian lineage of monotremes we investigated whether the melatonin receptor has the ability to bind melatonin in the platypus (Ornithorhynchus anatinus), and evaluated its pharmacological profile...
2018: PloS One
https://www.readbyqxmd.com/read/29488024/evolution-through-cold-and-deep-waters-the-molecular-phylogeny-of-the-lithodidae-crustacea-decapoda
#6
Sally Hall, Sven Thatje
The objectives of this work are to use gene sequence data to assess the hypothesis that the Lithodinae arose from ancestors with uncalcified abdomens in shallow waters of the North-East Pacific, investigate the monophyly and interrelationships of genera within the Lithodinae and to estimate the scale and minimum number of biogeographic transitions from the shallow environment to the deep sea and vice versa. To do this, phylogenetic analysis from three mitochondrial and three nuclear markers was conducted using minimum evolution, maximum likelihood and Bayesian methods...
February 27, 2018: Die Naturwissenschaften
https://www.readbyqxmd.com/read/29417889/female-mate-choice-based-on-male-nuptial-coloration-in-pale-chub-zacco-platypus
#7
Daisuke Takahashi
Males of many animals exhibit conspicuous secondary sexual traits, which are often the result of sexual selection. During the breeding period of the pale chub (Pisces: Cyprinidae), males show various sexual traits, such as long anal fins, breeding tubercles on the head, and/or conspicuous red and greenish-blue nuptial colorations. Although these conspicuous sexual dimorphisms and dichromatisms indicate that this can serve as a model species for understanding sexual selection, it is unclear whether these male sexual traits are related to female mate choice...
February 2018: Zoological Science
https://www.readbyqxmd.com/read/29372906/structural-characterization-of-a-novel-monotreme-specific-protein-with-antimicrobial-activity-from-the-milk-of-the-platypus
#8
Janet Newman, Julie A Sharp, Ashwantha Kumar Enjapoori, John Bentley, Kevin R Nicholas, Timothy E Adams, Thomas S Peat
Monotreme lactation protein (MLP) is a recently identified protein with antimicrobial activity. It is present in the milk of monotremes and is unique to this lineage. To characterize MLP and to gain insight into the potential role of this protein in the evolution of lactation, the crystal structure of duck-billed platypus (Ornithorhynchus anatinus) MLP was determined at 1.82 Å resolution. This is the first structure to be reported for this novel, mammalian antibacterial protein. MLP was expressed as a FLAG epitope-tagged protein in mammalian cells and crystallized readily, with at least three space groups being observed (P1, C2 and P21)...
January 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29372309/more-sex-chromosomes-than-autosomes-in-the-amazonian-frog-leptodactylus-pentadactylus
#9
T Gazoni, C F B Haddad, H Narimatsu, D C Cabral-de-Mello, M L Lyra, P P Parise-Maltempi
Heteromorphic sex chromosomes are common in eukaryotes and largely ubiquitous in birds and mammals. The largest number of multiple sex chromosomes in vertebrates known today is found in the monotreme platypus (Ornithorhynchus anatinus, 2n = 52) which exhibits precisely 10 sex chromosomes. Interestingly, fish, amphibians, and reptiles have sex determination mechanisms that do or do not involve morphologically differentiated sex chromosomes. Relatively few amphibian species carry heteromorphic sex chromosomes, and when present, they are frequently represented by only one pair, either XX:XY or ZZ:ZW types...
January 26, 2018: Chromosoma
https://www.readbyqxmd.com/read/29360868/a-simple-snp-genotyping-method-reveals-extreme-invasions-of-non-native-haplotypes-in-pale-chub-opsariichthys-platypus-a-common-cyprinid-fish-in-japan
#10
Shigeru Kitanishi, Norio Onikura, Takahiko Mukai
Biological invasion by non-native subspecies or populations is one of the most serious threats to ecosystems, because these species might be easily established in the introduced area and can negatively affect native populations through competition and hybridization. Pale chub Opsariichthys platypus, one of the most common fish in East Asia, exhibits clear genetic differentiation among regional populations; however, introgression and subsequent loss of genetic integrity have been occurring throughout Japan due to the artificial introduction of non-native conspecifics...
2018: PloS One
https://www.readbyqxmd.com/read/29307115/bioinformatic-analyses-of-zona-pellucida-genes-in-vertebrates-and-their-expression-in-nile-tilapia
#11
Tianli Wu, Yunying Cheng, Zhilong Liu, Wenjing Tao, Shuqing Zheng, Deshou Wang
Zona pellucida (ZP) genes encode ZP glycoproteins which constitute the coat surrounding oocytes and early embryos. Genome-wide identification of ZP genes is still lacking in vertebrates, especially in fish species. Herein, we conducted bioinformatic analyses of the ZP genes of the Nile tilapia and other vertebrates. Totally 16, 9, 17, 27, 21, 20, 26, 19, 14,11, 24, 17, 9, 18, 8, 11, 9, 8, 5, and 4 ZP genes belonging to 5 subfamilies (ZPA, ZPB, ZPC, ZPD, and ZPAX) were found in the sea lamprey, elephant shark, coelacanth, spotted gar, zebrafish, medaka, stickleback, Nile tilapia, Amazon molly, platyfish, seahorse, Northern snakehead, cavefish, tetraodon, clawed frog, turtle, chicken, platypus, kangaroo rat, and human genomes, respectively...
April 2018: Fish Physiology and Biochemistry
https://www.readbyqxmd.com/read/29284563/a-novel-ehrlichia-species-in-blood-and-ixodes-ornithorhynchi-ticks-from-platypuses-ornithorhynchus-anatinus-in-queensland-and-tasmania-australia
#12
Alexander W Gofton, Siew-May Loh, Amanda D Barbosa, Andrea Paparini, Amber Gillett, James Macgregor, Charlotte L Oskam, Una M Ryan, Peter J Irwin
Worldwide, Ehrlichia spp. are emerging infectious organisms of domestic animals and people, however, most Ehrlichia spp. naturally infect wildlife reservoirs causing mainly asymptomatic infections. Australian ecosystems have been under-explored for these potentially pathogenic organisms, and recent studies have identified a range of novel Ehrlichia, and their sister genera, Anaplasma and 'Candidatus Neoehrlichia' species, from native Australian ticks. We used bacterial 16S rRNA (16S) next-generation sequencing and genus-specific PCR to profile the bacterial communities in platypus (Ornithorhynchus anatinus) blood samples and platypus ticks (Ixodes ornithorhynchi), and identified a high prevalence of Ehrlichia sequences...
February 2018: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/29215911/weird-animals-sex-and-genome-evolution
#13
Jennifer A Marshall Graves
Making my career in Australia exposed me to the tyranny of distance, but it gave me opportunities to study our unique native fauna. Distantly related animal species present genetic variation that we can use to explore the most fundamental biological structures and processes. I have compared chromosomes and genomes of kangaroos and platypus, tiger snakes and emus, devils (Tasmanian) and dragons (lizards). I particularly love the challenges posed by sex chromosomes, which, apart from determining sex, provide stunning examples of epigenetic control and break all the evolutionary rules that we currently understand...
February 15, 2018: Annual Review of Animal Biosciences
https://www.readbyqxmd.com/read/29180746/numts-colonization-in-mammalian-genomes
#14
F M Calabrese, D L Balacco, R Preste, M A Diroma, R Forino, M Ventura, M Attimonelli
The colonization of the nuclear genome by mitochondrial DNA is an ongoing process in eukaryotes and plays an important role in genomic variability. Notwithstanding the DNA sequence availability of about 100 complete eukaryotic genomes, up to now NumtS distribution has been fully reported for a small number of sequenced eukaryotic species. With the aim to clarify the time and way of NumtS evolution, we explored the genomic distribution of NumtS in 23 eukaryotic species using an intra/interspecies in silico approach based on a cross-species similarity search and deeply investigate the evolution of NumtS in mammals...
November 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29161408/landscape-of-dna-methylation-on-the-marsupial-x
#15
Shafagh A Waters, Alexandra M Livernois, Hardip Patel, Denis O'Meally, Jeff M Craig, Jennifer A Marshall Graves, Catherine M Suter, Paul D Waters
DNA methylation plays a key role in maintaining transcriptional silence on the inactive X chromosome of eutherian mammals. Beyond eutherians, there are limited genome wide data on DNA methylation from other vertebrates. Previous studies of X borne genes in various marsupial models revealed no differential DNA methylation of promoters between the sexes, leading to the conclusion that CpG methylation plays no role in marsupial X-inactivation. Using reduced representation bisulfite sequencing, we generated male and female CpG methylation profiles in four representative vertebrates (mouse, gray short-tailed opossum, platypus and chicken)...
November 17, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29032097/comparative-assessment-of-the-adverse-outcome-of-wastewater-effluents-by-integrating-oxidative-stress-and-histopathological-alterations-in-endemic-fish
#16
Palas Samanta, Hyungjoon Im, Jisu Yoo, Hwanggoo Lee, Nan-Young Kim, Wonky Kim, Soon-Jin Hwang, Woo-Keun Kim, Jinho Jung
This study evaluated the adverse effect of wastewater effluents on three fish species, Carassius auratus, Zacco platypus, and Zacco koreanus, collected in the Eungcheon, Mihocheon, and Busocheon streams, respectively. Fish gills, liver, and kidneys from the mixing zone (MZ) and sites upstream (US) and downstream (DS) of the MZ were analyzed for oxidative stress responses and histology. Catalase and glutathione S-transferase activity was significantly higher at MZ and DS than from US (p<0.05), indicating induction of antioxidant defense mechanisms...
February 15, 2018: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/29026079/a-long-range-cis-regulatory-element-for-class-i-odorant-receptor-genes
#17
Tetsuo Iwata, Yoshihito Niimura, Chizuru Kobayashi, Daichi Shirakawa, Hikoyu Suzuki, Takayuki Enomoto, Kazushige Touhara, Yoshihiro Yoshihara, Junji Hirota
Individual olfactory sensory neurons express a single odorant receptor gene from either class I genes residing in a single cluster on a single chromosome or class II genes spread over multiple clusters on multiple chromosomes. Here, we identify an enhancer element for mouse class I genes, the J element, that is conserved through mammalian species from the platypus to humans. The J element regulates most class I genes expression by exerting an effect over ~ 3 megabases within the whole cluster. Deletion of the trans J element increases the expression frequencies of class I genes from the intact J allele, indicating that the allelic exclusion of class I genes depends on the activity of the J element...
October 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/28949902/marsupial-and-monotreme-cathelicidins-display-antimicrobial-activity-including-against-methicillin-resistant-staphylococcus-aureus
#18
Emma Peel, Yuanyuan Cheng, Julianne T Djordjevic, Michael Kuhn, Tania Sorrell, Katherine Belov
With the growing demand for new antibiotics to combat increasing multi-drug resistance, a family of antimicrobial peptides known as cathelicidins has emerged as potential candidates. Expansions in cathelicidin-encoding genes in marsupials and monotremes are of specific interest as the peptides they encode have evolved to protect immunologically naive young in the harsh conditions of the pouch and burrow. Our previous work demonstrated that some marsupial and monotreme cathelicidins have broad-spectrum antibacterial activity and kill resistant bacteria, but the activity of many cathelicidins is unknown...
September 27, 2017: Microbiology
https://www.readbyqxmd.com/read/28922870/male-mutation-bias-is-the-main-force-shaping-chromosomal-substitution-rates-in-monotreme-mammals
#19
Vivian Link, Diana Aguilar-Gómez, Ciro Ramírez-Suástegui, Laurence D Hurst, Diego Cortez
In many species, spermatogenesis involves more cell divisions than oogenesis, and the male germline, therefore, accumulates more DNA replication errors, a phenomenon known as male mutation bias. The extent of male mutation bias (α) is estimated by comparing substitution rates of the X, Y, and autosomal chromosomes, as these chromosomes spend different proportions of their time in the germlines of the two sexes. Male mutation bias has been characterized in placental and marsupial mammals as well as birds, but analyses in monotremes failed to detect any such bias...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28919547/deep-sequencing-to-resolve-complex-diversity-of-apicomplexan-parasites-in-platypuses-and-echidnas-proof-of-principle-for-wildlife-disease-investigation
#20
Jan Šlapeta, Stefan Saverimuttu, Larry Vogelnest, Cheryl Sangster, Frances Hulst, Karrie Rose, Paul Thompson, Richard Whittington
The short-beaked echidna (Tachyglossus aculeatus) and the platypus (Ornithorhynchus anatinus) are iconic egg-laying monotremes (Mammalia: Monotremata) from Australasia. The aim of this study was to demonstrate the utility of diversity profiles in disease investigations of monotremes. Using small subunit (18S) rDNA amplicon deep-sequencing we demonstrated the presence of apicomplexan parasites and confirmed by direct and cloned amplicon gene sequencing Theileria ornithorhynchi, Theileria tachyglossi, Eimeria echidnae and Cryptosporidium fayeri...
September 13, 2017: Infection, Genetics and Evolution
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