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https://www.readbyqxmd.com/read/28931057/challenges-and-advances-for-transcriptome-assembly-in-non-model-species
#1
Arnaud Ungaro, Nicolas Pech, Jean-François Martin, R J Scott McCairns, Jean-Philippe Mévy, Rémi Chappaz, André Gilles
Analyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly. Given the limits of mapping reads to a reference when it is highly divergent, as is frequently the case for non-model species, we evaluate whether using blastn would outperform mapping methods for read assignment in such situations (>15% divergence). We demonstrate its high performance by using simulated reads of lengths corresponding to those generated by the most common sequencing platforms, and over a realistic range of genetic divergence (0% to 30% divergence)...
2017: PloS One
https://www.readbyqxmd.com/read/28929561/one-pot-three-component-sulfonimidamide-synthesis-exploiting-the-sulfinylamine-reagent-n-sulfinyltritylamine-trnso
#2
Thomas Q Davies, Adrian Hall, Michael C Willis
Sulfonimidamides are increasingly important molecules in medicinal chemistry and agrochemistry, but their preparation requires lengthy synthetic sequences, which has likely limited their use. We describe a one-pot de novo synthesis of sulfonimidamides from widely available organometallic reagents and amines. This convenient and efficient process uses a stable sulfinylamine reagent, N-sulfinyltritylamine (TrNSO), available in one step on 10 gram scale, as a linchpin. In contrast to classical approaches starting from thiols or their derivatives, our TrNSO-based approach facilitates the rapid assembly of the three reaction components into a variety of differentially substituted sulfonimidamides containing medicinally relevant moieties, including pyridines and indoles...
September 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28928460/molecular-dissection-of-transcriptional-reprogramming-of-steviol-glycosides-synthesis-in-leaf-tissue-during-developmental-phase-transitions-in-stevia-rebaudiana-bert
#3
Gopal Singh, Gagandeep Singh, Pradeep Singh, Rajni Parmar, Navgeet Paul, Radhika Vashist, Mohit Kumar Swarnkar, Ashok Kumar, Sanatsujat Singh, Anil Kumar Singh, Sanjay Kumar, Ram Kumar Sharma
Stevia is a natural source of commercially important steviol glycosides (SGs), which share biosynthesis route with gibberellic acids (GAs) through plastidal MEP and cytosolic MVA pathways. Ontogeny-dependent deviation in SGs biosynthesis is one of the key factor for global cultivation of Stevia, has not been studied at transcriptional level. To dissect underlying molecular mechanism, we followed a global transcriptome sequencing approach and generated more than 100 million reads. Annotation of 41,262 de novo assembled transcripts identified all the genes required for SGs and GAs biosynthesis...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28924510/development-of-est-ssr-markers-for-taxillus-nigrans-loranthaceae-in-southwestern-china-using-next-generation-sequencing
#4
Ning Miao, Lei Zhang, Maoping Li, Liqiang Fan, Kangshan Mao
PREMISE OF THE STUDY: We developed transcriptome microsatellite markers (simple sequence repeats) for Taxillus nigrans (Loranthaceae) to survey the genetic diversity and population structure of this species. METHODS AND RESULTS: We used Illumina HiSeq data to reconstruct the transcriptome of T. nigrans by de novo assembly and used the transcriptome to develop a set of simple sequence repeat markers. Overall, 40 primer pairs were designed and tested; 19 of them amplified successfully and demonstrated polymorphisms...
August 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28923556/de-novo-assembly-and-transcriptome-characterization-of-the-freshwater-prawn-palaemonetes-argentinus-implications-for-a-detoxification-response
#5
C Fernando García, Nicolas Pedrini, Arturo Sánchez-Paz, Carlos S Reyna-Blanco, Sabrina Lavarias, Adriana Muhlia-Almazán, Analía Fernández-Giménez, Aldana Laino, Enrique de-la-Re-Vega, German Lukaszewicz, Alonso A López-Zavala, Luis G Brieba, Michael F Criscitello, Jesús S Carrasco-Miranda, Karina D García-Orozco, Adrian Ochoa-Leyva, Enrique Rudiño-Piñera, Alejandro Sanchez-Flores, Rogerio R Sotelo-Mundo
Palaemonetes argentinus, an abundant freshwater prawn species in the northern and central region of Argentina, has been used as a bioindicator of environmental pollutants as it displays a very high sensitivity to pollutants exposure. Despite their extraordinary ecological relevance, a lack of genomic information has hindered a more thorough understanding of the molecular mechanisms potentially involved in detoxification processes of this species. Thus, transcriptomic profiling studies represent a promising approach to overcome the limitations imposed by the lack of extensive genomic resources for P...
September 8, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28923029/mitochondrial-genomes-reveal-recombination-in-the-presumed-asexual-fusarium-oxysporum-species-complex
#6
Balázs Brankovics, Peter van Dam, Martijn Rep, G Sybren de Hoog, Theo A J van der Lee, Cees Waalwijk, Anne D van Diepeningen
BACKGROUND: The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties. RESULTS: A total of 61 complete mitogenomes of FOSC strains were de novo assembled and annotated. Length variations and intron patterns support the separation of three phylogenetic species...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28923015/transcriptome-analysis-of-pseudostellaria-heterophylla-in-response-to-the-infection-of-pathogenic-fusarium-oxysporum
#7
Xianjin Qin, Hongmiao Wu, Jun Chen, Linkun Wu, Sheng Lin, Muhammad Umar Khan, Mohammad Reza Boorboori, Wenxiong Lin
BACKGROUND: Pseudostellaria heterophylla (P. heterophylla), a herbaceous perennial, belongs to Caryophyllaceae family and is one of the Chinese herbal medicine with high pharmacodynamic value. It can be used to treat the spleen deficiency, anorexia, weakness after illness and spontaneous perspiration symptoms. Our previous study found that consecutive monoculture of Pseudostellaria heterophylla could lead to the deterioration of the rhizosphere microenvironment. The specialized forms of pathogenic fungus Fusarium oxysporum f...
September 18, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28922823/de-novo-genome-assembly-of-camptotheca-acuminata-a-natural-source-of-the-anti-cancer-compound-camptothecin
#8
Dongyan Zhao, John P Hamilton, Gina M Pham, Emily Crisovan, Krystle Wiegert-Rininger, Brieanne Vaillancourt, Dean DellaPenna, C Robin Buell
Camptotheca acuminata is 1 of a limited number of species that produce camptothecin, a pentacyclic quinoline alkaloid with anti-cancer activity due to its ability to inhibit DNA topoisomerase. While transcriptome studies have been performed previously with various camptothecin-producing species, no genome sequence for a camptothecin-producing species is available to date. We generated a high-quality de novo genome assembly for C. acuminata representing 403 174 860 bp on 1394 scaffolds with an N50 scaffold size of 1752 kbp...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28921169/effects-of-acute-salt-stress-on-modulation-of-gene-expression-in-a-malaysian-salt-tolerant-indigenous-rice-variety-bajong
#9
Brandon Pei Hui Yeo, Mrinal Bhave, Siaw San Hwang
The small genome size of rice relative to wheat and barley, together with its salt sensitivity, make it an ideal candidate for studies of salt stress response. Transcriptomics has emerged as a powerful technique to study salinity responses in many crop species. By identifying a large number of differentially expressed genes (DEGs) simultaneously after the stress induction, it can provide crucial insight into the immediate responses towards the stressor. In this study, a Malaysian salt-tolerant indigenous rice variety named Bajong and one commercial rice variety named MR219 were investigated for their performance in plant growth and ion accumulation properties after salt stress treatment...
September 18, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/28919018/de-novo-transcriptome-assembly-of-the-calanoid-copepod-neocalanus-flemingeri-a-new-resource-for-emergence-from-diapause
#10
Vittoria Roncalli, Matthew C Cieslak, Stephanie A Sommer, Russell R Hopcroft, Petra H Lenz
Copepods, small planktonic crustaceans, are key links between primary producers and upper trophic levels, including many economically important fishes. In the subarctic North Pacific, the life cycle of copepods like Neocalanus flemingeri includes an ontogenetic migration to depth followed by a period of diapause (a type of dormancy) characterized by arrested development and low metabolic activity. The end of diapause is marked by the production of the first brood of eggs. Recent temperature anomalies in the North Pacific have raised concerns about potential negative effects on N...
September 14, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28916360/trancriptome-profiles-of-amur-sturgeon-spleen-in-response-to-yersinia-ruckeri-infection
#11
Shaowu Li, Ying Zhang, Yongsheng Cao, Di Wang, Hongbai Liu, Tongyan Lu
Yersinia ruckeri (YR) is the causative agent of yersiniosis which has caused significant economic losses in fish culture worldwide, including in Amur sturgeon (Acipenser schrenckii) culture. To better understand the mechanism of the immune responses to YR in Amur sturgeon, the transcriptomic profiles of the spleens from YR-infected and non-infected groups were obtained using RNA-seq techniques. The de novo assemblies yielded totally 145 670 unigenes from the two libraries. The total numbers of transcripts in YR-infected and non-infected groups were from 110 893 to 147 336, with the mean length varying from 560 to 631 (N50: from 882 to 1083)...
September 12, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28910776/fastetch-a-fast-sketch-based-assembler-for-genomes
#12
Priyanka Ghosh, Ananth Kalyanaraman
De novo genome assembly describes the process of reconstructing an unknown genome from a large collection of short (or long) reads sequenced from the genome. A single run of a Next-Generation Sequencing (NGS) technology can produce billions of short reads, making genome assembly computationally demanding (both in terms of memory and time). One of the major computational steps in modern day short read assemblers involves the construction and use of a string data structure called the de Bruijn graph. In fact, a majority of short read assemblers build the complete de Bruijn graph for the set of input reads, and subsequently traverse and prune low-quality edges, in order to generate genomic "contigs"-the output of assembly...
September 11, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28905880/mutations-in-rars-cause-a-hypomyelination-disorder-akin-to-pelizaeus-merzbacher-disease
#13
Michael Nafisinia, Nara Sobreira, Lisa Riley, Wendy Gold, Birgit Uhlenberg, Claudia Weiß, Corinne Boehm, Kristina Prelog, Robert Ouvrier, John Christodoulou
Pelizaeus-Merzbacher disease (PMD) is a rare Mendelian disorder characterised by central nervous system hypomyelination. PMD typically manifests in infancy or early childhood and is caused by mutations in proteolipid protein-1 (PLP1). However, variants in several other genes including gap junction protein gamma 2 (GJC2) can also cause a similar phenotype and are referred to PMD-like disease (PMLD). Whole-exome sequencing in two siblings presenting with clinical symptoms of PMD revealed a homozygous variant in the arginyl-tRNA synthetase (RARS) gene: NM_002887...
October 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28905330/complete-chloroplast-genome-sequences-of-two-endangered-phoebe-lauraceae-species
#14
Yingang Li, Wuqin Xu, Wentao Zou, Dongyue Jiang, Xinhong Liu
BACKGROUND: Phoebe (Lauraceae) comprises of evergreen trees or shrubs with approximately 100 species, distributed in tropical and subtropical Asia and Neotropical America. A total of 34 species and three varieties occur in China. Despite of economic and ecological value, only limited genomic resources are available for this genus. RESULTS: We sequenced the two complete chloroplast (cp) genomes of Phoebe chekiangensis and P. bournei using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly...
September 13, 2017: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/28904649/harnessing-whole-genome-sequencing-in-medical-mycology
#15
REVIEW
Christina A Cuomo
PURPOSE OF REVIEW: Comparative genome sequencing studies of human fungal pathogens enable identification of genes and variants associated with virulence and drug resistance. This review describes current approaches, resources, and advances in applying whole genome sequencing to study clinically important fungal pathogens. RECENT FINDINGS: Genomes for some important fungal pathogens were only recently assembled, revealing gene family expansions in many species and extreme gene loss in one obligate species...
2017: Current Fungal Infection Reports
https://www.readbyqxmd.com/read/28904206/a-disease-associated-frameshift-mutation-in-caveolin-1-disrupts-caveolae-formation-and-function-through-introduction-of-a-de-novo-er-retention-signal
#16
Courtney A Copeland, Bing Han, Ajit Tiwari, Eric D Austin, James E Loyd, James D West, Anne K Kenworthy
Caveolin-1 (CAV1) is an essential component of caveolae and is implicated in numerous physiological processes. Recent studies have identified heterozygous mutations in the CAV1 gene in patients with pulmonary arterial hypertension (PAH), but the mechanisms by which these mutations impact caveolae assembly and contribute to disease remain unclear. To address this question, we examined the consequences of a familial PAH-associated frameshift mutation in CAV1, P158PfsX22, on caveolae assembly and function. We show that C-terminus of the CAV1 P158 protein contains a functional ER-retention signal that inhibits ER exit and caveolae formation and accelerates CAV1 turnover in Cav1(-/-) MEFs...
September 13, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28903539/kollector-transcript-informed-targeted-de-novo-assembly-of-gene-loci
#17
Erdi Kucuk, Justin Chu, Benjamin P Vandervalk, S Austin Hammond, René L Warren, Inanc Birol
No abstract text is available yet for this article.
September 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28902884/development-of-est-ssr-markers-in-flowering-chinese-cabbage-brassica-campestris-l-ssp-chinensis-var-utilis-tsen-et-lee-based-on-de-novo-transcriptomic-assemblies
#18
Jingfang Chen, Ronghua Li, Yanshi Xia, Guihua Bai, Peiguo Guo, Zhiliang Wang, Hua Zhang, Kadambot H M Siddique
Flowering Chinese cabbage is one of the most important vegetable crops in southern China. Genetic improvement of various agronomic traits in this crop is underway to meet high market demand in the region, but the progress is hampered by limited number of molecular markers available in this crop. This study aimed to develop EST-SSR markers from transcriptome sequences generated by next-generation sequencing. RNA-seq of eight cabbage samples identified 48,975 unigenes. Of these unigenes, 23,267 were annotated in 56 gene ontology (GO) categories, 6,033 were mapped to 131 KEGG pathways, and 7,825 were assigned to clusters of orthologous groups (COGs)...
2017: PloS One
https://www.readbyqxmd.com/read/28902847/first-insights-in-the-variability-of-borrelia-recurrentis-genomes
#19
Durdica Marosevic, Gabriele Margos, Reinhard Wallich, Andreas Wieser, Andreas Sing, Volker Fingerle
BACKGROUND: Borrelia recurrentis is the causative agent of louse-borne relapsing fever, endemic to the Horn of Africa. New attention was raised in Europe, with the highest number of cases (n = 45) reported among migrants in 2015 in Germany and sporadically from other European countries. So far only one genome was sequenced, hindering the development of specific molecular diagnostic and typing tools. Here we report on modified culture conditions for B. recurrentis and the intraspecies genome variability of six isolates isolated and cultured in different years in order to explore the possibility to identify new targets for typing and examine the molecular epidemiology of the pathogen...
September 13, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28900436/molecular-resources-from-transcriptomes-in-the-brassicaceae-family
#20
Lua Lopez, Eva M Wolf, J Chris Pires, Patrick P Edger, Marcus A Koch
The rapidly falling costs and the increasing availability of large DNA sequence data sets facilitate the fast and affordable mining of large molecular markers data sets for comprehensive evolutionary studies. The Brassicaceae (mustards) are an important species-rich family in the plant kingdom with taxa distributed worldwide and a complex evolutionary history. We performed Simple Sequence Repeats (SSRs) mining using de novo assembled transcriptomes from 19 species across the Brassicaceae in order to study SSR evolution and provide comprehensive sets of molecular markers for genetic studies within the family...
2017: Frontiers in Plant Science
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