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de novo assembly

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https://www.readbyqxmd.com/read/28229564/diversification-of-hox-gene-clusters-in-osteoglossomorph-fish-in-comparison-to-other-teleosts-and-the-spotted-gar-outgroup
#1
Kyle J Martin, Peter W H Holland
An ancient genome duplication (TGD or 3R) occurred in teleost fish after divergence from the lineage leading to gar. This genome duplication is shared by the three extant teleost lineages: Osteoglossomorpha (bony-tongues), Elopomorpha (eels and tarpons), and Clupeocephala (a large clade including salmon, carp, medaka, zebrafish, cichlids, pufferfish, stickleback, and ∼26,000 other species). After TGD, different clupeocephalan species retained different gene duplicates; this is seen clearly in Hox gene clusters but extends to all genes...
February 23, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28228764/de-novo-transcriptome-assembly-of-chinese-kale-and-global-expression-analysis-of-genes-involved-in-glucosinolate-metabolism-in-multiple-tissues
#2
Shuanghua Wu, Jianjun Lei, Guoju Chen, Hancai Chen, Bihao Cao, Changming Chen
Chinese kale, a vegetable of the cruciferous family, is a popular crop in southern China and Southeast Asia due to its high glucosinolate content and nutritional qualities. However, there is little research on the molecular genetics and genes involved in glucosinolate metabolism and its regulation in Chinese kale. In this study, we sequenced and characterized the transcriptomes and expression profiles of genes expressed in 11 tissues of Chinese kale. A total of 216 million 150-bp clean reads were generated using RNA-sequencing technology...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28228093/comparative-profiling-of-hepatopancreas-transcriptomes-in-satiated-and-starving-pomacea-canaliculata
#3
Lei Yang, Tian-Yin Cheng, Fei-Yan Zhao
BACKGROUND: Although Pomacea canaliculata is native to South and Central America, it has become one of the most abundant invasive species worldwide and causes extensive damage to agriculture and horticulture. Conventional physical and chemical techniques have been used to eliminate P. canaliculata, but the effects are not ideal. Therefore, it is important to devise a new method based on a greater understanding of the biology of P. canaliculata. However, the molecular mechanisms underlying digestion and absorption in P...
February 22, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28228091/exploring-the-transcriptome-of-non-model-oleaginous-microalga-dunaliella-tertiolecta-through-high-throughput-sequencing-and-high-performance-computing
#4
Lina Yao, Kenneth Wei Min Tan, Tin Wee Tan, Yuan Kun Lee
BACKGROUND: RNA-Seq technology has received a lot of attention in recent years for microalgal global transcriptomic profiling. It is widely used in transcriptome-wide analysis of gene expression., particularly for microalgal strains with potential as biofuel sources. However, insufficient genomic or transcriptomic information of non-model microalgae has limited the understanding of their regulatory mechanisms and hampered genetic manipulation to enhance biofuel production. As such, an optimal microalgal transcriptomic database construction is a subject of urgent investigation...
February 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28225773/whole-genome-duplication-and-molecular-evolution-in-cornus-l-cornaceae-insights-from-transcriptome-sequences
#5
Yan Yu, Qiuyun Xiang, Paul S Manos, Douglas E Soltis, Pamela S Soltis, Bao-Hua Song, Shifeng Cheng, Xin Liu, Gane Wong
The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework...
2017: PloS One
https://www.readbyqxmd.com/read/28225089/the-hidden-perils-of-read-mapping-as-a-quality-assessment-tool-in-genome-sequencing
#6
B Lehri, A M Seddon, A V Karlyshev
This article provides a comparative analysis of the various methods of genome sequencing focusing on verification of the assembly quality. The results of a comparative assessment of various de novo assembly tools, as well as sequencing technologies, are presented using a recently completed sequence of the genome of Lactobacillus fermentum 3872. In particular, quality of assemblies is assessed by using CLC Genomics Workbench read mapping and Optical mapping developed by OpGen. Over-extension of contigs without prior knowledge of contig location can lead to misassembled contigs, even when commonly used quality indicators such as read mapping suggest that a contig is well assembled...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28225035/deep-sequencing-and-transcriptome-analyses-to-identify-genes-involved-in-secoiridoid-biosynthesis-in-the-tibetan-medicinal-plant-swertia-mussotii
#7
Yue Liu, Yi Wang, Fengxian Guo, Lin Zhan, Toni Mohr, Prisca Cheng, Naxin Huo, Ronghui Gu, Danning Pei, Jiaqing Sun, Li Tang, Chunlin Long, Luqi Huang, Yong Q Gu
Swertia mussotii Franch. is an important traditional Tibetan medicinal plant with pharmacological properties effective in the treatment of various ailments including hepatitis. Secoiridoids are the major bioactive compounds in S. mussotii. To better understand the secoiridoid biosynthesis pathway, we generated transcriptome sequences from the root, leaf, stem, and flower tissues, and performed de novo sequence assembly, yielding 98,613 unique transcripts with an N50 of 1,085 bp. Putative functions could be assigned to 35,029 transcripts (35...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28224052/compacting-and-correcting-trinity-and-oases-rna-seq-de-novo-assemblies
#8
Cédric Cabau, Frédéric Escudié, Anis Djari, Yann Guiguen, Julien Bobe, Christophe Klopp
BACKGROUND: De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved...
2017: PeerJ
https://www.readbyqxmd.com/read/28220138/de-novo-transcriptome-assembly-of-phomopsis-liquidambari-provides-insights-into-genes-associated-with-different-lifestyles-in-rice-oryza-sativa-l
#9
Jun Zhou, Xin Li, Yan Chen, Chuan-Chao Dai
The mechanisms that trigger the switch from endophytic fungi to saprophytic fungi are largely unexplored. Broad host range Phomopsis liquidambari is established in endophytic and saprophytic systems with rice (Oryza sativa L.). Endophytic P. liquidambari promotes rice growth, increasing rice yield and improving the efficiency of nitrogen fertilizer. This species's saprophytic counterpart can decompose rice litterfall, promoting litter organic matter cycling and the release of nutrients and improving the soil microbial environment...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28220135/differential-gene-expression-analysis-in-polygonum-minus-leaf-upon-24-h-of-methyl-jasmonate-elicitation
#10
Reyhaneh Rahnamaie-Tajadod, Kok-Keong Loke, Hoe-Han Goh, Normah M Noor
Polygonum minus is an herbal plant that grows in Southeast Asian countries and traditionally used as medicine. This plant produces diverse secondary metabolites such as phenolic compounds and their derivatives, which are known to have roles in plant abiotic and biotic stress responses. Methyl jasmonate (MeJA) is a plant signaling molecule that triggers transcriptional reprogramming in secondary metabolism and activation of defense responses against many biotic and abiotic stresses. However, the effect of MeJA elicitation on the genome-wide expression profile in the leaf tissue of P...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28219787/a-novel-archaeal-species-belonging-to-methanoculleus-genus-identified-via-de-novo-assembly-and-metagenomic-binning-process-in-biogas-reactors
#11
Panagiotis G Kougias, Stefano Campanaro, Laura Treu, Xinyu Zhu, Irini Angelidaki
Recently, a first comprehensive catalogue of microbial genomes populating biogas reactors treating manure and agro-industrial residues was determined by sequencing samples collected from 22 biogas reactors including laboratory and full scale. Among the archaeal community, one of the most abundant methanogens belongs to Methanoculleus genus and for this reason it was provisionally named Methanoculleus sp. DTU006. Its full length 16S rRNA sequence is 97% similar to Methanoculleus marisnigri JR1 and to Methanoculleus palmolei DSM 4273...
February 17, 2017: Anaerobe
https://www.readbyqxmd.com/read/28217442/whole-genome-sequencing-and-analysis-of-campylobacter-coli-yh502-from-retail-chicken-reveals-a-plasmid-borne-type-vi-secretion-system
#12
Sandeep Ghatak, Yiping He, Sue Reed, Terence Strobaugh, Peter Irwin
Campylobacter is a major cause of foodborne illnesses worldwide. Campylobacter infections, commonly caused by ingestion of undercooked poultry and meat products, can lead to gastroenteritis and chronic reactive arthritis in humans. Whole genome sequencing (WGS) is a powerful technology that provides comprehensive genetic information about bacteria and is increasingly being applied to study foodborne pathogens: e.g., evolution, epidemiology/outbreak investigation, and detection. Herein we report the complete genome sequence of Campylobacter coli strain YH502 isolated from retail chicken in the United States...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28216796/design-and-synthesis-of-nanofibers-of-self-assembled-de-novo-glycoconjugates-towards-mucosal-lining-restoration-and-anti-inflammatory-drug-delivery
#13
Jie Zhou, Michael O'Keeffe, Gongxian Liao, Fan Zhao, Cox Terhorst, Bing Xu
The medical practice for IBD is solely based on anti-inflammatory drugs, but the outcome is far from ideal. Our long-term research goal is to seek a better clinical outcome by combining the anti-inflammatory therapy with physical mucus layer restoration. As the first step towards that objective, we choose to develop self-assembled hydrogels of de novo glycoconjugates that consist of anti-inflammatory drugs and glycopeptides. By covalently linking peptides (e.g., nap-phe-phe-lys), saccharides (e.g., glucosamine), and an anti-inflammatory drug (i...
October 6, 2016: Tetrahedron
https://www.readbyqxmd.com/read/28216038/de-novo-transcriptome-of-the-muga-silkworm-antheraea-assamensis-helfer
#14
Hasnahana Chetia, Debajyoti Kabiraj, Deepika Singh, Ponnala Vimal Mosahari, Suradip Das, Pragya Sharma, Kartik Neog, Swagata Sharma, P Jayaprakash, Utpal Bora
Antheraea assamensis (Lepidoptera: Saturniidae), is a semi-domesticated silkworm known to be endemic to Assam and the adjoining hilly areas of Northeast India. It is the only producer of a unique, commercially important variety of golden silk called "muga silk". Herein, we report the de novo transcriptome of A. assamensis reared on Machilus bombycina leaves for the first time. Short reads generated by high throughput sequencing of cDNA libraries from multiple tissues, viz. alimentary canal, silk gland and residual body were assembled into transcripts via a de novo assembly pipeline followed by functional annotation and classification...
February 16, 2017: Gene
https://www.readbyqxmd.com/read/28212394/de-novo-transcriptome-analysis-and-microsatellite-marker-development-for-population-genetic-study-of-a-serious-insect-pest-rhopalosiphum-padi-l-hemiptera-aphididae
#15
Xinle Duan, Kang Wang, Sha Su, Ruizheng Tian, Yuting Li, Maohua Chen
The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not been investigated. In this study, we used transcriptome information obtained by RNA-Seq to develop polymorphic microsatellites for investigating population genetics in this species. The transcriptome of R. padi was sequenced on an Illumina HiSeq 2000 platform...
2017: PloS One
https://www.readbyqxmd.com/read/28212382/de-novo-assembly-of-the-sea-trout-salmo-trutta-m-trutta-skin-transcriptome-to-identify-putative-genes-involved-in-the-immune-response-and-epidermal-mucus-secretion
#16
Magdalena Malachowicz, Roman Wenne, Artur Burzynski
In fish, the skin is a multifunctional organ and the first barrier against pathogens. Salmonids differ in their susceptibility to microorganisms due to varied skin morphology and gene expression patterns. The brown trout is a salmonid species with important commercial and ecological value in Europe. However, there is a lack of knowledge regarding the genes involved in the immune response and mucus secretion in the skin of this fish. Thus, we characterized the skin transcriptome of anadromous brown trout using next-generation sequencing (NGS)...
2017: PloS One
https://www.readbyqxmd.com/read/28210266/a-phylogenetic-analysis-of-chloroplast-genomes-elucidates-the-relationships-of-the-six-economically-important-brassica-species-comprising-the-triangle-of-u
#17
Peirong Li, Shujiang Zhang, Fei Li, Shifan Zhang, Hui Zhang, Xiaowu Wang, Rifei Sun, Guusje Bonnema, Theo J A Borm
The Brassica genus comprises many economically important worldwide cultivated crops. The well-established model of the Brassica genus, U's triangle, consists of three basic diploid plant species (Brassica rapa, Brassica oleracea, and Brassica nigra) and three amphidiploid species (Brassica napus, Brassica juncea, and Brassica carinata) that arose through interspecific hybridizations. Despite being extensively studied because of its commercial relevance, several aspects of the origin of the Brassica species and the relationships within and among these six species still remain open questions...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28210265/rna-seq-of-guar-cyamopsis-tetragonoloba-l-taub-leaves-de-novo-transcriptome-assembly-functional-annotation-and-development-of-genomic-resources
#18
Umesh K Tanwar, Vikas Pruthi, Gursharn S Randhawa
Genetic improvement in industrially important guar (Cyamopsis tetragonoloba, L. Taub.) crop has been hindered due to the lack of sufficient genomic or transcriptomic resources. In this study, RNA-Seq technology was employed to characterize the transcriptome of leaf tissues from two guar varieties, namely, M-83 and RGC-1066. Approximately 30 million high-quality pair-end reads of each variety generated by Illumina HiSeq platform were used for de novo assembly by Trinity program. A total of 62,146 non-redundant unigenes with an average length of 679 bp were obtained...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28209812/sequencing-and-de-novo-assembly-of-the-complete-chloroplast-genome-of-the-peruvian-carrot-arracacia-xanthorrhiza-bancroft
#19
Javier Santiago Alvarado, Diane Hinojosa López, Isaury Maldonado Torres, María Margarita Meléndez, Rosalinda Aybar Batista, Vivek K Raxwal, Juan A Negrón Berríos, Alok Arun
Arracacia xanthorrhiza is an important secondary food crop in South America and Puerto Rico. The lack of crop protection and improvement strategies leads to infections damaging the storage roots. Here, we report the annotated complete chloroplast genome sequence of A. xanthorrhiza as a step toward developing genomic resources for this crop.
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28209181/de-novo-sequencing-and-comparative-transcriptome-analysis-of-adventitious-root-development-induced-by-exogenous-indole-3-butyric-acid-in-cuttings-of-tetraploid-black-locust
#20
Jine Quan, Seng Meng, Erhui Guo, Sheng Zhang, Zhong Zhao, Xitian Yang
BACKGROUND: Indole-3-butyric acid (IBA) is applied to the cuttings of various plant species to induce formation of adventitious roots (ARs) in commercial settings. Tetraploid black locust is an attractive ornamental tree that is drought resistant, sand tolerant, can prevent sand erosion and has various commercial uses. To further elucidate the mechanisms of AR formation, we used Illumina sequencing to analyze transcriptome dynamics and differential gene expression at four developmental stages in control (CK) and IBA-treated groups...
February 16, 2017: BMC Genomics
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