scholarly journals Genome Update of Botrytis cinerea Strains B05.10 and T4

2012 ◽  
Vol 11 (11) ◽  
pp. 1413-1414 ◽  
Author(s):  
Martijn Staats ◽  
Jan A. L. van Kan
Keyword(s):  
Botrytis Cinerea ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Rna Seq ◽  
High Coverage ◽  
Protein Coding ◽  
Content Type ◽  
Gene Predictor ◽  
Structure Annotation ◽  
Expressed Sequence

ABSTRACT We report here an update of the Botrytis cinerea strains B05.10 and T4 genomes, as well as an automated preliminary gene structure annotation. High-coverage de novo assemblies and reference-based alignments led to a correction of wrong base calls, elimination of sequence gaps, and improved joining of contigs. The new assemblies have substantially lower numbers of scaffolds and a concomitant increase in the N 50 .The list of protein-coding genes was generated using the evidence-driven gene predictor Augustus, with expressed sequence tag evidence and RNA-Seq data as input.

scholarly journals Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse

2015 ◽  
Vol 36 (5) ◽  
pp. 809-819 ◽  
Author(s):  
Gireesh K. Bogu ◽  
Pedro Vizán ◽  
Lawrence W. Stanton ◽  
Miguel Beato ◽  
Luciano Di Croce ◽  
...  
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
De Novo ◽  
Noncoding Rnas ◽  
Mouse Cell ◽  
Long Noncoding Rnas ◽  
Chromatin State ◽  
Rna Seq ◽  
Gene Encoding ◽  
Protein Coding

Discovering and classifying long noncoding RNAs (lncRNAs) across all mammalian tissues and cell lines remains a major challenge. Previously, mouse lncRNAs were identified using transcriptome sequencing (RNA-seq) data from a limited number of tissues or cell lines. Additionally, associating a few hundred lncRNA promoters with chromatin states in a single mouse cell line has identified two classes of chromatin-associated lncRNA. However, the discovery and classification of lncRNAs is still pending in many other tissues in mouse. To address this, we built a comprehensive catalog of lncRNAs by combining known lncRNAs with high-confidence novel lncRNAs identified by mapping andde novoassembling billions of RNA-seq reads from eight tissues and a primary cell line in mouse. Next, we integrated this catalog of lncRNAs with multiple genome-wide chromatin state maps and found two different classes of chromatin state-associated lncRNAs, including promoter-associated (plncRNAs) and enhancer-associated (elncRNAs) lncRNAs, across various tissues. Experimental knockdown of an elncRNA resulted in the downregulation of the neighboring protein-codingKdm8gene, encoding a histone demethylase. Our findings provide 2,803 novel lncRNAs and a comprehensive catalog of chromatin-associated lncRNAs across different tissues in mouse.

scholarly journals Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis

2018 ◽  
Vol 6 (16) ◽  
pp. e00265-18 ◽  
Author(s):  
Stewart T. G. Burgess ◽  
Kathryn Bartley ◽  
Edward J. Marr ◽  
Harry W. Wright ◽  
Robert J. Weaver ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Gene Prediction ◽  
Draft Genome ◽  
Psoroptes Ovis ◽  
Protein Coding ◽  
Content Type ◽  
Sheep Scab ◽  
Draft Genome Assembly ◽  
Intense Pruritus

ABSTRACT Sheep scab, caused by infestation with Psoroptes ovis, is highly contagious, results in intense pruritus, and represents a major welfare and economic concern. Here, we report the first draft genome assembly and gene prediction of P. ovis based on PacBio de novo sequencing. The ∼63.2-Mb genome encodes 12,041 protein-coding genes.

scholarly journals Draft Genome Sequence of Escherichia coli KL53

2018 ◽  
Vol 6 (13) ◽  
Author(s):  
Katarina Soltys ◽  
Silvia Vavrova ◽  
Jaroslav Budis ◽  
Lenka Palkova ◽  
Gabriel Minarik ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Clinical Isolate ◽  
Genome Sequence ◽  
De Novo ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Tellurite Resistance ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes

ABSTRACT Here, we report the draft genome sequence of a clinical isolate of the uropathogenic strain Escherichia coli KL53. A total of 5,083,632 bp was de novo assembled into 170 contigs containing 89 RNAs and 5,034 protein-coding genes. Remarkable is the presence of the tellurite resistance ( ter ) operon on a plasmid.

scholarly journals Application of EST-SSR markers developed from the transcriptome of Torreya grandis (Taxaceae), a threatened nut-yielding conifer tree

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5606 ◽  
Author(s):  
Jun Zeng ◽  
Jie Chen ◽  
Yixuan Kou ◽  
Yujin Wang
Keyword(s):  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Population Genetic Analysis ◽  
Protein Databases ◽  
Genetic Groups ◽  
Conifer Tree ◽  
Torreya Grandis ◽  
Expressed Sequence ◽  
Distribution Frequency

Torreya grandis (Taxaceae) is an ancient conifer species endemic to southeast China. Because of its nutrient-rich and delicious seeds, this species has been utilized for centuries by the Chinese. However, transcriptome data and transcriptome-derived microsatellite markers for population genetics studies are still insufficient for understanding of this species’ genetic basis. In this study, a transcriptome from T. grandis leaves was generated using Illumina sequencing. A total of 69,920 unigenes were generated after de novo assembly, and annotated by searching against seven protein databases. In addition, 2,065 expressed sequence tag–simple sequence repeats (EST-SSRs) were detected, with the distribution frequency of 2.75% of total unigenes and average number of 0.03 SSRs per unigene. Among these EST-SSRs, 1,339 primer pairs were successfully designed, and 106 primer pairs were randomly selected for the development of potential molecular markers. Among them, 11 EST-SSR markers revealed a moderate level of genetic diversity, and were used to investigate the population structure of T. grandis. Two different genetic groups within this species were revealed using these EST-SSR markers, indicating that these markers developed in this study can be effectively applied to the population genetic analysis of T. grandis.

scholarly journals De novo transcriptome assembly of the Italian white truffle (Tuber magnatum Pico)

2018 ◽  
Author(s):  
Federico Vita ◽  
Amedeo Alpi ◽  
Edoardo Bertolini
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Rna Seq ◽  
Genetic Studies ◽  
Protein Coding ◽  
Important Species ◽  
White Truffle ◽  
Tuber Magnatum ◽  
Insight Into

AbstractThe Italian white truffle (Tuber magnatum Pico) is a gastronomic delicacy that dominates the worldwide truffle market. Despite its importance, the genomic resources currently available for this species are still limited. Here we present the first de novo transcriptome assembly of T. magnatum. Illumina RNA-seq data were assembled using a single-k-mer approach into 22,932 transcripts with N50 of 1,524 bp. Our approach allowed to predict and annotate 12,367 putative protein coding sequences, reunited in 6,723 loci. In addition, we identified 2,581 gene-based SSR markers. This work provides the first publicly available reference transcriptome for genomics and genetic studies providing insight into the molecular mechanisms underlying the biology of this important species.

scholarly journals Identification of sugarcane genes involved in the purine synthesis pathway

2001 ◽  
Vol 24 (1-4) ◽  
pp. 251-255 ◽  
Author(s):  
Mario A. Jancso ◽  
Susana A. Sculaccio ◽  
Otavio H. Thiemann
Keyword(s):  
Expressed Sequence Tag ◽  
De Novo ◽  
Statistical Significance ◽  
Local Alignment ◽  
Central Importance ◽  
Purine Nucleotides ◽  
Nucleotide Synthesis ◽  
Purine Synthesis ◽  
Search Tool ◽  
Expressed Sequence

Nucleotide synthesis is of central importance to all cells. In most organisms, the purine nucleotides are synthesized de novo from non-nucleotide precursors such as amino acids, ammonia and carbon dioxide. An understanding of the enzymes involved in sugarcane purine synthesis opens the possibility of using these enzymes as targets for chemicals which may be effective in combating phytopathogen. Such an approach has already been applied to several parasites and types of cancer. The strategy described in this paper was applied to identify sugarcane clusters for each step of the de novo purine synthesis pathway. Representative sequences of this pathway were chosen from the National Center for Biotechnology Information (NCBI) database and used to search the translated sugarcane expressed sequence tag (SUCEST) database using the available basic local alignment search tool (BLAST) facility. Retrieved clusters were further tested for the statistical significance of the alignment by an implementation (PRSS3) of the Monte Carlo shuffling algorithm calibrated using known protein sequences of divergent taxa along the phylogenetic tree. The sequences were compared to each other and to the sugarcane clusters selected using BLAST analysis, with the resulting table of p-values indicating the degree of divergence of each enzyme within different taxa and in relation to the sugarcane clusters. The results obtained by this strategy allowed us to identify the sugarcane proteins participating in the purine synthesis pathway.

scholarly journals Small RNAs Are Implicated in Regulation of Gene and Transposable Element Expression in the Protist Trichomonas vaginalis

mSphere ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Sally D. Warring ◽  
Frances Blow ◽  
Grace Avecilla ◽  
Jordan C. Orosco ◽  
Steven A. Sullivan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Small Rna ◽  
Trichomonas Vaginalis ◽  
Repetitive Elements ◽  
Rna Seq ◽  
Transmitted Infection ◽  
Protein Coding ◽  
Content Type ◽  
Rna Molecules ◽  
Sexually Transmitted

ABSTRACT Trichomonas vaginalis is the causative agent of trichomoniasis, the most prevalent nonviral sexually transmitted infection worldwide. Repetitive elements, including transposable elements (TEs) and virally derived repeats, comprise more than half of the ∼160-Mb T. vaginalis genome. An intriguing question is how the parasite controls its potentially lethal complement of mobile elements, which can disrupt transcription of protein-coding genes and genome functions. In this study, we generated high-throughput RNA sequencing (RNA-Seq) and small RNA-Seq data sets in triplicate for the T. vaginalis G3 reference strain and characterized the mRNA and small RNA populations and their mapping patterns along all six chromosomes. Mapping the RNA-Seq transcripts to the genome revealed that the majority of genes predicted within repetitive elements are not expressed. Interestingly, we identified a novel species of small RNA that maps bidirectionally along the chromosomes and is correlated with reduced protein-coding gene expression and reduced RNA-Seq coverage in repetitive elements. This novel small RNA family may play a regulatory role in gene and repetitive element expression. Our results identify a possible small RNA pathway mechanism by which the parasite regulates expression of genes and TEs and raise intriguing questions as to the role repeats may play in shaping T. vaginalis genome evolution and the diversity of small RNA pathways in general. IMPORTANCE Trichomoniasis, caused by the protozoan Trichomonas vaginalis, is the most common nonviral sexually transmitted infection in humans. The millions of cases each year have sequelae that may include complications during pregnancy and increased risk of HIV infection. Given its evident success in this niche, it is paradoxical that T. vaginalis harbors in its genome thousands of transposable elements that have the potential to be extremely detrimental to normal genomic function. In many organisms, transposon expression is regulated by the activity of endogenously expressed short (∼21 to 35 nucleotides [nt]) small RNA molecules that effect gene silencing by targeting mRNAs for degradation or by recruiting epigenetic silencing machinery to locations in the genome. Our research has identified small RNA molecules correlated with reduced expression of T. vaginalis genes and transposons. This suggests that a small RNA pathway is a major contributor to gene expression patterns in the parasite and opens up new avenues for investigation into small RNA biogenesis, function, and diversity.

scholarly journals Assembly and validation of conserved long non-coding RNAs in the ruminant transcriptome

2018 ◽  
Author(s):  
Stephen J. Bush ◽  
Charity Muriuki ◽  
Mary E. B. McCulloch ◽  
Iseabail L. Farquhar ◽  
Emily L. Clark ◽  
...  
Keyword(s):  
Developmental Stages ◽  
De Novo ◽  
Expression Profiles ◽  
Rna Seq ◽  
Protein Coding ◽  
Stochastic Sampling ◽  
Single Dataset ◽  
Non Coding Rnas ◽  
Low Levels ◽  
Species Mapping

AbstractmRNA-like long non-coding RNAs (lncRNA) are a significant component of mammalian transcriptomes, although most are expressed only at low levels, with high tissue-specificity and/or at specific developmental stages. In many cases, therefore, lncRNA detection by RNA-sequencing (RNA-seq) is compromised by stochastic sampling. To account for this and create a catalogue of ruminant lncRNA, we comparedde novoassembled lncRNA derived from large RNA-seq datasets in transcriptional atlas projects for sheep and goats with previous lncRNA assembled in cattle and human. Few lncRNA could be reproducibly assembled from a single dataset, even with deep sequencing of the same tissues from multiple animals. Furthermore, there was little sequence overlap between lncRNA assembled from pooled RNA-seq data. We combined positional conservation (synteny) with cross-species mapping of candidate lncRNA to identify a consensus set of ruminant lncRNA and then used the RNA-seq data to demonstrate detectable and reproducible expression in each species. The majority of lncRNA were encoded by single exons, and expressed at < 1 TPM. In sheep, 20-30% of lncRNA had expression profiles significantly correlated with neighbouring protein-coding genes, suggesting association with enhancers. Alongside substantially expanding the ruminant lncRNA repertoire, the outcomes of our analysis demonstrate that stochastic sampling can be partly overcome by combining RNA-seq datasets from related species. This has practical implications for the future discovery of lncRNA in other species.

scholarly journals Bioinformatic and experimental evidence for suicidal and catalytic plant THI4s

2020 ◽  
Author(s):  
Jaya Joshi ◽  
Guillaume A.W. Beaudoin ◽  
Jenelle A. Patterson ◽  
Jorge D. García-García ◽  
Catherine E. Belisle ◽  
...  
Keyword(s):  
Active Site ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Indirect Evidence ◽  
Grain Filling ◽  
Prima Facie ◽  
Major Type ◽  
In Planta ◽  
Grain Filling Period ◽  
Expressed Sequence

ABSTRACTLike fungi and some prokaryotes, plants use a thiazole synthase (THI4) to make the thiazole precursor of thiamin. Fungal THI4s are suicide enzymes that destroy an essential active-site Cys residue to obtain the sulfur atom needed for thiazole formation. In contrast, certain prokaryotic THI4s have no active-site Cys, use sulfide as sulfur donor, and are truly catalytic. The presence of a conserved active-site Cys in plant THI4s and other indirect evidence implies that they are suicidal. To confirm this, we complemented the Arabidopsis tz-1 mutant, which lacks THI4 activity, with a His-tagged Arabidopsis THI4 construct. LC-MS analysis of tryptic peptides of the THI4 extracted from leaves showed that the active-site Cys was predominantly in desulfurated form, consistent with THI4 having a suicide mech-anism in planta. Unexpectedly, transcriptome datamining and deep proteome profiling showed that barley, wheat, and oat have both a widely expressed canonical THI4 with an active-site Cys, and a THI4-like paralog (non-Cys THI4) that has no active-site Cys and is the major type of THI4 in devel-oping grains. Transcriptomic evidence also indicated that barley, wheat, and oat grains synthesize thiamin de novo, implying that their non-Cys THI4s synthesize thiazole. Structure modeling supported this inference, as did demonstration that non-Cys THI4s have significant capacity to complement thia-zole auxotrophy in Escherichia coli. There is thus a prima facie case that non-Cys cereal THI4s, like their prokaryotic counterparts, are catalytic thiazole synthases. Bioenergetic calculations show that, relative to suicide THI4s, such enzymes could save substantial energy during the grain filling period.AbbreviationsDHAla, dehydroalanine; EST, expressed sequence tag; FDR, false discovery rate; IPTG, β-D-1-thiogalactopyranoside

scholarly journals A Novel Software and Method for the Efficient Development of Polymorphic SSR Loci Based on Transcriptome Data

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 917
Author(s):  
Ruizheng Tian ◽  
Cunhuan Zhang ◽  
Yixiao Huang ◽  
Xin Guo ◽  
Maohua Chen
Keyword(s):  
Expressed Sequence Tag ◽  
The Body ◽  
Pea Aphid ◽  
New Method ◽  
Transcriptome Data ◽  
Rna Seq ◽  
Ssr Loci ◽  
Polymorphic Microsatellite ◽  
Expressed Sequence ◽  
Simple Sequence

Traditional methods for developing polymorphic microsatellite loci without reference sequences are time-consuming and labor-intensive, and the polymorphisms of simple sequence repeat (SSR) loci developed from expressed sequence tag (EST) databases are generally poor. To address this issue, in this study, we developed a new software (PSSRdt) and established an effective method for directly obtaining polymorphism details of SSR loci by analyzing diverse transcriptome data. The new method includes three steps, raw data processing, PSSRdt application, and loci extraction and verification. To test the practicality of the method, we successfully obtained 1940 potential polymorphic SSRs from the transcript dataset combined with 44 pea aphid transcriptomes. Fifty-two SSR loci obtained by the new method were selected for validating the polymorphic characteristics by genotyping in pea aphid individuals. The results showed that over 92% of SSR loci were polymorphic and 73.1% of loci were highly polymorphic. Our new software and method provide an innovative approach to microsatellite development based on RNA-seq data, and open a new path for the rapid mining of numerous loci with polymorphism to add to the body of research on microsatellites.

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