scholarly journals De novo transcriptome sequencing and comparative analysis of midgut tissues of four non-model insects pertaining to Hemiptera, Coleoptera, Diptera and Lepidoptera

2017 ◽  
Author(s):  
Rajesh K. Gazara ◽  
Christiane Cardoso ◽  
Daniel Bellieny-Rabelo ◽  
Clélia Ferreira ◽  
Walter R. Terra ◽  
...  
Keyword(s):  
Spodoptera Frugiperda ◽  
De Novo ◽  
Morphological Diversity ◽  
Evolutionary Information ◽  
De Novo Transcriptome ◽  
Cytochrome P450 Genes ◽  
Computational Strategy ◽  
Shed Light ◽  
Dysdercus Peruvianus

ABSTRACTDespite the great morphological diversity of insects, there is a regularity in their digestive functions, which is apparently related to their physiology. In the present work we report the de novo midgut transcriptomes of four non-model insects from four distinct orders: Spodoptera frugiperda (Lepidoptera), Musca domestica (Diptera), Tenebrio molitor (Coleoptera) and Dysdercus peruvianus (Hemiptera). We employed a computational strategy to merge assemblies obtained with two different algorithms, which substantially increased the quality of the final transcriptomes. Unigenes were annotated and analyzed using the eggNOG database, which allowed us to assign some level of functional and evolutionary information to 79.7% to 93.1% of the transcriptomes. We found interesting transcriptional patterns, such as: i) the intense use of lysozymes in digestive functions of M. domestica larvae, which are streamlined and adapted to feed on bacteria; ii) the up-regulation of orthologous UDP-glycosyl transferase and cytochrome P450 genes in the whole midguts different species, supporting the presence of an ancient defense frontline to counter xenobiotics; iii) evidence supporting roles for juvenile hormone binding proteins in the midgut physiology, probably as a way to activate genes that help fight anti-nutritional substances (e.g. protease inhibitors). The results presented here shed light on the digestive and structural properties of the digestive systems of these distantly related species. Furthermore, the produced datasets will also be useful for scientists studying these insects.

scholarly journals TransRate: reference free quality assessment of de-novo transcriptome assemblies

2015 ◽  
Author(s):  
Richard D Smith-Unna ◽  
Chris Boursnell ◽  
Rob Patro ◽  
Julian M Hibberd ◽  
Steven Kelly
Keyword(s):  
Quality Assessment ◽  
De Novo ◽  
De Novo Transcriptome ◽  
Rna Molecules

TransRateis a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only sequenced reads as the input,TransRatemeasures the quality of individual contigs and whole assemblies, enabling assembly optimization and comparison.TransRatecan accurately evaluate assemblies of conserved and novel RNA molecules of any kind in any species. We show that it is more accurate than comparable methods and demonstrate its use on a variety of data.

scholarly journals Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

2016 ◽  
Author(s):  
Cédric Cabau ◽  
Frédéric Escudié ◽  
Anis Djari ◽  
Yann Guiguen ◽  
Julien Bobe ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Error Rates ◽  
Rna Seq ◽  
De Novo Transcriptome ◽  
Software Packages ◽  
Redundancy Reduction ◽  
Assembly Pipeline ◽  
Free Open Source

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. Results We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1,3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Conclusion Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an ease to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available at http://www.sigenae.org/drap .

scholarly journals Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

2016 ◽  
Author(s):  
Cédric Cabau ◽  
Frédéric Escudié ◽  
Anis Djari ◽  
Yann Guiguen ◽  
Julien Bobe ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Error Rates ◽  
Rna Seq ◽  
De Novo Transcriptome ◽  
Software Packages ◽  
Redundancy Reduction ◽  
Assembly Pipeline ◽  
Free Open Source

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. Results We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1,3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Conclusion Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an ease to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available at http://www.sigenae.org/drap .

scholarly journals Comprehensive transcriptome analysis of grafting onto Artemisia scoparia  W. to affect the aphid resistance of chrysanthemum (Chrysanthemum morifolium T. )

2019 ◽  
Author(s):  
Xue-ying Zhang(Former Corresponding Author) ◽  
Xian-zhi Sun(New Corresponding Author) ◽  
Sheng Zhang ◽  
Fang-fang Liu ◽  
Jing-hui Yang ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Chrysanthemum Morifolium ◽  
De Novo Transcriptome Assembly ◽  
Rna Seq ◽  
De Novo Transcriptome ◽  
Biotic And Abiotic Stresses ◽  
Yield And Quality ◽  
Artemisia Scoparia

Abstract Aphid ( Macrosiphoniella sanbourni ) stress drastically influences the yield and quality of chrysanthemum, and grafting has been widely used to improve tolerance to biotic and abiotic stresses. However, the effect of grafting on the resistance of chrysanthemum to aphids remains unclear. Therefore, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze the self - rooted grafted chrysanthemum ( Chrysanthemum morifolium 'Hangbaiju') and the grafted Artermisia-chrysanthemum ( grafted onto Artemisia scoparia ) transcription response to aphid stress.

scholarly journals Impact of sequencing data filtering on the quality of de novo transcriptome assembly

2021 ◽  
Vol 270 ◽  
pp. 01014
Author(s):  
Yakov Meger ◽  
Ekaterina Vodiasova ◽  
Anastasiya Lantushenko
Keyword(s):  
Input Data ◽  
De Novo ◽  
Transcriptome Assembly ◽  
De Novo Transcriptome Assembly ◽  
Data Filtering ◽  
Sequencing Data ◽  
De Novo Transcriptome ◽  
Filtering Algorithm ◽  
Required Quality

There are many assemblers with different algorithms that are used for de novo transcriptome assembly. At the same time, the filtering stage, which is one of the key stages, also has several approaches and algorithms. However, to date, there are only few studies on the effect of the degree of filtration on the de novo transcriptome assembly, specially for single-end reads. In this paper, we analyzed transcriptomes obtained using two of the most common software (rnaSPADES and Trinity), and also applied various approaches to the stage of filtering reads. The key differences between the two assemblies were shown and the parameters that were sensitive to the degree of filtering and the length of the input reads were identified. An efficient two-stage filtering algorithm was also proposed, which allows one to preserve the volume of input data as much as possible with the required quality of all reads after filtering and trimming.

The Baluch, Sunnism and the State in Iran

2017 ◽  
Author(s):  
Stéphane A. Dudoignon
Keyword(s):  
South Asia ◽  
South Asian ◽  
Social Life ◽  
The State ◽  
First Century ◽  
Local Democracy ◽  
Oasis Area ◽  
Shed Light

Since 2002, Sunni jihadi groups have been active in Iranian Baluchistan without managing to plunge the region into chaos. This book suggests that a reason for this, besides Tehran’s military responses, has been the quality of Khomeini and Khamenei’s relationship with a network of South-Asia-educated Sunni ulama (mawlawis) originating from the Sarbaz oasis area, in the south of Baluchistan. Educated in the religiously reformist, socially conservative South Asian Deoband School, which puts the madrasa at the centre of social life, the Sarbazi ulama had taken advantage, in Iranian territory, of the eclipse of Baluch tribal might under the Pahlavi monarchy (1925-79). They emerged then as a bulwark against Soviet influence and progressive ideologies, before rallying to Khomeini in 1979. Since the turn of the twenty-first century, they have been playing the role of a rampart against Salafi propaganda and Saudi intrigues. The book shows that, through their alliance with an Iranian Kurdish-born Muslim-Brother movement and through the promotion of a distinct ‘Sunni vote’, they have since the early 2000s contributed towards – and benefitted from – the defence by the Reformist presidents Khatami (1997-2005) and Ruhani (since 2013) of local democracy and of the minorities’ rights. They endeavoured to help, at the same time, preventing the propagation of jihadism and Sunni radicalisation to Iran – at least until the ISIS/Daesh-claimed attacks of June 2017, in Tehran, shed light on the limits of the Islamic Republic’s strategy of reliance on Deobandi ulama and Muslim-Brother preachers in the country’s Sunni-peopled peripheries.

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