SeqTrim — A Validation and Trimming Tool for All Purpose Sequence Reads

Falgueras, Juan; Lara, Antonio Jiménez; Cantón, Francisco R.; Pérez-Trabado, Guillermo; Claros, M. Gonzalo

doi:10.1007/978-3-540-74972-1_46

Cited by 5 publications

(6 citation statements)

References 13 publications

(18 reference statements)

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“…In order to estimate the number of different Unigenes identified, two independent steps of filtering were performed to remove any possible source of contamination from the final transcriptome and to avoid redundancy as far as possible. On the one hand, sequences without blast results were analyzed using SeqTrimNext software (advanced version of SeqTrim, Falgueras et al, 2007 ) with a specific template customized for Roche 454 GS-FLX plant transcriptomic data. To identify and reject sequences from inoculated organisms an additional comparison was performed with a database containing sequences from O. novo-ulmi and O. ulmi genomes ( Forgetta et al, 2013 ; Khoshraftar et al, 2013 ), from D. concentrica (48 sequences in GenBank database) and sequences from D. eschscholzii genome ( Ng et al, 2012 ).…”

Section: Methodsmentioning

confidence: 99%

Massive sequencing of Ulmus minor’s transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease

et al. 2015

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Elms, especially Ulmus minor and U. americana, are carrying out a hard battle against Dutch elm disease (DED). This vascular wilt disease, caused by Ophiostoma ulmi and O. novo-ulmi, appeared in the twentieth century and killed millions of elms across North America and Europe. Elm breeding and conservation programmes have identified a reduced number of DED tolerant genotypes. In this study, three U. minor genotypes with contrasted levels of tolerance to DED were exposed to several biotic and abiotic stresses in order to (i) obtain a de novo assembled transcriptome of U. minor using 454 pyrosequencing, (ii) perform a functional annotation of the assembled transcriptome, (iii) identify genes potentially involved in the molecular response to environmental stress, and (iv) develop gene-based markers to support breeding programmes. A total of 58,429 putative unigenes were identified after assembly and filtering of the transcriptome. 32,152 of these unigenes showed homology with proteins identified in the genome from the most common plant model species. Well-known family proteins and transcription factors involved in abiotic, biotic or both stresses were identified after functional annotation. A total of 30,693 polymorphisms were identified in 7,125 isotigs, a large number of them corresponding to single nucleotide polymorphisms (SNPs; 27,359). In a subset randomly selected for validation, 87% of the SNPs were confirmed. The material generated may be valuable for future Ulmus gene expression, population genomics and association genetics studies, especially taking into account the scarce molecular information available for this genus and the great impact that DED has on elm populations.

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Section: Methodsmentioning

confidence: 99%

Massive sequencing of Ulmus minor’s transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease

et al. 2015

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“…Clones with confirmed single inserts were sequenced single-pass (McGill University and Génome Québec Innovation Center). Sequences were base called using phred (Green 2002 ) and trimmed using SeqTrim (Falgueras et al 2007 ). The sequences appear in public sequence databases under the GenBank accession numbers GW696871 to GW698115.…”

Section: Methodsmentioning

confidence: 99%

PR-10, defensin and cold dehydrin genes are among those over expressed in Oxytropis (Fabaceae) species adapted to the arctic

Archambault

Strömvik

2011

Funct Integr Genomics

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In many studied plants, typical responses to cold treatment include up-regulating the hydrophilic COR/LEA genes and down-regulating photosynthesis-related genes, carbohydrate metabolism, GDSL-motif lipase, hormone metabolism and oxidative regulation genes. However, next to nothing is known about gene expression in arctic plants, which are actually adapted to a harsh, cold environment. The molecular mechanisms behind the many specific adaptations of arctic plants, such as slow growth, well-developed root systems and short stature, are not well understood. In this study, we examine whole plantlet transcriptome differences between two arctic and two temperate Oxytropis (Fabaceae) species, grown under their respective controlled environmental conditions. Gene expression differences are analyzed using cDNA library subtraction followed by expressed sequence tags sequencing and annotation. Sequences from a total of nearly 2,000 clones cluster into 121 and 368 unique genes from the arctic and from the temperate plants, respectively. The predominant biological process for genes from the arctic-enriched library is “response to stimulus”. A concurrent overexpression of pathogenesis-related class 10 proteins (PR-10), plant defensin and cold dehydrin genes is a novel feature for species adapted to stressful growth environment. The temperate-enriched genes are involved in photosynthesis, translation and nucleosome assembly. Interestingly, both arctic and temperate-enriched libraries also contain genes involved in ribosome biogenesis and assembly, however of different types. Real-time reverse transcription PCR of cold dehydrin and two PR-10 genes, as well as the light harvesting complex b1 genes demonstrates that the gene expression is dependent on species and growth conditions.Electronic supplementary materialThe online version of this article (doi:10.1007/s10142-011-0223-6) contains supplementary material, which is available to authorized users.

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“…Selected clones were single-pass sequenced (Macrogen Inc., Seoul, Korea). Sequences were trimmed using SeqTrim v0.098 -w0.19 29 e-values lower than 1 × 10 -10 were considered significant. Functional classification was performed according to KEGG.…”

Section: Methodsmentioning

confidence: 99%

Combined Proteomic and Transcriptomic Analysis Identifies Differentially Expressed Pathways Associated to Pinus radiata Needle Maturation

et al. 2010

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Needle differentiation is a very complex process that leads to the formation of a mature photosynthetic organ from pluripotent needle primordia. The proteome and transcriptome of immature and fully developed needles of Pinus radiata D. Don were compared to described changes in mRNA and protein species that characterize the needle maturation developmental process. A total of 856 protein spots were analyzed, defining a total of 280 spots as differential between developmental stages, from which 127 were confidently identified. A suppressive subtractive library (2048 clones, 274 non redundant contigs) was built, and 176 genes showed to be differentially expressed. The Joint data analysis of proteomic and transcriptomic results provided a broad overview of differentially expressed pathways associated with needle maturation and stress-related pathways. Proteins and genes related to energy metabolism pathways, photosynthesis, and oxidative phosphorylation were overexpressed in mature needles. Amino acid metabolism, transcription, and translation pathways were overexpressed in immature needles. Interestingly, stress related proteins were characteristic of immature tissues, a fact that may be linked to defense mechanisms and the higher growth rate and morphogenetic competence exhibited by these needles. Thus, this work provides an overview of the molecular changes affecting proteomes and transcriptomes during P. radiata needle maturation, having an integrative vision of the functioning and physiology of this process.

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SeqTrim — A Validation and Trimming Tool for All Purpose Sequence Reads

Cited by 5 publications

References 13 publications

Massive sequencing of Ulmus minor’s transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease

Massive sequencing of Ulmus minor’s transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease

PR-10, defensin and cold dehydrin genes are among those over expressed in Oxytropis (Fabaceae) species adapted to the arctic

Combined Proteomic and Transcriptomic Analysis Identifies Differentially Expressed Pathways Associated to Pinus radiata Needle Maturation

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