Annocript: a flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs

Musacchia, Francesco; Basu, Swaraj; Petrosino, Giuseppe; Salvemini, Marco; Sanges, Remo

doi:10.1093/bioinformatics/btv106

Cited by 102 publications

(79 citation statements)

References 20 publications

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“…The model built on the training data was applied to the entire repeat masked assembly, together with external support from homologous proteins aligned using E xonerate (Slater & Birney, 2005). The predicted gene models were annotated using A nnocript (Musacchia et al ., 2015). …”

Section: Methodsmentioning

confidence: 99%

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

et al. 2017

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Summary Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process in phytoplankton is poorly defined. Using the marine planktonic diatom Pseudo‐nitzschia multistriata, we investigated the cell response to cues released during sexual reproduction, an event that demands strong regulatory mechanisms and impacts on population dynamics.We sequenced the genome of P. multistriata and performed phylogenomic and transcriptomic analyses, which allowed the definition of gene gains and losses, horizontal gene transfers, conservation and evolutionary rate of sex‐related genes. We also identified a small number of conserved noncoding elements.Sexual reproduction impacted on cell cycle progression and induced an asymmetric response of the opposite mating types. G protein‐coupled receptors and cyclic guanosine monophosphate (cGMP) are implicated in the response to sexual cues, which overall entails a modulation of cell cycle, meiosis‐related and nutrient transporter genes, suggesting a fine control of nutrient uptake even under nutrient‐replete conditions.The controllable life cycle and the genome sequence of P. multistriata allow the reconstruction of changes occurring in diatoms in a key phase of their life cycle, providing hints on the evolution and putative function of their genes and empowering studies on sexual reproduction.

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Section: Methodsmentioning

confidence: 99%

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

et al. 2017

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“…We used the Annocript pipeline21 to annotate these 77 hypothetical DEGs. Annocript successfully annotated 29 DEGs, based on the data at the Swiss-Prot (SP) and UniRef90 databases22 (Supplementary Table S6).…”

Section: Resultsmentioning

confidence: 99%

“…To annotate the hypothetical DEGs, we used the custom pipeline Annocript21 (https://github.com/frankMusacchia/Annocript/tree/master/GUIDE). We used Swiss-Prot (SP) and UniRef9022 (version: August 2015) databases for blastp searches with the following parameters: word_size = 4; e-value = 10 −5 ; num_descriptions = 5; num_alignments = 5; threshold = 18.…”

Section: Methodsmentioning

confidence: 99%

MerR and ChrR mediate blue light induced photo-oxidative stress response at the transcriptional level in Vibrio cholerae

Tardu

Bulut

Kavaklı

2017

Sci Rep

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Blue light (BL) is a major environmental factor that affects the physiology, behavior, and infectivity of bacteria as it contributes to the generation of reactive oxygen species (ROS) while increasing photo-oxidative stress in cells. However, precise photo-oxidative response mechanism in non-phototrophic bacteria is yet to be elucidated. In this study, we investigated the effect of BL in Vibrio cholerae by using genetics and transcriptome profiling. Genome-wide analysis revealed that transcription of 6.3% of V. cholerae genes were regulated by BL. We further showed that BL enhances ROS production, which is generated through the oxidative phosphorylation. To understand signaling mechanisms, we generated several knockouts and analyzed their transcriptome under BL exposure. Studies with a double-knockout confirm an anti-sigma factor (ChrR) and putative metalloregulatory-like protein (MerR) are responsible for the genome-wide regulation to BL response in V. cholerae. Collectively, these results demonstrate that MerR-like proteins, in addition to ChrR, are required for V. cholerae to mount an appropriate response against photo-oxidative stress induced by BL. Outside its natural host, V. cholerae can survive for extended periods in natural aquatic environments. Therefore, the regulation of light response for V. cholerae may be a critical cellular process for its survival in these environments.

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“…Final transcriptomes were then annotated with Annocript (version 1.2, Musacchia et al 2015) using the UniProt Reference Clusters (UniRef) database (version February 2016;Suzek et al 2015). Transcripts with significant blast hits (E value < 1e−5) against possible contaminants (plants, fungus, mites, and bacteria) in UniRef were removed from the final dataset and were also used to identify other contaminants based on cluster analysis from Corset, as described in Araujo et al (2016).…”

Section: Transcriptome Assemblymentioning

confidence: 99%

RNA-Seq reveals that mitochondrial genes and long non-coding RNAs may play important roles in the bivoltine generations of the non-social Neotropical bee Tetrapedia diversipes

2017

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-In animals, voltinism is a result of evolutionary adaptations to environmental conditions. These evolutionary adaptations may profoundly affect the population structure and social organization level. To study the bivoltinism of the solitary bee Tetrapedia diversipes , we performed comparative transcriptomics analyses of foundresses and larvae from the two reproductive generations (G1 and G2) produced per year by this bee. Most of the differentially expressed genes (DEGs) were found between foundresses: 52 DEGs between adults, but only one between the larvae. Among the DEGs in foundresses, 46 were higher expressed in G1 and most of them (38) have no functional annotation defined in the database. Interestingly, mitochondrial genes and long non-coding RNAs were the only type of identified transcripts in the set of upregulated genes. These results highlight the importance of developing studies on non-model species and suggest that maternal genes may be of importance for determining larval diapause in T. diversipes .transcriptome / bivoltinism / diapause / solitary bee / RNA-Seq

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Annocript: a flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs

Abstract: remo.sanges@szn.it.

Cited by 102 publications

References 20 publications

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

MerR and ChrR mediate blue light induced photo-oxidative stress response at the transcriptional level in Vibrio cholerae

RNA-Seq reveals that mitochondrial genes and long non-coding RNAs may play important roles in the bivoltine generations of the non-social Neotropical bee Tetrapedia diversipes

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