Venus flytrap carnivorous lifestyle builds on herbivore defense strategies

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

Although the concept of botanical carnivory has been known since Darwin's time, the molecular mechanisms that allow animal feeding remain unknown, primarily due to a complete lack of genomic information. Here, we show that the transcriptomic landscape of the Dionaea trap is dramatically shifted toward signal transduction and nutrient transport upon insect feeding, with touch hormone signaling and protein secretion prevailing. At the same time, a massive induction of general defense responses is accompanied by the repression of cell death–related genes/processes. We hypothesize that the carnivory syndrome of Dionaea evolved by exaptation of ancient defense pathways, replacing cell death with nutrient acquisition.

Related collections

Most cited references 105

Record: found
Abstract: found
Article: found

Is Open Access

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Bo Li, Colin Dewey (2011)

Background RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes, as it is difficult to determine which transcripts are isoforms of the same gene. A second significant issue is the design of RNA-Seq experiments, in terms of the number of reads, read length, and whether reads come from one or both ends of cDNA fragments. Results We present RSEM, an user-friendly software package for quantifying gene and isoform abundances from single-end or paired-end RNA-Seq data. RSEM outputs abundance estimates, 95% credibility intervals, and visualization files and can also simulate RNA-Seq data. In contrast to other existing tools, the software does not require a reference genome. Thus, in combination with a de novo transcriptome assembler, RSEM enables accurate transcript quantification for species without sequenced genomes. On simulated and real data sets, RSEM has superior or comparable performance to quantification methods that rely on a reference genome. Taking advantage of RSEM's ability to effectively use ambiguously-mapping reads, we show that accurate gene-level abundance estimates are best obtained with large numbers of short single-end reads. On the other hand, estimates of the relative frequencies of isoforms within single genes may be improved through the use of paired-end reads, depending on the number of possible splice forms for each gene. Conclusions RSEM is an accurate and user-friendly software tool for quantifying transcript abundances from RNA-Seq data. As it does not rely on the existence of a reference genome, it is particularly useful for quantification with de novo transcriptome assemblies. In addition, RSEM has enabled valuable guidance for cost-efficient design of quantification experiments with RNA-Seq, which is currently relatively expensive.

0 comments Cited 4904 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

BLAST+: architecture and applications

Christiam Camacho, George Coulouris, Vahram Avagyan … (2009)

Background Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications. Results We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes. The program can now retrieve masking information for database sequences from the BLAST databases. A new modular software library can now access subject sequence data from arbitrary data sources. We introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options. The strategy files can be uploaded to and downloaded from the NCBI BLAST web site. Conclusion The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences. We have also improved the user interface of the command-line applications.

0 comments Cited 4487 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

Felipe A. Simão, Robert Waterhouse, Panagiotis Ioannidis … (2015)

Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50.

0 comments Cited 3599 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Journal

Journal ID (nlm-ta): Genome Res

Journal ID (iso-abbrev): Genome Res

Journal ID (hwp): genome

Journal ID (pmc): genome

Journal ID (publisher-id): GENOME

Title: Genome Research

Publisher: Cold Spring Harbor Laboratory Press

ISSN (Print): 1088-9051

ISSN (Electronic): 1549-5469

Publication date (Print): June 2016

Publication date PMC-release: June 2016

Volume: 26

Issue: 6

Pages: 812-825

Affiliations

[1 ]Center for Computational and Theoretical Biology, Campus Hubland Nord; Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, D-97218 Würzburg, Germany;

[2 ]Institute for Molecular Plant Physiology and Biophysics, Biocenter, University of Würzburg, 97082 Würzburg, Germany;

[3 ]Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany;

[4 ]Department of Animal Ecology and Tropical Biology, Biocenter, Am Hubland, 97074 Würzburg, Germany;

[5 ]Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;

[6 ]Bioorganic Chemistry Department, Max-Planck-Institute for Chemical Ecology, 07745 Jena, Germany;

[7 ]Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, 40225 Düsseldorf, Germany

Author notes

[8]

Present address: Max-Planck-Institute for Developmental Biology, Department of Molecular Biology, 72076 Tübingen, Germany

Corresponding author: hedrich@ 123456botanik.uni-wuerzburg.de

Author information

Felix Bemm http://orcid.org/0000-0001-6557-4898

Rainer Hedrich http://orcid.org/0000-0003-3224-1362

Article

Medline ID: 9509184

DOI: 10.1101/gr.202200.115

PMC ID: 4889972

PubMed ID: 27197216

SO-VID: 09358963-789c-46df-87c4-a18d941d5e0b

License:

This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

History

Date received : 20 November 2015

Date accepted : 7 April 2016

Page count

Pages: 14

Funding

Funded by: European Research Council http://dx.doi.org/10.13039/501100000781

Award ID: FP/20010-2015

Award ID: 250194

Funded by: King Saud University http://dx.doi.org/10.13039/501100002383

Award ID: IRG14-08

Comments

Comment on this article

scite_

Cited by 34

See all cited by

Most referenced authors 3,005

See all reference authors

- Version 1
- Version 1

Venus flytrap carnivorous lifestyle builds on herbivore defense strategies

Read this article at

Abstract

Related collections

ScienceOpen Research

Most cited references 105

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

BLAST+: architecture and applications

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

Author and article information

Journal

Affiliations

Author notes

Author information

Article

History

Page count

Funding

Categories

Comments

Comment on this article

Similar content 127

Cited by 34

Most referenced authors 3,005