FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci

Rambaldi, Davide; Ciccarelli, Francesca D.

doi:10.1093/bioinformatics/btp381

Cited by 100 publications

(74 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…68). EPDR transcripts were then used as queries to identify the correct intron/exon architecture of the genes in the genome assemblies (schematic created using FancyGene 69 ). An alignment of the manually curated GBR EPDRs was created using AliView 70 (see Supplementary Note 8) and assessed for the possession of signal peptides using SignalP 4.1 (ref.…”

Section: Letter Researchmentioning

confidence: 99%

The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest

Hall

Kocot

Baughman

et al. 2017

Nature

175

237

View full text Add to dashboard Cite

The crown-of-thorns starfish (COTS, the Acanthaster planci species group) is a highly fecund predator of reef-building corals throughout the Indo-Pacific region 1 . COTS population outbreaks cause substantial loss of coral cover, diminishing the integrity and resilience of reef ecosystems 2-6 . Here we sequenced genomes of COTS from the Great Barrier Reef, Australia and Okinawa, Japan to identify gene products that underlie species-specific communication and could potentially be used in biocontrol strategies. We focused on water-borne chemical plumes released from aggregating COTS, which make the normally sedentary starfish become highly active. Peptide sequences detected in these plumes by mass spectrometry are encoded in the COTS genome and expressed in external tissues. The exoproteome released by aggregating COTS consists largely of signalling factors and hydrolytic enzymes, and includes an expanded and rapidly evolving set of starfish-specific ependymin-related proteins. These secreted proteins may be detected by members of a large family of olfactory-receptor-like G-protein-coupled receptors that are expressed externally, sometimes in a sex-specific manner. This study provides insights into COTS-specific communication that may guide the generation of peptide mimetics for use on reefs with COTS outbreaks.COTS are extremely fecund mass spawners 7 , which predisposes them to population outbreaks that result in a pronounced loss of live coral cover and associated biodiversity. These outbreaks have a higher impact on reef health and resilience than the combined effects of coral bleaching and disease, and increase the susceptibility of reefs to other potentially detrimental events, such as severe storms [2][3][4][5][6] (Supplementary Note 1).Although a range of local in situ control measures have been applied with some success (Supplementary Note 1), mitigation of COTS outbreaks on the necessary regional scale requires mass-deployed, species-specific strategies. In this context, genome-encoded COTSspecific attractants that underpin spawning aggregations have substantial potential as biocontrol agents. To identify attractants, we sequenced the genomes of two wild-caught individuals separated by over 5,000 km, one from the Great Barrier Reef (GBR), Australia and the other from Okinawa (OKI), Japan (Fig. 1c, d and Extended Data Fig. 1). We also sequenced transcriptomes from external organs, and proteins released into the seawater by COTS that were aggregating or were in the presence of their main predator, the giant triton Charonia tritonis (Fig. 1b).We generated separate 384 megabase (Mb) draft assemblies for the GBR and OKI genomes (Extended Data COTS genes are labelled and are marked with red lines; other asteroids, two shades of orange and yellow lines; sea urchins, dark green; hemichordates, light green; molluscs, pink; annelids, purple; cnidarians, black; and vertebrates, blue. The three clades to which COTS sequences belong are indicated by the outer circle. The asterisk denotes the fish-specific tru...

show abstract

Section: Letter Researchmentioning

confidence: 99%

The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest

Hall

Kocot

Baughman

et al. 2017

Nature

175

237

View full text Add to dashboard Cite

show abstract

“…The alignments were used to construct a maximum likelihood phylogenetic tree with RAxML (version 8.1.12) software using a gamma distribution and LG4X model (Le et al 2012;Stamatakis 2014). Conserved AS events in SR families between maize and sorghum exon-intron gene structure were visualized by Fancygene version 1.4 (Rambaldi and Ciccarelli 2009). …”

Section: Conserved As In Sr and Hnrnp Proteinsmentioning

confidence: 99%

Evolutionarily Conserved Alternative Splicing Across Monocots

et al. 2017

View full text Add to dashboard Cite

One difficulty when identifying alternative splicing (AS) events in plants is distinguishing functional AS from splicing noise. One way to add confidence to the validity of a splice isoform is to observe that it is conserved across evolutionarily related species. We use a high throughput method to identify junction-based conserved AS events from RNA-Seq data across nine plant species, including five grass monocots (maize, sorghum, rice, Brachpodium, and foxtail millet), plus two nongrass monocots (banana and African oil palm), the eudicot Arabidopsis, and the basal angiosperm Amborella. In total, 9804 AS events were found to be conserved between two or more species studied. In grasses containing large regions of conserved synteny, the frequency of conserved AS events is twice that observed for genes outside of conserved synteny blocks. In plant-specific RS and RS2Z subfamilies of the serine/arginine (SR) splicefactor proteins, we observe both conservation and divergence of AS events after the whole genome duplication in maize. In addition, plant-specific RS and RS2Z splice-factor subfamilies are highly connected with R2R3-MYB in STRING functional protein association networks built using genes exhibiting conserved AS. Furthermore, we discovered that functional protein association networks constructed around genes harboring conserved AS events are enriched for phosphatases, kinases, and ubiquitylation genes, which suggests that AS may participate in regulating signaling pathways. These data lay the foundation for identifying and studying conserved AS events in the monocots, particularly across grass species, and this conserved AS resource identifies an additional layer between genotype to phenotype that may impact future crop improvement efforts.

show abstract

“…The coding sequences and the genome sequences from SL2.40 were analyzed using FancyGene (Rambaldi and Ciccarelli, 2009 …”

Section: Comparison Of the Yabby Domain Sequence And Structurementioning

confidence: 99%

Identification and expression analysis of YABBY family genes associated with fruit shape in tomato (Solanum lycopersicum L.)

Han¹,

Liu²,

Jiang³

et al. 2015

Genet. Mol. Res.

View full text Add to dashboard Cite

ABSTRACT. YABBY family genes play important roles in the development of leaf, flower, and fruit. The purpose of this research was to integrate all the YABBY genes and analyze the correlation between gene expression and fruit shape in tomato. Scanning of 24 genomes of sequenced species demonstrated that YABBY genes were very normal and stable in flowering plants except the seedless plants. Nine YABBY genes in tomato were computationally and experimentally characterized. The phylogeny was constructed based on whole proteins or the YABBY domain, and five distinct clades were observed as described in other angiosperms. A comparison of the expression patterns in tomatoes with large differences in fruit shape and/or size suggested that during the fruit development, YABBY genes had both negative and positive functions. The obtained information could provide a deeper understanding of the evolution of YABBY genes and can also be useful for tomato yield and shape breeding.

show abstract

FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci

Cited by 100 publications

References 9 publications

The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest

The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest

Evolutionarily Conserved Alternative Splicing Across Monocots

Identification and expression analysis of YABBY family genes associated with fruit shape in tomato (Solanum lycopersicum L.)

Contact Info

Product

Resources

About