Phylogenetic annotation and genomic architecture of opsin genes in Crustacea

Pérez‐Moreno, Jorge L.; DeLeo, Danielle M.; Palero, Ferran; Bracken‐Grissom, Heather D.

doi:10.1007/s10750-018-3678-9

Cited by 14 publications

(30 citation statements)

References 96 publications

(12 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Tissue‐specific (eye and photophore) reference transcriptomes were assembled de novo with Trinity v2.8.4 (Grabherr et al., 2011; Haas et al., 2013) using in silico read normalization, a minimum contig length of 200 bp and a k‐mer size of 23, which has proven to be the optimal k‐mer size for these crustacean RNA‐seq data sets (i.e. Bracken‐Grissom et al, 2020; Pérez‐Moreno, DeLeo, Palero, & Bracken‐Grissom, 2018). A comprehensive reference assembly containing both tissue types was also assembled for downstream gene expression comparisons between tissue types.…”

Section: Methodsmentioning

confidence: 99%

“…Each tissue‐specific transcriptome was analysed using the Phylogenetically‐Informed Annotation (PIA) tool (Speiser et al., 2014), modified for command‐line use (Pérez‐Moreno et al, 2018), which characterizes putative visual opsins and phototransduction pathway genes in a phylogenetic context. Assemblies were run through PIA using a pipeline previously described in Pérez‐Moreno et al.…”

Section: Methodsmentioning

confidence: 99%

“…Assemblies were run through PIA using a pipeline previously described in Pérez‐Moreno et al. (2018). In brief, these tools extract all open‐reading frames (ORFs), identify light interaction (LIT) genes via BLAST searches against a database of known visual genes, and align and subsequently place significant hits into precomputed gene phylogenies to differentiate between false positives and genes of interest.…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Illuminating the impact of diel vertical migration on visual gene expression in deep‐sea shrimp

DeLeo

Bracken‐Grissom

2020

Molecular Ecology

Self Cite

View full text Add to dashboard Cite

Diel vertical migration (DVM) of marine animals represents one of the largest migrations on our planet. Migrating fauna are subjected to a variety of light fields and environmental conditions that can have notable impacts on sensory mechanisms, including an organism's visual capabilities. Among deep‐sea migrators are oplophorid shrimp that vertically migrate hundreds of metres to feed in shallow waters at night. These species also have bioluminescent light organs that emit light during migrations to aid in camouflage. The organs have recently been shown to contain visual proteins (opsins) and genes that infer light sensitivity. Knowledge regarding the impacts of vertical migratory behaviour, and fluctuating environmental conditions, on sensory system evolution is unknown. In this study, the oplophorid Systellaspis debilis was either collected during the day from deep waters or at night from relatively shallow waters to ensure sampling across the vertical distributional range. De novo transcriptomes of light‐sensitive tissues (eyes/photophores) from the day/night specimens were sequenced and analysed to characterize opsin diversity and visual/light interaction genes. Gene expression analyses were also conducted to quantify expression differences associated with DVM. Our results revealed an expanded opsin repertoire among the shrimp and differential opsin expression that may be linked to spectral tuning during the migratory process. This study sheds light on the sensory systems of a bioluminescent invertebrate and provides additional evidence for extraocular light sensitivity. Our findings further suggest opsin co‐expression and subsequent fluctuations in opsin expression may play an important role in diversifying the visual responses of vertical migrators.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Illuminating the impact of diel vertical migration on visual gene expression in deep‐sea shrimp

DeLeo

Bracken‐Grissom

2020

Molecular Ecology

Self Cite

View full text Add to dashboard Cite

show abstract

“…Page -39with all crab data restricted to only a few eubrachyurans. Nevertheless, visual pigments play a critical role in the activation of the phototransduction signaling cascade, and consist of an opsin protein bound to a chromophore (Pérez-Moreno et al, 2018). To date, the few studies that use 825!…”

Section: Visual Pigments and Phototransductionmentioning

confidence: 99%

“…As genomic data are generated for additional crab species, visual pigments should be targeted by eye-specific transcriptomics and/or the design of genomic probes based on 890! previous visual pigment annotations (Speiser et al, 2014;Schott et al, 2017;Pérez-Moreno et al, 2018). Tracing the evolution of photoreceptor genes and eye morphology across a robust crab tree could be an informative first step to reconstructing the evolutionary history of vision across this iconic group.…”

Section: !mentioning

confidence: 99%

Evolution of crab eye structures and the utility of ommatidia morphology in resolving phylogeny

Luque

Allison

Bracken‐Grissom

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

Image-forming compound eyes are such a valuable adaptation that similar visual systems have 20! evolved independently across crustaceans. But if different compound eye types have evolved independently multiple times, how useful are eye structures and ommatidia morphology for resolving phylogenetic relationships? Crabs are ideal study organisms to explore these questions because they have a good fossil record extending back into the Jurassic, they possess a great variety of optical designs, and details of eye form can be compared between extant and 25! fossil groups. True crabs, or Brachyura, have been traditionally divided into two groups based on the position of the sexual openings in males and females: the so-called 'Podotremata' (females bearing their sexual openings on the legs), and the Eubrachyura, or 'higher' true crabs (females bearing their sexual openings on the thorax). Although Eubrachyura appears to be monophyletic, the monophyly of podotreme crabs remains controversial and therefore requires 30! exploration of new character systems. The earliest podotremous lineages share the plesiomorphic condition of 'mirror' reflecting superposition eyes with most shrimp, lobsters, and anomurans (false crabs and allies). The optical mechanisms of fossil and extant podotreme groups more closely related to Eubrachyura, however, are still poorly investigated. To better judge the phylogenetic utility of compound eye form, we investigated the distribution of eye 35! types in fossil and extant podotreme crabs. Our findings suggest the plesiomorphic 'mirror'eyes-seen in most decapod crustaceans including the earliest true crabs-has been lost in several 'higher' podotremes and in eubrachyurans. We conclude that the secondary retention of larval apposition eyes has existed in eubrachyurans and some podotremes since at least the Early Cretaceous, and that the distribution of eye types among true crabs supports a 40! paraphyletic podotreme grade, as suggested by recent molecular and morphological phylogenetic studies. We also review photoreceptor structure and visual pigment evolution, currently known in crabs exclusively from eubrachyuran representatives. These topics are critical for future expansion of research on podotremes to deeply investigate the homology of eye types across crabs. 45!

show abstract

Preface: Recent advances in Crustacean Genomics

et al. 2018

Self Cite

View full text Add to dashboard Cite

Applications of next generation sequencing have expanded rapidly over recent years, unveiling many new and exciting areas of genomic research. This includes novel insights into physiology, reproductive biology, response to environmental challenges, and their evolutionary history. Despite their importance, crustaceans still lack genomic resources compared with other widely-studied groups such as insects and vertebrates. The present volume integrates a collection of contributions from the speakers, and compiles the main results presented during the symposium. Following the structure of the Crustacean Genomics workshop, contributed papers have been arranged in two main blocks, a first set of studies focused on the use of transcriptomics to investigate crustacean physiology and reproduction while the second set focused on molecular systematics and evolutionary studies.

show abstract

Phylogenetic annotation and genomic architecture of opsin genes in Crustacea

Cited by 14 publications

References 96 publications

Illuminating the impact of diel vertical migration on visual gene expression in deep‐sea shrimp

Illuminating the impact of diel vertical migration on visual gene expression in deep‐sea shrimp

Evolution of crab eye structures and the utility of ommatidia morphology in resolving phylogeny

Preface: Recent advances in Crustacean Genomics

Contact Info

Product

Resources

About