Dataset Information

Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation.

ABSTRACT: Cladobranchia (Gastropoda: Nudibranchia) is a diverse (approx. 1000 species) but understudied group of sea slug molluscs. In order to fully comprehend the diversity of nudibranchs and the evolution of character traits within Cladobranchia, a solid understanding of evolutionary relationships is necessary. To date, only two direct attempts have been made to understand the evolutionary relationships within Cladobranchia, neither of which resulted in well-supported phylogenetic hypotheses. In addition to these studies, several others have addressed some of the relationships within this clade while investigating the evolutionary history of more inclusive groups (Nudibranchia and Euthyneura). However, all of the resulting phylogenetic hypotheses contain conflicting topologies within Cladobranchia. In this study, we address some of these long-standing issues regarding the evolutionary history of Cladobranchia using RNA-Seq data (transcriptomes). We sequenced 16 transcriptomes and combined these with four transcriptomes from the NCBI Sequence Read Archive. Transcript assembly using Trinity and orthology determination using HaMStR yielded 839 orthologous groups for analysis. These data provide a well-supported and almost fully resolved phylogenetic hypothesis for Cladobranchia. Our results support the monophyly of Cladobranchia and the sub-clade Aeolidida, but reject the monophyly of Dendronotida.

SUBMITTER: Goodheart JA

PROVIDER: S-EPMC4593679 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

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Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation.

Goodheart Jessica A JA Bazinet Adam L AL Collins Allen G AG Cummings Michael P MP

Royal Society open science 20150923 9

Cladobranchia (Gastropoda: Nudibranchia) is a diverse (approx. 1000 species) but understudied group of sea slug molluscs. In order to fully comprehend the diversity of nudibranchs and the evolution of character traits within Cladobranchia, a solid understanding of evolutionary relationships is necessary. To date, only two direct attempts have been made to understand the evolutionary relationships within Cladobranchia, neither of which resulted in well-supported phylogenetic hypotheses. In additi ...[more]

PMID: 26473045

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Project description:The impact of predator-prey interactions on the evolution of many marine invertebrates is poorly understood. Since barriers to genetic exchange are less obvious in the marine realm than in terrestrial or freshwater systems, non-allopatric divergence may play a fundamental role in the generation of biodiversity. In this context, shifts between major prey types could constitute important factors explaining the biodiversity of marine taxa, particularly in groups with highly specialized diets. However, the scarcity of marine specialized consumers for which reliable phylogenies exist hampers attempts to test the role of trophic specialization in evolution. In this study, RNA-Seq data is used to produce a phylogeny of Cladobranchia, a group of marine invertebrates that feed on a diverse array of prey taxa but mostly specialize on cnidarians. The broad range of prey type preferences allegedly present in two major groups within Cladobranchia suggest that prey type shifts are relatively common over evolutionary timescales.In the present study, we generated a well-supported phylogeny of the major lineages within Cladobranchia using RNA-Seq data, and used ancestral state reconstruction analyses to better understand the evolution of prey preference. These analyses answered several fundamental questions regarding the evolutionary relationships within Cladobranchia, including support for a clade of species from Arminidae as sister to Tritoniidae (which both preferentially prey on Octocorallia). Ancestral state reconstruction analyses supported a cladobranchian ancestor with a preference for Hydrozoa and show that the few transitions identified only occur from lineages that prey on Hydrozoa to those that feed on other types of prey.There is strong phylogenetic correlation with prey preference within Cladobranchia, suggesting that prey type specialization within this group has inertia. Shifts between different types of prey have occurred rarely throughout the evolution of Cladobranchia, indicating that this may not have been an important driver of the diversity within this group.

Project description:Ischemic stroke (IS) is one of the main causes of morbidity and disability worldwide due to its complex mechanism. Anemia was characterized as a risk factor of IS because the direct connection between central nervous system, blood supply, and tissue oxygen delivery. As the key oxygen-carrying molecule in the blood, hemoglobin (Hb) may be decisive in the destiny of penumbral area or influence the brain recovery and neurologic function, which could finally affect the outcome of IS. However, more detailed information on the expression levels of Hb related genes were still lacking possibly because the concentration of Hb was determined by the genes' expression several hours ago, which may make the research more difficult to perform. This time gap between gene expressions and protein concentration could make these genes predictive bio-markers for IS outcome. In this study, we choose 28 IS patients, of which 12 were suffering from anemia. Statistical analysis results showed that the outcomes of the patients were different when dividing them into two groups characterized by Hb concentration. 2 sex and age matched patients were first chosen to perform RNA-seq analysis on, on two occasions at two different time points, after which the Hb counts were tested at least 24 h after sequencing. Results showed that the outcome of anemia patients was poor compared with non-anemia patients. Two other patients were then chosen for analysis which excluded the coincidence of other factors. The results showed that the low value of Hb under 13 g/dL in men were closely related to the poor outcome of IS patients. Differently expressed Hb related genes were tested and six genes were shown to be positively correlated with the recovery degree of IS patients: ELANE, FGF23, HBB, PIEZO1, RASA4, and PRTN3. Gene CPM was shown to be negatively correlated with clinical outcomes. All of the seven genes were validated to be related to strokes using real-time PCR or literature searches. Taken together, these genes could be considered as new predictors for the recovery of IS patients.

Dataset Information

Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation.

Publications

Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation.

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