Dataset Information

Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods.

ABSTRACT: RNA editing, a post-transcriptional process, allows the diversification of proteomes beyond the genomic blueprint; however it is infrequently used among animals for this purpose. Recent reports suggesting increased levels of RNA editing in squids thus raise the question of the nature and effects of these events. We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites. Editing is enriched in the nervous system, affecting molecules pertinent for excitability and neuronal morphology. The genomic sequence flanking editing sites is highly conserved, suggesting that the process confers a selective advantage. Due to the large number of sites, the surrounding conservation greatly reduces the number of mutations and genomic polymorphisms in protein-coding regions. This trade-off between genome evolution and transcriptome plasticity highlights the importance of RNA recoding as a strategy for diversifying proteins, particularly those associated with neural function. PAPERCLIP.

SUBMITTER: Liscovitch-Brauer N

PROVIDER: S-EPMC5499236 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods.

Liscovitch-Brauer Noa N Alon Shahar S Porath Hagit T HT Elstein Boaz B Unger Ron R Ziv Tamar T Admon Arie A Levanon Erez Y EY Rosenthal Joshua J C JJC Eisenberg Eli E

Cell 20170401 2

RNA editing, a post-transcriptional process, allows the diversification of proteomes beyond the genomic blueprint; however it is infrequently used among animals for this purpose. Recent reports suggesting increased levels of RNA editing in squids thus raise the question of the nature and effects of these events. We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites. Editing is enriched in t ...[more]

PMID: 28388405

Similar Datasets

Project description:Streptomycetes are filamentous soil-dwelling bacteria. They are best known as the producers of a great variety of natural products such as antibiotics, antifungals, antiparasitics, and anticancer agents and the decomposers of organic substances for carbon recycling. They are also model organisms for the studies of gene regulatory networks, morphological differentiation, and stress response. The availability of sets of genomes from closely related Streptomyces strains makes it possible to assess the mechanisms underlying genome plasticity and systems adaptation.We present the results of a comprehensive analysis of the genomes of five Streptomyces species with distinct phenotypes. These streptomycetes have a pan-genome comprised of 17,362 orthologous families which includes 3,096 components in the core genome, 5,066 components in the dispensable genome, and 9,200 components that are uniquely present in only one species. The core genome makes up about 33%-45% of each genome repertoire. It contains important genes for Streptomyces biology including those involved in gene regulation, secretion, secondary metabolism and morphological differentiation. Abundant duplicate genes have been identified, with 4%-11% of the whole genomes composed of lineage-specific expansions (LSEs), suggesting that frequent gene duplication or lateral gene transfer events play a role in shaping the genome diversification within this genus. Two patterns of expansion, single gene expansion and chromosome block expansion are observed, representing different scales of duplication.Our results provide a catalog of genome components and their potential functional roles in gene regulatory networks and metabolic networks. The core genome components reveal the minimum requirement for streptomycetes to sustain a successful lifecycle in the soil environment, reflecting the effects of both genome evolution and environmental stress acting upon the expressed phenotypes. A better understanding of the LSE gene families will, on the other hand, bring a wealth of new insights into the mechanisms underlying strain-specific phenotypes, such as the production of novel antibiotics, pathogenesis, and adaptive response to environmental challenges.

Project description:BackgroundThe Subclass Coleoidea (Class Cephalopoda) accommodates the diverse present-day internally shelled cephalopod mollusks (Spirula, Sepia and octopuses, squids, Vampyroteuthis) and also extinct internally shelled cephalopods. Recent Spirula represents a unique coleoid retaining shell structures, a narrow marginal siphuncle and globular protoconch that signify the ancestry of the subclass Coleoidea from the Paleozoic subclass Bactritoidea. This hypothesis has been recently supported by newly recorded diverse bactritoid-like coleoids from the Carboniferous of the USA, but prior to this study no fossil cephalopod indicative of an endochochleate branch with an origin independent from subclass Bactritoidea has been reported.Methodology/principal findingsTwo orthoconic conchs were recovered from the Early Eocene of Seymour Island at the tip of the Antarctic Peninsula, Antarctica. They have loosely mineralized organic-rich chitin-compatible microlaminated shell walls and broadly expanded central siphuncles. The morphological, ultrustructural and chemical data were determined and characterized through comparisons with extant and extinct taxa using Scanning Electron Microscopy/Energy Dispersive Spectrometry (SEM/EDS).Conclusions/significanceOur study presents the first evidence for an evolutionary lineage of internally shelled cephalopods with independent origin from Bactritoidea/Coleoidea, indicating convergent evolution with the subclass Coleoidea. A new subclass Paracoleoidea Doguzhaeva n. subcl. is established for accommodation of orthoconic cephalopods with the internal shell associated with a broadly expanded central siphuncle. Antarcticerida Doguzhaeva n. ord., Antarcticeratidae Doguzhaeva n. fam., Antarcticeras nordenskjoeldi Doguzhaeva n. gen., n. sp. are described within the subclass Paracoleoidea. The analysis of organic-rich shell preservation of A. nordenskjoeldi by use of SEM/EDS techniques revealed fossilization of hyposeptal cameral soft tissues. This suggests that a depositional environment favoring soft-tissue preservation was the factor enabling conservation of the weakly mineralized shell of A. nordenskjoeldi.

Dataset Information

Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods.

Publications

Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets