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Eurytemora carolleeae strain:Atlantic clade

ABSTRACT: Eurytemora carolleeae strain:Atlantic clade Genome sequencing and assembly

PROVIDER: PRJNA203087 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR1043119_1.fastq.gz	Fastqsanger.gz
	SRR1043119_2.fastq.gz	Fastqsanger.gz
	SRR2452640_1.fastq.gz	Fastqsanger.gz
	SRR2452640_2.fastq.gz	Fastqsanger.gz

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Eurytemora carolleeae

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The Genome Architecture of the Copepod Eurytemora carolleeae - the Highly Invasive Atlantic Clade of the Eurytemoraaffinis Species Complex.

Project description:Copepods are among the most abundant organisms on the planet and play critical functions in aquatic ecosystems. Among copepods, populations of the Eurytemora affinis species complex are numerically dominant in many coastal habitats and serve as food sources for major fisheries. Intriguingly, certain populations possess the unusual capacity to invade novel salinities on rapid time scales. Despite their ecological importance, high-quality genomic resources have been absent for calanoid copepods, limiting our ability to comprehensively dissect the genome architecture underlying the highly invasive and adaptive capacity of certain populations. Here, we present the first chromosome-level genome of a calanoid copepod, from the Atlantic clade (Eurytemora carolleeae) of the E. affinis species complex. This genome was assembled using high-coverage PacBio long-read and Hi-C sequences of an inbred line, generated through 30 generations of full-sib mating. This genome, consisting of 529.3 Mb (contig N50 = 4.2 Mb, scaffold N50 = 140.6 Mb), was anchored onto four chromosomes. Genome annotation predicted 20,262 protein-coding genes, of which ion transport-related gene families were substantially expanded based on comparative analyses of 12 additional arthropod genomes. Also, we found genome-wide signatures of historical gene body methylation of the ion transport-related genes and the significant clustering of these genes on each chromosome. This genome represents one of the most contiguous copepod genomes to date and is among the highest quality marine invertebrate genomes. As such, this genome provides an invaluable resource to help yield fundamental insights into the ability of this copepod to adapt to rapidly changing environments.

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Eurytemora affinis

Project description:Eurytemora affinis overview

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Eurytemora affinis strain:Wimereux

Project description:Eurytemora affinis strain:Wimereux Transcriptome or Gene expression

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Eurytemora affinis

Project description:Eurytemora affinis Raw sequence reads

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Eurytemora carolleeae in the Laurentian Great Lakes revealed by phylogenetic and morphological analysis.

Project description:In the Laurentian Great Lakes, specimens of Eurytemora have been reported as E. affinis since its invasion in the late 1950s. During an intensive collection of aquatic invertebrates for morphological and molecular identification in Western Lake Erie in 2012-2013, several specimens of Eurytemora were collected. Analysis of these specimens identified them as the recently described species E. carolleeae Alekseev and Souissi 2011. This result led us to assess E. carolleeae's identifying features, geographic distribution and historical presence in the Laurentian Great Lakes in view of its recent description in 2011. Cytochrome oxidase I (COI) DNA sequences of Eurytemora specimens were identified as closer (2 - 4% different) to recently described E. carolleeae than to most Eurytemora affinis sequences (14% different). Eurytemora from other areas of the Great Lakes and from North American rivers as far west as South Dakota (Missouri River) and east to Delaware (Christina River) also keyed to E. carolleeae. Morphological analysis of archival specimens from 1962 and from all the Great Lakes were identified as E. carolleeae. Additionally, Eurytemora drawings in previous publications from studies in the Holarctic region were reassessed to determine if these specimens were E. carolleeae. Additional morphological characters that may distinguish the North American E. carolleeae from other taxa are also described. We conclude that E. carolleeae is the correct name for the species of Eurytemora that has inhabited the Great Lakes since its invasion, as established by both morphological and COI sequence comparisons to reference keys and sequence databases in present and archival specimens.

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Project description:Clade

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